Leporid Genera Research Articles

Illuminating the obscured phylogenetic radiation of South AmericanSylvilagusGray, 1867 (Lagomorpha: Leporidae)

Largely shallow and putatively explosive divergences in the family Leporidae (rabbits and hares; order: Lagomorpha) have resulted in phylogenetic relationships that remain currently unresolved. These rapid radiations in different branches of the leporid tree have resulted in conflicting phylogenetic hypotheses. However, this phylogenetic incongruence may also result from inadequate taxon or character sampling, due to the high number of extinct and difficult to sample extant species, and highly conserved morphological characters. Sylvilagus (cottontail rabbits) constitute about 30% of the known extant leporid species. New species are routinely being recognized, and phylogenetic relationships with respect to other leporid genera, and within the genus, have failed to be recovered with certainty. Within Sylvilagus, the South American S. brasiliensis is the most widespread and poorly known taxon, likely comprising multiple species. Here, we reanalyze previously published molecular data from phylogenetic studies on Leporidae, focusing on the S. brasiliensis group, and assessing phylogenetic relationships using bifurcating trees and split networks to identify phylogenetic regions with polytomies. We estimate differentiation and phylogenetic relationships of molecular lineages within the S. brasiliensis group. Our analyses suggest that this group contains a number of divergent taxa, well differentiated from other cottontail species. We discern two major polytomies during leporid diversification. The first, at the base of the leporid radiation, likely resulted from a combination of hard (rapid radiation) and soft polytomies (high number of unsampled extinct species). The second polytomy likely resulted from a rapid radiation during the initial diversification of the genus Sylvilagus. We conclude that only a molecular phylogeny based on a broader taxonomic representation will fully resolve leporid phylogeny.

Host-Specific Glycans Are Correlated with Susceptibility to Infection by Lagoviruses, but Not with Their Virulence.

Rabbit hemorrhagic disease virus (RHDV) and European brown hare syndrome virus (EBHSV) are two lagoviruses from the family Caliciviridae that cause fatal diseases in two leporid genera, Oryctolagus and Lepus, respectively. In the last few years, several examples of host jumps of lagoviruses among leporids were recorded. In addition, a new pathogenic genotype of RHDV emerged, and many nonpathogenic strains of lagoviruses have been described. The molecular mechanisms behind host shifts and the emergence of virulence are unknown. Since RHDV uses glycans of the histo-blood group antigen type as attachment factors to initiate infection, we studied if glycan specificities of the new pathogenic RHDV genotype, nonpathogenic lagoviruses, and EBHSV potentially play a role in determining the host range and virulence of lagoviruses. We observed binding to A, B, or H antigens of the histo-blood group family for all strains known to primarily infect European rabbits (Oryctolagus cuniculus), which have recently been classified as GI strains. However, we could not explain the emergence of virulence, since similar glycan specificities were found in several pathogenic and nonpathogenic strains. In contrast, EBHSV, recently classified as GII.1, bound to terminal β-linked N-acetylglucosamine residues of O-glycans. Expression of these attachment factors in the upper respiratory and digestive tracts in three lagomorph species (Oryctolagus cuniculus, Lepuseuropaeus, and Sylvilagus floridanus) showed species-specific patterns regarding susceptibility to infection by these viruses, indicating that species-specific glycan expression is likely a major contributor to lagovirus host specificity and range.IMPORTANCE Lagoviruses constitute a genus of the family Caliciviridae comprising highly pathogenic viruses, RHDV and EBHSV, that infect rabbits and hares, respectively. Recently, nonpathogenic strains were discovered and new pathogenic strains have emerged. In addition, host jumps between lagomorphs have been observed. The mechanisms responsible for the emergence of pathogenicity and host species range are unknown. Previous studies showed that RHDV strains attach to glycans expressed in the upper respiratory and digestive tracts of rabbits, the likely portals of virus entry. Here, we studied the glycan-binding properties of novel pathogenic and nonpathogenic strains looking for a link between glycan binding and virulence or between glycan specificity and host range. We found that glycan binding did not correlate with virulence. However, expression of glycan motifs in the upper respiratory and digestive tracts of lagomorphs revealed species-specific patterns associated with the host ranges of the virus strains, suggesting that glycan diversity contributes to lagovirus host ranges.

Evolution of viral sensing RIG-I-like receptor genes in Leporidae genera Oryctolagus, Sylvilagus, and Lepus

One of the most severe European rabbit (Oryctolagus cuniculus) pathogens is myxoma virus (MYXV), a rabbit-specific leporipoxvirus that causes the highly lethal disease myxomatosis. Other leporid genera, Sylvilagus and Lepus, encompass species with variable susceptibilities to MYXV, but these do not develop the lethal form of the disease. The protective role of the retinoic acid-inducible gene-I (RIG-I/DDX58) in sensing MYXV in nonpermissive human myeloid cells prompted the study of the RIG-I-like receptor (RLR) family evolution in the three leporid genera. This viral-sensor family also includes the melanoma differentiation-associated factor 5 (MDA5/IFIH1), and the laboratory of genetics and physiology 2 (LGP2/DHX58). Considering specifically the MYXV susceptible host (European rabbit) and one of the virus natural long-term hosts (Sylvilagus bachmani, brush rabbit), the amino acid differences of positively selected sites in RIG-I between the two species were located in the protein region responsible for viral RNA recognition and binding, the repressor domain. Such differences might play a determinant role in how MYXV is sensed. When looking for episodic selection on MDA5 and LGP2 of the eastern cottontail (Sylvilagus floridanus), we also uncovered evidence of selective pressures that might be exerted by a species-specific leporipoxvirus, the Shope fibroma virus. Finally, a putative alternative splicing case was identified in Oryctolagus and Lepus MDA5 isoforms, corresponding to the deletion of one specific exon. This study provided the first insights into the evolution of the leporid RLR gene family that helps illuminate the origins of the species-specific innate responses to pathogens and more specifically to MYXV.

Lagomorphs (rabbits, pikas and hares) do not use telomere-directed replicative aging in vitro

Telomere shortening is used for replicative aging in primates and ungulates but not rodents. We examined telomere biology in rabbits to expand the comparative biology of telomere-directed replicative senescence within mammals. The order Lagomorpha consists of two families; Leporidae and Ochotonidae. We examined telomere biology in species representing three leporid genera (European White Rabbit, Black-tailed Jack Rabbit, and Swamp Rabbit) and the monotypic ochotonid genus (North American Pika). Of the leporids one species was a laboratory strain and the others were wild caught. The leporids neither exhibited cellular senescence after sustained periods in culture nor displayed detectable telomerase activity. Continued culture was possible because of their extremely long telomeric arrays. Immunofluorescence showed robust telomere signals at chromosome ends and significant internal chromosomal staining in some instances. Pika was unique in displaying endogenous telomerase activity throughout time in culture. These results show that it is unlikely that lagomorphs use telomere shortening and replicative senescence as a tumor protective mechanism.

Isolation and characterization of six polymorphic microsatellite loci in South African hares (Lepus saxatilis F. Cuvier, 1823 and Lepus capensis Linnaeus, 1758)

AbstractWe have developed six novel, polymorphic microsatellite markers for the scrub hare, Lepus saxatilis. These markers have been tested for 150 scrub hares and 67 Cape hares from different localities across southern Africa. All six loci amplified consistently well and most were highly polymorphic. Four loci amplified consistently in five different leporid genera. The microsatellites presented here will be useful for phylogeographical studies in the scrub hare and other leporidae.

Pliocene Leporidae (Lagomorpha, Mammalia) from the Upper Siwaliks of India: Implications for phylogenetic relationships

ABSTRACT New studies based on enamel microstructure, as well as morphometric and morphologic comparative analyses have led to the revision of the Siwalik leporids described to date. A dp3 has been placed in Pliosiwalagus whitei, and a p3 previously assigned to Pliosiwalagus whitei has been placed in Pliosiwalagus sp. A specimen with p3p4, previously assigned to Caprolagus sivalensis has been reassigned to the genus Pliosiwalagus. A generalized phylogeny of Old World leporids has been suggested. Enamel microstructure studies of various leporid genera reveal difference in distribution of radial and irregular enamel within the thin and thick enamel of p3s and p4s. Morphological differences among the p3s of fossil and extant leporid genera of Asia, Europe and Africa have been quantified using “Thin Plate Spline” program. Results from this analysis support the interpretations based on morphological similarities.

Multiple substitutions affect the phylogenetic utility of cytochrome b and 12S rDNA data: examining a rapid radiation in leporid (Lagomorpha) evolution.

Partial sequences of two mitochondrial genes, the 12S ribosomal gene (739 bp) and the cytochrome b gene (672 bp), were analyzed in hopes of reconstructing the evolutionary relationships of 11 leporid species, representative of seven genera. However, partial cytochrome b sequences were of little phylogenetic value in this study. A suite of pairwise comparisons between taxa revealed that at the intergeneric level, the cytochrome b gene is saturated at synonymous coding positions due to multiple substitution events. Furthermore, variation at the nonsynonymous positions is limited, rendering the cytochrome b gene of little phylogenetic value for assessing the relationships between leporid genera. If the cytochrome b data are analyzed without accounting for these two classes of nucleotides (i.e., synonymous and nonsynonymous sites), one may incorrectly conclude that signal exists in the cytochrome b data. The mitochondrial 12S rRNA gene, on the other hand, has not experienced excessive saturation at either stem or loop positions. Phylogenies reconstructed from the 12S rDNA data support hypotheses based on fossil evidence that African rock rabbits (Pronolagus) are outside of the main leporid stock and that leporids experienced a rapid radiation. However, the molecular data suggest that this radiation event occurred in the mid-Miocene several millions of years earlier than the Pleistocene dates suggested by paleontological evidence.