The adaptive genomic landscape of beak morphology in Darwin's finches

Neotropics as a Cradle for Adaptive Radiations

Neotropical ecosystems are renowned for numerous examples of adaptive radiation in both plants and animals resulting in high levels of biodiversity and endemism. However, we still lack a comprehensive review of the abiotic and biotic factors that contribute to these adaptive radiations. To fill this gap, we delve into the geological history of the region, including the role of tectonic events such as the Andean uplift, the formation of the Isthmus of Panama, and the emergence of the Guiana and Brazilian Shields. We also explore the role of ecological opportunities created by the emergence of new habitats, as well as the role of key innovations, such as novel feeding strategies or reproductive mechanisms. We discuss different examples of adaptive radiation, including classic ones like Darwin's finches and Anolis lizards, and more recent ones like bromeliads and lupines. Finally, we propose new examples of adaptive radiations mediated by ecological interactions in their geological context. By doing so, we provide insights into the complex interplay of factors that contributed to the remarkable diversity of life in the Neotropics and highlight the importance of this region in understanding the origins of biodiversity.

Molecular Innovations Shaping Beak Morphology in Birds

The beak, a pivotal evolutionary trait characterized by high morphological diversity and plasticity, has enabled birds to survive mass extinction events and subsequently radiate into diverse ecological niches worldwide. This remarkable ecological adaptability underscores the importance of uncovering the molecular mechanisms shaping avian beak morphology, particularly benefiting from the rapidly advancing archives of genomics and epigenomics. We review the latest advancements in understanding how genetic and epigenetic innovations control or regulate beak development and drive beak morphological adaptation and diversification over the past two decades. We conclude with several recommendations for future endeavors, expanding to more bird lineages, with a focus on beak shape and the lower beak, and conducting functional experiments. By directing research efforts toward these aspects and integrating advanced omics techniques, the complex molecular mechanisms involved in avian beak evolution and morphogenesis will be deeply interpreted.

The genetic basis of dispersal in a vertebrate metapopulation

Dispersal affects evolutionary processes by changing population size and genetic composition, influencing the viability and persistence of populations. Investigating which mechanisms underlie variation in dispersal phenotypes and whether populations harbour adaptive potential for dispersal is crucial to understanding the eco-evolutionary dynamics of this important trait. Here, we investigate the genetic architecture of dispersal among successfully recruited individuals in an insular metapopulation of house sparrows. We use an extensive long-term individual-based ecological data set and high-density single-nucleotide polymorphism (SNP) genotypes for over 2500 individuals. We conducted a genome-wide association study (GWAS), and found a relationship between dispersal probability and a SNP located near genes known to regulate circadian rhythm, glycogenesis and exercise performance, among other functions. However, this SNP only explained 3.8% of variance, suggesting that dispersal is a polygenic trait. We then used an animal model to estimate heritable genetic variation (σA 2 ), which composes 10% of the total variation in dispersal probability. Finally, we investigated differences in σA 2 across populations occupying ecologically relevant habitat types (farm vs. non-farm) using a genetic groups animal model. We found different adaptive potentials across habitats, with higher mean breeding value, σA 2 , and heritability for the habitat presenting lower dispersal rates, suggesting also different roles of environmental variation. Our results suggest a complex genetic architecture of dispersal and demonstrate that adaptive potential may be environment dependent in key eco-evolutionary traits. The eco-evolutionary implications of such environment dependence and consequent spatial variation are likely to become ever more important with the increased fragmentation and loss of suitable habitats for many natural populations.

Community-wide genome sequencing reveals 30 years of Darwin's finch evolution

A fundamental goal in evolutionary biology is to understand the genetic architecture of adaptive traits. Using whole-genome data of 3955 of Darwin's finches on the Galápagos Island of Daphne Major, we identified six loci of large effect that explain 45% of the variation in the highly heritable beak size of Geospiza fortis, a key ecological trait. The major locus is a supergene comprising four genes. Abrupt changes in allele frequencies at the loci accompanied a strong change in beak size caused by natural selection during a drought. A gradual change in Geospiza scandens occurred across 30 years as a result of introgressive hybridization with G. fortis. This study shows how a few loci with large effect on a fitness-related trait contribute to the genetic potential for rapid adaptive radiation.

Molecular mechanisms of adaptive evolution in wild animals and plants

Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.

Genotype-environment associations across spatial scales reveal the importance of putative adaptive genetic variation in divergence

Identifying areas of high evolutionary potential is a judicious strategy for developing conservation priorities in the face of environmental change. For wide-ranging species occupying heterogeneous environments, the evolutionary forces that shape distinct populations can vary spatially. Here, we investigate patterns of genomic variation and genotype-environment associations in the hermit thrush (Catharus guttatus), a North American songbird, at broad (across the breeding range) and narrow spatial scales (at a hybrid zone). We begin by building a genoscape or map of genetic variation across the breeding range and find five distinct genetic clusters within the species, with the greatest variation occurring in the western portion of the range. Genotype-environment association analyses indicate higher allelic turnover in the west than in the east, with measures of temperature surfacing as key predictors of putative adaptive genomic variation rangewide. Since broad patterns detected across a species' range represent the aggregate of many locally adapted populations, we investigate whether our broadscale analysis is consistent with a finer scale analysis. We find that top rangewide temperature-associated loci vary in their clinal patterns (e.g., steep clines vs. fixed allele frequencies) across a hybrid zone in British Columbia, suggesting that the environmental predictors and the associated candidate loci identified in the rangewide analysis are of variable importance in this particular region. However, two candidate loci exhibit strong concordance with the temperature gradient in British Columbia, suggesting a potential role for temperature-related barriers to gene flow and/or temperature-driven ecological selection in maintaining putative local adaptation. This study demonstrates how patterns identified at the broad (macrogeographic) scale can be validated by investigating genotype-environment correlations at the local (microgeographic) scale. Furthermore, our results highlight the importance of considering the spatial distribution of putative adaptive variation when assessing population-level sensitivity to climate change and other stressors.

Rapid adaptive radiation of Darwin's finches depends on ancestral genetic modules

Recent adaptive radiations are models for investigating mechanisms contributing to the evolution of biodiversity. An unresolved question is the relative importance of new mutations, ancestral variants, and introgressive hybridization for phenotypic evolution and speciation. Here, we address this issue using Darwin's finches and investigate the genomic architecture underlying their phenotypic diversity. Admixture mapping for beak and body size in the small, medium, and large ground finches revealed 28 loci showing strong genetic differentiation. These loci represent ancestral haplotype blocks with origins predating speciation events during the Darwin's finch radiation. Genes expressed in the developing beak are overrepresented in these genomic regions. Ancestral haplotypes constitute genetic modules for selection and act as key determinants of the unusual phenotypic diversity of Darwin's finches. Such ancestral haplotype blocks can be critical for how species adapt to environmental variability and change.

Evolutionary Divergence and Radula Diversification in Two Ecomorphs from an Adaptive Radiation of Freshwater Snails

(1) Background: Adaptive diversification of complex traits plays a pivotal role in the evolution of organismal diversity. In the freshwater snail genus Tylomelania, adaptive radiations were likely promoted by trophic specialization via diversification of their key foraging organ, the radula. (2) Methods: To investigate the molecular basis of radula diversification and its contribution to lineage divergence, we used tissue-specific transcriptomes of two sympatric Tylomelania sarasinorum ecomorphs. (3) Results: We show that ecomorphs are genetically divergent lineages with habitat-correlated abundances. Sequence divergence and the proportion of highly differentially expressed genes are significantly higher between radula transcriptomes compared to the mantle and foot. However, the same is not true when all differentially expressed genes or only non-synonymous SNPs are considered. Finally, putative homologs of some candidate genes for radula diversification (hh, arx, gbb) were also found to contribute to trophic specialization in cichlids and Darwin’s finches. (4) Conclusions: Our results are in line with diversifying selection on the radula driving Tylomelania ecomorph divergence and indicate that some molecular pathways may be especially prone to adaptive diversification, even across phylogenetically distant animal groups.

Molecular parallelism in signaling function across different sexually selected ornaments in a warbler

Extravagant ornaments are thought to signal male quality to females choosing mates, but the evidence linking ornament size to male quality is controversial, particularly in cases in which females prefer different ornaments in different populations. Here, we use whole-genome sequencing and transcriptomics to determine the genetic basis of ornament size in two populations of a widespread warbler, the common yellowthroat (Geothlypis trichas). Within a single subspecies, females in a Wisconsin population prefer males with larger black masks as mates, while females in a New York population prefer males with larger yellow bibs. Despite being produced by different pigments in different patches on the body, the size of the ornament preferred by females in each population was linked to numerous genes that function in many of the same core aspects of male quality (e.g., immunity and oxidative balance). These relationships confirm recent hypotheses linking the signaling function of ornaments to male quality. Furthermore, the parallelism in signaling function provides the flexibility for different types of ornaments to be used as signals of similar aspects of male quality. This could facilitate switches in female preference for different ornaments, a potentially important step in the early stages of divergence among populations.

Comparative Genomics and Evolution of Avian Specialized Traits

Genomic data are important for understanding the origin and evolution of traits. Under the context of rapidly developing of sequencing technologies and more widely available genome sequences, researchers are able to study evolutionary mechanisms of traits via comparative genomic methods. Compared with other vertebrates, bird genomes are relatively small and exhibit conserved synteny with few repetitive elements, which makes them suitable for evolutionary studies. Increasing genomic progress has been reported on the evolution of powered flight, body size variation, beak morphology, plumage colouration, high-elevation colonization, migration, and vocalization. By summarizing previous studies, we demonstrate the genetic bases of trait evolution, highlighting the roles of small-scale sequence variation, genomic structural variation, and changes in gene interaction networks. We suggest that future studies should focus on improving the quality of reference genomes, exploring the evolution of regulatory elements and networks, and combining genomic data with morphological, ecological, behavioural, and developmental biology data.

Low genome-wide divergence between two lizard populations with high adaptive phenotypic differentiation

Usually, adaptive phenotypic differentiation is paralleled by genetic divergence between locally adapted populations. However, adaptation can also happen in a scenario of nonsignificant genetic divergence due to intense gene flow and/or recent differentiation. While this phenomenon is rarely published, findings on incipient ecologically driven divergence or isolation by adaptation are relatively common, which could confound our understanding about the frequency at which they actually occur in nature. Here, we explore genome-wide traces of divergence between two populations of the lacertid lizard Psammodromus algirus separated by a 600 m elevational gradient. These populations seem to be differentially adapted to their environments despite showing low levels of genetic differentiation (according to previously studies of mtDNA and microsatellite data). We performed a search for outliers (i.e., loci subject to selection) trying to identify specific loci with FST statistics significantly higher than those expected on the basis of overall, genome-wide estimates of genetic divergence. We find that local phenotypic adaptation (in terms of a wide diversity of characters) was not accompanied by genome-wide differentiation, even when we maximized the chances of unveiling such differentiation at particular loci with FST-based outlier detection tests. Instead, our analyses confirmed the lack of genome-wide differentiation on the basis of more than 70,000 SNPs, which is concordant with a scenario of local adaptation without isolation by environment. Our results add evidence to previous studies in which local adaptation does not lead to any kind of isolation (or early stages of ecological speciation), but maintains phenotypic divergence despite the lack of a differentiated genomic background.

Fur colour in the Arctic fox: genetic architecture and consequences for fitness

Genome-wide association studies provide good opportunities for studying the genetic basis of adaptive traits in wild populations. Yet, previous studies often failed to identify major effect genes. In this study, we used high-density single nucleotide polymorphism and individual fitness data from a wild non-model species. Using a whole-genome approach, we identified the MC1R gene as the sole causal gene underlying Arctic fox Vulpes lagopus fur colour. Further, we showed the adaptive importance of fur colour genotypes through measures of fitness that link ecological and evolutionary processes. We found a tendency for blue foxes that are heterozygous at the fur colour locus to have higher fitness than homozygous white foxes. The effect of genotype on fitness was independent of winter duration but varied with prey availability, with the strongest effect in years of increasing rodent populations. MC1R is located in a genomic region with high gene density, and we discuss the potential for indirect selection through linkage and pleiotropy. Our study shows that whole-genome analyses can be successfully applied to wild species and identify major effect genes underlying adaptive traits. Furthermore, we show how this approach can be used to identify knowledge gaps in our understanding of interactions between ecology and evolution.

An island-hopping bird reveals how founder events shape genome-wide divergence

When populations colonize new areas, both strong selection and strong drift can be experienced due to novel environments and small founding populations, respectively. Empirical studies have predominantly focused on the phenotype when assessing the role of selection, and limited neutral-loci when assessing founder-induced loss of diversity. Consequently, the extent to which processes interact to influence evolutionary trajectories is difficult to assess. Genomic-level approaches provide the opportunity to simultaneously consider these processes. Here, we examine the roles of selection and drift in shaping genomic diversity and divergence in historically documented sequential island colonizations by the silvereye (Zosterops lateralis). We provide the first empirical demonstration of the rapid appearance of highly diverged genomic regions following population founding, the position of which are highly idiosyncratic. As these regions rarely contained loci putatively under selection, it is most likely that these differences arise via the stochastic nature of the founding process. However, selection is required to explain rapid evolution of larger body size in insular silvereyes. Reconciling our genomic data with these phenotypic patterns suggests there may be many genomic routes to the island phenotype, which vary across populations. Finally, we show that accelerated divergence associated with multiple founding steps is the product of genome-wide rather than localized differences, and that diversity erodes due to loss of rare alleles. However, even multiple founder events do not result in divergence and diversity levels seen in evolutionary older subspecies, and therefore do not provide a shortcut to speciation as proposed by founder-effect speciation models.

Chromosome-Level Genome Assembly of the Common Chaffinch (Aves: Fringilla coelebs): A Valuable Resource for Evolutionary Biology

The common chaffinch, Fringilla coelebs, is one of the most common, widespread, and well-studied passerines in Europe, with a broad distribution encompassing Western Europe and parts of Asia, North Africa, and the Macaronesian archipelagos. We present a high-quality genome assembly of the common chaffinch generated using Illumina shotgun sequencing in combination with Chicago and Hi-C libraries. The final genome is a 994.87-Mb chromosome-level assembly, with 98% of the sequence data located in chromosome scaffolds and a N50 statistic of 69.73 Mb. Our genome assembly shows high completeness, with a complete BUSCO score of 93.9% using the avian data set. Around 7.8% of the genome contains interspersed repetitive elements. The structural annotation yielded 17,703 genes, 86.5% of which have a functional annotation, including 7,827 complete universal single-copy orthologs out of 8,338 genes represented in the BUSCO avian data set. This new annotated genome assembly will be a valuable resource as a reference for comparative and population genomic analyses of passerine, avian, and vertebrate evolution.

Testing the influence of crushing surface variation on seed-cracking performance among beak morphs of the African seedcracker Pyrenestes ostrinus

Extreme phenotypic polymorphism is an oft-cited example of evolutionary theory in practice. Although these morphological variations are assumed to be adaptive, few studies have biomechanically tested such hypotheses. Pyrenestes ostrinus (the African seedcracker finch) shows an intraspecific polymorphism in beak size and shape that is entirely diet driven and allelically determined. Three distinct morphs feed upon soft sedge seeds during times of abundance, but during lean times switch to specializing on three different species of sedge seeds that differ significantly in hardness. Here, we test the hypothesis that beak morphology is directly related to consuming seeds of different hardness. We used a novel experimental analysis to test how beak morphology affects the efficiency of cracking sedge seeds of variable hardness, observing that neither mandibular ramus width nor crushing surface morphology had significant effects on the ability to crack different seed types. It is likely that feeding performance is correlated with other aspects of beak size and shape, such as beak depth and strength, muscle force or gape. Our results highlight how even seemingly straightforward examples of adaptive selection in nature can be complex in practice.

Genomic variation, population history and within-archipelago adaptation between island bird populations

Oceanic island archipelagos provide excellent models to understand evolutionary processes. Colonization events and gene flow can interact with selection to shape genetic variation at different spatial scales. Landscape-scale variation in biotic and abiotic factors may drive fine-scale selection within islands, while long-term evolutionary processes may drive divergence between distantly related populations. Here, we examine patterns of population history and selection between recently diverged populations of the Berthelot's pipit (Anthus berthelotii), a passerine endemic to three North Atlantic archipelagos. First, we use demographic trees and f3 statistics to show that genome-wide divergence across the species range is largely shaped by colonization and bottlenecks, with evidence of very weak gene flow between populations. Then, using a genome scan approach, we identify signatures of divergent selection within archipelagos at single nucleotide polymorphisms (SNPs) in genes potentially associated with craniofacial development and DNA repair. We did not detect within-archipelago selection at the same SNPs as were detected previously at broader spatial scales between archipelagos, but did identify signatures of selection at loci associated with similar biological functions. These findings suggest that similar ecological factors may repeatedly drive selection between recently separated populations, as well as at broad spatial scales across varied landscapes.

Polygenic basis for adaptive morphological variation in a threatened Aotearoa | New Zealand bird, the hihi (Notiomystis cincta)

To predict if a threatened species can adapt to changing selective pressures, it is crucial to understand the genetic basis of adaptive traits, especially in species historically affected by severe bottlenecks. We estimated the heritability of three hihi (Notiomystis cincta) morphological traits known to be under selection (nestling tarsus length, body mass and head-bill length) using 523 individuals and 39 699 single nucleotide polymorphisms (SNPs) from a 50 K Affymetrix SNP chip. We then examined the genetic architecture of the traits via chromosome partitioning analyses and genome-wide association scans (GWAS). Heritabilities estimated using pedigree relatedness or genomic relatedness were low. For tarsus length, the proportion of genetic variance explained by each chromosome was positively correlated with its size, and more than one chromosome explained significant variation for body mass and head-bill length. Finally, GWAS analyses suggested many loci of small effect contributing to trait variation for all three traits, although one locus (an SNP within an intron of the transcription factor HEY2) was tentatively associated with tarsus length. Our findings suggest a polygenic nature for the morphological traits, with many small effect size loci contributing to the majority of the variation, similar to results from many other wild populations. However, the small effective population size, polygenic architecture and already low heritabilities suggest that both the total response and rate of response to selection are likely to be limited in hihi.

Precipitation and vegetation shape patterns of genomic and craniometric variation in the central African rodent Praomys misonnei

Predicting species' capacity to respond to climate change is an essential first step in developing effective conservation strategies. However, conservation prioritization schemes rarely take evolutionary potential into account. Ecotones provide important opportunities for diversifying selection and may thus constitute reservoirs of standing variation, increasing the capacity for future adaptation. Here, we map patterns of environmentally associated genomic and craniometric variation in the central African rodent Praomys misonnei to identify areas with the greatest turnover in genomic composition. We also project patterns of environmentally associated genomic variation under future climate change scenarios to determine where populations may be under the greatest pressure to adapt. While precipitation gradients influence both genomic and craniometric variation, vegetation structure is also an important determinant of craniometric variation. Areas of elevated environmentally associated genomic and craniometric variation overlap with zones of rapid ecological transition underlining their importance as reservoirs of evolutionary potential. We also find that populations in the Sanaga river basin, central Cameroon and coastal Gabon are likely to be under the greatest pressure from climate change. Lastly, we make specific conservation recommendations on how to protect zones of high evolutionary potential and identify areas where populations may be the most susceptible to climate change.

An empirical comparison of population genetic analyses using microsatellite and SNP data for a species of conservation concern

BACKGROUND

Use of genomic tools to characterize wildlife populations has increased in recent years. In the past, genetic characterization has been accomplished with more traditional genetic tools (e.g., microsatellites). The explosion of genomic methods and the subsequent creation of large SNP datasets has led to the promise of increased precision in population genetic parameter estimates and identification of demographically and evolutionarily independent groups, as well as questions about the future usefulness of the more traditional genetic tools. At present, few empirical comparisons of population genetic parameters and clustering analyses performed with microsatellites and SNPs have been conducted.

RESULTS

Here we used microsatellite and SNP data generated from Gunnison sage-grouse (Centrocercus minimus) samples to evaluate concordance of the results obtained from each dataset for common metrics of genetic diversity (HO, HE, FIS, AR) and differentiation (FST, GST, DJost). Additionally, we evaluated clustering of individuals using putatively neutral (SNPs and microsatellites), putatively adaptive, and a combined dataset of putatively neutral and adaptive loci. We took particular interest in the conservation implications of any differences. Generally, we found high concordance between microsatellites and SNPs for HE, FIS, AR, and all differentiation estimates. Although there was strong correlation between metrics from SNPs and microsatellites, the magnitude of the diversity and differentiation metrics were quite different in some cases. Clustering analyses also showed similar patterns, though SNP data was able to cluster individuals into more distinct groups. Importantly, clustering analyses with SNP data suggest strong demographic independence among the six distinct populations of Gunnison sage-grouse with some indication of evolutionary independence in two or three populations; a finding that was not revealed by microsatellite data.

CONCLUSION

We demonstrate that SNPs have three main advantages over microsatellites: more precise estimates of population-level diversity, higher power to identify groups in clustering methods, and the ability to consider local adaptation. This study adds to a growing body of work comparing the use of SNPs and microsatellites to evaluate genetic diversity and differentiation for a species of conservation concern with relatively high population structure and using the most common method of obtaining SNP genotypes for non-model organisms.

Galapagos Islands Endemic Vertebrates: A Population Genetics Perspective

The organisms of the Galapagos Islands played a central role in the development of the theory of evolution by Charles Darwin. Examination of the population genetics factors of many of these organisms with modern molecular methods has expanded our understanding of their evolution. Here, I provide a perspective on how selection, gene flow, genetic drift, mutation, and inbreeding have contributed to the evolution of 6 iconic Galapagos species: flightless cormorant, pink iguana, marine iguana, Galapagos hawk, giant tortoises, and Darwin's finches. Because of the inherent biological differences among these species that have colonized the Galapagos, different population genetic factors appear to be more or less important in these different species. For example, the Galapagos provided novel environments in which strong selection took place and the Darwin's finches diversified to produce new species and the cormorant adapted to the nutrient-rich western shores of the Galapagos by losing its ability to fly and genomic data have now identified candidate genes. In both the pink iguana, which exists in one small population, and the Galapagos hawk, which has small population sizes, genetic drift has been potentially quite important. There appears to be very limited interisland gene flow in the flightless cormorant and the Galapagos hawk. On the other hand, both the marine iguana and some of the Darwin's finches appear to have significant interisland gene flow. Hybridization between species and subspecies has also introduced new adaptive variation, and in some cases, hybridization might have resulted in despeciation. Overall, new population genetics and genomics research has provided additional insight into the evolution of vertebrate species in the Galapagos.

Genome-wide association analyses reveal polygenic genomic architecture underlying divergent shell morphology in Spanish Littorina saxatilis ecotypes

Gene flow between diverging populations experiencing dissimilar ecological conditions can theoretically constrain adaptive evolution. To minimize the effect of gene flow, alleles underlying traits essential for local adaptation are predicted to be located in linked genome regions with reduced recombination. Local reduction in gene flow caused by selection is expected to produce elevated divergence in these regions. The highly divergent crab-adapted and wave-adapted ecotypes of the marine snail Littorina saxatilis present a model system to test these predictions. We used genome-wide association (GWA) analysis of geometric morphometric shell traits associated with microgeographic divergence between the two L. saxatilis ecotypes within three separate sampling sites. A total of 477 snails that had individual geometric morphometric data and individual genotypes at 4,066 single nucleotide polymorphisms (SNPs) were analyzed using GWA methods that corrected for population structure among the three sites. This approach allowed dissection of the genomic architecture of shell shape divergence between ecotypes across a wide geographic range, spanning two glacial lineages. GWA revealed 216 quantitative trait loci (QTL) with shell size or shape differences between ecotypes, with most loci explaining a small proportion of phenotypic variation. We found that QTL were evenly distributed across 17 linkage groups, and exhibited elevated interchromosomal linkage, suggesting a genome-wide response to divergent selection on shell shape between the two ecotypes. Shell shape trait-associated loci showed partial overlap with previously identified outlier loci under divergent selection between the two ecotypes, supporting the hypothesis of diversifying selection on these genomic regions. These results suggest that divergence in shell shape between the crab-adapted and wave-adapted ecotypes is produced predominantly by a polygenic genomic architecture with positive linkage disequilibrium among loci of small effect.

Eco-evolutionary feedbacks between prey densities and linkage disequilibrium in the predator maintain diversity

Diversity occurs at multiple scales. Within a single population, there is diversity in genotypes and phenotypes. At a larger scale, within ecological communities, there is diversity in species. A number of studies have investigated how diversity at these two scales influence each other through what has been termed eco-evolutionary feedbacks. Here we study a three-species ecological module called apparent competition, in which the predator is evolving in a trait that determines its interaction with two prey species. Unlike previous studies on apparent competition, which employed evolutionary frameworks with very simple genetics, we study an eco-evolutionary model in which the predator's trait is determined by two recombining diallelic loci, so that its mean and variance can evolve, as well as associations (linkage disequilibrium) between the loci. We ask how eco-evolutionary feedbacks with these two loci affect the coexistence of the prey species and the maintenance of polymorphisms within the predator species. We uncover a novel eco-evolutionary feedback between the prey densities and the linkage disequilibrium between the predator's loci. Through a stability analysis, we demonstrate how these feedbacks affect polymorphisms at both loci and, among others, may generate stable cycling.

Growth factor gene IGF1 is associated with bill size in the black-bellied seedcracker Pyrenestes ostrinus

Pyrenestes finches are unique among birds in showing a non-sex-determined polymorphism in bill size and are considered a textbook example of disruptive selection. Morphs breed randomly with respect to bill size, and differ in diet and feeding performance relative to seed hardness. Previous breeding experiments are consistent with the polymorphism being controlled by a single genetic factor. Here, we use genome-wide pooled sequencing to explore the underlying genetic basis of bill morphology and identify a single candidate region. Targeted resequencing reveals extensive linkage disequilibrium across a 300 Kb region containing the insulin-like growth factor 1 (IGF1) gene, with a single 5-million-year-old haplotype associating with phenotypic dominance of the large-billed morph. We find no genetic similarities controlling bill size in the well-studied Darwin’s finches (Geospiza). Our results show how a single genetic factor may control bill size and provide a foundation for future studies to examine this phenomenon within and among avian species.

Pyrenestes finches have a bill size polymorphism thought to be maintained by disruptive selection. Here, the authors identify a single candidate region, including insulin-like growth factor 1, differentiating small and large bill size morphs and a wider region differentiating the mega-billed morph.

The old and new faces of morphology: the legacy of D'Arcy Thompson's 'theory of transformations' and 'laws of growth'

In 1917, the publication of On Growth and Form by D'Arcy Wentworth Thompson challenged both mathematicians and naturalists to think about biological shapes and diversity as more than a confusion of chaotic forms generated at random, but rather as geometric shapes that could be described by principles of physics and mathematics. Thompson's work was based on the ideas of Galileo and Goethe on morphology and of Russell on functionalism, but he was first to postulate that physical forces and internal growth parameters regulate biological forms and could be revealed via geometric transformations in morphological space. Such precise mathematical structure suggested a unifying generative process, as reflected in the title of the book. To Thompson it was growth that could explain the generation of any particular biological form, and changes in ontogeny, rather than natural selection, could then explain the diversity of biological shapes. Whereas adaptationism, widely accepted in evolutionary biology, gives primacy to extrinsic factors in producing morphological variation, Thompson's 'laws of growth' provide intrinsic directives and constraints for the generation of individual shapes, helping to explain the 'profusion of forms, colours, and other modifications' observed in the living world.