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Molecular Phylogeography (molecular + phylogeography)
Selected AbstractsConsistent geographic structure among multiple nuclear sequences and cpDNA polymorphisms of Cardamine nipponica Franch. et Savat. (Brassicaceae)MOLECULAR ECOLOGY, Issue 13 2008HAJIME IKEDA Abstract Molecular phylogeography has inferred the history of differentiation between regions and/or among populations following the Pleistocene climatic oscillations, mostly based on the genetic structure of organelle DNA. However, such genetic structure only reflects the history of a single gene, and studies based on single-copy genes of nuclear DNA (nDNA) are required for phylogeography, although their efficiency remains unclear. To examine the utility of nDNA loci, the genetic structures of three genes from Cardamine nipponica, which is closely related to the model species Arabidopsis thaliana, were elucidated: the nDNA genes DET1, PHYA, PHYE, as well as chloroplast DNA (cpDNA). In 279 individuals collected from throughout the range of the species, strong genetic differentiation between northern and central Japan was found for all loci. This result suggested that populations in central Japan experienced a different history from those in northern Japan during the Pleistocene climatic oscillations. In addition, the evidence of refugia at the edges of the distribution, where the genetic structure was less influenced by colonization following range expansion, was shown for several loci. The specific genetic structure within the southernmost populations of northern Japan suggested that this region was also isolated during range expansion. Hence, the consistent history among loci and a more detailed history from several loci indicated that cpDNA can represent the history of vicariance and demonstrated the efficiency of single-copy nuclear genes in phylogeography. [source] A mitochondrial phylogeography of Brachidontes variabilis (Bivalvia: Mytilidae) reveals three cryptic speciesJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 4 2007M. Sirna Terranova Abstract This study examined genetic variation across the range of Brachidontes variabilis to produce a molecular phylogeography. Neighbour joining (NJ), minimum evolution (ME) and maximum parsimony (MP) trees based on partial mitochondrial DNA sequences of 16S-rDNA and cytochrome oxidase (COI) genes revealed three monophyletic clades: (1) Brachidontes pharaonis s.l. from the Mediterranean Sea and the Red Sea; (2) B. variabilis from the Indian Ocean; (3) B. variabilis from the western Pacific Ocean. Although the three clades have never been differentiated by malacologists employing conventional morphological keys, they should be ascribed to the taxonomic rank of species. The nucleotide divergences between Brachidontes lineages (between 10.3% and 23.2%) were substantially higher than the divergence between congeneric Mytilus species (2.3,6.7%) and corresponded to interspecific divergences found in other bivalvia, indicating that they should be considered three different species. Analysis of the 16S-rDNA sequences revealed heteroplasmy, indicating dual uniparental inheritance (DUI) of mtDNA in the species of Brachidontes collected in the Indian Ocean, but not in the species in the Pacific nor in the species in the Red Sea and the Mediterranean Sea. When we employed the conventional estimate of the rate of mitochondrial sequence divergence (2% per million years), the divergence times for the three monophyletic lineages were 6,11 Myr for the Indian Ocean and Pacific Ocean Brachidontes sp. and 6.5,9 Myr for the Red Sea and Indian Ocean Brachidontes sp. Thus, these species diverged from one another during the Miocene (23.8,5.3 Myr). We infer that a common ancestor of the three Brachidontes species probably had an Indo-Pacific distribution and that vicariance events, linked to Pleistocene glaciations first and then to the opening of the Red Sea, produced three monophyletic lineages. Riassunto Lo studio filogeografico č stato condotto su tutto l'areale di Brachidontes variabilis (Krauss, 1848) attraverso l'analisi di sequenze mitocondriali (16S-rDNA e COI) che hanno separato i campioni in tre cladi monofiletici. Diversi algoritmi (NJ, ME e MP) hanno elaborato alberi con la stessa topologia, in cui č possibile riconoscere: (1) Brachidontes pharaonis s.l. dell'area Mar Mediterraneo , Mar Rosso; (2) Brachidontes variabilis dell' Oceano Indiano; (3) Brachidontesvariabilis dell'Oceano Pacifico. Il loro grado di divergenza č sufficientemente alto da potere ascrivere al rango di specie i singoli cladi, nonostante non siano stati ancora individuati i caratteri tassonomici distintivi, a causa della grande variazione morfologica. La divergenza nucleotidica tra le tre linee di Brachidontes era compresa tra 10.3% e 23.2%, in un range di valori superiori a quelli trovati nel confronto tra specie congeneriche di Mytilus sp (2.3,6.7%). Utilizzando il tasso evolutivo, che convenzionalmente viene applicato ai valori di divergenza genetica di geni mitocondriali (2% per milioni di anni), si sono ricavati tempi di divergenza corrispondenti a 6,11 milioni di anni tra Oceano Indiano e Pacifico, e a 6.5,9 milioni di anni tra Mar Rosso e Oceano Indiano. Le tre linee evolutive sembrano essersi separate durante il Miocene. Probabilmente un comune antenato con distribuzione Indo-Pacifica puň essere andato incontro a processi di vicarianza e/o di dispersione legati alle glaciazioni pleistoceniche prima e all'apertura del Mar Rosso dopo. [source] Combined ecological niche modelling and molecular phylogeography revealed the evolutionary history of Hordeum marinum (Poaceae) , niche differentiation, loss of genetic diversity, and speciation in Mediterranean Quaternary refugiaMOLECULAR ECOLOGY, Issue 8 2007SABINE S. JAKOB Abstract The Hordeum marinum species group consists of two annual grasses of western Eurasian saline meadows or marshes. The two grasses split in the Quaternary about two million years ago. Hordeum marinum and the diploid of Hordeum gussoneanum (2×) co-occur throughout the Mediterranean basin, while the autotetraploid cytotype of H. gussoneanum (4×) overlaps with its diploid progenitor geographically only in the utmost Eastern Mediterranean, extending from there eastwards into Asia. Using chloroplast sequences of the trnL-F region, six newly developed chloroplast microsatellite loci, ecological predictive models based on climate data, and the present geographical distribution of the two species we analysed differentiation processes in the H. marinum group. The chloroplast data indicated clear differences in the history of both species. For H. marinum we found a subdivision between genetically variable populations from the Iberian Peninsula and the more uniform populations from the remaining Mediterranean. As an explanation, we assume Pleistocene fragmentation of an earlier widespread population and survival in an Iberian and a Central Mediterranean glacial refuge. Chloroplast variation was completely absent within the cytotypes of H. gussoneanum, indicating a severe and recent genetic bottleneck. Due to this lack of chloroplast variation only the combination of ecological habitat modelling with molecular data analyses allowed conclusions about the history of this taxon. The distribution areas of the two cytotypes of H. gussoneanum overlap today in parts of Turkey, indicating an area with similar climate conditions during polyploid formation. However, after its origin the polyploid cytotype underwent a pronounced ecological shift, compared to its diploid progenitor, allowing it to colonize mountainous inland habitats between the Mediterranean basin and Afghanistan. The extant sympatric occurrence of H. marinum and H. gussoneanum 2× in the Mediterranean region is interpreted as a result of secondary contact after fast Holocene range expansion out of different ice age refugia. [source] Substantial genetic substructuring in southeastern and alpine Australia revealed by molecular phylogeography of the Egernia whitii (Lacertilia: Scincidae) species groupMOLECULAR ECOLOGY, Issue 5 2005DAVID G. CHAPPLE Abstract Palaeoclimatic events and biogeographical processes since the mid-Tertiary are believed to have strongly influenced the evolution and distribution of the terrestrial vertebrate fauna of southeastern Australia. We examined the phylogeography of the temperate-adapted members of the Egernia whitii species group, a group of skinks that comprise both widespread low- to mid-elevation (E. whitii) and montane-restricted species (Egernia guthega, Egernia montana), in order to obtain important insights into the influence of past biogeographical processes on the herpetofauna of southeastern Australia. Sequence data were obtained from all six temperate-adapted species within the E. whitii species group, and specifically from across the distributional ranges of E. whitii, E. guthega and E. montana. We targeted a fragment of the ND4 mitochondrial gene (696 bp) and analysed the data using maximum likelihood and Bayesian methods. Our data reveal a deep phylogeographical break in the east Gippsland region of Victoria between ,northern' (Queensland, New South Wales, Australian Capital Territory) and ,southern' (Victoria, Tasmania, South Australia) populations of E. whitii. This divergence appears to have occurred during the late Miocene,Pliocene, with the Gippsland basin possibly forming a geographical barrier to dispersal. Substantial structuring within both the ,northern' and the ,southern' clades is consistent with the effects of Plio,Pleistocene glacial-interglacial cycles. Pleistocene glacial cycles also appear to have shaped the phylogeographical patterns observed in the alpine species, E. guthega and E. montana. We used our results to examine the biogeographical process that led to the origin and subsequent diversification of the lowland and alpine herpetofauna of southeastern Australia. [source] History and evolution of the arctic flora: in the footsteps of Eric HulténMOLECULAR ECOLOGY, Issue 2 2003Richard J. Abbott Abstract A major contribution to our initial understanding of the origin, history and biogeography of the present-day arctic flora was made by Eric Hultén in his landmark book Outline of the History of Arctic and Boreal Biota during the Quarternary Period, published in 1937. Here we review recent molecular and fossil evidence that has tested some of Hultén's proposals. There is now excellent fossil, molecular and phytogeographical evidence to support Hultén's proposal that Beringia was a major northern refugium for arctic plants throughout the Quaternary. In contrast, most molecular evidence fails to support his proposal that contemporary east and west Atlantic populations of circumarctic and amphi-Atlantic species have been separated throughout the Quaternary. In fact, populations of these species from opposite sides of the Atlantic are normally genetically very similar, thus the North Atlantic does not appear to have been a strong barrier to their dispersal during the Quaternary. Hultén made no detailed proposals on mechanisms of speciation in the Arctic; however, molecular studies have confirmed that many arctic plants are allopolyploid, and some of them most probably originated during the Holocene. Recurrent formation of polyploids from differentiated diploid or more low-ploid populations provides one explanation for the intriguing taxonomic complexity of the arctic flora, also noted by Hultén. In addition, population fragmentation during glacial periods may have lead to the formation of new sibling species at the diploid level. Despite the progress made since Hultén wrote his book, there remain large gaps in our knowledge of the history of the arctic flora, especially about the origins of the founding stocks of this flora which first appeared in the Arctic at the end of the Pliocene (approximately 3 Ma). Comprehensive analyses of the molecular phylogeography of arctic taxa and their relatives together with detailed fossil studies are required to fill these gaps. [source] | ||||||||||