Dryad Data Repository

Appendix 3

Fri, 03 Feb 2012 16:09:58 GMT

Plots of regression analyses between proportion of variable sites, proportion of informative sites, clade support index, level of discordance, and precision of species trees.

Appendix 6

Fri, 03 Feb 2012 16:10:08 GMT

Species trees estimated in *BEAST with variable numbers of loci using phased and unphased data.

Simulated gene trees for Mesquite

Fri, 03 Feb 2012 16:09:52 GMT

Input file for Mesquite in nexus format containing 100 simulated gene trees for a species tree of 8 species and 3 sequences/species. The number of deep coalescences for each gene tree was calculated in Mesquite to group gene trees in three categories of discordance with the species tree. See more details in online Appendix 7.

Output files from Phase analyses

Fri, 03 Feb 2012 16:09:42 GMT

Concatenated output files in text format of analyses with the software Phase to phase DNA sequence data from 19 nuclear loci of 16 species of the Liolaemus darwinii group

Input files for BEAST analyses

Fri, 03 Feb 2012 16:09:49 GMT

Compressed file containing input files in xml format for estimating species trees with the software *BEAST using DNA sequence data from 20 loci of 16 species of the Liolaemus darwinii group

Appendix 8

Fri, 03 Feb 2012 16:10:14 GMT

Phylogenetic trees estimated in previous studies of the Liolaemus darwinii group.

Appendix 7

Fri, 03 Feb 2012 16:10:11 GMT

Simulation of 100 gene trees from a pre-specified species tree to analyze the relationship between accuracy of species-tree estimation and the distribution of gene-tree discordance.

Alignments of unphased DNA sequences

Fri, 03 Feb 2012 16:09:39 GMT

Concatenated text files in nexus format of DNA sequences from 20 loci of 16 species of the Liolaemus darwinii group

Appendix 4

Fri, 03 Feb 2012 16:10:01 GMT

Gene trees estimated in *BEAST using the full data set. Branch lengths are in units of substitutions per site.

Appendix 5

Fri, 03 Feb 2012 16:10:04 GMT

Species trees estimated in *BEAST using: phased data, variable population size and tree priors, and 200 million generations. Species tree estimated with BEST using the full data set.

Appendix 2

Fri, 03 Feb 2012 16:09:55 GMT

Sequence alignments of unphased data for 20 loci

Alignments of phased DNA sequences

Fri, 03 Feb 2012 16:09:46 GMT

Concatenated text files in nexus format of phased DNA sequences from 19 nuclear loci of 16 species of the Liolaemus darwinii group

pmc

Thu, 02 Feb 2012 15:15:15 GMT

An R package containing functions to perform the method described in the package, manual for these functions, and a vignette demonstrating how the package is used to replicate the results of this study.

Data from: Is your phylogeny informative? Measuring the power of comparative methods

Thu, 02 Feb 2012 15:15:08 GMT

Phylogenetic comparative methods may fail to produce meaningful results when either the underlying model is inappropriate or the data contain insufficient information to inform the inference. The ability to measure the statistical power of these methods has become crucial to ensure that data quantity keeps pace with growing model complexity. Through simulations, we show that commonly applied model choice methods based on information criteria can have remarkably high error rates; this can be a problem because methods to estimate the uncertainty or power are not widely known or applied. Furthermore, the power of comparative methods can depend significantly on the structure of the data. We describe a Monte Carlo based method which addresses both of these challenges, and show how this approach both quantifies and substantially reduces errors relative to information criteria. The method also produces meaningful confidence intervals for model parameters. We illustrate how the power to distinguish different models, such as varying levels of selection, varies both with number of taxa and structure of the phylogeny. We provide an open-source implementation in the pmc (“Phylogenetic Monte Carlo”) package for the R programming language. We hope such power analysis becomes a routine part of model comparison in comparative methods.

Fleskes_etal_Table S1_REV

Thu, 02 Feb 2012 17:38:47 GMT

Table S1. Microsoft Excel file containing data used in the analysis of bird use of grain and non-grain fields treated with two types of post-harvest flooding that differed in depth and duration (Flood-type [FLD] fields were flooded with <1 cm–1.5 m water for >1 week; Irrigated-type [IRG] fields were flooded with <1 cm–15 cm water for <1 week) in the Tulare Basin of California, 19 August–6 December 2005. Surveys were grouped by time of day into early-day (< 4 hours post sunrise), mid-day (> 4 hours post sunrise and > 4 hours before sunset) and late-day (< 4 hours before sunset) periods. Counts for each survey are presented by species and for waterfowl (includes ducks and geese), other waterbirds (includes coots, shorebirds, grebes, pelicans, herons, egrets, gulls, and terns), non-waterbirds (includes passerines, raptors, and vultures) and total birds (See Table 1 for species).

reproductive traits

Fecundity, egg hatching success

developmental traits

larval time, pupal time, pupal mass, growth rate

selection

Selection on cold tolerance

Data from: Response to selection on cold tolerance is constrained by inbreeding

Thu, 02 Feb 2012 18:28:46 GMT

The evolutionary potential of any given population is of fundamental importance for its longer-term prospects. Modern land-use practices often result in small and isolated populations, increasing extinction risk through reduced genetic diversity caused by inbreeding or drift. Concomitant genetic erosion may further interfere with a population’s evolutionary potential. In this study we investigate the consequences of inbreeding on evolutionary potential (the ability to increase cold resistance) in the tropical butterfly Bicyclus anynana. We applied artificial selection to chill-coma recovery time, starting from three levels of inbreeding (outbred control, one or two full-sib matings). Ten generations of selection produced highly divergent phenotypes, with the lines selected for increased cold tolerance showing by ca. 28% shorter recovery times after cold exposure relative to unselected controls. Correlated responses to selection in 10 life history and stress resistance traits were essentially absent. Inbred lines showed a weaker response to selection, thus indicating a reduced evolutionary potential. Inbreeding depression was still measurable in some traits after the course of selection. Traits more closely related to fitness showed a clear fitness rebound, suggesting a trait-specific impact of purging. Our findings have important implications for the longer-term survival of small populations in fragmented landscapes.

cold and heat stress

cold and heat tolerance after selection

longevity and survival

longevity control, longevity after cold shock and survival after heat shock

Chloroplast_Peru-Galapagos

Arlequin data file for the chloroplast markers

IMa_Gal_2pops

IMA2 data file using microsatellite data

Data from: Recent colonization of the Galapagos by the tree Geoffroea spinosa Jacq. (Leguminosae)

Thu, 02 Feb 2012 18:48:55 GMT

This study puts together genetic data and an Approximate Bayesian Computation (ABC) approach to infer the time at which the tree Geoffroea spinosa colonized the Galapagos Islands. The genetic diversity and differentiation between Peru and Galapagos population samples, estimated using three chloroplast spacers and six microsatellite loci, reveal significant differences between two mainland regions separated by the Andes mountains (Inter Andean versus Pacific Coast) as well as a significant genetic differentiation of island populations. Microsatellites identify two distinct geographic clusters, the Galapagos and the mainland, and chloroplast markers show a private haplotype in the Galapagos. The nuclear distinctiveness of the InterAndean populations suggests current restricted pollen flow, but chloroplast points to cross-Andean dispersals via seeds, indicating that the Andes might not be an effective biogeographical barrier. The ABC analyses clearly point to the colonization of the Galapagos within the last 160,000 years and possibly as recently as 4,750 YA (475 generations). Founder events associated with colonization of the two islands where the species occurs are detected, with Española having been colonized after Floreana. We discuss two non-mutually exclusive possibilities of colonization of the islands, natural dispersal versus human introduction. Because Floreana is dated as 1.5 MYA, we consider that the young age for the colonization of the island indicated by the ABC analysis favors a human introduction over a natural dispersal scenario.

Microsatellites_Peru-Galapagos

Arlequin data file for micorsatellite markers

field

Morphological measurements for all the field caught individuals

Data from: Niche specialization influences adaptive phenotypic plasticity in threespine stickleback

Wed, 01 Feb 2012 17:34:00 GMT

Phenotypic plasticity may be favoured in generalist populations if it increases niche width even in temporally constant environments. Phenotypic plasticity can increase the frequency of extreme phenotypes in a population and thus allow it to make use of a wide resource spectrum. Here we test the prediction that generalist populations should be more plastic than specialists. In a common garden experiment, we show that solitary generalist populations of threespine sticklebacks inhabiting small coastal lakes of British Columbia have a higher degree of morphological plasticity than the more specialized sympatric limnetic and benthic species. The ancestral marine stickleback showed similar low levels of plasticity to sympatric sticklebacks, implying that the greater plasticity of the generalist population has evolved recently. Measurements of wild populations show that those with mean trait values intermediate between the benthic and limnetic values indeed have higher morphological variation. Our data indicate that plasticity can evolve rapidly after colonization of a new environment in response to changing niche use.

experiment

Morphological measurements for all the experimental individuals

Data from: Body size evolution on islands: are adult size variations in tiger snakes a non-adaptive consequence of selection on birth size?

Wed, 01 Feb 2012 17:40:17 GMT

Mean adult size has been used as the traditional measure of body size to explain trends of insular gigantism and dwarfism in a wide array of taxa. However, patterns of variation in body size at birth have surprisingly received little attention, leaving open the possibility that adult body size differences are non-adaptive consequences of selection acting on neonate body size. Here, I used an empirical and correlative approach to test this hypothesis in a mosaic of 12 island and mainland snake populations in Australia. Data collected on 597 adult and 1084 neonate tiger snakes showed that (1) both adult and neonate mean body size varied strongly across populations; (2) prey diversity and size convincingly explained birth size variations: birth size, notably gape size, correlated with prey size; (3) neonate snout-vent length was significantly correlated with neonate gape size; and (4) neonate snout-vent length was significantly correlated with adult snout-vent length. Post-natal growth rates recorded under common garden conditions differed across populations and were correlated with mean prey size. These data collectively suggest that (1) prey size is the main driver for the evolution of body size at birth in gape-limited predators; (2) adult size variations may reflect selective forces acting on earlier life stages; and (3) adult size variations may also reflect resource availability during ontogeny (notably prey diversity).

Aubret 53172

Excel file contains 4 sheets. First sheet titled Adult Tiger snakes contains field data collected on Adult Tiger snakes (sex, body mass and snout-vent length). Sheet titled Mothers litters and neonates contains laboratory and museum data about reproductive output in female tiger snakes for several populations. For each female is given birth date, mean litter body mass (calculated average body mass for all neonates in a given litter), mean litter svl (calculated average snout vent length for all neonates in a given litter), and mean litter jaw (calculated average jaw length for all neonates in a given litter). Sheet titled Prey contains data collected in Museum collection for prey available at each study site. Latin names are given with body mass and maximum circumference of each prey item. Sheet titled Growth experiment contains experimental data on growth rate and food consumption in neonate Tiger snakes from several populations. Headings indicate for each mother its population of origin, neonate identification number, birth date and morphometrics at birth. Body mass and snout vent length are recorded every two months until the end of the experiment. Column titled Total growth in body mass indicates the difference in body mass between the start and the end of the experiment. The two last columns are Total food (total amount of food consumed by each neonate over the course of the experiment) and Length of experiment (total duration of the experiment). Conversion rates were calculated (column titled Increase in body mass per g of food) and daily growth rates in body mass (increase in body mass in mg per day). Similar calculation were made for snout vent length (increase in svl per g of food; increase in svl in mm per day).

Data from: The direct and ecological costs of an ant-plant symbiosis

Wed, 01 Feb 2012 17:50:27 GMT

How strong is selection for cheating in mutualisms? The answer depends on the type and magnitude of the costs of the mutualism. Here, we investigated the direct and ecological costs of plant defense by ants in the association between Cordia nodosa, a myrmecophytic plant, and Allomerus octoarticulatus, a phytoecious ant. Cordia nodosa trees produce food and housing to reward ants that protect them against herbivores. For nearly a year, we manipulated the presence of A. octoarticulatus ants and most insect herbivores on C. nodosa in a full factorial experiment. Ants increased plant growth when herbivores were present, but decreased plant growth when herbivores were absent, showing that hosting ants can be costly to plants. However, we did not detect a cost to ant colonies of defending host plants against herbivores. Although this asymmetry in costs suggests that the plants may be under stronger selection than the ants to cheat by withholding investment in their partner, the costs to C. nodosa are probably at least partly ecological, arising because ants tend scale insects on their host plants. We argue that ecological costs should favor resistance or traits other than cheating, and thus that neither partner may face much temptation to cheat.

DataAmNat53179file2

See readme file

DataAmNat53179file1

fluctuationDomains

Wed, 01 Feb 2012 17:21:51 GMT

R package containing the software used to simulate, analyze, and visualize the data considered in this publication.

Data from: The B-matrix harbours significant and sex-specific constraints on the evolution of multi-character sexual dimorphism

Tue, 10 Jan 2012 19:34:10 GMT

The extent to which sexual dimorphism can evolve within a population depends on an interaction between sexually divergent selection and constraints imposed by a genetic architecture that is shared between males and females. The degree of constraint within a population is normally inferred from the intersexual genetic correlation, rmf. However, such bivariate correlations ignore the potential constraining effect of genetic covariances between other sexually co-expressed traits. Using the fruit fly Drosophila serrata, a species that exhibits mutual mate preference for blends of homologous contact pheromones, we tested the impact of between-sex between-trait genetic covariances using an extended version of the genetic variance-covariance matrix, G, that includes Lande’s (1980) between-sex covariance matrix, B. We find that including B greatly reduces the degree to which male and female traits are predicted to diverge in the face of divergent phenotypic selection. However, the degree to which B alters the response to selection differs between the sexes. The overall rate of male trait evolution is predicted to decline, but its direction remains relatively unchanged, whereas the opposite is found in females. We emphasise the importance of considering the B-matrix in microevolutionary studies of constraints on the evolution of sexual dimorphism.

Data from: The biogeography of Sulawesi revisited: is there evidence for a vicariant origin of taxa on Wallace’s “anomalous island”?

Wed, 18 Jan 2012 21:42:33 GMT

Sulawesi, the largest island in the Indonesian biodiversity hotspot region Wallacea, hosts a diverse endemic fauna whose origin has been debated for more than 150 years. We use a comparative approach based on dated phylogenies and geological constraints to test the role of vicariance versus dispersal in the origin of Sulawesi taxa. Most divergence time estimates for the split of Sulawesi lineages from their sister groups postdate relevant tectonic vicariant events, suggesting that the island was predominantly colonized by dispersal. Vicariance cannot be refuted for 20 % of the analyzed taxa, though. While vicariance across Wallace’s Line was only supported for one arthropod taxon, divergence time estimates were consistent with a “tectonic dispersal” vicariance hypothesis from the East in three (invertebrate and vertebrate) taxa. Speciation on Sulawesi did not occur before the Miocene, which is consistent with geological evidence for more extensive land on the island from that time. The Pliocene onset of periodic sea-level changes may have played a role in increasing the potential for dispersal to Sulawesi. A more extensive taxon sampling in Wallacea will be crucial for refining our understanding of the region’s biogeography and for testing hypotheses on the origin of taxa on its most important island.

Data from: Genetic basis of adaptation in Arabidopsis thaliana: local adaptation at the seed dormancy QTL DOG1

Thu, 19 Jan 2012 19:48:47 GMT

Local adaptation provides an opportunity to study the genetic basis of adaptation and investigate the allelic architecture of adaptive genes. We study DELAY OF GERMINATION 1 (DOG1), a gene controlling natural variation in seed dormancy in Arabidopsis thaliana and investigate evolution of dormancy in 41 populations distributed in four regions separated by natural barriers. Using F_ST and Q_ST comparisons, we compare variation at DOG1 with neutral markers and quantitative variation in seed dormancy. Patterns of genetic differentiation among populations suggest that the gene DOG1 contributes to local adaptation. Although Q_ST for seed dormancy is not different from F_ST for neutral markers, a correlation with variation in summer precipitation supports that seed dormancy is adaptive. We characterize dormancy variation in several F_2-populations and show that a series of functionally distinct alleles segregate at the DOG1 locus. Theoretical models have shown that the number and effect of alleles segregating at QTLs have important consequences for adaptation. Our results provide support to models postulating a large number of alleles at quantitative trait loci involved in adaptation.

Data from: Increased energy promotes size-based niche availability in marine mollusks

Tue, 10 Jan 2012 20:13:56 GMT

Variation in chemical energy, i.e., food, availability is posited to cause variation in body size. However, examinations of the relationship are rare and primarily limited to amniotes and zooplankton. Moreover, the relationship between body size and chemical energy may be impacted by phylogenetic history, clade specific ecology, and heterogeneity of chemical energy in space and time. Considerable work remains to both document patterns in body size over gradients in food availability and understanding the processes potentially generating them. Here, we examine the functional relationship between body size and chemical energy availability over a broad assortment of marine mollusks varying in habitat and mobility. We demonstrate that chemical energy availability is likely driving body size patterns across habitats. We find that lower food availability decreases size-based niche availability by setting hard constraints on maximum size and potentially on minimum size depending on clade-specific ecology. Conversely, higher food availability promotes greater niche availability and potentially promotes evolutionary innovation with regard to size. We posit based on these findings and previous work that increases in chemical energy are important to the diversification of Metazoans through size-mediated niche processes.

BTped

Full blue tit pedigree. This dataset comprises 3,090 individual blue tits and a total of 4,024 breeding events between 2001 and 2008.

GTped

Full great tit pedigree. Our full dataset for great tits comprises 12,724 individuals and a total of 19,395 breeding events between 1947 and 2008.

Data from: Integrating candidate gene and quantitative genetic approaches to understand variation in timing of breeding in wild tit populations

Tue, 31 Jan 2012 21:03:45 GMT

Two commonly used techniques for estimating the effect of genes on traits in wild populations are the candidate gene approach and quantitative genetic analyses. However, whether these two approaches measure the same underlying processes remains unresolved. Here we use these two methods to test if they are alternative or complementary approaches to understanding genetic variation in the timing of reproduction – a key trait involved in adaptation to climate change - in wild tit populations. Our analyses of the candidate gene Clock show weak correlates with timing variables in blue tits, but no association in great tits, confirming earlier results. Quantitative genetic analyses revealed very low levels of both direct (female) and indirect (male) additive genetic variation in timing traits for both species, in contrast to previous studies on these traits, and much lower than generally assumed. Hence, neither method suggests strong genetic effects on timing of breeding in birds and further work should seek to assess the generality of these conclusions. We discuss how differences in the genetic control of traits, species life-history and confounding environmental variables may determine how useful integrating these two techniques is to understand phenotypic variation in wild populations.

Data from: Environmental and genetic influences on body mass and resting metabolic rates (RMR) in a natural population of weasel Mustela nivalis

Mon, 12 Dec 2011 18:55:10 GMT

Body mass (BM) and resting metabolic rates (RMR) are two inexorably linked traits strongly related to mammalian life histories. Yet, there have been no studies attempting to estimate heritable variation and covariation of BM and RMR in natural populations. We used a marker-based approach to construct a pedigree and then the ‘animal model’ to estimate narrow sense heritability (h^2) of these traits in a free-living population of weasels Mustela nivalis – a small carnivore characterised by a wide range of BM and extremely high RMR. The most important factors affecting BM of weasels were sex and habitat type, whereas RMR was significantly affected only by seasonal variation of this trait. All environmental factors had only small effect on estimates of additive genetic variance of both BM and RMR. The amount of additive genetic variance associated with BM and estimates of heritability were high and significant in males (h^2 = 0.61), but low and not significant in females (h^2 = 0.32), probably due to small sample size for the latter sex. The results from the two-trait model revealed significant phenotypic (r_P = 0.62) and genetic correlation (r_A = 0.89) between BM and whole body RMR. The estimate of heritability of whole body RMR (0.54) and body mass corrected RMR (0.45) were lower than estimates of heritability for BM. Both phenotypic and genetic correlations between body mass corrected RMR and BM had negative signals (r_P = -0.42 and r_A = -0.58). Our results indicate that total energy expenditures of individuals can quickly evolve through concerted changes in BM and RMR.

Data from: Bird use of fields treated post-harvest with two types of flooding in Tulare Basin, California

Thu, 02 Feb 2012 17:38:45 GMT

We surveyed birds on grain and non-grain fields in the Tulare Basin of California treated post-harvest with two types of flooding that varied in duration and depth of water applied (Flooded-type fields [FLD]: <1 cm–1.5 m for >1 week; Irrigated-type fields [IRG]: <1–15 cm water for <1 week at a time). Our goal was to compare use of these field types by birds to guide habitat conservation in the region. During 19 August–6 December 2005, we counted a total of 80,316 birds during 23 surveys of 5 FLD (4 wheat, 1 alfalfa) fields and 8,225 birds during 38 surveys of 33 IRG (23 cotton, 4 tomato, 3 wheat, 1 alfalfa, 1 oat, 1 fallow) fields. We recorded 14 waterfowl (13 duck, 1 goose), 29 other waterbird (coots, shorebirds, grebes, pelicans, herons, egrets, gulls, terns), and 14 non-waterbird (passerines, raptors, and vultures) species on FLD fields compared to 5 duck, 14 other waterbird, and 9 non-waterbird species on IRG fields. Species composition differed by field type; waterfowl (FLD vs. IRG, 16.2% vs. 1.3%) and other waterbirds (80.4% vs. 71.6%) comprised a greater percentage and non-waterbirds (3.5% vs. 27.1%) a lower percentage of birds on FLD than on IRG fields. The modeled density estimate of waterfowl was 108 times greater on FLD than IRG fields and 7.4 times greater on grain than non-grain fields. The density estimate of other waterbirds was 11.8 times greater on FLD than IRG fields and 4.4 times greater on grain than non-grain fields. The density estimate of non-waterbirds was 14.3 times greater on grain than non-grain fields but did not differ by flood type. Long duration (i.e., >1 week) flooding increased waterbird use of grain fields in the Tulare Basin more than in the northern Central Valley. Thus, even though water costs are high in the Tulare Basin, if net benefit to waterbirds is considered, management programs that increase availability of FLD-type fields (especially grain) in the Tulare Basin may be a cost-effective option to help meet waterbird habitat conservation goals in the Central Valley of California.

MorrisseyEtAlEvolution2012Data

R data file containing a list. The list is composed of two elements: (1) a data frame containing individual phenotypic measures and covariates, and (2) the pedigree.

Data from: The prediction of adaptive evolution: empirical application of the secondary theorem of selection and comparison to the breeder's equation

Mon, 30 Jan 2012 18:02:34 GMT

Adaptive evolution occurs when fitness covaries with genetic merit for a trait (or traits). The breeder’s equation (BE), in both its univariate and multivariate forms, allows us to predict this process by combining estimates of selection on phenotype with estimates of genetic (co)variation. However, predictions are only valid if all factors causal for trait-fitness covariance are measured. While this requirement will rarely (if ever) be met in practice, it can be avoided by applying Robertson’s secondary theorem of selection (STS). The STS predicts evolution by directly estimating the genetic basis of trait-fitness covariation with out any explicit model of selection. Here we apply the BE and STS to four morphological traits measured in Soay sheep (Ovis aries) from St. Kilda. Despite apparently positive selection on heritable size traits, sheep are not getting larger. However, while the BE predicts increasing size the STS does not, a discrepancy that suggests unmeasured factors are upwardly biasing our estimates of selection on phenotype. We suggest this is likely to be a general issue, and that wider application of the STS could offer at least a partial resolution to the common discrepancy between naive expectations and observed trait dynamics in natural populations.

DRYAD FILES

Mon, 30 Jan 2012 18:18:20 GMT

This is a zipped folder of all of the data files and scripts to run the statistical analyses associated with the manuscript.

Data from: Panmixia supports divergence with gene flow in Darwin’s small ground finch, Geospiza fuliginosa, on Santa Cruz, Galápagos Islands

Mon, 30 Jan 2012 18:54:26 GMT

The divergence-with-gene-flow model of speciation has a strong theoretical basis with a growing number of plausible examples in nature, but remains hotly debated. Darwin’s finches of the Galápagos Archipelago have played an important role in our understanding of speciation processes. Recent studies suggest that this group may also provide insights into speciation via divergence with gene flow. On the island of Santa Cruz, recent studies found evidence for adaptive divergence in Darwin’s small ground finch, Geospiza fuliginosa, between ecologically contrasting arid and humid zones. Despite the short geographical distance between these zones, strong disruptive selection during low rainfall periods is expected to generate and maintain adaptive divergence. Conversely, during high rainfall periods, when disruptive selection is predicted to be weakened, population divergence in adaptive traits is expected to break down. Because periods of low and high rainfall irregularly alternate, the geographical pattern of adaptive divergence can be assumed to break down and, importantly, regenerate in situ. Here, we use microsatellite allele frequency data to assess the genetic population structure of G. fuliginosa on Santa Cruz. We sample 21 sites and four ecological zones across the island. We reject hypotheses of population substructure linked to ecological and geographical differences among sites in favour of a single panmictic population. Panmixia infers high levels of gene flow within Santa Cruz, which favours selection over genetic drift as a valid process generating phenotypic divergence in G. fuliginosa on Santa Cruz. We discuss how our findings may support classic adaptation, phenotypic plasticity, matching habitat choice, or any combination of these three processes.

Galligan et alPanmixiadata

Allele size data for 12 microsatellites

Gratten_etal_Dryad

Data from: Selection and microevolution of coat pattern are cryptic in a wild population of sheep

Mon, 30 Jan 2012 19:10:43 GMT

Understanding the maintenance of genetic variation in natural populations is a core aim of evolutionary genetics. Insight can be gained by quantifying selection at the level of the genotype, as opposed to the phenotype. Here, we show that in a natural population of Soay sheep which is polymorphic for coat pattern, recessive genetic variants at the causal gene, agouti signalling protein (ASIP), are associated with reduced lifetime fitness. This was due primarily to a reduction in juvenile survival of uniformly coloured (self-type) sheep, which are homozygous recessive, and occurs despite significantly higher reproductive success in surviving self-type adults. Consistent with their relatively low fitness, we show that the frequency of self-type individuals has declined from 1985 to 2008. Remarkably though, the frequency of the underlying self-allele has increased, because the frequency of heterozygous individuals (who harbour the majority of all self alleles) has increased. Indeed, the ratio of observed:expected heterozygous individuals has increased during the study, such that there is now a significant excess of heterozygotyes. By employing gene-dropping simulations, we show that microevolutionary trends in the frequency and excess of ASIP heterozygotes are too pronounced to be caused by genetic drift. Studying this polymorphism at the level of phenotype rather than underlying genotype would have failed to detect cryptic fitness differences. We would also have been unable to rule out genetic drift as an evolutionary force driving genetic change. This highlights the importance of resolving the underlying genetic basis of phenotypic variation in explaining evolutionary dynamics.