Human-mediated introduction of introgressed deer across Wallace's line: Historical biogeography of Rusa unicolor and R. timorensis

Global phylogeographical distribution of Gloeoporus dichrous

Phylogeographic analyses are efficient in ecological and evolutionary studies to discover the origin of a lineage, its dispersal routes, and the divergence of ancestral traits. Studies on widespread wood-decay fungi have revealed the phylogenetic division of several polypores based on geographical distribution. In this study, specimens of Gloeoporus dichrous, a cosmopolitan polypore species, were collected globally and analyzed for their geographic distribution. Multi-marker Bayesian molecular clock and haplotype analyses revealed a clear division of G. dichrous populations by continent. The species diverged from its neighboring clades 10.3 (16.0-5.6) million years ago, with Asian and North American populations at the center of divergence. Possible dispersal mechanisms and pathways are predicted and discussed based on the evaluated transfer routes. The biogeography of G. dichrous analyzed in this study represents a fraction of the polypore evolution and may advance the understanding of the overall evolution of wood-decay fungi.

First mitogenome phylogeny of the sun bear Helarctos malayanus reveals a deep split between Indochinese and Sundaic lineages

The sun bear Helarctos malayanus is one of the most endangered ursids, and to date classification of sun bear populations has been based almost exclusively on geographic distribution and morphology. The very few molecular studies focussing on this species were limited in geographic scope. Using archival and non-invasively collected sample material, we have added a substantial number of complete or near-complete mitochondrial genome sequences from sun bears of several range countries of the species' distribution. We here report 32 new mitogenome sequences representing sun bears from Cambodia, Thailand, Peninsular Malaysia, Sumatra, and Borneo. Reconstruction of phylogenetic relationships revealed two matrilines that diverged ~295 thousand years ago: one restricted to portions of mainland Indochina (China, Cambodia, Thailand; "Mainland clade"), and one comprising bears from Borneo, Sumatra, Peninsular Malaysia but also Thailand ("Sunda clade"). Generally recent coalescence times in the mitochondrial phylogeny suggest that recent or historical demographic processes have resulted in a loss of mtDNA variation. Additionally, analysis of our data in conjunction with shorter mtDNA sequences revealed that the Bornean sun bear, classified as a distinct subspecies (H. m. euryspilus), does not harbor a distinctive matriline. Further molecular studies of H. malayanus are needed, which should ideally include data from nuclear loci.

OUP accepted manuscript

Globally, many wild deer populations are actively studied or managed for conservation, hunting, or damage mitigation purposes. These studies require reliable estimates of population state parameters, such as density or abundance, with a level of precision that is fit for purpose. Such estimates can be difficult to attain for many populations that occur in situations that are poorly suited to common survey methods. We evaluated the utility of combining camera trap survey data, in which a small proportion of the sample is individually recognizable using natural markings, with spatial mark–resight (SMR) models to estimate deer density in a variety of situations. We surveyed 13 deer populations comprising four deer species (Cervus unicolor, C. timorensis, C. elaphus, Dama dama) at nine widely separated sites, and used Bayesian SMR models to estimate population densities and abundances. Twelve surveys provided sufficient data for analysis and seven produced density estimates with coefficients of variation (CVs) ≤ 0.25. Estimated densities ranged from 0.3 to 24.6 deer km⁻². Camera trap surveys and SMR models provided a powerful and flexible approach for estimating deer densities in populations in which many detections were not individually identifiable, and they should provide useful density estimates under a wide range of conditions that are not amenable to more widely used methods. In the absence of specific local information on deer detectability and movement patterns, we recommend that at least 30 cameras be spaced at 500–1,000 m and set for 90 days. This approach could also be applied to large mammals other than deer.

Population genomics of free-ranging Great Plains white-tailed and mule deer reflects a long history of interspecific hybridization

Hybridization is a natural process at species-range boundaries that may variably promote the speciation process or break down species barriers but minimally will influence management outcomes of distinct populations. White-tailed deer (Odocoileus virginianus) and mule deer (Odocoileus hemionus) have broad and overlapping distributions in North America and a recognized capacity for interspecific hybridization. In response to contemporary environmental change to any of one or multiple still-unknown factors, mule deer range is contracting westward accompanied by a westward expansion of white-tailed deer, leading to increasing interactions, opportunities for gene flow, and associated conservation implications. To quantify genetic diversity, phylogenomic structure, and dynamics of hybridization in sympatric populations of white-tailed and mule deer, we used mitochondrial cytochrome b data coupled with SNP loci discovered with double-digest restriction site-associated DNA sequencing. We recovered 25,018 SNPs across 92 deer samples from both species, collected from two regions of western Kansas. Eight individuals with unambiguous external morphology representing both species were of hybrid origin (8.7%), and represented the product of multi-generational backcrossing. Mitochondrial data showed both ancient and recent directional discordance with morphological species assignments, reflecting a legacy of mule deer males mating with white-tailed deer females. Mule deer had lower genetic diversity than white-tailed deer, and both mitochondrial and nuclear data suggest contemporary mule deer effective population decline. Landscape genetic analyses show relative isolation between the two study regions for white-tailed deer, but greater connectivity among mule deer, with predominant movement from north to south. Collectively, our results suggest a long history of gene flow between these species in the Great Plains and hint at evolutionary processes that purge incompatible functional genomic elements as a result of hybridization. Surviving hybrids evidently may be reproductive, but with unknown consequences for the future integrity of these species, population trajectories, or relative susceptibility to emerging pathogens.

Population genetics of Sambar (Rusa unicolor) from the Western Himalayas: preliminary findings

BACKGROUND

The sambar (Rusa unicolor) is one of the largest deer distributed across diverse habitats of India and threatened due to habitat loss, changes in the land-use patterns, illegal poaching, and anthropogenic disturbances. Here, we report the first population genetics account of sambar deer from the Western Himalayas.

METHODS AND RESULTS

We observed relatively compromised genetic diversity (π = 0.0008 ± 0.0006 at mtDNA and Ho = 0.499 ± 0.056 at nDNA). We identified 60 unique individuals using a select panel of seven loci (P_ID sib cum 1.60E-03). Bayesian skyline plot showed a stable demographic history since the past 8 kyr with a decline in recent years. The population lacked genetic structuring, likely due to the contiguous distribution and large dispersal patterns of sambar.

CONCLUSION

The preliminary findings are valuable in exploring the utility of genetic diversity in monitoring the sambar population, estimating density following capture-recapture analysis, and aid to the conservation planning of sambar in large landscapes.

Mitogenome Phylogeny Including Data from Additional Subspecies Provides New Insights into the Historical Biogeography of the Eurasian lynx Lynx lynx

Previous molecular studies of the wide-ranging Eurasian lynx Lynx lynx focused mainly on its northern Palearctic populations, with the consequence that the reconstruction of this species’ evolutionary history did not include genetic variation present in its southern Palearctic distribution. We sampled a previously not considered Asian subspecies (L. l. dinniki), added published data from another Asian subspecies (L. l. isabellinus), and reassessed the Eurasian lynx mtDNA phylogeny along with previously published data from northern Palearctic populations. Our mitogenome-based analyses revealed the existence of three major clades (A: Central Asia, B: SE Europe/SW Asia, C: Europe and Northern Asia) and at least five lineages, with diversification in Lynx lynx commencing at least 28kyr earlier than hitherto estimated. The subspecies L. l. isabellinus harbors the most basal matriline, consistent with the origin of Lynx lynx in this subspecies’ current range. L. l. dinniki harbors the second most basal matriline, which is related to, and may be the source of, the mtDNA diversity of the critically endangered Balkan lynx L. l. balcanicus. Our results suggest that the Anatolian peninsula was a glacial refugium for Eurasian lynx, with previously unconsidered implications for the colonization of Europe by this species.

Evolutionary history of Sundaland shrews (Eulipotyphla: Soricidae: Crocidura) with a focus on Borneo

The hyperdiverse shrew genus Crocidura is one of few small mammal genera distributed across Sundaland and all of its boundaries. This represents a rare opportunity to study the geological history of this region through the evolutionary history of these shrews. We generate a phylogeny of all recognized species of Sundaland Crocidura and show that most speciation events took place during the Pleistocene, prior to the inundation of the Sunda Shelf around 400 000 years ago. We find east–west differentiation within two separate lineages on Borneo, and that the current taxonomy of its two endemic species does not reflect evolutionary history, but ecophenotypic variation of plastic traits related to elevation. Sulawesi shrews are monophyletic, with a single notable exception: the black-footed shrew (C. nigripes). We show that the black-footed shrew diverged from its relatives on Borneo recently, suggesting a human-assisted breach of Wallace’s line. Overall, the number of Crocidura species, especially on Borneo, probably remains an underestimate.

A review of the genus Rusa in the indo-malayan archipelago and conservation efforts

Genus Rusa, belonging to the deer family Cervidae is native to the Indo-Malaya Archipelago (IMA). However, detailed information on the Rusa genus in the IMA is limited. This review provides comprehensive information on the Rusa genus in the IMA including, threats and conservation efforts. There are four species of deer in Rusa genus, which is Sambar deer (Rusa unicolor), Javan deer (Rusa timorensis), Visayan spotted deer (Rusa alfredi) and Philippine deer (Rusa marianna). Despite their wide distribution in the South Asian and Southeast Asian regions, they are under serious threats. Some conservation efforts that are being done to protect and conserve them among others are; (1) facilities protection, (2) habitat enrichment programme, (3) Ex-situ conservation, (4) legislations, and (5) captive breeding. Conservation through genetics is also an important step in conserving these species. Recommendations for conservation of the genus are also discussed; 1. maintenance of ecosystem. 2. more effective monitoring system on the existing protected area. 3. ex-situ conservation, and 4. habitat monitoring.

Multiplex PCRs for the specific identification of marsupial and deer species from faecal samples as a basis for non-invasive epidemiological studies of parasites

Background

The specific identification of animals through the analysis of faecal DNA is important in many areas of scientific endeavour, particularly in the field of parasitology.

Methods

Here, we designed and assessed two multiplex PCR assays using genetic markers in a mitochondrial cytochrome b (cytb) gene region for the unequivocal identification and discrimination of animal species based on the specific amplification of DNA from faecal samples collected from water catchment areas in Victoria, Australia. One of these assays differentiates three marsupial species (eastern grey kangaroo, swamp wallaby and common wombat) and the other distinguishes three deer species (fallow, red and sambar deer). We tested these two assays using a total of 669 faecal samples, collected as part of an ongoing programme to monitor parasites and microorganisms in these animals.

Results

These two PCR assays are entirely specific for these animal species and achieve analytical sensitivities of 0.1–1.0 picogram (pg). We tested 669 faecal samples and found that some previous inferences of species based on faecal morphology were erroneous. We were able to molecularly authenticate all of the 669 samples.

Conclusions

We have established PCR assays that accurately distinguish the faecal samples of some of the prominent large mammalian herbivores found within a water catchment system in the state of Victoria, Australia. The multiplex assays for marsupials and deer produce amplicons that are easily differentiable based on their size on an agarose gel, and can be readily sequenced for definitive species authentication. Although established for marsupials and deer, the methodology used here can be applied to other host-parasite study systems to ensure data integrity.

Widespread hybridization in the introduced hog deer population of Victoria, Australia, and its implications for conservation

In Australia, many species have been introduced that have since undergone drastic declines in their native range. One species of note is the hog deer (Axis porcinus) which was introduced in the 1860s to Victoria, Australia, and has since become endangered in its native range throughout South-East Asia. There is increased interest in using non-native populations as a source for genetic rescue; however, considerations need to be made of the genetic suitability of the non-native population. Three mitochondrial markers and two nuclear markers were sequenced to assess the genetic variation of the Victorian population of hog deer, which identified that the Victorian population has hybrid origins with the closely related chital (Axis axis), a species that is no longer present in the wild in Victoria. In addition, the mitochondrial D-loop region within the Victorian hog deer is monomorphic, demonstrating that mitochondrial genetic diversity is very low within this population. This study is the first to report of long-term persistence of hog deer and chital hybrids in a wild setting, and the continual survival of this population suggests that hybrids of these two species are fertile. Despite the newly discovered hybrid status in Victorian hog deer, this population may still be beneficial for future translocations within the native range. However, more in-depth analysis of genetic diversity within the Victorian hog deer population and investigation of hybridization rates within the native range are necessary before translocations are attempted.