BACKGROUND
our recent history of domesticating plants and animals  <cit>  offers a diversity of genetic systems to study evolution in action  <cit> .
crop and livestock breeders often provoke relatively large phenotypic changes across successive generations conditioned on available standing genetic variation found in wild progenitor populations.
such changes demonstrate the formidable power of directional selection over relatively short periods of time.
in fact, charles darwin devoted the opening chapter of “on the origins of species” to artificial selection in order to introduce natural selection as the principal driver of evolutionary change  <cit> .
in his two-volume follow-up devoted specifically to domestication, darwin noted that “selection may be followed either methodically and intentionally, or unconsciously and unintentionally”  <cit> .
these histories can also be modeled as a co-evolutionary framework between humans and the crops and livestock they cultivate  <cit> , whether the selective pressures were intentional or not.
while domesticates usually have reduced effective population sizes relative to their ancestral populations, there still remains ample variation for selection to act upon.
numerous loci involved in animal and crop domestication are found to harbor positive selection coefficients  <cit>  and selectively swept regions  <cit> .
in domestic chickens, genomic sequences from multiple lines reveal the presence of selective sweeps leading to the discovery of causative agents in growth differences between domestic lines  <cit> .
in household pets, selection for certain behavioral and sensory traits  <cit>  have produced signatures of positive selection in vision and hearing genes in domesticated cats  <cit>  and neural development genes in dogs  <cit> .
the growing literature on crop, livestock, and pet domestication reveals that long-term selection by humans can generate strong signals of selection at the genomic level and provides a new lens into the strength and target of selection during our recent domesticated past.
animals bred in the laboratory as model organisms may also be adapted to human conditions, and over a much shorter time period.
studies comparing laboratory strains of mice and nematodes have identified genetic differences in genes involved in behavior  <cit>  and metabolism  <cit>  suggesting adaptation to novel conditions in the laboratory .
over a century ago, drosophila melanogaster was brought into the laboratory initially as a teaching tool  <cit> , and its fast generation time and relative ease of maintenance quickly made the fruit fly an important genetics research tool  <cit>  in such varied fields such as development, physiology, and evolution.
canton-s, the oldest known wildtype fly stock, was captured by calvin bridges over a century ago from a natural population in canton, ohio, and first debuted in his seminal  <dig> paper on “non-disjunction as proof of the chromosome theory of heredity”  <cit> .
approximately a decade later, donald lancefield, another product of thomas morgan’s prolific lab at columbia university, extracted oregon-r from a population in roseburg, oregon  <cit> .
many commonly used fly stocks eventually coalesce ancestrally to these old north american laboratory stalwarts, canton-s and oregon-r , which were independently extracted from populations in north america and themselves possessing relatively recent african origins .fig.
<dig> hypothetical genealogical relationship of laboratory strains in relation to global populations of d. melanogaster and the closely related species, d. simulans.
the five lab strains are indicated in red with hypothetical ancestral relationships marked as a dotted line.
estimated time since common ancestors are indicated below
with at least a dozen generations per year, d. melanogaster lab stocks have been isolated from their wild ancestors for over a thousand generations, providing ample time to sufficiently diverge.
it is known among fruit fly researchers that behavioral traits of laboratory vs. wild d. melanogaster are distinct, with lab-reared flies far tamer and more manageable than those found in the wild.
although lab-reared flies are generally maintained under relatively standard conditions of temperature, light, and diet, selective pressures in the lab are very different than those found in the wild providing the potential for strong selection for human-accommodating phenotypes and/or the relaxation of selection on traits adapted in nature  <cit> .
on the other hand, domesticates are generally less reproductively fit than their wild relatives  <cit>  and may exhibit similar less optimal behavioral phenotypes.
lab stocks typically experience drastic decreases in population size and higher levels of inbreeding ultimately decreasing the efficacy of selection to rid lines of continually re-occurring deleterious alleles  <cit> .
whether these phenotypic differences in lab strains are driven by conscious selection, inadvertent selection, a relaxation in selection, or are simply the fixation of deleterious mutations, is not known.
its relatively recent and well-documented history, access to multiple isolated lines reared in similar environmental settings, well-characterized functional annotations, and the availability of hundreds of genomes from extensively sampled extant populations including a closely related species, make d. melanogaster an ideal model system to study the evolutionary processes that underlie rapid phenotypic change.
here, we investigate genetic differences between common laboratory stains of d. melanogaster to those recently caught from nature to examine whether this important, centuries-old genetic model has evolved convergent domesticated behaviors by adapting to a bottled existence or being inundated by low-fitness alleles.
we first document behavioral differences between lab-reared and wild-caught flies with respect to their general activity and locomotory abilities.
we then identify snps that are differentiated between the genomes of laboratory and wild strains to evaluate the roles of selection vs. drift in flies isolated in bottles.
among uniquely derived alleles found only in lab strains we find patterns of drift and selection across, respectively, low and high frequency classes, when comparing evolutionary parameters such as grantham distance, missense to silent mutations, positional distribution within codons, and levels of codon bias.
we further characterize putative regions under sustained selection among lab strains and find longer than expected haplotypes near high-frequency derived snps, also enriched in neuro-sensory genes.
finally, we suggest that this neurogenetic class, residing on a disproportionately large fraction of the genome relative to other functional classes, provides a large mutational target for genetic variation to accumulate and selection to act upon.
thus, the genomics of fly domestication reveal an interplay of evolutionary forces with mutation and selection on a large neurogenetic class of genes playing a pivotal role in d. melanogaster’s brief, but distinguished, history in the laboratory.
RESULTS
behavior
although it is well-known among drosophilists that lab strains are much slower and easier to handle than live flies, literature documenting these differences is lacking.
we first confirm anecdotal reports of differences in the overall activity between laboratory stocks  and flies from wild populations .
on average, flies from lab strains are significantly less active than wild-caught individuals using different measures of locomotion including standard and angular velocities  and time-spent moving vs. stationary .
lab strains also demonstrate less responsiveness in the form of interactions between individuals compared to wild-caught lines where the latter’s movement is more uniformly distributed and gradually increases with proximity to neighbors .
flies from laboratory strains do not appear to follow this relationship with motion uncorrelated to the proximity with their nearest neighbor .
overall, these results provide general support for a convergence of slow-moving and less responsive behavior in lab strains.
genetic variation in lab strains
after applying filters for quality and missing data, a total of  <dig> , <dig> base pairs were analyzed across five reassembled laboratory strains of d. melanogaster,  <dig> genomes from  <dig> global populations including an extensively sampled population from north america , and one closely related species, d. simulans.
among  <dig> , <dig> polymorphic sites,  <dig>  % are non-singletons and used for subsequent analyses .
to test for signals of domestication, we used three defined categories of snps differentiated between lab strains and populations of d. melanogaster from nature: lab-specific snps and two types of highly differentiated fst  snps, depending on whether the derived allele is found at a higher frequency among lab strains , or in a representative natural population .
while distinct, some overlap exists between the lab-specific and fst*lab>wild analysis categories: out of a total  <dig>  differentiated snps,  <dig> snps are common to these two snp classes .
in contrast, fst*wild>lab snps are unique and relatively rare .fig.
<dig> characterization of derived snps differentiated between lab strains and a wild d. melanogaster population.
a number and overlap of lab-specific snps  with fst*lab>wild snps .
the total number of fst*wild>lab snps  is also shown.
b site frequency distribution of lab-specific snps, per chromosome.
c genic characterization of lab-specific snps found in the majority  of laboratory strains, across chromosomal arms
lab-specific snps
the number of lab-specific snps is  <dig> , with  <dig>  and  <dig>  snps located in genic and cds regions, respectively .
the total number of lab-specific snps is significantly larger than a subsample of five random genomes from north carolina and comparison of the number of snps specific to this random subset against the entire north carolinian dataset  as well as the entire global dataset .
lab-specific snps represent only a small fraction  of the total snp variation found among global populations of d. melanogaster, including singletons.
lab-specific snps are distributed across all chromosome arms with a slight but significant enrichment across non-coding regions .
the x-chromosome is enriched for mid- and high-frequency lab-specific snps .
the number of fixed lab-specific snps  was  <dig>   <dig>  and  <dig>  respectively, in all genomic regions, genic, and cds regions .
genes containing fixed lab-specific snps are enriched for regulatory and signaling gene ontology  categories  and up-regulated in neural-sensory tissues .
fst*lab>wild snps
the number of derived snps with high fst  that harbor a greater frequency in the lab compared to the wild is  <dig> , with  <dig>  and  <dig>  in genic and cds regions respectively .
fst*lab>wild snps generally describe variants that are highly represented  among lab strains but have a low  allele frequency in global populations.
fst*lab>wild are uniformly distributed across chromosome arms and are enriched for genic regions .
the number of fst*lab>wild snps that are fixed  is  <dig>  and  <dig> , respectively, in all genomic regions and cds regions .
fst*lab>wild snps are functionally enriched in general developmental gene ontology categories .
fst*lab>wild snps are upregulated in several tissues including ganglion, larval cns, and ovary .
fst*wild>lab snps
a small proportion of fst* snps  are highly differentiated in the opposite direction.
these fst*wild>lab snps are found at low frequency  among lab strains but have high allele frequencies in global populations .
fst*wild>lab snps are enriched on the x-chromosome , across intergenic regions , and significantly enriched for neurogenetic genes .
specifically, this snp category is significantly enriched in nervous system development and photoreceptor development gene ontologies and is upregulated in neural, visual, and ovarian tissues .
evolutionary relationships
phylogenetic analyses on lab-specific snps and fst* snps were performed to provide insight on the origin and relationship among isolated lab stocks .
the lab-specific consensus snp tree reveals canton-s as ancestral to the three oregon-r strains and the w <dig> strain, as expected .
the fst* snp consensus tree similarly shows a distinct lab monophyletic clade with similar bootstrap support for lab strain topology .
a distinct origin among lab strains is also seen using a random set of  <dig>  polymorphic sites among lab and wild strains .
the branch lengths of the lab strains dramatically differ between trees indicating each lab strain’s distinctiveness  from each other  and the extant north american population .
the three congruent phylogenetic trees also revealed several surprises including the three oregon-r strains being paraphyletic, with ore- <dig> and ore- <dig> more similar to w <dig> than ore- <dig>  also, while the original oregon-r strain was independently sampled on the us west coast a few decades later, all lab strains appear to be derived from a single canton-s common ancestor , with the lab clade best supported next to extant populations from france, then north america.
genome-wide levels of selection
to detect differences in selective constraints in the lab, we estimate a series of evolutionary parameters  across five frequency bins of lab-specific snps located in coding regions.
we compare parameter estimates against similarly binned derived snps found only in the raleigh nc population along with simulation estimates expected under strict neutrality.
additional file 2: table s <dig> compares the nature and number of lab-differentiated snps to those found in the raleigh nc population across autosomes and x-chromosomes.
when not binned according to allele frequency, mean grantham scores, r/s, and c1/ ratios are similar to random simulations.
however, when grouped by frequency class, parameter estimates of medium to high frequency snps more closely follow a pattern of similarly binned snps from the wild rather than expected neutral patterns based on a random mutational model .fig.
<dig> frequency distribution of lab-specific , wild-caught , and neutrally simulated derived  snps across various evolutionary parameters.
a mean grantham score per replacement substitution.
b mean replacement/silent  ratio per snp per individual.
c mean ratio of the number of first codon position  snps to the number of second and third codon position  snps.
d mean proportion of non-preferred to preferred  codons and preferred to non-preferred  codons per individual.
for all panels, dotted black horizontal lines represent one standard deviation from the mean of  <dig> random simulations using d. simulans sequence data .
statistical significance determined using a wilcoxon rank-sum test.
asterisks indicate significant differences between lab-specific snps and snps derived from neutral simulations .
squares indicate significant differences between lab-specific snps and snps derived from the raleigh nc population
effective population size
the effective population size is a strong determinant of the effectiveness of selection and drift  <cit> .
watterson’s theta, Θs  <cit> , was estimated across non-overlapping 50 kb windows to compare the amount of genetic variation from an extant population to that found among all lab strains.
like previous genome-wide estimates of nucleotide diversity from the raleigh nc population , our estimates of Θ similarly fluctuate across genomic regions with a genome-wide average of Θnc =  <dig>  .
although laboratory strains do not collectively comprise a true interbreeding population, we estimate Θlab to provide a relative measure of ancestral ne.
laboratory nucleotide diversity varies along the genome in a similar fashion as the raleigh nc population with a genome-wide mean of Θlab =  <dig>  , indicating at least a two-fold reduction in ancestral ne.
extended haplotype blocks
regions of extended homozygosity present potential signals of positive selection.
we observe a mean haplotype length for all lab vs. wild differentiated classes of snps  of 653 bp .
among lab-specific snps, long outlier haplotypes were only found within the high frequency class ≥ <dig>  and were significantly larger than all other frequency classes .
under a neutral model, we would expect similar haplotype lengths across all frequency classes.
in addition, we have run simulations in which we choose sites at random and estimate haplotype lengths.
using  <dig> replicates, the random site haplotype lengths are at least two standard errors lower than the observed 5/ <dig> haplotype lengths.
a total of  <dig>  large haplotype block outliers  were identified ranging in length from  <dig>  bp to  <dig>  bp and were significantly enriched  on the x-chromosome .
candidate lab-specific, fst*lab>wild, and fst*wild>lab haplotype blocks contain, respectively,  <dig>   <dig>  and  <dig> genes.
genes found within these lab-specific candidate haplotype blocks are enriched for neurogenetic gene ontology categories along with functional classes related to regulation and behavior responses  as well as other significant functional categories .
however, when normalized by gene length, significant go category enrichments in large lab-specific haplotype blocks disappear.
within large fst*lab>wild haplotype blocks, genes are enriched for go classes involved with axon guidance, post-embryonic system development, and regulation , even after normalizing for gene length.
no significant go enrichment is found in the four genes contained within large fst*wild>lab haplotype blocks.fig.
<dig> lab-specific snp haplotype length across frequency class.
boxplot of extended haplotype length surrounding lab-specific snps across derived frequency allele classes
fig.
<dig> neurogenetic enrichment of extended haplotype blocks and fst*wild>lab snp genomic distribution.
in the top panel, colored rectangles indicates haplotype blocks surrounding lab-differentiated snps .
size distribution of haplotype blocks per frequency class is found in fig.
<dig>  presence of known neurogenetic genes in each block is indicated by purple arrows.
in the bottom panel, fst scan identifies derived snps in genic regions with higher allele frequency in the raleigh nc population relative to the laboratory strains .
dotted line indicates cutoff for fst*wild>lab snps .
of the  <dig> fst* snps found in genic regions, snps are significantly enriched for neurogenetic genes .
snps found within neurogenetic genes are shaded in purple
fst*lab>wild
fst*lab>wild
fst*lab>wild
fst*lab>wild
fst*lab>wild
fst*lab>wild
fst*lab>wild
fst*lab>wild
fst*lab>wild
fst*lab>wild
fst*lab>wild
anumber of genes from gene ontology  from flybase fb2015_05
**p-value calculated using benjamini-hochberg correction
gene ontologies within each snp type are ranked by p-value.
no significant gene ontology class was found for haplotypes classified for significantly differentiated snps in which the derived snp is found in lower frequency in the wild
discussion
phenotypic and genetic differences in laboratory stocks
the captive genetic model, drosophila melanogaster, reveals hallmark features consistent with domestication.
laboratory strains show significant differences in behavior from their relatively recently isolated wild progenitors .
previous studies comparing lab and wild-caught lines of d. melanogaster also report differences in egg and larval survival  <cit>  and life history traits such as pre-adult development, early fecundity, and remating frequency  <cit> .
these traits comprise a suite of behavioral, physiological, and reproductive characters  <cit>  that have converged across multiple strains evolving independently under similar laboratory conditions.
furthermore, it previously has been demonstrated that these traits can quickly evolve significant differences in as little as 8– <dig> generations  <cit> .
it is paradoxical that domesticates, typically derived from small founder populations and maintained at very low effective population sizes, can effectively adapt to human conditions.
from a population genetics perspective, we may expect the opposite: that small captive populations and lower ne propagate the segregation and eventual fixation of deleterious mutations, thus, imposing a potentially large mutational burden on laboratory strains  <cit> .
our evolutionary parameter analysis reveals such drift-like signatures at the low end of the site frequency spectrum.
estimates of grantham distances, r/s ratios, codon positional fraction, and codon bias support a general genome-wide reduction in selection on low-frequency derived alleles in the lab  where mildly deleterious alleles may persist for longer periods of time  <cit> .
with a decrease in effective population size across each strain, inbreeding and drift dominate, which in turn, can quickly fix allelic and associated phenotypic changes across successive generations of captivity.
short-term isolation studies in drosophila have shown similar rapid changes across a variety of phenotypes  <cit>  with reductions in performance levels  <cit> ).
thus, the accumulation and fixation of mildly deleterious alleles, particularly on larger neurogenetic genes , and subsequent inbreeding depression  <cit>  may promote both the rapid nature of domestication and its associated convergence of common behavioral traits.
these docile and non-aggressive traits may alternatively be described as “lethargic” , a term commonly applied to inbred, and often sickly, drosophila stocks.
when did these changes occur?
our results suggest that these changes towards a domesticated phenotype likely began very early on based on available standing genetic variation of the progenitor population.
while heterozygosity in each contemporary isofemale lab strain is virtually zero , as a whole, these five lab strains collectively only harbor a two-fold genome-wide decrease in nucleotide diversity, Θlab, relative to a large contemporary population from raleigh nc .
this diversity estimate primarily reflects the amount of genetic variation captured in each of the five lines from an ancestral population.
the five lab strains share ~ <dig>  derived snps with extant global populations  indicating that laboratory stocks collectively extracted a significant fraction d. melanogaster genetic variation at their time of capture.
the importance of ancestral standing genetic variation can also be seen in the  <dig>  lab-specific snps.
in theory, these snps represent any of the following: i) de novo mutations that arose in the lab, ii) genetic variation that previously existed in an extinct north american population, or iii) a subset of genetic variation that has been completely lost in extant global populations.
we estimate that only a small fraction of these snps can be generated de novo .
the remainder of the lab-specific snps was probably lost in extant wild populations during the last century.
strong evidence supports a recent global sweep in d. melanogaster that dramatically reduced species-wide genetic variation after these particular lab strains were collected  <cit> .
thus, from the large pool of available genetic variation from their north american progenitor populations, canton-s and oregon-r likely experienced similar selection pressures on common genetic variants  during the earliest generations of lab domestication  <cit> .
a phylogenetic analysis of shared lab/wild snps also supports a distinct origin of all lab strains .
however, whether the lab strain monophyly is the result of an extinct progenitor population or the loss of global variation is unknown.
the inclusion of more sequenced lab strains may differentiate between these two hypotheses.
adaptation in the lab
caenorhabditis elegans, like d. melanogaster, has been lab-cultured for over 50 years, and harbors pronounced differences in longevity and fertility when compared to wild isolates  <cit> .
genome sequencing in the nematode identified snps differentiated between wild and long-term laboratory strains enriched for cell cycle and metabolic/growth genes  <cit> .
their results suggest the presence of strong selection early in nematode domestication for optimal growth under rich nutrient conditions similar to the significant go term, “behavioral response to nutrients”, found among lab-specific snps in fruit flies .
laboratory mice have similarly been shown to converge certain phenotypes including melatonin deficiency  <cit> , and a lack of aggression and tameness  <cit> .
the results from our evolutionary parameter analysis, when limited to lab-specific snps in the mid- to high frequency range, support that common phenotypic signals of domestication observed in the captive fruit fly have been strongly shaped by selection.
these derived snps, found in the majority of lab strains, show similar evolutionary patterns to high frequency snps from the wild and not to neutral expectations, unlike low-frequency snps .
the laboratory setting presents an immediate change in the fitness landscape, permitting rapid and significant changes in phenotype that would be detrimental to their fitness in the wild, across relatively few generations  <cit> .
inadvertent human habituation and unintentional conditioning may be the primary selective agent for such known differences among lab strains as faster development and reproductive time  <cit> .
for instance, flies that rarely escape the bottle or benchtop may be selected due to human carelessness while fly stocks are transferred to new vials/bottles, or “flipped”.
our behavioral results support such a convergent shift towards less active and responsive flies .
from our genomic analysis, we find that neurogenetic genes, involved in such biological processes as neurogenesis and axon development, are enriched in extended haplotype blocks common to differentiated snps  found at high allele frequencies , with an overrepresentation of fixations on the x-chromosome.
these genes affect locomotion and visual cues suggesting lab selection on genes involved in behavioral responses.
while an excess of long extended haplotypes on high frequency lab-specific snps support an adaptive shift towards domesticated phenotypes, a relaxation of selection on certain loci involved in behavior may have co-occurred in the lab.
conditions in the laboratory are often optimized for growth and reproduction, reducing the natural ability of flies to escape predators or compete for food and mates.
thus, a relaxation of selection on activity levels, aggressiveness, and responsiveness, critical in the wild, may also drive the behavioral differences that converged across lab strains.
characters involved in mating, driven by the sparsity of mates in the vicinity, is a key difference between domestic and wild species  <cit> .
our behavioral results, showing a reduction in interactive activity in lab flies, is consistent with this hypothesis.
in addition, our go analysis of shared fst*wild>lab snps, in which the derived allele is more frequent in the raleigh nc population than lab strains, finds a significant enrichment of the neurogenetic functional class, even when corrected for gene size.
these snps are found in different genes than the snps harbored in long extended haplotype blocks, suggesting an extensive cache of genes involved in behavioral differences between flies reared in the lab and those found in the wild.
a similar decrease in behavioral activity was observed in lab strains of mice  <cit> , with backcrossing to wild mice isolates allowing them to regain these previously lost behavioral functions  <cit> .
the use of inbred laboratory strains of d. melanogaster presented unique analytical challenges that differ from other domesticated studies.
due to initial and recurrent inbreeding and the lack of an interbreeding population, laboratory strains violate most population genetic models used to infer selection.
in this study, the site frequency spectrum is only applied across isolated lab strains as a framework to bin our observed data and could not be used to infer population genetic parameters.
despite these difficulties, our results reveal an interplay of drift and selection at work in the lab.
first, we find genome-wide levels of selective constraints in the lab that are significantly lower than a sampled north american population.
this pattern is likely caused by low effective population sizes in bottles that promote the accumulation of mildly deleterious mutations under drift-like conditions, which we also observe in low frequency alleles.
second, we observe derived snps that are highly differentiated between the lab and a north american population to be significantly enriched in neurogenetic genes, suggesting a differential fitness landscape in behavior.
this functional enrichment takes into account the number of genes in each functional class as well as their size.
third, we find signatures of positive selection on extended haplotypes in both lab-specific and highly differentiated snps.
these, too, are significantly enriched in neurogenetic genes.
fourth, there’s an enrichment of these changes on the x-chromosome .
the preferential role of the x-chromosome is seen in marked differences in the site frequency spectrum between the x-chromosome and autosomes  and in the enrichment of long haplotype blocks on the x-chromosome .
since many of these long x-linked haplotype blocks are fixed in all five lab strains, the fixation of hemizygous loci likely occurred early in fly domestication.
preferential role for neurogenetic genes
our results suggest a central role for neurogenetic genes in domestication.
lab-specific snps found in the majority of lab strains are strongly enriched for this functional class, as are highly differentiated snps found in high frequency in the wild .
large outlier haplotype blocks also contain an overrepresentation of neurogenetic genes .
in most fly labs, inadvertent selection is inevitable: more active, reactive, and sensory-prone flies  have a higher probability of escaping during routine stock transfers.
hence, fly researchers may have unconsciously selected for lethargic flies over thousands of generations in the lab.
selected genes, enriched for sensory functions in eye photoreceptors and peripheral nervous system, can explain these behavioral shifts seen in lab strains.
the significance of neurogenetic genes in changing activity and response behaviors across a relatively short evolutionary time period may also relate to how behaviors involved in premating isolation  can swiftly and easily develop in a population by drift and selection.
recently, wilkins et al.
<cit>  proposed a general hypothesis to explain the convergence of various phenotypic traits that differentiate mammalian domesticates from their wild progenitors.
these traits are collectively known as the “domestication syndrome”  <cit>  and, in mammals, include such morphological modifications as depigmentation, facial skeletal, and floppy ears as well as behavioral shifts towards docility and tameness  <cit> .
wilkins et al.
<cit>  argue that a developmental deficit in neural crest genes can generate each of these differences, thus, explaining the commonality of these traits across domesticated mammals.
our results extend the behavioral component of the domestication syndrome to non-vertebrates but through a more general genomic mechanism based on the predominance of mutations on neurogenetic genes affecting overall locomotion and activity.
in drosophila, genes from this ontological category are among the largest in gene number and gene size, providing a large mutational target for rapid behavioral change .
currently,  <dig>  out of  <dig>  genes are characterized as “neurogenetic” , and 24 % of known fly genes are expressed in the brain and nervous system  <cit> .
we propose that a large mutational target  <cit>  of neurogenetic genes can explain the rapid evolution of behavior in animal taxa., these neurogenomic loci collectively provide a large genomic substrate for variation to accumulate, and then selection and drift to act, to quickly transform behavior within a relatively short time frame.
CONCLUSIONS
tameness and docility are hallmark features of domestication and the product of artificial selection by breeders.
our results challenge the traditional notion that relatively submissive laboratory animals are solely the product of cumulating deleterious mutations and demonstrate how unconscious selection for human-favored traits plays an important role in driving rapid phenotypic change in the lab.
selection on a large pool of available genetic variation during the early stages of fly domestication, followed by strong and recurrent inbreeding, allow for the successive roles of adaptation and drift in shaping the genetic architecture of domesticated phenotypic traits in a bottle.
our study finds that the genes and phenotypes in fruit fly domestication are enriched in, respectively, neurogenetic and behavioral function, providing a starting point to decode the genomic basis of domestication and promoting its study in genetic model systems such as drosophila.
a detailed mapping of these genes and their snps to specific behaviors will not only be informative about the selective pressures that we have inadvertently applied to our immediate biotic environment, but may also provide new general insight on the divergence and isolation of populations.

 our recent history of domesticating plants and animals offers a diversity of genetic systems to study evolution in action. crop and livestock breeders often provoke relatively large phenotypic changes across successive generations conditioned on available standing genetic variation found in wild progenitor populations. such changes demonstrate the formidable power of directional selection over relatively short periods of time. in fact, charles darwin devoted the opening chapter of “on the origins of species” to artificial selection in order to introduce natural selection as the principal driver of evolutionary change. in his two-volume follow-up devoted specifically to domestication, darwin noted that “selection may be followed either methodically and intentionally, or unconsciously and unintentionally”. these histories can also be modeled as a co-evolutionary framework between humans and the crops and livestock they cultivate, whether the selective pressures were intentional or not. while domesticates usually have reduced effective population sizes relative to their ancestral populations, there still remains ample variation for selection to act upon. numerous loci involved in animal and crop domestication are found to harbor positive selection coefficients and selectively swept regions. in domestic chickens, genomic sequences from multiple lines reveal the presence of selective sweeps leading to the discovery of causative agents in growth differences between domestic lines. in household pets, selection for certain behavioral and sensory traits have produced signatures of positive selection in vision and hearing genes in domesticated cats and neural development genes in dogs. the growing literature on crop, livestock, and pet domestication reveals that long-term selection by humans can generate strong signals of selection at the genomic level and provides a new lens into the strength and target of selection during our recent domesticated past. animals bred in the laboratory as model organisms may also be adapted to human conditions, and over a much shorter time period. studies comparing laboratory strains of mice and nematodes have identified genetic differences in genes involved in behavior and metabolism suggesting adaptation to novel conditions in the laboratory. over a century ago, drosophila melanogaster was brought into the laboratory initially as a teaching tool, and its fast generation time and relative ease of maintenance quickly made the fruit fly an important genetics research tool in such varied fields such as development, physiology, and evolution. canton-s, the oldest known wildtype fly stock, was captured by calvin bridges over a century ago from a natural population in canton, ohio, and first debuted in his seminal paper on “non-disjunction as proof of the chromosome theory of heredity”. approximately a decade later, donald lancefield, another product of thomas morgan’s prolific lab at columbia university, extracted oregon-r from a population in roseburg, oregon. many commonly used fly stocks eventually coalesce ancestrally to these old north american laboratory stalwarts, canton-s and oregon-r, which were independently extracted from populations in north america and themselves possessing relatively recent african origins.fig. hypothetical genealogical relationship of laboratory strains in relation to global populations of d. melanogaster and the closely related species, d. simulans. the five lab strains are indicated in red with hypothetical ancestral relationships marked as a dotted line. estimated time since common ancestors are indicated below with at least a dozen generations per year, d. melanogaster lab stocks have been isolated from their wild ancestors for over a thousand generations, providing ample time to sufficiently diverge. it is known among fruit fly researchers that behavioral traits of laboratory vs. wild d. melanogaster are distinct, with lab-reared flies far tamer and more manageable than those found in the wild. although lab-reared flies are generally maintained under relatively standard conditions of temperature, light, and diet, selective pressures in the lab are very different than those found in the wild providing the potential for strong selection for human-accommodating phenotypes and/or the relaxation of selection on traits adapted in nature. on the other hand, domesticates are generally less reproductively fit than their wild relatives and may exhibit similar less optimal behavioral phenotypes. lab stocks typically experience drastic decreases in population size and higher levels of inbreeding ultimately decreasing the efficacy of selection to rid lines of continually re-occurring deleterious alleles. whether these phenotypic differences in lab strains are driven by conscious selection, inadvertent selection, a relaxation in selection, or are simply the fixation of deleterious mutations, is not known. its relatively recent and well-documented history, access to multiple isolated lines reared in similar environmental settings, well-characterized functional annotations, and the availability of hundreds of genomes from extensively sampled extant populations including a closely related species, make d. melanogaster an ideal model system to study the evolutionary processes that underlie rapid phenotypic change. here, we investigate genetic differences between common laboratory stains of d. melanogaster to those recently caught from nature to examine whether this important, centuries-old genetic model has evolved convergent domesticated behaviors by adapting to a bottled existence or being inundated by low-fitness alleles. we first document behavioral differences between lab-reared and wild-caught flies with respect to their general activity and locomotory abilities. we then identify snps that are differentiated between the genomes of laboratory and wild strains to evaluate the roles of selection vs. drift in flies isolated in bottles. among uniquely derived alleles found only in lab strains we find patterns of drift and selection across, respectively, low and high frequency classes, when comparing evolutionary parameters such as grantham distance, missense to silent mutations, positional distribution within codons, and levels of codon bias. we further characterize putative regions under sustained selection among lab strains and find longer than expected haplotypes near high-frequency derived snps, also enriched in neuro-sensory genes. finally, we suggest that this neurogenetic class, residing on a disproportionately large fraction of the genome relative to other functional classes, provides a large mutational target for genetic variation to accumulate and selection to act upon. thus, the genomics of fly domestication reveal an interplay of evolutionary forces with mutation and selection on a large neurogenetic class of genes playing a pivotal role in d. melanogaster’s brief, but distinguished, history in the laboratory.  behavior although it is well-known among drosophilists that lab strains are much slower and easier to handle than live flies, literature documenting these differences is lacking. we first confirm anecdotal reports of differences in the overall activity between laboratory stocks and flies from wild populations. on average, flies from lab strains are significantly less active than wild-caught individuals using different measures of locomotion including standard and angular velocities and time-spent moving vs. stationary. lab strains also demonstrate less responsiveness in the form of interactions between individuals compared to wild-caught lines where the latter’s movement is more uniformly distributed and gradually increases with proximity to neighbors. flies from laboratory strains do not appear to follow this relationship with motion uncorrelated to the proximity with their nearest neighbor. overall, these results provide general support for a convergence of slow-moving and less responsive behavior in lab strains. genetic variation in lab strains after applying filters for quality and missing data, a total of, base pairs were analyzed across five reassembled laboratory strains of d. melanogaster, genomes from global populations including an extensively sampled population from north america, and one closely related species, d. simulans. among, polymorphic sites,  % are non-singletons and used for subsequent analyses. to test for signals of domestication, we used three defined categories of snps differentiated between lab strains and populations of d. melanogaster from nature: lab-specific snps and two types of highly differentiated fst snps, depending on whether the derived allele is found at a higher frequency among lab strains, or in a representative natural population. while distinct, some overlap exists between the lab-specific and fst*lab>wild analysis categories: out of a total differentiated snps, snps are common to these two snp classes. in contrast, fst*wild>lab snps are unique and relatively rare.fig. characterization of derived snps differentiated between lab strains and a wild d. melanogaster population. a number and overlap of lab-specific snps with fst*lab>wild snps. the total number of fst*wild>lab snps is also shown. b site frequency distribution of lab-specific snps, per chromosome. c genic characterization of lab-specific snps found in the majority of laboratory strains, across chromosomal arms lab-specific snps the number of lab-specific snps is, with and snps located in genic and cds regions, respectively. the total number of lab-specific snps is significantly larger than a subsample of five random genomes from north carolina and comparison of the number of snps specific to this random subset against the entire north carolinian dataset as well as the entire global dataset. lab-specific snps represent only a small fraction of the total snp variation found among global populations of d. melanogaster, including singletons. lab-specific snps are distributed across all chromosome arms with a slight but significant enrichment across non-coding regions. the x-chromosome is enriched for mid- and high-frequency lab-specific snps. the number of fixed lab-specific snps was and respectively, in all genomic regions, genic, and cds regions. genes containing fixed lab-specific snps are enriched for regulatory and signaling gene ontology categories and up-regulated in neural-sensory tissues. fst*lab>wild snps the number of derived snps with high fst that harbor a greater frequency in the lab compared to the wild is, with and in genic and cds regions respectively. fst*lab>wild snps generally describe variants that are highly represented among lab strains but have a low allele frequency in global populations. fst*lab>wild are uniformly distributed across chromosome arms and are enriched for genic regions. the number of fst*lab>wild snps that are fixed is and, respectively, in all genomic regions and cds regions. fst*lab>wild snps are functionally enriched in general developmental gene ontology categories. fst*lab>wild snps are upregulated in several tissues including ganglion, larval cns, and ovary. fst*wild>lab snps a small proportion of fst* snps are highly differentiated in the opposite direction. these fst*wild>lab snps are found at low frequency among lab strains but have high allele frequencies in global populations. fst*wild>lab snps are enriched on the x-chromosome, across intergenic regions, and significantly enriched for neurogenetic genes. specifically, this snp category is significantly enriched in nervous system development and photoreceptor development gene ontologies and is upregulated in neural, visual, and ovarian tissues. evolutionary relationships phylogenetic analyses on lab-specific snps and fst* snps were performed to provide insight on the origin and relationship among isolated lab stocks. the lab-specific consensus snp tree reveals canton-s as ancestral to the three oregon-r strains and the w strain, as expected. the fst* snp consensus tree similarly shows a distinct lab monophyletic clade with similar bootstrap support for lab strain topology. a distinct origin among lab strains is also seen using a random set of polymorphic sites among lab and wild strains. the branch lengths of the lab strains dramatically differ between trees indicating each lab strain’s distinctiveness from each other and the extant north american population. the three congruent phylogenetic trees also revealed several surprises including the three oregon-r strains being paraphyletic, with ore- and ore- more similar to w than ore- also, while the original oregon-r strain was independently sampled on the us west coast a few decades later, all lab strains appear to be derived from a single canton-s common ancestor, with the lab clade best supported next to extant populations from france, then north america. genome-wide levels of selection to detect differences in selective constraints in the lab, we estimate a series of evolutionary parameters across five frequency bins of lab-specific snps located in coding regions. we compare parameter estimates against similarly binned derived snps found only in the raleigh nc population along with simulation estimates expected under strict neutrality. additional file 2: table s compares the nature and number of lab-differentiated snps to those found in the raleigh nc population across autosomes and x-chromosomes. when not binned according to allele frequency, mean grantham scores, r/s, and c1/ ratios are similar to random simulations. however, when grouped by frequency class, parameter estimates of medium to high frequency snps more closely follow a pattern of similarly binned snps from the wild rather than expected neutral patterns based on a random mutational model.fig. frequency distribution of lab-specific, wild-caught, and neutrally simulated derived snps across various evolutionary parameters. a mean grantham score per replacement substitution. b mean replacement/silent ratio per snp per individual. c mean ratio of the number of first codon position snps to the number of second and third codon position snps. d mean proportion of non-preferred to preferred codons and preferred to non-preferred codons per individual. for all panels, dotted black horizontal lines represent one standard deviation from the mean of random simulations using d. simulans sequence data. statistical significance determined using a wilcoxon rank-sum test. asterisks indicate significant differences between lab-specific snps and snps derived from neutral simulations. squares indicate significant differences between lab-specific snps and snps derived from the raleigh nc population effective population size the effective population size is a strong determinant of the effectiveness of selection and drift. watterson’s theta, Θs, was estimated across non-overlapping 50 kb windows to compare the amount of genetic variation from an extant population to that found among all lab strains. like previous genome-wide estimates of nucleotide diversity from the raleigh nc population, our estimates of Θ similarly fluctuate across genomic regions with a genome-wide average of Θnc = . although laboratory strains do not collectively comprise a true interbreeding population, we estimate Θlab to provide a relative measure of ancestral ne. laboratory nucleotide diversity varies along the genome in a similar fashion as the raleigh nc population with a genome-wide mean of Θlab = , indicating at least a two-fold reduction in ancestral ne. extended haplotype blocks regions of extended homozygosity present potential signals of positive selection. we observe a mean haplotype length for all lab vs. wild differentiated classes of snps of 653 bp. among lab-specific snps, long outlier haplotypes were only found within the high frequency class ≥ and were significantly larger than all other frequency classes. under a neutral model, we would expect similar haplotype lengths across all frequency classes. in addition, we have run simulations in which we choose sites at random and estimate haplotype lengths. using replicates, the random site haplotype lengths are at least two standard errors lower than the observed 5/ haplotype lengths. a total of large haplotype block outliers were identified ranging in length from  bp to  bp and were significantly enriched on the x-chromosome. candidate lab-specific, fst*lab>wild, and fst*wild>lab haplotype blocks contain, respectively, and genes. genes found within these lab-specific candidate haplotype blocks are enriched for neurogenetic gene ontology categories along with functional classes related to regulation and behavior responses as well as other significant functional categories. however, when normalized by gene length, significant go category enrichments in large lab-specific haplotype blocks disappear. within large fst*lab>wild haplotype blocks, genes are enriched for go classes involved with axon guidance, post-embryonic system development, and regulation, even after normalizing for gene length. no significant go enrichment is found in the four genes contained within large fst*wild>lab haplotype blocks.fig. lab-specific snp haplotype length across frequency class. boxplot of extended haplotype length surrounding lab-specific snps across derived frequency allele classes fig. neurogenetic enrichment of extended haplotype blocks and fst*wild>lab snp genomic distribution. in the top panel, colored rectangles indicates haplotype blocks surrounding lab-differentiated snps. size distribution of haplotype blocks per frequency class is found in fig.  presence of known neurogenetic genes in each block is indicated by purple arrows. in the bottom panel, fst scan identifies derived snps in genic regions with higher allele frequency in the raleigh nc population relative to the laboratory strains. dotted line indicates cutoff for fst*wild>lab snps. of the fst* snps found in genic regions, snps are significantly enriched for neurogenetic genes. snps found within neurogenetic genes are shaded in purple fst*lab>wild fst*lab>wild fst*lab>wild fst*lab>wild fst*lab>wild fst*lab>wild fst*lab>wild fst*lab>wild fst*lab>wild fst*lab>wild fst*lab>wild anumber of genes from gene ontology from flybase fb2015_05 **p-value calculated using benjamini-hochberg correction gene ontologies within each snp type are ranked by p-value. no significant gene ontology class was found for haplotypes classified for significantly differentiated snps in which the derived snp is found in lower frequency in the wild discussion phenotypic and genetic differences in laboratory stocks the captive genetic model, drosophila melanogaster, reveals hallmark features consistent with domestication. laboratory strains show significant differences in behavior from their relatively recently isolated wild progenitors. previous studies comparing lab and wild-caught lines of d. melanogaster also report differences in egg and larval survival and life history traits such as pre-adult development, early fecundity, and remating frequency. these traits comprise a suite of behavioral, physiological, and reproductive characters that have converged across multiple strains evolving independently under similar laboratory conditions. furthermore, it previously has been demonstrated that these traits can quickly evolve significant differences in as little as 8– generations. it is paradoxical that domesticates, typically derived from small founder populations and maintained at very low effective population sizes, can effectively adapt to human conditions. from a population genetics perspective, we may expect the opposite: that small captive populations and lower ne propagate the segregation and eventual fixation of deleterious mutations, thus, imposing a potentially large mutational burden on laboratory strains. our evolutionary parameter analysis reveals such drift-like signatures at the low end of the site frequency spectrum. estimates of grantham distances, r/s ratios, codon positional fraction, and codon bias support a general genome-wide reduction in selection on low-frequency derived alleles in the lab where mildly deleterious alleles may persist for longer periods of time. with a decrease in effective population size across each strain, inbreeding and drift dominate, which in turn, can quickly fix allelic and associated phenotypic changes across successive generations of captivity. short-term isolation studies in drosophila have shown similar rapid changes across a variety of phenotypes with reductions in performance levels ). thus, the accumulation and fixation of mildly deleterious alleles, particularly on larger neurogenetic genes, and subsequent inbreeding depression may promote both the rapid nature of domestication and its associated convergence of common behavioral traits. these docile and non-aggressive traits may alternatively be described as “lethargic”, a term commonly applied to inbred, and often sickly, drosophila stocks. when did these changes occur? our results suggest that these changes towards a domesticated phenotype likely began very early on based on available standing genetic variation of the progenitor population. while heterozygosity in each contemporary isofemale lab strain is virtually zero, as a whole, these five lab strains collectively only harbor a two-fold genome-wide decrease in nucleotide diversity, Θlab, relative to a large contemporary population from raleigh nc. this diversity estimate primarily reflects the amount of genetic variation captured in each of the five lines from an ancestral population. the five lab strains share ~ derived snps with extant global populations indicating that laboratory stocks collectively extracted a significant fraction d. melanogaster genetic variation at their time of capture. the importance of ancestral standing genetic variation can also be seen in the lab-specific snps. in theory, these snps represent any of the following: i) de novo mutations that arose in the lab, ii) genetic variation that previously existed in an extinct north american population, or iii) a subset of genetic variation that has been completely lost in extant global populations. we estimate that only a small fraction of these snps can be generated de novo. the remainder of the lab-specific snps was probably lost in extant wild populations during the last century. strong evidence supports a recent global sweep in d. melanogaster that dramatically reduced species-wide genetic variation after these particular lab strains were collected. thus, from the large pool of available genetic variation from their north american progenitor populations, canton-s and oregon-r likely experienced similar selection pressures on common genetic variants during the earliest generations of lab domestication. a phylogenetic analysis of shared lab/wild snps also supports a distinct origin of all lab strains. however, whether the lab strain monophyly is the result of an extinct progenitor population or the loss of global variation is unknown. the inclusion of more sequenced lab strains may differentiate between these two hypotheses. adaptation in the lab caenorhabditis elegans, like d. melanogaster, has been lab-cultured for over 50 years, and harbors pronounced differences in longevity and fertility when compared to wild isolates. genome sequencing in the nematode identified snps differentiated between wild and long-term laboratory strains enriched for cell cycle and metabolic/growth genes. their results suggest the presence of strong selection early in nematode domestication for optimal growth under rich nutrient conditions similar to the significant go term, “behavioral response to nutrients”, found among lab-specific snps in fruit flies. laboratory mice have similarly been shown to converge certain phenotypes including melatonin deficiency, and a lack of aggression and tameness. the results from our evolutionary parameter analysis, when limited to lab-specific snps in the mid- to high frequency range, support that common phenotypic signals of domestication observed in the captive fruit fly have been strongly shaped by selection. these derived snps, found in the majority of lab strains, show similar evolutionary patterns to high frequency snps from the wild and not to neutral expectations, unlike low-frequency snps. the laboratory setting presents an immediate change in the fitness landscape, permitting rapid and significant changes in phenotype that would be detrimental to their fitness in the wild, across relatively few generations. inadvertent human habituation and unintentional conditioning may be the primary selective agent for such known differences among lab strains as faster development and reproductive time. for instance, flies that rarely escape the bottle or benchtop may be selected due to human carelessness while fly stocks are transferred to new vials/bottles, or “flipped”. our behavioral results support such a convergent shift towards less active and responsive flies. from our genomic analysis, we find that neurogenetic genes, involved in such biological processes as neurogenesis and axon development, are enriched in extended haplotype blocks common to differentiated snps found at high allele frequencies, with an overrepresentation of fixations on the x-chromosome. these genes affect locomotion and visual cues suggesting lab selection on genes involved in behavioral responses. while an excess of long extended haplotypes on high frequency lab-specific snps support an adaptive shift towards domesticated phenotypes, a relaxation of selection on certain loci involved in behavior may have co-occurred in the lab. conditions in the laboratory are often optimized for growth and reproduction, reducing the natural ability of flies to escape predators or compete for food and mates. thus, a relaxation of selection on activity levels, aggressiveness, and responsiveness, critical in the wild, may also drive the behavioral differences that converged across lab strains. characters involved in mating, driven by the sparsity of mates in the vicinity, is a key difference between domestic and wild species. our behavioral results, showing a reduction in interactive activity in lab flies, is consistent with this hypothesis. in addition, our go analysis of shared fst*wild>lab snps, in which the derived allele is more frequent in the raleigh nc population than lab strains, finds a significant enrichment of the neurogenetic functional class, even when corrected for gene size. these snps are found in different genes than the snps harbored in long extended haplotype blocks, suggesting an extensive cache of genes involved in behavioral differences between flies reared in the lab and those found in the wild. a similar decrease in behavioral activity was observed in lab strains of mice, with backcrossing to wild mice isolates allowing them to regain these previously lost behavioral functions. the use of inbred laboratory strains of d. melanogaster presented unique analytical challenges that differ from other domesticated studies. due to initial and recurrent inbreeding and the lack of an interbreeding population, laboratory strains violate most population genetic models used to infer selection. in this study, the site frequency spectrum is only applied across isolated lab strains as a framework to bin our observed data and could not be used to infer population genetic parameters. despite these difficulties, our results reveal an interplay of drift and selection at work in the lab. first, we find genome-wide levels of selective constraints in the lab that are significantly lower than a sampled north american population. this pattern is likely caused by low effective population sizes in bottles that promote the accumulation of mildly deleterious mutations under drift-like conditions, which we also observe in low frequency alleles. second, we observe derived snps that are highly differentiated between the lab and a north american population to be significantly enriched in neurogenetic genes, suggesting a differential fitness landscape in behavior. this functional enrichment takes into account the number of genes in each functional class as well as their size. third, we find signatures of positive selection on extended haplotypes in both lab-specific and highly differentiated snps. these, too, are significantly enriched in neurogenetic genes. fourth, there’s an enrichment of these changes on the x-chromosome. the preferential role of the x-chromosome is seen in marked differences in the site frequency spectrum between the x-chromosome and autosomes and in the enrichment of long haplotype blocks on the x-chromosome. since many of these long x-linked haplotype blocks are fixed in all five lab strains, the fixation of hemizygous loci likely occurred early in fly domestication. preferential role for neurogenetic genes our results suggest a central role for neurogenetic genes in domestication. lab-specific snps found in the majority of lab strains are strongly enriched for this functional class, as are highly differentiated snps found in high frequency in the wild. large outlier haplotype blocks also contain an overrepresentation of neurogenetic genes. in most fly labs, inadvertent selection is inevitable: more active, reactive, and sensory-prone flies have a higher probability of escaping during routine stock transfers. hence, fly researchers may have unconsciously selected for lethargic flies over thousands of generations in the lab. selected genes, enriched for sensory functions in eye photoreceptors and peripheral nervous system, can explain these behavioral shifts seen in lab strains. the significance of neurogenetic genes in changing activity and response behaviors across a relatively short evolutionary time period may also relate to how behaviors involved in premating isolation can swiftly and easily develop in a population by drift and selection. recently, wilkins et al. proposed a general hypothesis to explain the convergence of various phenotypic traits that differentiate mammalian domesticates from their wild progenitors. these traits are collectively known as the “domestication syndrome” and, in mammals, include such morphological modifications as depigmentation, facial skeletal, and floppy ears as well as behavioral shifts towards docility and tameness. wilkins et al. argue that a developmental deficit in neural crest genes can generate each of these differences, thus, explaining the commonality of these traits across domesticated mammals. our results extend the behavioral component of the domestication syndrome to non-vertebrates but through a more general genomic mechanism based on the predominance of mutations on neurogenetic genes affecting overall locomotion and activity. in drosophila, genes from this ontological category are among the largest in gene number and gene size, providing a large mutational target for rapid behavioral change. currently, out of genes are characterized as “neurogenetic”, and 24 % of known fly genes are expressed in the brain and nervous system. we propose that a large mutational target of neurogenetic genes can explain the rapid evolution of behavior in animal taxa., these neurogenomic loci collectively provide a large genomic substrate for variation to accumulate, and then selection and drift to act, to quickly transform behavior within a relatively short time frame.  tameness and docility are hallmark features of domestication and the product of artificial selection by breeders. our results challenge the traditional notion that relatively submissive laboratory animals are solely the product of cumulating deleterious mutations and demonstrate how unconscious selection for human-favored traits plays an important role in driving rapid phenotypic change in the lab. selection on a large pool of available genetic variation during the early stages of fly domestication, followed by strong and recurrent inbreeding, allow for the successive roles of adaptation and drift in shaping the genetic architecture of domesticated phenotypic traits in a bottle. our study finds that the genes and phenotypes in fruit fly domestication are enriched in, respectively, neurogenetic and behavioral function, providing a starting point to decode the genomic basis of domestication and promoting its study in genetic model systems such as drosophila. a detailed mapping of these genes and their snps to specific behaviors will not only be informative about the selective pressures that we have inadvertently applied to our immediate biotic environment, but may also provide new general insight on the divergence and isolation of populations. 
our results demonstrate that lab animals can quickly evolve domesticated behaviors via unconscious selection by humans early on a broad pool of disproportionately large neurogenetic targets followed by the fixation of accumulated deleterious mutations on functionally similar targets. from reassembled genomes of common lab strains, we identify unique, derived variants not present in global populations. however, high-frequency lab snps found in most or all lab strains reveal an enrichment of x-linked loci and neuro-sensory genes across large extended haplotypes. among random mutations that continuously accumulate in the laboratory, we detect common adaptive signatures in domesticated lab strains of fruit flies. decreased selective constraints across low frequency snps are different from patterns found in the wild and more similar to neutral expectations, suggesting an overall accumulation of deleterious mutations. yet whether this divergence is due to inadvertent selection in the lab or the fixation of deleterious mutations remains unknown. model organisms reared for prolonged periods in the laboratory also exhibit similar shifts towards these domesticated behaviors. behavioradaptationpurifying selectionpositive selectionextended haplotypesdomestication genomicsmodel organismsdomestication syndromehttp://dx.doi.org/ /100000076directorate for biological sciences1407006kulathinal rob j. issue-copyright-statement© the author 2016
 domesticated animals quickly evolve docile and submissive behaviors after isolation from their wild conspecifics. model organisms reared for prolonged periods in the laboratory also exhibit similar shifts towards these domesticated behaviors. yet whether this divergence is due to inadvertent selection in the lab or the fixation of deleterious mutations remains unknown.  here, we compare the genomes of lab-reared and wild-caught drosophila melanogaster to understand the genetic basis of these recently endowed behaviors common to laboratory models. from reassembled genomes of common lab strains, we identify unique, derived variants not present in global populations. decreased selective constraints across low frequency snps are different from patterns found in the wild and more similar to neutral expectations, suggesting an overall accumulation of deleterious mutations. however, high-frequency lab snps found in most or all lab strains reveal an enrichment of x-linked loci and neuro-sensory genes across large extended haplotypes. among shared polymorphisms, we also find highly differentiated snps, in which the derived allele is higher in frequency in the wild, enriched for similar neurogenetic ontologies, indicative of relaxed selection on more active wild alleles in the lab.  among random mutations that continuously accumulate in the laboratory, we detect common adaptive signatures in domesticated lab strains of fruit flies. our results demonstrate that lab animals can quickly evolve domesticated behaviors via unconscious selection by humans early on a broad pool of disproportionately large neurogenetic targets followed by the fixation of accumulated deleterious mutations on functionally similar targets. electronic supplementary material the online version of this article contains supplementary material, which is available to authorized users. keywords behavioradaptationpurifying selectionpositive selectionextended haplotypesdomestication genomicsmodel organismsdomestication syndromehttp://dx.doi.org/ /100000076directorate for biological sciences1407006kulathinal rob j. issue-copyright-statement© the author 2016 