Using historical genome‐wide DNA to unravel the confused taxonomy in a songbird lineage that is extinct in the wild

Baveja, Pratibha; Garg, Kritika M.; Chattopadhyay, Balaji; Sadanandan, Keren R.; Prawiradilaga, Dewi M.; Yuda, Pramana; Lee, Jessica G.H.

doi:10.1111/eva.13149

Cited by 14 publications

(10 citation statements)

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“…Target enrichment protocols have been shown to be highly effective at capturing historical DNA for phylogenomic studies ( Bryson et al, 2016 ; van der Valk et al, 2017 ; Chattopadhyay et al, 2019 ; Baveja et al, 2020 ). We designed loci specifically targeting both conserved exons and variable intronic regions of the Zosterops genome ( Chattopadhyay et al, 2019 ).…”

Section: Methodsmentioning

confidence: 99%

Phylogenomics of white-eyes, a ‘great speciator’, reveals Indonesian archipelago as the center of lineage diversity

Gwee

Garg

Chattopadhyay

et al. 2020

eLife

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Archipelagoes serve as important ‘natural laboratories’ which facilitate the study of island radiations and contribute to the understanding of evolutionary processes. The white-eye genus Zosterops is a classical example of a ‘great speciator’, comprising c. 100 species from across the Old World, most of them insular. We achieved an extensive geographic DNA sampling of Zosterops by using historical specimens and recently collected samples. Using over 700 genome-wide loci in conjunction with coalescent species tree methods and gene flow detection approaches, we untangled the reticulated evolutionary history of Zosterops, which comprises three main clades centered in Indo-Africa, Asia, and Australasia, respectively. Genetic introgression between species permeates the Zosterops phylogeny, regardless of how distantly related species are. Crucially, we identified the Indonesian archipelago, and specifically Borneo, as the major center of diversity and the only area where all three main clades overlap, attesting to the evolutionary importance of this region.

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Section: Methodsmentioning

confidence: 99%

Phylogenomics of white-eyes, a ‘great speciator’, reveals Indonesian archipelago as the center of lineage diversity

Gwee

Garg

Chattopadhyay

et al. 2020

eLife

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“…In sixteen visits, we made a more detailed morphological assessment to establish what proportion of the trade comprised jalla-type bird and flowerior contra-type birds, involving a total of 1613 birds (Table 1). Morphologically these species are recognizable by the extent of bare red/orange facial skin and eye color [13].…”

Section: Discussionmentioning

confidence: 99%

“…Planning a reintroduction program for the species following release protocols approved by international bodies first requires proper research on the species' in situ status, genetic load, and original range distribution, along with good understanding of the events behind the extinction of the Javan pied starling in nature. The first steps in this process have already been taken [13,14], and in east Java, the Prigen Conservation Breeding Ark, a collaborative breeding project in which, amongst others, Taman Safari Indonesia participates, has been established with the aim of setting up an insurance population for future release.…”

Section: Role Of Zoos In the Conservation Of Javan Pied Starlingmentioning

confidence: 99%

“…Baveja et al [13] and van Balen and Collar [14] set out the case that the Javan pied starling Gracupica jalla is a distinct species that is extinct in the wild. Baveja et al [13], using historic and contemporary genetic samples, provided support for the recognition of G. jalla from Java and Bali as distinct from other pied starling species from mainland Asia (G. floweri, G. contra, G. supercilliaris: pied starlings do not occur on the Thai-Malay Peninsula, Borneo, and most of Sumatra, and G. jalla is geographically isolated). Previously considered part of a wide ranged Asian pied starling complex, in 2016 its IUCN threat status was assessed as Critically Endangered [15].…”

Section: Introductionmentioning

confidence: 99%

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Large-Scale Trade in a Songbird That Is Extinct in the Wild

et al. 2021

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Indonesia is at the epicenter of the Asian Songbird Crisis, i.e., the recognition that the cage bird trade has a devastating impact on numerous imperiled bird species in Asia. The Javan pied starling Gracupica jalla, only in the last five years recognized as distinct from the pied starlings of mainland Southeast Asia, has been declared extinct the wild in 2021. Up until the 1980s, it used to be one of the most common open countryside birds on the islands of Java and Bali, Indonesia. From the early 2000s onwards, the species is commercially bred to meet the demand from the domestic cagebird trade. We conducted 280 market surveys in 25 bird markets in Java and Bali between April 2014 and March 2020, with 15 markets being surveyed at least six times. We recorded 24,358 Javan pied starlings, making it one of the most commonly observed birds in the markets. We established that, conservatively, around 40% of the birds in the market were sold within one week and used this to estimate that at a minimum ~80,000 Javan pied starlings are sold in the bird markets on Java and Bali. The latter represents a monetary value of USD 5.2 million. We showed that prices were low in the 1980s, when all birds were sourced from the wild. It became more varied and differentiated in the 2000s when a combination of now expensive wild-caught and cheaper captive-bred birds were offered for sale, and prices stabilized in the 2010s when most, if not all birds were commercially captive-bred. Javan pied starlings are not protected under Indonesian law, and there are no linked-up conservation efforts in place to re-establish a wild population on the islands, although small-scale releases do take place.

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“…Frandsen et al 2020;Robinson et al 2021a) and delineating management units (Barbosa et al 2018) starting from almost any type of sample (e.g. museum collections and biobanks; Baveja et al 2020). Likewise, the inclusion of species specific genomic analysis generates unseen possibilities to reach predefined long-term conservation goals whether that is to e.g.…”

Section: Defining Ex Situ Populations and Their Relationship To In Situ Populations Using Genomicsmentioning

confidence: 99%

New developments in the field of genomic technologies and their relevance to conservation management

et al. 2021

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Recent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for conservation applications. Many of these tools are well developed and used by other life science fields, while others are still in development. Considering these technological possibilities, choosing the right tool(s) from the toolbox is crucial and can pose a challenging task. With this in mind, we strive to inspire, inform and illuminate managers and practitioners on how conservation efforts can benefit from the current genomic and biotechnological revolution. With inspirational case studies we show how new technologies can help resolve some of the main conservation challenges, while also informing how implementable the different technologies are. We here focus specifically on small population management, highlight the potential for genetic rescue, and discuss the opportunities in the field of gene editing to help with adaptation to changing environments. In addition, we delineate potential applications of gene drives for controlling invasive species. We illuminate that the genomic toolbox offers added benefit to conservation efforts, but also comes with limitations for the use of these novel emerging techniques.

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Using historical genome‐wide DNA to unravel the confused taxonomy in a songbird lineage that is extinct in the wild

Cited by 14 publications

References 109 publications

Phylogenomics of white-eyes, a ‘great speciator’, reveals Indonesian archipelago as the center of lineage diversity

Phylogenomics of white-eyes, a ‘great speciator’, reveals Indonesian archipelago as the center of lineage diversity

Large-Scale Trade in a Songbird That Is Extinct in the Wild

New developments in the field of genomic technologies and their relevance to conservation management

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