Genomic insights into the evolutionary relationships and demographic history of kiwi
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Genomic insights into the evolutionary relationships and demographic history of kiwi. / Westbury, Michael V.; De Cahsan, Binia; Shepherd, Lara D.; Holdaway, Richard N.; Duchene, David A.; Lorenzen, Eline D.
In: PLoS ONE, Vol. 17, No. 10, e0266430, 2022.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Genomic insights into the evolutionary relationships and demographic history of kiwi
AU - Westbury, Michael V.
AU - De Cahsan, Binia
AU - Shepherd, Lara D.
AU - Holdaway, Richard N.
AU - Duchene, David A.
AU - Lorenzen, Eline D.
N1 - Publisher Copyright: © 2022 Westbury et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PY - 2022
Y1 - 2022
N2 - Kiwi are a unique and emblematic group of birds endemic to New Zealand. Deep-time evolutionary relationships among the five extant kiwi species have been difficult to resolve, in part due to the absence of pre-Quaternary fossils to inform speciation events. Here, we utilise single representative nuclear genomes of all five extant kiwi species (great spotted kiwi, little spotted kiwi, Okarito brown kiwi, North Island brown kiwi, and southern brown kiwi) and investigate their evolutionary histories with phylogenomic, genetic diversity, and deep-time (past million years) demographic analyses. We uncover relatively low levels of gene-tree phylogenetic discordance across the genomes, suggesting clear distinction between species. However, we also find indications of post-divergence gene flow, concordant with recent reports of interspecific hybrids. The four species for which unbiased levels of genetic diversity could be calculated, due to the availability of reference assemblies (all species except the southern brown kiwi), show relatively low levels of genetic diversity, which we suggest reflects a combination of older environmental as well as more recent anthropogenic influence. In addition, we suggest hypotheses regarding the impact of known past environmental events, such as volcanic eruptions and glacial periods, on the similarities and differences observed in the demographic histories of the five kiwi species over the past million years.
AB - Kiwi are a unique and emblematic group of birds endemic to New Zealand. Deep-time evolutionary relationships among the five extant kiwi species have been difficult to resolve, in part due to the absence of pre-Quaternary fossils to inform speciation events. Here, we utilise single representative nuclear genomes of all five extant kiwi species (great spotted kiwi, little spotted kiwi, Okarito brown kiwi, North Island brown kiwi, and southern brown kiwi) and investigate their evolutionary histories with phylogenomic, genetic diversity, and deep-time (past million years) demographic analyses. We uncover relatively low levels of gene-tree phylogenetic discordance across the genomes, suggesting clear distinction between species. However, we also find indications of post-divergence gene flow, concordant with recent reports of interspecific hybrids. The four species for which unbiased levels of genetic diversity could be calculated, due to the availability of reference assemblies (all species except the southern brown kiwi), show relatively low levels of genetic diversity, which we suggest reflects a combination of older environmental as well as more recent anthropogenic influence. In addition, we suggest hypotheses regarding the impact of known past environmental events, such as volcanic eruptions and glacial periods, on the similarities and differences observed in the demographic histories of the five kiwi species over the past million years.
U2 - 10.1371/journal.pone.0266430
DO - 10.1371/journal.pone.0266430
M3 - Journal article
C2 - 36215252
AN - SCOPUS:85139573045
VL - 17
JO - PLoS ONE
JF - PLoS ONE
SN - 1932-6203
IS - 10
M1 - e0266430
ER -
ID: 337657054