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1.
Proc Natl Acad Sci U S A ; 121(15): e2319506121, 2024 Apr 09.
Artigo em Inglês | MEDLINE | ID: mdl-38557186

RESUMO

Genomes are typically mosaics of regions with different evolutionary histories. When speciation events are closely spaced in time, recombination makes the regions sharing the same history small, and the evolutionary history changes rapidly as we move along the genome. When examining rapid radiations such as the early diversification of Neoaves 66 Mya, typically no consistent history is observed across segments exceeding kilobases of the genome. Here, we report an exception. We found that a 21-Mb region in avian genomes, mapped to chicken chromosome 4, shows an extremely strong and discordance-free signal for a history different from that of the inferred species tree. Such a strong discordance-free signal, indicative of suppressed recombination across many millions of base pairs, is not observed elsewhere in the genome for any deep avian relationships. Although long regions with suppressed recombination have been documented in recently diverged species, our results pertain to relationships dating circa 65 Mya. We provide evidence that this strong signal may be due to an ancient rearrangement that blocked recombination and remained polymorphic for several million years prior to fixation. We show that the presence of this region has misled previous phylogenomic efforts with lower taxon sampling, showing the interplay between taxon and locus sampling. We predict that similar ancient rearrangements may confound phylogenetic analyses in other clades, pointing to a need for new analytical models that incorporate the possibility of such events.


Assuntos
Evolução Biológica , Genoma , Animais , Filogenia , Genoma/genética , Aves , Recombinação Genética
2.
Nat Rev Genet ; 21(8): 476-492, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32472059

RESUMO

Recombination is a central biological process with implications for many areas in the life sciences. Yet we are only beginning to appreciate variation in the recombination rate along the genome and among individuals, populations and species. Spurred by technological advances, we are now able to bring variation in this key biological parameter to centre stage. Here, we review the conceptual implications of recombination rate variation and guide the reader through the assumptions, strengths and weaknesses of genomic inference methods, including population-based, pedigree-based and gamete-based approaches. Appreciation of the differences and commonalities of these approaches is a prerequisite to formulate a unifying and comparative framework for understanding the molecular and evolutionary mechanisms shaping, and being shaped by, recombination.


Assuntos
Evolução Molecular , Genética Populacional , Genômica , Recombinação Genética , Animais , Evolução Biológica , Mapeamento Cromossômico , Testes Genéticos , Variação Genética , Genômica/métodos , Humanos , Miose
3.
PLoS Genet ; 19(9): e1010901, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-37747941

RESUMO

The evolution of genetic sex determination is often accompanied by degradation of the sex-limited chromosome. Male heterogametic systems have evolved convergent, epigenetic mechanisms restoring the resulting imbalance in gene dosage between diploid autosomes (AA) and the hemizygous sex chromosome (X). Female heterogametic systems (AAf Zf, AAm ZZm) tend to only show partial dosage compensation (0.5 < Zf:AAf < 1) and dosage balance (0.5

Assuntos
Cromatina , Corvos , Animais , Feminino , Masculino , Cromatina/genética , Corvos/genética , Epigênese Genética , Metilação , Mecanismo Genético de Compensação de Dose , Cromossomos Sexuais
4.
Mol Biol Evol ; 41(6)2024 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-38743589

RESUMO

Chromosomal inversions are structural mutations that can play a prominent role in adaptation and speciation. Inversions segregating across species boundaries (trans-species inversions) are often taken as evidence for ancient balancing selection or adaptive introgression, but can also be due to incomplete lineage sorting. Using whole-genome resequencing data from 18 populations of 11 recognized munia species in the genus Lonchura (N = 176 individuals), we identify four large para- and pericentric inversions ranging in size from 4 to 20 Mb. All four inversions cosegregate across multiple species and predate the numerous speciation events associated with the rapid radiation of this clade across the prehistoric Sahul (Australia, New Guinea) and Bismarck Archipelago. Using coalescent theory, we infer that trans-specificity is improbable for neutrally segregating variation despite substantial incomplete lineage sorting characterizing this young radiation. Instead, the maintenance of all three autosomal inversions (chr1, chr5, and chr6) is best explained by selection acting along ecogeographic clines not observed for the collinear parts of the genome. In addition, the sex chromosome inversion largely aligns with species boundaries and shows signatures of repeated positive selection for both alleles. This study provides evidence for trans-species inversion polymorphisms involved in both adaptation and speciation. It further highlights the importance of informing selection inference using a null model of neutral evolution derived from the collinear part of the genome.


Assuntos
Inversão Cromossômica , Animais , Seleção Genética , Especiação Genética , Evolução Molecular , Passeriformes/genética
5.
Genome Res ; 32(4): 671-681, 2022 04.
Artigo em Inglês | MEDLINE | ID: mdl-35149543

RESUMO

One of the defining features of transposable elements (TEs) is their ability to move to new locations in the host genome. To minimize the potentially deleterious effects of de novo TE insertions, hosts have evolved several mechanisms to control TE activity, including recombination-mediated removal and epigenetic silencing; however, increasing evidence suggests that silencing of TEs is often incomplete. The crow family experienced a recent radiation of LTR retrotransposons (LTRs), offering an opportunity to gain insight into the regulatory control of young, potentially still active TEs. We quantified the abundance of TE-derived transcripts across several tissues in 15 Eurasian crows (Corvus (corone) spp.) raised under common garden conditions and find evidence for ineffective TE suppression on the female-specific W Chromosome. Using RNA-seq data, we show that ∼9.5% of all transcribed TEs had considerably greater (average, 16-fold) transcript abundance in female crows and that >85% of these female-biased TEs originated on the W Chromosome. After accounting for differences in TE density among chromosomal classes, W-linked TEs were significantly more highly expressed than TEs residing on other chromosomes, consistent with ineffective silencing on the former. Together, our results suggest that the crow W Chromosome acts as a source of transcriptionally active TEs, with possible negative fitness consequences for female birds analogous to Drosophila (an X/Y system), in which overexpression of Y-linked TEs is associated with male-specific aging and fitness loss ("toxic Y").


Assuntos
Elementos de DNA Transponíveis , Evolução Molecular , Animais , Aves , Drosophila , Epigênese Genética , Feminino , Masculino , Cromossomos Sexuais/genética
6.
Genome Res ; 32(2): 324-336, 2022 02.
Artigo em Inglês | MEDLINE | ID: mdl-34907076

RESUMO

Hybridization is thought to reactivate transposable elements (TEs) that were efficiently suppressed in the genomes of the parental hosts. Here, we provide evidence for this "genomic shock hypothesis" in the fission yeast Schizosaccharomyces pombe In this species, two divergent lineages (Sp and Sk) have experienced recent, likely human-induced, hybridization. We used long-read sequencing data to assemble genomes of 37 samples derived from 31 S. pombe strains spanning a wide range of ancestral admixture proportions. A comprehensive TE inventory revealed exclusive presence of long terminal repeat (LTR) retrotransposons. Sequence analysis of active full-length elements, as well as solo LTRs, revealed a complex history of homologous recombination. Population genetic analyses of syntenic sequences placed insertion of many solo LTRs before the split of the Sp and Sk lineages. Most full-length elements were inserted more recently, after hybridization. With the exception of a single full-length element with signs of positive selection, both solo LTRs and, in particular, full-length elements carry signatures of purifying selection indicating effective removal by the host. Consistent with reactivation upon hybridization, the number of full-length LTR retrotransposons, varying extensively from zero to 87 among strains, significantly increases with the degree of genomic admixture. This study gives a detailed account of global TE diversity in S. pombe, documents complex recombination histories within TE elements, and provides evidence for the "genomic shock hypothesis."


Assuntos
Schizosaccharomyces , Elementos de DNA Transponíveis/genética , Evolução Molecular , Genoma Fúngico , Humanos , Retroelementos/genética , Schizosaccharomyces/genética , Sequências Repetidas Terminais/genética
7.
Nat Rev Genet ; 18(2): 87-100, 2017 02.
Artigo em Inglês | MEDLINE | ID: mdl-27840429

RESUMO

As populations diverge, genetic differences accumulate across the genome. Spurred by rapid developments in sequencing technology, genome-wide population surveys of natural populations promise insights into the evolutionary processes and the genetic basis underlying speciation. Although genomic regions of elevated differentiation are the focus of searches for 'speciation genes', there is an increasing realization that such genomic signatures can also arise by alternative processes that are not related to population divergence, such as linked selection. In this Review, we explore methodological trends in speciation genomic studies, highlight the difficulty in separating processes related to speciation from those emerging from genome-wide properties that are not related to reproductive isolation, and provide a set of suggestions for future work in this area.


Assuntos
Evolução Biológica , Fluxo Gênico , Especiação Genética , Ilhas Genômicas , Seleção Genética/genética , Animais , Variação Genética/genética , Genoma , Genômica , Humanos , Modelos Genéticos
8.
Syst Biol ; 70(4): 786-802, 2021 06 16.
Artigo em Inglês | MEDLINE | ID: mdl-33367817

RESUMO

The phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance because of strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here, we used high-coverage genome-wide sequencing for 14 of the 15 species of Otariidae to elucidate the phylogeny of the family and its bearing on the taxonomy and biogeographical history. Despite extreme topological discordance among gene trees, we found a fully supported species tree that agrees with the few well-accepted relationships and establishes monophyly of the genus Arctocephalus. Our data support a relatively recent trans-hemispheric dispersal at the base of a southern clade, which rapidly diversified into six major lineages between 3 and 2.5 Ma. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be nonmonophyletic, with California (Zalophus californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Zalophus wollebaeki) with evidence for introgression between the two genera. Overall, the high degree of genealogical discordance was best explained by incomplete lineage sorting resulting from quasi-simultaneous speciation within the southern clade with introgresssion playing a subordinate role in explaining the incongruence among and within prior phylogenetic studies of the family. [Hybridization; ILS; phylogenomics; Pleistocene; Pliocene; monophyly.].


Assuntos
Substâncias Explosivas , Otárias , Leões-Marinhos , Animais , Sequência de Bases , Otárias/genética , Filogenia , Leões-Marinhos/genética
9.
Mol Biol Evol ; 37(1): 260-279, 2020 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-31504782

RESUMO

The ratio of nonsynonymous over synonymous sequence divergence, dN/dS, is a widely used estimate of the nonsynonymous over synonymous fixation rate ratio ω, which measures the extent to which natural selection modulates protein sequence evolution. Its computation is based on a phylogenetic approach and computes sequence divergence of protein-coding DNA between species, traditionally using a single representative DNA sequence per species. This approach ignores the presence of polymorphisms and relies on the indirect assumption that new mutations fix instantaneously, an assumption which is generally violated and reasonable only for distantly related species. The violation of the underlying assumption leads to a time-dependence of sequence divergence, and biased estimates of ω in particular for closely related species, where the contribution of ancestral and lineage-specific polymorphisms to sequence divergence is substantial. We here use a time-dependent Poisson random field model to derive an analytical expression of dN/dS as a function of divergence time and sample size. We then extend our framework to the estimation of the proportion of adaptive protein evolution α. This mathematical treatment enables us to show that the joint usage of polymorphism and divergence data can assist the inference of selection for closely related species. Moreover, our analytical results provide the basis for a protocol for the estimation of ω and α for closely related species. We illustrate the performance of this protocol by studying a population data set of four corvid species, which involves the estimation of ω and α at different time-scales and for several choices of sample sizes.


Assuntos
Evolução Molecular , Técnicas Genéticas , Modelos Genéticos , Mutação Silenciosa , Animais , Corvos/genética , Polimorfismo Genético
10.
Mol Biol Evol ; 37(2): 469-474, 2020 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-31633794

RESUMO

Theory predicts that deleterious mutations accumulate more readily in small populations. As a consequence, mutation load is expected to be elevated in species where life-history strategies and geographic or historical contingencies reduce the number of reproducing individuals. Yet, few studies have empirically tested this prediction using genome-wide data in a comparative framework. We collected whole-genome sequencing data for 147 individuals across seven crow species (Corvus spp.). For each species, we estimated the distribution of fitness effects of deleterious mutations and compared it with proxies of the effective population size Ne. Island species with comparatively smaller geographic range sizes had a significantly increased mutation load. These results support the view that small populations have an elevated risk of mutational meltdown, which may contribute to the higher extinction rates observed in island species.


Assuntos
Mutação , Passeriformes/genética , Sequenciamento Completo do Genoma/veterinária , Animais , Evolução Molecular , Aptidão Genética , Características de História de Vida , Modelos Genéticos , Passeriformes/classificação , Filogenia , Densidade Demográfica , Seleção Genética
11.
Mol Ecol ; 30(4): 973-986, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33305388

RESUMO

Very few animals habitually manufacture and use tools. It has been suggested that advanced tool behaviour co-evolves with a suite of behavioural, morphological and life history traits. In fact, there are indications for such an adaptive complex in tool-using crows (genus Corvus species). Here, we sequenced the genomes of two habitually tool-using and ten non-tool-using crow species to search for genomic signatures associated with a tool-using lifestyle. Using comparative genomic and population genetic approaches, we screened for signals of selection in protein-coding genes in the tool-using New Caledonian and Hawaiian crows. While we detected signals of recent selection in New Caledonian crows near genes associated with bill morphology, our data indicate that genetic changes in these two lineages are surprisingly subtle, with little evidence at present for convergence. We explore the biological explanations for these findings, such as the relative roles of gene regulation and protein-coding changes, as well as the possibility that statistical power to detect selection in recently diverged lineages may have been insufficient. Our study contributes to a growing body of literature aiming to decipher the genetic basis of recently evolved complex behaviour.


Assuntos
Corvos , Características de História de Vida , Comportamento de Utilização de Ferramentas , Animais , Corvos/genética , Havaí
12.
Mol Ecol ; 30(23): 6162-6177, 2021 12.
Artigo em Inglês | MEDLINE | ID: mdl-34416064

RESUMO

Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically, the probability of inbreeding mediated by mating system and/or population demography. Here, we investigated whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global data set of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstructed demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We found a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population size, were autozygous at hundreds of short ROH (<1 Mb), reflecting high background relatedness due to coalescence of haplotypes deep within the pedigree. In contrast, longer and therefore younger ROH (>1.5 Mb) were found in low latitude populations, and populations of known conservation concern. These include a Scottish killer whale, for which 37.8% of the autosomes were comprised of ROH >1.5 Mb in length. The fate of this population, in which only two adult males have been sighted in the past five years, and zero fecundity over the last two decades, may be inextricably linked to its demographic history and consequential inbreeding depression.


Assuntos
Orca , Animais , Genoma , Homozigoto , Endogamia , Masculino , Polimorfismo de Nucleotídeo Único , Densidade Demográfica , Orca/genética
13.
Mol Biol Evol ; 36(9): 1975-1989, 2019 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-31225876

RESUMO

Mutation and recombination are key evolutionary processes governing phenotypic variation and reproductive isolation. We here demonstrate that biodiversity within all globally known strains of Schizosaccharomyces pombe arose through admixture between two divergent ancestral lineages. Initial hybridization was inferred to have occurred ∼20-60 sexual outcrossing generations ago consistent with recent, human-induced migration at the onset of intensified transcontinental trade. Species-wide heritable phenotypic variation was explained near-exclusively by strain-specific arrangements of alternating ancestry components with evidence for transgressive segregation. Reproductive compatibility between strains was likewise predicted by the degree of shared ancestry. To assess the genetic determinants of ancestry block distribution across the genome, we characterized the type, frequency, and position of structural genomic variation using nanopore and single-molecule real-time sequencing. Despite being associated with double-strand break initiation points, over 800 segregating structural variants exerted overall little influence on the introgression landscape or on reproductive compatibility between strains. In contrast, we found strong ancestry disequilibrium consistent with negative epistatic selection shaping genomic ancestry combinations during the course of hybridization. This study provides a detailed, experimentally tractable example that genomes of natural populations are mosaics reflecting different evolutionary histories. Exploiting genome-wide heterogeneity in the history of ancestral recombination and lineage-specific mutations sheds new light on the population history of S. pombe and highlights the importance of hybridization as a creative force in generating biodiversity.


Assuntos
Variação Genética , Hibridização Genética , Schizosaccharomyces/genética , Epistasia Genética , Variação Estrutural do Genoma , Isolamento Reprodutivo , Sequenciamento Completo do Genoma
14.
Genome Res ; 27(5): 697-708, 2017 05.
Artigo em Inglês | MEDLINE | ID: mdl-28360231

RESUMO

Accurate and contiguous genome assembly is key to a comprehensive understanding of the processes shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DNA. As a key feature of genome architecture associated with centromeric and subtelomeric regions, it locally influences meiotic recombination. In this study, we assess the impact of large tandem repeat arrays on the recombination rate landscape in an avian speciation model, the Eurasian crow. We assembled two high-quality genome references using single-molecule real-time sequencing (long-read assembly [LR]) and single-molecule optical maps (optical map assembly [OM]). A three-way comparison including the published short-read assembly (SR) constructed for the same individual allowed assessing assembly properties and pinpointing misassemblies. By combining information from all three assemblies, we characterized 36 previously unidentified large repetitive regions in the proximity of sequence assembly breakpoints, the majority of which contained complex arrays of a 14-kb satellite repeat or its 1.2-kb subunit. Using whole-genome population resequencing data, we estimated the population-scaled recombination rate (ρ) and found it to be significantly reduced in these regions. These findings are consistent with an effect of low recombination in regions adjacent to centromeric or subtelomeric heterochromatin and add to our understanding of the processes generating widespread heterogeneity in genetic diversity and differentiation along the genome. By combining three different technologies, our results highlight the importance of adding a layer of information on genome structure that is inaccessible to each approach independently.


Assuntos
Mapeamento de Sequências Contíguas/normas , Genoma , Sequências de Repetição em Tandem , Animais , Cromatina/genética , Cromatina/metabolismo , Mapeamento de Sequências Contíguas/métodos , Corvos/genética , Recombinação Homóloga , Análise de Sequência de DNA/métodos , Análise de Sequência de DNA/normas
15.
J Evol Biol ; 33(5): 727-733, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32069366

RESUMO

Within hybrid zones of socially monogamous species, the number of mating opportunities with a conspecific can be limited. As a consequence, individuals may mate with a heterospecific (social) partner despite possible fitness costs to their hybrid offspring. Extra-pair copulations with a conspecific may thus arise as a possible post hoc strategy to reduce the costs of hybridization. We here assessed the rate of extra-pair paternity in the hybrid zone between all-black carrion crows (Corvus (corone) corone) and grey hooded crows (C. (c.) cornix) and tested whether extra-pair paternity (EPP) was more likely in broods where parents differed in plumage colour. The proportion of broods with at least one extra-pair offspring and the proportion of extra-pair offspring were low overall (6.98% and 2.90%, respectively) with no evidence of hybrid broods having higher EPP rates than purebred nests.


Assuntos
Corvos/genética , Hibridização Genética , Comportamento Sexual Animal , Animais , Europa (Continente) , Feminino , Masculino , Paternidade
16.
Mol Ecol ; 28(9): 2406-2422, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30849214

RESUMO

Despite an increasing appreciation of the importance of host-microbe interactions in ecological and evolutionary processes, the factors shaping microbial communities in wild populations remain poorly understood. We therefore exploited a natural experiment provided by two adjacent Antarctic fur seal (Arctocephalus gazella) colonies of high and low social density and combined 16S rRNA metabarcoding with microsatellite profiling of mother-offspring pairs to investigate environmental and genetic influences on skin microbial communities. Seal-associated bacterial communities differed profoundly between the two colonies, despite the host populations themselves being genetically undifferentiated. Consistent with the hypothesis that social stress depresses bacterial diversity, we found that microbial alpha diversity was significantly lower in the high-density colony. Seals from one of the colonies that contained a stream also carried a subset of freshwater-associated bacteria, indicative of an influence of the physical environment. Furthermore, mothers and their offspring shared similar microbial communities, in support of the notion that microbes may facilitate mother-offspring recognition. Finally, a significant negative association was found between bacterial diversity and heterozygosity, a measure of host genetic quality. Our study thus reveals a complex interplay between environmental and host genetic effects, while also providing empirical support for the leash model of host control, which posits that bacterial communities are driven not only by bottom-up species interactions, but also by top-down host regulation. Taken together, our findings have broad implications for understanding host-microbe interactions as well as prokaryotic diversity in general.


Assuntos
Otárias/microbiologia , Microbiota/genética , Pele/microbiologia , Fatores Etários , Animais , Regiões Antárticas , Comportamento Animal , Feminino , Variação Genética , Heterozigoto , Masculino , Mães , RNA Ribossômico 16S , Fatores Sexuais , Comportamento Social
17.
Mol Ecol ; 28(2): 484-502, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-30187987

RESUMO

Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.


Assuntos
Metagenômica , Microbiota/genética , Pele/microbiologia , Orca/microbiologia , Animais , Regiões Antárticas , Diatomáceas/genética , Geografia , Orca/parasitologia
18.
Mol Ecol ; 28(14): 3427-3444, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31131963

RESUMO

Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global data set of killer whale genomes in a rare attempt to elucidate global population structure in a nonhuman species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during postglacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.


Assuntos
Fluxo Gênico , Genoma , Orca/genética , Alelos , Animais , Regiões Antárticas , Sequência de Bases , Núcleo Celular/genética , DNA Mitocondrial/genética , Deriva Genética , Variação Genética , Geografia , Cadeias de Markov , Modelos Genéticos , Filogenia , Análise de Componente Principal
19.
PLoS Biol ; 14(1): e1002350, 2016 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-26745372

RESUMO

Recent advancements in animal tracking technology and high-throughput sequencing are rapidly changing the questions and scope of research in the biological sciences. The integration of genomic data with high-tech animal instrumentation comes as a natural progression of traditional work in ecological genetics, and we provide a framework for linking the separate data streams from these technologies. Such a merger will elucidate the genetic basis of adaptive behaviors like migration and hibernation and advance our understanding of fundamental ecological and evolutionary processes such as pathogen transmission, population responses to environmental change, and communication in natural populations.


Assuntos
Ecologia/tendências , Genômica/tendências , Sequenciamento de Nucleotídeos em Larga Escala , Distribuição Animal , Animais , Transmissão de Doença Infecciosa , Previsões , Fluxo Gênico , Estudos de Associação Genética
20.
J Exp Biol ; 222(Pt 5)2019 03 08.
Artigo em Inglês | MEDLINE | ID: mdl-30718374

RESUMO

Functional validation of candidate genes involved in adaptation and speciation remains challenging. Here, we exemplify the utility of a method quantifying individual mRNA transcripts in revealing the molecular basis of divergence in feather pigment synthesis during early-stage speciation in crows. Using a padlock probe assay combined with rolling circle amplification, we quantified cell-type-specific gene expression in the histological context of growing feather follicles. Expression of Tyrosinase Related Protein 1 (TYRP1), Solute Carrier Family 45 member 2 (SLC45A2) and Hematopoietic Prostaglandin D Synthase (HPGDS) was melanocyte-limited and significantly reduced in follicles from hooded crow, explaining the substantially lower eumelanin content in grey versus black feathers. The central upstream Melanocyte Inducing Transcription Factor (MITF) only showed differential expression specific to melanocytes - a feature not captured by bulk RNA-seq. Overall, this study provides insight into the molecular basis of an evolutionary young transition in pigment synthesis, and demonstrates the power of histologically explicit, statistically substantiated single-cell gene expression quantification for functional genetic inference in natural populations.


Assuntos
Corvos/fisiologia , Plumas/fisiologia , Regulação da Expressão Gênica , Especiação Genética , Pigmentação/genética , Pigmentos Biológicos/genética , RNA Mensageiro/genética , Animais , Cor , Corvos/genética , Plumas/crescimento & desenvolvimento , Melanócitos/metabolismo , Pigmentos Biológicos/biossíntese
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