Birds in space and time: genetic changes accompanying anthropogenic habitat fragmentation in the endangered black‐capped vireo (<i>Vireo atricapilla</i>)

Athrey, Giridhar; Barr, Kelly R.; Lance, Richard F.; Leberg, Paul L.

doi:10.1111/j.1752-4571.2011.00233.x

Cited by 37 publications

(58 citation statements)

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“…The remaining isolated remnant populations are expected (6,7) and observed (8)(9)(10) to lose genetic variation via drift and inbreeding (with a few notable exceptions, e.g., ref. 11), which may further hasten their decline (12).…”

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Predictable allele frequency changes due to habitat fragmentation in the Glanville fritillary butterfly

Fountain

Nieminen

Sirén

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Describing the evolutionary dynamics of now extinct populations is challenging, as their genetic composition before extinction is generally unknown. The Glanville fritillary butterfly has a large extant metapopulation in the Åland Islands in Finland, but declined to extinction in the nearby fragmented southwestern (SW) Finnish archipelago in the 20th century. We genotyped museum samples for 222 SNPs across the genome, including SNPs from candidate genes and neutral regions. SW Finnish populations had significantly reduced genetic diversity before extinction, and their allele frequencies gradually diverged from those in contemporary Åland populations over 80 y. We identified 15 outlier loci among candidate SNPs, mostly related to flight, in which allele frequencies have changed more than the neutral expectation. At outlier loci, allele frequencies in SW Finland shifted in the same direction as newly established populations deviated from old local populations in contemporary Åland. Moreover, outlier allele frequencies in SW Finland resemble those in fragmented landscapes as opposed to continuous landscapes in the Baltic region. These results indicate selection for genotypes associated with good colonization capacity in the highly fragmented landscape before the extinction of the populations. Evolutionary response to habitat fragmentation may have enhanced the viability of the populations, but it did not save the species from regional extinction in the face of severe habitat loss and fragmentation. These results highlight a potentially common situation in changing environments: evolutionary changes are not strong enough to fully compensate for the direct adverse effects of environmental change and thereby rescue populations from extinction.

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confidence: 99%

Predictable allele frequency changes due to habitat fragmentation in the Glanville fritillary butterfly

Fountain

Nieminen

Sirén

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…2008; Athrey et al. 2012a). Our molecular assessment of BCVI history provides a perspective that might otherwise be lacking for assessing current population trends.…”

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confidence: 99%

“…2008; Athrey et al. 2012a), mtDNA sequences (Zink et al. 2010), and nuclear gene sequences (this study).…”

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confidence: 99%

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Fluctuating fire regimes and their historical effects on genetic variation in an endangered shrubland specialist

Vázquez‐Miranda

Barr

Farquhar

et al. 2015

Ecology and Evolution

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The Pleistocene was characterized by worldwide shifts in community compositions. Some of these shifts were a result of changes in fire regimes, which influenced the distribution of species belonging to fire‐dependent communities. We studied an endangered juniper–oak shrubland specialist, the black‐capped vireo (Vireo atricapilla). This species was locally extirpated in parts of Texas and Oklahoma by the end of the 1980s as a result of habitat change and loss, predation, brood parasitism, and anthropogenic fire suppression. We sequenced multiple nuclear loci and used coalescence methods to obtain a deeper understanding of historical population trends than that typically available from microsatellites or mtDNA. We compared our estimated population history, a long‐term history of the fire regime and ecological niche models representing the mid‐Holocene, last glacial maximum, and last interglacial. Our Bayesian skyline plots showed a pattern of historical population fluctuation that was consistent with changing fire regimes. Genetic data suggest that the species is genetically unstructured, and that the current population should be orders of magnitude larger than it is at present. We suggest that fire suppression and habitat loss are primary factors contributing to the recent decline of the BCVI, although the role of climate change since the last glacial maximum is unclear at present.

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“…Similar to IM models, Approximate Bayesian Computation (ABC) modelling (Beaumont, 2010)$/ has been used to estimate past effective population sizes and bottlenecks (Husemann et al, 2015, Spurgin et al, 2014b, Athrey et al, 2012, Allentoft et al, 2014, divergence times Joseph, 2012, Barber andKlicka, 2010) and the amount of gene flow (Illera et al, 2014). In contrast to IM models, however, ABC modelling allows for the comparison of multiple scenarios that differ in the amount and timing of gene flow.…”

Section: Formation and Distribution Of Hybrid Zonesmentioning

confidence: 99%

Crossing species boundaries : the hybrid histories of the true geese

Ottenburghs¹

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. Crossing Species Boundaries: The Hybrid Histories of the True Geese. PhD thesis, Wageningen University, the Netherlands. Hybridization, the interbreeding of different species, is a common phenomenon in birds: about 16% of bird species is known to have hybridized with at least one other species. Numerous avian hybrid zones have been studied from a morphological or genetic perspective, often documenting the interspecific exchange of genetic material by hybridization and backcrossing (i.e. introgression). The incidence of hybridization varies among bird orders with the Anseriformes (waterfowl: ducks, geese and swans) showing the highest propensity to hybridize. In this thesis, I provide a genomic perspective on the role of hybridization in the evolutionary history of one particular anseriform tribe, the Anserini or "True Geese", which comprises 17 species divided over two genera: Anser and Branta . The diversification of this bird group took place in the late Pliocene and the early Pleistocene (between four and two million years ago), conceivably driven by a global cooling trend that led to the establishment of a circumpolar tundra belt and the emergence of temperate grasslands. Most species show a steady population increase during this period, followed by population subdivision during the Last Glacial Maximum about 110,000 to 12,000 years ago. The combination of large effective population sizes and occasional range shifts facilitated contact between the diverging goose species, resulting in high levels of interspecific gene flow. Introgressive hybridization might have enabled these goose populations to quickly adapt to changing environments by transferring of advantageous alleles across species boundaries, increasing standing genetic variation or expanding phenotypic variation of certain traits (e.g., beak morphology). Hybridization seems to be a common and integral component in the evolution and diversification of geese. The pervasiveness of rapid speciation and hybridization in geese complicates the attempt to capture their evolutionary history in a phylogenetic tree, therefore I advocate a phylogenetic network approach. Indeed, trying to capture the complex diversification of the True Geese in a branching tree can be regarded as a wild goose chase. Abstract TABLE OF CONTENTS

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Birds in space and time: genetic changes accompanying anthropogenic habitat fragmentation in the endangered black‐capped vireo (Vireo atricapilla)

Cited by 37 publications

References 88 publications

Predictable allele frequency changes due to habitat fragmentation in the Glanville fritillary butterfly

Predictable allele frequency changes due to habitat fragmentation in the Glanville fritillary butterfly

Fluctuating fire regimes and their historical effects on genetic variation in an endangered shrubland specialist

Crossing species boundaries : the hybrid histories of the true geese

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