Home About us Contact
|
Home About us Contact | ||
|
|
||
Mitochondrial Data (mitochondrial + data)
Selected AbstractsTo see in different seas: spatial variation in the rhodopsin gene of the sand goby (Pomatoschistus minutus)MOLECULAR ECOLOGY, Issue 20 2009MAARTEN H. D. LARMUSEAU Abstract Aquatic organisms living in a range of photic environments require specific mechanisms to tune their visual pigments. Maximum absorbance (,max) of retinal rods in populations of the marine demersal sand goby, (Pomatoschistus minutus; Gobiidae, Teleostei) correlates with the local optic environment. It has been shown that this is not regulated through a physiological response by exchanging the rhodopsin chromophore. To test for evolutionary adaptation, the sequence of the rhodopsin (RH1) gene was analysed in 165 Pomatoschistus minutus individuals from seven populations across its distribution range. Analysis showed a high level of intraspecific polymorphism at the RH1 gene, including nonsynonymous mutations on amino acids, known as spectral tuning sites. Population differentiation at these sites was in agreement with the observed differentiation in ,max values. Analyses of dN/dS substitution rate ratios and likelihood ratio tests under site-specific models detected a significant signal of positive Darwinian selection on the RH1 gene. A strong discrepancy in differentiation was noticed between RH1 gene variation and the presumably neutral microsatellites and mitochondrial data. Samples did not cluster according to geographical or historical proximity with regards to RH1, but according to the general photic conditions of the habitat environment of the sand goby. This study highlights the usefulness of sensory genes, like rhodopsin, for studying the characteristics of local adaptation in marine nonmodel organisms. [source] Huge populations and old species of Costa Rican and Panamanian dirt frogs inferred from mitochondrial and nuclear gene sequencesMOLECULAR ECOLOGY, Issue 10 2003A. J. Crawford Abstract Molecular genetic data were used to investigate population sizes and ages of Eleutherodactylus (Anura: Leptodactylidae), a species-rich group of small leaf-litter frogs endemic to Central America. Population genetic structure and divergence was investigated for four closely related species surveyed across nine localities in Costa Rica and Panama. DNA sequence data were collected from a mitochondrial gene (ND2) and a nuclear gene (c- myc). Phylogenetic analyses yielded concordant results between loci, with reciprocal monophyly of mitochondrial DNA haplotypes for all species and of c- myc haplotypes for three of the four species. Estimates of genetic differentiation among populations (FST) based upon mitochondrial data were always higher than nuclear-based FST estimates, even after correcting for the expected fourfold lower effective population size (Ne) of the mitochondrial genome. Comparing within-population variation and the relative mutation rates of the two genes revealed that the Ne of the mitochondrial genome was 15-fold lower than the estimate of the nuclear genome based on c- myc. Nuclear FST estimates were , 0 for the most proximal pairs of populations, but ranged from 0.5 to 1.0 for all other pairs, even within the same nominal species. The nuclear locus yielded estimates of Ne within localities on the order of 105. This value is two to three orders of magnitude larger than any previous Ne estimate from frogs, but is nonetheless consistent with published demographic data. Applying a molecular clock model suggested that morphologically indistinguishable populations within one species may be 107 years old. These results demonstrate that even a geologically young and dynamic region of the tropics can support very old lineages that harbour great levels of genetic diversity within populations. The association of high nucleotide diversity within populations, large divergence between populations, and high species diversity is also discussed in light of neutral community models. [source] Origin, diversification and conservation status of talus snails in the Pinaleño Mountains: a conservation biogeographic studyANIMAL CONSERVATION, Issue 3 2010K. F. Weaver Abstract For many taxa, determining conservation status and priority is impeded by lack of adequate taxonomic and range data. For these problematic groups, we propose combining molecular techniques with careful geographic sampling to evaluate the validity, extent and phylogenetic relatedness of the proposed units of diversity. We employed such a strategy to document monophyletic lineages, range extents and phylogenetic relatedness for talus snails (genus Sonorella) in the Pinaleño Mountains of Arizona, an isolated range that has the most vertical relief of any of the sky islands in Arizona. Three of the four species found in the Pinaleño Mountains have been considered candidate species for protection under the Endangered Species Act. Further, one of these taxa, Sonorella macrophallus, is of particular concern and was protected under an USFS conservation agreement until 2004, due to its presumed endemicity to a narrow portion of one canyon. We collected a large dataset of 12S and COI mitochondrial DNA, and subsamples of reproductive morphology from specimens collected throughout the Pinaleños and from adjacent ranges (e.g. the Huachucas, Chiricahuas and Santa Catalinas). We generated a phylogeny based on the mitochondrial data, and matched clades with named species utilizing reproductive morphology. Our results show that both S. macrophallus and Sonorella imitator are relatively widespread across the Pinaleños while Sonorella grahamensis and Sonorella christenseni are restricted to very small areas. These results dramatically change our previous knowledge about range extents, especially for S. macrophallus. Given these results, land managers may need to reassess the status of all four Sonorella species. Finally, all Sonorella species from the Pinaleños are more closely related to each other than to other taxa on other ranges. This result strongly suggests that diversification of the four Sonorella species in the Pinaleños occurred in situ. [source] Mitochondrial and Y Chromosome Diversity in the English-Speaking CaribbeanANNALS OF HUMAN GENETICS, Issue 6 2007J. Benn Torres Summary The transatlantic slave trade lasted over three centuries and represents one of the largest forced migrations in human history. The biological repercussions are not well understood especially in African-Caribbean populations. This paper explores the effects of the forced migration, isolation, and admixture on genetic diversity using mitochondrial and Y chromosome markers for 501 individuals from Dominica, Grenada, Jamaica, St. Kitts, St. Lucia, St. Thomas, St. Vincent, and Trinidad. Genetic diversity and population genetic structure analyses of mitochondrial data and Y chromosome data indicate that there was no post-migration loss in genetic diversity in the African derived lineages. Genetic structure was observed between the islands for both genetic systems. This may be due to isolation, differences in the number and source of Africans imported, depopulation of indigenous populations, and/or differences in colonization history. Nearly 10% of the individuals belonged to a non-African mitochondrial haplogroup. In contrast, Y chromosome admixture estimates showed that there was nearly 30% European contribution to these Caribbean populations. This study sheds light on the history of Africans in the Americas as well as contributing to our understanding of the nature and extent of diversity within the African Diaspora. [source] Genetic relationships of the western Mediterranean painted frogs based on allozymes and mitochondrial markers: evolutionary and taxonomic inferences (Amphibia, Anura, Discoglossidae)BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2006ZANGARI FRANCESCA Allozymes and sequencing of mitochondrial cytochrome b (cyt b) and 12S genes were used to reconstruct the genetic structure and phylogenetic relationships of all Discoglossus taxa described so far (except the probably extinct D. nigriventer). This is the first time that a comprehensive study on the Discoglossus painted frogs has used nuclear and mitochondrial markers, evidencing a discordant pattern between the two datasets. Comparison of these discrepancies suggests a role of stochastic sorting of ancestral polymorphisms, possibly associated with male-biased dispersal and present or past secondary contact. The genetic relationships between taxa with intermediate levels of divergence were well defined by allozyme data, but showed short internodes and low bootstrap values for mitochondrial data, suggesting a rapid radiation of their lineages during the Messinian Lago Mare phase. The results provide information about the taxonomic status of D. galganoi and D. jeanneae, considered as subspecies, and indicate D. pictus as nonmonophyletic, confirming D. scovazzi as a distinct species. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 87, 515,536. [source] | ||||||||||