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  • 1
    Online Resource
    Online Resource
    Genomic and geographic diversification of a “great-speciator” ( Rhipidura rufifrons )
    Oxford University Press (OUP) ; 2023
    In:  Ornithology Vol. 140, No. 1 ( 2023-02-14)
    Details
    In: Ornithology, Oxford University Press (OUP), Vol. 140, No. 1 ( 2023-02-14)
    Abstract: The radiation of so-called “great speciators” represents a paradox among the myriad of avian radiations endemic to the southwest Pacific. In such radiations, lineages otherwise capable of dispersing across vast distances of open ocean differentiate rapidly and frequently across relatively short geographic barriers. Here, we evaluate the phylogeography of the Rufous Fantail (Rhipidura rufifrons). Although a presumed “great-speciator”, no formal investigations across its range have been performed. Moreover, delimitation of lineages within R. rufifrons, and the biogeographic implications of those relationships, remain unresolved. To investigate whether R. rufifrons represents a great speciator we identified thousands of single nucleotide polymorphisms for 89 individuals, representing 19 described taxa. Analyses recovered 7 divergent lineages and evidence of gene flow between geographically isolated populations. We also found plumage differences to be a poor proxy for evolutionary relationships. Given the relatively recent divergence dates for the clade (1.35–2.31 mya), rapid phenotypic differentiation, and evidence for multiple independent lineages within the species complex, we determine that R. rufifrons possesses the characteristics of a great speciator.
    Type of Medium: Online Resource
    ISSN: 0004-8038 , 2732-4613
    URL: Article
    DOI: 10.1093/ornithology/ukac049
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2065970-2
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Population connectivity across a highly fragmented distribution: Phylogeography of the Chalcophaps doves
    Elsevier BV ; 2022
    In:  Molecular Phylogenetics and Evolution Vol. 166 ( 2022-01), p. 107333-
    Details
    In: Molecular Phylogenetics and Evolution, Elsevier BV, Vol. 166 ( 2022-01), p. 107333-
    Type of Medium: Online Resource
    ISSN: 1055-7903
    URL: Article
    DOI: 10.1016/j.ympev.2021.107333
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2022
    detail.hit.zdb_id: 1471402-4
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    Library preparation method and DNA source influence endogenous DNA recovery from 100‐year‐old avian museum specimens
    Wiley ; 2023
    In:  Ecology and Evolution Vol. 13, No. 8 ( 2023-08)
    Details
    In: Ecology and Evolution, Wiley, Vol. 13, No. 8 ( 2023-08)
    Abstract: Museum specimens collected prior to cryogenic tissue storage are increasingly being used as genetic resources, and though high‐throughput sequencing is becoming more cost‐efficient, whole genome sequencing (WGS) of historical DNA (hDNA) remains inefficient and costly due to its short fragment sizes and high loads of exogenous DNA, among other factors. It is also unclear how sequencing efficiency is influenced by DNA sources. We aimed to identify the most efficient method and DNA source for collecting WGS data from avian museum specimens. We analyzed low‐coverage WGS from 60 DNA libraries prepared from four American Robin ( Turdus migratorius ) and four Abyssinian Thrush ( Turdus abyssinicus ) specimens collected in the 1920s. We compared DNA source (toepad versus incision‐line skin clip) and three library preparation methods: (1) double‐stranded DNA (dsDNA), single tube (KAPA); (2) single‐stranded DNA (ssDNA), multi‐tube (IDT); and (3) ssDNA, single tube (Claret Bioscience). We found that the ssDNA, multi‐tube method resulted in significantly greater endogenous DNA content, average read length, and sequencing efficiency than the other tested methods. We also tested whether a predigestion step reduced exogenous DNA in libraries from one specimen per species and found promising results that warrant further study. The ~10% increase in average sequencing efficiency of the best‐performing method over a commonly implemented dsDNA library preparation method has the potential to significantly increase WGS coverage of hDNA from bird specimens. Future work should evaluate the threshold for specimen age at which these results hold and how the combination of library preparation method and DNA source influence WGS in other taxa.
    Type of Medium: Online Resource
    ISSN: 2045-7758 , 2045-7758
    URL: Issue
    URL: Article
    DOI: 10.1002/ece3.v13.8
    DOI: 10.1002/ece3.10407
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 2635675-2
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  • 4
    Online Resource
    Online Resource
    Relationships of morphological groups in the northern flicker superspecies complex ( Colaptes auratus & C. chrysoides )
    Informa UK Limited ; 2017
    In:  Systematics and Biodiversity Vol. 15, No. 3 ( 2017-05-04), p. 183-191
    Details
    In: Systematics and Biodiversity, Informa UK Limited, Vol. 15, No. 3 ( 2017-05-04), p. 183-191
    Type of Medium: Online Resource
    ISSN: 1477-2000 , 1478-0933
    URL: Article
    DOI: 10.1080/14772000.2016.1238020
    Language: English
    Publisher: Informa UK Limited
    Publication Date: 2017
    detail.hit.zdb_id: 2110629-0
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Multiple and Independent Phases of Transposable Element Amplification in the Genomes of Piciformes (Woodpeckers and Allies)
    Oxford University Press (OUP) ; 2018
    In:  Genome Biology and Evolution Vol. 10, No. 6 ( 2018-06-01), p. 1445-1456
    Details
    In: Genome Biology and Evolution, Oxford University Press (OUP), Vol. 10, No. 6 ( 2018-06-01), p. 1445-1456
    Type of Medium: Online Resource
    ISSN: 1759-6653
    URL: Article
    DOI: 10.1093/gbe/evy105
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2018
    detail.hit.zdb_id: 2495328-3
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  • 6
    Online Resource
    Online Resource
    The Genomic Signature of Allopatric Speciation in a Songbird Is Shaped by Genome Architecture (Aves: Certhia americana )
    Oxford University Press (OUP) ; 2021
    In:  Genome Biology and Evolution Vol. 13, No. 8 ( 2021-08-03)
    Details
    In: Genome Biology and Evolution, Oxford University Press (OUP), Vol. 13, No. 8 ( 2021-08-03)
    Abstract: The genomic signature of speciation with gene flow is often attributed to the strength of divergent selection and recombination rate in regions harboring targets for selection. In contrast, allopatric speciation provides a different geographic context and evolutionary scenario, whereby introgression is limited by isolation rather than selection against gene flow. Lacking shared divergent selection or selection against hybridization, we would predict the genomic signature of allopatric speciation would largely be shaped by genomic architecture—the nonrandom distribution of functional elements and chromosomal characteristics—through its role in affecting the processes of selection and drift. Here, we built and annotated a chromosome-scale genome assembly for a songbird (Passeriformes: Certhia americana). We show that the genomic signature of allopatric speciation between its two primary lineages is largely shaped by genomic architecture. Regionally, gene density and recombination rate variation explain a large proportion of variance in genomic diversity, differentiation, and divergence. We identified a heterogeneous landscape of selection and neutrality, with a large portion of the genome under the effects of indirect selection. We found higher proportions of small chromosomes under the effects of indirect selection, likely because they have relatively higher gene density. At the chromosome scale, differential genomic architecture of macro- and microchromosomes shapes the genomic signatures of speciation: chromosome size has: 1) a positive relationship with genetic differentiation, genetic divergence, rate of lineage sorting in the contact zone, and proportion neutral evolution and 2) a negative relationship with genetic diversity and recombination rate.
    Type of Medium: Online Resource
    ISSN: 1759-6653
    URL: Article
    DOI: 10.1093/gbe/evab120
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2495328-3
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  • 7
    Online Resource
    Online Resource
    A genomic investigation of the putative contact zone between divergent Brown Creeper ( Certhia americana ) lineages: chromosomal patterns of genetic differentiation
    Canadian Science Publishing ; 2016
    In:  Genome Vol. 59, No. 2 ( 2016-02), p. 115-125
    Details
    In: Genome, Canadian Science Publishing, Vol. 59, No. 2 ( 2016-02), p. 115-125
    Abstract: Sky islands, or montane forest separated by different lowland habitats, are highly fragmented regions that potentially limit gene flow between isolated populations. In the sky islands of the Madrean Archipelago (Arizona, USA), various taxa display different phylogeographic patterns, from unrestricted gene flow among sky islands to complex patterns with multiple distinct lineages. Using genomic-level approaches allows the investigation of differential patterns of gene flow, selection, and genetic differentiation among chromosomes and specific genomic regions between sky island populations. Here, we used thousands of SNPs to investigate the putative contact zone of divergent Brown Creeper (Certhia americana) lineages in the Madrean Archipelago sky islands. We found the two lineages to be completely allopatric (during the breeding season) with a lack of hybridization and gene flow between lineages and no genetic structure among sky islands within lineages. Additionally, the two lineages inhabit different climatic and ecosystem conditions and have many local primary song dialects in the southern Arizona mountain ranges. We identified a positive relationship between genetic differentiation and chromosome size, but the sex chromosome (Z) was not found to be an outlier. Differential patterns of genetic differentiation per chromosome may be explained by genetic drift—possibly in conjunction with non-random mating and non-random gene flow—due to variance in recombination rates among chromosomes.
    Type of Medium: Online Resource
    ISSN: 0831-2796 , 1480-3321
    URL: Article
    DOI: 10.1139/gen-2015-0093
    Language: English
    Publisher: Canadian Science Publishing
    Publication Date: 2016
    detail.hit.zdb_id: 2020635-5
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  • 8
    Online Resource
    Online Resource
    Diversification in wild populations of the model organism Anolis carolinensis : A genome‐wide phylogeographic investigation
    Wiley ; 2016
    In:  Ecology and Evolution Vol. 6, No. 22 ( 2016-11), p. 8115-8125
    Details
    In: Ecology and Evolution, Wiley, Vol. 6, No. 22 ( 2016-11), p. 8115-8125
    Abstract: The green anole ( Anolis carolinensis ) is a lizard widespread throughout the southeastern United States and is a model organism for the study of reproductive behavior, physiology, neural biology, and genomics. Previous phylogeographic studies of A. carolinensis using mitochondrial DNA and small numbers of nuclear loci identified conflicting and poorly supported relationships among geographically structured clades; these inconsistencies preclude confident use of A. carolinensis evolutionary history in association with morphological, physiological, or reproductive biology studies among sampling localities and necessitate increased effort to resolve evolutionary relationships among natural populations. Here, we used anchored hybrid enrichment of hundreds of genetic markers across the genome of A. carolinensis and identified five strongly supported phylogeographic groups. Using multiple analyses, we produced a fully resolved species tree, investigated relative support for each lineage across all gene trees, and identified mito‐nuclear discordance when comparing our results to previous studies. We found fixed differences in only one clade—southern Florida restricted to the Everglades region—while most polymorphisms were shared between lineages. The southern Florida group likely diverged from other populations during the Pliocene, with all other diversification during the Pleistocene. Multiple lines of support, including phylogenetic relationships, a latitudinal gradient in genetic diversity, and relatively more stable long‐term population sizes in southern phylogeographic groups, indicate that diversification in A. carolinensis occurred northward from southern Florida.
    Type of Medium: Online Resource
    ISSN: 2045-7758 , 2045-7758
    URL: Issue
    URL: Article
    DOI: 10.1002/ece3.2016.6.issue-22
    DOI: 10.1002/ece3.2547
    Language: English
    Publisher: Wiley
    Publication Date: 2016
    detail.hit.zdb_id: 2635675-2
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  • 9
    Online Resource
    Online Resource
    Impact of host demography and evolutionary history on endosymbiont molecular evolution: A test in carpenter ants (genus Camponotus ) and their Blochmannia endosymbionts
    Wiley ; 2022
    In:  Ecology and Evolution Vol. 12, No. 7 ( 2022-07)
    Details
    In: Ecology and Evolution, Wiley, Vol. 12, No. 7 ( 2022-07)
    Abstract: Obligate endosymbioses are tight associations between symbionts and the hosts they live inside. Hosts and their associated obligate endosymbionts generally exhibit codiversification, which has been documented in taxonomically diverse insect lineages. Host demography (e.g., effective population sizes) may impact the demography of endosymbionts, which may lead to an association between host demography and the patterns and processes of endosymbiont molecular evolution. Here, we used whole‐genome sequencing data for carpenter ants (Genus Camponotus; subgenera Camponotus and Tanaemyrmex ) and their Blochmannia endosymbionts as our study system to address whether Camponotus demography shapes Blochmannia molecular evolution. Using whole‐genome phylogenomics, we confirmed previous work identifying codiversification between carpenter ants and their Blochmannia endosymbionts. We found that Blochmannia genes have evolved at a pace ~30× faster than that of their hosts' molecular evolution and that these rates are positively associated with host rates of molecular evolution. Using multiple tests for selection in Blochmannia genes, we found signatures of positive selection and shifts in selection strength across the phylogeny. Host demography was associated with Blochmannia shifts toward increased selection strengths, but not associated with Blochmannia selection relaxation, positive selection, genetic drift rates, or genome size evolution. Mixed support for relationships between host effective population sizes and Blochmannia molecular evolution suggests weak or uncoupled relationships between host demography and Blochmannia population genomic processes. Finally, we found that Blochmannia genome size evolution was associated with genome‐wide estimates of genetic drift and number of genes with relaxed selection pressures.
    Type of Medium: Online Resource
    ISSN: 2045-7758 , 2045-7758
    URL: Issue
    URL: Article
    DOI: 10.1002/ece3.v12.7
    DOI: 10.1002/ece3.9026
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2635675-2
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  • 10
    Online Resource
    Online Resource
    Supplemental Information 1: Supplementary figures and tables.
    PeerJ ; 2017
    In:  PeerJ Vol. 5 ( 2017-05-18), p. e3335-
    Details
    In: PeerJ, PeerJ, Vol. 5 ( 2017-05-18), p. e3335-
    Abstract: Topographically complex regions often contain the close juxtaposition of closely related species along elevational gradients. The evolutionary causes of these elevational replacements, and thus the origin and maintenance of a large portion of species diversity along elevational gradients, are usually unclear because ecological differentiation along a gradient or secondary contact following allopatric diversification can produce the same pattern. We used reduced representation genomic sequencing to assess genetic relationships and gene flow between three parapatric pairs of closely related songbird taxa ( Arachnothera spiderhunters, Chloropsis leafbirds, and Enicurus forktails) along an elevational gradient in Borneo. Each taxon pair presents a different elevational range distribution across the island, yet results were uniform: little or no gene flow was detected in any pairwise comparisons. These results are congruent with an allopatric “species-pump” model for generation of species diversity and elevational parapatry of congeners on Borneo, rather than in situ generation of species by “ecological speciation” along an elevational gradient.
    Type of Medium: Online Resource
    ISSN: 2167-8359
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.7717/peerj.3335
    DOI: 10.7717/peerj.3335/fig-1
    DOI: 10.7717/peerj.3335/fig-2
    DOI: 10.7717/peerj.3335/fig-3
    DOI: 10.7717/peerj.3335/fig-4
    DOI: 10.7717/peerj.3335/table-1
    DOI: 10.7717/peerj.3335/table-2
    DOI: 10.7717/peerj.3335/supp-1
    Language: English
    Publisher: PeerJ
    Publication Date: 2017
    detail.hit.zdb_id: 2703241-3
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