Home About us Contact
|
Home About us Contact | ||
|
|
||
Mitochondrial Lineages (mitochondrial + lineage)
Selected AbstractsGenetic variation and phylogeography of free-living mouse species (genus Mus) in the Balkans and the Middle EastMOLECULAR ECOLOGY, Issue 22 2007M. MACHOLÁN Abstract This work presents a study of the distribution and pattern of variation throughout the ranges of three free-living mouse species of the genus Mus,M. macedonicus, M. spicilegus, and a M. cypriacus , based on sequencing of two segments of the mitochondrial DNA (mtDNA) control region. The study shows a similar level of variability in the three species and suggests their recent population expansion. The highest proportion of variation is found within populations indicating low genetic structuring. Phylogenetic analysis confirms the significant divergence of a mitochondrial lineage of M. macedonicus from Israel, recently described as a new subspecies, M. macedonicus spretoides. Conversely, no genetic hiatus is revealed between European and Asian populations of M. macedonicus macedonicus. Although phylogenetic relationships among M. spicilegus populations could not be unravelled precisely, the results suggest a recent westward expansion of the species. The mtDNA divergence between M. macedonicus and M. spicilegus is 7.3%, suggesting their split between c. 700 000 and 1 million years ago. These dates correspond with a coalescent estimate about 720 000 years ago. On the other hand, M. cypriacus appeared almost twice as divergent from the former species (4.5%) as from the latter (8.8%) suggesting a divergence of c. 430 000,610 000 years ago (coalescent , 490 000 years ago) and 830 000,1.2 million years ago (coalescent , 780 000 years ago), respectively. Approximate times of population expansion have also been estimated for all taxa and groups of populations. Existence of several glacial refuges and various colonization scenarios are discussed; since all estimated divergence times fall within interglacial periods it seems that climatic oscillations did not play a crucial role in the evolution of the three species. [source] Genetic evaluation of a proposed introduction: the case of the greater prairie chicken and the extinct heath henMOLECULAR ECOLOGY, Issue 7 2004Eric P. Palkovacs Abstract Population introduction is an important tool for ecosystem restoration. However, before introductions should be conducted, it is important to evaluate the genetic, phenotypic and ecological suitability of possible replacement populations. Careful genetic analysis is particularly important if it is suspected that the extirpated population was unique or genetically divergent. On the island of Martha's Vineyard, Massachusetts, the introduction of greater prairie chickens (Tympanuchus cupido pinnatus) to replace the extinct heath hen (T. cupido cupido) is being considered as part of an ecosystem restoration project. Martha's Vineyard was home to the last remaining heath hen population until its extinction in 1932. We conducted this study to aid in determining the suitability of greater prairie chickens as a possible replacement for the heath hen. We examined mitochondrial control region sequences from extant populations of all prairie grouse species (Tympanuchus) and from museum skin heath hen specimens. Our data suggest that the Martha's Vineyard heath hen population represents a divergent mitochondrial lineage. This result is attributable either to a long period of geographical isolation from other prairie grouse populations or to a population bottleneck resulting from human disturbance. The mtDNA diagnosability of the heath hen contrasts with the network of mtDNA haplotypes of other prairie grouse (T. cupido attwateri, T. pallidicinctus and T. phasianellus), which do not form distinguishable mtDNA groupings. Our findings suggest that the Martha's Vineyard heath hen was more genetically isolated than are current populations of prairie grouse and place the emphasis for future research on examining prairie grouse adaptations to different habitat types to assess ecological exchangeability between heath hens and greater prairie chickens. [source] Body shape vs. colour associated initial divergence in the Telmatherina radiation in Lake Matano, Sulawesi, IndonesiaJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 3 2007D. ROY Abstract Highly polymorphic colouration patterns are often associated with sexual selection in fish and can be the initial cause of divergence among closely related taxa. Here we use genetic, body colour and geometric morphometric data collected on 118 fish from Lake Matano, Sulawesi, Indonesia to test if colouration is the initial cause of divergence in the radiating Telmatherina genus. Results reveal that all Telmatherina previously described in this system can be categorized into three mitochondrial lineages and that colouration is only weakly associated with early divergence. Clade-specific body shapes, however, likely adapted to microenvironments are key to the initial divergence in this system. Data also show that although colourations were not likely instrumental in seeding divergence in these fish, they appear to have developed in parallel within each clade. Our results are consistent with an emerging pattern repeated in many vertebrate radiations, whereby divergence by colouration or other display traits is preceded by specialization to environmental adaptive peaks. [source] Differentiation of golden-ringed dragonfly Anotogaster sieboldii (Selys, 1854) (Cordulegastridae: Odonata) in the insular East Asia revealed by the mitochondrial gene genealogy with taxonomic implicationsJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 2 2008T. Kiyoshi Abstract Molecular phylogeographical analyses of Anotogaster sieboldii (Selys, 1854) were conducted to reveal the differentiation process of insular populations. The gene genealogy based on 845 bp of the mitochondrial genes (cytochrome oxidase subunit I and subunit II) indicated that A. sieboldii includes two deeply separated lineages. These two major lineages seem to have differentiated in Miocene before the formation of the insular East Asia. One lineage includes three inner clades that correspond to the populations of northern area (the Japanese main islands, Korean Peninsula, Yakushima), Amamioshima and Okinawajima. Populations of Central Ryukyu, including Amamioshima and Okinawajima, might have been divided from the northern populations in early Pleistocene. The other major lineage includes populations of the Yaeyama Group, Taiwan and East China. The former two populations were reconstructed as a reciprocal monophyletic group. Populations of Taiwan and Yaeyama Groups would have been separated from the continental ones in Pleistocene. These two highly divergent lineages should be recognized as distinct species. Furthermore, the mitochondrial lineages revealed six genetically distinct and geographically isolated assemblages: (1) northern populations, (2) Amamioshima, (3) Okinawajima, (4) Yaeyama Group, (5) Taiwan and (6) East China. Zusammenfassung An der Libelle Anotogaster sieboldii wurden molekulare phylogeographische Analysen durchgeführt, um ihre Differenzierungen in Insel-Populationen zu erkennen. Die Gen-Genealogie (basierend auf 845 bp mitochondrialer Gene (COI und COII) zeigte, dass A. sieboldii zwei weit getrennte Abstammungslinien enthält, die sich wahrscheinlich im Miozän vor der Bildung der ostasiatischen Inselwelt differenzierten. Eine Abstammungslinie schließt drei Gruppierungen ein, die den Populationen in den nördlichen Gebieten entsprechen: die japanischen Hauptinseln, die koreanische Halbinsel Yakushima, Amamioshima sowie Okinawajima. Die Populationen von Zentral-Ryukyu, einschließlich Amamioshima und Okinawajima, ist möglicherweise im frühen Pleistozän von den nördlichen Populationen getrennt worden. Die andere größere Abstammungslinie schließt die Populationen der Yaeyama-Gruppe, Taiwan und das Östliche China ein. Zwei dieser Populationen wurden als Teil einer entsprechenden monophyletischen Gruppe rekonstruiert; die Populationen von Taiwan und die Yaeyama-Gruppe sind danach im Pleistozän von den kontinentalen Populationen getrennt worden. Diese zwei sehr differierenden Abstammungslinien sollten als verschiedene Spezies betrachtet werden. Weiterhin werden sechs genetisch verschiedene und geographisch isolierte Gruppierungen deutlich: (1) die nördlichen Populationen, (2) Amamioshima, (3) Okinawajima, (4) die Yaeyama-Gruppe, (5) Taiwan und (6) die Population im östlichen China. [source] Defining reproductively isolated units in a cryptic and syntopic species complex using mitochondrial and nuclear markers: the brooding brittle star, Amphipholis squamata (Ophiuroidea)MOLECULAR ECOLOGY, Issue 7 2008E. BOISSIN Abstract At a time when biodiversity is threatened, we are still discovering new species, and particularly in the marine realm. Delimiting species boundaries is the first step to get a precise idea of diversity. For sympatric species which are morphologically undistinguishable, using a combination of independent molecular markers is a necessary step to define separate species. Amphipholis squamata, a cosmopolitan brittle star, includes several very divergent mitochondrial lineages. These lineages appear totally intermixed in the field and studies on morphology and colour polymorphism failed to find any diagnostic character. Therefore, these mitochondrial lineages may be totally interbreeding presently. To test this hypothesis, we characterized the genetic structure of the complex in the French Mediterranean coast using sequences of mitochondrial DNA (16S) and for the first time, several nuclear DNA markers (introns and microsatellites). The data revealed six phylogenetic lineages corresponding to at least four biological species. These sibling species seem to live in syntopy. However, they seem to display contrasted levels of genetic diversity, suggesting they have distinct demographic histories and/or life-history traits. Genetic differentiation and isolation-by-distance within the French Mediterranean coasts are revealed in three lineages, as expected for a species without a free larval phase. Finally, although recombinant nuclear genotypes are common within mitochondrial lineages, the data set displays a total lack of heterozygotes, suggesting a very high selfing rate, a feature likely to have favoured the formation of the species complex. [source] Around or across the Carpathians: colonization model of the Danube basin inferred from genetic diversification of stone loach (Barbatula barbatula) populationsMOLECULAR ECOLOGY, Issue 5 2008ALENA, EDIVÁ Abstract Despite increasing information about postglacial recolonization of European freshwater systems, very little is known about pre-Pleistocene history. We used data on the recent distribution and phylogenetic relationships of stone loach mitochondrial lineages to reconstruct the initial colonization pattern of the Danube river system, one of the most important refuges for European freshwater ichthyofauna. Fine-scale phylogeography of the Danubian populations revealed five highly divergent lineages of pre-Pleistocene age and suggested the multiple origin of the Danubian stone loach. The mean sequence divergence among lineages extended from 7.0% to 13.4%, which is the highest intraspecific divergence observed so far within this river system. Based on the phylogeographical patterns, we propose the following hypothesis to relate the evolution and dispersal of the studied species with the evolution of the Danube river system and the Carpathian Mountains: (i) during the warmer period in the Miocene, the areas surrounding the uplifting Alps and Carpathians served as mountainous refuges for cold-water adapted fish and promoted the diversification of its populations, and (ii) from these refuges, colonization of the emerging Danube river system may have taken place following the retreat of the Central Paratethys. Co-existence of highly divergent mtDNA lineages in a single river system shows that range shifts in response to climatic changes during the Quaternary did not cause extensive genetic homogenization in the stone loach populations. However, the wide distribution of some mtDNA lineages indicates that the Pleistocene glaciations promoted the dispersal and mixing of populations through the lowlands. [source] Refugial isolation and secondary contact in the dyeing poison frog Dendrobates tinctoriusMOLECULAR ECOLOGY, Issue 14 2006BRICE P. NOONAN Abstract Recent palaeoclimactic research suggests that fluctuating environmental conditions throughout the Pleistocene of Amazonia occurred with previously unrecognized frequency. This has resulted in a theoretical shift from glacially influenced fluctuations to those driven by precessional rhythms. This theoretical revolution has a profound impact on expectations of biotic diversity within biogeographical regions that have long been based on the idea of large-scale landscape fragmentation associated with increased aridity and glacial cycles. Generally speaking, this shifts phylogeographical expectations from that of (i) large areas of sympatry of closely related (but not sister) species whose origins lie in separate refugia, and current distributions are the results of cyclic connectivity of those two refugia (refuge hypothesis), to that of (ii) fine scale genetic structure, often associated with elevation, and divergence well below expected speciation levels [disturbance,vicariance (DV) hypothesis]. To date there have been few tests of the expectations of the DV hypothesis based on empirical studies of Neotropical floral and faunal communities. Herein we examine phylogeographical structure of Dendrobates tinctorius, an amphibian species endemic to the uplands of the eastern Guiana Shield, based on sampling of 114 individuals from 24 localities. Phylogenetic, nested clade, and dispersal,vicariance (DIVA) analyses of cytochrome b sequence data reveal the presence of two mitochondrial lineages that are associated with previously identified western and eastern uplands of this area. The geographical distribution of mitochondrial haplotypes and the results of DIVA and coalescent analyses suggest that there has been extensive secondary contact between these lineages indicating a complex history of connectivity between these western and eastern highlands, supporting the predictions of the DV hypothesis. [source] Isolation and development of microsatellite markers for the Japanese dormouse, Glirulus japonicusMOLECULAR ECOLOGY RESOURCES, Issue 2 2009S. P. YASUDA Abstract Eight microsatellite markers were developed for the Japanese dormouse (Glirulus japonicus), a natural monument and near-threatened species in Japan. The markers amplify in individuals from all of the mitochondrial lineages detected in a previous study. Numerous polymorphisms were detected in specimens from a local population in central Honshu (11,21 alleles per locus; n = 31) and from the entire distribution range of the species (19,41 alleles per locus; n = 152). These microsatellites will be useful in conservation genetic studies of G. japonicus. [source] A fine map for maternal lineage analysis by mitochondrial hypervariable region in 12 Chinese goat breedsANIMAL SCIENCE JOURNAL, Issue 4 2009Yan-Ping WU ABSTRACT As the fast pace of genomic research continues to identify mitochondrial lineages in animals, it has become apparent that many independent studies are needed to support a robust phylogenetic inference. The aim of this study was thus to further characterize the maternal lineage, proposed to originate in southwestern region of China, using a wider survey of diverse goat breeds in China. To this end, we sequenced the mitochondrial hypervariable region 1 (HVR1) of the mtDNA control region in 145 goats of 12 Chinese breeds. Phylogenetic analysis revealed that Chinese goats were classified into four distinct lineages (A, B, C and D) as previously reported. A Mantel test and the analysis of Analysis of Molecular Variance (ANOVA) indicated that there was not an obvious geographic structure among Chinese goat breeds. Population expansion analysis based on mismatch distribution and Fu's Fs statistic indicate that two expansion events in Chinese goats occurred respectively at about 11 and 29 mutational time units ago, revealing two star-like subclades in lineage B corresponding to two population expansion events. Moreover, lineage B sequences were presented only in the breeds of southwestern or surrounding regions of China. Multiple lines of evidence from this study and previous studies indicate that for Chinese goats mtDNA lineage B originated from the southwestern region of China. [source] Deeply divergent mitochondrial lineages reveal patterns of local endemism in chironomids of the Australian Wet TropicsAUSTRAL ECOLOGY, Issue 3 2009MATT N. KROSCH Abstract The Wet Tropics bioregion of north-eastern Australia has been subject to extensive fluctuations in climate throughout the late Pliocene and Pleistocene. Cycles of rainforest contraction and expansion of dry sclerophyll forest associated with such climatic fluctuations are postulated to have played a major role in driving geographical endemism in terrestrial rainforest taxa. Consequences for the distributions of aquatic organisms, however, are poorly understood. The Australian non-biting midge species Echinocladius martini Cranston (Diptera: Chironomidae), although restricted to cool, well-forested freshwater streams, has been considered to be able to disperse among populations located in isolated rainforest pockets during periods of sclerophyllous forest expansion, potentially limiting the effect of climatic fluctuations on patterns of endemism. In this study, mitochondrial COI and 16S data were analysed for E. martini collected from eight sites spanning the Wet Tropics bioregion to assess the scale and extent of phylogeographic structure. Analyses of genetic structure showed several highly divergent cryptic lineages with restricted geographical distributions. Within one of the identified lineages, strong genetic structure implied that dispersal among proximate (<1 km apart) streams was extremely restricted. The results suggest that vicariant processes, most likely due to the systemic drying of the Australian continent during the Plio-Pleistocene, might have fragmented historical E. martini populations and, hence, promoted divergence in allopatry. [source] Phylogeography of the last surviving populations of Rhodian and Anatolian fallow deer (Dama dama dama L., 1758)BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2008MARCO MASSETI The European fallow deer (Dama dama dama) is one of the most widespread cervids, and its distribution has been heavily affected by man. At present, only one wild autochthonous population is reputed to survive in Anatolia, but its census size is dramatically decreasing. This means that a significant portion of the ancestral genetic diversity of this taxon is seriously threatened. In the present study, a portion of the mitochondrial DNA (D-loop) in 37 D. d. dama specimens from three Mediterranean sites, Turkey, the island of Rhodes (Greece), and the Italian Peninsula, and seven individuals of the Persian fallow deer, Dama dama mesopotamica, was sequenced, and the results from the data analysis are interpreted in light of current archaeozoological and biogeographical knowledge. We conclude that: (1) D. d. mesopotamica is strongly differentiated from D. d. dama, confirming the results of previous genetic studies and (2) the Rhodian populations of D. d. dama, founded by humans in Neolithic times, possess a set of mitochondrial lineages, found in no other study populations. The persistence of these haplotypes is particularly significant because human-mediated processes (e.g. domestication) usually result in genetic depletion and erosion of an ancestral genetic pool. In the case of the Rhodes' population of fallow deer, we hypothesize that, during the foundation of this population, humans unknowingly preserved a remarkable portion of the original genetic diversity of the source population(s). © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 93, 835,844. [source] | ||||||||||