Phylogenetic studies of pantherine cats (Felidae) based on multiple genes, with novel application of nuclear beta-fibrinogen intron 7 to carnivores

Genetic diversity and structure of the binturong Arctictis binturong (Carnivora: Viverridae) – status of the elusive Palawan binturong and implications for conservation

The binturong or bearcat is a forest mesocarnivore ranging from Nepal to Indonesia and the Philippines. Several subspecies of binturongs are recognized but a revision is needed. The binturong from Palawan was described as a species and is now considered a subspecies, but its status has never been checked using molecular approaches. Owing to its restricted range and the pressure on its habitat, the Palawan binturong may be endangered. It is, therefore, of crucial importance to clarify its taxonomic status, particularly for the management of captive populations. We sequenced one nuclear and two mitochondrial markers for binturongs from locations across the species range and from zoos. Our results provide an assessment of the genetic polymorphism and structure within the binturong, resulting in two groups, corresponding to the Indochinese and the Sundaic regions. Within the latter were found the Palawan binturongs on one side, and an individual from Sulu archipelago (a locality not reported before) on the other side. The Palawan binturongs form a monophyletic group, genetically close to Bornean binturongs, which suggests that they may have dispersed from Borneo, and represents a lineage worth preserving, but which is not a separate species nor a separate subspecies.

Iliac auricular surface morphofunctional study in felidae

Felids show remarkable phenotypic similarities and are conservative in behavioral and ecological traits. In contrast, they display a large range in body mass from around 1kg to more than 300kg. Body size and locomotory specializations correlate to skull, limb and vertebral skeleton morphology. With an increase in body mass, felids prey selection switches from small to large, from using a rapid skull or spine lethal bite for small prey, to sustained suffocating bite for large prey. Dietary specialization correlates to skull and front limbs morphology but no correlation was found on the spine or on the hind limb. The morphology of the sacroiliac junction in relation to ecological factors remained to be described. We are presenting a study of the overall shape of the iliac auricular surface with qualitative and quantitative analyses of its morphology. Our results demonstrate that body mass, prey selection, and bite type, crucially influence the auricular surface, where no significant effect of locomotor specialization was found. The outline of the surface is significantly more elevated dorso-caudally and the joint surface shows an irregular W-shape topography in big cats whereas the surface in small cats is smoother with a C-shape topography and less of an elevated ridge. Biomechanically, we suggest that a complex auricular surface increases joint stiffness and provides more support in heavier cats, an advantage for subduing big prey successfully during a sustained bite.

Phylogeography of the heavily poached African common pangolin (Pholidota, Manis tricuspis) reveals six cryptic lineages as traceable signatures of Pleistocene diversification

Knowledge on faunal diversification in African rainforests remains scarce. We used phylogeography to assess (i) the role of Pleistocene climatic oscillations in the diversification of the African common pangolin (Manis tricuspis) and (ii) the utility of our multilocus approach for taxonomic delineation and trade tracing of this heavily poached species. We sequenced 101 individuals for two mitochondrial DNA (mtDNA), two nuclear DNA and one Y-borne gene fragments (totalizing 2602 bp). We used a time-calibrated, Bayesian inference phylogenetic framework and conducted character-based, genetic and phylogenetic delineation of species hypotheses within African common pangolins. We identified six geographic lineages partitioned into western Africa, Ghana, the Dahomey Gap, western central Africa, Gabon and central Africa, all diverging during the Middle to Late Pleistocene. MtDNA (cytochrome b + control region) was the sole locus to provide diagnostic characters for each of the six lineages. Tree-based Bayesian delimitation methods using single- and multilocus approaches gave high support for 'species' level recognition of the six African common pangolin lineages. Although the diversification of African common pangolins occurred during Pleistocene cyclical glaciations, causative correlation with traditional rainforest refugia and riverine barriers in Africa was not straightforward. We conclude on the existence of six cryptic lineages within African common pangolins, which might be of major relevance for future conservation strategies. The high discriminative power of the mtDNA markers used in this study should allow an efficient molecular tracing of the regional origin of African common pangolin seizures.

The dynamic proliferation of CanSINEs mirrors the complex evolution of Feliforms

BACKGROUND

Repetitive short interspersed elements (SINEs) are retrotransposons ubiquitous in mammalian genomes and are highly informative markers to identify species and phylogenetic associations. Of these, SINEs unique to the order Carnivora (CanSINEs) yield novel insights on genome evolution in domestic dogs and cats, but less is known about their role in related carnivores. In particular, genome-wide assessment of CanSINE evolution has yet to be completed across the Feliformia (cat-like) suborder of Carnivora. Within Feliformia, the cat family Felidae is composed of 37 species and numerous subspecies organized into eight monophyletic lineages that likely arose 10 million years ago. Using the Felidae family as a reference phylogeny, along with representative taxa from other families of Feliformia, the origin, proliferation and evolution of CanSINEs within the suborder were assessed.

RESULTS

We identified 93 novel intergenic CanSINE loci in Feliformia. Sequence analyses separated Feliform CanSINEs into two subfamilies, each characterized by distinct RNA polymerase binding motifs and phylogenetic associations. Subfamily I CanSINEs arose early within Feliformia but are no longer under active proliferation. Subfamily II loci are more recent, exclusive to Felidae and show evidence for adaptation to extant RNA polymerase activity. Further, presence/absence distributions of CanSINE loci are largely congruent with taxonomic expectations within Feliformia and the less resolved nodes in the Felidae reference phylogeny present equally ambiguous CanSINE data. SINEs are thought to be nearly impervious to excision from the genome. However, we observed a nearly complete excision of a CanSINEs locus in puma (Puma concolor). In addition, we found that CanSINE proliferation in Felidae frequently targeted existing CanSINE loci for insertion sites, resulting in tandem arrays.

CONCLUSIONS

We demonstrate the existence of at least two SINE families within the Feliformia suborder, one of which is actively involved in insertional mutagenesis. We find SINEs are powerful markers of speciation and conclude that the few inconsistencies with expected patterns of speciation likely represent incomplete lineage sorting, species hybridization and SINE-mediated genome rearrangement.

Unraveling the effects of selection and demography on immune gene variation in free-ranging plains zebra (Equus quagga) populations

Demography, migration and natural selection are predominant processes affecting the distribution of genetic variation among natural populations. Many studies use neutral genetic markers to make inferences about population history. However, the investigation of functional coding loci, which directly reflect fitness, is critical to our understanding of species' ecology and evolution. Immune genes, such as those of the Major Histocompatibility Complex (MHC), play an important role in pathogen recognition and provide a potent model system for studying selection. We contrasted diversity patterns of neutral data with MHC loci, ELA-DRA and -DQA, in two southern African plains zebra (Equus quagga) populations: Etosha National Park, Namibia, and Kruger National Park, South Africa. Results from neutrality tests, along with observations of elevated diversity and low differentiation across populations, supported previous genus-level evidence for balancing selection at these loci. Despite being low, MHC divergence across populations was significant and may be attributed to drift effects typical of geographically separated populations experiencing little to no gene flow, or alternatively to shifting allele frequency distributions driven by spatially variable and fluctuating pathogen communities. At the DRA, zebra exhibited geographic differentiation concordant with microsatellites and reduced levels of diversity in Etosha due to highly skewed allele frequencies that could not be explained by demography, suggestive of spatially heterogeneous selection and local adaptation. This study highlights the complexity in which selection affects immune gene diversity and warrants the need for further research on the ecological mechanisms shaping patterns of adaptive variation among natural populations.

[Summary of phylogeny in family Felidae of Carnivora]

Felidae (cats) is one of the strict carnivorous groups in the order Carnivora, many of which are most familiar and spectacular to us. They are the top predators in the world. Thirty-six of 37 living cat species are considered as either "endangered" or "threatened". The relationships among species of the family Felidae, which evolved recently and rapidly, are difficult to resolve, and have been the subject of debate. Construction of a reliable Felidae phylogeny will be of evolutionarily significance and conservation value. In this paper, we summarized phylogeny of Felidae, including cytological, morphological and molecular evidence, and pointed out the existing phylogenetic problems. This review is expected to guide future researches of Felidae phylogeny, and to lay a theoretic foundation for the protection of this animal group.

Species boundaries and possible hybridization between the black mongoose (Galerella nigrata) and the slender mongoose (Galerella sanguinea)

Major climatic oscillations since the mid-Miocene climatic optimum are known to have played a key role in promoting speciation events. In this study we use molecular data to elucidate the evolutionary history of Galerella nigrata and link its divergence to known major climatic events. A total of 51 samples from G. nigrata and 17 from Galerella sanguinea were used to provide the first molecular evidence that G. nigrata may be a species in its own right. Both mitochondrial cytochrome b and the nuclear ß-fibrinogen intron seven sequences of G. nigrata form distinct monophyletic clades, separate from its sister species G. sanguinea. We estimate the divergence of these two species to have occurred 3.85-4.27 million years ago, coinciding with a period of the Plio-Pleistocene that was characterised by cooling global temperatures and strong aridity in southern Africa. However, evidence for potential hybridization between the two species was documented for ten individuals using phenotypic (pelage colouration) and/or molecular (nuclear and mtDNA sequences and microsatellite loci) data. There appeared to be a bias towards unidirectional hybridization with all potential hybrids showing mtDNA haplotypes from G. nigrata. We suggest that as the desert expanded across Namibia, G. sanguinea likely retreated with the savanna, leaving some mongooses stranded on the granite inselbergs of north-western Namibia. Subsequent adaptation of these mongooses to local conditions on granite inselbergs could have led to ecological speciation. Secondary contact zones would have been re-established with subsequent global warming events. It appears that the two species have not yet undergone complete reproductive isolation.

Mitogenomic analysis of the genus Panthera

The complete sequences of the mitochondrial DNA genomes of Panthera tigris, Panthera pardus, and Panthera uncia were determined using the polymerase chain reaction method. The lengths of the complete mitochondrial DNA sequences of the three species were 16990, 16964, and 16773 bp, respectively. Each of the three mitochondrial DNA genomes included 13 protein-coding genes, 22 tRNA, two rRNA, one O(L)R, and one control region. The structures of the genomes were highly similar to those of Felis catus, Acinonyx jubatus, and Neofelis nebulosa. The phylogenies of the genus Panthera were inferred from two combined mitochondrial sequence data sets and the complete mitochondrial genome sequences, by MP (maximum parsimony), ML (maximum likelihood), and Bayesian analysis. The results showed that Panthera was composed of Panthera leo, P. uncia, P. pardus, Panthera onca, P. tigris, and N. nebulosa, which was included as the most basal member. The phylogeny within Panthera genus was N. nebulosa (P. tigris (P. onca (P. pardus, (P. leo, P. uncia)))). The divergence times for Panthera genus were estimated based on the ML branch lengths and four well-established calibration points. The results showed that at about 11.3 MYA, the Panthera genus separated from other felid species and then evolved into the several species of the genus. In detail, N. nebulosa was estimated to be founded about 8.66 MYA, P. tigris about 6.55 MYA, P. uncia about 4.63 MYA, and P. pardus about 4.35 MYA. All these estimated times were older than those estimated from the fossil records. The divergence event, evolutionary process, speciation, and distribution pattern of P. uncia, a species endemic to the central Asia with core habitats on the Qinghai-Tibetan Plateau and surrounding highlands, mostly correlated with the geological tectonic events and intensive climate shifts that happened at 8, 3.6, 2.5, and 1.7 MYA on the plateau during the late Cenozoic period.

Oldest known pantherine skull and evolution of the tiger

The tiger is one of the most iconic extant animals, and its origin and evolution have been intensely debated. Fossils attributable to extant pantherine species-lineages are less than 2 MYA and the earliest tiger fossils are from the Calabrian, Lower Pleistocene. Molecular studies predict a much younger age for the divergence of modern tiger subspecies at <100 KYA, although their cranial morphology is readily distinguishable, indicating that early Pleistocene tigers would likely have differed markedly anatomically from extant tigers. Such inferences are hampered by the fact that well-known fossil tiger material is middle to late Pleistocene in age. Here we describe a new species of pantherine cat from Longdan, Gansu Province, China, Panthera zdanskyi sp. nov. With an estimated age of 2.55-2.16 MYA it represents the oldest complete skull of a pantherine cat hitherto found. Although smaller, it appears morphologically to be surprisingly similar to modern tigers considering its age. Morphological, morphometric, and cladistic analyses are congruent in confirming its very close affinity to the tiger, and it may be regarded as the most primitive species of the tiger lineage, demonstrating the first unequivocal presence of a modern pantherine species-lineage in the basal stage of the Pleistocene (Gelasian; traditionally considered to be Late Pliocene). This find supports a north-central Chinese origin of the tiger lineage, and demonstrates that various parts of the cranium, mandible, and dentition evolved at different rates. An increase in size and a reduction in the relative size of parts of the dentition appear to have been prominent features of tiger evolution, whereas the distinctive cranial morphology of modern tigers was established very early in their evolutionary history. The evolutionary trend of increasing size in the tiger lineage is likely coupled to the evolution of its primary prey species.

Dogs, cats, and kin: a molecular species-level phylogeny of Carnivora

Phylogenies underpin comparative biology as high-utility tools to test evolutionary and biogeographic hypotheses, inform on conservation strategies, and reveal the age and evolutionary histories of traits and lineages. As tools, most powerful are those phylogenies that contain all, or nearly all, of the taxa of a given group. Despite their obvious utility, such phylogenies, other than summary 'supertrees', are currently lacking for most mammalian orders, including the order Carnivora. Carnivora consists of about 270 extant species including most of the world's large terrestrial predators (e.g., the big cats, wolves, bears), as well as many of man's favorite wild (panda, cheetah, tiger) and domesticated animals (dog, cat). Distributed globally, carnivores are highly diverse ecologically, having occupied all major habitat types on the planet and being diverse in traits such as sociality, communication, body/brain size, and foraging ecology. Thus, numerous studies continue to address comparative questions within the order, highlighting the need for a detailed species-level phylogeny. Here we present a phylogeny of Carnivora that increases taxon sampling density from 28% in the most detailed primary-data study to date, to 82% containing 243 taxa (222 extant species, 17 subspecies). In addition to extant species, we sampled four extinct species: American cheetah, saber-toothed cat, cave bear and the giant short-faced bear. Bayesian analysis of cytochrome b sequences data-mined from GenBank results in a phylogenetic hypothesis that is largely congruent with prior studies based on fewer taxa but more characters. We find support for the monophyly of Carnivora, its major division into Caniformia and Feliformia, and for all but one family within the order. The only exception is the placement of the kinkajou outside Procyonidae, however, prior studies have already cast doubt on its family placement. In contrast, at the subfamily and genus level, our results indicate numerous problems with current classification. Our results also propose new, controversial hypotheses, such as the possible placement of the red panda (Ailuridae) sister to canids (Canidae). Our results confirm previous findings suggesting that the dog was domesticated from the Eurasian wolf (Canis lupus lupus) and are congruent with the Near East domestication of the cat. In sum, this study presents the most detailed species-level phylogeny of Carnivora to date and a much needed tool for comparative studies of carnivoran species. To demonstrate one such use, we perform a phylogenetic analysis of evolutionary distinctiveness (EDGE), which can be used to help establish conservation priorities. According with those criteria, and under one of the many possible sets of parameters, the highest priority Carnivora species for conservation of evolutionary diversity include: monk seals, giant and red panda, giant otter, otter civet, Owston's palm civet, sea otter, Liberian mongoose, spectacled bear, walrus, binturong, and the fossa.

[Intra-individual allele heterozygotes in phylogenetic analysis]

The study of evolutionary relationships among organisms is vital in evolutionary biology. To reconstruct a reliable species phylogeny, one of the most important issues is to choose proper molecular markers and take full advantage of phylogenetic information contained in these markers. Intra-individual allele heterozygotes (IIAHs) have been commonly detected in intron phylogenetic studies. How to incorporate IIAHs into phylogenetic framework has been a focus in current studies. In this review, the conception, isolation, and analytic methods of IIAHs in phylogeny were summarized.

Molecular phylogeny of the Herpestidae (Mammalia, Carnivora) with a special emphasis on the Asian Herpestes

Until now, phylogenetic studies of the mongooses (Carnivora, Herpestidae) have not included an exhaustive sampling of the Asian members of this family. In this study, we used mitochondrial (Cytochrome b and ND2), nuclear (beta-fibrinogen intron 7 and Transthyretin intron 1) sequences from almost all of the recognized mongoose species to produce a well-resolved phylogeny of the Herpestidae. We also performed molecular dating analyses to infer divergence dates of the different lineages within the Herpestidae. Our results confirmed the paraphyly of the Herpestes genus and other phylogenetic relationships, which previously had only been moderately supported. The Asian herpestid species were found to form a monophyletic group within the Herpestidae. Within the Asian species, a cyto-nuclear conflict was discovered between the small Indian mongoose (Herpestes auropunctatus), the Indian gray mongoose (Herpestes edwardsii) and the Javan mongoose (Herpestes javanicus), which may have occurred through interspecific hybridization. This study inferred an Early Miocene origin for the Herpestidae and a Middle Miocene origin for the Asian mongooses.

New insights into the evolution of intronic sequences of the beta-fibrinogen gene and their application in reconstructing mustelid phylogeny

Mustelidae is the largest and most diverse family in the order Carnivora. The phylogenetic relationships among the subfamilies have especially long been a focus of study. Herein we are among the first to employ two new introns (4 and 7) of the nuclear beta-fibrinogen gene to clarify these enigmatic problems. In addition, two previously available nuclear (IRBP exon 1 and TTR intron 1) and one mt (ND2) data sets were also combined and analyzed simultaneously with the newly obtained sequence data in this study. Detailed characterizations of the two intronic regions not only reveal the remarkable occurrences of short interspersed element (SINE) insertion events, providing a new example supporting the attractive hypothesis that attrition of an earlier retroposition may offer a proper environment for successive retropositions by forming a "dimer-like" structure, but also demonstrate their utility in the resolution of mustelid phylogeny. All of our analyses confirm the assemblage of Mustelinae, Lutrinae, and Melinae with confidence; moreover, two clades within Mustelinae were clearly recognized, i.e., genera Mustela and Martes. Notably, genus Martes of Mustelinae was found to branch off first, followed by Melinae and then a clade containing Lutrinae and genus Mustela of Mustelinae, indicating paraphyly of Mustelinae. In addition, Mephitinae diverges before the other mustelids and the monophyletic Procyonidae in all cases, supporting its elevation to a separate family. Additional independent genetic markers are still in need to resolve the trichotomy among Mephitinae and the other two carnivoran clades, Ailuridae and Procyonidae/non-mephitine Mustelidae.

Molecular evolution study in China: progress and future promise

China has a large land area with highly diverse topography, climate and vegetation, and animal resources and is ranked eighth in the world and first in the Northern Hemisphere on richness of biodiversity. Even though little work on molecular evolution had been reported a decade ago, studies on both the evolution of macromolecules and the molecular phylogeny have become active in China in recent years. This review highlights some of the interesting and important developments in molecular evolution study in China. Chinese scientists have made significant contribution on the methods inferring phylogeny and biogeography of animals and plants in East Asia using molecular data. Studies on population and conservation genetics of animals and plants, such as Golden monkey and Chinese sturgeon, provided useful information for conserving the endangered species. East and South Asia has been demonstrated to be one of the centres of domestication. Origin and evolution of genes and gene families have been explored, which shed new insight on the genetic mechanism of adaptation. In the genomic era, Chinese researchers also made a transition from single-gene to a genomic investigation approach. Considering the fact that amazing progress has been made in the past few years, and more and more talented young scientists are entering field, the future of molecular evolution study in China holds much promise.

Clouded leopard phylogeny revisited: support for species recognition and population division between Borneo and Sumatra

BACKGROUND

The clouded leopard (Neofelis nebulosa) is one of the least known cat species and depletion of their forested habitats puts it under heavy pressure. Recently reclassification of Bornean clouded leopards (N. nebulosa diardi) to species level (N.diardi) was suggested based on molecular and morphological evidence. Since the genetic results were based solely on three Bornean samples we re-evaluated this partition using additional samples of Bornean clouded leopards (N = 7) and we were also able to include specimens from Sumatra (N = 3), which were lacking in previous analysis.

RESULTS

We found strong support for the distinction between N. nebulosa and N. diardi based on three fragments of mtDNA (900 bp) and 18 microsatellites. Forty-one fixed mitochondrial nucleotide differences and non-overlapping allele sizes in 8 of 18 microsatellite loci distinguished N. nebulosa and N. diardi. This is equivalent to the genetic divergence among recognized species in the genus Panthera. Sumatran clouded leopards clustered with specimens from Borneo, suggesting that Sumatran individuals also belong to N. diardi. Additionally, a significant population subdivision was apparent among N. diardi from Sumatra and Borneo based on mtDNA and microsatellite data.

CONCLUSION

Referring to their origin on two Sunda Islands we propose to give N. diardi the common name "Sundaland clouded leopard". The reduced gene flow between Borneo and Sumatra might suggest the recognition of two subspecies of N. diardi. Based on this reclassification of clouded leopards not only species, but also the populations on Borneo and Sumatra should be managed separately and a higher priority should be placed to protect the different populations from extinction.

Indel evolution of mammalian introns and the utility of non-coding nuclear markers in eutherian phylogenetics

Nuclear DNA intron sequences are increasingly used to investigate evolutionary relationships among closely related organisms. The phylogenetic usefulness of intron sequences at higher taxonomic levels has, however, not been firmly established and very few studies have used these markers to address evolutionary questions above the family level. In addition, the mechanisms driving intron evolution are not well understood. We compared DNA sequence data derived from three presumably independently segregating introns (THY, PRKC I and MGF) across 158 mammalian species. All currently recognized extant eutherian mammalian orders were included with the exception of Cingulata, Dermoptera and Scandentia. The total aligned length of the data was 6366 base pairs (bp); after the exclusion of autapomorphic insertions, 1511 bp were analyzed. In many instances the Bayesian and parsimony analyses were complementary and gave significant posterior probability and bootstrap support (>80) for the monophyly of Afrotheria, Euarchontoglires, Laurasiatheria and Boreoeutheria. Apart from finding congruent support when using these methods, the intron data also provided several indels longer than 3 bp that support, among others, the monophyly of Afrotheria, Paenungulata, Ferae and Boreoeutheria. A quantitative analysis of insertions and deletions suggested that there was a 75% bias towards deletions. The average insertion size in the mammalian data set was 16.49 bp +/- 57.70 while the average deletion was much smaller (4.47 bp +/- 14.17). The tendency towards large insertions and small deletions is highlighted by the observation that out of a total of 17 indels larger than 100 bp, 15 were insertions. The majority of indels (>60% of all events) were 1 or 2 bp changes. Although the average overall indel substitution rate of 0.00559 per site is comparable to that previously reported for rodents and primates, individual analyses among different evolutionary lineages provide evidence for differences in the formation rate of indels among the different mammalian groups.

Phylogenetics of the woodrat genus Neotoma (Rodentia: Muridae): implications for the evolution of phenotypic variation in male external genitalia

Interspecific morphological variation in animal genitalia has long attracted the attention of evolutionary biologists because of the role genital form may play in the generation and/or maintenance of species boundaries. Here we examine the origin and evolution of genital variation in rodents of the muroid genus Neotoma. We test the hypothesis that a relatively rare genital form has evolved only once in Neotoma. We use four mitochondrial and four nuclear markers to evaluate this hypothesis by establishing a phylogenetic framework in which to examine genital evolution. We find intron seven of the beta-fibrinogen gene to be a highly informative nuclear marker for the levels of differentiation that characterize Neotoma with this locus evolving at a rate slower than cytochrome b but faster than 12S. We estimate phylogenetic relationships within Neotoma using both maximum parsimony and maximum likelihood-based Bayesian methods. Our Bayesian and parsimony reconstructions differ in significant ways, but we show that our parsimony analysis may be influenced by long-branch attraction. Furthermore, our estimate of Neotoma phylogeny remains consistent across various data partitioning strategies in the Bayesian analyses. Using ancestral state reconstruction, we find support for the monophyly of taxa that possess the relatively rare genital form. However, we also find support for the independent evolution of the common genital form and discuss possible underlying developmental shifts that may have contributed to our observed patterns of morphological evolution.

Phylogeny of the caniform carnivora: evidence from multiple genes

The monophyletic group Caniformia in the order Carnivora currently comprises seven families whose relationships remain contentious. The phylogenetic positions of the two panda species within the Caniformia have also been evolutionary puzzles over the past decades, especially for Ailurus fulgens (the red panda). Here, new nuclear sequences from two introns of the beta-fibrinogen gene (beta-fibrinogen introns 4 and 7) and a complete mitochondrial (mt) gene (ND2) from 17 caniform representatives were explored for their utilities in resolving higher-level relationships in the Caniformia. In addition, two previously available nuclear (IRBP exon 1 and TTR intron 1) data sets were also combined and analyzed simultaneously with the newly obtained sequence data in this study. Combined analyses of four nuclear and one mt genes (4417 bp) recover a branching order in which almost all nodes were strongly supported. The present analyses provide evidence in favor of Ailurus fulgens as the closest taxon to the procyonid-mustelid (i.e., Musteloidea sensu stricto) clade, followed by pinnipeds (i.e., Otariidae and Phocidae), Ursidae (including Ailuropoda melanoleuca), and Canidae, the most basal lineage in the Caniformia. The potential utilities of different genes in the context of caniform phylogeny were also evaluated, with special attention to the previously unexplored beta-fibrinogen intron 4 and 7 genes.

Evolutionary implications of multiple SINE insertions in an intronic region from diverse mammals

An analysis of the nuclear beta-fibrinogen intron 7 locus from 30 taxa representing 12 placental orders of mammals reveals the enriched occurrences of short interspersed element (SINE) insertion events. Mammalian-wide interspersed repeats (MIRs) are present at orthologous sites of all examined species except those in the order Rodentia. The higher substitution rate in mouse and a rare MIR deletion from rat account for the absence of MIR in the rodents. A minimum of five lineage-specific SINE sequences are also found to have independently inserted into this intron in Carnivora, Artiodactyla and Lagomorpha. In the case of Carnivora, the unique amplification pattern of order-specific CAN SINE provides important evidence for the "pan-carnivore" hypothesis of this repeat element and reveals that the CAN SINE family may still be active today. Particularly interesting is the finding that all identified lineage-specific SINE elements show a strong tendency to insert within or in very close proximity to the preexisting MIRs for their efficient integrations, suggesting that the MIR element is a hot spot for successive insertions of other SINEs. The unexpected MIR excision as a result of a random deletion in the rat intron locus and the non-random site targeting detected by this study indicate that SINEs actually have a greater insertional flexibility and regional specificity than had previously been recognized. Implications for SINE sequence evolution upon and following integration, as well as the fascinating interactions between retroposons and the host genomes are discussed.