Mountain- and brown hare genetic polymorphisms to survey local adaptations and conservation status of the heath hare (Lepus timidus sylvaticus, Nilsson 1831).

We provide the first whole genome sequences from three specimens of the mountain hare subspecies the heath hare (Lepus timidus sylvaticus), along with samples from two mountain hares (Lepus timidus timidus) and two brown hares (Lepus europaeus) from Sweden. The heath hare has a unique grey winter pelage as compared to other mountain hares (white) and brown hares (mostly brown), and face regional extinction, likely due to competitive exclusion from the non-native brown hare. Whole genome resequencing from the seven hare specimens were mapped to the Lepus timidus pseudoreference genome and used for detection of 11,363,883 polymorphic nucleotide positions. The data presented here could be useful for addressing local adaptations and conservation status of mountain hares and brown hares in Sweden, including unique subspecies.

Experimental rewilding may restore abandoned wood-pastures if policy allows.

Large herbivores play key roles in terrestrial ecosystems. Continuous defaunation processes have produced cascade effects on plant community composition, vegetation structure, and even climate. Wood-pastures were created by traditional management practices that have maintained open structures and biodiversity for millennia. In Europe, despite the broad recognition of their biological importance, such landscapes are declining due to land-use changes. This calls for finding urgent solutions for wood-pasture conservation. To test whether introducing an ecological replacement of an extinct wild horse could have positive effects on wood-pasture restoration, we designed a 3-year rewilding experiment. Horses created a more open wood-pasture structure by browsing on seedlings and saplings, affected tree composition via selective browsing and controlled the colonization of woody vegetation in grassland-dominated areas. Thus, rewilding could be a potential avenue for wood-pasture restoration and biodiversity conservation. However, such benefits may not materialize without a necessary paradigm and political shift.

Ethical Considerations for Wildlife Reintroductions and Rewilding.

The recovery of many populations of large carnivores and herbivores in major parts of Europe and North America offers ecosystem services and opportunities for sustainable utilization of wildlife. Examples of services are hunting, meat, and skin, along with less invasive utilization such as ecotourism and wildlife spotting. An increasing number of studies also point out the ecosystem function, landscape engineering, and cascading effects of wildlife as values for human existence, biodiversity conservation, and ecosystem resilience. Within this framework, the concept of rewilding has emerged as a means to add to the wilderness through either supplementary release of wildlife species already present or reintroduction of species formerly present in a certain area. The latter involves translocation of species from other geographical areas, releases from captivity, feralization, retro-breeding, or de-domestication of breeds for which the wild ancestor is extinct. While all these initiatives aim to reverse some of the negative human impacts on life on earth, some pose challenges such as conflicts of interest between humans and wildlife in, for example, forestry, agriculture, traffic, or disease dynamics (e.g., zoonosis). There are also welfare aspects when managing wildlife populations with the purpose to serve humans or act as tools in landscape engineering. These welfare aspects are particularly apparent when it comes to releases of animals handled by humans, either from captivity or translocated from other geographical areas. An ethical values clash is that translocation can involve suffering of the actual individual, while also contributing to reintroduction of species and reestablishment of ecological functions. This paper describes wildlife recovery in Europe and North America and elaborates on ethical considerations raised by the use of wildlife for different purposes, in order to find ways forward that are acceptable to both the animals and humans involved. The reintroduction ethics aspects raised are finally formulated in 10 guidelines suggested for management efforts aimed at translocating wildlife or reestablishing wilderness areas.

Widespread introgression of mountain hare genes into Fennoscandian brown hare populations.

In Fennoscandia, mountain hare (Lepus timidus) and brown hare (Lepus europaeus) hybridize and produce fertile offspring, resulting in gene flow across the species barrier. Analyses of maternally inherited mitochondrial DNA (mtDNA) show that introgression occur frequently, but unavailability of appropriate nuclear DNA markers has made it difficult to evaluate the scale- and significance for the species. The extent of introgression has become important as the brown hare is continuously expanding its range northward, at the apparent expense of the mountain hare, raising concerns about possible competition. We report here, based on analysis of 6833 SNP markers, that the introgression is highly asymmetrical in the direction of gene flow from mountain hare to brown hare, and that the levels of nuclear gene introgression are independent of mtDNA introgression. While it is possible that brown hares obtain locally adapted alleles from the resident mountain hares, the low levels of mountain hare alleles among allopatric brown hares suggest that hybridization is driven by stochastic processes. Interspecific geneflow with the brown hare is unlikely to have major impacts on mountain hare in Fennoscandia, but direct competition may.

Identification of a Bitter-Taste Receptor Gene Repertoire in Different Lagomorphs Species.

The repertoires of bitter-taste receptor (T2R) gene have been described for several animal species, but these data are still scarce for Lagomorphs. The aim of the present work is to identify potential repertoires of T2R in several Lagomorph species, covering a wide geographical distribution. We studied these genes in Lepus timidus, L. europaeus, Oryctolagus cuniculus algirus, Romerolagus diazi, and Sylvilagus floridanus, using O. cuniculus cuniculus as control species for PCR and DNA sequencing. We studied the identities of the DNA sequences and built the corresponding phylogenetic tree. Sequencing was successful for both subspecies of O. cuniculus for all T2R genes studied, for five genes in Lepus, and for three genes in R. diazi and S. floridanus. We describe for the first time the partial repertoires of T2R genes for Lagomorphs species, other than the common rabbit. Our phylogenetic analyses indicate that sequence proximity levels follow the established taxonomic classification.

LaGomiCs-Lagomorph Genomics Consortium: An International Collaborative Effort for Sequencing the Genomes of an Entire Mammalian Order.

The order Lagomorpha comprises about 90 living species, divided in 2 families: the pikas (Family Ochotonidae), and the rabbits, hares, and jackrabbits (Family Leporidae). Lagomorphs are important economically and scientifically as major human food resources, valued game species, pests of agricultural significance, model laboratory animals, and key elements in food webs. A quarter of the lagomorph species are listed as threatened. They are native to all continents except Antarctica, and occur up to 5000 m above sea level, from the equator to the Arctic, spanning a wide range of environmental conditions. The order has notable taxonomic problems presenting significant difficulties for defining a species due to broad phenotypic variation, overlap of morphological characteristics, and relatively recent speciation events. At present, only the genomes of 2 species, the European rabbit (Oryctolagus cuniculus) and American pika (Ochotona princeps) have been sequenced and assembled. Starting from a paucity of genome information, the main scientific aim of the Lagomorph Genomics Consortium (LaGomiCs), born from a cooperative initiative of the European COST Action "A Collaborative European Network on Rabbit Genome Biology-RGB-Net" and the World Lagomorph Society (WLS), is to provide an international framework for the sequencing of the genome of all extant and selected extinct lagomorphs. Sequencing the genomes of an entire order will provide a large amount of information to address biological problems not only related to lagomorphs but also to all mammals. We present current and planned sequencing programs and outline the final objective of LaGomiCs possible through broad international collaboration.

Characteristics of spermatozoa and reproductive organs in relation to age and body weight in Swedish moose (Alces alces).

Knowledge of the reproductive biology of game species is vital for sustainable management. In moose (Alces alces), research in reproductive characteristics has focused on the female, whereas there are few studies in male moose. The aim of the present study was to investigate sperm morphology and chromatin integrity (SCSA), and their relationships with testicular and epididymal features, as well as temporal aspects with respect to the hunting season. In total, 143 male moose aged 1.5-11.5 years were sampled from 2008 to 2011. The proportion of normal spermatozoa (PNS) ranged from 1.5% to 82.0%, with a mean of 51%, and the %DFI (DNA fragmentation index) ranged from 2.5% to 36.7% (mean 9.5). PNS decreased temporally, and was positively associated with carcass and testes weight. Body weight and testes weight had positive effect on PNS regardless of age. No effect of any explanatory variables was observed on the DFI. The testis/body weight ratio of moose (0.033%) is among the lowest reported among mammals, indicating a less polygynous mating system than in roe deer and red deer. For reproduction success in moose, a high body weight in males is favorable, as is a balanced sex ratio. Thus, males should not be harvested prior to the time when the majority of females have passed their first oestrus of the season.

Reproductive characteristics in female Swedish moose (Alces alces), with emphasis on puberty, timing of oestrus, and mating.

BACKGROUND: The moose (Alces alces) is an intensively managed keystone species in Fennoscandia. Several aspects of reproduction in moose have not been fully elucidated, including puberty, timing of mating and oestrus, and the length of the oestrus period. These aspects are relevant for an adaptive management of moose with respect to harvest, population size, demography and environmental conditions. Therefore, an investigation of female moose reproduction was conducted during the moose-hunting period in southern Sweden from 2008 to 2011. RESULTS: A total of 250 reproductive organs and information on carcass weight and age was collected from four different hunting areas (provinces of Öland, Småland, Södermanland, and Västergötland) in southern Sweden. The results showed that puberty in female moose varied with carcass weight, age, and time of season. The period for oestrous/mating lasted from about mid September to the beginning of November. CONCLUSIONS: The oestrus period (predominantly for heifers) is longer than previously reported and was not finished when the hunting period started. Sampling the uterine cervix to detect spermatozoa was a useful method to determine if mating had occurred. To avoid hunting of moose during oestrus, we suggest that the hunting period should be postponed by at least 14 days in southern Sweden.

Genetic divergence in the small Indian mongoose (Herpestes auropunctatus), a widely distributed invasive species.

The combination of founder events, random drift and new selective forces experienced by introduced species typically lowers genetic variation and induces differentiation from the ancestral population. Here, we investigate microsatellite differentiation between introduced and native populations of the small Indian mongoose (Herpestes auropunctatus). Many expectations based on introduction history, such as loss of alleles and relationships among populations, are confirmed. Nevertheless, when applying population assignment methods to our data, we observe a few specimens that are incorrectly assigned and/or appear to have a mixed ancestry, despite estimates of substantial population differentiation. Thus, we suggest that population assignments of individuals should be viewed as tentative and that there should be agreement among different algorithms before assignments are applied in conservation or management. Further, we find no congruence between previously reported morphological differentiation and the sorting of microsatellite variation. Some introduced populations have retained much genetic variation while others have not, irrespective of morphology. Finally, we find alleles from the sympatric grey mongoose (Herpestes edwardsii) in one small Indian mongoose within the native range, suggesting an alternative explanation for morphological differentiation involving a shift in female preferences in allopatry.

Introgression from Lepus europaeus to L. timidus in Russia revealed by mitochondrial single nucleotide polymorphisms and nuclear microsatellites.

Hybridisation among wild mammal populations may lead to introgression of genes and genomes over the species barrier. In Sweden, in northern Europe, and on the Iberian Peninsula in southern Europe, mitochondrial DNA from L. timidus occurs among L. europaeus specimens, presumably as a result of interspecific hybridisation. In Russia, the species are believed to hybridise as well, but no investigations have confirmed introgression. Here we develop species diagnostic single nucleotide polymorphisms in the mitochondrial genomes and combine them with analysis of nuclear microsatellite markers to investigate hybridisation and introgression in 71 Lepus specimens from Russia. A total of 58 specimens are typical representatives of either species. An additional nine specimens have slightly intermediate genotypes, potentially as a result of introgression of nuclear genes. Finally, we find three specimens with L. europaeus mitochondrial genome and apparent L. timidus nuclear genome. This indicates that the reciprocal transfer of mtDNA occur among Russian populations of these species. Our observation differs from previous observations of mtDNA introgression in Sweden and Iberia, and provides further support for a reticulated mode of introgression within the genus Lepus.