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Divergent Clades (divergent + clade)
Selected AbstractsGenetic population structure of the net-winged midge, Elporia barnardi (Diptera: Blephariceridae) in streams of the south-western Cape, South Africa: implications for dispersalFRESHWATER BIOLOGY, Issue 1 2003M. J. Wishart SUMMARY 1.,The net-winged midges (Diptera: Blephariceridae), with highly specific habitat requirements and specialised morphological adaptations, exhibit high habitat fidelity and a limited potential for dispersal. Given the longitudinal and hierarchical nature of lotic systems, along with the geological structure of catchment units, we hypothesise that populations of net-winged midge should exhibit a high degree of population sub-structuring. 2.,Sequence variation in the cytochrome c oxidase subunit I (COI) region of the mitochondrial DNA (mtDNA) was examined to determine patterns of genetic variation and infer historical and contemporary processes important in the genetic structuring of populations of Elporia barnardi. The DNA variation was examined at sites within streams, between streams in the same range, and between mountain ranges in the south-western Cape of South Africa. 3.,Twenty-five haplotypes, 641 bp in length, were identified from the 93 individuals sampled. A neighbour-joining tree revealed two highly divergent clades (,5%) corresponding to populations from the two mountain ranges. A number of monophyletic groups were identified within each clade, associated with individual catchment units. 4.,The distribution of genetic variation was examined using analysis of molecular variance (amova). This showed most of the variation to be distributed among the two ranges (,80%), with a small percentage (,15%) distributed among streams within each range. Similarly, variation among streams on Table Mountain was primarily distributed among catchment units (86%). A Mantel's test revealed a significant relationship between genetic differentiation and geographical distance, suggesting isolation by distance (P < 0.001). 5.,Levels of sequence divergence between the two major clades, representing the two mountain ranges, are comparable with those of some intra-generic species comparisons. Vicariant events, such as the isolation of the Peninsula mountain chain and Table Mountain, may have been important in the evolution of what is now a highly endemic fauna. 6.,The monophyletic nature of the catchment units suggests that dispersal is confined to the stream environment and that mountain ridges provide effective physical barriers to dispersal of E. barnardi. [source] The Bassian Isthmus and the major ocean currents of southeast Australia influence the phylogeography and population structure of a southern Australian intertidal barnacle Catomerus polymerus (Darwin)MOLECULAR ECOLOGY, Issue 8 2008KATHERINE L. YORK Abstract Southern Australia is currently divided into three marine biogeographical provinces based on faunal distributions and physical parameters. These regions indicate eastern and western distributions, with an overlap occurring in the Bass Strait in Victoria. However, studies indicate that the boundaries of these provinces vary depending on the species being examined, and in particular on the mode of development employed by that species, be they direct developers or planktonic larvae dispersers. Mitochondrial DNA sequence analysis of the surf barnacle Catomerus polymerus in southern Australia revealed an east,west phylogeographical split involving two highly divergent clades (cytochrome oxidase I 3.5 ± 0.76%, control region 6.7 ± 0.65%), with almost no geographical overlap. Spatial genetic structure was not detected within either clade, indicative of a relatively long-lived planktonic larval phase. Five microsatellite loci indicated that C. polymerus populations exhibit relatively high levels of genetic divergence, and fall into four subregions: eastern Australia, central Victoria, western Victoria and Tasmania, and South Australia. FST values between eastern Australia (from the eastern mitochondrial DNA clade) and the remaining three subregions ranged from 0.038 to 0.159, with other analyses indicating isolation by distance between the subregions of western mitochondrial origin. We suggest that the east,west division is indicative of allopatric divergence resulting from the emergence of the Bassian land-bridge during glacial maxima, preventing gene flow between these two lineages. Subsequently, contemporary ecological conditions, namely the East Australian, Leeuwin, and Zeehan currents and the geographical disjunctions at the Coorong and Ninety Mile Beach are most likely responsible for the four subregions indicated by the microsatellite data. [source] Contrasting demographic history and phylogeographical patterns in two Indo-Pacific gastropodsMOLECULAR ECOLOGY, Issue 2 2008ERIC D. CRANDALL Abstract Marine species with ranges that span the Indo-Australian Archipelago (IAA) exhibit a range of phylogeographical patterns, most of which are interpreted in the context of vicariance between Indian and Pacific Ocean populations during Pliocene and Pleistocene low sea-level stands. However, patterns often vary among ecologically similar taxa, sometimes even within genera. This study compares phylogeographical patterns in two species of highly dispersive neritid gastropod, Nerita albicilla and Nerita plicata, with nearly sympatric ranges that span the Indo-Pacific. Mitochondrial COI sequences from > 1000 individuals from 97 sites reveal similar phylogenies in both species (two divergent clades differing by 3.2% and 2.3%, for N. albicilla and N. plicata, respectively). However, despite ecological similarity and congeneric status, the two species exhibit phylogeographical discordance. N. albicilla has maintained reciprocal monophyly of Indian and Pacific Ocean populations, while N. plicata is panmictic between oceans, but displays a genetic cline in the Central Pacific. Although this difference might be explained by qualitatively different demographic histories, parameter estimates from three coalescent models indicate that both species have high levels of gene flow between demes (2Nem > 75), and share a common history of population expansion that is likely associated with cyclical flooding of continental shelves and island lagoons following low sea-level stands. Results indicate that ecologically similar, codistributed species may respond very differently to shared environmental processes, suggesting that relatively minor differences in traits such as pelagic larval duration or microhabitat association may profoundly impact phylogeographical structure. [source] Contrasting patterns in genetic diversity following multiple invasions of fresh and brackish watersMOLECULAR ECOLOGY, Issue 12 2006DAVID W. KELLY Abstract Biological invasions may combine the genetic effects of population bottlenecks and selection and thus provide valuable insight into the role of such processes during novel environmental colonizations. However, these processes are also influenced by multiple invasions, the number of individuals introduced and the degree of similarity between source and receiving habitats. The amphipod Gammarus tigrinus provides a useful model to assess these factors, as its invasion history has involved major environmental transitions. This species is native to the northwest Atlantic Ocean, although it invaded both brackish and freshwater habitats in the British Isles after introduction more than 65 years ago. It has also spread to similar habitats in Western Europe and, most recently, to Eastern Europe, the Baltic Sea, and the Laurentian Great Lakes. To examine sources of invasion and patterns of genetic change, we sampled populations from 13 native estuaries and 19 invaded sites and sequenced 542 bp of the mitochondrial COI gene. Strong native phylogeographical structure allowed us to unambiguously identify three allopatrically evolved clades (2.3,3.1% divergent) in invading populations, indicative of multiple introductions. The most divergent clades occurred in the British Isles and mainland Europe and were sourced from the St Lawrence and Chesapeake/Delaware Bay estuaries. A third clade was found in the Great Lakes and sourced to the Hudson River estuary. Despite extensive sampling, G. tigrinus did not occur in freshwater at putative source sites. Some European populations showed reduced genetic diversity consistent with bottlenecks, although selection effects cannot be excluded. The habitat distribution of clades in Europe was congruent with the known invasion history of secondary spread from the British Isles. Differences in salinity tolerance among lineages were suggested by patterns of habitat colonization by different native COI clades. Populations consisting of admixtures of the two invading clades were found principally at recently invaded fresh and brackish water sites in Eastern Europe, and were characterized by higher genetic diversity than putative source populations. Further studies are required to determine if these represent novel genotypes. Our results confirm that biological invasions need not result in diminished genetic diversity, particularly if multiple source populations, each with distinctive genetic composition, contribute to the founding populations. [source] Multiple introductions promote range expansion of the mollusc Cyclope neritea (Nassariidae) in France: evidence from mitochondrial sequence dataMOLECULAR ECOLOGY, Issue 6 2006B. SIMON-BOUHET Abstract Since the 1970s, the nassariid gastropod Cyclope neritea has been extending its range north along the French Atlantic coasts from the Iberian Peninsula. This may be due to natural spread because of the recent warming of the northeastern Atlantic. However, human-mediated introductions related to shellfish culture may also be a probable explanation for this sudden range expansion. To examine these two hypotheses, we carried out a comprehensive study based on mitochondrial gene sequences (cytochrome oxidase I) of the five recently colonized French bays as well as 14 populations located in the recognized native range of the species. From a total of 594 individuals, we observed 29 haplotypes to split into three divergent clades. In the native range, we observed a low molecular diversity, strong genetic structure and agreement between geography and gene genealogies. Along the French coasts, we observed the opposite: high genetic diversity and low genetic structure. Our results show that recurrent human-mediated introductions from several geographical areas in the native range may be a source for the French Atlantic populations. However, despite the low dispersal ability of C. neritea, the isolation-by-distance pattern in France suggested that this gastropod may have been present (although unnoticed) on the French Atlantic coasts before the 1970s. As C. neritea shows characteristics of a cryptogenic species, the classification of Atlantic populations as either native or introduced is not straightforward. Cryptogenic species should be studied further to determine the status of new populations close to their recognized native range. [source] Patterns of population subdivision, gene flow and genetic variability in the African wild dog (Lycaon pictus)MOLECULAR ECOLOGY, Issue 7 2001D. J. Girman Abstract African wild dogs are large, highly mobile carnivores that are known to disperse over considerable distances and are rare throughout much of their geographical range. Consequently, genetic variation within and differentiation between geographically separated populations is predicted to be minimal. We determined the genetic diversity of mitochondrial DNA (mtDNA) control region sequences and microsatellite loci in seven populations of African wild dogs. Analysis of mtDNA nucleotide diversity suggests that, historically, wild dog populations have been small relative to other large carnivores. However, population declines due to recent habitat loss have not caused a dramatic reduction in genetic diversity. We found one historical and eight recent mtDNA genotypes in 280 individuals that defined two highly divergent clades. In contrast to a previous, more limited, mtDNA analysis, sequences from these clades are not geographically restricted to eastern or southern African populations. Rather, we found a large admixture zone spanning populations from Botswana, Zimbabwe and south-eastern Tanzania. Mitochondrial and microsatellite differentiation between populations was significant and unique mtDNA genotypes and alleles characterized the populations. However, gene flow estimates (Nm) based on microsatellite data were generally greater than one migrant per generation. In contrast, gene flow estimates based on the mtDNA control region were lower than expected given differences in the mode of inheritance of mitochondrial and nuclear markers which suggests a male bias in long-distance dispersal. [source] Phylogeography and population structure of an ecotonal marsupial, Bettongia tropica, determined using mtDNA and microsatellitesMOLECULAR ECOLOGY, Issue 12 2000L. C. Pope Abstract The northern bettong, Bettongia tropica, is an endangered species of Potoroidae with a restricted distribution in the wet tropics of north Queensland, Australia. The species is only found within a thin strip of sclerophyll forest along the western margin of rainforest. This tight association with rainforest boundaries is predicted to have resulted in population isolation as rainforest contracted during the Pleistocene, though some have proposed that the northern bettong was not present in the wet tropics until the late Pleistocene. The dispersal ability of the species, and of the family, is not known. This study examined gene flow among populations within areas of continuous habitat complemented by a broader analysis of phylogeography. Individuals trapped at each of the four known regions (one region was subsampled at three different sites), were sequenced for 547 base pairs of the mitochondrial DNA (mtDNA) control region and typed for seven microsatellite loci. The mtDNA phylogeny showed congruence with a biogeographical hypothesis, a relatively deep split suggesting historical isolation in separate northern and southern refugia. The two divergent clades were both present within the Lamb Range, indicating an expansion from these refuges and subsequent admixture at one site. mtDNA allele frequencies indicated relatively limited gene flow within the Lamb Range over distances as short as nine km. Tests of population divergence using microsatellites (FST and assignment tests) strongly supported this result. A molecular signal indicative of a recent bottleneck was unexpectedly detected in one of the Lamb Range subpopulations. This lead us to examine the behaviour of the statistics used in this bottleneck test under a linear stepping-stone model with varying migration rates. We found that it may be more difficult to detect molecular signatures for recent bottlenecks under conditions of very low migration rates than for isolated populations and, conversely, that ,false' bottleneck signatures may be observed at higher migration rates. The Lamb Range FST estimate clearly fell within the category of potentially ,false' bottleneck signals. Despite relatively limited gene flow, evidence for asymmetric dispersal suggests more complicated population dynamics than a simple linear stepping-stone model. [source] The comparative phylogeography of Neotropical mammals: patterns of intraspecific mitochondrial DNA variation among bats contrasted to nonvolant small mammalsMOLECULAR ECOLOGY, Issue 9 2000A. D. Ditchfield Abstract The major aim of this study was to compare the phylogeographic patterns of codistributed bats and small nonvolant Neotropical mammals. Cytochrome b sequences (mitochondrial DNA) were obtained for a total of 275 bats representing 17 species. The tissue samples were collected in coastal Brazil, and were available from Mexico and the Guyana. The study concentrates on four species (Artibeus lituratus, Carollia perspicillata, Sturnira lilium and Glossophaga soricina) which were well represented. The other 13 species were sequenced to test the generality of the patterns observed. In general, sequence divergence values within species were low, with most bat species presenting less than 4% average sequence divergence, and usually between 1 and 2.5%. Clades of highly similar haplotypes enjoyed broad distribution on a continental scale. These clades were not usually geographically structured, and at a given locality the number of haplotypes was high (8,10). As distance increased, some moderately divergent clades were found, although the levels of divergence were low. This suggests a geographical effect that varied depending on species and scale. Small nonvolant mammals almost invariably have high levels of sequence divergence (> 10%) for cytochrome b over much shorter distances (< 1000 km). The grain of intraspecific variation found in small nonvolant mammals is much finer than in bats. Low levels of geographical structuring cannot be attributed to a slower evolutionary rate of bat DNA in relation to other mammalian taxa. The phylogeographic pattern of bats contrasts sharply with the pattern found for Neotropical rodents and marsupials. [source] Evolutionarily independent genes and genomes and insights on genetic structure, evolution and conservation of the collis group of dartersANIMAL CONSERVATION, Issue 4 2009K. J. Oswald Abstract Comparing variation across evolutionarily independent characters, notably nuclear and mitochondrial genes, yields a more robust estimate of diversification than is generally recovered from individual characters. Patterns of variation across multiple molecular markers from the mitochondrial (16SrRNA, cytochrome b) and nuclear (ldhA6 and aldB) genomes were examined from six populations of Etheostoma collis and two populations of Etheostoma saludae, species aligned in the collis groups. Phylogenetic analyses revealed that sequence variation among individuals from the Roanoke, Tar and Neuse Rivers and the Catawba and Pee Dee Rivers, respectively, form highly supported, deeply divergent clades. Relationships of alleles sampled from Saluda River E. saludae and Cape Fear River E. collis to these lineages are unresolved, but all groups are reciprocally monophyletic for both nuclear and mtDNA loci. Phylogenetic analyses suggest that historical factors have had a strong influence on the distribution of genetic variation among populations. Genetic variation within the collis group is consistent with all previously proposed taxonomic hypotheses for the collis group, providing no taxonomic insights. From a conservation standpoint, each population of the collis group is an ESU, thereby warranting a drainage-specific management strategy. [source] Population genetic structure and conservation of Asian elephants (Elephas maximus) across IndiaANIMAL CONSERVATION, Issue 4 2005T. N. C. Vidya This study examines the population genetic structure of Asian elephants (Elephas maximus) across India, which harbours over half the world's population of this endangered species. Mitochondrial DNA control region sequences and allele frequencies at six nuclear DNA microsatellite markers obtained from the dung of free-ranging elephants reveal low mtDNA and typical microsatellite diversity. Both known divergent clades of mtDNA haplotypes in the Asian elephant are present in India, with southern and central India exhibiting exclusively the , clade of Fernando et al. (2000), northern India exhibiting exclusively the , clade and northeastern India exhibiting both, but predominantly the , clade. A nested clade analysis revealed isolation by distance as the principal mechanism responsible for the observed haplotype distributions within the , and , clades. Analyses of molecular variance and pairwise population FST tests based on both mitochondrial and microsatellite DNA suggest that northern-northeastern India, central India, Nilgiris (in southern India) and Anamalai-Periyar (in southern India) are four demographically autonomous population units and should be managed separately. In addition, evidence for female philopatry, male-mediated gene flow and two possible historical biogeographical barriers is described. [source] Deep genetic divergences among morphologically similar and parapatric Skistodiaptomus (Copepoda: Calanoida: Diaptomidae) challenge the hypothesis of Pleistocene speciationBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2009RYAN A. THUM We used mitochondrial [cytochrome c oxidase subunit I (CO I), cytochrome b, and 16S] and nuclear [internal transcribed spacer (ITS) phylogenies of Skistodiaptomus copepods to test hypotheses of Pleistocene divergence and speciation within the genus. Mitochondrial (mt)DNA sequence divergences do not support hypotheses for Pleistocene speciation and instead suggest much more ancient speciation events in the genus. Skistodiaptomus oregonensis and Skistodiaptomus pygmaeus (i.e. two morphologically similar and parapatric species) exhibited uncorrected mtDNA sequence divergences exceeding 20%. Similarly, we identified three divergent clades of Skistodiaptomus pallidus that exhibited mtDNA sequence divergences exceeding 15%, suggesting that even intraspecific divergence within this morphospecies predates the Pleistocene. We found clear evidence of CO I pseudogenes in S. pygmaeus, but their presence did not lead to significant overestimates of sequence divergences for this gene. Substitution saturation and strong purifying selection have most likely led to underestimates of sequence divergences and divergence times among Skistodiaptomus. The widespread phenomenon of morphological stasis among genetically divergent copepod groups indicates that speciation often occurs with little or no morphological change. Instead, morphological evolution may occur idiosyncratically after speciation and create discordant patterns of morphological similarity, shared ancestry and divergence time. Cryptic species complexes are therefore common in copepods, and morphological species concepts underestimate their true species diversity. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 96, 150,165. [source] | ||||||||||