Inherited Mitochondrial DNA (inherited + mitochondrial_dna)

Distribution by Scientific Domains


Selected Abstracts


Inferences from DNA data: population histories, evolutionary processes and forensic match probabilities

JOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES A (STATISTICS IN SOCIETY), Issue 2 2003
Ian J. Wilson
Summary. We develop a flexible class of Metropolis,Hastings algorithms for drawing inferences about population histories and mutation rates from deoxyribonucleic acid (DNA) sequence data. Match probabilities for use in forensic identification are also obtained, which is particularly useful for mitochondrial DNA profiles. Our data augmentation approach, in which the ancestral DNA data are inferred at each node of the genealogical tree, simplifies likelihood calculations and permits a wide class of mutation models to be employed, so that many different types of DNA sequence data can be analysed within our framework. Moreover, simpler likelihood calculations imply greater freedom for generating tree proposals, so that algorithms with good mixing properties can be implemented. We incorporate the effects of demography by means of simple mechanisms for changes in population size and structure, and we estimate the corresponding demographic parameters, but we do not here allow for the effects of either recombination or selection. We illustrate our methods by application to four human DNA data sets, consisting of DNA sequences, short tandem repeat loci, single-nucleotide polymorphism sites and insertion sites. Two of the data sets are drawn from the male-specific Y-chromosome, one from maternally inherited mitochondrial DNA and one from the , -globin locus on chromosome 11. [source]


Sex-biased gene flow and colonization in the Formosan lesser horseshoe bat: inference from nuclear and mitochondrial markers

JOURNAL OF ZOOLOGY, Issue 3 2008
S.- F. Chen
Abstract Sex-biased behaviours are expected to play an important role in partitioning genetic variance in animal populations. Comparing genetic structure at markers with different modes of inheritance provides a means of detecting these behaviours and their consequences for population genetic structure. In colonially breeding mammals, the common combination of female philopatry and male vagility can promote contrasting patterns of genetic differentiation between the sexes, both via their effects on recurrent gene flow and on colonization. We examined sex differences in gene flow and structure by comparing maternally inherited mitochondrial DNA (mtDNA) and biparentally inherited autosomal loci in the Formosan lesser horseshoe bat Rhinolophus monoceros. We found that genetic partitioning was higher at mtDNA than autosomal markers in both sexes, indicative of female-biased philopatry and male-biased dispersal. Across Taiwan, isolation-by-distance was detected for all sex/marker combinations but was steeper for mtDNA than for nuclear markers. We suggest that isolation-by-distance shown from mtDNA at large scales is likely to reflect the stepwise founding of new breeding colonies by females during colonization. In contrast, no isolation-by-distance was found at smaller distances of up to 100 km, indicating that gene flow and/or recent shared ancestry homogenises genetic structure among nearby sites. Our results highlight the value of an indirect genetic approach to understanding sex-biased behaviours and their consequences in a little-studied species. [source]


Phylogeography of Douglas-fir based on mitochondrial and chloroplast DNA sequences: testing hypotheses from the fossil record

MOLECULAR ECOLOGY, Issue 9 2010
PAUL F. GUGGER
Abstract The integration of fossil and molecular data can provide a synthetic understanding of the ecological and evolutionary history of an organism. We analysed range-wide maternally inherited mitochondrial DNA and paternally inherited chloroplast DNA sequence data with coalescent simulations and traditional population genetic methods to test hypotheses of population divergence generated from the fossil record of Douglas-fir (Pseudotsuga menziesii), an ecologically and economically important western North American conifer. Specifically, we tested (i) the hypothesis that the Pliocene orogeny of the Cascades and Sierra Nevada caused the divergence of coastal and Rocky Mountain Douglas-fir varieties; and (ii) the hypothesis that multiple glacial refugia existed on the coast and in the Rocky Mountains. We found that Douglas-fir varieties diverged about 2.11 Ma (4.37 Ma,755 ka), which could be consistent with a Pliocene divergence. Rocky Mountain Douglas-fir probably resided in three or more glacial refugia. More variable molecular markers would be required to detect the two coastal refugia suggested in the fossil record. Comparison of mitochondrial DNA and chloroplast DNA variation revealed that gene flow via pollen linked populations isolated from seed exchange. Postglacial colonization of Canada from coastal and Rocky Mountain refugia near the ice margin at the Last Glacial Maximum produced a wide hybrid zone among varieties that formed almost exclusively by pollen exchange and chloroplast DNA introgression, not seed exchange. Postglacial migration rates were 50,165 m/year, insufficient to track projected 21st century warming in some regions. Although fossil and genetic data largely agree, each provides unique insights. [source]


Phylogeography of a northeast Asian spruce, Picea jezoensis, inferred from genetic variation observed in organelle DNA markers

MOLECULAR ECOLOGY, Issue 16 2007
M. AIZAWA
Abstract Range-wide genetic variation of the widespread cold-temperate spruce Picea jezoensis was studied throughout northeast Asia using maternally inherited mitochondrial DNA and paternally inherited chloroplast DNA markers. This study assessed 33 natural populations including three varieties of the species in Japan, Russia, China, and South Korea. We depicted sharp suture zones in straits around Japan in the geographical distribution pattern of mitochondrial haplotypes (GST = 0.901; NST = 0.934). In contrast, we detected possible extensive pollen flow without seed flow across the straits around Japan during the past population history in the distribution pattern of chloroplast haplotypes (GST = 0.233; NST = 0.333). The analysis of isolation by distance of the species implied that by acting as a barrier for the movement of seeds and pollen, the sharp suture zones contributed considerably to the level of genetic differentiation between populations. Constructed networks of mitochondrial haplotypes allowed inference of the phylogeographical history of the species. We deduced that the disjunction with Kamchatka populations reflects range expansion and contraction to the north of the current distribution. Within Japan, we detected phylogeographically different types of P. jezoensis between Hokkaido and Honshu islands; P. jezoensis in Honshu Island may have colonized this region from the Asian continent via the Korean peninsula and the species in Hokkaido Island is likely to have spread from the Asian continent via Sakhalin through land bridges. Japanese endemism of mitochondrial haplotypes in Hokkaido and Honshu islands might have been promoted by separation of these islands from each other and from the Asian continent by the straits during the late Quaternary. [source]


Hybrid origin of a swordtail species (Teleostei: Xiphophorus clemenciae) driven by sexual selection

MOLECULAR ECOLOGY, Issue 3 2006
AXEL MEYER
Abstract The swordlike exaggerated caudal fin extensions of male swordtails are conspicuous traits that are selected for through female choice. Swords are one of only few examples where the hypothesis of a pre-existing bias is believed to apply for the evolution of a male trait. Previous laboratory experiments demonstrated that females prefer males with longer swords and even females from some swordless species show an affiliation for males of sworded species. Earlier phylogenetic studies based on maternally inherited mitochondrial DNA placed the sworded southern swordtail Xiphophorus clemenciae with swordless platies, contradicting its morphology-based evolutionary affinities. The analyses of new nuclear DNA markers now recover its traditional phylogenetic placement with other southern swordtails, suggesting that this species was formed by an ancient hybridization event. We propose that sexual selection through female choice was the likely process of hybrid speciation, by mating of platy females with males of an ancestral swordtail lineage. In artificial crosses of descendent species from the two potential ancestral lineages of X. clemenciae the hybrid and backcross males have swords of intermediate lengths. Additionally, mate choice experiments demonstrate that hybrid females prefer sworded males. These experimental lines of evidence make hybridization through xeno-specific sexual selection by female choice the likely mechanism of speciation. [source]


Combining paternally and maternally inherited mitochondrial DNA for analysis of population structure in mussels

MOLECULAR ECOLOGY, Issue 6 2004
Robert A. Krebs
Abstract Sequence divergence for a fragment of the 16S rRNA gene was compared to identify the advantages in using mitochondrial genes that descend separately through the female and male lineages to examine population structure. The test compared divergence among four local species of freshwater mussels (Unionidae) and was extended to multiple populations of one species, Pyganodon grandis. For the same gene, the male-inherited sequences diverged at a faster rate, producing longer branch lengths in the phylogenies. Of particular use were sequences extracted from P. grandis populations from the southern region of the Lake Erie watershed (Ohio, USA); five male-inherited haplotypes were found. Only one change was observed in the female-inherited form in this region. Therefore, more rapid evolution has occurred in the male form of the gene, and this form provided stronger evidence of geographical isolation among populations. A combination of analyses on haplotypes derived through males and females creates complementary opportunities to identify evolutionary relationships caused by drift and migration in mussels. [source]