A distinct new subspecies of the white-rumped shama Copsychus malabaricus at imminent risk of extinction

Wu, Meng Yue; Rheindt, Frank E.

doi:10.1007/s10336-022-01977-2

Cited by 1 publication

(7 citation statements)

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“…We prepared whole-genome libraries for a total of 60 individuals ( supplementary table S2, Supplementary Material online) to generate genomes at a mean coverage of 8×, spanning 14 out of the 15 widely recognized taxa of the white-rumped shama complex following the taxonomy of Roberts et al (2020) plus the newly described taxon ngae ( Wu and Rheindt 2022 ), making for a total of 15 sampled taxa. The only missing form was the long-extinct taxon mirabilis from tiny Panaitan Island near Java, for which we were not able to source historic DNA material.…”

Section: Resultsmentioning

confidence: 99%

“…The members of the white-rumped shama Copsychus malabaricus complex constitute a songbird radiation that is assumed to be relatively well-inventoried in taxonomic terms, although species boundaries have been shifting somewhat among the 16 taxa widely recognized in this complex (including 15 traditional ones and one recently described to science, ngae ; Wu and Rheindt 2022 ) ( supplementary table S1, Supplementary Material online). They are widely known across Asia for their melodious songs and striking plumages, and range among the most popular cagebirds in the Southeast Asian and global bird trade ( Nash 1993 ).…”

Section: Introductionmentioning

confidence: 99%

“…Currently, the International Union for the Conservation of Nature (IUCN) classifies all recognized species of this complex as of “Least Concern” ( BirdLife International 2021 ). However, member taxa in Southeast Asia are reported to be in rapid decline, with some populations on the brink of extinction or even extirpated due to a steep rise in trade and habitat loss over <2 decades ( Eaton et al 2015 , 2016 ; Irham 2016 ; Rheindt et al 2019 ; Wu and Rheindt 2022 ). The species complex is therefore listed among the top 12 priority groups for conservation by IUCN’s Asian Songbird Trade Specialist Group ( Lee et al 2016 ).…”

Section: Introductionmentioning

confidence: 99%

“…Previous phylogenetic work on the C. malabaricus complex has only included a subset of taxa, with full resolution still outstanding ( Lim et al 2010 , 2017 ; Sangster et al 2010 ; Chua et al 2015 ; Wu and Rheindt 2022 ). Most prior work has relied on the signal of few DNA markers, chiefly restricted to the mitochondrion ( Lim et al 2010 ; Sangster et al 2010 ; Chua et al 2015 ), with all the associated susceptibility to artifacts of genetic introgression and single-marker phylogenetics ( Ballard and Whitlock 2004 ; Hurst and Jiggins 2005 ; Rheindt et al 2009 ; Rheindt and Edwards 2011 ).…”

Section: Introductionmentioning

confidence: 99%

“…Most prior work has relied on the signal of few DNA markers, chiefly restricted to the mitochondrion ( Lim et al 2010 ; Sangster et al 2010 ; Chua et al 2015 ), with all the associated susceptibility to artifacts of genetic introgression and single-marker phylogenetics ( Ballard and Whitlock 2004 ; Hurst and Jiggins 2005 ; Rheindt et al 2009 ; Rheindt and Edwards 2011 ). The only studies using genome-wide sequencing methods exhibited a restricted sampling regime limited to 3–9 out of 16 taxa ( Lim et al 2017 ; Wu and Rheindt 2022 ).…”

Section: Introductionmentioning

confidence: 99%

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Genomes From Historic DNA Unveil Massive Hidden Extinction and Terminal Endangerment in a Tropical Asian Songbird Radiation

Lau

et al. 2022

Molecular Biology and Evolution

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Quantifying the magnitude of the global extinction crisis is important but remains challenging, as many extinction events pass unnoticed owing to our limited taxonomic knowledge of the world’s organisms. The increasing rarity of many taxa renders comprehensive sampling difficult, further compounding the problem. Vertebrate lineages such as birds, which are thought to be taxonomically well understood, are therefore used as indicator groups for mapping and quantifying global extinction. To test whether extinction patterns are adequately gauged in well-studied groups, we implemented ancient-DNA protocols and retrieved whole genomes from the historic DNA of museum specimens in a widely known songbird radiation of shamas (genus Copsychus) that is assumed to be of least conservation concern. We uncovered cryptic diversity and an unexpected degree of hidden extinction and terminal endangerment. Our analyses reveal that >40% of the phylogenetic diversity of this radiation is already either extinct in the wild or nearly so, including the two genomically most distinct members of this group (omissus and nigricauda), which have so far flown under the conservation radar as they have previously been considered subspecies. Comparing the genomes of modern samples with those from roughly a century ago, we also found a significant decrease in genetic diversity and a concomitant increase in homozygosity affecting various taxa, including small-island endemics that are extinct in the wild as well as subspecies that remain widespread across the continental scale. Our application of modern genomic approaches demonstrates elevated levels of allelic and taxonomic diversity loss in a songbird clade that has not been listed as globally threatened, highlighting the importance of ongoing reassessments of extinction incidence even across well-studied animal groups. Key words: extinction, introgression, white-rumped shama, conservation.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%