The hidden history of the snowshoe hare,Lepus americanus: extensive mitochondrial DNA introgression inferred from multilocus genetic variation

Patterns of evolution in MHC class II DQA and DQB exon 2 genes of Alpine mountain hares, Lepus timidus varronis, and sympatric and parapatric brown hares, L. europaeus, from Switzerland

In natural populations, hybridization is known to occur between a wide range of species. However, its evolutionary significance is less clear. Genes involved in fighting pathogens are considered excellent candidates for studying adaptive introgression, although both introgression and balancing selection can generate similar patterns of diversity and differentiation. Here, we compared DQA and DQB MHC class II and microsatellite allelic diversity of sympatric and parapatric mountain (Lepus timidus) and brown hare (L. europaeus) populations from Switzerland. We detected higher genetic diversity in brown hares compared to mountain hares at both MHC and microsatellite loci. We consider the observed patterns of microsatellite diversity both for L. europaeus and L. timidus as result of stochastic demographic processes while the pattern of MHC polymorphism of the studied hare populations can be explained by pathogen-driven selection. Rare bidirectional gene flow between both hare species seems to occur specifically for MHC alleles. However, the high number of shared alleles showing similar high frequency in both species suggests that reciprocally exchanged MHC alleles are being maintained via balancing selection. Adaptation to similar pathogen communities can also lead to parallel selection of MHC alleles. Positive selection, recombination and mutations have played different roles in shaping the patterns of MHC allelic diversity in and differentiation between both species. Results for the latter evolutionary forces do not show a better matching between the sympatric populations compared to the parapatric ones, suggesting a minor role of introgression for the observed evolutionary patterns of the studied hare species.

Characterising Mitochondrial Capture in an Iberian Shrew

Mitochondrial introgression raises questions of biogeography and of the extent of reproductive isolation and natural selection. Previous phylogenetic work on the Sorex araneus complex revealed apparent mitonuclear discordance in Iberian shrews, indicating past hybridisation of Sorex granarius and the Carlit chromosomal race of S. araneus, enabling introgression of the S. araneus mitochondrial genome into S. granarius. To further study this, we genetically typed 61 Sorex araneus/coronatus/granarius from localities in Portugal, Spain, France, and Andorra at mitochondrial, autosomal, and sex-linked loci and combined our data with the previously published sequences. Our data are consistent with earlier data indicating that S. coronatus and S. granarius are the most closely related of the three species, confirming that S. granarius from the Central System mountain range in Spain captured the mitochondrial genome from a population of S. araneus. This mitochondrial capture event can be explained by invoking a biogeographical scenario whereby S. araneus was in contact with S. granarius during the Younger Dryas in central Iberia, despite the two species currently having disjunct distributions. We discuss whether selection favoured S. granarius with an introgressed mitochondrial genome. Our data also suggest recent hybridisation and introgression between S. coronatus and S. granarius, as well as between S. araneus and S. coronatus.

Molecular phenotyping uncovers differences in basic housekeeping functions among closely related species of hares ( Lepus spp., Lagomorpha: Leporidae)

Speciation is a fundamental evolutionary process, which results in genetic differentiation of populations and manifests as discrete morphological, physiological and behavioural differences. Each species has travelled its own evolutionary trajectory, influenced by random drift and driven by various types of natural selection, making the association of genetic differences between the species with the phenotypic differences extremely complex to dissect. In the present study, we have used an in vitro model to analyse in depth the genetic and gene regulation differences between fibroblasts of two closely related mammals, the arctic/subarctic mountain hare (Lepus timidus Linnaeus) and the temperate steppe-climate adapted brown hare (Lepus europaeus Pallas). We discovered the existence of a species-specific expression pattern of 1623 genes, manifesting in differences in cell growth, cell cycle control, respiration, and metabolism. Interspecific differences in the housekeeping functions of fibroblast cells suggest that speciation acts on fundamental cellular processes, even in these two interfertile species. Our results help to understand the molecular constituents of a species difference on a cellular level, which could contribute to the maintenance of the species boundary.

Bidirectional hybridisation and introgression between introduced European brown hare, Lepus europaeus and the endemic Irish hare, L. timidus hibernicus

Introduced non-native species can threaten native species through interspecific hybridisation and genetic introgression. We assessed the prevalence of hybridisation and introgression between introduced European brown hare, Lepus europaeus, and the endemic Irish hare, L. timidus hibernicus. Roadkill hares (n = 56) were sequenced for a 379bp section of the mitochondrial DNA D-loop and a 474bp segment of the nuclear transferrin (Tf) gene. A species-specific indel in the transferrin gene was present in L.t. hibernicus and absent in L. europaeus. Excluding three hares from which molecular data could not be recovered, 28 hares (53%) were native L.t. hibernicus, 7 (13%) were non-native L. europaeus and 18 (34%) were hybrids; of which 5 (28%) were first generation (F1) involving bidirectional crosses with mismatched nuclear and mtDNA (3 ♂ europaeus x ♀ hibernicus and 2 ♂ hibernicus x ♀ europaeus). Mixed nuclear transferrin sequences suggested 13 (72%) of hybrids were at least 2nd generation (F2) with 9 (69%) possessing L.t. hibernicus and 4 (31%) L. europaeus mtDNA (the latter indicative of hybrid backcrossing with the non-native). The prevalence of hybridisation at similar mountain-brown hare contact zones throughout Europe is notably lower (4–16%) and typically unidirectional (♂ europaeus x ♀ timidus). A high prevalence of bidirectional hybridisation and introgression (in association with projected climate change) may favour the introduced species over the native. Genetic surveillance and population monitoring are needed to further explore the potential conservation implications of European brown hare in Ireland.

Counteracting forces of introgressive hybridization and interspecific competition shape the morphological traits of cryptic Iberian Eptesicus bats

Cryptic species that coexist in sympatry are likely to simultaneously experience strong competition and hybridization. The first phenomenon would lead to character displacement, whereas the second can potentially promote morphological similarity through adaptive introgression. The main goal of this work was to investigate the effect of introgressive hybridization on the morphology of cryptic Iberian Eptesicus bats when facing counteracting evolutionary forces from interspecific competition. We found substantial overlap both in dentition and in wing morphology traits, though mainly in individuals in sympatry. The presence of hybrids contributes to a fifth of this overlap, with hybrids showing traits with intermediate morphometry. Thus, introgressive hybridization may contribute to species adaptation to trophic and ecological space responding directly to the macro-habitats characteristics of the sympatric zone and to local prey availability. On the other hand, fur shade tended to be browner and brighter in hybrids than parental species. Colour differences could result from partitioning of resources as an adaptation to environmental factors such as roost and microhabitats. We argue that a balance between adaptive introgression and niche partitioning shapes species interactions with the environment through affecting morphological traits under selection.

Conflicting nuclear and mitogenome phylogenies reveal ancient mitochondrial replacement between two North American species of collared lemmings (Dicrostonyx groenlandicus, D. hudsonius)

Collared lemmings (Dicrostonyx) are cold adapted rodents, keystone animals in the tundra communities and the model taxa in studies of Arctic genetic diversity and Quaternary paleontology. We examined mitochondrial and nuclear genomic variation to reconstruct phylogenetic relationships among the Eurasian D. torquatus and North American D. groenlandicus, D. hudsonius and evaluate biogeographic hypothesis of the two colonization events of North America from Eurasia based on morphological variation in dental traits. The nuclear and mitogenome phylogenies support reciprocal monophyly of each species but reveal conflicting relationships among species. The mitogenome tree likely reflects ancient mitochondrial replacement between currently isolated D. groenlandicus and D. hudsonius. The nuclear genome phylogeny reveals species cladogenesis and supports the hypothesis that D. hudsonius with primitive and distinct molar morphology represents a relic of the first migration event from Eurasia to North America. Species widely distributed in the North American Arctic, D. groenlandicus, with advanced dental morphology originated from a later colonization event across the Bering Land Bridge. This study shows ancient mitochondrial capture between two Arctic species and emphasizes the importance of multilocus approaches for phylogenetic inference.

The evolutionary pathways for local adaptation in mountain hares

Understanding the evolution of local adaptations is a central aim of evolutionary biology and key for the identification of unique populations and lineages of conservation relevance. By combining RAD sequencing and whole‐genome sequencing, we identify genetic signatures of local adaptation in mountain hares (Lepus timidus) from isolated and distinctive habitats of its wide distribution: Ireland, the Alps and Fennoscandia. Demographic modelling suggested that the split of these mountain hares occurred around 20 thousand years ago, providing the opportunity to study adaptive evolution over a short timescale. Using genome‐wide scans, we identified signatures of extreme differentiation among hares from distinct geographic areas that overlap with area‐specific selective sweeps, suggesting targets for local adaptation. Several identified candidate genes are associated with traits related to the uniqueness of the different environments inhabited by the three groups of mountain hares, including coat colour, ability to live at high altitudes and variation in body size. In Irish mountain hares, a variant of ASIP, a gene previously implicated in introgression‐driven winter coat colour variation in mountain and snowshoe hares (L. americanus), may underlie brown winter coats, reinforcing the repeated nature of evolution at ASIP moulding adaptive seasonal colouration. Comparative genomic analyses across several hare species suggested that mountain hares’ adaptive variants appear predominantly species‐specific. However, using coalescent simulations, we also show instances where the candidate adaptive variants have been introduced via introgressive hybridization. Our study shows that standing adaptive variation, including that introgressed from other species, was a crucial component of the post‐glacial dynamics of species.

Hybridization with mountain hares increases the functional allelic repertoire in brown hares

Brown hares (Lepus europaeus Pallas) are able to hybridize with mountain hares (L. timidus Linnaeus) and produce fertile offspring, which results in cross-species gene flow. However, not much is known about the functional significance of this genetic introgression. Using targeted sequencing of candidate loci combined with mtDNA genotyping, we found the ancestral genetic diversity in the Finnish brown hare to be small, likely due to founder effect and range expansion, while gene flow from mountain hares constitutes an important source of functional genetic variability. Some of this variability, such as the alleles of the mountain hare thermogenin (uncoupling protein 1, UCP1), might have adaptive advantage for brown hares, whereas immunity-related MHC alleles are reciprocally exchanged and maintained via balancing selection. Our study offers a rare example where an expanding species can increase its allelic variability through hybridization with a congeneric native species, offering a route to shortcut evolutionary adaptation to the local environmental conditions.

Whole-genome sequencing reveals asymmetric introgression between two sister species of cold-resistant leaf beetles

A large number of genetic variation studies have identified cases of mitochondrial genome introgression in animals, indicating that reproductive barriers among closely related species are often permeable. Because of its sheer size, the impact of hybridization on the evolution of the nuclear genome is more difficult to apprehend. Only a few studies have explored it recently thanks to recent progress in DNA sequencing and genome assembly. Here, we analysed whole-genome sequence variation among multiple individuals of two sister species of leaf beetles inside their hybrid zone, in which asymmetric mitochondrial genome introgression had previously been established. We used a machine learning approach based on computer simulations for training to identify regions of the nuclear genome that were introgressed. We inferred asymmetric introgression of ≈2% of the genome, in the same direction that was observed for the mitochondrial genome. Because a previous study based on a reduced-representation sequencing approach was not able to detect this introgression, we conclude that whole-genome sequencing is necessary when the fraction of the introgressed genome is small. We also analysed the whole-genome sequence of a hybrid individual, demonstrating that hybrids have the capacity to backcross with the species for which virtually no introgression was observed. Our data suggest that one species has recently invaded the range of the other and/or some alleles that where transferred from the invaded into the invading species could be under positive selection and may have favoured the adaptation of the invading species to the Alpine environment.

Lagomorpha as a Model Morphological System

Due to their global distribution, invasive history, and unique characteristics, European rabbits are recognizable almost anywhere on our planet. Although they are members of a much larger group of living and extinct mammals [Mammalia, Lagomorpha (rabbits, hares, and pikas)], the group is often characterized by several well-known genera (e.g., Oryctolagus, Sylvilagus, Lepus, and Ochotona). This representation does not capture the extraordinary diversity of behavior and form found throughout the order. Model organisms are commonly used as exemplars for biological research, but there are a limited number of model clades or lineages that have been used to study evolutionary morphology in a more explicitly comparative way. We present this review paper to show that lagomorphs are a strong system in which to study macro- and micro-scale patterns of morphological change within a clade that offers underappreciated levels of diversity. To this end, we offer a summary of the status of relevant aspects of lagomorph biology.

The Legacy of Recurrent Introgression during the Radiation of Hares

Hybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification of Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1-4 individuals per species), spanning the global distribution of the genus, and two outgroups. We used a coalescent framework to infer species relationships and divergence times, despite extensive genealogical discordance. We found high levels of allele sharing among species and show that this reflects extensive incomplete lineage sorting and temporally layered hybridization. Our results revealed recurrent introgression at all stages along the Lepus radiation, including recent gene flow between extant species since the last glacial maximum but also pervasive ancient introgression occurring since near the origin of the hare lineages. We show that ancient hybridization between northern hemisphere species has resulted in shared variation of potential adaptive relevance to highly seasonal environments, including genes involved in circadian rhythm regulation, pigmentation, and thermoregulation. Our results illustrate how the genetic legacy of ancestral hybridization may persist across a radiation, leaving a long-lasting signature of shared genetic variation that may contribute to adaptation. [Adaptation; ancient introgression; hybridization; Lepus; phylogenomics.].

Identifying model violations under the multispecies coalescent model using P2C2M.SNAPP

Phylogenetic estimation under the multispecies coalescent model (MSCM) assumes all incongruence among loci is caused by incomplete lineage sorting. Therefore, applying the MSCM to datasets that contain incongruence that is caused by other processes, such as gene flow, can lead to biased phylogeny estimates. To identify possible bias when using the MSCM, we present P2C2M.SNAPP. P2C2M.SNAPP is an R package that identifies model violations using posterior predictive simulation. P2C2M.SNAPP uses the posterior distribution of species trees output by the software package SNAPP to simulate posterior predictive datasets under the MSCM, and then uses summary statistics to compare either the empirical data or the posterior distribution to the posterior predictive distribution to identify model violations. In simulation testing, P2C2M.SNAPP correctly classified up to 83% of datasets (depending on the summary statistic used) as to whether or not they violated the MSCM model. P2C2M.SNAPP represents a user-friendly way for researchers to perform posterior predictive model checks when using the popular SNAPP phylogenetic estimation program. It is freely available as an R package, along with additional program details and tutorials.

The population genetics of crypsis in vertebrates: recent insights from mice, hares, and lizards

By combining well-established population genetic theory with high-throughput sequencing data from natural populations, major strides have recently been made in understanding how, why, and when vertebrate populations evolve crypsis. Here, we focus on background matching, a particular facet of crypsis that involves the ability of an organism to conceal itself through matching its color to the surrounding environment. While interesting in and of itself, the study of this phenotype has also provided fruitful population genetic insights into the interplay of strong positive selection with other evolutionary processes. Specifically, and predicated upon the findings of previous candidate gene association studies, a primary focus of this recent literature involves the realization that the inference of selection from DNA sequence data first requires a robust model of population demography in order to identify genomic regions which do not conform to neutral expectations. Moreover, these demographic estimates provide crucial information about the origin and timing of the onset of selective pressures associated with, for example, the colonization of a novel environment. Furthermore, such inference has revealed crypsis to be a particularly useful phenotype for investigating the interplay of migration and selection—with examples of gene flow constraining rates of adaptation, or alternatively providing the genetic variants that may ultimately sweep through the population. Here, we evaluate the underlying evidence, review the strengths and weaknesses of the many population genetic methodologies used in these studies, and discuss how these insights have aided our general understanding of the evolutionary process.

The evolutionary history of the Cape hare (Lepus capensis sensu lato): insights for systematics and biogeography

Inferring the phylogeography of species with large distributions helps deciphering major diversification patterns that may occur in parallel across taxa. Here, we infer the evolutionary history of the Cape hare, Lepus capensis sensu lato, a species distributed from southern Africa to Asia, by analyzing variation at 18 microsatellites and 9 DNA (1 mitochondrial and 8 nuclear) sequenced loci, from field and museum-collected samples. Using a combination of assignment and coalescent-based methods, we show that the Cape hare is composed of five evolutionary lineages, distributed in distinct biogeographic regions-north-western Africa, eastern Africa, southern Africa, the Near East and the Arabian Peninsula. A deep phylogenetic break possibly dating to the Early Pleistocene was inferred between the African and Asian L. capensis groups, and the latter appear more closely related to other Eurasian hare species than to African Cape hares. The inferred phylogeographic structure is shared by numerous taxa distributed across the studied range, suggesting that environmental changes, such as the progressive aridification of the Saharo-Arabian desert and the fluctuations of savannah habitats in Sub-Saharan Africa, had comparable impacts across species. Fine-scale analyses of the western Sahara-Sahel populations showed rich fragmentation patterns for mitochondrial DNA but not for microsatellites, compatible with the environmental heterogeneity of the region and female philopatry. The complex evolutionary history of L. capensis sensu lato, which possibly includes interspecific gene flow, is not reflected by taxonomy. Integrating evolutionary inference contributes to an improved characterization of biodiversity, which is fundamental to foster the conservation of relevant evolutionary units.

Contrasting phylogeographic histories between the continent and islands of East Asia: Massive mitochondrial introgression and long-term isolation of hares (Lagomorpha: Lepus)

Hares of the genus Lepus are distributed worldwide, and introgressive hybridization is thought to be pervasive among species, leading to reticulate evolution and taxonomic confusion. Here, we performed phylogeographic analyses of the following species of hare across East Asia: L. timidus, L. mandshuricus, L. coreanus, and L. brachyurus collected from far-eastern Russia, South Korea, and Japan. Nucleotide sequences of one mitochondrial DNA and eight nuclear gene loci were examined, adding sequences of hares in China from databases. All nuclear DNA analyses supported the clear separation of three phylogroups: L. timidus, L. brachyurus, and the L. mandshuricus complex containing L. coreanus. On the other hand, massive mitochondrial introgression from two L. timidus lineages to the L. mandshuricus complex was suggested in continental East Asia. The northern population of the L. mandshuricus complex was mainly associated with introgression from the continental lineage of L. timidus, possibly since the last glacial period, whereas the southern population of the L. mandshuricus complex experienced introgression from another L. timidus lineage related to the Hokkaido population, possibly before the last glacial period. In contrast to continental hares, no evidence of introgression was found in L. brachyurus in the Japanese Archipelago, which showed the oldest divergence amongst East Asian hare lineages. Our findings suggest that glacial-interglacial climate changes in the circum-Japan Sea region promoted distribution shifts and introgressive hybridization among continental hare species, while the geographic structure of the region contributed to long-term isolation of hares on the islands, preventing inter-species gene flow.

The Volcano Rabbit in the Phylogenetic Network of Lagomorphs

The order Lagomorpha unifies pikas (Ochotonidae) and the hares plus rabbits (Leporidae). Phylogenetic reconstructions of the species within Leporidae based on traditional morphological or molecular sequence data provide support for conflicting hypotheses. The retroposon presence/absence patterns analyzed in this study revealed strong support for the broadly accepted splitting of lagomorphs into ochotonids and leporids with Pronolagus as the first divergence in the leporid tree. Furthermore, the retroposon presence/absence patterns nested the rare volcano rabbit, Romerolagus diazi, within an unresolved network of deeper leporid relationships and provide the first homoplasy-free image of incomplete lineage sorting and/or ancestral hybridization/introgression in rapidly radiated Leporidae. At the same time, the strongest retroposon presence/absence signal supports the volcano rabbit as a separate branch between the Pronolagus junction and a unified cluster of the remaining leporids.

Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares

Snowshoe hares (Lepus americanus) maintain seasonal camouflage by molting to a white winter coat, but some hares remain brown during the winter in regions with low snow cover. We show that cis-regulatory variation controlling seasonal expression of the Agouti gene underlies this adaptive winter camouflage polymorphism. Genetic variation at Agouti clustered by winter coat color across multiple hare and jackrabbit species, revealing a history of recurrent interspecific gene flow. Brown winter coats in snowshoe hares likely originated from an introgressed black-tailed jackrabbit allele that has swept to high frequency in mild winter environments. These discoveries show that introgression of genetic variants that underlie key ecological traits can seed past and ongoing adaptation to rapidly changing environments.

The puzzling phylogeography of the haplochromine cichlid fish Astatotilapia burtoni

Astatotilapia burtoni is a member of the "modern haplochromines," the most species-rich lineage within the family of cichlid fishes. Although the species has been in use as research model in various fields of research since almost seven decades, including developmental biology, neurobiology, genetics and genomics, and behavioral biology, little is known about its spatial distribution and phylogeography. Here, we examine the population structure and phylogeographic history of A. burtoni throughout its entire distribution range in the Lake Tanganyika basin. In addition, we include several A. burtoni laboratory strains to trace back their origin from wild populations. To this end, we reconstruct phylogenetic relationships based on sequences of the mitochondrial DNA (mtDNA) control region (d-loop) as well as thousands of genomewide single nucleotide polymorphisms (SNPs) derived from restriction-associated DNA sequencing. Our analyses reveal high population structure and deep divergence among several lineages, however, with discordant nuclear and mtDNA phylogenetic inferences. Whereas the SNP-based phylogenetic hypothesis uncovers an unexpectedly deep split in A. burtoni, separating the populations in the southern part of the Lake Tanganyika basin from those in the northern part, analyses of the mtDNA control region suggest deep divergence between populations from the southwestern shoreline and populations from the northern and southeastern shorelines of Lake Tanganyika. This phylogeographic pattern and mitochondrial haplotype sharing between populations from the very North and the very South of Lake Tanganyika can only partly be explained by introgression linked to lake-level fluctuations leading to past contact zones between otherwise isolated populations and large-scale migration events.

Mitochondrial and nuclear DNA reveals reticulate evolution in hares (Lepus spp., Lagomorpha, Mammalia) from Ethiopia

For hares (Lepus spp., Leporidae, Lagomorpha, Mammalia) from Ethiopia no conclusive molecular phylogenetic data are available. To provide a first molecular phylogenetic model for the Abyssinian Hare (Lepus habessinicus), the Ethiopian Hare (L. fagani), and the Ethiopian Highland Hare (L. starcki) and their evolutionary relationships to hares from Africa, Eurasia, and North America, we phylogenetically analysed mitochondrial ATPase subunit 6 (ATP6; n = 153 / 416bp) and nuclear transferrin (TF; n = 155 / 434bp) sequences of phenotypically determined individuals. For the hares from Ethiopia, genotype composition at twelve microsatellite loci (n = 107) was used to explore both interspecific gene pool separation and levels of current hybridization, as has been observed in some other Lepus species. For phylogenetic analyses ATP6 and TF sequences of Lepus species from South and North Africa (L. capensis, L. saxatilis), the Anatolian peninsula and Europe (L. europaeus, L. timidus) were also produced and additional TF sequences of 18 Lepus species retrieved from GenBank were included as well. Median joining networks, neighbour joining, maximum likelihood analyses, as well as Bayesian inference resulted in similar models of evolution of the three species from Ethiopia for the ATP6 and TF sequences, respectively. The Ethiopian species are, however, not monophyletic, with signatures of contemporary uni- and bidirectional mitochondrial introgression and/ or shared ancestral polymorphism. Lepus habessinicus carries mtDNA distinct from South African L. capensis and North African L. capensis sensu lato; that finding is not in line with earlier suggestions of its conspecificity with L. capensis. Lepus starcki has mtDNA distinct from L. capensis and L. europaeus, which is not in line with earlier suggestions to include it either in L. capensis or L. europaeus. Lepus fagani shares mitochondrial haplotypes with the other two species from Ethiopia, despite its distinct phenotypic and microsatellite differences; moreover, it is not represented by a species-specific mitochondrial haplogroup, suggesting considerable mitochondrial capture by the other species from Ethiopia or species from other parts of Africa. Both mitochondrial and nuclear sequences indicate close phylogenetic relationships among all three Lepus species from Ethiopia, with L. fagani being surprisingly tightly connected to L. habessinicus. TF sequences suggest close evolutionary relationships between the three Ethiopian species and Cape hares from South and North Africa; they further suggest that hares from Ethiopia hold a position ancestral to many Eurasian and North American species.

Variation of partial transferrin sequences and phylogenetic relationships among hares (Lepus capensis, Lagomorpha) from Tunisia

North African hares are currently included in cape hares, Lepus capensis sensu lato, a taxon that may be considered a superspecies or a complex of closely related species. The existing molecular data, however, are not unequivocal, with mtDNA control region sequences suggesting a separate species status and nuclear loci (allozymes, microsatellites) revealing conspecificity of L. capensis and L. europaeus. Here, we study sequence variation in the intron 6 (468 bp) of the transferrin nuclear gene, of 105 hares with different coat colour from different regions in Tunisia with respect to genetic diversity and differentiation, as well as their phylogenetic status. Forty-six haplotypes (alleles) were revealed and compared phylogenetically to all available TF haplotypes of various Lepus species retrieved from GenBank. Maximum Likelihood, neighbor joining and median joining network analyses concordantly grouped all currently obtained haplotypes together with haplotypes belonging to six different Chinese hare species and the African scrub hare L. saxatilis. Moreover, two Tunisian haploypes were shared with L. capensis, L timidus, L. sinensis, L. yarkandensis, and L. hainanus from China. These results indicated the evolutionary complexity of the genus Lepus with the mixing of nuclear gene haplotypes resulting from introgressive hybridization or/and shared ancestral polymorphism. We report the presence of shared ancestral polymorphism between North African and Chinese hares. This has not been detected earlier in the mtDNA sequences of the same individuals. Genetic diversity of the TF sequences from the Tunisian populations was relatively high compared to other hare populations. However, genetic differentiation and gene flow analyses (AMOVA, F_ST, Nm) indicated little divergence with the absence of geographically meaningful phylogroups and lack of clustering with coat colour types. These results confirm the presence of a single hare species in Tunisia, but a sound inference on its phylogenetic position would require additional nuclear markers and numerous geographically meaningful samples from Africa and Eurasia.

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.

Complete mitochondrial DNA sequence of Lepus sinensis (Leporidae: Lepus)

In the present study, we determined the complete nucleotide sequence of the mitochondrial (mt) genome of Chinese hare, Lepus sinensis (Leporidae: Lepus) by using polymerase chain reaction (PCR) technique. The entire mtDNA sequence is 17438 nucleotides long and contains 13 protein-coding genes, 2 ribosomal tRNA 22 transfer RNA gens and one long non-coding region known as the control region. The mt gene arrangement of L. sinensis is identical to those typical for vertebrates.