Population genetic studies of marine species sometimes find no clear patterns of genetic differen... more Population genetic studies of marine species sometimes find no clear patterns of genetic differentiation, but signals of geographic gene flow typified by isolation by distance (IBD) due to high dispersal ability. A previous study of mitochondrial DNA of the yellowfin goby Acanthogobius flavimanus indicated that this species also does not have clearly differentiated population groups around the Japanese archipelago, in contrast with other coastal goby species that have highly differentiated groups between the Sea of Japan and Pacific Ocean populations. Here, to clearly reveal phylogeographic structures of the yellowfin goby around the Japanese archipelago, we conducted large-scale RAD-sequencing analysis of their nuclear genomic SNP loci. As a result, IBD patterns were confirmed across the yellowfin goby populations, and the larval dispersal distance of this species was revealed to be approximately 19 km on average. In addition, different larval dispersal distances were estimated for its Sea of Japan and Pacific Ocean populations, suggesting that different coastal environments and/or ecological features may affect its dispersal rates. These results would provide foundations for ecological and conservation studies of the yellowfin goby and coastal fishes having similar dispersal strategy to this species.
Organisms respond to the fluctuations in field environments differently throughout their lives de... more Organisms respond to the fluctuations in field environments differently throughout their lives depending on their genetic variations. However, how such genetic variations affect environmental responses of organisms under field conditions, that is, the genotype × environment interaction (G×E), remains unclear. In the present study, we developed a method to identify the loci influencing gene expression dynamics (GED) in field-grown rice. We cultivated chromosome segment substitution lines (CSSLs) from Koshihikari and Takanari rice varieties1 in the field, and conducted approximately 900 time-series RNA sequencing (RNA-Seq) (bihourly-sampling for 16 d during 4 months). This novel analytical approach identified more than one thousand expression dynamics quantitative trait loci (edQTLs), which cause differences in GED between Koshihikari and Takanari. Based on the edQTLs, we successfully predicted the GED under environments different from training environments and in rice cultivars with ...
Stacksbinder (available at https ://ps.agr.ryuko ku.ac.jp/stack sbind er/) is a web-based tool fo... more Stacksbinder (available at https ://ps.agr.ryuko ku.ac.jp/stack sbind er/) is a web-based tool for summarizing the output of software Stacks, which is widely used to analyze restriction site-associated DNA sequencing (RAD-Seq) data. Although summarization is an essential step in RAD-Seq analysis, no specific tools exist for summarizing and visualizing these data. Stacksbinder generates a summary report by using files exported from Stacks. The report is HTML-based and easy to browse in any environment. It consists of plots and tables containing information that can be used to assess the quality of experiments and determine the filtering of single nucleotide polymorphisms.
Gene expression levels exhibit stochastic variations among genetically identical organisms under ... more Gene expression levels exhibit stochastic variations among genetically identical organisms under the same environmental conditions. In many recent transcriptome analyses based on RNA sequencing (RNA-seq), variations in gene expression levels among replicates were assumed to follow a negative binomial distribution, although the physiological basis of this assumption remains unclear. In this study, RNA-seq data were obtained from Arabidopsis thaliana under eight conditions (21-27 replicates), and the characteristics of gene-dependent empirical probability density function (ePDF) profiles of gene expression levels were analyzed. For A. thaliana and Saccharomyces cerevisiae, various types of ePDF of gene expression levels were obtained that were classified as Gaussian, power law-like containing a long tail, or intermediate. These ePDF profiles were well fitted with a Gauss-power mixing distribution function derived from a simple model of a stochastic transcriptional network containing a...
Using genome-wide SNP data obtained from high-throughput techniques based on double digest restri... more Using genome-wide SNP data obtained from high-throughput techniques based on double digest restriction site-associated DNA sequencing (ddRAD-seq), we elucidated the migration history and genetic diversity of the Japanese population of the ecologically important brown seaweed Sargassum thunbergii (Mertens ex Roth) Kuntze. STRUCTURE and NeighborNet analyses showed a clear genetic differentiation among populations of four geographic regions: Kyushu (POP1); Sea of Japan (POP2); Hokkaido and Tohoku (POP3); and Pacific coast from Kyushu to Kanto (POP4). Approximate Bayesian Computation (ABC) analysis indicated that POP4 diverged first, followed by the separation between POP2 (the largest effective population size) and POP3; POP1 was the last to form, shaped by the mixture of POP2 (73%) and POP4 (27%). High genetic diversity was detected in POP1 and POP2, whereas low genetic diversity was detected in POP3 and POP4. These results indicated that S. thunbergii populations of Kyushu and the Se...
Motivation: Gene expression levels exhibit stochastic variations among genetically identical orga... more Motivation: Gene expression levels exhibit stochastic variations among genetically identical organisms under the same environmental conditions. In many recent transcriptome analyses based on RNA sequencing (RNA-seq), variations in gene expression levels among replicates were assumed to follow a negative binomial distribution although the physiological basis of this assumption remain unclear. Results: In this study, RNA-seq data were obtained from Arabidopsis thaliana under eight conditions (21-27 replicates), and the characteristics of gene-dependent distribution profiles of gene expression levels were analyzed. For A. thaliana and Saccharomyces cerevisiae, the distribution profiles could be described by a Gauss-power mixing distribution derived from a simple model of a stochastic transcriptional network containing a feedback loop. The distribution profiles of gene expression levels were roughly classified as Gaussian, power law-like containing a long tail, and mixed. The fitting fu...
Taishu horses are a native Japanese breed, of which only 41 individuals remained on Tsushima Isla... more Taishu horses are a native Japanese breed, of which only 41 individuals remained on Tsushima Island in 2018. Their genetic diversity is considered lower than that of other Japanese native horse breeds; thus, it needs to be investigated for sustainable conservation of this breed. Historical records revealed that several Taishu individuals were released areas off-Tsushima Island in mid-1980s. At present, Taishu horses living outside of Tsushima Island, hereafter referred to as Non-Tsushima Taishus (NTTs), are tagged. However, the genetic structure of the NTT individuals remains unclear, and such individuals are not included in the current mating plans for Taishu horses. Herein, we examined the genetic structure of 18 NTT individuals by comparing their genomic (SNP) information with that of individuals on Tsushima Island (TT), four other native Japanese breeds, and one Anglo-Arabian breed by using ddRAD-seq. We found that all individuals related to the Taishu can be grouped in one cluster, which was separated from other horse breeds. Patterns of specific and shared SNPs in NTT individuals closely resembled those of TT individuals, suggesting very minor genetic differences. Meanwhile, the heterozygosity of NTT individuals was slightly higher than that of TT individuals, and many NTT individuals were of fertile age, suggesting that the pedigree of NTT individuals would be useful in breed conservation plans for Taishu horses. Based on their genomic information, we also reconstructed the pedigree structures of four NTT individuals with no family information. The inclusion of NTT individuals in future mating plans on Tsushima Island may be an effective and feasible method for conserving the Taishu horse breed in Japan.
Evolution of mating systems has become one of the most important research areas in evolutionary b... more Evolution of mating systems has become one of the most important research areas in evolutionary biology. Cyrtomium falcatum is a homosporous fern species native to eastern Asia. Two subspecies belonging to a sexual diploid race of C. falcatum are recognized: subsp. littorale and subsp. australe. Subspecies littorale shows intermediate selfing rates, while subsp. australe is an obligate outcrosser. We aimed to evaluate the process of mating system evolution and divergence for the two subspecies using restriction site associated DNA sequencing (RAD-seq). The results showed that subsp. littorale had lower genetic diversity and stronger genetic drift than subsp. australe. Fluctuations in the effective population size over time were evaluated by extended Bayesian skyline plot and Stairway plot analyses, both of which revealed a severe population bottleneck about 20,000 years ago in subsp. littorale. This bottleneck and the subsequent range expansion after the LGM appear to have played an...
Background: Fitness trade-offs of plastic traits between alternative environments are a prerequis... more Background: Fitness trade-offs of plastic traits between alternative environments are a prerequisite for the evolution of phenotypic plasticity; however, the costs associated with plastic traits have yet not been determined. Most empirical studies have assessed the costs of plastic traits by investigating a minimum of two environments (to elicit plasticity) and only two or even one environment to evaluate the consequences of plasticity. In contrast, in nature, organisms are constantly subjected to multiple environments, and the expression and magnitude of the costs of plastic traits are occasionally context-dependent. Objective: To analyze the costs of plastic traits across multiple environments. Methods: We determined the benefits and costs of two plastic responses (predator- and prey-induced morphologies) of larvae of the salamander Hynobius retardatus to larval survival, metamorphic timing, and body size at metamorphosis in three different environments [by using tadpoles of an an...
Nuclear sequence markers are useful tool for the study of the history of populations and adaptati... more Nuclear sequence markers are useful tool for the study of the history of populations and adaptation. However, it is not easy to obtain multiple nuclear primers for organisms with poor or no genomic sequence information. Here we used the genomes of organisms that have been fully sequenced to design comprehensive sets of primers to amplify polymorphic genomic fragments of multiple nuclear genes in non-sequenced organisms. First, we identified a large number of candidate polymorphic regions that were flanked on each side by conserved regions in the reference genomes. We then designed primers based on these conserved sequences and examined whether the primers could be used to amplify sequences in target species, montane brown frog (Rana ornativentris), anole lizard (Anolis sagrei), guppy (Poecilia reticulata), and fruit fly (Drosophila melanogaster), for population genetic analysis. We successfully obtained polymorphic markers for all target species studied. In addition, we found that s...
In most animal species, the hatchling stage is a highly vulnerable life history stage. In many fi... more In most animal species, the hatchling stage is a highly vulnerable life history stage. In many fish and amphibian species, hatchling abundance varies substantially among sites and years, with the result that selection strength in conspecific interactions such as cannibalism is also variable. The variability of selection leads species to evolve phenotypic plasticity, and adaptive trait changes in hatchlings that depend on the density of conspecifics can therefore be expected. However, plasticity strategies in response to cannibalistic interactions in this vulnerable life history stage have received little attention.Because cannibalism success is dependent on the size balance between predator capturing organ and prey body, and also on the prey-capturing ability of the cannibal and the escape ability of its prey, we hypothesize that hatchlings will exhibit faster growth and development in response to conspecific interactions. We performed a series of experiments to test this hypothesis...
ABSTRACT In most animal species, the hatchling stage is a highly vulnerable life history stage. I... more ABSTRACT In most animal species, the hatchling stage is a highly vulnerable life history stage. In many fish and amphibian species, hatchling abundance varies substantially among sites and years, with the result that selection strength in conspecific interactions such as cannibalism is also variable. The variability of selection leads species to evolve phenotypic plasticity, and adaptive trait changes in hatchlings that depend on the density of conspecifics can therefore be expected. However, plasticity strategies in response to cannibalistic interactions in this vulnerable life history stage have received little attention.Because cannibalism success is dependent on the size balance between predator capturing organ and prey body, and also on the prey-capturing ability of the cannibal and the escape ability of its prey, we hypothesize that hatchlings will exhibit faster growth and development in response to conspecific interactions. We performed a series of experiments to test this hypothesis, using pre-feeding larvae of a cannibalistic salamander (Hynobius retardatus).Many traits of the hatchlings reared with conspecifics were larger than the same traits in those reared alone, because the former hatchlings grew faster and were more advanced developmentally. The time to the beginning of feeding was shorter, and swimming speed as an indicator of escape performance was faster, for hatchlings reared with conspecifics.Hatchlings reared with conspecifics more successfully cannibalized small hatchlings and were also highly resistant to being cannibalized by large conspecifics, compared with hatchlings reared alone. These differences in cannibalism success and avoidance of cannibalization were well explained by differences in gape and head size, respectively, between the interacting hatchlings. Therefore, acceleration of growth and development of hatchlings in the proximate presence of conspecifics may confer significant fitness advantages on hatchlings in a high-density cannibalistic situation.Developmental and growth plasticity may thus be a powerful adaptive mechanism that allows individuals to respond to the dynamic character of salamander populations in nature.This article is protected by copyright. All rights reserved.
Nuclear sequence markers are useful tool for the study of the history of populations and adaptati... more Nuclear sequence markers are useful tool for the study of the history of populations and adaptation. However, it is not easy to obtain multiple nuclear primers for organisms with poor or no genomic sequence information. Here we used the genomes of organisms that have been fully sequenced to design comprehensive sets of primers to amplify polymorphic genomic fragments of multiple nuclear genes in non-sequenced organisms. First, we identified a large number of candidate polymorphic regions that were flanked on each side by conserved regions in the reference genomes. We then designed primers based on these conserved sequences and examined whether the primers could be used to amplify sequences in target species, montane brown frog (Rana ornativentris), anole lizard (Anolis sagrei), guppy (Poecilia reticulata), and fruit fly (Drosophila melanogaster), for population genetic analysis. We successfully obtained polymorphic markers for all target species studied. In addition, we found that sequence identities of the regions between the primer sites in the reference genomes affected the experimental success of DNA amplification and identification of polymorphic loci in the target genomes, and that exonic primers had a higher success rate than intronic primers in amplifying readable sequences. We conclude that this comparative genomic approach is a time-and cost-effective way to obtain polymorphic markers for nonsequenced organisms, and that it will contribute to the further development of evolutionary ecology and population genetics for non-sequenced organisms, aiding in the understanding of the genetic basis of adaptation.
Phenotypic plasticity can have strong impacts on predator-prey interactions. Although much work h... more Phenotypic plasticity can have strong impacts on predator-prey interactions. Although much work has examined the effects of inducible defences, less understood is how inducible offences in predators affect predator-prey interactions and predator and prey phenotypes. Here, we examine the impacts of an inducible offence on the interactions and life histories of a cohort of predatory Hynobius retardatus salamander larvae and their prey, Rana pirica tadpoles. We examined larval (duration, survival) and post-metamorphic (size) traits of both species after manipulating the presence/absence of tadpoles and salamanders with offensive (broadened gape width) or non-offensive phenotypes in pond enclosures. Offensive phenotype salamanders reduced tadpole survival and metamorph emergence by 58% compared to tadpole-only treatments, and by over 30% compared to non-offensive phenotypes. Average time to metamorphosis of frogs was delayed by 30% in the presence of salamanders, although this was independent of salamander phenotype. Thus, offensive phenotype salamanders reduced the number of tadpoles remaining in the pond over time by reducing tadpole survival, not by altering patterns of metamorph emergence. Offensive phenotypes also caused tadpoles to metamorphose 19% larger than no salamander treatments and 6% larger than non-offensive phenotype treatments. Pooled across salamander treatments, tadpoles caused salamanders to reach metamorphosis faster and larger. Moreover, in the presence of tadpoles, offensive phenotype salamanders metamorphosed 25% faster and 5% larger than non-offensive phenotype salamanders, but in their absence, neither their size nor larval period differed from non-offensive phenotype individuals. To our knowledge, this study is the first to demonstrate that inducible offences in predators can have strong impacts on predator and prey phenotypes across multiple life stages. Since early metamorphosis at a larger size has potential fitness advantages, the impacts of offensive phenotypes on frog and salamander life histories likely have significant consequences for individuals and populations. Furthermore, increased predation on tadpoles likely causes offensive phenotype individuals to have strong impacts on pond communities. Future studies should examine the fitness consequences of morphological and life-history plasticity across multiple life stages and should address the population and community level consequences of offensive phenotypes.
The guppy is known to exhibit remarkable interindividual variations in spectral sensitivity of mi... more The guppy is known to exhibit remarkable interindividual variations in spectral sensitivity of middle to long wavelength-sensitive (M/LWS) cone photoreceptor cells. The guppy has four M/LWS-type opsin genes (LWS-1, LWS-2, LWS-3 and LWS-4) that are considered to be responsible for this sensory variation. However, the allelic variation of the opsin genes, particularly in terms of their absorption spectrum, has not been explored in wild populations. Thus, we examined nucleotide variations in the four M/LWS opsin genes as well as blue-sensitive SWS2-B and ultraviolet-sensitive SWS1 opsin genes for comparison and seven non-opsin nuclear loci as reference genes in 10 guppy populations from various light environments in Trinidad and Tobago. For the first time, we discovered a potential spectral variation (180 Ser/Ala) in LWS-1 that differed at an amino acid site known to affect the absorption spectra of opsins. Based on a coalescent simulation of the nucleotide variation of the reference genes, we showed that the interpopulation genetic differentiation of two opsin genes was significantly larger than the neutral expectation. Furthermore, this genetic differentiation was significantly related to differences in dissolved oxygen (DO) level, and it was not explained by the spatial distance between populations. The DO levels are correlated with eutrophication that possibly affects the color of aquatic environments. These results suggest that the population diversity of opsin genes is significantly driven by natural selection and that the guppy could adapt to various light environments through color vision changes.
Background The guppy (Poecilia reticulata) is an important model organism for studying sexual sel... more Background The guppy (Poecilia reticulata) is an important model organism for studying sexual selection; male guppies have complex and conspicuous pigmentation, and female guppies exhibit preferences for males with specific color spots. Understanding the genetic basis underlying pigmentation variation in the guppy is important for exploring the factors causing the maintenance of color polymorphism in wild populations. Findings We focused on the melanic black pigmentation of guppies, and examined genetic variations in the melanocortin 1 receptor (MC1R) gene because variation in this gene is known to contribute to polymorphism of melanin pigmentation in several animal species. The complete coding sequence of the guppy MC1R gene was determined, and two different MC1R alleles (963 and 969 bp) were found in wild populations. Ornamental strain guppies with a 963-bp MC1R tended to show less black pigmentation than those with a 969-bp MC1R, although the association between MC1R genotype and black pigmentation disappeared in the F2 offspring. Conclusions The guppy MC1R gene showed variation in the five wild Trinidadian populations we examined, and these populations also differed in terms of allele frequencies. We identified a significant association between black pigmentation and MC1R genotype in fish obtained from aquarium shops. However, the results from F2 families suggest that there are other genes that modify the effects of the MC1R gene.
Population genetic studies of marine species sometimes find no clear patterns of genetic differen... more Population genetic studies of marine species sometimes find no clear patterns of genetic differentiation, but signals of geographic gene flow typified by isolation by distance (IBD) due to high dispersal ability. A previous study of mitochondrial DNA of the yellowfin goby Acanthogobius flavimanus indicated that this species also does not have clearly differentiated population groups around the Japanese archipelago, in contrast with other coastal goby species that have highly differentiated groups between the Sea of Japan and Pacific Ocean populations. Here, to clearly reveal phylogeographic structures of the yellowfin goby around the Japanese archipelago, we conducted large-scale RAD-sequencing analysis of their nuclear genomic SNP loci. As a result, IBD patterns were confirmed across the yellowfin goby populations, and the larval dispersal distance of this species was revealed to be approximately 19 km on average. In addition, different larval dispersal distances were estimated for its Sea of Japan and Pacific Ocean populations, suggesting that different coastal environments and/or ecological features may affect its dispersal rates. These results would provide foundations for ecological and conservation studies of the yellowfin goby and coastal fishes having similar dispersal strategy to this species.
Organisms respond to the fluctuations in field environments differently throughout their lives de... more Organisms respond to the fluctuations in field environments differently throughout their lives depending on their genetic variations. However, how such genetic variations affect environmental responses of organisms under field conditions, that is, the genotype × environment interaction (G×E), remains unclear. In the present study, we developed a method to identify the loci influencing gene expression dynamics (GED) in field-grown rice. We cultivated chromosome segment substitution lines (CSSLs) from Koshihikari and Takanari rice varieties1 in the field, and conducted approximately 900 time-series RNA sequencing (RNA-Seq) (bihourly-sampling for 16 d during 4 months). This novel analytical approach identified more than one thousand expression dynamics quantitative trait loci (edQTLs), which cause differences in GED between Koshihikari and Takanari. Based on the edQTLs, we successfully predicted the GED under environments different from training environments and in rice cultivars with ...
Stacksbinder (available at https ://ps.agr.ryuko ku.ac.jp/stack sbind er/) is a web-based tool fo... more Stacksbinder (available at https ://ps.agr.ryuko ku.ac.jp/stack sbind er/) is a web-based tool for summarizing the output of software Stacks, which is widely used to analyze restriction site-associated DNA sequencing (RAD-Seq) data. Although summarization is an essential step in RAD-Seq analysis, no specific tools exist for summarizing and visualizing these data. Stacksbinder generates a summary report by using files exported from Stacks. The report is HTML-based and easy to browse in any environment. It consists of plots and tables containing information that can be used to assess the quality of experiments and determine the filtering of single nucleotide polymorphisms.
Gene expression levels exhibit stochastic variations among genetically identical organisms under ... more Gene expression levels exhibit stochastic variations among genetically identical organisms under the same environmental conditions. In many recent transcriptome analyses based on RNA sequencing (RNA-seq), variations in gene expression levels among replicates were assumed to follow a negative binomial distribution, although the physiological basis of this assumption remains unclear. In this study, RNA-seq data were obtained from Arabidopsis thaliana under eight conditions (21-27 replicates), and the characteristics of gene-dependent empirical probability density function (ePDF) profiles of gene expression levels were analyzed. For A. thaliana and Saccharomyces cerevisiae, various types of ePDF of gene expression levels were obtained that were classified as Gaussian, power law-like containing a long tail, or intermediate. These ePDF profiles were well fitted with a Gauss-power mixing distribution function derived from a simple model of a stochastic transcriptional network containing a...
Using genome-wide SNP data obtained from high-throughput techniques based on double digest restri... more Using genome-wide SNP data obtained from high-throughput techniques based on double digest restriction site-associated DNA sequencing (ddRAD-seq), we elucidated the migration history and genetic diversity of the Japanese population of the ecologically important brown seaweed Sargassum thunbergii (Mertens ex Roth) Kuntze. STRUCTURE and NeighborNet analyses showed a clear genetic differentiation among populations of four geographic regions: Kyushu (POP1); Sea of Japan (POP2); Hokkaido and Tohoku (POP3); and Pacific coast from Kyushu to Kanto (POP4). Approximate Bayesian Computation (ABC) analysis indicated that POP4 diverged first, followed by the separation between POP2 (the largest effective population size) and POP3; POP1 was the last to form, shaped by the mixture of POP2 (73%) and POP4 (27%). High genetic diversity was detected in POP1 and POP2, whereas low genetic diversity was detected in POP3 and POP4. These results indicated that S. thunbergii populations of Kyushu and the Se...
Motivation: Gene expression levels exhibit stochastic variations among genetically identical orga... more Motivation: Gene expression levels exhibit stochastic variations among genetically identical organisms under the same environmental conditions. In many recent transcriptome analyses based on RNA sequencing (RNA-seq), variations in gene expression levels among replicates were assumed to follow a negative binomial distribution although the physiological basis of this assumption remain unclear. Results: In this study, RNA-seq data were obtained from Arabidopsis thaliana under eight conditions (21-27 replicates), and the characteristics of gene-dependent distribution profiles of gene expression levels were analyzed. For A. thaliana and Saccharomyces cerevisiae, the distribution profiles could be described by a Gauss-power mixing distribution derived from a simple model of a stochastic transcriptional network containing a feedback loop. The distribution profiles of gene expression levels were roughly classified as Gaussian, power law-like containing a long tail, and mixed. The fitting fu...
Taishu horses are a native Japanese breed, of which only 41 individuals remained on Tsushima Isla... more Taishu horses are a native Japanese breed, of which only 41 individuals remained on Tsushima Island in 2018. Their genetic diversity is considered lower than that of other Japanese native horse breeds; thus, it needs to be investigated for sustainable conservation of this breed. Historical records revealed that several Taishu individuals were released areas off-Tsushima Island in mid-1980s. At present, Taishu horses living outside of Tsushima Island, hereafter referred to as Non-Tsushima Taishus (NTTs), are tagged. However, the genetic structure of the NTT individuals remains unclear, and such individuals are not included in the current mating plans for Taishu horses. Herein, we examined the genetic structure of 18 NTT individuals by comparing their genomic (SNP) information with that of individuals on Tsushima Island (TT), four other native Japanese breeds, and one Anglo-Arabian breed by using ddRAD-seq. We found that all individuals related to the Taishu can be grouped in one cluster, which was separated from other horse breeds. Patterns of specific and shared SNPs in NTT individuals closely resembled those of TT individuals, suggesting very minor genetic differences. Meanwhile, the heterozygosity of NTT individuals was slightly higher than that of TT individuals, and many NTT individuals were of fertile age, suggesting that the pedigree of NTT individuals would be useful in breed conservation plans for Taishu horses. Based on their genomic information, we also reconstructed the pedigree structures of four NTT individuals with no family information. The inclusion of NTT individuals in future mating plans on Tsushima Island may be an effective and feasible method for conserving the Taishu horse breed in Japan.
Evolution of mating systems has become one of the most important research areas in evolutionary b... more Evolution of mating systems has become one of the most important research areas in evolutionary biology. Cyrtomium falcatum is a homosporous fern species native to eastern Asia. Two subspecies belonging to a sexual diploid race of C. falcatum are recognized: subsp. littorale and subsp. australe. Subspecies littorale shows intermediate selfing rates, while subsp. australe is an obligate outcrosser. We aimed to evaluate the process of mating system evolution and divergence for the two subspecies using restriction site associated DNA sequencing (RAD-seq). The results showed that subsp. littorale had lower genetic diversity and stronger genetic drift than subsp. australe. Fluctuations in the effective population size over time were evaluated by extended Bayesian skyline plot and Stairway plot analyses, both of which revealed a severe population bottleneck about 20,000 years ago in subsp. littorale. This bottleneck and the subsequent range expansion after the LGM appear to have played an...
Background: Fitness trade-offs of plastic traits between alternative environments are a prerequis... more Background: Fitness trade-offs of plastic traits between alternative environments are a prerequisite for the evolution of phenotypic plasticity; however, the costs associated with plastic traits have yet not been determined. Most empirical studies have assessed the costs of plastic traits by investigating a minimum of two environments (to elicit plasticity) and only two or even one environment to evaluate the consequences of plasticity. In contrast, in nature, organisms are constantly subjected to multiple environments, and the expression and magnitude of the costs of plastic traits are occasionally context-dependent. Objective: To analyze the costs of plastic traits across multiple environments. Methods: We determined the benefits and costs of two plastic responses (predator- and prey-induced morphologies) of larvae of the salamander Hynobius retardatus to larval survival, metamorphic timing, and body size at metamorphosis in three different environments [by using tadpoles of an an...
Nuclear sequence markers are useful tool for the study of the history of populations and adaptati... more Nuclear sequence markers are useful tool for the study of the history of populations and adaptation. However, it is not easy to obtain multiple nuclear primers for organisms with poor or no genomic sequence information. Here we used the genomes of organisms that have been fully sequenced to design comprehensive sets of primers to amplify polymorphic genomic fragments of multiple nuclear genes in non-sequenced organisms. First, we identified a large number of candidate polymorphic regions that were flanked on each side by conserved regions in the reference genomes. We then designed primers based on these conserved sequences and examined whether the primers could be used to amplify sequences in target species, montane brown frog (Rana ornativentris), anole lizard (Anolis sagrei), guppy (Poecilia reticulata), and fruit fly (Drosophila melanogaster), for population genetic analysis. We successfully obtained polymorphic markers for all target species studied. In addition, we found that s...
In most animal species, the hatchling stage is a highly vulnerable life history stage. In many fi... more In most animal species, the hatchling stage is a highly vulnerable life history stage. In many fish and amphibian species, hatchling abundance varies substantially among sites and years, with the result that selection strength in conspecific interactions such as cannibalism is also variable. The variability of selection leads species to evolve phenotypic plasticity, and adaptive trait changes in hatchlings that depend on the density of conspecifics can therefore be expected. However, plasticity strategies in response to cannibalistic interactions in this vulnerable life history stage have received little attention.Because cannibalism success is dependent on the size balance between predator capturing organ and prey body, and also on the prey-capturing ability of the cannibal and the escape ability of its prey, we hypothesize that hatchlings will exhibit faster growth and development in response to conspecific interactions. We performed a series of experiments to test this hypothesis...
ABSTRACT In most animal species, the hatchling stage is a highly vulnerable life history stage. I... more ABSTRACT In most animal species, the hatchling stage is a highly vulnerable life history stage. In many fish and amphibian species, hatchling abundance varies substantially among sites and years, with the result that selection strength in conspecific interactions such as cannibalism is also variable. The variability of selection leads species to evolve phenotypic plasticity, and adaptive trait changes in hatchlings that depend on the density of conspecifics can therefore be expected. However, plasticity strategies in response to cannibalistic interactions in this vulnerable life history stage have received little attention.Because cannibalism success is dependent on the size balance between predator capturing organ and prey body, and also on the prey-capturing ability of the cannibal and the escape ability of its prey, we hypothesize that hatchlings will exhibit faster growth and development in response to conspecific interactions. We performed a series of experiments to test this hypothesis, using pre-feeding larvae of a cannibalistic salamander (Hynobius retardatus).Many traits of the hatchlings reared with conspecifics were larger than the same traits in those reared alone, because the former hatchlings grew faster and were more advanced developmentally. The time to the beginning of feeding was shorter, and swimming speed as an indicator of escape performance was faster, for hatchlings reared with conspecifics.Hatchlings reared with conspecifics more successfully cannibalized small hatchlings and were also highly resistant to being cannibalized by large conspecifics, compared with hatchlings reared alone. These differences in cannibalism success and avoidance of cannibalization were well explained by differences in gape and head size, respectively, between the interacting hatchlings. Therefore, acceleration of growth and development of hatchlings in the proximate presence of conspecifics may confer significant fitness advantages on hatchlings in a high-density cannibalistic situation.Developmental and growth plasticity may thus be a powerful adaptive mechanism that allows individuals to respond to the dynamic character of salamander populations in nature.This article is protected by copyright. All rights reserved.
Nuclear sequence markers are useful tool for the study of the history of populations and adaptati... more Nuclear sequence markers are useful tool for the study of the history of populations and adaptation. However, it is not easy to obtain multiple nuclear primers for organisms with poor or no genomic sequence information. Here we used the genomes of organisms that have been fully sequenced to design comprehensive sets of primers to amplify polymorphic genomic fragments of multiple nuclear genes in non-sequenced organisms. First, we identified a large number of candidate polymorphic regions that were flanked on each side by conserved regions in the reference genomes. We then designed primers based on these conserved sequences and examined whether the primers could be used to amplify sequences in target species, montane brown frog (Rana ornativentris), anole lizard (Anolis sagrei), guppy (Poecilia reticulata), and fruit fly (Drosophila melanogaster), for population genetic analysis. We successfully obtained polymorphic markers for all target species studied. In addition, we found that sequence identities of the regions between the primer sites in the reference genomes affected the experimental success of DNA amplification and identification of polymorphic loci in the target genomes, and that exonic primers had a higher success rate than intronic primers in amplifying readable sequences. We conclude that this comparative genomic approach is a time-and cost-effective way to obtain polymorphic markers for nonsequenced organisms, and that it will contribute to the further development of evolutionary ecology and population genetics for non-sequenced organisms, aiding in the understanding of the genetic basis of adaptation.
Phenotypic plasticity can have strong impacts on predator-prey interactions. Although much work h... more Phenotypic plasticity can have strong impacts on predator-prey interactions. Although much work has examined the effects of inducible defences, less understood is how inducible offences in predators affect predator-prey interactions and predator and prey phenotypes. Here, we examine the impacts of an inducible offence on the interactions and life histories of a cohort of predatory Hynobius retardatus salamander larvae and their prey, Rana pirica tadpoles. We examined larval (duration, survival) and post-metamorphic (size) traits of both species after manipulating the presence/absence of tadpoles and salamanders with offensive (broadened gape width) or non-offensive phenotypes in pond enclosures. Offensive phenotype salamanders reduced tadpole survival and metamorph emergence by 58% compared to tadpole-only treatments, and by over 30% compared to non-offensive phenotypes. Average time to metamorphosis of frogs was delayed by 30% in the presence of salamanders, although this was independent of salamander phenotype. Thus, offensive phenotype salamanders reduced the number of tadpoles remaining in the pond over time by reducing tadpole survival, not by altering patterns of metamorph emergence. Offensive phenotypes also caused tadpoles to metamorphose 19% larger than no salamander treatments and 6% larger than non-offensive phenotype treatments. Pooled across salamander treatments, tadpoles caused salamanders to reach metamorphosis faster and larger. Moreover, in the presence of tadpoles, offensive phenotype salamanders metamorphosed 25% faster and 5% larger than non-offensive phenotype salamanders, but in their absence, neither their size nor larval period differed from non-offensive phenotype individuals. To our knowledge, this study is the first to demonstrate that inducible offences in predators can have strong impacts on predator and prey phenotypes across multiple life stages. Since early metamorphosis at a larger size has potential fitness advantages, the impacts of offensive phenotypes on frog and salamander life histories likely have significant consequences for individuals and populations. Furthermore, increased predation on tadpoles likely causes offensive phenotype individuals to have strong impacts on pond communities. Future studies should examine the fitness consequences of morphological and life-history plasticity across multiple life stages and should address the population and community level consequences of offensive phenotypes.
The guppy is known to exhibit remarkable interindividual variations in spectral sensitivity of mi... more The guppy is known to exhibit remarkable interindividual variations in spectral sensitivity of middle to long wavelength-sensitive (M/LWS) cone photoreceptor cells. The guppy has four M/LWS-type opsin genes (LWS-1, LWS-2, LWS-3 and LWS-4) that are considered to be responsible for this sensory variation. However, the allelic variation of the opsin genes, particularly in terms of their absorption spectrum, has not been explored in wild populations. Thus, we examined nucleotide variations in the four M/LWS opsin genes as well as blue-sensitive SWS2-B and ultraviolet-sensitive SWS1 opsin genes for comparison and seven non-opsin nuclear loci as reference genes in 10 guppy populations from various light environments in Trinidad and Tobago. For the first time, we discovered a potential spectral variation (180 Ser/Ala) in LWS-1 that differed at an amino acid site known to affect the absorption spectra of opsins. Based on a coalescent simulation of the nucleotide variation of the reference genes, we showed that the interpopulation genetic differentiation of two opsin genes was significantly larger than the neutral expectation. Furthermore, this genetic differentiation was significantly related to differences in dissolved oxygen (DO) level, and it was not explained by the spatial distance between populations. The DO levels are correlated with eutrophication that possibly affects the color of aquatic environments. These results suggest that the population diversity of opsin genes is significantly driven by natural selection and that the guppy could adapt to various light environments through color vision changes.
Background The guppy (Poecilia reticulata) is an important model organism for studying sexual sel... more Background The guppy (Poecilia reticulata) is an important model organism for studying sexual selection; male guppies have complex and conspicuous pigmentation, and female guppies exhibit preferences for males with specific color spots. Understanding the genetic basis underlying pigmentation variation in the guppy is important for exploring the factors causing the maintenance of color polymorphism in wild populations. Findings We focused on the melanic black pigmentation of guppies, and examined genetic variations in the melanocortin 1 receptor (MC1R) gene because variation in this gene is known to contribute to polymorphism of melanin pigmentation in several animal species. The complete coding sequence of the guppy MC1R gene was determined, and two different MC1R alleles (963 and 969 bp) were found in wild populations. Ornamental strain guppies with a 963-bp MC1R tended to show less black pigmentation than those with a 969-bp MC1R, although the association between MC1R genotype and black pigmentation disappeared in the F2 offspring. Conclusions The guppy MC1R gene showed variation in the five wild Trinidadian populations we examined, and these populations also differed in terms of allele frequencies. We identified a significant association between black pigmentation and MC1R genotype in fish obtained from aquarium shops. However, the results from F2 families suggest that there are other genes that modify the effects of the MC1R gene.
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Papers by Ayumi Tezuka