A Bigger Toolbox: Biotechnology in Biodiversity Conservation

Trends in biotechnology, Journal Year: 2016, Volume and Issue: 35(1), P. 55 - 65

Published: July 14, 2016

Language: Английский

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A comparison of genomic islands of differentiation across three young avian species pairs

Molecular Ecology, Journal Year: 2018, Volume and Issue: 27(23), P. 4839 - 4855

Published: Sept. 6, 2018

Abstract Detailed evaluations of genomic variation between sister species often reveal distinct chromosomal regions high relative differentiation (i.e., “islands differentiation” in F ST ), but there is much debate regarding the causes this pattern. We briefly review prominent models islands and compare patterns three closely related pairs New World warblers with goal evaluating support for four models. Each pair (MacGillivray's/mourning warblers; Townsend's/black‐throated green Audubon's/myrtle warblers) consists forms that were likely separated western eastern North American refugia during cycles Pleistocene glaciations have now come into contact Canada, where each a narrow hybrid zone. show strong differences their heterogeneity , suggesting differing selective forces and/or responses to similar among pairs. Across most genome, levels within‐group nucleotide diversity ( π Within ) are almost as large between‐group distance Between within pair, recent common ancestry gene flow. In two pairs, pattern peaks having low suggests sweeps spread geographically differentiated groups, followed by local differentiation. This “sweep‐before‐differentiation” model consistent signatures flow yellow‐rumped warbler complex. These findings add our growing understanding speciation complex process can involve phases adaptive introgression partially populations.

Language: Английский

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Avian SDMs: current state, challenges, and opportunities

Journal of Avian Biology, Journal Year: 2017, Volume and Issue: 48(12), P. 1483 - 1504

Published: Oct. 23, 2017

Quantifying species distributions using distribution models (SDMs) has emerged as a central method in modern biogeography. These empirical link occurrence data with spatial environmental information. Since their emergence the 1990s, thousands of scientific papers have used SDMs to study organisms across entire tree life, birds commanding considerable attention. Here, we review current state avian and point challenges future opportunities for specific applications, ranging from conservation biology, invasive predicting seabird distributions, more general topics such modeling diversity, niche evolution seasonal at biogeographic scale. While been criticized being phenomenological nature, inability explicitly account variety processes affecting populations, conclude that they remain powerful tool learn about past, current, – least when limitations assumptions are recognized addressed. We close our by providing an outlook on prospects synergies other disciplines which can play important role.

Language: Английский

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Fine scale mapping of genomic introgressions within the Drosophila yakuba clade

PLoS Genetics, Journal Year: 2017, Volume and Issue: 13(9), P. e1006971 - e1006971

Published: Sept. 5, 2017

The process of speciation involves populations diverging over time until they are genetically and reproductively isolated. Hybridization between nascent species was long thought to directly oppose speciation. However, the amount interspecific genetic exchange (introgression) mediated by hybridization remains largely unknown, although recent progress in genome sequencing has made measuring introgression more tractable. A natural place look for individuals with admixed ancestry (indicative introgression) is regions where co-occur. In west Africa, D. santomea yakuba hybridize on island São Tomé, while teissieri nearby Bioko. this report, we quantify genomic extent three Drosophila clade (D. yakuba, santomea), teissieri). We sequenced genomes 86 from all species. also developed applied a new statistical framework, using hidden Markov approach, identify introgression. found that occurred both pairs but most introgressed segments small (on order few kilobases). After ruling out retention ancestral polymorphism as an explanation these similar regions, find sizes haplotypes indicate not (>1,000 generations ago). additionally show cases, rarer X chromosomes than autosomes which consistent sex playing large role reproductive isolation. Even though two have stable contemporary hybrid zones, providing opportunity ongoing gene flow, our results currently rare.

Language: Английский

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Behavioral Isolation and Incipient Speciation in Birds

Annual Review of Ecology Evolution and Systematics, Journal Year: 2018, Volume and Issue: 49(1), P. 1 - 24

Published: May 18, 2018

Behavioral changes, such as those involved in mating, foraging, and migration, can generate reproductive barriers between populations. Birds, particular, are known for their great diversity these behaviors, so behavioral isolation is often proposed to be the major driver of speciation. Here, we review empirical evidence evaluate importance early stages avian Experimentally measured mating preferences indicate that changes behavior result premating barriers, with strength depending on extent divergence signals. Differences migratory foraging also play important roles generating However, because imperfect, extrinsic postzygotic form selection against hybrids having intermediate phenotypes, an role diversification, especially completing speciation process.

Language: Английский

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Avian Coloration Genetics: Recent Advances and Emerging Questions

Journal of Heredity, Journal Year: 2021, Volume and Issue: 112(5), P. 395 - 416

Published: March 23, 2021

Abstract The colorful phenotypes of birds have long provided rich source material for evolutionary biologists. Avian plumage, beaks, skin, and eggs—which exhibit a stunning range cryptic conspicuous forms—inspired early work on adaptive coloration. More recently, avian color has fueled discoveries the physiological, developmental, and—increasingly—genetic mechanisms responsible phenotypic variation. relative ease with which traits can be quantified made an attractive system uncovering links between phenotype genotype. Accordingly, field coloration genetics is burgeoning. In this review, we highlight recent advances emerging questions associated genetic underpinnings bird color. We start by describing breakthroughs related to 2 pigment classes: carotenoids that produce red, yellow, orange in most psittacofulvins similar colors parrots. then discuss structural colors, are produced interaction light nanoscale materials greatly extend plumage palette. Structural remain understudied—but paradigm changing. next explore how arise from interactions among pigmentary may controlled genes co-expressed or co-regulated. also identify opportunities investigate mediating within-feather micropatterning bare parts eggs. conclude spotlighting research areas—mechanistic vision production, speciation—that been invigorated insights, trend likely continue as new genomic approaches applied non-model species.

Language: Английский

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Sex chromosome inversions enforce reproductive isolation across an avian hybrid zone

Molecular Ecology, Journal Year: 2018, Volume and Issue: 28(6), P. 1246 - 1262

Published: Sept. 19, 2018

Abstract Across hybrid zones, the sex chromosomes are often more strongly differentiated than autosomes. This is regularly attributed to greater frequency of reproductive incompatibilities accumulating on and their exposure in heterogametic sex. Working within an avian zone, we explore possibility that chromosome inversions differentially accumulate Z compared autosomes thereby contribute differentiation. We analyse northern Australian zone between two subspecies long‐tailed finch ( Poephila acuticauda ), first described based differences bill colour, using reduced‐representation genomic sequencing for 293 individuals over a 1,530‐km transect. Autosomal differentiation minimal. In contrast, 75% highly shows steep cline, which displaced 350 km west cline colour. Differentiation associated with or putative chromosomal inversions, each predominating one subspecies. If reduce recombination incompatibilities, they selectively favoured should therefore zones. argue this predisposes chromosome. One region affecting colour Z, but main candidates 8. displacement centres suggest has not contributed inversion accumulation. Based width, however, both isolation established pair

Language: Английский

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Avian introgression in the genomic era

Avian Research, Journal Year: 2017, Volume and Issue: 8(1)

Published: Nov. 21, 2017

Introgression, the incorporation of genetic material from one (sub)species into gene pool another by means hybridization and backcrossing, is a common phenomenon in birds can provide important insights speciation process. In last decade, toolkit for studying introgression has expanded together with development molecular markers. this review, we explore how genomic data, most recent step methodological progress, impacts different aspects study avian introgression. First, detection hybrids backcrosses improved dramatically. The widely used software package STRUCTURE. Phylogenetic discordance (i.e. loci resulting discordant trees) introgression, although it should be regarded as starting point further analyses, not definitive proof Specifically, disentangling other biological processes, such incomplete lineage sorting, remains challenging endeavour, new techniques, D-statistic, are being developed. addition, phylogenetics might require shift trees to networks. Second, hybrid zones geographical or cline analysis led complex interplay between speciation. However, because each zone just single snapshot continuously changing interaction, studied across temporal and/or spatial scales. A third powerful tool genome scan. debate on which evolutionary processes underlie landscape still ongoing, question whether involved reproductive isolation cluster 'islands speciation' they scattered throughout genome. Exploring landscapes tree life will an exciting field research. Finally, findings these methods incorporated specific scenarios, consequently tested using modelling approach. All all, perspective our understanding evolution general.

Language: Английский

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A comparative assessment ofSNPand microsatellite markers for assigning parentage in a socially monogamous bird

Molecular Ecology Resources, Journal Year: 2016, Volume and Issue: 17(2), P. 183 - 193

Published: Aug. 4, 2016

Abstract Single‐nucleotide polymorphisms ( SNP s) are preferred over microsatellite markers in many evolutionary studies, but have only recently been applied to studies of parentage. Evaluations s and microsatellites for assigning parentage mostly focused on special cases that require a relatively large number heterozygous loci, such as species with low genetic diversity or complex social structures. We developed 120 from transcriptome assembled using RNA ‐sequencing songbird the most common avian mating system—social monogamy. compared effectiveness 97 novel six previously described paternity black‐throated blue warbler, Setophaga caerulescens . show full panel (mean H o = 0.19) was powerful multiallelic 0.86). Paternity assignments two marker types were agreement 92% offspring. Filtering individual samples by 50% call rate 75% maximized offspring assigned 95% confidence s. also found 40 0.37) had similar power assign These findings demonstrate small variable can be effective analyses socially monogamous species. suggest development is advantageous high‐throughput genotyping plan address range ecological questions.

Language: Английский

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More than skin and bones: Comparing extraction methods and alternative sources of DNA from avian museum specimens

Molecular Ecology Resources, Journal Year: 2019, Volume and Issue: 20(5), P. 1220 - 1227

Published: Sept. 3, 2019

Next-generation sequencing has greatly expanded the utility and value of museum collections by revealing specimens as genomic resources. As field genomics grows, so does need for extraction methods that maximize DNA yields. For avian specimens, established method extracting from toe pads works well most specimens. However, some especially those birds are very small or large, can be a poor source DNA. In this study, we apply two (phenol-chloroform silica column) to three different sources (toe pad, skin punch bone) 10 historical We show modified phenol-chloroform protocol yielded significantly more than column (e.g., Qiagen DNeasy Blood & Tissue Kit) across all tissue types. extractions using contained longer fragments on average protocol, probably result loss through column. While punches bone fragments, proved reliable alternative might appealing when pad impractical. Overall, found bird contain substantial amounts studies under scenarios, but consistently provides high quantities required current protocols.

Language: Английский

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