Aberrantly plumaged orioles from the Trans-Fly savannas of New Guinea and their ecological and evolutionary significance

Joseph, Leo; Dolman, Gaynor; Iova, Bulisa; Jønsson, Knud A.; Campbell, Catriona D.; Mason, Ian J.; Drew, Alex

doi:10.1080/01584197.2019.1605831

Cited by 8 publications

(3 citation statements)

References 19 publications

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“…To our knowledge, this study is the first to comprehensively test the hypothesis of introgression across the Arafura Shelf using genome‐wide SNPs from whole‐genome resequencing (Joseph, Bishop, et al, 2019; Joseph, Dolman, et al, 2019; Kearns et al, 2014), although several studies have investigated patterns of gene flow in this region with other data types, especially mtDNA and RADseq (Andersen et al, 2021; Dorrington et al, 2020; Edwards, 1993a; Joseph, Bishop, et al, 2019; Kearns et al, 2011, 2014; Lamb et al, 2019; Peñalba et al, 2019; Toon et al, 2017). Species histories of other Australo‐Papuan taxa might also be shaped by reticulate evolution around the ancient Lake Carpentaria.…”

Section: Discussionmentioning

confidence: 99%

Whole‐genome phylogeography of the blue‐faced honeyeater (Entomyzon cyanotis) and discovery and characterization of a neo‐Z chromosome

et al. 2022

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Whole‐genome surveys of genetic diversity and geographic variation often yield unexpected discoveries of novel structural variation, which long‐read DNA sequencing can help clarify. Here, we report on whole‐genome phylogeography of a bird exhibiting classic vicariant geographies across Australia and New Guinea, the blue‐faced honeyeater (Entomyzon cyanotis), and the discovery and characterization of a novel neo‐Z chromosome by long‐read sequencing. Using short‐read genome‐wide SNPs, we inferred population divergence events within E. cyanotis across the Carpentarian and other biogeographic barriers during the Pleistocene (~0.3–1.7 Ma). Evidence for introgression between nonsister populations supports a hypothesis of reticulate evolution around a triad of dynamic barriers around Pleistocene Lake Carpentaria between Australia and New Guinea. During this phylogeographic survey, we discovered a large (134 Mbp) neo‐Z chromosome and we explored its diversity, divergence and introgression landscape. We show that, as in some sylvioid passerine birds, a fusion occurred between chromosome 5 and the Z chromosome to form a neo‐Z chromosome; and in E. cyanotis, the ancestral pseudoautosomal region (PAR) appears nonrecombinant between Z and W, along with most of the fused chromosome 5. The added recombination‐suppressed portion of the neo‐Z (~37.2 Mbp) displays reduced diversity and faster population genetic differentiation compared with the ancestral‐Z. Yet, the new PAR (~17.4 Mbp) shows elevated diversity and reduced differentiation compared to autosomes, potentially resulting from introgression. In our case, long‐read sequencing helped clarify the genomic landscape of population divergence on autosomes and sex chromosomes in a species where prior knowledge of genome structure was still incomplete.

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Section: Discussionmentioning

confidence: 99%

Whole‐genome phylogeography of the blue‐faced honeyeater (Entomyzon cyanotis) and discovery and characterization of a neo‐Z chromosome

et al. 2022

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“…One, a focused study of mitochondrial DNA diversity in a suite of New Guinean birds, shows how much remains to be learned even of their basic taxonomy (Jønsson et al 2019). Two others (Joseph et al 2019a(Joseph et al , 2019b emphasise that the birds of New Guinean savannahs, despite having been reasonably well inventoried, are among the least-studied avifaunas in the entire region and still hold many surprises.…”

Section: Faunistics Systematics and Biogeographymentioning

confidence: 99%

Ornithology of New Guinea and the Indo-Pacific Islands: introduction to the special issue ofEmu – Austral Ornithologyand a dedication to Paul Igag

Joseph

Heinsohn

Mack

2019

Emu - Austral Ornithology

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“…Phuong et al, 2017), generating conflicting patterns across the genome and making it difficult to identify causative links between pattern and process. Most cases confidently associating mitonuclear discordance with an underlying evolutionary process involve dramatic discordance caused by mitochondrial capture (Andersen et al, 2021; Joseph et al, 2021; Kearns et al, 2014; McElroy et al, 2020; Mikkelsen & Weir, 2022), directional introgression across a hybrid zone (Del‐Rio et al, 2022) or recent hybridization resulting in mismatched mitochondrial and nuclear genomes in a single individual (Joseph et al, 2019; Joseph & Moritz, 1993). In contrast, few studies have identified mitonuclear discordance resulting mainly from ILS (except see Firneno et al, 2020; Wang et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers

et al. 2023

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Many organisms possess multiple discrete genomes (i.e. nuclear and organellar), which are inherited separately and may have unique and even conflicting evolutionary histories. Phylogenetic reconstructions from these discrete genomes can yield different patterns of relatedness, a phenomenon known as cytonuclear discordance. In many animals, mitonuclear discordance (i.e. discordant evolutionary histories between the nuclear and mitochondrial genomes) has been widely documented, but its causes are often considered idiosyncratic and inscrutable. We show that a case of mitonuclear discordance in Todiramphus kingfishers can be explained by extensive genome‐wide incomplete lineage sorting (ILS), likely a result of the explosive diversification history of this genus. For these kingfishers, quartet frequencies reveal that the nuclear genome is dominated by discordant topologies, with none of the internal branches in our consensus nuclear tree recovered in >50% of genome‐wide gene trees. Meanwhile, a lack of inter‐species shared ancestry, non‐significant pairwise tests for gene flow, and little evidence for meaningful migration edges between species, leads to the conclusion that gene flow cannot explain the mitonuclear discordance we observe. This lack of evidence for gene flow combined with evidence for extensive genome‐wide gene tree discordance, a hallmark of ILS, leads us to conclude that the mitonuclear discordance we observe likely results from ILS, specifically deep coalescence of the mitochondrial genome. Based on this case study, we hypothesize that similar demographic histories in other ‘great speciator’ taxa across the Indo‐Pacific likely predispose these groups to high levels of ILS and high likelihoods of mitonuclear discordance.

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Aberrantly plumaged orioles from the Trans-Fly savannas of New Guinea and their ecological and evolutionary significance

Cited by 8 publications

References 19 publications

Whole‐genome phylogeography of the blue‐faced honeyeater (Entomyzon cyanotis) and discovery and characterization of a neo‐Z chromosome

Whole‐genome phylogeography of the blue‐faced honeyeater (Entomyzon cyanotis) and discovery and characterization of a neo‐Z chromosome

Ornithology of New Guinea and the Indo-Pacific Islands: introduction to the special issue ofEmu – Austral Ornithologyand a dedication to Paul Igag

Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers

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