Sorting out tigers (Panthera tigris): mitochondrial sequences, nuclear inserts, systematics, and conservation genetics

Abstract

Sequences from complete mitochondrial cytochrome b genes of 34 tigers support the hypothesis that Sumatran tigers are diagnostically distinct from mainland populations. None of the latter, including Bengals, Siberians, or Indochinese tigers, were found to have fixed diagnostic characters. Phylogenetic analysis of these sequences confirms these results. Within the framework of a phylogenetic species concept, current evidence thus supports the recognition of two distinct taxa, and within the context of this definition they could be ranked at the species level. This paper also documents a previously unrecognized nuclear insert of mitochondrial DNA that includes, minimally, mitochondrial homologues of a control region that lacks the feline mitochondrial repeat sequences, a complete cytochrome b gene, and complete tRNA Thr and tRNA Pro genes. In a phylogenetic analysis of the nuclear cytochrome b-like sequences and various feline mitochondrial sequences, the nuclear insert clusters with lion mitochondrial cytochrome b sequences, which suggests the insert is at least as old as the split between lions and tigers. The results of this study emphasize the importance of doing more to conserve Sumatran tigers. Because they are underrepresented in zoos relative to Bengals and Siberians, an effort should be made to increase captive breeding stocks of Sumatrans. That Sumatrans are a distinct taxonomic entity relative to mainland populations can be used in educational programs to increase conservation efforts within Indonesia.

Phylogeography and Genetic Ancestry of Tigers (Panthera tigris)

“…In our first hypothesis, two groups were considered: the P. t. sumatrae island population and all contemporary mainland populations ( P. t. altaica, P. t. corbetti I, P. t. corbetti II, P. t. tigris) . This recently proposed model (Cracraft et al 1998; Kitchener 1999; Kitchener and Dugmore 2000) presumes continuous habitat distribution on the mainland. The second scenario considered tigers as three groups: the Sumatran population (P. t. sumatrae), the Amur tigers (P. t. altaica), which presently are isolated from other tiger populations by more than their maximum known dispersal distance (Mazak 1996), and a group of the other mainland tigers subspecies.…”

“…Foremost among these has been the limited sample size of “voucher specimens” (defined as individuals that were verified as wild-born from a specific geographic locale or captive-born from geographically verified wild-born parents). In addition, the presence of Numt, a nuclear pseudogene insertion of cytoplasmic mitochondrial DNA (mtDNA) in tiger autosomes (Lopez et al 1994; Johnson et al 1996; Cracraft et al 1998; J. H. Kim, A. Antunes, S.-J. Luo, J. Menninger, W. G. Nash, et al, personal communication) has made it difficult to utilize universal mammalian primer sets for mitochondrial genes, because they will coamplify Numt.…”

Detection of mitochondrial insertions in the nucleus (NuMts) of Pleistocene and modern muskoxen

“…the process leading to loss of function of a locus following duplication or transposition), which is mostly expected for coding loci (graph not shown). Up to date, shifts in base composition of D-loop Numts have not been studied, as cases of noncoding Numts have rarely been reported [4,9,10,16-18]. …”

Increasing numbers of bird species result from taxonomic progress, not taxonomic inflation

“…Refined species taxonomies may inform biogeographic study of microendemic biota (Wilmé et al 2006), enable more precise estimation of cladogenesis (e.g. Tobias et al 2008), inform the study of adaptation (Zink & McKitrick 1995) and help to identify conservation priorities (Daugherty et al 1990;Cracraft et al 1998 …”