Complex histories of gene flow and a mitochondrial capture event in a nonsister pair of birds

Andersen, Michael J.; McCullough, Jenna M.; Gyllenhaal, Ethan F.; Mapel, Xena Marie; Haryoko, Tri; Jønsson, Knud A.; Joseph, Leo

doi:10.1111/mec.15856

Cited by 29 publications

(25 citation statements)

References 105 publications

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“…3f , Table S3 ). This observation contradicts the hypothesis of mitochondrial introgression, though mitochondrial introgression has previously been reported with negligible signs of nuclear introgression (Good et al 2015 ; Andersen et al 2020 ). Taken together, the mitonuclear discordance can be explained by both post-divergence gene flow and ILS.…”

Section: Discussioncontrasting

confidence: 59%

“…S4 ). This paraphyly could potentially be attributable to ILS or mitochondrial introgression, and differentiating between these two scenarios remains a challenging endeavor (Holder et al 2001 ; Buckley et al 2006 but see Andersen et al 2020 ). If ILS is responsible for the observed discordance, it would require retention of shared mitochondrial haplotypes between O. t. traillii and O. t. robinsoni .…”

Section: Discussionmentioning

confidence: 99%

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Utilizing museomics to trace the complex history and species boundaries in an avian-study system of conservation concern

et al. 2022

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A taxonomic classification that accurately captures evolutionary history is essential for conservation. Genomics provides powerful tools for delimiting species and understanding their evolutionary relationships. This allows for a more accurate and detailed view on conservation status compared with other, traditionally used, methods. However, from a practical and ethical perspective, gathering sufficient samples for endangered taxa may be difficult. Here, we use museum specimens to trace the evolutionary history and species boundaries in an Asian oriole clade. The endangered silver oriole has long been recognized as a distinct species based on its unique coloration, but a recent study suggested that it might be nested within the maroon oriole-species complex. To evaluate species designation, population connectivity, and the corresponding conservation implications, we assembled a de novo genome and used whole-genome resequencing of historical specimens. Our results show that the silver orioles form a monophyletic lineage within the maroon oriole complex and that maroon and silver forms continued to interbreed after initial divergence, but do not show signs of recent gene flow. Using a genome scan, we identified genes that may form the basis for color divergence and act as reproductive barriers. Taken together, our results confirm the species status of the silver oriole and highlight that taxonomic revision of the maroon forms is urgently needed. Our study demonstrates how genomics and Natural History Collections (NHC) can be utilized to shed light on the taxonomy and evolutionary history of natural populations and how such insights can directly benefit conservation practitioners when assessing wild populations.

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Section: Discussioncontrasting

confidence: 59%

Section: Discussionmentioning

confidence: 99%

Utilizing museomics to trace the complex history and species boundaries in an avian-study system of conservation concern

et al. 2022

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“…Mito-nuclear discordance has been increasingly found in phylogeographic studies within and among conspecific populations and closely related species ( Avise et al 2016 ). This intriguing phenomenon may be caused by various biological processes, such as female-linked selection (e.g., Fossøy et al 2016 ), sex-biased dispersal (e.g., Roycroft et al 2019 ), mitochondrial capture through introgression (e.g., Andersen et al 2021 ), and invasions by reproductive parasites (e.g., Wolbachia spp., Arif et al 2021 ). In this study, mito-nuclear discordance was mainly observed in the populations located in the hybrid zone, which suggested that the hybrid populations of NMBT and HLQQ incorporating both the western and eastern genetic components detected by the nuclear data were completely grouped into the eastern lineage based on the mitochondrial data.…”

Section: Discussionmentioning

confidence: 99%

Climate Warming Since the Holocene Accelerates West–East Communication for the Eurasian Temperate Water Strider SpeciesAquarius paludum

Yuan

Damgaard

et al. 2022

Molecular Biology and Evolution

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Holocene climate warming has dramatically altered biological diversity and distributions. Recent human-induced emissions of greenhouse gases will exacerbate global warming and thus induce threats to cold-adapted taxa. However, the impacts of this major climate change on transcontinental temperate species are still poorly understood. Here, we generated extensive genomic datasets for a water strider, Aquarius paludum, which was sampled across its entire distribution in Eurasia and used these datasets in combination with ecological niche modeling (ENM) to elucidate the influence of the Holocene and future climate warming on its population structure and demographic history. We found that A. paludum consisted of two phylogeographic lineages that diverged in the middle Pleistocene, which resulted in a “west–east component” genetic pattern that was probably triggered by Central Asia-Mongoxin aridification and Pleistocene glaciations. The diverged western and eastern lineages had a second contact in the Holocene, which shaped a temporary hybrid zone located at the boundary of the arid–semiarid regions of China. Future predictions detected a potentially novel northern corridor to connect the western and eastern populations, indicating west–east gene flow would possibly continue to intensify under future warming climate conditions. Further integrating phylogeographic and ENM analyses of multiple Eurasian temperate taxa based on published studies reinforced our findings on the “west–east component” genetic pattern and the predicted future northern corridor for A. paludum. Our study provided a detailed paradigm from a phylogeographic perspective of how transcontinental temperate species differ from cold-adapted taxa in their response to climate warming.

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“…Mito-nuclear discordance is being increasingly detected in speciation studies, especially among recently diverged lineages (Andersen et al, 2021;Bonnet et al, 2017;Firneno et al, 2020;Mao & Rossiter, 2020;Toews & Brelsford, 2012). Introgression and incomplete lineage sorting (ILS) are two different processes that mainly caused phenomenon of mito-nuclear discordance.…”

Section: Chinensis and L Oratoria And Underlying Factorsmentioning

confidence: 99%

Species delimitation of rice seed bugs complex: Insights from mitochondrial genomes and ddRAD‐seq data

Xue

Zheng

et al. 2021

Zoologica Scripta

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Members of the genus Leptocorisa have for long been known as major pests of rice in the East region (China, 2009) and most Leptocorisa species feed on rice, with some species seriously damaged pest in southern China and adjoining countries (Ahmad, 1965;Hsiao et al., 1977;Litsinger et al., 2015). Rice seed bugs are one of the few pests that feed directly on developing rice spikelets in the field (Litsinger et al., 2015). It is reported that adults and nymphs suck out the developing rice grains at the

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Complex histories of gene flow and a mitochondrial capture event in a nonsister pair of birds

Abstract: This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Cited by 29 publications

References 105 publications

Utilizing museomics to trace the complex history and species boundaries in an avian-study system of conservation concern

Utilizing museomics to trace the complex history and species boundaries in an avian-study system of conservation concern

Climate Warming Since the Holocene Accelerates West–East Communication for the Eurasian Temperate Water Strider SpeciesAquarius paludum

Species delimitation of rice seed bugs complex: Insights from mitochondrial genomes and ddRAD‐seq data

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