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  1. Matsui M, Hamidy A, Murphy RW, Khonsue W, Yambun P, Shimada T, et al.
    Mol Phylogenet Evol, 2010 Jul;56(1):259-72.
    PMID: 20302957 DOI: 10.1016/j.ympev.2010.03.014
    By investigating genealogical relationships, we estimated the phylogenetic history and biogeography in the megophryid genus Leptobrachium (sensu lato, including Vibrissaphora) from southern China, Indochina, Thailand and the Sundaland. The genealogical relationships among the 30 named and unnamed taxa were estimated using 2009 bp of sequences from the mitochondrial DNA genes 12S rRNA, tRNA(val), and 16S rRNA using maximum parsimony, maximum likelihood, and Bayesian inference methods. The genus Leptobrachium was a well-supported monophyletic group that contained two major clades. One clade had three subclades primarily from disjunct regions including Borneo, Peninsular Malaysia and Java, and Thailand. The Bornean subclade included one species each from the Philippines and Sumatra. The other major clade consisted of two subclades, one from Indochina and the other from southern China (Vibrissaphora). Divergence times estimated an old evolutionary history of each subclade, one that could not be explained by the geohistory of Southeast Asian major landmasses.
  2. Borzée A, Kielgast J, Wren S, Angulo A, Chen S, Magellan K, et al.
    Biol Conserv, 2021 Mar;255:108973.
    PMID: 35125500 DOI: 10.1016/j.biocon.2021.108973
    Emerging infectious diseases are on the rise in many different taxa, including, among others, the amphibian batrachochytrids, the snake fungal disease and the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) virus, responsible for Coronavirus disease 2019 (COVID-19) in mammals. Following the onset of the pandemic linked to COVID-19, eastern Asia has shown strong leadership, taking actions to regulate the trade of potential vector species in several regions. These actions were taken in response to an increase in public awareness, and the need for a quick reaction to mitigate against further pandemics. However, trade restrictions rarely affect amphibians, despite the risk of pathogen transmission, directly, or indirectly through habitat destruction and the loss of vector consumption. Thus, species that help alleviate the risk of zoonoses or provide biological control are not protected. Hence, in view of the global amphibian decline and the risk of zoonoses, we support the current wildlife trade regulations and support measures to safeguard wildlife from overexploitation. The current period of regulation overhaul should be used as a springboard for amphibian conservation. To mitigate risks, we suggest the following stipulations specifically for amphibians. I) Restrictions to amphibian farming in eastern Asia, in relation to pathogen transmission and the establishment of invasive species. II) Regulation of the amphibian pet trade, with a focus on potential vector species. III) Expansion of the wildlife trade ban, to limit the wildlife-human-pet interface. The resulting actions will benefit both human and wildlife populations, as they will lead to a decrease in the risk of zoonoses and better protection of the environment.

    SIGNIFICANCE STATEMENT: There is an increasing number of emerging infectious diseases impacting all species, including amphibians, reptiles and mammals. The latest threat to humans is the virus responsible for COVID-19, and the resulting pandemic. Countries in eastern Asia have taken steps to regulate wildlife trade and prevent further zoonoses thereby decreasing the risk of pathogens arising from wild species. However, as amphibians are generally excluded from regulations we support specific trade restrictions: I) Restrictions to amphibian farming; II) regulation of the amphibian pet trade; III) expansion of the wildlife trade ban. These restrictions will benefit both human and wildlife populations by decreasing the risks of zoonoses and better protecting the environment.

  3. Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, et al.
    Nature, 2021 Apr;592(7856):737-746.
    PMID: 33911273 DOI: 10.1038/s41586-021-03451-0
    High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.
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