Evolution: What Darwin Did Not know by then..!

Table of Contents: Foreword. 1, A brief history of evolution. 2, How to brand a species? 3, Concepts in evolution which we all know. 4, Variations, more-variations & quantitative traits. 5, Species branding’s role in Darwinian speciation. 6, Different prospects of species branding. 7, Environment’s roles. 8, Species branding in populations. 9, A case study with microbes. 10, Resurfacing of past theories. Final word. FAQs. Mind map for this book. References. List of figures. Acknowledgements. Word cloud for this book. Back cover. Foreword: We all know that during the days of Darwin, the field of microscopy was at its infancy, and genetics did not exist as a field at all... at these times Darwin made remarkable achievements in the understanding of the origins of life... but science has come a long way since the days of Darwin... This book discusses about the concepts Darwin would have probably worked on, if he would be living (amongst us) in these days. The days of information superhighways, exponential growth in genomic knowledge and the unfortunate information overload that has come with it. Though this book is basic it can be called a research edition, in the sense that it requires at least some prior knowledge in the subject area to continue to understand and enjoy reading it. I wish you to have a good time. Dedication: This book is dedicated towards the betterment of science and the human understanding… ~~~ Figure:1 Evolution chandelier. [1] 1 A brief history of evolution Neo-darwinism Also called as 'modern synthesis', neo-darwinism is a combination of both classical darwinism and the mendelian genetic theory. M odern synthesis has been widely accepted, but its views on speciation are still under debate. Neodarwinists insisted that speciation happens by gradual accumulation of small genetic changes over time. According to them this also includes gradual changes to the morphology over time, as one species gets converted into a narrowly distinct species. With this being a theory, confirmation for these events which happened during evolution over extended periods of time could be done only by studying the fossil remains. And the fossils tell a different story. Punctuations in fossils In spite of the neo-darwinian claim of gradualism, fossil evidences have-not shown gradual stages of evolution from one species into its closely related species. Evolutionary trees drawn using these fossils show, rapid 'bursts' of speciation followed by long periods of 'stasis' where the species stayed unchanged. This model of evolution is referred to as 'punctuated equilibrium' Fig:2 and has been widely accepted [2, 3]. The absence of fossils which are missing links connecting two given genera (inter- genera/ family /order missing-links), persuaded the non-darwinists to question the neo-darwinian views on speciation through fine gradations. And this successfully influenced the supporters of neodarwinism; to accept and accommodate this fact by making changes to their theory. Figure:2 Punctuated equilibrium. [4] Neo-darwinian speciation With speciation being an occasional event, the neodarwinians subsequently claimed that the genotypic and specially the phenotypic gradualism happen in isolation at secluded locations like an island separated by water barrier (/river) Fig:3&4 or far side of a mountain range which divided terrain acting as a land barrier [5-7]. Neo-darwinists also claim that under these circumstances the fossils of the ‘intergenera/ family /order missing-links’ could have been preserved, in remote sites away from where the common fossils are found, but would not-have been unearthed until this day. With this being a theory, the presence of these remote fossils has not-been confirmed. Figure:3 Neo-darwinian speciation. [8] Figure:4 Neo-darwinian speciation. [9] Morphological discontinuity Darwin was aware of this problem and he believed that the 'morphological discontinuity' which was seen in fossils of his time, was because of incomplete fossil records. He hoped that as more fossils get unearthed in the future it would include ‘inter- genera/ family /order fossils’, which he believed would only add strength to his theory. But paleontology has come a long way ever since Darwin's days. M ost of the fossil types being unearthed now are previously known ones, and new fossil types are rarely being uncovered nowadays. Also the mathematical models in paleontology suggest that fossil records are nearly complete [10]. Artifacts theory Darwin and his supporters also believed in the 'artifacts theory'. According to which the fossil record was punctuated as it was full of artifacts; and all species are not-equally represented, since many species did-not get fossilized. They specifically claimed that organisms with soft bodies are notrepresented as they were difficult to be fossilized and to be part of the record. The artifacts theory has been disproved recently with the excavation of soft bodied animal fossils in south-China Fig:5&6 [11]. Figure:5 Photograph and interpretive drawing of M iddle Cambrian cnidarian jellyfish fossil in lateral view. [12] Figure:6 Cubozoan embryo fossils from the Lower Cambrian Kuanchuanpu Formation, Shaanxi, South China. Analyzed in detail through computed microtomography (M icro-CT) and scanning electron microscopy (SEM ) without coating. [13] Punctuations in taxa Apart from the fact that fossils fail to support gradual speciation, the branching patterns observed in higher order taxa of both plants and animals also fail to support gradualism. Systematics and cladistics have shown that major features of 'body plans' (phyla) and their associated components arose not-in the gradual way [14]. So biologists are on a constant search for alternatives to Darwin's gradualism all through the past one and a half century. Alternatives to neo-darwinism Though many alternatives to darwinism have been proposed, the famous ones are those which support nongradual speciation. These include saltationism, mutationism, systemic mutation, quantum evolution, quantum speciation, hopeful monster hypothesis etc. They have gained some recognition after the emergence of the field of developmental biology (evo-devo) in the 1980s, but they lack the popularity which darwinism still holds. The Species Problem A species is a group of any given organism, which are capable of breeding inbetween them. In population terms: they are a population of a given organism which breed among themselves, but donot breed with a different population of that organism. It is observed that in many species of fishes, insects; the distinction between the many different species is not very clear. So one is unable to draw the line of demarkation in between those species. This is known to scientists as the 'Species Problem' or 'Darwin's Problem'. But every species is capable of distinguishing itself from its neighbouring species. How that is done.., will be discussed in detail in the next chapter. M oving in to the next chapter, we will be shifting gears to learn how a species gets branded, and about the hypothesis of species branding. ~~~ 2 How to brand a species? What makes a given species unique? How is a given species capable of distinguishing itself from its neighbouring species? These subjects are discussed in this chapter in detail. Species branding factors & 'the hypothesis of species branding' Today we see branding and trade marking happening all around us. Each commercial brand tries to achieve a brand identity, which highlights its unique innovations from the rest of the pack. Similarly in nature (it appears that) each species tries to brand itself; so as to protect all the phenotypic novelties it develops, from getting dispersed among the other species. Species branding factors (SBFs) are the molecular factors which ‘tag’ a given species thereby preventing it from reproducing with any other species, but enabling reproduction with the same species. Some of the proteins involved during fertilization have been known to be good examples for primary species branding factors. These proteins are part of all the three steps of the fertilization process; hence they ensure species-specificity at multiple levels. These include: 1, Chemotaxis of sperm towards the ovum. 2, Sperm and egg interaction through membrane surface proteins. 3, Fusion of the nuclei from the egg and sperm. Let’s discuss each of these in detail. 1) Chemotaxis of sperm occurs at a species specific manner for eg: a monkey’s sperm does not get attracted to human ovum. This phenomena has been documented in several species of echinoderms, molluscs, urochordates, and cnidarians [15, 16]. For example: the protein 'resact' in the sperm’s surface acts as a chemoattractant receptor-protein; which enables the sperm migration towards the ovum, as found in the sea urchin Fig:7 Arbacia punctulata [17]. This receptor protein differs in different organisms and is specific to its unique chemoattractant, there by acting as a species branding factor. Figure:7 The small peptide RESACT acts as a chemoattractant for the sea urchin sperm. When receptors on the surface of the sperm bind RESACT; and then a signal transduction cascade involving cyclic GM P (cGM P) is set in motion, triggering faster sperm swimming. [18] 2) Sperm and egg interaction is also species specific. As seen in the sea urchins, surface proteins of the sperm such as 'bindin' attach with, receptors such as 'EBR1' on the egg’s vitelline membrane [19]. In the mouse sperm, a transmembrane protein called 'fertilin' Fig:8, enables its binding to the protein 'integrin' Fig:8 present on the egg’s membrane [2022]. These surface proteins associated with reproduction are good examples of SBFs. Figure:8 The molecules on the sperm surface, such as fertilin and cyritestin, may be involved in sperm–egg binding. Okabe and colleagues found that sperm’s Izumo protein is essential for membrane fusion. On the egg, CD9 is required for fusion and might collaborate with other proteins such as integrins or glycosylphosphatidylinositol (GPI)-anchored proteins. [23] 3) Fusion of the nuclei from the egg and sperm is also species specific; which is brought by the action of 'fusogenic' proteins. These proteins have been reported to be similar to the fusogenic proteins found in some viruses, like the 'HA protein' of influenza virus Fig:9 [24, 25] and the 'F protein' of Sendai virus Fig:10 [26]; where they bring forth the viral and cell fusions. Bindin and fertilin are also believed to promote fusion of the nuclei in sea urchins and mouse respectively. These fusogenic proteins which vary across different organisms serve as SBFs. Figure:9 Influenza-A viruses are enveloped, negative strand RNA viruses. The virus enters the cell by receptor-mediated endocytosis, viral HA binds to host cell receptors that contain terminal α-2,6-linked or α-2,3-linked sialic acid (α-2,6-SA or α-2,3-SA) moieties. [27] Figure:10 Fusion mechanism in the 'F protein' of Sendai virus according to the “viral fusion pore” model of Lee K. [28] Nuclear gate keepers (NGK) Fig:11 [29] are good examples of secondary SBFs. They are proteins which are stationed at the nuclear pores Fig:12 where they prevent the entry of genetic material from another species through viruses. They are highly species specific and thus prevent breeding across species. Proteins such as bindin and NGK are probably the fastest evolving proteins and are able to diverge rapidly when compared to other proteins of the organism. They brand a given species, preventing its interbreeding and enabling it to diverge far from the parental species. In doing so these SBFs spear head the process of speciation. Figure:11 Structure of the nuclear pore complex (NPC), an assembly of 456 proteins that controls the flow of molecules between the DNA-storing nucleus and the rest of the cell. [30] Figure:12 Nuclear pore complexes on the nuclear membranes of frog oocytes as seen from the cytoplasm. [31] Prokaryotes do-not have a nucleus and so the NGKs. But prokaryotes are also known to have evolved similar mechanisms to protect and brand their own genomes. Archaebacteria as well as eubacteria possess the restriction- modification system; [32, 33] which chop any foreign DNA entering their cell. They would also safeguard and brand their genome by methylating it at unique sites. Codon bias Fig:13 and GC content which varies between organisms also play a vital role in branding, by providing the host DNA an upper hand over any foreign DNA that might have sneaked into the cell. Figure:13 Codon positions. [34] Comparative analysis of the codon usage of all ORFs of CrleGV (black) and CpGV (gray). The nucleotide bias of the first and second codon positions are given to the left. The dinucleotides and the encoded amino acids are given on the outer circle. The nucleotide distribution of the third codon position is given to the right. Legend: Cryptophlebia leucotreta granulovirus (CrleGV) Cydia pomonella granulovirus (CpGV) Figure:14 Codon usage rose plots for four representatives of different genera of Vibrio…[35] There are also other genetic factors which aid in species branding and speciation, like the 'interspersed repeats' Fig:15 [36]. These repetitive DNA stretches get scattered within newly evolving 'copies of a gene'. They preserve the new gene from being replaced by the 'original gene' through homologous recombination Fig:16&17. The original gene might exist as a paralogue Fig:18 in the same genome, or might enter from another individual through mating. The interspersed repeats thereby protect and enable the new copy to diverge, by accumulating mutations and to evolve new functions. Figure:15 Categories of repetitive nuclear elements. [37] Figure:16 Direct repeats excising DNA. Figure:17 Inverted repeats flipping DNA. Figure:18 Shared ancestry among homologous proteins across a gene family. [38] Let us keep aside the species branding factors for a while and discuss the different concepts in evolution which we all know about. ~~~ 3 Concepts in evolution which we all know The variations seen among, the members of a given species or in-between two seperate species; is due to the occurance of the many micro and macro-mutational events. This chapter discusses them in detail. Micro-mutation and micro-evolution M icro-mutations are small changes that happen to the genome of an organism like point mutations, small scale duplications, gene level rearrangements, minor recombinations etc. These mutations mostly bring about changes to the genotype and may go unnoticed (silent mutation), but rarely they do produce phenotypic changes. If the change results in a slight phenotype then it is called micro-evolution, but on the other hand if it is a quite remarkably altered phenotype then it is termed as macro-evolution. As one knows, not-all mutations cause evolution. For example: a point mutation in ‘hot spots’ like a developmental gene [39, 40] or at an active site of a protein Fig:19, or a promoter of a gene Fig:20&21 or an yet to be discovered switch in the neighborhood of the gene has a better chance of resulting in a new phenotype, than one that occurs in an ubiquitous gene, the loop region Fig:22 of a protein or intron of a gene Fig:23 etc. As obvious the outcome being a micro or macro-evolution depends upon the degree of phenotypic effect the mutation produces; with micro-evolution generally referred to as a neo-darwinian mode of gradual evolution. Figure:19 Active site as seen in the induced fit model of enzyme action. [41] Promoter–Prokaryotic Figure:20 A simple regulatory region of DNA located upstream of the gene. [42] Promoter–Eukaryotic Figure:21 Eukaryotic promoters are extremely diverse and are difficult to characterize. They typically lie upstream of the gene and can have regulatory elements several kilobases away from the transcriptional start site. [43] Figure:22 A simple protein structure with clearly visible; loop, α-helix and β-sheets (Structure of pancreatic RNase A). [44] Figure:23 M ost eukaryotic genes, have coding regions (exons) interrupted by non-coding regions (introns). [45] Macro-mutation and macro-evolution M acro-mutations are large changes that occur in the genome of an organism like gross mutations, large scale duplications Fig:24, genome level rearrangements Fig:25, major recombinations Fig:26 etc, which results in big changes to the genome. These changes generally get reflected as new phenotype but may also go unnoticed by just contributing to the genotype. Here again, the scale of the phenotypic effect will determine if it is a macro- or a micro-evolution. Genome duplications mostly result in an enhanced new phenotype or macro-evolution. M acro-evolution being a relatively rare event, the evidences for genome duplication events can be seen in the sequenced genomes of organisms which live today. For example: gene shuffling in antifreeze gene [46] (where macro-evolution happens through micro-mutations), genome duplications in fishes and other organisms Fig:27 [47, 48] (where macro-evolution happens through macro-mutations), macro-evolution of insect body plans [49] etc.. Figure:24 Global gene duplication: distribution of the duplicated genes on the 21 Tetraodon chromosomes. [50] These duplications are most likely brought about by a heightened activity of transposons and small scale recombination events through repetitive elements. Figure:25 Genomic rearrangements can be triggered by a multitude of factors. The inner ring shows four broad categories and the outer ring shows components within these categories. [51] Figure:26 Crossover recombination (at the chromosomal level) between repeated DNA sequences at non-allelic positions can generate a deletion, a duplication, an inversion or an isodicentric chromosome. [52] Figure:27 Genome duplication: Hox clusters are indicative of whole-genome duplication events which happened across life forms. [53] M acro-evolution occurs abruptly (at random) and much less frequent than micro-evolution. This is the reason why one is not-able to observe it, when one goes looking for it. But one can catch an event of macro-evolution if one would observe an organism continuously for many thousands of generations. So within a human life span one can observe macro-evolution only in organisms with very short generation times, like the microbe E. coli Fig:29 [54-56] with a generation time of only 20 minutes or the viruses Fig:30 [5759]. Figure:28 M utations in terms of evolution. Long term evolution studies: Saltation seen in E. coli [56] · Prof. C. Lenski has been running an adaptive evolution experiment in an asexual Escherichia coli (ones without conjugation capabilities) ever since 24 th February 1988. The populations have reached the milestone of 50,000 generations in February 2010. · Prof. Lenski's laboratory at M ichigan State University cultures these E. coli in a minimal growth medium with citrate as the main food source (and another food source in minimal amounts provided just for survival needs). The point to note is that wild-type E. coli cannot grow on citrate when oxygen is present (Cit-). · These E. coli are grown in flasks and 1% of each population is transferred to a flask of fresh growth medium in regular intervals. Samples are also regularly frozen as glycerol stabs. · Around generation 33,127, the experimenters noticed a dramatically expanded population-size in one of the samples; they found clones in this population could grow on the citrate. These bacteria evolved the ability to grow on citrate under the oxygen-rich conditions of the experiment. · They also found the ability to use citrate could spontaneously re-evolve in a subset of genetically pure clones isolated from earlier time points in the population's history. Such re-evolution of citrate use was never observed in clones isolated from before generation 20,000. · Examination of samples of the population frozen at earlier time points led to the discovery that a citrate-using variant (Cit+) had evolved in the population at some point between generations 31,000 and 31,500. · The researchers have also found that, all Cit+ clones had duplication mutations of a 2933 base pair segment. A macro-evolutionary event has in fact happened in this case, most likely through micro-duplication (micromutation). One should note that in this laboratory experiment, more than 31,000 generations and trillions and trillions of individual organisms were involved; during Prof. Lenski’s scanning for the evolution of a single phenotype (Cit+) in an organism which is limited in its genome size and complexity. Figure:29 Prof. C. Lenski’s long term lines of E.coli on 25th June 2008 close-up of citrate mutant (middle flask). [56, 60] Figure:30 The circulating influenza-A viruses change by mutation, so antibodies become less effective at neutralizing the virus. Therefore infections can occur repeatedly throughout one’s lifetime as new subtypes of influenza-A emerge. [61] These adaptive mutations confering extreme disease resistance, could be considered as macro-evolution due to micro-mutations; happening at the level of the surface antigens. M acro-evolution can also occur due to unanticipated (sudden) expression of silent micro-mutations (genotypic changes) that have been silently building up over successive generations, known as hidden evolution. Hsp90 is a good example for this [62-65]. Under stress it releases the expression (phenotypic expression) of a variety of mutations in the developmental control proteins which had been accumulating until then. One has to get himself aware that evolution need-not necessarily and always be micro-evolutions brought about by micro-mutations. Sequenced genomes of organisms hold proof for the occurrence of macro-mutations and macroevolutions, but they are known to happen on an infrequent scale. Apart from micro and macro-mutations; variation can be brought about in any organism through genetic fluctuations called quantitative traits, which is discussed in the next chapter. Tip: From now-on in this book; one has to be bit careful while reading through words like micro-mutation, micro-evolution, macro-mutation and macro-evolution. They have been defined on relative terms and have been applied in their corresponding context, but unfortunately could be little confusing to any-one reading this book for the first time. Especially in exceptional cases where micro-mutation leads to macro-evolution. In case of any mix-up, please remember to go through chapter-3: “ concepts in evolution which we all know”. ~~~ 4 Variations, more-variations and quantitative traits While the variations we discussed in the previous chapter may considered as the 'real' variations found in the organisms, there are also transcient variations which tend to fluctuate in betwen generations. They are known as the Quantitative traits; these variations when occuring in nature, can easily mislead even expert scientists and must be taken in to account. Quantitative traits As obvious, variations in morphology are seen in members of any given species that exists today (at least due to SNPs). These variations are necessarily-not the products of micro-evolution, but are the quantitative traits brought about by polygenic effects. These traits are nothing but heritable 'fluctuations'. They never contribute to the gradual process of evolution because the population still remains as a single species, is interbreedable and the traits are mostly ' reversible' . They are the reason behind the variations seen in M endel's peas Fig:31; for example the height: which has been known to 'fluctuate between generations' and has-not continued to increase (grow taller) through evolution. The different breeds of dogs Fig:32&33 may also be treated as quantitative traits, because of their ability to interbreed and the reversibility of certain traits. Though micro-evolution happens today, what appears like gradual evolution in most cases is actually heritable 'fluctuations' (quantitative traits) [66-68], which are rather widespread. Figure:31 M endel examined the inheritance patterns of seven different pea-plant characters. For each character, one of the two parent traits disappeared in the F1 hybrids, but reappeared in approximately one quarter of the F2 generation (not shown here). [69] Figure:32 A taller breed of dog with one of the smallest breeds…[70] Figure:33 Some of the different breeds of dogs. [71] The effects of quantitative traits on paleontology, where classification is primarily done based on morphology; remains an open question. Especially some of the admired 'transitional fossils' (missing links) with fine-gradations in morphology might-not be the products of micro-evolution. But they would be the variants brought about by quantitative traits (when living in favorable natural environments). Fossils of these kind of variants which slightly differ in morphology, could enable the curators to arrange them as 'series of specimens' Fig:33 and to present them as evidence for the 'different stages of progression' of micro-evolution. If we could give some thought to our minds: imagine what if today’s dog species get fossilized and are dug up by future paleontologists? What if their fossilized skeletons are neatly arranged to explain the micro-evolution of dogs; starting with the little chihuahua and ending up with the great danes, with a few missing links getting discovered once in a while! So it would be better ‘not’ to use morphological variations as a criterion in any way, when gauging the finegradations of 'micro-evolution' in the organisms that exist today. But it would be wise to use the degree of incapacity to interbreed (hybridize) caused by the “divergence of species branding factors”, as the chief criterion to measure the progress of micro-evolution. Let's go through this in detail in the next chapter. ~~~ 5 Species branding’s role in Darwinian speciation Speciation concepts The following speciation concepts have been framed based on the degree of difficulty to interbreed, experienced due to the divergence of species branding factors. It could be theorized that as speciation proceeds; the least separate species interbreed even in the wild, then there are the once that are a bit-further away which interbreed only under captivity, those that are still-further interbreed only by invitro means (IVF) and with being further-apart they are clearly distinct species and they don't interbreed. Lets look in to these in detail. 1) Inbreeding evasion: From the classical definition of species, species are a group of organisms which are not-capable of interbreeding with other species in the wild. As observed during inbreeding evasion where the process of speciation appears to begin; the newly formed variants mostly prefer mating with similar variants, than breeding with dissimilar variants. For example: two groups of Drosophila pseudoobscura, were fed with two different types of food for eight generations Fig:34 [72]. At the end of the experiment they preferred mating only with those individuals; who had consumed the same food type (similar variants), over mating with those that had consumed the other food type (dissimilar variants). In this sense Drosophila pseudoobscura consuming a certain type of fruit in the wild Fig:35 for successive generations, will avoid breeding with variants of the same species which have been consuming another type of food for several generations. Figure:34 Inbreeding evasion experiment as observed by Diane Dodd in fruit flies. [73] Figure:35 Diane Dodd’s fruit fly experiment happening in nature. [74, 75] The interruption in breeding between morphologically identical Drosophila pseudoobscura (reproductive isolation) may be caused by factors such as, the epigenic switches like methylation. They could isolate the 'new variant' of a species by avoiding it from mating with other members of the same species, there by initiating the process of origination of a new species. There is also the possibility that the reproductive isolation could be due to simple reasons such as preference due to body odor, caused by consuming different food types. In any case, inbreeding evasion could be considered as an initiating event in the long run towards speciation. Difference in bird songs/ mating calls (behavioral isolation), reproduction at different times of the year (temporal isolation) etc, could be the result of inbreeding evasion; and could be taken as the extrinsic (external) outcomes of inbreeding evasion. 2) Interbreeding in captivity: As speciation proceeds further, inbreeding evasion and geographic grouping leads to new morphological groups like the finches that bear unique beak shapes. Some of these variants are capable of interbreeding in captivity, while they do-not normally interbreed in the wild. For example: interbreeding has been reported between several species of Darwin's finches which are known to interbreed more often in the lab than in the wild. This ability to interbreed shows that the species branding factors of these finches are still the same. From their breeding pattern they can no more be considered as distinct species, but have to be regarded as different breeds (dissimilar variants) of a single species. After Darwin had left the Galapagos Islands, continued research on the Darwin's finches has observed that the different species of finches that were celebrated by Darwin Fig:36 do in fact interbreed with each other even in the wild. Geospiza fortis has been reported to interbreed with G. magnirostris [76], G. fuliginosa interbreed with G. fortis [77], G. scandens interbreed with G. fortis [78]. Figure:36 Drawings of the different heads and beaks of finches that Darwin observed in the Galapagos Islands. Recent studies in molecular biology on Darwin’s finches confirm that their beak morphology is the outcome of five different genes (polygenic) Fig:37 [80] i.e. Bmp4, Calmodulin, TgfβIIr, β-catenin, Dkk3. This adds support to the view that the different species of Darwin's finches can be considered as mere variations Fig:38 and those that interbreed may actually belong to a single species Fig:39. Reports of the different species of Darwin's finches interbreeding in the wild, questions the very definition of species. The classical definition of species, as organisms which do-not interbreed with other species in the wild, seems to be fragile and may need an update. Because interbreeding happens among the finch species; in captivity and even in the wild, one can be sure that no species branding has happened in them. But in some organisms, it has been reported that; the outcome of the captive interbreeding is sterile progeny or lethal zygotes. This sterility or lethality could be due to incompatibility among gene pairs (Dobzhansky-M uller gene pairs), of the two hybridizing species. These gene pairs are known to be compatible when breeding with-in members of their own species. With two different species of Drosophila (D. melanogaster & D. simulans) hybridizing; they essentially have the same chromosome number, which means their genomes might not differ by macro-mutations. But most likely differ by micro-mutations like the Dobzhansky-M uller gene pairs. Upon confirmation, these gene pairs might also be considered as new species branding factors. Figure:37 The distinct beak morphologies in Geospiza are generated by differences in the time and place of expression of different genes: Bmp4, Calmodulin, TGFβIIr, β-catenin, Dkk3. Through their action on different skeletal tissues, different genes alter independent dimensions of growth. [81] Figure:38 The beak of the sharp-beaked finch, G. difficilis, represents a basal morphology for Geospiza. Expression and function of the genes bring changes in beak dimensions of the more derived species. [82] Figure:39 Functional analysis of : TGFβIIr, β-catenin, Dkk3 etc, in the chicken model system. [83] 3) Interbreeding in vitro: As speciation diverges the dissimilar variants further, they interbreed not-even in captivity; but only through in vitro means in the lab such as in vitro fertilization Fig:40. This could be because of some ‘primary’ species branding factors which have diverged quickly. This could include the cell surface proteins which are needed for the entry process of the sperm in to the ovum. In vitro fertilization overrides these proteins by the injection of sperm directly into the ovum. For example: stickle back fishes are found in the northern hemisphere where their different species vary in features like body size, body shape, presence or absence of the defensive armor, size & pattern of skeletal structures, etc.. M ore than 40 different species of stickleback fishes have been classified. Among them some species can interbreed through laboratory mating, while there are some other species which can interbreed only through in vitro fertilization [84, 85]. Because these variants yield to interbreeding through in vitro manipulations, this makes us understand that only the primary species branding factors (those proteins involved in chemotaxis and Sperm egg surface interaction) have diverged and their secondary species branding factors have-not diverged far enough. So these stickle back variants cannot be called as distinct species. Therefore, they may be considered (together with the finches) as 'un-established species'. But one can be sure that branding, has happened to a certain extend in these stickle back variants. Figure:40 Three spined stickle backs. [86] Figure:41 The standard in vitro fertilization procedure. [87] 4) Fully branded species: With further deviation of the diverged variants, their 'species branding process' gets completed. As a result they can never interbreed either in the wild or in captivity or even with the help of in vitro techniques like in vitro fertilization. At this stage they may be authenticated as separate species or as stable morphological forms. These stable species have the potency to establish themselves in large numbers and to leave behind ample fossils. A stable species is one which has distinguished its species branding factors far-away from its species of origin such that; both the primary and secondary species branding factors have diverged. As it is widely accepted, a species radiates into different morphological variants; when a new niche is born or when a former niche gets vacant following a mass extinction event OR due to artificial selection. From the above sections it is evident that; all these progenitors of a species like a few finch varieties and some of the stickle back fish variants may-not be classified as different species, as they interbreed. But they could be only considered as different morphological variants or subspecies. It could take a while until stable species emerge out from among these variants. It could also be that only the stable species leave behind the ample amount of fossils required to be discovered through excavations in the future. Apart from the fossils of stable species, fossils of all other variants obviously would be found in limited numbers and might be perceived as the rare missing links. From what has been discussed till now, one gets to know that the species branding factors are an independent entity from factors such as micro& macromutation/evolution. The different prospects of speciation are discussed in the next chapter. Speciation can have several prospective results depending upon, whether it involves micro- or macro-mutations and if it involves the SBFs or not. ~~~ 6 Different prospects of species branding The species branding hypothesis acts as an unifying hypothesis on evolution; and explains the various aspects of evolution, which are discussed in this chapter. Figure:42 The prospects of micro-mutations and macromutations in terms of SBFs. Prospects of micro-mutation Case 1: Micro-mutations involving both SBF and non-SBF genes (Darwinian speciation) Apart from micro-mutations happening to SBF genes (during Darwinian speciation), over time micro-mutations also happen to the non-SBF genes. As seen in the previous chapter we come to know that micro-mutations happening in the genes of the species branding factors (SBF) could result in the origin of a new sub-species. These new subspecies over time could speciate in to new species. This process of speciation passes through different stages of speciation like inbreeding evasion, capacity of inter-breeding only in captivity, capacity of inter-breeding only by in vitro means and the establishment of stable species. These radiating new species slowly get ‘adapted’ to the environment by occupying a micro-niche. Case 2: Micro-mutations involving only SBF genes (Cryptic species) Cryptic species can be explained with the help of species branding factors. The cryptic species originate when a given litter of progeny differ, in its species branding factors from the parent’s SBFs. Interbreeding among the members of the litter (in course of time) would give rise to a population of the new cryptic species; which look exactly similar to the parental species in all means. But are incapable of interbreeding with it. Examples for cryptic species include tetrahymena; species of flies, fungi, fishes, corals etc. Case 3: Micro-mutations involving non-SBF genes (Variants / Quantitative traits) · M ost micro-mutations result in new genotypes. These new genotypic variations are primarily due to the single nucleotide polymorphisms (SNPs), but majority of these SNPs do-not exhibit phenotypes. · Relatively rarely, micro-mutations produce new phenotypes. This may be the result of SNPs Fig:43 (the exceptional ones) which are capable of exhibiting a phenotype. Or can be due to small scale duplications, gene level rearrangements, minor recombinations etc. These minor mutations are generally located in, or around the vicinity of a gene; and could be associated with quantitative traits (QTL). Together they could produce different morphological variants or breeds, which may not be evolutionarily beneficial (as their features tend to fluctuate over generations). · M icro-mutations can also lead to macro-evolution as seen in the case of Prof. C. Lenski's experiment on E.coli which was discussed earlier in chapter 3. Figure:43 S ickle cell anemia is an example of a SNP which produces a phenotype and happens in a non-SBF gene. But this deleterious SNP is not-evolutionarily beneficial. [88, 89] Prospects of macro-mutation M acro-mutations almost always result in macroevolution by bringing about major changes to the genome; these changes may include changes to the SBFs or not. Case 4: Macro-mutations involving both SBF and non-SBF genes (Speciation through saltation) Genome level duplication brings about major changes to the genome of a given organism Fig:44 possibly through duplications and shuffling. This could include changes occuring to both the SBF and non-SBF genes. But because copies of the original SBFs are possibly present; this will permit continued mating with the parental population, resulting in hybrids (of the same species). With the huge incrementations to the genome produced as a result of the duplication, it would probably take at least a few generations for the nascent mutant to settle down into a relatively stable form. The mutant mating with the parental population would only assist the smooth occurrence of this process. Over time hybrid SBFs would be generated which would enable inbreeding only among the new hybrids. The intensity of phenotypical innovation brought about by this event will determine if a new species, or a genus or order or class is produced. With new features not-found in any of its relatives; the organism would sneak into a new ecological niche if possible into a new ecosystem, thereby ‘adopting’ a new environment. Eg: 2R & 3R genome duplications which happened during the evolution of fishes were macroduplication events, Fig:27 they were most likely accompanied by co-duplication of the corresponding SBFs. By this way fishes have colonized the oceans. Insect body plans have evolved through genome duplication events (macro-evolution through macro-mutations). Through this way insects have colonized the earth. Figure:44 How to pass from the bony vertebrate’s last common ancestor genome (12 chromosomes) to the genomes of humans and Tetraodon. M odel derived from the study of synteny groups between those two modern vertebrates. [90] Case 5: Macro-mutation involving non-SBF genes (Hybrid species) As a fact two phenotypically different species like lion and tiger have been known to mate and produce hybrid progeny (liger/tion). In the first place this process shows that the SBFs of the two given species have-not diverged and are compatible (it is only that the non-SBF genes differ massively). As observed, the difference in the chromosome numbers between the hybridising species pair (see example); is indicative of macro-mutations which had already diverged their non-SBF genes. But their ability to mate shows that they have compatible (same) SBFs. But unlike case-4, where the hybridization process (mixing and matching of genes) happens within the same species and occurs as a smooth progression that gets on perfecting over generations. In case-5, the hybridization occurs between two different species and instantly in a single generation. This only leads to more defects than innovations, especially in the reproductive genes. As observed in many cases, the offspring are often substandard and sterile. So obviously the SBFs have no evolutionary role to play. As examples: Tiger and lion though belonging to different species can mate to produce offspring Fig:45&46; similarly horse (64 chromosomes) and donkey (62 chromosomes) can mate producing the mule/hinny (63 chromosomes) Fig:48&49, which are mostly sterile. One could infer that the SBFs are same in the two related species, so they are capable of matting to produce offspring. But the difference in their chromosome numbers shows that macroevolution (at the non-SBF genes) had seperated them. These different morphological variants (hybrids) which are produced are mostly evolutionarily non-beneficial. The occurrence of this type of hybrids in fish [91], amphibian [92], birds [93] & mammals [94] etc only reminds us on the presence of, these many pairs of animals holding compatible SBFs (primary) in between them. The fact that these hybrids occur very rarely, could also explain the scarcity of the intermediate types of some fossil records. Pl Note: Deletion of one/few chromosomes in a given genome (organism) is also M acro-mutation. This can give rise to a new hybrid-species. The new species will have a relatively compact genome and can hybridize with the parental species; provided it still contains the SBF gene in its genome. Eg., It is possible that through chromosomal deletion events: The Wild horse (66 Chr) >> gave>> Domestic Horse (64 Chr) >> gave>> Donkey (62 Chromosomes). During the origin of these hybrid species, their primary SBFs remain unaltered...! Figure:45 Tion. [95] Figure:46 Liger. [96] Figure:47 Leopon. [97] Figure:48 M ule. [98] Figure:49 Hinny. [99] Figure:50 Zorse. [100] Figure:51 Zonkey. [101] [Figure:52 Cama. [102 For a whole list of hybrid animals please refer to: http://www.messybeast.com/genetics/hybrid-cats.htm ~~~ 7 Environment’s roles The environment which is an external factor obviously plays the prominent role in shaping the evolution of organisms. Some organisms like the puffer fish have had such severe 'negative environmental pressure' (purifying selection) that they lost the extra genes by deletion and have resulted in having compact genomes. On the other hand fishes in the artic and antartic have evolved antifreeze proteins which give them an advantage over the environment or in other words they are under 'positive environmental pressure' (adaptive selection). There exists a third type of external pressure which is the 'neutral environmental pressure' seen in organisms like the lungfish and coelacanth. This neutral pressure allows them to continue having their rudimentary hind legs instead of fins. The Great Barrier Reef today stands as an example of evolution through co-operation among varied organisms. And much evidence has accumulated in this topic of ecology. But many of the symbiotic relationships among organisms probably were not revealed during the times of Darwin, that Darwin was biased towards evolution through natural selection (negative selection) and not adaptive selection (positive selection) which his colleague Alfred Russel Wallace believed in. In other words, Wallace emphasized on the importance of adaptation to the environment for survival and Darwin emphasized on competition even-between individuals of the same species for survival. But unfortunately misinterpretation of science by policy makers led to wars of historic proportions. But today’s world is relatively much peaceful and well developed, now we know that cooperation, collaboration, mergers and accusations are all part of the game. Evidence for possitive selection can also be found in microbes. This include the cyanobacteria that entered in to an endo-symbiotic relationship with the eukaryotes, becoming the chloroplast. Similarly the aerobic bacteria became mitochondria. And the amoeba transformed in to the white blood cells. Evolution in action While the neo-darwinian views insist on evolution only through gradualism the other darwinian concepts like selection, adaptation, survival etc. are widely acknowledged as visible proofs for evolution happening even today. To quote a few examples of evolution in action: environmental selection either natural or artificial (the peppered moth Biston betularia) [103], the survivor is the fittest and it can propagate (the cane toad of Australia) [104], adaptation to the environment (Italian wall lizard Podarcis sicula evolution in the island of Pod M rčaru [105] (possibly macroevolution), the yellow bellied three-toed lizard Saiphos equalis of Australia which either lays eggs or gives live birth as an adaptation to coastal regions or inland area [106], adaptive variations (Darwin's finches) [107, 108], evolution of drug resistance in bacteria [109, 110], and viruses [111, 112] (mostly saltation), etc. As we know, population genetics has a prominent role to play in evolution. Species branding and its role in the population aspects of evolution are discussed in detail in the next chapter. ~~~ 8 Species branding in populations All the different concepts discussed so far in this book can be interpreted in terms of population biology, this chapter has the details. Sympatric speciation Fig:53&54 Obviously variations can be observed in any given species. They may be in the form of genetic variations which are not-visible, or the phenotypic variations which are the visible products of some of the micro-/macro-mutations. Just to iterate: phenotypic variations (those which are not fluctuations) may be caused by micro-evolutions (mostly micro-mutations) or macro-evolution (either micro or macromutations). During sympatric speciation, most likely microevolution happens frequently. But in the course of time most organisms which evolved through micro-evolution get filtered; as these slight mutants are incapable of competing with their established originator, for the existing niche. But most organisms that evolved through macro-evolution obviously could have the fitness to occupy the existing niche (or even a new niche). Unfortunately these macro-evolved organisms may still retain the ability to reproduce with the originator species (if branding had-not occurred in them), so the new characters which they had acquired may get dissipated by interbreeding. But if species branding would have taken place in them, then they are capable of: becoming fully branded species (in course of time), populating in vast numbers and leaving behind huge amounts of fossils. As against the other less fortunate macro-evolvants; which do-not undergo species branding and are unable to establish themselves. And so they become rare fossils; (these macro-evolvants which exhibit ‘unique phenotypes’ might give rise to those rare fossils, which are generally considered as the ‘misfits’ among a series of fossils). Figure:53 Various types of speciation among populations. [113] Figure:54 Various types of speciation among populations. [114] Allopatric speciation: Unlike sympatric speciation which we looked at earlier, micro-evolvants have a better chance to survive in allopatric speciation Fig:53&54; since these organisms move to a different location (founder event), separated by a physical barrier (vicariant). In this new location micro-evolutions may give the evolvants an upper hand, even over a native of this location. But in other case if macro-evolution would take place in this location, then without doubt it could give the evolvants a much better leverage. If individuals of these evolved organisms would move back to the originator’s primary location, (before species branding had taken place in them); then they would only be capable of forming hybrids with the originator population. But if these evolvants had undergone species branding in advance, then phenotypically and reproductively they stay as distinct species; even if they were to get back to the originator’s primary location. Species branding in microbial populations: Due to their small size and short generation times; very large number of variations (genotypic and phenotypic) can be seen in a given microbial species. But even strains which have evolved unique phenotypes do-not branch off in to new species. Instead these phenotypes are shared with other strains through horizontal gene transfer processes; such as conjugation, fusion, by means of viruses etc.. When a given strain finds a niche for itself, and if species branding would take place in it; then this strain can be said to have successfully established as a new species. So by now any genotypic or phenotypic innovation that would take place in the new species, is retained (confined) within the species; and necessarily need-not be shared with peers. The next chapter of this book involves an insilico case study using different bacterial varieties. ~~~ 9 A case study with mammals and microbes The following text in this section has to be taken with a pinch of salt, as the available data is not-exhaustive. While natural selection (through reproductive isolation) is an extrinsic source for speciation (hindering gene flow); species branding is the intrinsic factor for the same. To find out how species branding happens intrinsically, one could try to understand how species branding happens in the primary SBFs of M ammals and of the simple systems like M icrobes. This chapter deals with case studies carried out in the mammalian and microbial systems, by studying their genomes through insilico means. 1, Mammalian bioinformatics-case studies: Earlier in chapter 2 we had discussed a bit, about the interaction of proteins on the surface of sperm and egg during the fertilization process. In this section we will be dealing with them in detail. IZUM O1 is a cell surface protein which was identified in 2005 [115] ; and is found on the surface of the sperm cells. Homologues for this protein are found across many mammalian sequenced genomes. JUNO is its counterpart found in the surface of the egg cells. First identified in 2014 [116], it also has homologues across many mammalian sequenced genomes. Empirical studies have confirmed the binding of IZUM O1 with the JUNO protein, and crystal structures have also been made available for this pair. This confirms the docking between IZUM O1 with JUNO; with this pair of proteins serving as a lock & a key, in between the fertilizing egg & sperm. This promissing protein pair is capable of revealing us vital information about species hybridisation, species branding and the species problem; than ever before. So a detailed case study involving IZUM O1 & JUNO proteins, was done through bioinformatics means. Donkey and the Horses: Donkey ( Equus asinus) has 62 chromosomes, while the Domestic horse ( Equus caballus) has 64 chromosomes and the Wild horse (E quus przewalskii) has 66 chromosomes. In spite of the difference in their chromosomal numbers; they are capable of interbreeding with one another, and producing hybrids like hinny, mule etc. A comparison of the IZUM O1 proteins and the JUNO proteins from these mammals shows that; their sequences align Fig:55&56 very well with one another (~100% identity). Pl NOTE: In all the below alignments the color Red represents 'identical amino acids' among the aligned protein sequences; while the color Blue represents 'mismatches' which are the non-identical amino acids. And Green indicates the Sequence ids. Figure:55 An alignment of three isoforms of the Egg-surface protein IZUM O, from three different Equus species. Figure:56 An alignment of the Sperm-surface protein JUNO from the different Equus species. Inference : The Equus species alignments show absolutely No mismatches, when thier IZUM O proteins were aligned. While they show just a single mismatch in their aligned JUNO proteins. This high level of identity among these species branding factors (IZUM O and JUNO) reflects the fact that Equus species can easily form hybrids. Figure:57 The names of the hybrids, formed between the different Equus species [117]. Pl Note: The genome sequences of Zebra and Pony are yet to be available. Source: http://messybeast.com/genetics/hybridequines.htm Mouse and Rat: M ouse ( Mus musculus) Fig:60 has 40 chromosomes, while the Rat ( Rattus norvegicus) Fig:60 has 42 chromosomes. Serious efforts to interbreed them have all failed [118]. Sequence comparison of the IZUM O1 proteins and the JUNO proteins from both the organisms shows that Fig:58&59; there are serious mismatches in between the two aligned sequences along the entire stretch. Figure:58 An alignment of the Egg-surface protein IZUM O from Rat and M ouse. Figure:59 An alignment of the Sperm-surface protein JUNO from Rat and M ouse, with mouse having two isoforms of the protein. Inference: The alignment between Rat and M ouse shows large number of mismatches, at both the IZUM O & JUNO proteins. This result is perfectly in-line with the known fact that, efforts to breed a rat and a mouse over many centuries have all failed..! Figure:60 A picture of M ouse and Rat [119]. Camel Species: Arabian camel ( Camelus dromedarius), the Bacterian camel ( Camelus bactrianus) and the Wild Bacterian camel ( Camelus ferus) all of them Fig:63 have 74 chromosomes as part of their respective genomes. They do, but rarely interbreed with one another, producing hybrids like Bukht. A comparison of the IZUM O1 proteins and the JUNO proteins from these Camelids shows that Fig:61&62; their sequences align with one another considerably. Figure:61 An alignment of the Egg-surface protein IZUM O from three different Camelus species. Figure:62 An alignment of the Sperm-surface protein JUNO from three different Camelus species. Inference: The alignment between the different Camelids shows few mismatches. This alignment does not show a vast diference as observed in the case of 'Rat vs M ouse' or is highly identical as in the case of the 'Equus Spps'; but falls in between. This co-relates with the fact that, hybrids do occur among the Camelus but relatively rarely. Figure:63 A picture of the different Camelids and their hybridization pattern [120]. Sheep and Goat: Sheep ( Ovis aries) Fig:66 has 54 chromosomes, while the Goat ( Capra hircus) Fig:66 has 60 chromosomes. In spite of the difference in their chromosome numbers; they do but rarely interbreed with one another, producing hybrids like geep or shoat Fig:67. A comparison of their, IZUM O1 proteins and the JUNO proteins; results in their sequences aligning with one another considerably Fig:64&65. Figure:64 An alignment of the Egg-surface protein IZUM O from Goat and Sheep. Figure:65 An alignment of the Sperm-surface protein JUNO from Goat and Sheep. Inference : The sequence alignment seen between goat and sheep is similar to Camelids, showing few mismatches. Again supporting the fact that hybrids do occur between them, but relatively rarely. Figure:66 Picture of a goat and sheep pair [121]. Figure:67 Picture of a geep/shout [122]. The above case study involving four different sets of mammals reveals, the three distinct levels in their ability to hybridize: 1) With Equus Spps being the first; having high sequence identity and are easy to hybridize. 2) Then comes the 'Camelids' and 'Goat vs Sheep'; where the sequence identity is fairly identical and they rarely hybridize. 3) Finally the 'Rat vs M ouse'; showing high degree of difference between their sequences, corelating well with their inability to hybridize. Confirmational test LEAD: The case studies done so far fall in favor of the Species Branding Hypothesis; suggesting that IZUM O1 & JUNO proteins act as potential Species branding factors. But the role of these proteins can be confirmed; only when the corresponding proteins from some of the Cryptic species sets would be sequenced. Upon sequencing, if one finds that the sequences of a given Cryptic species would differ; then it would help one confirm that these proteins in fact play a major role in species hybridisation. In this case these the proteins would also play a vital role in the origin of a new species. 2, Microbial bioinformatics-case studies: To find out how the 'process of species branding' occurs, one could try to understand how it has happened in simple systems like microbes. Which in turn could be learnt by looking at, how the restriction enzymes have evolved across various bacteria. Studies in Bacteria suggests that Species branding can happen at a smaller or in a larger scale. Micro-species branding: Just like micro-mutation or micro-evolution, species branding can also happen at a smaller scale. HinP1I and M spI the restriction modification systems can be considered as a good example for this. Their tight structural superimposition and the trivial difference between their restriction-cleavage sites, is a good example for micro-species branding Fig:68&69. Figure:68 Structural superimposition of HinP1I (green) and M spI (cyan). [123] Figure:69 As visible both the restriction enzymes differ only slightly in their cleavage sites. [124] Macro-species branding: Similarly like macro-mutation and macro-evolution, large scale species branding can also be seen in the microbial restriction modification systems. Examples for these kinds of restriction modification systems, can be seen from figure Fig:70. The figure shows how diverse the restriction enzymes can be and how modular evolution has taken place in them. Figure:70 M acro-species branding among restriction enzymes. [125] Legend: The topology diagram with triangles represents β-strands, circles represents α– and 310-helices, and connecting lines represents loops. Shaded shapes are the conserved ones and white ones are novel. Structural distance matrix using PDB files: For making any comparison in between restriction enzymes; one has to look to structural information, since sequence similarity among them is highly limited. In an in silico experiment by TR Singh et al, multiple structure files of restriction enzymes in PDB format were compared to write an output file containing the set of distance matrices Fig:71. The distance matrix scores correspond to the level of difference between the various restriction enzymes. Figure:71 Structural distance matrix using PDB files. [126] Phylogenetic tree made using the derived distance matrix: To visualize the relation between the various restriction enzymes; the distance matrix scores in between the various restriction enzymes (as computed by TR Singh et al) were used to generate a phylogenetic tree Fig:72 by using the program FITCH. Figure:72 Phylogenetic tree made using the derived distance matrix. Interpreting the phylogenetic tree: given below are examples for micro-species branding and macro-species branding, their phylum and class are also included. Examples for micro-species branding {MspI & HinP1I} Moraxella catarrhalis [M spI] Phylum: Proteobacteria Class: γ-proteobacteria & Haemophilus influenzae [HinP1I] Phylum: Proteobacteria Class: γ-proteobacteria Examples for macro-species branding {EcoRV & [BamHI + SdaI]} E.coli [EcoRV] Phylum: Proteobacteria Class: γ-proteobacteria & Bacillus amyloliquefaciens [BamHI] Phylum: Firmicutes Class: Bacilli + Streptomyces Spps [SdaI] Phylum:Actinobacteria Class:Actinobacteria M icro-species branding can be easily differentiated from macro-species branding by looking at the above highlighted class and phyla in the phylogenetic tree of bacterial groups Fig:73. In the case of microbes the restriction enzymes act as primary SBFs during speciation; while antibiotic production, virulence, zymic activity, codon bias etc. can be considered as the secondary SBFs during this speciation process. Figure:73 Universal phylogenetic tree of bacterial groups. [127] ~~~ 10 Resurfacing of past theories The recent availability of genome information is making the evolutionary histories of many organisms to be re-written [120, 121]. The genomic era is also generating new evidences to support former theories of evolution like lamarckism. In a debate between gradual versus punctuated change one could make an educated guess that darwinism is right in the sense that gradualism does occur often at the genotypic level. Saltationism is also right in its own sense that 'morphological discontinuity/punctuation' occur typically at the phenotypic level, seen as noticeable changes to the morphology. Neo-lamarckism and epigenetic inheritance Surprisingly, the discarded theory of lamarckism has also earned recognition in recent years as neo-lamarckism or soft-inheritance. According to which characteristics acquired during an individual's lifetime can be transmitted to their offspring in non-mendelian ways. Epigenetics [122-124] explains how this non-genetic inheritance happens and describes the molecular events behind it. The environment is known to affect regulatory proteins like hormones which in turn methylate the DNA at unique sites, thereby switching on and off the expression of specific genes. Though this DNA gets inherited the mendelian way; by being bonded to it are the modifications, (e.g. methylation) that are possibly passed on as well. Therefore, the genes are inherited either switched on or off; which in turn influences the phenotypic characters of the new generation. So in the end characters acquired during one's lifetime could be passed on to his progeny through epigenetic inheritance. It should be emphasized however, that all current hypotheses about epigenetic inheritance should be taken with a grain of salt. Looking at the punctuations seen in the fossils, one gets the feeling that macro-mutations could have led the vertical evolutionary process, while micro-mutations contributed mainly towards horizontal (lateral) evolution. Figure:61 An illustration of micro and macro-evolution (from the phenotypic perspective). With X-axis as time and Y-axis as phenotypic innovation. ~~~ Final word With the advent of the era of systems and synthetic biology, a more holistic approach to life science could be expected in the near future. The system of species branding and the various factors associated with it could be revealed to us sooner than we would imagine for it to happen. Cambrian evolution, evo-nhancer hypothesis and other concepts will be discussed in a separate book which is in the making… for the mean time I will be happy to have your comments posted to me: joseph.on.evolution@gmail.com Figure:62 Darwin commenting about his theory in his book; ‘On the origin of species: by means of natural selection or, the preservation of favored races in the struggle for life’. [125] With evidences for saltation found in the sequenced genomes of organisms [125-127]; Darwin mentioning about “slight modifications” in his book makes one doubt, if his statement could be correct? But Darwin cannot be considered wrong, Fig:62 as genotypic evolution mostly happens gradually and phenotypic evolution mainly occurs as noticeable saltations (as supported by Prof. C. Lenski’s experiment and the punctuations seen in fossils). Having said this, darwinism and saltationism can be considered as the two sides of the same coin; Richard Goldschmidt, Stephen Jay Gould and others observed the phenotypic changes or saltation that was obviously seen in both the living organisms and the fossils. While darwinist like Susumu Ohno tried to explain the saltations through genotypic causes (like genome duplications) which brought about the huge phenotypic changes in organisms. The problem with present day Darwinists is that: They seem to mistake, the much frequently occuring quantitative traits, for the less prevalent microevolutions. They supposedly under estimate the power of saltations. Especially those macro-evolutions which are brought about by micro-mutations. They seem to ignore the possibility of phenotypic innovations evolving rapidly, due to micro-mutations occuring at the evolutionary hot-spots. And they appear not to accept the ground reality about the fossil records. They wrongly believe that speciation happens at the level of populations, following a gradual phyletic tree. While it specifically happens at the level of SBFs, following a (relatively) 'punctuated' evolutionary tree Fig:61. This work of literature just tries to give a ‘big sketch’ on speciation by making a consensus out of the data available to us. But the big picture will be revealed to us, only when genomic sequences of many more organisms become available. With many genome projects in the line, there is much hope that this would become a reality. Undoubtedly natural selection has its hand over any and every aspect of evolution. But during the origin of new species, speciesbranding is the intrinsic factor which drives speciation; while natural selection has to be taken as the extrinsic factor which influences speciation from the exterior. ~~~ FAQs (Frequently asked questions) · How could the spectrum of related fossils originate? When we look at the different breeds of dogs we see that they are the quantitative traits of the dog species. It is just that the dog quantitative traits have been segregated by means of artificial selection. Similarly quantitative traits can be found in any given organism, which when segregated by means of natural selection; give rise to a spectrum of variants of that organism. These variants generally leave behind a spectrum of related fossils. Among them the variant which eventually establishes itself would leave behind the ‘most fossils’, in other words would leave behind the ‘most common’ fossil-type. And the other variants together would leave behind a spectrum of ‘rare fossil types’. · How could we differentiate the variants seen during speciation through micro-evolution (Darwinian speciation), from their quantitative traits? For example Darwin observed variants of finches which are a good example of speciation thorough microevolution; but the question remains as how do these variants differ from the quantitative traits of the finches..? The answer is simple: it does not matter if they are variants or quantitative traits, if species branding has taken place in them; then speciation through micro-evolution has happened in them, if it has not then they will be considered as mere quantitative traits. From observations most Darwin’s finches seem to be mere quantitative traits, that were separated by means of natural selection; as they tend to interbreed in nature. But the ones which do not interbreed, could be considered as the non-QTL variants; formed as the result of micro-evolution. · How could unique fossils originate? We know that during sympatric speciation a new species originates from among the native organisms. Under these circumstances of absence of any natural barriers, the newly formed species most likely is a macro-evolvant which survives the competition, as micro-evolvants easily perish in this environment. Under these circumstances unique organisms and organisms which originate by saltation tent to evolve. These organisms leave behind the unique fossils which do not have any missing links to connect them to the other related organisms’ fossils. · What are the evidences against the popular belief that 99% species of organisms that lived on the face of the earth did not get fossilized? The artifacts hypothesis claimed that fleshy parts of organisms get fossilized extremly rarely and so claimed that 99% of species types did not get fossilized. This hypothesis has been disproved by the unearthing of jelly fish fossils in south china. Furthermore, with the scarcity of the missing links, just the common fossils are being repeatedly unearthed during fossil hunting expeditions (even at different continents). This shows the inequality in numbers among the different types of organisms which lived on the face of the earth. The major fossils must belong to the organisms which had established themselves. M issing links which surface once in a while could belong to the un-established variants or quantitative traits. And the unique fossils might belong to unique organisms, which were sparse in numbers. Hence an evolutionary tree drawn using phyletic gradualism can be wrong; but a tree drawn using punctuated equilibrium (with the common fossils) can be considered viable. · Are there any examples for saltation? Saltation or macro-evolution being a rare event can happen approximately once in a thousand generations of an organism. So observing saltations in most organisms is not possible with in a human life span of about 70 years. But saltation has been experimentally proved to happen in the lab, using the bacteria E. coli which has a generation time of only 20 mins. Sequenced genomes also provide us with evidences for the occurrence of saltation events. Richard Goldschmidt, one of the lead proponents of Saltation exclaimed this in simple terms that “a reptile laid an egg and a bird hatched out of it..”! · What is species branding? For example chimpanzees cannot reproduce by mating with humans. In other terms sperm from a chimpanzee cannot recognize a human ovum. Some how humans have branded their sperm such that, they could mate between the different breeds of humans and not with chimpanzees. This kind of molecular branding seen in each organism is called as species branding. · Do humans have quantitative traits? The different breeds of humans like caucasian Europeans, native Africans, Asians, aboriginal Australians and others may be considered as the quantitative traits in humans. For example: M ulatto children are born, when a black parent and a white parent get in to family relationship. But on the other hand when two mulatto parents get in to relationship, their characters can get segregated the mendelian way and totally black or totally white children could be born. This was the case with mulatto parents Kylee hodgson and Remi horder who gave birth to twins Kian and Remee Fig:76. Figure:76 Quantitative traits of humans in action. [136] This reversibility of ancestral characters confirms that the different breeds of humans are none but quantitative traits found in the human species. · What are evolutionary hot spots? Some key genes like the developmental genes; and some mutational hotspots like the protein active sites, gene promoters, could accelerate the evolutionary process; they could be treated as evolutionary hotspots. · What could be the reason behind donkey and horse mating in spite of being different species? As obvious donkey and horse must have had a common ancestor. Their ability to mate to produce offspring shows us that they have the same species branding factors. M ost likely macro-mutations had occurred to their common ancestor, so that they differ morphologically and genetically from each other. · Are evolution and speciation two different things? Evolution literally means change; any change that occurs in an organism is evolution. For example the human species has learnt to use its brain in phenomenally dexterous ways in just over the past two decades. This means humans have evolved over the recent years. Speciation is different from evolution; it is about the origin of a new species. For example if a breed of humans are unable to interbreed with another; then speciation has happened in the new breed, and a new species of humans can be believed to have risen. But in reality no such cases have been reported. Also cryptic species of humans have not been reported. So humans have evolved over the years but have not yet speciated. Evolution and speciation are two different things. To cut the long story short, speciation happens in the case of cryptic species. But in the case of hybrid species evolution happens. ~~~ Contents of this book as Mind map: NOTE: (Pl zoom-in [+] to view in a mobile device/ Best viewed on a computer screen) References: 1. http://a 1.s 6i mg.com/cdn/0015/p/5194445_16325308_l z.jpg Evolution chandelier. 2.Goul d, S.J., & El dredge, Ni l es , Punctuated equilibria: the tempo and mode of evolution reconsidered. Pa l eobi ol ogy, 1977. 3 (2)(115-151): p. p.145. 3.Ma tti l a , T.M. a nd F. Bokma , Extant mammal body masses suggest punctuated equilibrium. Proc Bi ol Sci , 2008. 275(1648): p. 2195-9. 4. http://upl oa d.wi ki medi a .org/wi ki pedi a /commons /6/69/Punctua tedequi l i bri um.s vg, Punctuated equilibrium. 5.Butl i n, R.K., J. Ga l i ndo, a nd J.W. Gra ha me, Review. Sympatric, parapatric or allopatric: the most important way to classify speciation? Phi l os Tra ns R Soc Lond B Bi ol Sci , 2008. 363(1506): p. 2997-3007. 6.Hos ki n, C.J., et a l ., Reinforcement drives rapid allopatric speciation. Na ture, 2005. 437(7063): p. 1353-6. 7.Ma ri e Curi e SPECIATION Network, B.R., Debel l e A, Kerth C, Snook RR, Beukeboom LW, Ca s ti l l o Ca ja s RF, Di a o W, Ma a n ME, Pa ol ucci S, Wei s s i ng FJ, va n de Za nde L, Hoi kka l a A, Geuveri nk E, Jenni ngs J, Ka nka re M, Knott KE, Tyukma eva VI, Zouma da ki s C, Ri tchi e MG, Ba rker D, Immonen E, Ki rkpa tri ck M, Noor M, Ma ci a s Ga rci a C, Schmi tt T, Schi l thui zen M., What do we need to know about speciation? Trends Ecol Evol , 2012. 8. http://i ma ge.tutorvi s ta .com/content/heredi tyevol uti on/a l l opa tri c-s peci a ti on.jpeg, Neo- darwinian speciation. 9. http://i 1.yti mg.com/vi /2bPX0f120nc/hqdefa ul t.jpg, Neo-darwinian speciation 2. 10.Uyeda , J.C., et a l ., The million-year wait for macroevolutionary bursts. Proc Na tl Aca d Sci U S A, 2011. 108(38): p. 15908-13. 11.D.G. Shu, H.L.L., S. Conwa y Morri s , X.L. Zha ng, S.X. Hu, L. Chen, J. Ha n, M. Zhu, Y. Li , a nd a nd L.Z. Chen, Lower Cambrian vertebrates from south China. Na ture, 1999. 12.Ca rtwri ght P, H.S., Hendri cks JR, Ja rra rd RD, et a l ., Photograph and interpretive drawing of Middle Cambrian cnidarian jellyfish in lateral view (scale bar 5 mm), i n Exceptionally Preserved Jellyfishes from the Middle Cambrian. PLoS ONE 2(10): e1121. doi:10.1371/journal.pone.0001121. 13. http://www.ncbi .nl m.ni h.gov/pmc/a rti cl es /PMC3741300/fi gure/pone0070741-g002/, Cubozoan embryos from the Lower Cambrian Kuanchuanpu Formation, Shaanxi, South China. Analyzed in detail through computed microtomography (Micro-CT) and scanning electron microscopy (SEM) without coating. (scale bar 300 µm), i n PLoS One. 2013; 8(8): e70741. Published online 2013 August 12. doi: 10.1371/journal.pone.0070741. 14.Verga ra -Si l va , F., Plants and the conceptual articulation of evolutionary developmental biology. Bi ol . Phi l os , 2003: p. 18, 249–284. 15.Mi l l er, R.L., Sperm chemo-orientation in the metazoa. Bi ol ogy of Ferti l i za ti on, Vol . 2. 1985, New York: Aca demi c Pres s . 275–337. 16.Yos hi da , M., K. Ina ba , a nd M. Mori s a wa , Sperm chemotaxis during the process of fertilization in the ascidians Ciona savignyi and Ciona intestinalis. Dev Bi ol , 1993. 157(2): p. 497-506. 17.Wa rd, G.E., et a l ., Chemotaxis of Arbacia punctulata spermatozoa to resact, a peptide from the egg jelly layer. J Cel l Bi ol , 1985. 101(6): p. 2324-9. 18. http://worms .zool ogy.wi s c.edu/dd2/echi no/fert/chemota xi s /chemota xi s .html The small peptide RESACT acts as a chemoattractant for sea urchin sperm. When receptors on the surface of the sperm bind RESACT, a signal transduction cascade involving cyclic GMP (cGMP) is set in motion, triggering faster sperm swimming. 19.Ka mei , N. a nd C.G. Gl a be, The species-specific egg receptor for sea urchin sperm adhesion is EBR1,a novel ADAMTS protein. Genes Dev, 2003. 17(20): p. 2502-7. 20.Al berts , B., Molecular biology of the cell. 4th ed. 2002, New York: Ga rl a nd Sci ence. xxxi v, 1463, [86] p. 21.Eva ns , J.P. a nd H.M. Fl orma n, The state of the union: the cell biology of fertilization. Na t Cel l Bi ol , 2002. 4 Suppl: p. s 57-63. 22.Yua n, R., P. Pri ma koff, a nd D.G. Myl es , A role for the disintegrin domain of cyritestin, a sperm surface protein belonging to the ADAM family, in mouse sperm-egg plasma membrane adhesion and fusion. J Cel l Bi ol , 1997. 137(1): p. 105-12. 23. http://www.na ture.com/na ture/journa l /v434/n7030/i ma ges /434152a f1.2.jpg, The molecules on the sperm surface, such as fertilin and cyritestin, may be involved in sperm–egg binding; Okabe and colleagues find that Izumo is essential for membrane fusion. On the egg, CD9 is required for fusion and might collaborate with other proteins such as integrins or glycosylphosphatidylinositol (GPI)-anchored proteins. , i n Developmental biology: Sperm–egg fusion unscrambled Richard Schultz and Carmen Williams Nature 434, 152-153(10 March 2005). 24.Ha mi l ton, B.S., G.R. Whi tta ker, a nd S. Da ni el , Influenza virus-mediated membrane fusion: determinants of hemagglutinin fusogenic activity and experimental approaches for assessing virus fusion. Vi rus es , 2012. 4(7): p. 1144-68. 25.Pl otch, S.J., et a l ., Inhibition of influenza A virus replication by compounds interfering with the fusogenic function of the viral hemagglutinin. J Vi rol , 1999. 73(1): p. 140-51. 26.Ba ga i , S., et a l ., Hemagglutinin-neuraminidase enhances F protein-mediated membrane fusion of reconstituted Sendai virus envelopes with cells. J Vi rol , 1993. 67(6): p. 3312-8. 27. http://www.s pri ngeri ma ges .com/Ima ges /Bi omedi ci ne/110.1007_s 12035-012-8320-7-4, Infectious Agents and Neurodegeneration, Journal: Molecular Neurobiology Vol. 46 Issue 3. 28. http://educa ti on.expa s y.org/i ma ges /Fus i on.jpg, Fusion mechanism in the 'F protein' of Sendai virus according to the ﾓ viral fusion poreﾔ model of Lee K. 29.Ca pel s on, M., C. Doucet, a nd M.W. Hetzer, Nuclear pore complexes: guardians of the nuclear genome. Col d Spri ng Ha rb Symp Qua nt Bi ol , 2011. 75: p. 585-97. 30. http://publ i ca ti ons .ni gms .ni h.gov/bi obea t/08-0116/08-01-16-1.jpg, Structure of the nuclear po re complex (NPC), an assembly of 456 proteins that controls the flow of molecules between the DNA- storing nucleus and the rest of the cell. , i n Featured in the January 16, 2008, issue of Biomedical Beat. 31. http://l ea rn.geneti cs .uta h.edu/content/cel l s /membra nes /i ma ges /Nucl ea rPore.jpg Nuclear pore complexes on the nuclear membranes of frog oocytes as seen from the cytoplasm. 32.Wi l s on, G.G., Organization of restriction-modification systems. Nucl ei c Aci ds Res , 1991. 19(10): p. 2539-66. 33.Wi l s on, G.G. a nd N.E. Murra y, Restriction and modification systems. Annu Rev Genet, 1991. 25: p. 585-627. 34. http://ori gi n-a rs .el s -cdn.com/content/i ma ge/1-s 2.0S0042682203005154-gr6.jpg, Codon positions. 35. http://openi .nl m.ni h.gov/i mgs /512/152/2777879/2777879_14712148-9-258-5.png, Codon usage rose plots for four representatives of different vibrio genera. 36.Jurka , J., W. Ba o, a nd K.K. Koji ma , Families of transposable elements, population structure and the origin of species. Bi ol Di rect, 2011. 6: p. 44. 37. http://bi o3400.ni cerweb.com/Locked/medi a /ch12/repeti ti ve_DNA.html Categories of repetitive nuclear elements. 38. http://a ngel .el te.hu/fi j/ol d- homepa ge/okt/gbi /ki eg/i mg/ncbi -homol ogorthol og-pa ra l og.gi f, Shared ancestry amon g homologous proteins across a gene family. 39.Doebl ey, J., A. Stec, a nd L. Hubba rd, The evolution of apical dominance in maize. Na ture, 1997. 386(6624): p. 485-8. 40.Wa ng, H., et a l ., The origin of the naked grains of maize. Na ture, 2005. 436(7051): p. 714-9. 41. http://i ws .col l i n.edu/bi opa ge/fa cul ty/mccul l och/1406/outl i nes /cha pter%206/Gp07l 10.JPG Active site as seen in the induced fit model of enzyme action. 42. http://cnx.org/content/m44523/l a tes t/Fi gure_15_02_01.jpg A simple regulatory region of DNA located upstream of the gene, i n Module by OpenStax College. info@openstaxcollege.org. 43. http://voer.edu.vn:2013/0.1/mfi l es /55378/get, Eukaryotic promoters are extremely diverse and are difficult to characterize. They typically lie upstream of the gene and can have regulatory elements several kilobases away from the transcriptional start site., in Module by OpenStax College. info@openstaxcollege.org. 44. http://en.wi ki pedi a .org/wi ki /Pa ncrea ti c_ri bonucl ea s e A simple protein structure with clearly visible loop, α-helix and β-sheets (Structure of pancreatic RNase A). 45. http://www.genome.gov/Ima ges /EdKi t/bi o2i _l a rge.gi f Most eukaryotic genes, coding regions (exons) are interrupted by non-coding regions (introns). 46.Logs don, J.M., Jr. a nd W.F. Dool i ttl e, Origin of antifreeze protein genes: a cool tale in molecular evolution. Proc Na tl Aca d Sci U S A, 1997. 94(8): p. 3485-7. 47.Cui , L., et a l ., Widespread genome duplications throughout the history of flowering plants. Genome Res , 2006. 16(6): p. 738-49. 48.Penni s i , E., Molecular evolution. Genome duplications: the stuff of evolution? Sci ence, 2001. 294(5551): p. 2458-60. 49.Rons ha ugen, M., N. McGi nni s , a nd W. McGi nni s , Hox protein mutation and macroevolution of the insect body plan. Na ture, 2002. 415(6874): p. 914-7. 50. http://www.cns .fr/s pi p/IMG/ca che311x315/Fi gure04-311x315.gi f, Gene duplication: Global distribution of the duplicated genes on the 21 Tetraodon chromosomes., in Nature 431, 946957 (21 October 2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype Olivier Jaillon. 51. http://www.na ture.com/nrg/journa l /v11/n12/i ma ges /nrg2883f1.jpg, Genomic rearrangements can be triggered by a multitude of factors. The inner ring shows four broad categories and the outer ring shows components within these categories., in Triggers for genomic rearrangements: insights into genomic, cellular and environmental influences Reviews Genetics 11, 819-829 (December 2010). 52. http://www.na ture.com/nrm/journa l /v11/n3/i ma ges /nrm2849f2.jpg, Crossover recombination between repeated DNA sequences at non-allelic positions can generate a deletion, a duplication, an inversion or an isodicentric chromosome., in Genome destabilization by homologous recombination in the germ line Nature Reviews Molecular Cell Biology 11, 182-195 (March 2010). 53. http://openi .nl m.ni h.gov/i mgs /512/162/1845163/1845163_pbi o.0050101.g005.png Genome duplication: Hox clusters are indicative of whole-genome duplication events, in Survey Sequencing and Comparative Analysis of the Elephant Shark (Callorhinchus milii) Genome PLoS Biol. (2007). 54.Lens ki , R.E., E. coli as a model organism in evolutionary genetics. Evol uti ona ry Geneti cs : Concepts a nd Ca s e Studi es ., ed. C.W.F.a .J.B. Wol f. 2006, New York: Oxford Uni vers i ty Pres s . 485-487. 55.Lens ki , R.E., Microbial evolution in action. Mi crobi ol ogy Toda y, 2004(31): p. 158. 56. http://en.wi ki pedi a .org/wi ki /Es cheri chi a _col i _l ongterm_evol uti on_experi ment, Escherichia coli long-term evolution experiment. 57.Hol mes , E.C., Viral evolution in the genomic age. PLoS Bi ol , 2007. 5(10): p. e278. 58.Iyer, L.M., et a l ., Evolutionary genomics of nucleocytoplasmic large DNA viruses. Vi rus Res , 2006. 117(1): p. 156-84. 59.Si mons en, L., et a l ., The genesis and spread of reassortment human influenza A/H3N2 viruses conferring adamantane resistance. Mol Bi ol Evol , 2007. 24(8): p. 1811-20. 60. http://upl oa d.wi ki medi a .org/wi ki pedi a /commons /thumb/e/e8/Lens ki 's _l ongterm_l i nes _of_E._col i _on_25_June_2008, c.u.o.c.m.j.p.-L., C_Lenski_ﾒ s longterm lines of E.coli on 25 June 2008 close-up of citrate mutant. 61. http://www.i nfl uenza centre.org/a bouti nfl uenza .htm The circulating influenza-A viruses change by mutation, so antibodies become less effective at neutralizing the virus. Therefore infections can occur repeatedly throughout oneﾒ s lifetime as new subtypes of influenza-A emerge. 62.Fos ti ni s , Y., et a l ., Heat shock protein HSP90 and its association with the cytoskeleton: a morphological study. Bi ochem Cel l Bi ol , 1992. 70(9): p. 779-86. 63.Quei ts ch, C., T.A. Sa ngs ter, a nd S. Li ndqui s t, Hsp90 as a capacitor of phenotypic variation. Na ture, 2002. 417(6889): p. 618-24. 64.Rutherford, S.L. a nd S. Li ndqui s t, Hsp90 as a capacitor for morphological evolution. Na ture, 1998. 396(6709): p. 336-42. 65.Wa gner, G.P., C.H. Chi u, a nd T.F. Ha ns en, Is Hsp90 a regulator of evolvability? J Exp Zool , 1999. 285(2): p. 116-8. 66.Ma cka y, T.F., E.A. Stone, a nd J.F. Ayrol es , The genetics of quantitative traits: challenges and prospects. Na t Rev Genet, 2009. 10(8): p. 565-77. 67.Pa ra n, I. a nd D. Za mi r, Quantitative traits in plants: beyond the QTL. Trends Genet, 2003. 19(6): p. 303-6. 68.Pl omi n, R., C.M. Ha worth, a nd O.S. Da vi s , Common disorders are quantitative traits. Na t Rev Genet, 2009. 10(12): p. 872-8. 69. http://a pps .cms fq.edu.ec/bi ol ogyexpl ori ngl i fe/text/cha pter10/concept10.2.html Mendel examined the inheritance patterns of seven different pea-plant characters. For each character, one of the two parent traits disappeared in the F1 hybrids, but reappeared in approximately one quarter of the F2 generation (not shown here). 70. http://www.nyda i l ynews .com/news /ca l i forni a grea t-da ne-gi bs on-dubbed-worl d-ta l l es tdog-di ed-bone-ca ncer-a rti cl e-1.397372, A taller breed of dog with one of the smallest breeds…. 71. http://www.remmeer.com/i ma ges /SR/SRDogBreeds .html , Some of the differen t breeds of dogs…. 72.Dodd, D.M.B., Reproductive Isolation as a Consequence of Adaptive Divergence in Drosophila pseudoobscura. Evol uti on, 1989. Vol. 43(No. 6): p. 13081311. 73. http://bi o4es obi l 2009.wordpres s .com/2010/04/27/unders ta ndi ngs peci a ti on/, Inbreeding evasion experiment as observed by Diane Dodd in fruit flies. 74. http://evol uti on.berkel ey.edu/evol i bra ry/a rti cl e/0_0_0/evo_40 Diane Doddﾒ s fruit fly experiment happening in nature. 75. http://evol uti on.berkel ey.edu/evol i bra ry/a rti cl e/evo_44 Diane Doddﾒ s fruit fly experiment happening in nature. 76.Huber, S.K., et a l ., Reproductive isolation of sympatric morphs in a population of Darwin's finches. Proc Bi ol Sci , 2007. 274(1619): p. 1709-14. 77.Gra nt P. R., G.B.R., Phenotypic and genetic effects of hybridization in Darwin's finches. Evol uti on, 1994(48): p. 297–316. 78.Gra nt, P.R. a nd B.R. Gra nt, Unpredictable evolution in a 30-year study of Darwin's finches. Sci ence, 2002. 296(5568): p. 707-11. 79. http://utda i l ybea con.com/photos /2012/feb/9/cha rl es da rwi ns -fi nches -2-9/, Darwin's drawings of the different heads and beaks he found among the finches on the Galapagos Islands. 80.Ma l l a ri no, R., et a l ., Two developmental modules establish 3D beak-shape variation in Darwin's finches. Proc Na tl Aca d Sci U S A, 2011. 108(10): p. 4057-62. 81. http://www.pna s .org/content/108/10/4057/F5.expa ns i on.html The distinct beak morphologies in Geospiza are generated by differences in the time and place of expression of different genes: Bmp4, Calmodulin, TGFβIIr, β-catenin, Dkk3. Through their action on different skeletal tissues, different genes alter independent dimensions of growth., in PNAS Two developmental modules establish 3D beak-shape variation in Darwin's finches. 82. http://www.pna s .org/content/108/10/4057/F5.expa ns i on.html The beak of the sharp-beaked finch, G. difficilis, represents a basal morphology for Geospiza. Expression and function of the genes bring changes in beak dimensions of the more derived species. +, positive effect; 0, no effect; −, negative effect; pmx, premaxillary bone; pnc, prenasal cartilage., in PNAS Two developmental modules establish 3D beak-shape variation in Darwin's finches. 83. http://www.pna s .org/content/108/10/4057/F3.expa ns i on.html Functional analysis of TGFβIIr, β-catenin, and Dkk3 in the chicken model system., in PNAS Two developmental modules establish 3D beak-shape variation in Darwin's finches. 84.Bel l , M.A.F., S. A., The evolutionary biology of the threespine stickleback. 1994, Oxford: Oxford Uni vers i ty Pres s . 85.Choua rd, T., Evolution: Revenge of the hopeful monster. Na ture, 2010. 463(7283): p. 864-7. 86. http://www.hel s i nki .fi /bi os ci /egru/i ma ges /Kol mi pi i kki _pa rvi _rgb.jpg Three spined stickle back. 87. http://www.ca l i forni a i vf.com/, The standard in vitro fertilization procedure. 88. http://evol uti on.berkel ey.edu/evol i bra ry/i ma ges /evo/hemogl obi n.gi f Sickle cell anemia is an example of a SNP which produced a phenotype But this deleterious SNP is not-evolutionarily beneficial. 89. http://medi a .l a necc.edu/us ers /s nydert/225Lectures /06A/thumbna i l s /s i ckl ecel l .png Sickle cell anemia is an example of a SNP which produced a phenotype But this deleterious SNP is not-evolutionarily beneficial. 90. http://www.cns .fr/s pi p/Tetra odon-ni grovi ri di s -a fi s h-wi th.html , How to pass from the bo ny vertebrateﾒ s last common ancestor genome (12 chromosomes) to the genomes of humans and Tetraodon. Model derived from the study of synteny groups between those two modern vertebrates. 91. http://en.wi ki pedi a .org/wi ki /Ca tegory:Fi s h_hybri ds , Fish hybrids. 92. http://en.wi ki pedi a .org/wi ki /Ca tegory:Amphi bi a _hybri ds Hybrid Amphibians. 93. http://en.wi ki pedi a .org/wi ki /Ca tegory:Bi rd_hybri ds , Hybrid Birds. 94. http://en.wi ki pedi a .org/wi ki /Ca tegory:Ma mma l _hybri ds Hybrid Mammals. 95. http://1.bp.bl ogs pot.com/EjIEVqVXm1s /TwNE6I0_8bI/AAAAAAAAHYk/s ry5BeRml d8/s 1600/l i gron.bmp Tion. 96. http://3.bp.bl ogs pot.com/-tgqzdkx0yo/Tvk2yymd5SI/AAAAAAAAAts /2IxfHS6_EZo/s 1600/Li ger4.jpg Liger. 97. http://3.bp.bl ogs pot.com/_2ys VkCtH1s /TITp8eH_oII/AAAAAAAACw4/ZvUfEFuyCGs /s 400/l eopon+ (1).jpg, Leopon. 98. http://upl oa d.wi ki medi a .org/wi ki pedi a /commons /e/e0/Jua nci to.jpg Mule. 99. http://upl oa d.wi ki medi a .org/wi ki pedi a /commons /9/96/Ol d_hi nny_i n_Okl a homa .jpg Hinny. 100. http://hors ea ndponyti mes .com/res ources /i ma ges /Zebroi d.jpg Zorse. 101. http://a -za ni ma l s .com/medi a /a ni ma l s /i ma ges /ori gi na l /zonkey2.jpg Zonkey. 102. http://i 1-news .s oftpedi a s ta ti c.com/i ma ges /news 2/10-Ama zi ng-Fa cts About-Ca mel s -6.jpg, Cama. 103.Ha rt, A.G., et a l ., Evidence for contemporary evolution during Darwin's lifetime. Curr Bi ol , 2010. 20(3): p. R95. 104.Urba n, M.C., et a l ., The cane toad's (Chaunus [Bufo] marinus) increasing ability to invade Australia is revealed by a dynamically updated range model. Proc Bi ol Sci , 2007. 274(1616): p. 1413-9. 105.Los os , J.B., et a l ., Experimental studies of adaptive differentiation in Bahamian Anolis lizards. Geneti ca , 2001. 112-113: p. 399-415. 106.Li nvi l l e, B.J., et a l ., Placental calcium provision in a lizard with prolonged oviductal egg retention. J Comp Phys i ol B, 2010. 180(2): p. 221-7. 107.Petren, K., et a l ., Comparative landscape genetics and the adaptive radiation of Darwin's finches: the role of peripheral isolation. Mol Ecol , 2005. 14(10): p. 2943-57. 108.Tebbi ch, S., K. Sterel ny, a nd I. Tes chke, The tale of the finch: adaptive radiation and behavioural flexibility. Phi l os Tra ns R Soc Lond B Bi ol Sci , 2010. 365(1543): p. 1099-109. 109.Al bri ch, W.C., D.L. Monnet, a nd S. Ha rba rth, Antibiotic selection pressure and resistance in Streptococcus pneumoniae and Streptococcus pyogenes. Emerg Infect Di s , 2004. 10(3): p. 5147. 110.Bennett, P.M., Plasmid encoded antibiotic resistance: acquisition and transfer of antibiotic resistance genes in bacteria. Br J Pha rma col , 2008. 153 Suppl 1: p. S347-57. 111.Chen, R., M.E. Qui nones -Ma teu, a nd L.M. Ma ns ky, Drug resistance, virus fitness and HIV-1 mutagenesis. Curr Pha rm Des , 2004. 10(32): p. 4065-70. 112.Yi m, H.J., et a l ., Evolution of multi-drug resistant hepatitis B virus during sequential therapy. Hepa tol ogy, 2006. 44(3): p. 703-12. 113. http://en.wi ki pedi a .org/wi ki /Fi l e:Speci a ti on_modes .s vg Various types of speciation among populations. 114. http://evol uti on.berkel ey.edu/evos i te/evo101/VC1a Modes Speci a ti on.s html Various types of speciation among populations. 115.Na oka zu Inoue, Ma s a hi to Ika wa , Aya ko Is ota ni , a nd Ma s a ru Oka be, The immunoglobulin superfamily protein Izumo is required for sperm to fuse with eggs. Na ture, 2005 Ma r 10. 434(7030): 234-238. 116. Enri ca Bi a nchi , Brenda n Doe, Da vi d Goul di ng, Sa nger Mous e Geneti cs Project, a nd Ga vi n J. Wri ght, Juno is the egg Izumo receptor and is essential for mammalian fertilisation. Na ture, 2014 Apr 24. 508(7497): 483–487. 117. http://mes s ybea s t.com/geneti cs /hybri dequi nes .htm, The names of the hybri ds, formed between the different Equus species. 118. http://www.ra tbeha vi or.org/Ra tMous eHybri d.htm, S erious efforts to interbreed them have all failed. 119. http://www.mous eprobl em.ca /wpcontent/upl oa ds /2015/10/mous e_vs _ra t.jpg, A picture of Mouse and Rat. 120. https ://s -medi a -ca chea k0.pi ni mg.com/ori gi na l s /7d/ee/6d/7dee6d11a 3b6e5f0553945312f5701ff.jpg picture of the different Camelids and their hybridization pattern. 121. http://mtda ta .ru/u18/photo8939/203747790070/ori gi na l .jpg, Picture of a goat and sheep pair. 122. https ://s ta ti c.s ta nda rd.co.uk/s 3fs publ i c/thumbna i l s /i ma ge/2014/04/04/20/geep.jpg of a geep/shout. 123.Ya ng, Z., et a l ., Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI. Nucl ei c Aci ds Res , 2005. 33(6): p. 1892-901. 124. https ://www.neb.com/products /res tri cti onendonucl ea s es , As visible both the re striction enzymes differ only slightly in their recognition sites. 125.Pi ngoud, V., et a l ., Evolutionary relationship between different subgroups of restriction endonucleases. J Bi ol Chem, 2002. 277(16): p. 14306-14. 126.Si ngh, T.R. a nd K.R. Pa rda s a ni , In silico analysis of evolutionary patterns in restriction endonucleases. In Si l i co Bi ol , 2009. 9(1-2): p. 45-53. 127. http://www.ba cteri a l phyl ogeny.com/i mg/ta xonomy/ma i n_tree.jpg Phylogenetic tree of bacterial groups. 128.Brown, K.S., Deep Green rewrites evolutionary history of plants. Sci ence, 1999. 285(5430): p. 990-1. 129.Da l ton, R., Ancient DNA set to rewrite human history. Na ture, 2010. 465(7295): p. 148-9. 130.Ba ni s ter, C.E., Review of Epigenetics: A Reference Manual: A book edited by Jeffrey M. Craig and Nicholas C. Wong. Epi geneti cs , 2011. 7(8): p. 963-4. 131.Ca s a des us , J. a nd D. Low, Epigenetic gene regulation in the bacterial world. Mi crobi ol Mol Bi ol Rev, 2006. 70(3): p. 830-56. 132.Cha hwa n, R., S.N. Wonta ka l , a nd S. Roa , The multidimensional nature of epigenetic information and its role in disease. Di s cov Med, 2011. 11(58): p. 233-43. 133. http://cros s fi rea pol ogeti cs .fi l es .wordpres s .com/2011/06/da rwi n- brea kdown.jpg, Darwin commenting about his theory in the book origin of species. 134. http://www.evol uti onnews .org/2013/07/exon_s huffl i ng074401.html Jonathan, Exon Shuffling, and the Origins of Protein Folds. 2013, July 15. 135.Ma rcotte, E.M., et a l ., Detecting protein function and protein-protein interactions from genome sequences. Sci ence, 1999. 285(5428): p. 751-3. 136. https ://mul a ttodi a ri es .fi l es .wordpres s .com/2015/03/145223_twi ns fa mi l y740896_jpga 4009876ce786f8b37f46ca 1bfa 71684.jpeg Quantitative traits of humans in action. NOTE: • The URLs are references as per accessed on 16.04.2014 • This book has extracts from the PhD thesis:“The actinome of Dictyostelium amoebae: comparative in silico and in vivo characterization”, submitted to the Ludwig-MaximiliansUniversity, Munich, Germany. List of figures Figure:1 Evolution chandelier. Figure:2 Punctuated equilibrium. Figure:3 Neo-darwinian speciation. Figure:4 Neo-darwinian speciation. Figure:5 Photograph and interpretive drawing of M iddle Cambrian cnidarian jellyfish in lateral view. Figure:6 Cubozoan embryos from the Lower Cambrian Kuanchuanpu Formation, Shaanxi, South China. Analyzed in detail through computed microtomography (M icro-CT) and scanning electron microscopy (SEM ) without coating. Figure:7 The small peptide RESACT acts as a chemoattractant for sea urchin sperm. When receptors on the surface of the sperm bind RESACT, a signal transduction cascade involving cyclic GM P (cGM P) is set in motion, triggering faster sperm swimming. Figure:8 The molecules on the sperm surface, such as fertilin and cyritestin, may be involved in sperm–egg binding; Okabe and colleagues find that Izumo is essential for membrane fusion. On the egg, CD9 is required for fusion and might collaborate with other proteins such as integrins or glycosylphosphatidylinositol (GPI)-anchored proteins. Figure:9 Influenza-A viruses are enveloped, negative strand RNA viruses. The virus enters the cell by receptor-mediated endocytosis, viral HA binds to host cell receptors that contain terminal α-2,6-linked or α-2,3-linked sialic acid (α-2,6-SA or α-2,3-SA) moieties. Figure:10 Fusion mechanism in the 'F protein' of Sendai virus according to the “viral fusion pore” model of Lee K. Figure:11 Structure of the nuclear pore complex (NPC), an assembly of 456 proteins that controls the flow of molecules between the DNA-storing nucleus and the rest of the cell. Figure:12 Nuclear pore complexes on the nuclear membranes of frog oocytes as seen from the cytoplasm. Figure:13 Codon positions. Comparative analysis of the codon usage of all ORFs of CrleGV (black) and CpGV (gray). The nucleotide bias of the first and second codon positions are given to the left. The dinucleotides and the encoded amino acids are given on the outer circle. The nucleotide distribution of the third codon position is given to the right. Figure:14 Codon usage rose plots for two representatives of different species of Vibrio. Figure:15 Categories of repetitive nuclear elements. Figure:16 Direct repeats excising DNA. Figure:17 Inverted repeats flipping DNA. Figure:18 Shared ancestry among homologous proteins across a gene family. Figure:19 Active site as seen in the induced fit model of enzyme action. Figure:20 A simple regulatory region of DNA located upstream of the gene. Figure:21 Eukaryotic promoters are extremely diverse and are difficult to characterize. They typically lie upstream of the gene and can have regulatory elements several kilobases away from the transcriptional start site. Figure:22 A simple protein structure with clearly visible loop, α-helix and β-sheets (Structure of pancreatic RNase A). Figure:23 M ost eukaryotic genes, coding regions (exons) are interrupted by non-coding regions (introns). Figure:24 Global gene duplication: distribution of the duplicated genes on the 21 Tetraodon chromosomes. These duplications are most likely brought about by a heightened activity of transposons and small scale recombination events through repetitive elements. Figure:25 Genomic rearrangements can be triggered by a multitude of factors. The inner ring shows four broad categories and the outer ring shows components within these categories. Figure:26 Crossover recombination (at the chromosomal level) between repeated DNA sequences at non-allelic positions can generate a deletion, a duplication, an inversion or an isodicentric chromosome. Figure:27 Genome duplication: Hox clusters are indicative of whole-genome duplication events which happened across life forms. Figure:28 M utations in terms of evolution. Figure:29 Prof. C.Lenski’s long term lines of E.coli on 25th June 2008 close-up of citrate mutant. Figure:30 The circulating influenza-A viruses change by mutation, so antibodies become less effective at neutralizing the virus. Therefore infections can occur repeatedly throughout one’s lifetime as new subtypes of influenza-A emerge This could be considered as a macro-evolution happening at the level of the surface antigens. Figure:31 M endel examined the inheritance patterns of seven different pea-plant characters. For each character, one of the two parent traits disappeared in the F1 hybrids, but reappeared in approximately one quarter of the F2 generation (not shown here). Figure:32 A taller breed of dog with one of the smallest breeds… Figure:33 Some of the different breeds of dogs… Figure:34 Inbreeding evasion experiment as observed by Diane Dodd in fruit flies. Figure:35 Diane Dodd’s fruit fly experiment happening in nature. Figure:36 Drawings of the different heads and beaks of finches that Darwin observed in the Galapagos Islands. Figure:37 The distinct beak morphologies in Geospiz a are generated by differences in the time and place of expression of different genes: Bmp4, Calmodulin, TGFβIIr, β-catenin, Dkk3. Through their action on different skeletal tissues, different genes alter independent dimensions of growth. Figure:38 The beak of the sharp-beaked finch, G. difficilis, represents a basal morphology for Geospiza. Expression and function of the genes bring changes in beak dimensions of the more derived species. Figure:39 Functional analysis of TGFβIIr, β-catenin, and Dkk3 in the chicken model system. Figure:40 Three spined stickle back. Figure:41 The standard in vitro fertilization procedure. Figure:42 The prospects of micro-mutations and macromutations in terms of SBFs. Figure:43 S ickle cell anemia is an example of a SNP which produces a phenotype and happens in a non-SBF gene. But this deleterious SNP is not-evolutionarily beneficial. Figure:44 How to pass from the bony vertebrate’s last common ancestor genome (12 chromosomes) to the genomes of humans and Tetraodon. M odel derived from the study of synteny groups between those two modern vertebrates. Figure:45 Tion. Figure:46 Liger. Figure:47 Leopon. Figure:48 M ule. Figure:49 Hinny. Figure:50 Zorse. Figure:51 Zonkey. Figure:52 Cama. Figure:53 Various types of speciation among populations. Figure:54 Various types of speciation among populations. Figure:55 An alignment of three isoforms of the Egg-surface protein IZUM O, from three different Equus species. Figure:56 An alignment of the Sperm-surface protein JUNO from the different Equus species. Figure:57 The names of the hybrids, formed between the different Equus species. Figure:58 An alignment of the Egg-surface protein IZUM O from Rat and M ouse. Figure:59 An alignment of the Sperm-surface protein JUNO from Rat and M ouse, with mouse having two isoforms of the protein. Figure:60 A picture of M ouse and Rat. Figure:61 An alignment of the Egg-surface protein IZUM O from three different Camelus species. Figure:62 An alignment of the Sperm-surface protein JUNO from three different Camelus species. Figure:63 A picture of the different Camelids and their hybridization pattern. Figure:64 An alignment of the Egg-surface protein IZUM O from Goat and Sheep. Figure:65 An alignment of the Sperm-surface protein JUNO from Goat and Sheep. Figure:66 Picture of a goat and sheep pair. Figure:67 Picture of a geep/shout. Figure:68 Structural Superimposition of HinP1I (green) and M spI (cyan). Figure:69 As visible both the restriction enzymes differ only slightly in their cleavage sites. Figure:70 M acro-Species Branding among Restriction enzymes. Figure:71 Structural distance matrix using PDB files. Figure:72 Phylogenetic tree made using the derived distance matrix. Figure:73 Universal phylogenetic tree of bacterial groups. Figure:74 An illustration of micro- and macro-evolution (from the phenotypic perspective). Figure:75 Darwin commenting about his theory in the book; ‘On the origin of species: by means of natural selection or, the preservation of favoured races in the struggle for life’. Figure:76 Quantitative traits of humans in action. Cover picture: Adapted from the portrait of Charles Darwin by John Collier in 1883. Acknowledgements: I am very grateful to my Ph.D guide Prof. Michael S chleicher for his constant support and motivation; especially more so for his kindness. I am very fortunate to have had him as my doctor father; who (according to me) belongs to a rare breed of human individuals, who make decisions by not only listening to their brains but also to their hearts. I am very thankful to my friend Dr. Arasada Rajesh. I am also obliged to thank my friends in the M unich area namely, Sumathi, Sinnaiya Thavarasa, Selvakirubai, M ohan and Dr. Pandey and other good hearts. I am also thankful to my earlier teachers and professors who have developed in me a thirst for life-sciences; namely M r. Saravana Rajan, M r. Radha Krishnan, Prof. S. Krishna Swamy, Prof. K. Dharmalingam, Prof. S. Shanmuga Sundaram . I also acknowledge the support I had received from all my friends around the world, many of whom, I unfortunately am not in constant touch. I am thankful to my friends Kannan Sriram, Yathesh Kumar, M r. Gnanashekar, Danush Jeyan and late M r. Jawaharlal Paul. M ost of all, I cherish the support and motivation I received from my family members; my mother I. Daisy M ary, my father V.M Joseph, my sister Sophia Jegan, my uncle Prof. Henry Louis, Aunt Jesintha and other dear ones. ~~~ Word cloud for this book: