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

  title={Sorting out tigers (Panthera tigris): mitochondrial sequences, nuclear inserts, systematics, and conservation genetics},
  author={Joel Cracraft and Julie Feinstein and Jeffrey L. Vaughn and Kathleen M. Helm-Bychowski},
  journal={Animal Conservation},
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… 
Highly conserved D-loop-like nuclear mitochondrial sequences (Numts) in tiger (Panthera tigris)
Although the mtDNA D-loop sequence has a rapid rate of evolution, the 287-bp Numts are highly conserved; they are nearly identical in tiger subspecies and only 1.742% different between tiger and leopard, indicating that such sequences represent molecular 'fossils' that can shed light on evolution of the mitochondrial genome and may be the most appropriate outgroup for phylogenetic analysis.
Multiple nuclear pseudogenes of mitochondrial cytochrome b in Ctenomys (Caviomorpha, Rodentia) with either great similarity to or high divergence from the true mitochondrial sequence
It is suggested that there were two transfers of the cytochrome b gene from the mitochondrion to the nucleus; the first leading to sequences A–C and the second to the D sequence, which reinforces the necessity of great care in interpreting PCR-generated sequences, particularly those produced with universal primers.
Detection of mitochondrial insertions in the nucleus (NuMts) of Pleistocene and modern muskoxen
A case in which difficulties in ascertaining the organellar mtDNA sequence from modern samples hindered their comparison to ancient DNA sequences and multiple unique sequences from both hair and blood of one modern specimen were obtained.
Demography and Phylogenetic Utility of Numt Pseudogenes in the Southern Red-Backed Vole (Myodes gapperi)
Genome sequencing efforts will ultimately provide the data needed to fully characterize numt demography in different lineages, and it is predicted that numts will have phylogenetic utility as informative synapomorphies in closely related species.
Columba palumbus cyt b-like Numt sequence : comparison with functional homologue and the use of universal primers
Data from cytochrome b sequence did not support the existence of a geographically-based divergence among C. palumbus populations, which may indicate the persistence of gene flow, and several criteria used for detection of pseudogene amplification were discussed.
Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi‐terrestrial shrimps (Caridea: Lysmata, Exhippolysmata, and Merguia)
Analysis of mitochondrial genes commonly used for phylogenetic reconstruction suggest that all three mtDNA markers are equally useful for resolving phylogenetic relationships in the shrimps studied, and that PI profiling is not necessarily useful to estimate overall gene utility.
Phylogeography and Genetic Ancestry of Tigers (Panthera tigris)
To investigate the species' evolutionary history and to establish objective methods for subspecies recognition, voucher specimens of blood, skin, hair, and/or skin biopsies from 134 tigers with verified geographic origins or heritage across the whole distribution range were examined for molecular markers.
Analysis of variable sites between two complete South China tiger (Panthera tigris amoyensis) mitochondrial genomes
In order to investigate the mitochondrial genome of Panthera tigris amoyensis, two South China tigers (P25 and P27) were analyzed following 15 cymt-specific primer sets. The entire mtDNA sequence was
“COI-like” Sequences are Becoming Problematic in Molecular Systematic and DNA Barcoding Studies
An illustrated discussion about quality control, pseudogenes, and sequence composition in COI-like accessions across Crustacea from published and unpublished studies is illustrated.


Molecular evolution of mitochondrial 12S RNA and cytochrome b sequences in the pantherine lineage of Felidae.
DNA sequence comparisons of two mitochondrial DNA genes were used to infer phylogenetic relationships among 17 Felidae species, notably 15 in the previously described pantherine lineage, and suggested the recognition of a recently evolved monophyletic genus Panthera.
Insertions and duplications of mtDNA in the nuclear genomes of Old World monkeys and hominoids
Two divergent cytochrome b nuclear pseudogenes from orangutan cellular DNA are amplified and sequenced using oligonucleotide primers designed to match conserved regions of mammalian mitochondrial DNA (mtDNA) to find the source of DNA contamination of 'ancient' and forensic DNA.
Mitochondrial DNA-like sequence in the nuclear genome of an akodontine rodent.
When probed with both functional and nonfunctional gene fragments, MboI restriction digests revealed the same pattern, providing further evidence that the nonfunctional copy must be located in the nucleus.
A nuclear 'fossil' of the mitochondrial D-loop and the origin of modern humans
It is shown that human chromosome 11 carries a recent integration of the mitochondrial control region that can be used to gain further insight into the origin of the human mitochondrial gene pool.
Complete nucleotide sequences of the domestic cat (Felis catus) mitochondrial genome and a transposed mtDNA tandem repeat (Numt) in the nuclear genome.
Phylogenetic analysis of mitochondrial gene sequences confirms the recent transfer of the cytoplasmic mtDNA sequences to the domestic cat nucleus and recapitulates evolutionary relationships between mammal species.
Comparison of a mitochondrial gene and a corresponding nuclear pseudogene
  • P. Arctander
  • Biology
    Proceedings of the Royal Society of London. Series B: Biological Sciences
  • 1995
A direct comparison of a fragment of the mitochondrial gene coding for Cytochrome b and its assumed nuclear pseudogene in a phylogenetic context is presented, showing mitochondrial third position transitions are the fastest accumulating substitutions, here indicated to be at least up to 39 times faster than corresponding positions in the supposednuclear pseudogene.
Phylogenetic relationships among the major lineages of the birds-of-paradise (Paradisaeidae) using mitochondrial DNA gene sequences.
Complete mitochondrial cytochrome b gene sequences were determined from 12 species of the Australo-Papuan birds-of-paradise (Paradisaeidae) representing 9 genera and reveal a radiation of the main paradisaeinine lineages that took place over a relatively short evolutionary time scale.
The phylogenetic distances between 34 of the 37 extant species of Felidae were estimated using albumin immunological distances (AID) and the derived topology is highly consistent with the karyological disposition of these species, as well as with the fossil record of this family.
Applications of mitochondrial DNA analysis in conservation: a critical review
There are some relatively straightforward uses of mtDNA, preferably in conjunction with assays of nuclear variation, that can make a significant contribution to the long‐term planning and short‐term execution of species recovery plans.
The compatibility of the phylogenetic species concept with various biological needs for species and its use at the exclusion of alternative species concepts are discussed.