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

Abstract

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.

When birds of a feather flock together: Severe genomic erosion and the implications for genetic rescue in an endangered island passerine

“…We draw attention to the Fregate Island population (Figure 5b–d ), which did not suffer extirpation and serve as the founder population for all modern populations. While the historical heterozygosity estimates are low compared to those obtained from museum samples of other Copsychus species (Ng et al., 2017 ; Wu et al., 2022 ), heterozygosity is evenly distributed across the genome in our oldest pre‐bottleneck sample (Figure 5b ). In contrast, the sample from the bottleneck period reveals extended regions of reduced heterozygosity (Figure 5c ), and these regions are further extended along the genome in the post‐bottleneck sample (Figure 5d ).…”

Never judge a bird by its feathers: genetics unveils the true target of trafficking in morphologically similarCopsychusspecies

“…superciliaris, Lim et al 2010). More recently, through the generation of wholegenome re-sequencing data, Wu et al (2022) identified four full species within the existing C. malabaricus group. This has also created an extensive genomic database against which to test future cases of illegal poaching/trafficking of this recently CITES II listed species (CITES, 2023).…”

Library preparation method and DNA source influence endogenous DNA recovery from 100-year-old avian museum specimens

“…Now museum specimens commonly facilitate genomic studies via reduced representation (Bi et al, 2013; Linck, Hanna, Sellas, & Dumbacher, 2017; McCormack, Tsai, & Faircloth, 2016) and even whole genome sequencing (e.g. van der Valk, Díez-del-Molino, Marques-Bonet, Guschanski, & Dalén, 2019; Wu et al, 2022). Despite its increasing prevalence and dropping cost, sequencing whole genomes of museum specimens remains expensive because of the degraded nature of the historical DNA (hDNA).…”