Aim Advancement in ecological methods predicting species distributions is a crucial precondition for deriving sound management actions. Maximum entropy (MaxEnt) models are a popular tool to predict species distributions, as they are considered able to cope well with sparse, irregularly sampled data and minor location errors. Although a fundamental assumption of MaxEnt is that the entire area of interest has been systematically sampled, in practice, MaxEnt models are usually built from occurrence records that are spatially biased towards better‐surveyed areas. Two common, yet not compared, strategies to cope with uneven sampling effort are spatial filtering of occurrence data and background manipulation using environmental data with the same spatial bias as occurrence data. We tested these strategies using simulated data and a recently collated dataset on Malay civet Viverra tangalunga in Borneo. Location Borneo, Southeast Asia. Methods We collated 504 occurrence records of Malay civets from Borneo of which 291 records were from 2001 to 2011 and used them in the MaxEnt analysis (baseline scenario) together with 25 environmental input variables. We simulated datasets for two virtual species (similar to a range‐restricted highland and a lowland species) using the same number of records for model building. As occurrence records were biased towards north‐eastern Borneo, we investigated the efficacy of spatial filtering versus background manipulation to reduce overprediction or underprediction in specific areas. Results Spatial filtering minimized omission errors (false negatives) and commission errors (false positives). We recommend that when sample size is insufficient to allow spatial filtering, manipulation of the background dataset is preferable to not correcting for sampling bias, although predictions were comparatively weak and commission errors increased. Main Conclusions We conclude that a substantial improvement in the quality of model predictions can be achieved if uneven sampling effort is taken into account, thereby improving the efficacy of species conservation planning.

BackgroundElucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog.ResultsOur data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal.ConclusionsOur results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation.

BackgroundPigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection.ResultsA deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection.ConclusionsKey events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation. Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-017-0345-y) contains supplementary material, which is available to authorized users.

We describe Halmaheramys bokimekot Fabre, Pagès, Musser, Fitriana, Semiadi & Helgen gen. et sp. nov., a new genus and species of murine rodent from the North Moluccas, and study its phylogenetic placement using both molecular and morphological data. We generated a densely sampled mitochondrial and nuclear DNA data set that included most genera of Indo-Pacific Murinae, and used probabilistic methodologies to infer their phylogenetic relationships. To reconstruct their biogeographical history, we first dated the topology and then used a Lagrange analysis to infer ancestral geographic areas. Finally, we combined the ancestral area reconstructions with temporal information to compare patterns of murine colonization among Indo-Pacific archipelagos. We provide a new and comprehensive molecular phylogenetic reconstruction for Indo-Pacific Murinae, with a focus on the Rattus division. Using previous results and those presented in this study, we define a new Indo-Pacific group within the Rattus division, composed of Bullimus, Bunomys, Paruromys, Halmaheramys, Sundamys, and Taeromys. Our phylogenetic reconstructions revealed a relatively recent diversification from the Middle Miocene to Plio-Pleistocene associated with several major dispersal events. We identified two independent Indo-Pacific dispersal events from both western and eastern Indo-Pacific archipelagos to the isolated island of Halmahera, which led to the speciations of H. bokimekot gen. et sp. nov. and Rattus morotaiensis Kellogg, 1945. We propose that a Middle Miocene collision between the Halmahera and Sangihe arcs may have been responsible for the arrival of the ancestor of Halmaheramys to eastern Wallacea. Halmaheramys bokimekot gen. et sp. nov. is described in detail, and its systematics and biogeography are documented and illustrated.

The use of genome-wide genetic markers is an emerging approach for informing evidence-based management decisions for highly threatened species. Pangolins are the most heavily trafficked mammals across illegal wildlife trade globally, but Critically Endangered Sunda pangolins (Manis javanica) have not been widely studied in insular Southeast Asia. We used > 12,000 single nucleotide polymorphic markers (SNPs) to assign pangolin seizures from illegal trade of unknown origin to possible geographic sources via genetic clustering with pangolins of known origin. Our SNPs reveal three previously unrecognized genetic lineages of Sunda pangolins, possibly from Borneo, Java and Singapore/Sumatra. The seizure assignments suggest the majority of pangolins were traded from Borneo to Java. Using mitochondrial markers did not provide the same resolution of pangolin lineages, and to explore if admixture might explain these differences, we applied sophisticated tests of introgression using > 2,000 SNPs to investigate secondary gene flow between each of the three Sunda pangolin lineages. It is possible the admixture which we discovered is due to human-mediated movements of pangolins. Our findings impact a range of conservation actions, including tracing patterns of trade, repatriation of rescue animals, and conservation breeding. In order to conserve genetic diversity, we suggest that, pending further research, each pangolin lineage should as a precaution be protected and managed as an evolutionarily distinct conservation unit.

Gibbon ape leukemia virus (GALV) and koala retrovirus (KoRV) most likely originated from a cross-species transmission of an ancestral retrovirus into koalas and gibbons via one or more intermediate as-yet-unknown hosts. A virus highly similar to GALV has been identified in an Australian native rodent (Melomys burtoni) after extensive screening of Australian wildlife. GALV-like viruses have also been discovered in several Southeast Asian species, although screening has not been extensive and viruses discovered to date are only distantly related to GALV. We therefore screened 26 Southeast Asian rodent species for KoRV-and GALV-like sequences, using hybridization capture and high-throughput sequencing, in the attempt to identify potential GALV and KoRV hosts. Only the individuals belonging to a newly discovered subspecies of Melomys burtoni from Indonesia were positive, yielding an endogenous provirus very closely related to a strain of GALV. The sequence of the critical receptor domain for GALV infection in the Indonesian M. burtoni subsp. was consistent with the susceptibility of the species to GALV infection. The second record of a GALV in M. burtoni provides further evidence that M. burtoni, and potentially other lineages within the widespread subfamily Murinae, may play a role in the spread of GALV-like viruses. The discovery of a GALV in the most western part of the Australo-Papuan distribution of M. burtoni, specifically in a transitional zone between Asia and Australia (Wallacea), may be relevant to the cross-species transmission to gibbons in Southeast Asia and broadens the known distribution of GALVs in wild rodents. IMPORTANCEGibbon ape leukemia virus (GALV) and the koala retrovirus (KoRV) are very closely related, yet their hosts neither are closely related nor overlap geographically. Direct cross-species infection between koalas and gibbons is unlikely. Therefore, GALV and KoRV may have arisen via a cross-species transfer from an intermediate host whose range overlaps those of both gibbons and koalas. Using hybridization capture and high-throughput sequencing, we have screened a wide range of rodent candidate hosts from Southeast Asia for KoRV-and GALV-like sequences. Only a Melomys burtoni subspecies from Wallacea (Indonesia) was positive for GALV. We report the genome sequence of this newly identified GALV, the critical domain for infection of its potential cellular receptor, and its phylogenetic relationships with the other previously characterized GALVs. We hypothesize that Melomys burtoni, and potentially related lineages with an Australo-Papuan distribution, may have played a key role in crossspecies transmission to other taxa. The evolutionary mechanisms involved in cross-species transmissions (CSTs) of viruses are complex and generally poorly understood. Viral evolution, host contact rates, biological similarity in host defense systems (receptors, viral restriction factors), and host evolutionary relationships have been proposed as key factors in CST rates and outcomes (1). However, the...

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SUMMARYA study of growth and venison production from weaner red deer grazing pure tetraploid red clover (RC) or conventional perennial ryegrass/white clover (PRG) pasture was conducted in 1990, with the objective of attaining a minimum slaughter liveweight of 92 kg (50 kg carcass) by 12 months of age in the stags. Ten weaner red deer stags and ten weaner red deer hinds were randomly selected and rotationally grazed on either RC or PRG forage. In autumn and spring, forage allowances were 7 kgDM/hd/day and 8 kgDM/hd/day respectively. In winter, the animals from both groups were grazed together on PRG pasture, at a residual dry matter (DM) of 1100 kgDM/ha. Total nitrogen (N) concentration was higher in RC on offer than in PRG on offer (autumn 3·4 v. 3·1 %DM; spring 3·8 v. 3·1 %DM), whilst organic matter digestibility (OMD; autumn 80·5 v. 76·5%; spring 82·1 v. 80·3%) was also higher for RC on offer. Diet selected showed similar differences in total N concentration, but there were negligible differences between forages in OMD.Liveweight gains of RC and PRG stags were respectively 263 v. 192 g/day, 101 v. 106 g/day and 354 v. 341 g/day during autumn, winter and spring, with the corresponding values for hinds being 198. 173 g/day, 52 v. 53 g/day and 242 v. 218 g/day. At one year of age, stags grazing RC were 7 kg heavier and hinds 3 kg heavier than animals grazing PRG pasture. Animals grazing RC forage had higher voluntary feed intake (VFI) in both autumn (P < 0·10) and spring (P < 0·001), than animals grazing PRG pasture.All stags grazing RC forage reached the minimum slaughter liveweight by one year of age, compared to 75% of those grazing PRG pasture. At slaughter, stags that had grazed RC produced heavier carcass weights (59·9 v. 54·5 kg, P < 0·01), had higher carcass dressing percentage (55·3 v. 53·2 %; P < 0·01), and tended to have slightly greater carcass subcutaneous fat depth than stags grazing PRG pasture, but this effect disappeared when the data were corrected to equal carcass weight. All stags grazing RC produced velvet antler, relative to 75% of those grazing PRG; in stags producing harvestable velvet antler, there was no difference in antler weight between those grazing RC and PRG. It is concluded that RC offers potential as a special-purpose forage for the growth of weaner red deer.