Protein variation and its systematic implications for the South African Leporidae (Mammalia:Lagomorpha)

Analysis of 9 genetic loci by horizontal starch gel electrophoresis was performed on 203 specimens of South African representatives of the leporid genera Lepus and Pronolagus . Three loci were found to be polymorphic within samples of the various species of both genera: transferrin (Tf-I), esterase-1 (Es-I) and esterase-2 (Es-II). Only one system, carbonic anhydrase (CA-I), proved useful in species identification, this being restricted to the genus Lepus . Based on this system all Lepus specimens analysed would be assigned to one of two groups corresponding to the species L. capensis and L. saxatils .     

The rise and fall of the mountain hare (Lepus timidus) during Pleistocene glaciations: expansion and retreat with hybridization in the Iberian Peninsula

The climatic fluctuations during glaciations have affected differently arctic and temperate species. In the northern hemisphere, cooling periods induced the expansion of many arctic species to the south, while temperate species were forced to retract in southern refugia. Consequently, in some areas the alternation of these species set the conditions for competition and eventually hybridization. Hares in the Iberian Peninsula appear to illustrate this phenomenon. Populations of Iberian hare (Lepus granatensis), brown hare (Lepus europaeus) and broom hare (Lepus castroviejoi) in Northern Iberia harbour mitochondrial haplotypes from the mountain hare (Lepus timidus), a mainly boreal and arctic species presently absent from the peninsula. To understand the history of this past introgression we analysed sequence variation and geographical distribution of mitochondrial control region and cytochrome b haplotypes of L. timidus origin found in 378 specimens of these four species. Among 124 L. timidus from the Northern Palaearctic and the Alps we found substantial nucleotide diversity (2.3%) but little differentiation between populations. Based on the mismatch distribution of the L. timidus sequences, this could result from an expansion at a time of temperature decrease favourable to this arctic species. The nucleotide diversity of L. timidus mtDNA found in Iberian L. granatensis, L. europaeus and L. castroviejoi (183, 70 and 1 specimens, respectively) was of the same order as that in L. timidus over its range (1.9%), suggesting repeated introgression of multiple lineages. The structure of the coalescent of L. granatensis sequences indicates that hybridization with L. timidus was followed by expansion of the introgressed haplotypes, as expected during a replacement with competition, and occurred when temperatures started to rise, favouring the temperate species. Whether a similar scenario explains the introgression into Iberian L. europaeus remains unclear but it is possible that it hybridized with already introgressed L. granatensis.     

Invasion from the cold past: extensive introgression of mountain hare (Lepus timidus) mitochondrial DNA into three other hare species in northern Iberia

Mitochondrial DNA introgression from Lepus timidus into Lepus granatensis and Lepus europaeus was recently reported in Iberia, although L. timidus presumably retreated from this region at the end of the last ice age. Here we assess the extent of this ancient mtDNA introgression by RFLP analysis of 695 specimens representing the three hare species present in Iberia. The introgressed L. timidus lineage was found in 23 of the 37 populations sampled. It is almost fixed in L. europaeus across its Iberian range in the Pyrenean foothills, and in L. granatensis, which occupies the rest of the peninsula, it is predominant in the north and gradually disappears further south. We also found it in Lepus castroviejoi, a species endemic to Cantabria. Multiple hybridizations and, potentially, a selective advantage for the L. timidus lineage can explain the remarkable taxonomic and geographical range of this mitochondrial introgression.     

Pseudogenization of the MCP-2/CCL8 chemokine gene in European rabbit (genus Oryctolagus), but not in species of Cottontail rabbit (Sylvilagus) and Hare (Lepus)

ABSTRACT: BACKGROUND: Recent studies in human have highlighted the importance of the monocyte chemotactic proteins (MCP) in leukocyte trafficking and their effects in inflammatory processes, tumor progression, and HIV-1 infection. In European rabbit (Oryctolagus cuniculus) one of the prime MCP targets, the chemokine receptor CCR5 underwent a unique structural alteration. Until now, no homologue of MCP-2/CCL8a, MCP-3/CCL7 or MCP-4/CCL13 genes have been reported for this species. This is interesting, because at least the first two genes are expressed in most, if not all, mammals studied, and appear to be implicated in a variety of important chemokine ligand-receptor interactions. By assessing the Rabbit Whole Genome Sequence (WGS) data we have searched for orthologs of the mammalian genes of the MCP-Eotaxin cluster. RESULTS: We have localized the orthologs of these chemokine genes in the genome of European rabbit and compared them to those of leporid genera which do (i.e. Oryctolagus and Bunolagus) or do not share the CCR5 alteration with European rabbit (i.e. Lepus and Sylvilagus). Of the Rabbit orthologs of the CCL8, CCL7, and CCL13 genes only the last two were potentially functional, although showing some structural anomalies at the protein level. The ortholog of MCP-2/CCL8 appeared to be pseudogenized by deleterious nucleotide substitutions affecting exon1 and exon2. By analyzing both genomic and cDNA products, these studies were extended to wild specimens of four genera of the Leporidae family: Oryctolagus, Bunolagus, Lepus, and Sylvilagus. It appeared that the anomalies of the MCP-3/CCL7 and MCP-4/CCL13 proteins are shared among the different species of leporids. In contrast, whereas MCP-2/CCL8 was pseudogenized in every studied specimen of the Oryctolagus - Bunolagus lineage, this gene was intact in species of the Lepus - Sylvilagus lineage, and was, at least in Lepus, correctly transcribed. CONCLUSION: The biological function of a gene was often revealed in situations of dysfunction or gene loss. Infections with Myxoma virus (MYXV) tend to be fatal in European rabbit (genus Oryctolagus), while being harmless in Hares (genus Lepus) and benign in Cottontail rabbit (genus Sylvilagus), the natural hosts of the virus. This communication should stimulate research on a possible role of MCP-2/CCL8 in poxvirus related pathogenicity.     

A GENETIC ANALYSIS OF SYMPATRIC SUBPOPULATIONS OF THE SIBLING SPECIES LITTORINA SAXATILIS (OLIVI) AND LITTORINA ARCANA HANNAFORD ELLIS

A detailed analysis of shell characteristics (four parameters)and allozyme allele frequencies (eight to nine polymorphic loci)of sympatric Littorina saxatilis and Littorina arcana subpopulationsfrom Filey Brigg on the east coast of England supports theiridentification as closely related but separate species. Oneenzyme system, esterase-2, was nearly species diagnostic. Resultswere generally comparable with an earlier study of the two speciesfrom East Lothian, Scotland. Littorina saxatilis was again foundto be more variable than L. arcana. (Received 14 December 1983;     

Mitochondrial Cytochrome b Gene Sequence Diversity in the Korean Hare, Lepus coreanus Thomas (Mammalia, Lagomorpha)

Partial sequences of the mitochondrial cytochrome b gene of the Korean hare (Lepus coreanus) were analyzed to determine the degree of genetic diversity. Nine haplotypes were observed, and the maximum Tamura-Nei nucleotide distance among them was 2.8%, indicating that genetic diversity of L. coreanus is moderate. In order to clarify the Korean hare's taxonomic status and relationship with the Manchurian hare (L. mandshuricus) and the Chinese hare (L. sinensis), these nine haplotypes of the Korean hare were compared with 13 haplotypes from five other species of eastern Asian Lepus including L. mandshuricus and L. sinensis. The Korean hare was distinct in its cytochrome b gene, and it is confirmed that L. coreanus is a valid species, as noted by Jones and Johnson (1965, Univ. Kansas Publ. (Mus. Nat. Hist.) 16:357). Further analyses of mtDNA cytochrome b gene with additional specimens of L. coreanus from North Korea and other species of Lepus from eastern Asia are needed to clarify the taxonomic status of the divergent mtDNA clades of L. mandshuricus and L. sinensis.     

Sex-specific recombination rates in Parus major and P. caeruleus, an exception to Huxley's rule

Huxley's rule predicts lower recombination rates in the heterogametic sex than in the homogametic one. The genotyping of Parus major and P. caeruleus families at 8 microsatellite and 4 enzyme loci yielded contradicting data. Significant genotypic disequilibrium was observed between esterase-1, esterase-2 and esterase-3 in adults of P. major and between esterase-2/esterase-3 and esterase-2/microsatellite PK-12 in P. caeruleus. Support comes from linkage analyses of nuclear families. In P. major, the recombination rate of esterase-2/esterase -3 in males is significantly lower than in females (theta(male) = 0.076, theta(female) = 0.145). The opposite is found for the recombination rates of esterase-1/esterase-2 and esterase-2/esterase-3 in P. caeruleus (EST-1/EST-2: theta(female) = 0.218, theta(male) = 0.5, EST-2/EST-3: theta(female) = 0.109, theta(male) = 0.194). We conclude that the basis of differences in recombination rates cannot be heterogamety, per se, but must have multiple genetic causes including chromosomal rearrangments that have evolved after the cladogenesis of the two species.     

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.     

中国更新世兔属化石两新种

中国更新世兔属(Lepus)化石较为丰富,尤其是周口店各化石地点产出了大量的标本。但受条件的限制,缺乏对现生骨骼标本的研究与对比,分类位置混乱或仅鉴定为未定种。详细观察研究了中国科学院动物研究所保存的现生兔属8种的187件头骨标本,归纳整理出Lepus各个种头骨与牙齿特征的个体差异和年龄变化以及稳定的特征。主要稳定特征包括:鼻骨基本形态,如长度、前后相对宽度等;额骨两侧凹陷深浅;眶上突上翘程度;颞窝的深浅及宽度;成年个体上间顶骨愈合,或不完全愈合;门齿前齿沟的形态及白垩质充填的情况;门齿孔宽,腭桥长及翼内窝宽度的比例关系;颧骨高度,浅层咬肌窝及咬肌突腹面三角的形态(反映出咬肌的发育程度);吻部形态;下颌骨基本形态(冠状突、上升支、齿隙骨体、颏孔位置等);颊齿基本形态等。在对现生标本观察研究的基础上,详细描述了周口店第13地点的兔头骨及颅后骨骼,命名一新种德氏兔Lepus teilhardisp. nov.。新种以下列特征区别于已知兔属各种:颅全长平均大于90 mm,眶上突轻微上翘,前支稍短,后支发育;额骨两侧凹陷浅;咬肌突腹面中等大小;颧弓浅层咬肌窝较深;翼内窝宽度明显大于腭桥最小纵径;门齿孔较细长;颞窝上突起较高;枕外结节向下延伸成一低脊;听泡较大;外枕骨较宽,顶视几乎覆盖岩乳骨及部分听泡;I2前齿沟"V"字形,内、外两侧的前缘较平直且几乎持平,充填少量白垩质;下颌骨冠状突倾斜。陕西蓝田陈家窝子发现的翁氏兔(Lepus wongi)也归入该种内。将山东淄博孙家山发现的标本命名为淄博兔Lepus ziboensissp. nov.。该种门齿前齿沟浅窄,充填白垩质;齿隙明显较长;腭桥较长;翼内窝宽度与腭桥长度近乎相等;P2外前褶沟窄浅,内前褶沟亦较浅;p3在1件标本上可见较浅的前内褶沟。根据共生动物群分析,淄博兔的时代为早更新世晚期,参照测年数据德氏兔的时代可能从早更新世晚期至中更新世早期。     

Importance of biochemical marker genes in inbred strains of mice. Some problems on checking genetic purity of inbred strains (author's transl)

In order to check genetic purity of inbred strains of mice, we surveyed five biochemical variants in certain 69 strains, some of which had established from Japanese fancy mice. The loci examined were Hemoglobin beta-chain, Malic enzyme (supernatant form), Isocitrate dehydrogenase (supernatant form), Serum esterase-1, and Serum esterase-2. These loci were all in homozygous states as far as examined, however some subline divergences were found in a few strains, that is to say, sublines were found to be fixed with different alleles as some loci, Important of biochemical marker genes to check genetic purity of strains and several derived problems are mentioned.     

Home-loving boreal hare mitochondria survived several invasions in Iberia: the relative roles of recurrent hybridisation and allele surfing

Genetic introgression from a resident species into an invading close relative can result from repeated hybridisation along the invasion front and/or allele surfing on the expansion wave. Cases where the phenomenon is massive and systematic, such as for hares (genus Lepus) in Iberia, would be best explained by recurrent hybridisation but this is difficult to prove because the donor populations are generally extinct. In the Pyrenean foothills, Lepus europaeus presumably replaced Lepus granatensis recently and the present species border is parallel to the direction of invasion, so that populations of L. granatensis in the contact zone represent proxies of existing variation before the invasion. Among three pairs of populations sampled across this border, we find less differentiation of mitochondrial DNA (mtDNA) across than along it, as predicted under recurrent hybridisation at the invasion front. Using autosomal microsatellite loci and X- and Y-linked diagnostic loci, we show that admixture across the border is quasi-absent, making it unlikely that lack of interspecific mtDNA differentiation results from ongoing gene flow. Furthermore, we find that the local species ranges are climatically contrasted, making it also unlikely that ongoing ecology-driven movement of the contact account for mtDNA introgression. The lack of mtDNA differentiation across the boundary is mostly due to sharing of mtDNA from a boreal species currently extinct in Iberia (Lepus timidus) whose mitochondria have thus remained in place since the last deglaciation despite successive invasions by two other species. Home-loving mitochondria thus witness past species distribution rather than ongoing exchanges across stabilised contact zones.     

The ubiquitous mountain hare mitochondria: multiple introgressive hybridization in hares, genus Lepus

Climatic oscillations during the glaciations forced dramatic changes in species distributions, such that some presently temperate regions were alternately occupied by temperate and arctic species. These species could have met and hybridized during climatic transitions. This phenomenon happened for three hare species present in Iberia (Lepus granatensis, Lepus europaeus and Lepus castroviejoi), which display high frequencies of mitochondrial DNA (mtDNA) from Lepus timidus, an arctic/boreal species presently extinct in Iberia. Here, we extend our previous geographical survey to determine whether the distribution of this mtDNA lineage extends beyond the northern half of the Iberian Peninsula, where it is found at high frequencies. We also review the taxonomy, distribution and molecular phylogeny of the genus Lepus. The phylogenetic inference reveals the presence of L. timidus-like mtDNA in several other hare species in Asia and North America, suggesting that the mitochondrial introgression observed in Iberia might be generalized. Comparison with the available nuclear gene phylogenies suggests that introgression could have happened repeatedly, possibly during different climatic transitions. We discuss demographic and adaptive scenarios that could account for the repetition in time and space of this spectacular phenomenon and suggest ways to improve our understanding of its determinants and consequences. Such high levels of introgressive hybridization should discourage attempts to revise hare taxonomy based solely on mtDNA.     

Genic Heterogeneity within Electrophoretic "Alleles" and the Pattern of Variation among Loci in DROSOPHILA PSEUDOOBSCURA

An investigation, similar to our previously reported xanthine dehydrogenase study, was undertaken to examine the extent of hidden genic variation at nine loci (five larval proteins, three esterases and one aldehyde oxidase) by sequential application of various electrophoretic criteria employing pH, gel concentration and buffer variation. Polymorphic loci appear to fall into two distinct groups: weakly polymorphic, including larval protein 6, 7, 8, 10 and 13 and esterase-1 and -6; and highly polymorphic, including esterase-5, Xdh and possibly Ao. Monomorphic loci may belong to a third group different from all polymorphic loci. Bogota, a geographical isolate that is reproductively isolated from the mainland population, was found to be genetically distinct at four of the ten loci examined in detail so far, including Xdh, whereas previously it was found to be genetically distinct at none. These results are discussed in the light of balancing selection, neutral and mutation-selection hypotheses of genic variation in natural populations.     

The genomic legacy from the extinct Lepus timidus to the three hare species of Iberia: contrast between mtDNA, sex chromosomes and autosomes

Extensive interspecific genetic introgression is often reported, and appraising its genomic impact can serve to determine whether it results from selection on specific loci or from demographic processes affecting the whole genome. The three species of hares present in the Iberian Peninsula harbour high frequencies of mitochondrial DNA (mtDNA) from Lepus timidus, an arctic/boreal species now extinct in the region. This could result from the invasive replacement of L. timidus by the temperate species during deglaciation but should then have left traces in the nuclear genome. We typed single nucleotide polymorphisms (SNPs) discovered by sequencing 10 autosomal loci, two X-linked and one Y-linked in species-wide samples of the four taxa. Based on lineage-diagnostic SNPs, we detected no trace of L. timidus sex chromosomes in Iberia. From the frequencies of inferred haplotypes, autosomal introgression into L. granatensis appeared mostly sporadic but always widespread instead of restricted to the north as mtDNA. Autosomal introgression into Iberian L. europaeus , inhabiting the Pyrenean foothills, was hardly detectable, despite quasi-fixation of L. timidus mtDNA. L. castroviejoi , endemic to the Cantabrian Mountains and fixed for L. timidus mtDNA, showed little traces of autosomal introgression. The absence of sex-chromosome introgression presumably resulted from X-linked hybrid male unfitness. The contrasting patterns between the autosomes and mtDNA could reflect general gender asymmetric processes such as frequency-dependent female assortative mating, lower mtDNA migration and higher male dispersal, but adaptive mtDNA introgression cannot be dismissed. Additionally, we document reciprocal introgression between L. europaeus and both L. granatensis in Iberia and L. timidus outside Iberia.     

Ancient introgression of Lepus timidus mtDNA into L. granatensis and L. europaeus in the Iberian Peninsula

A 587 bp fragment of cytochrome b sequences from 90 individuals of 15 hare (Lepus) species and two outgroups were phylogenetically analysed and compared to an analysis derived from 474 bp sequences of the nuclear transferrin gene. Mountain hare (Lepus timidus) type mtDNA was observed in L. granatensis and L. europaeus from the Iberian Peninsula, far away from the extant distributional range of L. timidus. In addition to these two hare species, other hare species may also contain mtDNA from L. timidus. This species may have introgressed with other species of Lepus that occur within its present range, or where fossils indicate its historical presence during glacial periods. L. timidus mtDNA is common in the northern part of the L. granatensis range. Finally, we reassessed the phylogenetic relationships of the five European hare species based on both mitochondrial and nuclear DNA sequences.     

Hares on ice: phylogeography and historical demographics of Lepus arcticus, L. othus, and L. timidus (Mammalia: Lagomorpha)

Phylogeographical investigations of arctic organisms provide spatial and temporal frameworks for interpreting the role of climate change on biotic diversity in high-latitude ecosystems. Phylogenetic analyses were conducted on 473 base pairs of the mitochondrial control region in 192 arctic hares (Lepus arcticus, Lepus othus, Lepus timidus) and two individual Lepus townsendii. The three arctic hare species are closely related. All L. othus individuals form one well-supported clade, L. arcticus individuals form two well-supported clades, and L. timidus individuals are scattered throughout the phylogeny. Arctic hare distribution was altered dramatically following post-Pleistocene recession of continental ice sheets. We tested for genetic signatures of population expansion for hare populations now found in deglaciated areas. Historical demographic estimates for 12 arctic hare populations from throughout their range indicate that L. arcticus and L. othus persisted in two separate North American arctic refugia (Beringia and High Canadian Arctic) during glacial advances of the Pleistocene, while the high genetic diversity in L. timidus likely reflects multiple Eurasian refugia.     

河北秦皇岛柳江盆地中更新世野兔一新种

在河北秦皇岛柳江盆地山羊寨附近中更新世洞穴堆积中发现一种小型野兔化石:秦皇岛兔Lepus qinhuangdaoensis sp.nov.,该种以其个体小、p3后外褶沟深达内侧齿缘或贯穿整个齿冠面、部分标本p3具有釉岛及前内褶沟等特征区别于其他已知种。它是迄今为止所知的体形最小的野兔。     

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

We 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.     

中国更新世兔属化石的厘定

在对我国现生兔属各种骨骼特征研究的基础上,通过形态特征的观察与测量数据的分析,修订了已有的兔属化石材料。将周口店第1,2,6,20,山顶洞和东岭子洞等地点以及山东平邑发现的兔标本归入草兔Lepus capensis。以前被归入Lepus wongi种内的标本,除周口店第13地点及蓝田陈家窝子的应属于Lepus teilhardi外,其余地点的皆为Lepus capensis,因此L.wongi失去了原有的意义,为无效种。周口店第16地点的标本归入华南兔Lepus sinensis,是该种目前惟一的化石记录。辽宁营口金牛山的标本暂时归入东北兔Lepus mandschuricus。我国更新世共发现两个化石种和4个现生种。其中化石种Lepus teilhardi和L.ziboensis出现在早更新世晚期至中更新世早期,现生种L.capensis,L.mandschuricus,L.sinensis和L.comus分别出现在中更新世与晚更新世。初步讨论了兔属的起源,认为兔属可能起源于上新世的Trischizolagus。     

Electrophoretic identification of bird species involved in collisions with aircraft

• 1.1. The utility of biochemical genetic methods of bird identification was investigated for some common species which create a hazard for commercial aviation in Ireland.
• 2.2. Sixteen enzyme loci were assayed in eight species, using starch gel electrophoresis; three larids, three corvids and two columbids.
• 3.3. Genera were distinguishable using all but two loci.
• 4.4. Differences within genera were small, but all species except for the gulls Larus argentatus and L. marinus, could be identified using one or more loci.
• 5.5. Arising from the success of the method using fresh specimens, a protocol for the electrophoretic identification of traumatized remains of strikes is suggested.