从12S rRNA和Cyt b基因部分序列研究13种猫科动物的分子系统关系

为探讨中国猫科动物(Felidae)的系统发生关系,本文对中国产13种猫科动物的12SrRNA基因(约371bp)和细胞色素b基因(Cytb)部分序列(约355bp)进行了分析,并采用“最大简约法”和“最大似然法”构建了分子系统树。结果表明:在Cytb基因序列中,有113个位点存在变异(约为总位点数的31.8%),高于12SrRNA基因序列的44个变异位点(约为总位点数的11.9%);构建的分子系统树显示,猞猁(Lynxlynx)可能是中国最早起源的猫科动物,与其它猫科动物之间的亲缘关系较远,支持将其立为猞猁属(Lynx)的观点;草原斑猫(Felislibyca)、丛林猫(Felischaus)、兔狲(Otocolobusmanul)和荒漠猫(Felisbieti)具有较近的亲缘关系,支持将兔狲划归于猫属(Felis)的观点;金猫(Caopumatemminckii)、云猫(Pardofelismarmorata)具有较近的亲缘关系,但它们与猫属物种之间的亲缘关系可能较远,不支持将它们划归于猫属;豹猫(Ponailurusribengalensis)、渔猫(Prionailurusviverrinus)具有较近的亲缘关系,支持将它们同归于豹猫属(Ponailurus);云豹(Neofelisnebulosa)、豹(Pantherapardus)、雪豹(Unciauncia)、虎(Pantheratigris)具有较近的亲缘关系,支持将它们同归于豹属(Panthera)的观点     

Phylogenetic assessment of introns and SINEs within the Y chromosome using the cat family felidae as a species tree

The cat family Felidae was used as a species tree to assess the phylogenetic performance of genes, and their embedded SINE elements, within the nonrecombining region of the Y chromosome (NRY). Genomic segments from single-copy X-Y homologs SMCY, UBE1Y, and ZFY (3,604 bp) were amplified in 36 species of cat. These genes are located within the X-degenerate region of the NRY and are thought to be molecular "fossils" that ceased conventional recombination with the X chromosome early within the placental mammal evolution. The pattern and tempo of evolution at these three genes is significant in light of the recent, rapid evolution of the family over approximately 12 Myr and provides exceptional support for each of the eight recognized felid lineages, as well as clear diagnostic substitutions identifying nearly all species. Bootstrap support and Bayesian posterior probabilities are uniformly high for defining each of the eight monophyletic lineages. Further, the preferential use of specific target-site motifs facilitating SINE insertion is empirically supported by sequence analyses of SINEs embedded within the three genes. Target-site insertion is thought to explain the contradiction between intron phylogeny and results of the SMCY SINE phylogeny that unites distantly related species. Overall, our data suggest X-degenerate genes within the NRY are singularly powerful markers and offer a valuable patrilineal perspective in species evolution.     

Historical DNA reveals the phylogenetic position of the extinct Alpine lynx

During the last two centuries, lynx populations have undergone severe declines and extinctions in Europe. The Alpine lynx, once distributed across the whole Alpine arc, became extinct due to direct human prosecution and deprivation of its main prey in the 1930s. Similar to the Iberian lynx Lynx pardinus , its taxonomy has been subject to several controversies. Moreover, knowing the taxonomic status of the Alpine lynx will help to define conservation units of extant lynx populations in Europe. In this study, we investigated two mitochondrial DNA regions in museum specimens ( n =15) representing the autochthonous Alpine population and in samples from extant Eurasian lynx Lynx lynx populations in Europe and Asia ( n =17). Phylogenetic analysis (cytochrome b , 345 bp) placed the Alpine lynx within the Eurasian lynx lineage. Among all individuals examined, seven different haplotypes (control region, 300 bp) were observed but no unique Alpine haplotype was discovered. Haplotypes of the extinct Alpine population were identical to previously described haplotypes in Scandinavian lynx signifying a recent genetic ancestry with current European populations. Moreover, our genetic data suggest two distinct glacial refugia for the Carpathian and Balkan population. Overall this study demonstrates that historical DNA from extinct populations can help to disentangle the phylogenetic relationships and historical biogeography of taxa with only a limited number of extant populations remaining.     

An ecological reassessment of the southern African carnivore guild: a case study from Member 4, Sterkfontein, South Africa

The southern African late Pliocene to early Pleistocene carnivore guild was much larger than that of the present day. Understanding how this guild may have functioned is important for the reconstruction of carnivore-hominin interactions and to assess the potential for hominin scavenging in southern Africa. In modern ecosystems, the coexistence of larger carnivore species is constrained by several factors, which include high levels of interspecific competition. Here, the composition of the fossil carnivore guild is examined using Sterkfontein Member 4 (Cradle of Humankind, South Africa) as a case study. Sterkfontein Member 4 contains 10 larger carnivore taxa (body mass > 21.5 kg) and may also contain two Australopithecus species. Two possible causes of higher numbers of carnivore species in the South African fossil record are initially considered. First, that there is a bias introduced through comparing assemblages of differing sizes; second, carnivore biodiversity may have been artificially inflated due to previous taxonomic splitting of carnivore species, such as Crocuta. These possibilities are rejected and modern ecological data are used to construct a simple spatial model to determine how many carnivores could have co-existed. Although the resulting model indicates that the carnivore taxa present in Member 4 could have co-occurred, modern ecological studies indicate that it is highly unlikely that they would have co-existed simultaneously. Considering the complex depositional processes that operate in the southern African cave sites, it is proposed that the larger carnivore guild observed in the Sterkfontein Member 4 fossil assemblage is a palimpsest created by time-averaging. In light of this, we suggest that sites which have a large number of carnivore taxa should be examined for time-averaging, while those sites which have relatively few species may be a better reflection of carnivore communities.     

Phylogeny and Speciation of Felids

The phylogeny of the Felidae is reconstructed using a total evidence approach combining sequences from 12S rRNA, 16S rRNA, NADH-5, and cytochrome b genes with morphological and karyological characters. The 1504-character data set generated two equally parsimonious trees (CI = 0.413, 1795 steps) of which a strict consensus revealed one polytomy in the placement of the bay cat group. The tree supports several traditional groupings such as the genera Panthera and Lynx and the ocelot group of small South American felids, and it provides additional resolution of relationships within and among the major felid lineages. Combining phylogenetic, distributional, and ecological data indicates that vicariant speciation has played a relatively minor role in the diversification of the felids (approximately 26% of events), while sympatric speciation has been more important than expected on theoretical grounds (approximately 51.8% of events), although postspeciation dispersal may have blurred the boundaries between sympatric, parapatric, and peripheral isolate modes. An examination of ecological changes on the felid tree shows repeated patterns of resource partitioning in time (activity patterns), space (preferred habitat type), and food (as measured by body size) among closely related species. The rapid diversification of the cats thus appears to have been associated more with ecological than with geological separation.     

Dietary separation of sympatric carnivores identified by molecular analysis of scats

We studied the diets of four sympatric carnivores in the flooding savannas of western Venezuela by analysing predator DNA and prey remains in faeces. DNA was isolated and a portion of the cytochrome b gene of the mitochondrial genome amplified and sequenced from 20 of 34 scats. Species were diagnosed by comparing the resulting sequences to reference sequences generated from the blood of puma (Puma concolor), jaguar (Panthera onca), ocelot (Leopardus pardalus) and crab-eating fox (Cerdocyon thous). Scat size has previously been used to identify predators, but DNA data show that puma and jaguar scats overlap in size, as do those of puma, ocelot and fox. Prey-content analysis suggests minimal prey partitioning between pumas and jaguars. In field testing this technique for large carnivores, two potential limitations emerged: locating intact faecal samples and recovering DNA sequences from samples obtained in the wet season. Nonetheless, this study illustrates the tremendous potential of DNA faecal studies. The presence of domestic dog (Canis familiaris) in one puma scat and of wild pig (Sus scrofa), set as bait, in one jaguar sample exemplifies the forensic possibilities of this noninvasive analysis. In addition to defining the dietary habits of similar size sympatric mammals, DNA identifications from faeces allow wildlife managers to detect the presence of endangered taxa and manage prey for their conservation.     

猫科动物的分类——分子系统学框架和化石证据

猫科动物的演化关系传统上一直是富有争议的,这很大程度上造成了猫科在属一级的分类众说纷纭。新兴的分子生物学技术为我们理解猫科动物的系统发育提供了新的视角,本文回顾了近些年来的猫科分子系统学研究,以Johnson等（2006）和李钢等（2016）的研究结果为核心,同时结合确切的化石记录进行佐证,推断了猫科的演化历史。我们发现,分子系统学提出的现代猫科动物于晚中新世开始适应辐射、先后分化出了8个支系等观点,与化石证据基本吻合;但是分子系统学对部分支系起源的推断与化石证据存在差异。结合化石记录的分析,我们认为现代猫科8个支系中除狞猫支系和虎猫支系以外,其余均最有可能起源于亚洲,现代猫科动物在演化过程中至少经历了30次洲际迁徙。结合演化历史和形态学研究,我们遵循邱占祥等（2004）的观点,将现存的猫科动物全部归于猫亚科（Felinae）,并将现代猫亚科动物划分为15个属40个物种。     

Resolution of recent radiations within three evolutionary lineages of felidae using mitochondrial restriction fragment length polymorphism variation

Patterns of mitochondrial restriction fragment length polymorphism (RFLP) variation were used to resolve more recent relationships among the species of the Felidae ocelot lineage, domestic cat lineage, and pantherine lineage. Twenty-five of 28 restriction enzymes revealed site variation in at least 1 of 21 cat species. The ocelot lineage was resolved into three separate sistertaxa groups: Geoffroy's cat (Oncifelis geoffroyi) and kodkod (O. guigna), ocelot (Leopardus pardalis) and margay (L. wiedii), and pampas cat (Lynchailurus colocolo) and most of the tigrina samples (Leopardus tigrina). Within the domestic cat lineage, domestic cat (Felis catus), European wild cat (F. silvestris), and African wild cat (F. libyca) formed a monophyletic trichotomy, which was joined with sand cat (F. margarita) to a common ancestor. Jungle cat (F. chaus) and black-footed cat (F. nigripes) mtDNAs diverged earlier than those of the other domestic cat lineage species and are less closely related. Within the pantherine lineage, phylogenetic analysis identified two distinct groups, uniting lion (P. leo) with leopard (P. pardus) and tiger (P. tigris) with snow leopard (P. uncia).To whom correspondence should be addressed.     

Ecology and status of the jaguarundi Puma yagouaroundi: a synthesis of existing knowledge

相似文献