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

Cracraft, Joel; Feinstein, Julie; Vaughn, Jeffrey L.; Helm-Bychowski, Kathleen M.

doi:10.1017/s1367943098000080

Cited by 37 publications

(64 citation statements)

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“…The sequences of these PCR products were nearly identical to the DNA sequence of the numt (nuclear mtDNA insertion) known to exist in felid genomes, including the Amur tiger (AF053056; Cracraft et al 1998). Probable explanations for the numt amplification in only a few DNA extractions within the current study include differences between copy numbers of mitochondrial versus nuclear genes as well as the differential quality of DNA templates from non-invasively sampled materials.…”

Section: Resultsmentioning

confidence: 53%

“…The three outliers, all collected in the southeast corner of the main Sikhote-Alin population (Figure 1), represent two additional haplotypes, each differing from the common haplotype by a single step including: (1) a deletion of an adenine at position 94 within the HSV-1 region (2 individuals; 2.4%); and (2) a C/T transition at position 497 within the CCR (1 individual; 1.2%). Interestingly, none of the three haplotypes recovered in the wild population corresponded to the published P. t. altaica sequence originating from a captive individual, with the most common haplotype differing by a C/T transition at position 172 (GenBank AF053055; Cracraft et al 1998). This change is located in a long C stretch in the HSV-1 region which has been shown to be variable even within clones from the same individual (Jae-Heup et al 2001).…”

Section: Resultsmentioning

confidence: 97%

“…Editing and aligning of DNA sequences was carried out using Sequencer 4.1 (Gene Codes Corporation, Ann Arbor, MI). Fragments were further aligned to the published CR sequence of P. t. altaica (AF053055; Cracraft et al 1998) and P. tigris (Jae-Heup et al 2001), as well as to the sequences of the published CR numt (nuclear mtDNA insertion) for the same species (AF053056-AF053058; Cracraft et al 1998).…”

Section: Methodsmentioning

confidence: 99%

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Potential genetic consequences of a recent bottleneck in the Amur tiger of

Russello

Gladyshev

Miquelle

et al. 2004

Conservation Genetics

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The Amur tiger, Panthera tigris altaica, is a highly endangered felid whose range and population size has been severely reduced in recent times. At present, the wild population is estimated at 490 individuals, having rebounded from the 20-30 tigers remaining following a severe bottleneck in the 1940's. The current study presents preliminary data on the patterns and levels of genetic variation in the mitochondrial DNA control region using DNA extracted from non-invasively sampled faecal material, collected throughout the entire range of P. t. altaica in the Russian Far East. Analysis of 82 scat samples representing at least 27 individuals revealed extremely low levels of CR haplotype diversity, characterized by a single widespread haplotype (96.4%) and two rare variants, each differing by a single step within the hypervariable I (2.4%) and central conserved regions (1.2%), respectively. A comparison with previous data on cytochrome b variation in 14 captive individuals revealed a potentially greater amount of genetic variation represented in captivity relative to that found in the wild population. The extremely low levels of mitochondrial DNA variation in the wild population is discussed in light of the demographic processes that might have shaped these patterns as well as the potential bias introduced through analysis of fecal samples. These results highlight the continuing need to assess levels of genetic variation even in recovering populations that are increasing in number and underscore the important role that captive breeding programs may play in preserving remnant genetic diversity of endangered species.

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Section: Resultsmentioning

confidence: 53%

Section: Resultsmentioning

confidence: 97%

Section: Methodsmentioning

confidence: 99%

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Potential genetic consequences of a recent bottleneck in the Amur tiger of

Russello

Gladyshev

Miquelle

et al. 2004

Conservation Genetics

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“…Given the pervasiveness of insertions of mammalian mitochondrial DNA segments into the nuclear genome (Bensasson et al 2001), including carnivores (Lopez et al 1996;Cracraft et al 1998;Ishiguro et al 2002), we performed long-range PCR amplifications using two different primer pairs (L12616/H01177 and L12598/mtDNA11L, The majority of nuclear copies of mitochondrial DNA in animals are smaller than 1 kb (www.pseudogene.net; Woischnik and Moraes 2002). Furthermore, since it is highly unlikely that both primer pairs would fail to amplify the authentic target, sequence data that were consistent and unambiguous could be assumed to represent the mitochondrial DNA.…”

Section: Generation Of Complete Cytochrome B Sequencesmentioning

confidence: 99%

Species-specific mitochondrial DNA markers for identification of non-invasive samples from sympatric carnivores in the Iberian Peninsula

et al. 2007

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Genetic species identification of non-invasively collected samples has become an important tool in ecological research, management and conservation and wildlife forensics. This is especially true for carnivores, due to their elusive nature, and is crucial when several ecologically and phylogenetically close species, with similar faeces, hairs, bones and/or pelts, occur in sympatry. This is the case of the Iberian Peninsula, a region with a carnivore community of 16 species-about two-thirds of the European carnivore fauna. Here we present a simple, efficient and reliable PCR-based protocol, using a novel set of species-specific primers, for the unambiguous identification to species of non-invasively collected samples or forensic materials from Iberian carnivores. For each species, from the consensus of all cytochrome b haplotypes, found here and previously reported, we designed speciesspecific primer pairs for short fragments, the most likely to persist in low-quantity and degraded DNA samples. The predicted specificity of each primer pair was assessed through PCR of positive DNA extracts from the carnivore species, from an exhaustive array of potential prey and from humans. The robustness of PCR amplification for non-invasively sampled DNA was tested with scat samples. The primers did not produce false positives and correctly identified all carnivore samples to the species level. In comparison with sequencing and PCR-RFLP assays, our method is, respectively, cost-and time-effective, and is especially suited for monitoring surveys targeting multiple populations/species. It also introduces an approach that works for a whole community of carnivores living sympatrically over a large geographic area.

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“…The latter contained two additional sequences from GenBank (accession numbers AF053052 and X82300). One of them was taken from a lioness of unknown descent at the Brookfield Zoo (Cracraft et al 1998; Jean Dubach and Ann Petric, in correspondence with Wolfgang Frey) and clustered with Asian lions. The origin of the other (Árnason et al 1995) was not traceable at all.…”

Section: Resultsmentioning

confidence: 99%

Urgent call for further breeding of the relic zoo population of the critically endangered Barbary lion (Panthera leo leo Linnaeus 1758)

Bürger

Hemmer²

2005

Eur J Wildl Res

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Urgent call for further breeding of the relic zoo population of the critically endangered Barbary lion (Panthera leo leo Linnaeus 1758) Abstract The Barbary lion became extinct in the wild around 1942. Since the end of the 19th century, a last purebred captive breeding stock existed at the court of Morocco. The rest of these animals became the core exhibition of the new Rabat Zoo after passing through repeated bottlenecks and possibly some introgression events by foreign lions. This study uses mitochondrial DNA sequencing data to clarify the relationship among these lions and their subSaharan and Asian relatives. We analysed mitochondrial cytochrome b sequences obtained from a sample from a Barbary lion descended from a young female of the Barbary lion breeding group at the Rabat Zoo and various other members of the genus Panthera. In our cytochrome-b-based phylogenetic tree, the North African Barbary lion, represented by a biopsy sample from the Neuwied Zoo, joins the Asian lion clade, although it is slightly different from its Asian sister group. However, it is clearly distinct from subSaharan lions and can be considered as a genetically defined phylogeographic group of its own. Molecular dating of the extant sub-Saharan and Asian lion groups shows that the split between North African Barbary lions and Asian lions must be considerably more recent than 74-203 kilo years ago.

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

Cited by 37 publications

References 0 publications

Potential genetic consequences of a recent bottleneck in the Amur tiger of

Potential genetic consequences of a recent bottleneck in the Amur tiger of

Species-specific mitochondrial DNA markers for identification of non-invasive samples from sympatric carnivores in the Iberian Peninsula

Urgent call for further breeding of the relic zoo population of the critically endangered Barbary lion (Panthera leo leo Linnaeus 1758)

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