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

@article{Cracraft1998SortingOT,
  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},
  year={1998},
  volume={1}
}
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)
TLDR
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
TLDR
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
TLDR
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)
TLDR
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
TLDR
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)
TLDR
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)
TLDR
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
TLDR
An illustrated discussion about quality control, pseudogenes, and sequence composition in COI-like accessions across Crustacea from published and unpublished studies is illustrated.
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