Utility of nuclear DNA intron markers at lower taxonomic levels: Phylogenetic resolution among nine Tragelaphus spp.
MOLECULAR PHYLOGENETICS AND EVOLUTION
Authors: Willows-Munro, S; Robinson, TJ; Matthee, CA
Abstract
Phylogenetic relationships among the nine spiral-horn antelope species of the African bovid tribe Tragelaphini are controversial. In particular, mitochondrial DNA sequencing studies are not congruent with previous Morphological investigations. To test the utility of nuclear DNA intron markers at lower taxonomic levels and to provide additional data pertinent to tragelaphid evolution, we sequenced four nuclear DNA segments (MGF, PRKCI, SPTBN, and THY) and combined these data with mitochondrial DNA sequences from three genes (cytochrome b, 12S rRNA, and 16S rRNA). Our Molecular supermatrix comprised 4682 characters which were analyzed independently and in combination. Parsimony and model based phylogenetic analyses of the combined nuclear DNA data are congruent with those derived from the analysis of mitochondrial gene sequences. The corroboration between nuclear and mtDNA gene trees reject the possibility that genetic processes such as lineage sorting. gene duplication/deletion and hybrid speciation account for the conflict evident in the previously published phylogenies. It suggests rather that the morphological characters used to delimit the Tragelaphid species are subject to convergent evolution. Divergence times among species, calculated using a relaxed Bayesian molecular clock. are consistent with hypotheses proposing that climatic oscillations and their impact on habitats were the major forces driving speciation in the tribe Tragelaphini. (c) 2005 Elsevier Inc. All rights reserved.
Ancient hybridization and underestimated species diversity in Asian striped squirrels (genus Tamiops): inference from paternal, maternal and biparental markers
JOURNAL OF ZOOLOGY
Authors: Chang, S. -W.; Oshida, T.; Endo, H.; Nguyen, S. T.; Dang, C. N.; Nguyen, D. X.; Jiang, X.; Li, Z. -J.; Lin, L. -K.
Abstract
Current classification of the genus Tamiops is mainly based on pelage color pattern that is prone to seasonal variation or convergent adaptation to environmental selection. The arrangement of four species, Tamiops mcclellandii, Tamiops rodolphii, Tamiops swinhoei and Tamiops maritimus, is regarded as tentative due to difficulty in delineating species, especially the latter two species. We constructed multi-locus phylogenies of all four Tamiops species on the basis of paternal (Y-chromosomal SRY and SMCY7), maternal (mitochondrial cytochrome b gene) and biparental (autosomal IRBP, RAG1 and PRKCI) sequences. Maximum likelihood and Bayesian tree-constructing methods resulted in phylogenies with similar topologies. All genetic markers supported diversification of three main lineages: (1) T. mcclellandii; (2) T. rodolphii; (3) T. swinhoei-maritimus complex. On the basis of 24 T. maritimus from five localities and 10 T. swinhoei from four localities, T. swinhoei and T. maritimus were not reciprocally monophyletic. The six populations of the T. swinhoei-maritimus complex were monophyletic in all loci, except for autosomal loci in one T. maritimus population from Tam Dao, Vietnam. Autosomal phylogenies were more similar to Y-chromosomal than to mitochondrial phylogenies. Incongruence between nuclear and mitochondrial phylogenies indicates that either T. maritimus from Taiwan or T. maritimus from Phu Yen, Vietnam probably descended from ancient hybridization. Diversification of the three main Tamiops lineages was estimated to occur 8.8-6.7 million years ago (mya) and may have been affected by rapid uplift of the Himalayan Mountains in the western part of their range. Multiple divergences from 5.8 to 1.7 mya likely led to the formation of modern Tamiops species. All six populations of T. swinhoei-maritimus complex could be regarded as distinct species. Divergence among T. rodolphii populations in mitochondrial DNA was also at the interspecies level. Our analyses highlight the underestimation of species diversity in the genus Tamiops.