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

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Abstract

The pantherine lineage of the cat family Felidae (order: Carnivora) includes five big cats of genus Panthera and a great many midsized cats known worldwide. Presumably because of their recent and rapid radiation, the evolutionary relationship among pantherines remains ambiguous. We provide an independent assessment of the evolutionary history of pantherine lineage using two complete mitochondrial (mt) genes (ND2 and ND4) and the nuclear β-fibrinogen intron 7 gene, whose utility in carnivoran phylogeny was first explored. The available four mt (ND5, cytb, 12S, and 16SrRNA) and two nuclear (IRBP and TTR) sequence loci were also combined to reconstruct phylogeny of 14 closely related cat species. Our analyses of combined mt data (six genes; ≈3750 bp) and combined mt and nuclear data (nine genes; ≈6500 bp) obtained identical tree topologies, which were well-resolved and strongly supported for almost all nodes. Monophyly of Panthera genus in pantherine lineage was confirmed and interspecific affinities within this genus revealed a novel branching pattern, with P. tigris diverging first in Panthera genus, followed by P. onca, P. leo, and last two sister species P. pardus and P. uncia. In addition, close association of Neofelis nebulosa to Panthera, the phylogenetic redefinition of Otocolobus manul within the domestic cat group, and the relatedness of Acinonyx jubatus and Puma concolor were all important findings in the resulting phylogenies. The potential utilities of nine different genes for phylogenetic resolution of closely related pantherine species were also evaluated, with special interest in that of the novel nuclear β-fibrinogen intron 7.

Introduction

The Felidae, or cat family, is characterized by recent bursts of diversification within the last 10–15 million years (Johnson and O’Brien, 1997, Martin, 1980, Nowak, 1999, Werdelin, 1985). Thirty-eight cat species of this family are generally divided into the pantherine, domestic cat, and ocelot lineages (Ewer, 1973, Janczewski et al., 1995, Leyhausen, 1979, Masuda et al., 1996). The pantherine lineage, as the most recently evolved (within 1–8 MYA; Janczewski et al., 1995, Pecon Slattery et al., 1994) and largest felid group (around 20 cat species; Janczewski et al., 1995) has demonstrated great confusion in their taxonomy and phylogeny. These pantherine cats consist of five big cats of genus Panthera and a great many midsized cats species. They had been disputably assigned to 2–13 genera under various classification schemes in past studies (Ewer, 1973, Hemmer, 1978, Leyhausen, 1979, Nowak, 1999) and moreover, phylogenetic relationships among these pantherine species have also been controversial.

A wealth of molecular characters have been used to decipher feline evolutionary history, including protein electrophoresis, allozyme data, karyology, endogenous retroviruses, mitochondrial (mt) DNA sequences, sex chromosomes-linked genes, and chemical signals (Bininda-Emonds, 2001, Collier and O’Brien, 1985, Johnson and O’Brien, 1997, Lopez et al., 1994, O’Brien et al., 1987, Pecon Slattery and O’Brien, 1998, Reeves and O’Brien, 1984). However, little prior research focused nuclear genes at the DNA level. In the present paper, the seventh intron of the single-copy fibrinogen gene (β-chain; β-fibrinogen intron 7) from the nuclear genome was used for phylogenetic resolution among closely related pantherine cats. The utility of this gene segment has been successfully explored at different taxonomic levels in studies of birds (Johnson and Clayton, 2000, Moyle, 2004, Prychitko and Moore, 1997, Prychitko and Moore, 2000, Prychitko and Moore, 2003, Weibel and Moore, 2002) and reptiles (Creer et al., 2003, Giannasi et al., 2001), however, still lacking in those of mammals. Our work is the first to explore the potential of β-fibrinogen intron 7 as a genetic marker in carnivoran systematics. We also sequenced two large complete NADH dehydrogenase (ND2 and ND4) genes from mt genome, given the general thought that analysis of multiple independently inherited genes is especially effective in testing for congruence and estimating organismal phylogeny and, in addition, our previously reported nuclear interphotoreceptor retinoid-binding protein (IRBP) and transthyretin (TTR) genes (Yu et al., 2004b), together with four other available mtDNA characters (12SrRNA, cytochrome b, 16SrRNA, and ND5 genes; Janczewski et al., 1995, Johnson and O’Brien, 1997, Masuda et al., 1996) for the same set of cat species were also added to the present analyses.

Sequence data from 9 genes (three nuclear and six mt) of 12 pantherine cats and 2 domestic cats was analyzed, separately or in a variety of combinations here, with a view of (1) providing a broader understanding of interspecific relationships within the pantherine group, (2) assessing the utility of β-fibrinogen intron 7 as a novel marker in carnivoran phylogenetics, and (3) comparing evolutionary patterns of different genes and their values for resolution of low level feline questions.

Section snippets

DNA samples and PCR amplifications

Fourteen felids in the family Felidae were examined and listed in Table 1. All the five currently recognized members of genus Panthera in the pantherine lineage, including P. leo (lion), P. tigris (tiger), P. pardus (leopard), P. onca (jaguar), and P. uncia (snow leopard), and seven other pantherine cats, including Neofelis nebulosa (clouded leopard), Otocolobus manul (Pallas’s cat), Profelis temminckii (Asiatic golden cat), Prionailurus bengalensis (Asiatic leopard cat), Lynx lynx (lynx), Puma

Novel findings of SINE element in β-fibrinogen intronic segment

As mentioned above (see Section 2), two 239 bp large insertions (Gol-ins and Pal-ins) have occurred uniquely in Profelis temminckii (positions 96–334) and Otocolobus manul taxa (positions 587–825) β-fibrinogen intron 7, respectively. A BLAST search from GenBank database revealed that 225 bp of Gol-ins and Pal-ins exhibited the highest similarities to carnivoran-specific short interspersed element, i.e., CAN SINE family. The results from the RepeatMasker program (A.F.A. Smit and P. Green,

Monophyly and interspecific relationships of panthera genus

Traditionally, Panthera is composed of five recognized extant species. However, interspecific relationships within the genus have been equivocal probably due to extremely recent speciation (1–2 MYA; Kurten and Anderson, 1980, Wayne et al., 1989) resulting in short internodes that have not been resolved because of insufficient sequence data used in previous studies (see Fig. 4). In this paper, although individual genes examined failed to provide a well-supported phylogeny, the analyses of full

Supplementary materials

The sequences reported in this paper have been deposited in the GenBank database. Accession Nos. AY634369–AY634385 and AY634387–AY634405.

Acknowledgments

This work was supported by grants from National Natural Science Foundation of China (NSFC), Chinese Academy of Sciences and Program for S & T Fund Project of P.R. China (2001DEA10009-08). We thank Associate Editor Dr. Derek E Wildman’s help for improving the English of this manuscript.

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