Pangolin Genomes Offer Key Insights and Resources for the World's Most Trafficked Wild Mammals

Pangolins form a group of scaly mammals that are trafficked at record numbers for their meat and purported medicinal properties. Despite their conservation concern, knowledge of their evolution is limited by a paucity of genomic data. We aim to produce exhaustive genomic resources that include 3,238 orthologous genes and whole-genome polymorphisms to assess the evolution of all eight extant pangolin species. Robust orthologous gene-based phylogenies recovered the monophyly of the three genera and highlighted the existence of an undescribed species closely related to Southeast Asian pangolins. Signatures of middle Miocene admixture between an extinct, possibly European, lineage and the ancestor of Southeast Asian pangolins, provide new insights into the early evolutionary history of the group. Demographic trajectories and genome-wide heterozygosity estimates revealed contrasts between continental versus island populations and species lineages, suggesting that conservation planning should consider intraspecific patterns. With the expected loss of genomic diversity from recent, extensive trafficking not yet realized in pangolins, we recommend that populations be genetically surveyed to anticipate any deleterious impact of the illegal trade. Finally, we produce a complete set of genomic resources that will be integral for future conservation management and forensic endeavors for pangolins, including tracing their illegal trade. These comprise the completion of whole-genomes for pangolins through the hybrid assembly of the first reference genome for the giant pangolin (Smutsia gigantea) and new draft genomes (∼43x-77x) for four additional species, as well as a database of orthologous genes with over 3.4 million polymorphic sites.

How was genetic diversity transferred with translocations from ex situ to in situ? A case study of the European mink translocation to Hiiumaa Island in Estonia

The European mink (Mustela lutreola) is one of the most threatened small carnivores, listed as Critically Endangered on the IUCN Red List. Tallinn Zoo started a conservation breeding operation in 1980, which in 1992 was shaped into the European mink EEP Program to maintain a demographically and genetically healthy population in captivity. Since 2000, mink have been translocated on a yearly basis from the breeding facility in the zoo to Hiiumaa Island (Estonia) until the formation of the wild island population in 2016. Maintaining a healthy genetic structure in a captive population was a priority, so genetically the least valuable animals, according to calculations made by a population management program, were used for translocation. This study aims to assess the amount of genetic diversity passed from an ex situ population on to the island population. Comparisons of the genetic diversity were made by mitochondrial, microsatellite and nuclear markers. In addition, our results were combined with the pedigree data from the European mink EEP Studbook to further evaluate the flow of genetic diversity from the founder population to the established wild population. According to the findings, the island population's allelic richness was comparable to that of the founder population, and no evidence was found that its genetic structure had diverged from that of the founder population. It seems that the formation of the island population has been a gradual process of no more than the last seven yearly translocations.

Phylogeography of the Siberian weasel (Mustela sibirica), based on a mitochondrial DNA analysis

We investigated the genetic diversity and distribution pattern of mitochondrial DNA control-region haplotypes across the distributional range of the Siberian weasel (Mustela sibirica) in Eastern Eurasia. We identified 23 haplotypes from 65 individuals sampled from 21 localities. Our analyses showed two major phylogeographical groups: group I comprised continental Russia, Tsushima and Korea, and group II comprised China, Taiwan and Korea. Two novel haplotypes found in the Amur area and one from Gansu Province were closely related to the Tsushima and Taiwan clades, respectively. Phylogeographical and demographic analyses indicated a recent population expansion for group I, whereas no clear evidence for expansion was obtained for group II. The recent expansion of group I is also supported by historical records. Closely related haplotypes were found between the continental populations and the insular populations on Tsushima and Taiwan, suggesting that the ancestors of the insular populations immigrated from the continent via land bridges. The two groups could have evolved allopatrically in parts of eastern Asia differing in climate and vegetation.

The Anatolian glacial refugium and human-mediated colonization: a phylogeographical study of the stone marten (Martes foina) in Turkey

The Anatolian Peninsula, comprising most of modern Turkey, is situated at the junction of Europe, the Middle East and Asia. Together with its complex geomorphological and climatic history, this has given rise to a rich fauna and flora, which exhibits a wide range of historical biogeographical patterns. The stone marten (Martes foina) is a small carnivore that is found across the temperate Palaearctic region including Anatolia, where it is often associated with habitats modified by humans, but few genetic data exist for this species. We sequenced a 1840-bp region of the mitochondrial genome from 97 martens sampled across the peninsula and intron 7 of the nuclear β-fibrinogen gene from 53 of these. Two mitochondrial lineages were recovered, with overlapping eastern and western distributions, but there was no geographical structure for the autosomal marker. Coalescent analyses indicated that both of the lineages originated during the Last Glacial Maximum, one of them within an eastern Anatolian refugium and the other in a western Anatolian or Balkan refugium. The western lineage colonized most of Europe in the Holocene, while the eastern lineage may be endemic to Anatolia, from where it colonized the Iberian Peninsula via human translocation. The presence of at least one refugial stone marten population highlights the importance of Anatolia to the preservation of genetic variation and biodiversity.

Systematics and Distribution of Ferret Badgers Melogale (Mammalia, Mustelidae) in Vietnam: First Genetic Data

Genetic studies of the ferret badgers Melogale conducted in Vietnam have shown that this area is inhabited by three species, M. moschata, M. personata, and M. cucphuongensis, which can be attributed to sibling species (cryptic species). M. personata was found to be widespread not only in southern and central Vietnam, but also in the northern provinces (Lang Son, Ha Giang, Ninh Binh), while M. cucphuongensis was found in the provinces Lang Son, Ha Giang, Cao Bang, and Dak Lak, apart from Ninh Binh, from where it was described. The data obtained suggest a sympatric distribution of all three species over the Vietnam area and confirm sympatry of M. personata and M. moschata in southern Vietnam, which has been earlier established on the basis of morphological data.

Biogeography of Korea's top predator, the yellow-throated Marten: evolutionary history and population dynamics

BACKGROUND

Peninsulas often harvest high genetic diversity through repeated southward migrations of species during glacial maxima. Studies addressing within-species evolutionary responses to climate fluctuations in northeast Asia are limited compared to other regions of the world, and more so in the Korean Peninsula. In this study, we conducted the first population-level study of the yellow-throated marten, Martes flavigula, from the Korean Peninsula, Russian, Taiwanese and Chinese localities in a biogeographic framework using mitochondrial (cyt-b, nd2, cr) and nuclear gene sequencing (ghr).

RESULTS

Bayesian analyses revealed a rather young population, with a split from the most recent common ancestor at around 125 kya. Martes flavigula likely colonized the Korean Peninsula from Mainland China through the Yellow Sea twice, ca. 60 kya and 20 kya. Korean martens diversified during the Late Pleistocene with at least two dispersal events out of Korea, towards the southwest to Taiwan (ca. 80 kya) and towards the North into Russia and eastern China; most likely after the Last Glacial Maxima (ca. 20 kya). We argue that the lack of population structure and mixed populations is possibly a consequence of the high dispersal capability of the species. The Bayesian skyline plot revealed a population decline within the last 5000 years, suggesting potential negative biotic and anthropogenic effects in the area. We find that local populations are not genetically differentiated, therefore no perceptible population structure within Korea was found.

CONCLUSIONS

The topography and geography of the Korean Peninsula has played a pivotal role in its colonization. Connections between the Korean Peninsula and the Mainland through sea-level drops of the Yellow Sea at times of glacial maxima and the high dispersal capability of M. flavigula adds to the lack of geographical structure in this species and the paraphyly of Korean lineages.

Insular variation of the craniodental morphology in the Siberian weasel Mustela sibirica

We compared craniodental morphology among 5 populations of the Siberian weasel Mustela sibirica including 2 insular ones (Tsushima and Taiwan). Skulls of the insular individuals tended to be smaller than those of continental ones. Shape differences were also detected, but not so pronounced. Considering these results, the Taiwan population should be regarded as a distinct subspecies M. s. taivana from the mainland ones. The Tsushima population may also possibly be a distinct subspecies from the mainland ones, but more detailed studies using a larger number of specimens are needed for a conclusion. The introduced population in Honshu is also differentiated from the source population. This suggests a high morphological plasticity in M. sibirica.

Diversification, biogeographic pattern, and demographic history of Taiwanese Scutellaria species inferred from nuclear and chloroplast DNA

The ragged topography created by orogenesis generates diversified habitats for plants in Taiwan. In addition to colonization from nearby mainland China, high species diversity and endemism of plants is also present in Taiwan. Five of the seven Scutellaria species (Lamiaceae) in Taiwan, for example, are endemic to the island. Hypotheses of multiple sources or in situ radiation have arisen to explain the high endemism of Taiwanese species. In this study, phylogenetic analyses using both nuclear and chloroplast markers revealed the multiple sources of Taiwanese Scutellaria species and confirmed the rapid and recent speciation of endemic species, especially those of the "indica group" composed of S. indica, S. austrotaiwanensis, S. tashiroi, and S. playfairii. The common ancestors of the indica group colonized first in northern Taiwan and dispersed regionally southward and eastward. Climate changes during glacial/interglacial cycles led to gradual colonization and variance events in the ancestors of these species, resulting in the present distribution and genetic differentiation of extant populations. Population decline was also detected in S. indica, which might reflect a bottleneck effect from the glacials. In contrast, the recently speciated endemic members of the indica group have not had enough time to accumulate much genetic variation and are thus genetically insensitive to demographic fluctuations, but the extant lineages were spatially expanded in the coalescent process. This study integrated phylogenetic and population genetic analyses to illustrate the evolutionary history of Taiwanese Scutellaria of high endemism and may be indicative of the diversification mechanism of plants on continental islands.