From Atoms to Traits

Charles Darwin saw that random variations in organisms

provide fodder for evolution. Modern scientists are
revealing how that diversity arises from changes to DNA
and can add up to complex creatures or even cultures
BY DAVID M. KINGSLEY

0 n a shelf in a library in Texas sits a small

green volume, originally published 150years
ag6 and now generally recognized as one of the
most important scientific books ever written. Its
future success was not at all apparent when this
first-editioncopy of O n the Origin ofspecies was
printed, however. As Charles Darwin finished
the proofs of his new work, he drew up a short
self first arose. Once life began, though, Darwin
argued, organisms would slowly begmto change
and diversify through a completely natural pro-
cess: all living things vary; the differences are in-
herited. Those individualswith trait variants that
are favorable in the environment they inhabit
will thrive and produce more offspring than in-
dividuals with unfavorable variants. Advanta-
list of important colleagues who should receive geous traits will therefore accumulate over time
advance copies. He then anxiously awaited the by an inevitable process of "natural selection."
KEY CONCEPTS verdicts of the leading thinkers of his time. To convince readers of the cumulative power of
The idea that nature England's most famous living scientist in 1859 spontaneous variation and differential reproduc-
"selects" favorable varia- scribbled his reactions in notes found throughout tion, Darwin pointed to the huge changes in size
tions in organisms was that little green volume preserved at the Univer- and form that had occurred in domesticated
at the heart of Charles sity of Texas at Austin. Marked "from the au- plants, pigeons and dogs after only a few centu-
Darwin's theory of evolu- thor" on its frontispiece, it is the advance copy ries of selective breeding by humans.
tion, but how those varia-
that Darwin sent to Sir John Herschel, one of his Some of his scientificcolleagues instantly saw
tions arise was a mystery
in Darwin's time.
scientific heroes, whose own treatise on natural the power of Darwin's argument. "How stupid
philosophy had first inspired Darwin to become of me not to have thought of that!" exclaimed
Random changes in DNA a scientist. In the 1830sHerschel had memorably Thomas Henry Huxley, after reading his own
can give rise to changes described the origin of species as a "mystery of advance copy of Darwin's book. Unfortunately,
in an organism's traits, pro-
mysteries" that might occur by natural process- the reaction of the man whose opinion Darwin
viding a constant source
of variation.
es. Darwin quoted Herschel's words in the very said he valued "more than that of almost any oth-
first paragraph of the book, which laid out the er human being" was far less favorable. Herschel
Certain kinds of DNA chang- ingenious solution to the "mystery of mysteries" did not believe that useful new traits and species
es can produce major differ- that Darwin was offering to both Herschel and could arise from simple random variation, an
ences in form and function,
the world. idea he dismissed as the "law of higglety-piggle-
providing raw material for
the evolution of new species
Darwin's theory was at once sweeping and ty." In his personal copy of Origin of Species,
and even new human simple. He proposed that all living things on Herschel zeroed in on the fact that "favorable
cultures. -The Editors earth are descended from one or a few original - variations must 'occur' if anything is to be 'ef-
forms. He did not presume to know how Life it- fected.' " Darwin actually knew nothing about
A
January 2009
the origin of the variant traits themselves, and
Herschel felt that if Darwin could not explain the
source of variation, he did not really have a the-
b
ory sufficient to explain the origin of species.
In the 150 years since the debut of Darwin's
theory, key questions about how traits are passed
down to subsequent generations and how they
undergo evolutionary change have been resolved
by remarkable progress in the study of genes and
genomes. Darwin's scientific descendants study-
ing evolutionary biology today understand at
least the basic molecular underpinnings of the
beautiful diversity of plants and animals around
us. Like Darwin's theory itself, thecauses of vari-
ation are often simple, yet their effects are
profound. And fittingly, these in-
sights have come in a series of
steps, many of them just in time
for the successive SO-year anniversaries of Da
win's book.

Variation Revealed
Darwin was not only unable to say where vari-
ants came from, he did not explain how those
new traits could spread in subsequent genera-
tions. He believed in blending inheritance, the
idea that offspring take on characteristics inter-
mediate between their parents. But even Darwin
recognized that the theory was problematic
because if traits truly blended, then any rare new
variant would be progressively diluted by gener-
ations of breeding with the great mass of indi-

-
viduals that did not share the trait.
Confusion about blending inheritance was
swept away in 1900 by the rediscovery of Gregor

VARIATION in a pea plant, and

in all life, stems from DNA.
 I,%>+
4.5;p
JOHN HERSCHEL, a prominent
,i,r-
..;
,d5,,scientist of Charles Darwin's era,
I-.,,-
,-=;' x ,doubted the theory laid out in
+,- WWievm the -us8 may Ise of 'each
On the Origin of Species. Be- j
, as &pring from their m n k -
cause Darwin could not explain & in& s M t is the &acFp m u m
the cause of trait variations, the x,&GGd&bn, of meb differences, when
idea that nature selected the &0 &diVid~d,%8t *g Dl0
advantageous variants seemed m&mtiona .of .sjru.ctam*by w6eb Qe
incomplete. In his personal copy bebga on the fq$f+;tP;sem& a6:&b1ed to &q
of the book, Herschel wrote, Xdt4.t each atber,*d
"D. recognizes an unknown
cause of slight individual differ-
ences-but claims for 'natural
selection' the character of a 'suf-
ficient theory' in regard to the
results of those differences."

Mendel's famous breeding experiments with tosine, guanine and thymine (A, C, G, T),which
peas, conducted in the 1850s and 1860s. Differ- also form the foundation of a simple genetic lan-
ent pea plants in the Austrian monk's garden guage. Just like the 26 letters in the English al-
showed obvious morphological differences, such phabet, the four chemical letters in the DNA al-
as tall versus short stems, wrinkled versus smooth phabet can occur in any sequence along one
seeds, and so forth. When true-breeding pea strand of the helix, spelling out different instruc-
plants of contrasting types were crossed, the off- tions that are passed from parent to offspring.
spring usually resembled one of the two parents. The double-stranded helix provides a clear
With further crosses, both forms of a trait could mechanism for copying genetic information as
reappear in undiluted form in future generations, well. Cs always pair with Gs, and As pair with
however, demonstrating that the genetic infor- Ts across the middle of the DNA molecule, with
mation for alternative forms had not blended these affinities determined by the complementa-
away. Mendel's experiments changed the general ry size, shape and bonding properties of the cor-
perception of heritable variants from ephemeral
- -
responding chemical groups. When the two
and blendable to discreet entities passed from strands of the DNA helix are separated, the se-
THE AUTHOR parents to offspring, present even though they quence of letrers in each strand can therefore be
used as a template to rebuild the other strand.
ce patterns of Mendel's Watson and Crick's DNA structure immedi-
genetic factors" were, intriguingly, found to be ately suggested a possible physical basis for spon-
mirrored by the behavior of chromosomes in the taneous variation. Physical damage or mistakes
cell nucleus. At the SO-year anniversary of Ori- made in copying the DNA molecule prior to cell
gin of Species, the origin of variants was still un- division might alter its normal sequence of let-
known, but genetic information was becoming a ters. Mutations could take many different forms:
physical entity, and it was finally visible as threads substitution of a single letter for another at a
inside the nucleus. By the 100th anniversary of particular position in the polymer, deletion of a
of developmental biology at the the book's publication, hereditary information block of letters, duplication or insertion of new
Stanford University school of in chromosomes had already been traced to a letters, or inversion and translocation of the let-
Medicine and a Howard Hughes
Medical Institute investigator, His
- .
large acidic ~olvmer
<
called deoxvribonucleicacid ters already present. Such changes were still the-
(DNA).James D. Watson and Francis Crick had oretical at the time the structure was proposed.
studies of how genes control the
development and maintenance of proposed a structure for the DNA molecule in But as the 150th anniversary of Darwin's fa-
skeletonsand joints shed light on 1953, with stunning implications for our physi- mous publication approaches, large-scale se-
modern health problems aswell as cal understanding of heredity and variation. quencing methods have made it possible to read
on the evolution of new animal DNA is a long, two-stranded helix, with a entire genomes and to study genetic variation-
forms over the course Of millennia. backbone made of repetitive chains of sugar and the raw material for his proposed evolutionary
Kingsley has shown how several
basic genetic mechanisms work in phosphate. The two strands of the polymer are process-with unprecedented detail.
diverse organisms to create new held together by the complementary pairing be- By sequencing various organisms and their
traits in natural populations. tween four possible chemical bases: adenine, cy- offspring, then looking for any spontaneous

54 SCIENTIFIC A M E R I C A N January 2009

 Seeking Variatio
4 GEMMCLLES: Flme yews after Origin
of Species, Darwinput forth his
clearly shown that such mutationsdo occur fair- theory that a new variant version of
.
a trait might be passed from parent
ly regularly. (Of course, only mutations that oc-
to offspring, a d thus into the larger
cur in germ cells would be passed to offspring population, by "infinitely minute"
and therefore detectable in this manner.) Abso- particlesthat he called gemmules.
lute rates of mutation differ in different species 4ecfeted by ceik, the particleswould
but typically average per nucleotide per carry the essence of the body parts
generation for single base-pair substitutions. kem which they derived to the
rqxoductiw organs, to be absorbed
by the germ cells.
ticellularanimal with 100 million or even 10 bil-

4 MEMDECS FACTORS: EarbZOth-

century scientists rediscoveredthe
e hereditary information is passed down.
ideas of Gregor Mendel, who experi-
mentedwith pea plants during the
ikely than others, based on the chemical stabil- 1850%and 18605to derive detailed
and structural properties of the DNA bases. laws of irrheritance. Mendel pwited
In addition, some types of larger sequencechang- theexistenceof diirete facton
es occur much more frequently than the overall carrying trait information and ob-
average rate of single base-pair substitutions. served that each individual would
Stretches of DNA with eight or more identical carry two copies-ane from each
letters in a row, known as homopolymers, are parent-of a given factor. Although
very prone to copying errors during the process both were present, only one of the
of DNA replication, for example. So are regions copies would dominate and produce
the visible trait.
known as microsatellitesthat consist of sequenc-
es of two, three or more nucleotides repeated
over and over.
All these spontaneous changes within genom- THE DOUBLE HELIX: The DNA
es add up to a lot of diversity, even within a sin- moleculewas already recognizedas
gle species, including our own. In a historic mile- the vehicle for trait i n f a i o n when , '
stone, a reference sequence for the entire three- Francis Crick and James D. Watson
billion-base-pair human genome was completed discovered its structure in 1953. Thg >. ,'*

in 2003, and four years later the nearly complete paired strands joined by m p 1 m n - - i'
personal genome of Watson was published, tary chemical bases immediately A: i
making it possible to compare the two human suggested both an alphabetto ,%;

convey the genetic messageand a

sequences to each other and to that of Celera
mechanismfor it to change. Each .I
founder Craig Venter, whose genome sequence time a ceH &ides, it makes a eopy - :,,-
has also been made public. A side-by-side com-
parison of the three sequences offers several in-
of its drromwmes, providingan ' ' ;- .
apportunityf+x"fyposntobeintr~- , ',
teresting revelations. duced into the sequenceof bases. ,>;$?,\' .L

First, each individual's genome differs from *<- b

the reference sequence by roughly 3.3 million :

- .r

single base-pair changes, which corresponds to 1

.
variation in one of every 1,000 bases on average. 4 GENE REGULATION: Mendel 'sf-
Although deletions and insertions of larger DNA came to be known as genes, tradk a<,

stretches and whole genes are not as frequent as tionally Mined as stretchesof DNA ,
that encode a protein. Typos, wmu-
single base-pair changes (a few hundred thou-
tations, can alter or disable genes
sand instead of a few million events per genome),
directly, but in the pait decade scb 5%

these events account for the majority of total

entists haw also come toappreciate :.,i%
bases that differ between genomes, with up to 15 the importanceof another source of 2
million base pairs affected. Many entire genome variation: mutatiom that alter a .
+
regions have also recently been found to exist in DNA region responsible for regUIm ..
different copy numbers between individuals, ing when and where in the body a
which reflects an unappreciated level of genome >: gene is activated.

www.SciAm.com
structural variation whose implications scien- They know, for example, that Mendel's tall and
tists are only beginning to explore. Finally, the short pea plants differ by a single G to A substi-
sequence changes seen when comparing com- tution in a gene for the enzyme gibberellin oxi-
plete human genomes alter either the protein- dase. The so-called short variant of the gene
encoding or regulatory information or the copy changes a single amino acid in the enzyme,
number of a substantial proportion of all 23,000 which reduces enzyme activity and causes a 95
human genes, providing an abundant source of percent drop in the production of a growth-stim-
possible variation underlying many traits that ulating hormone in the stems of the pea plants.
differ between people. In contrast, Mendel's wrinkled seed trait re-
sults from the insertion of an 800-base-pair se-
The Molecular Basis of Traits quence in a gene for a starch-related enzyme. B
Herschel wanted an answer for how and why That inserted sequence interferes with the en- g
variants arose before he could accept Darwin's zyme's production, reducing starch synthesis
theory that natural selection acts on those traits, and producing changes in sugar and water con- .=.S
generating new living forms by completely nat- tent that lead to sweeter but wrinkly seeds. The .$$
$s
2;
ural processes. Today scientistsknow that spon- inserted sequence also appears at multiple 0th-
taneous changes in DNA are the simple "why" er locations in the pea genome, and it has all the t?
of variation, but the answer to "how" those hallmarks of a transposable element-a block
gs
so
mutations translate into trait differences is more of DNA code that can move from one place in gE
complex and makes for an activefield of research the genome to another. Such "jumping" ele- $2
u<
with implications far beyond evolution ments within genomes may be yet another
studies. common source of new genetic variants-
x:3c
3,
Biologists can now often connect the dots all either by inactivating genes or by creating new $f
the way from classic morphological and physi- regulatory sequences that change gene activity 22
ological traits in plants and animals to specific patterns. 3* 8>
changes in the atoms of the DNA double helix. One of the few generalizations evolutionary 22
January 2009
 differences such as these between individuals
might arise by natural processes, but bigger
structural differences between species could not
have done so. Many small changes can add up
to big ones, however. In addition, certain genes
have powerful effects on cell proliferation and
cell differentiation during embryonic develop-
ment, and changes in those control genes can
produce dramatic changes in the size, shape and
number of body parts. A subspecialty within
evolutionary biology that has come to be known
as evo-devo concentrates on studying the effects
of changes in important developmental genes
and the role they play in evolution.
The potent influence of such genes is illustrat-
ed by the modern maize plant, which looks com-
pletely different from a wild, weedy ancestor
called teosinte in Central America. Many of the
major structural differences between maize and STICKLEBACKS
teosinte map to a few key chromosome regions. ADAPT
Mutations in a regulatory area of a single gene
In just 10,000 generations,
that controls patterns of cell division during plant three-spinedstickleback fish
stem development account for much of the differ- have evolved myriad forms to
ence between an overall bush shape and a single, suit diverse environments.
central stalk. Changes in a second gene that is ac- Mutations affecting the activity
tive during seed development help to transform of three developmental-control
genes have produced striking
the stony, mineral-encased seeds of teosinte into anatomicalchanges, including
the softer, more exposed kernels of maize. An- the complete loss of pelvic hind
cient Mesoamerican farmers developed maize fins, large differences in bony
biologists can make about the nature of varia- from teosinte without any direct knowledge of armor and much lighter skin
color. In each fish pair shown
- tion is that one usually cannot tell just by look- DNA, genetics or development, of course. But by
below, a typical marine
2%
-- ing what the underlying genetic source of a trait mating plants with desirable properties, they un-
ancestor is on top and an
$4 variant is going to be. Darwin wrote extensively wittingly selected spontaneous variants in key evolved freshwater stickleback
3gg about dramatic morphological differences pres- developmental control genes and thereby con-
ent In pigeons, dogs and other domesticated ani- verted a bushy weed into a completely different
'3 - mals, for example. Today we know that the in- looking plant that is useful for human agricul-
a$
teresting traits in domesticated an~rnalsare ture in relat~velyfew steps.
ZZ based on many different types of DNA sequence Similar principles underlie the evolution "l
~2 change. new body forms in completely wild populations
s=
--
42 The difference between black and yellow col- of stickleback fish. When the last Ice Age ended
or in Labrador retrievers stems, for Instance, 10,000 years ago, migratory populations of
from a single base change that inactivates a sig- ocean fish colonized countless newly formed
nal receptor in the plgment cells of yellow dogs. lakes and streams in North America, Europe and
Increased muscle slze and improved racing per- Asia. These populations have since had approxi-
formance in whippet dogs have also been traced mately 10,000 generations to adapt to the new
to a s~nglebase-pair change, which inactivates a food sources, new predators, and new water col-
signal that normally suppresses muscle growth. ors, temperatures and salt concentrations found
In contrast, the special dorsal stripe of hair in in the freshwater environments. Today many
Rhodesian ridgeback dogs comes from the du- freshwater stickleback species show structural
plication of a 133,000-base-pair region contain- differences that are greater than those seen be-
ing three genes that encode a growth factor for tween different genera of fish, including 30-fold
fibroblastcells, which amps up production of the changes in the number or size of their bony plates,
growth factor. the presence or absence of entire fins, and major
Modern-day cr~ticsof Darwin and evolu- changes in jaw and body shape, tooth structures,
tionary theory have often suggested that small defensive spines and body color.

SCIENTIFIC AMERICAN 57
 Humans n e 4 only lo& akm-rndj
producednoveltraits, r&gin~Rd@
the changes @nabledentIreppu
example of such a Wf,
groups on different conti
possibilityof diredyan

Just as with maize, recent genetic studies show The Casual Concourse
that some of the large morphological changes of Atoms
can be mapped to a few important chromosome Humans can also look in the mirror and see fur-
regions. And the key genes within these regions ther examples of relatively recent variation pre-
turn out to encode central regulators ofdevelop- served by natural selection. Wecome in a variety
ment. They include a signaling molecule that of colors in different environments around the
controls the formation of many different surface world, and the lighter skin shades found in pop-
structures, another molecule that turns on bat- ulations at northern latitudes have recently been
teries of other genes involved in limb develop- traced to the combined effects of several genetic
Lactase regulatory sequence ment, and a secreted stem cell factor that con- changes, including single-base mutations in the
trols the migration and proliferation of precur- genes for a signal receptor and a transporter pro-
sor cells during embryonic development. tein active in pigment cells. Additional changes
The overall evolution of diverse new stickle- in DNA that regulate the migration, prolifera-
00 Distinct regionalmutations
No mutation back forms clearly involves multiple genes, but tion and survival of nascent pigment cells are
some of the same variants in particular devel- also suspected.
DISTINCT MUTATIONS in the same opmental regulators have been seen repeatedly A relative lack of variation in the DNA re-
regulatory region of DNA that in independent populations. The adaptation of gions flanking two of these pigment genes sug-
controls the lactase gene pre- these fish to their respective environments thus gests the light-skin variants were initially rare
dominate in different regions
demonstrates nicely how random variations and probably originated with a small number of
.
of the world. ,- . .. . - - ~
.
can give rise to major differences among organ- people. The variants would have then rapidly in-
isms, and if those changes confer an advantage, creased in frequency as ancient humans migrat-
natural selection will preserve them, again and ed into new environments with colder tempera-
again. tures and higher latitudes, where light skin more

' ' 5 8 - s C l E N T I F I C AMERICAN January 2009

 $$-,.'- -, * .- : . . -. ... !.,..
fermt lactose-tolerant populations have differ- p*,;*4c, ,
.
, ,,. ,. ,FG,n :
ent mutations in the key region-a striking ex- :<.?:. - -., - A+
.;I

ample of the repeated evdution of a similar trait $ -

by independent changes affecting one gene.
, ,ae,.L'.-- ,
I '. .
A

.
..
_ I - -+-,.
. . -
Another example of a recent nutrition-related -? '-- @
adaptation in humahs inwlves the multiplica- '"k
t i ~onf a complete gene. Whereas chimpanzees
Skifi Color ~ n l one
y copy of the gene for salivary amy-
Changes to at feastthreegenes have been linked to the trait or hw,an enzyme that digests starch in foad, hu-
liaht-coloredskirlL~hlchkbelieved to have amen ~nnorthern I mas show marked variation in the number of
~;ro~e.lightskin moret$as#y absorbs ultraviolet rays needed
to pmdttcqvitamin D, an&ntaae\nrhere sunliaht is limited. 1 anq&segene copies they carry. In someindivid-
uab, dupJlations of the gene have produced as
many as 10 copies along a single chromosome.
Bmple from cultures that eat diets rich in starch,
su& as rice, have higher average amylase gene
mpy numbers and higher amylase enzyme levels
in their saliva than do people from cultures that
rely 0x1hunting and fishing.
Dairy herding and agriculture both arose in
the past 10,000 years. Although that only cor-
responds to just 400 or so human generations,
major new sources of nutrition are clearly al-
ready leading to the accumulation of novel ge-
nt& wriants in populations that exploit those
hod wurces.
Herschel's most persistent objection to Dar-

I
Starch Digestion
win's theory was his feehng that useful new traits
People vary widely in the number of copies they carry ofa gene
for thestarch-digesting enzyme salivary a@%. Members of eould never appear from simple random varia-
cuttwes with starch-rich diets tend to haw higher numbersaf tion, In published comments and letters, he ar-
fhamylase gene and high levek of the enzyme in their mha
gwd that such characteristics would always re-
quire "mind, plan, design, to the plain and obvi-
readily makes vitamin D from limited sunlight. ous exclusion of the haphazard view of the
Similarly,strong molecular "signatures of se- subject and the casual concourse of atoms." Her- .
lection" have been found around a gene that schel was correct to point out that the origin of
controls the ability to digest lactose, the predom- variation was still a mystery in 1859. After 150
inant sugar in milk. Humans are mammals, years of additional research, however, we can MORE TO EXPLORE
nurse their young and produce an intestinal en- now catalogue a variety of spontaneous DNA se- cis-RegulatoryChanges in W t Li-
zyme that breaks lactose into the simpler sugars quence variants that occur every time a complex gand Expression and Parallel Evo-
glucose and galactose. Humans are also unique genome is passed from parents to offspring. lution of Pigmentationin Stickle-
among mammals in continuing to use the milk Only a tiny fraction of these changes are like- backs and Humans. Craig T. Miller
of other animals as a significant source of nutri- ly to improve, rather than degrade, the original et al. in Cell, Vol. 131, No. 6, pages
1179-11 89; December 14,2007.
tion well beyond childhood. This cultural inno- hereditary information and the trait that derives
vation has occurred independently in groups in from it. Nevertheless, sweeter peas, bigger mus- independentIntroductionof Two
Europe, Africa and the Middle East, using milk cles, faster running ability or improved ability to Lactase-Persistence Alleles into
derived from cattle, goats and camels. digest new foods have all arisen from simple new Human PopulationsReflects Dif-
An ability to digest milk in adulthood de- arrangements of atoms in the DNA sequence of ferent History of Adaptation to
Milk Culture. Nabil S. Enattah et al.
pends on a mutant form of the intestinal lactase peas, dogs and humans. Thus, the "casual con- in Am canier Journalof Human Genet-
gene, which in most mammals and most human course of atoms" clearly can generate interesting ics, Vol. 82, No. 1, pages 57-72; 2008.
5
groups, is active only during the infant nursing new traits. And the intrinsic variability of living
period. In humans from populations with a long organisms continues to provide the raw material Evolution: Constant Change and
6 history of dairy herding, however, a mutant by which, in Darwin's famous words at the end Common Threads. HHMl2005 Holi-
1 day Lectures on Science. Sean 0. Car-
5
form of the lactase gene continues to be active in of his small green book, Uendlessforms most roll and David M. Kingsley. Webcast or
adulthood. This genetic innovation has been beautiful and most wonderful, have been;and DVD available at wwv.hhmi.orgl
r
E

s linked to single base-pair changes in the regula- are being evolved." 4 biointeractivelevolution

SCIENTIFIC AMERICAN 59