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Phylogeographical Patterns (phylogeographical + pattern)
Selected AbstractsPhylogeographical pattern correlates with Pliocene mountain building in the alpine scree weta (Orthoptera, Anostostomatidae)MOLECULAR ECOLOGY, Issue 6 2000S. A. Trewick Abstract Most research on the biological effects of Pleistocene glaciation and refugia has been undertaken in the northern hemisphere and focuses on lowland taxa. Using single-strand conformation polymorphism (SSCP) analysis and sequencing of mitochondrial cytochrome oxidase I, we explored the intraspecific phylogeography of a flightless orthopteran (the alpine scree weta, Deinacrida connectens) that is adapted to the alpine zone of South Island, New Zealand. We found that several mountain ranges and regions had their own reciprocally monophyletic, deeply differentiated lineages. Corrected genetic distance among lineages was 8.4% (Kimura 2-parameter [K2P]) / 13% (GTR + I + ,), whereas within-lineage distances were only 2.8% (K2P) / 3.2% (GTR + I + ,). We propose a model to explain this phylogeographical structure, which links the radiation of D. connectens to Pliocene mountain building, and maintenance of this structure through the combined effects of mountain-top isolation during Pleistocene interglacials and ice barriers to dispersal during glacials. [source] Surviving glacial ages within the Biotic Gap: phylogeography of the New Zealand cicada Maoricicada campbelliJOURNAL OF BIOGEOGRAPHY, Issue 4 2009Kathy B. R. Hill Abstract Aim, New Zealand is an ideal location in which to investigate the roles of landscape and climate change on speciation and biogeography. An earlier study of the widespread endemic cicada Maoricicada campbelli (Myers) found two phylogeographically distinguishable major clades , northern South Island plus North Island (northern-SI + NI) and Otago. These two clades appeared to have diverged on either side of an area of the South Island known as the Biotic Gap. We sampled more intensively to test competing theories for this divergence. We aimed to discover if M. campbelli had survived within the Biotic Gap during recent glacial maxima, and if predicted areas of secondary contact between the two major clades existed. Location, New Zealand. Methods, We analysed mitochondrial DNA sequences (1520 bp; 212 individuals; 91 populations) using phylogenetic (maximum likelihood, Bayesian), population genetic (analysis of molecular variance) and molecular dating methods (Bayesian relaxed clock with improved priors). Results, We found strong geographical structuring of genetic variation. Our dating analyses suggest that M. campbelli originated 1.83,2.58 Ma, and split into the two major clades 1.45,2.09 Ma. The main subclades in the northern-SI + NI clade arose almost simultaneously at 0.69,1.03 Ma. Most subclades are supported by long internal branches and began to diversify 0.40,0.78 Ma. We found four narrow areas of secondary contact between the two major clades. We also found a difference between calling songs of the Otago vs. northern-SI + NI clades. Main conclusions, Phylogeographical patterns within M. campbelli indicate an early Pleistocene split into two major clades, followed by late Pleistocene range expansion and in situ population differentiation of subclades. The northern-SI + NI clade diversified so rapidly that the main subclade relationships cannot be resolved, and we now have little evidence for a disjunction across the Biotic Gap. Structure within the main subclades indicates rapid divergence after a common bottlenecking event, perhaps attributable to an extremely cold glacial maximum at c. 0.43 Ma. Clade structure and dating analyses indicate that M. campbelli survived in many refugia during recent glacial maxima, including within the Biotic Gap. The narrow overlap between the two major clades is attributed to recent contact during the current interglacial and slow gene diffusion. The two major clades appear to be in the early stages of speciation based on genetic and behavioural differences. [source] Distribution and population genetic structure of the Mediterranean pine shoot beetle Tomicus destruens in the Iberian Peninsula and Southern FranceAGRICULTURAL AND FOREST ENTOMOLOGY, Issue 2 2006Teresa Vasconcelos Abstract 1,The Mediterranean pine shoot beetle Tomicus destruens has long been indistinguishable from its congeneric Tomicus piniperda. Both species attack pines, and can be found in sympatry. The geographical distribution of T. destruens is still unclear in most of the Mediterranean Basin. 2,We aimed to describe the geographical distribution and zones of sympatry of both species in the Iberian Peninsula and France, and to study the molecular phylogeographical pattern of T. destruens. 3,Tomicus spp. adults were sampled in Portugal, Spain and France, and a portion of the mitochondrial genes COI and COII was sequenced for 84 individuals. Sequences were aligned to a data set previously obtained from French localities. 4,Tomicus destruens was found in all populations, except for one locality in Portugal and in the Landes (France). It was in sympatry with T. piniperda in two locations on Pinus pinaster and one location on Pinus radiata. 5,Within-population genetic diversity was high, but we found a significant pattern of spatial distribution of genetic variation, as well as a significant effect of the host tree. 6,The data suggest the existence of two glacial refugia, from which T. destruens recolonized its current range. One refugium was located in Portugal where the beetle probably evolved on P. pinaster. The corresponding haplotypes show a West,East frequency gradient. The other refugium was probably in the eastern range, where the beetles evolved on Pinus halepensis and P. pinea. The corresponding haplotypes show an East,West frequency gradient. [source] Fire and ice: volcanic and glacial impacts on the phylogeography of the New Zealand forest fern Asplenium hookerianumMOLECULAR ECOLOGY, Issue 21 2007LARA D. SHEPHERD Abstract In the Southern Hemisphere there has been little phylogeographical investigation of forest refugia sites during the last glacial. Hooker's spleenwort, Asplenium hookerianum, is a fern that is found throughout New Zealand. It is strongly associated with forest and is a proxy for the survival of woody vegetation during the last glacial maximum. DNA sequence data from the chloroplast trnL-trnF locus were obtained from 242 samples, including c. 10 individuals from each of 21 focal populations. Most populations contained multiple, and in many cases unique, haplotypes, including those neighbouring formerly glaciated areas, while the predominant inference from nested clade analysis was restricted gene flow with isolation by distance. These results suggest that A. hookerianum survived the last glacial maximum in widespread populations of sufficient size to retain the observed phylogeography, and therefore that the sheltering woody vegetation must have been similarly abundant. This is consistent with palynological interpretations for the survival in New Zealand of thermophilous forest species at considerably smaller distances from the ice sheets than recorded for the Northern Hemisphere. Eastern and central North Island populations of A. hookerianum were characterized by a different subset of haplotypes to populations from the remainder of the country. A similar east,west phylogeographical pattern has been detected in a diverse array of taxa, and has previously been attributed to recurrent vulcanism in the central North Island. [source] Phylogeographical structure, distribution and genetic variation of the green algae Ulva intestinalis and U. compressa (Chlorophyta) in the Baltic Sea areaMOLECULAR ECOLOGY, Issue 8 2004E. LESKINEN Abstract The marine algae Ulva intestinalis and U. compressa are morphologically plastic with many overlapping characters and are therefore difficult to distinguish from each other. The present distribution of U. intestinalis and U. compressa is investigated along the salinity gradient in the Baltic Sea area through analyses of internal transcribed spacer (ITS) sequence data. Also, the amount and distribution of intraspecific genetic polymorphism in the ITS region is studied allowing inferences on the phylogeographical pattern and postglacial recolonization of the Baltic Sea area. The data show that of the two species only U. intestinalis occurs in the Baltic Sea. The distribution of U. compressa is more restricted than previously reported, and it was not found in salinities lower than 15 ppt. All of Scandinavia and the Baltic Sea were covered with ice during the last ice age and the organisms in the Baltic Sea must have colonized the area after the ice had started to melt. The genetic diversity of U. intestinalis and U. compressa in the Baltic Sea and the neighbouring area was found to be reduced compared to that in the British Isles. This reduction may be the result of either a historical reduction of diversity or an adaptation of specific clones to the northern environmental conditions. [source] Mitochondrial phylogeography of the moor frog, Rana arvalisMOLECULAR ECOLOGY, Issue 6 2004W. Babik Abstract The moor frog Rana arvalis is a lowland species with a broad Eurasiatic distribution, from arctic tundra through forest to the steppe zone. Its present-day range suggests that glacial refugia of this frog were located outside southern European peninsulas. We studied the species-wide phylogeographical pattern using sequence variation in a 682 base pairs fragment of mtDNA cytochrome b gene; 223 individuals from 73 localities were analysed. Two main clades, A and B, differing by c. 3.6% sequence divergence were detected. The A clade is further subdivided into two subclades, AI and AII differing by 1.0%. All three lineages are present in the Carpathian Basin (CB), whereas the rest of the species range, including huge expanses of Eurasian lowlands, are inhabited solely by the AI lineage. We infer that AII and B lineages survived several glacial cycles in the CB but did not expand, at least in the present interglacial, to the north. The geographical distribution and genealogical relationships between haplotypes from the AI lineage indicate that this group had two glacial refugia, one located in the eastern part of the CB and the other probably in southern Russia. Populations from both refugia contributed to the colonization of the western part of the range, whereas the eastern part was colonized from the eastern refugium only. The effective population size as evidenced by ,ML is an order of magnitude higher in the AI lineage than in the AII and B lineages. Demographic expansion was detected in all three lineages. [source] Evolution on oceanic islands: molecular phylogenetic approaches to understanding pattern and processMOLECULAR ECOLOGY, Issue 6 2002B. C. Emerson Abstract By their very nature oceanic island ecosystems offer great opportunities for the study of evolution and have for a long time been recognized as natural laboratories for studying evolution owing to their discrete geographical nature and diversity of species and habitats. The development of molecular genetic methods for phylogenetic reconstruction has been a significant advance for evolutionary biologists, providing a tool for answering questions about the diversity among the flora and fauna on such islands. These questions relate to both the origin and causes of species diversity both within an archipelago and on individual islands. Within a phylogenetic framework one can answer fundamental questions such as whether ecologically and/or morphologically similar species on different islands are the result of island colonization or convergent evolution. Testing hypotheses about ages of the individual species groups or entire community assemblages is also possible within a phylogenetic framework. Evolutionary biologists and ecologists are increasingly turning to molecular phylogenetics for studying oceanic island plant and animal communities and it is important to review what has been attempted and achieved so far, with some cautionary notes about interpreting phylogeographical pattern on oceanic islands. [source] DNA barcode discovers two cryptic species and two geographical radiations in the invasive drosophilid Zaprionus indianusMOLECULAR ECOLOGY RESOURCES, Issue 3 2008AMIR YASSIN Abstract Comparing introduced to ancestral populations within a phylogeographical context is crucial in any study aiming to understand the ecological genetics of an invasive species. Zaprionus indianus is a cosmopolitan drosophilid that has recently succeeded to expand its geographical range upon three continents (Africa, Asia and the Americas). We studied the distribution of mitochondrial DNA (mtDNA) haplotypes for two genes (CO-I and CO-II) among 23 geographical populations. mtDNA revealed the presence of two well-supported phylogenetic lineages (phylads), with bootstrap value of 100%. Phylad I included three African populations, reinforcing the African-origin hypothesis of the species. Within phylad II, a distinct phylogeographical pattern was discovered: Atlantic populations (from the Americas and Madeira) were closer to the ancestral African populations than to Eastern ones (from Madagascar, Middle East and India). This means that during its passage from endemism to cosmopolitanism, Z. indianus exhibited two independent radiations, the older (the Eastern) to the East, and the younger (the Atlantic) to the West. Discriminant function analysis using 13 morphometrical characters was also able to discriminate between the two molecular phylads (93.34 ± 1.67%), although detailed morphological analysis of male genitalia using scanning electron microscopy showed no significant differences. Finally, crossing experiments revealed the presence of reproductive barrier between populations from the two phylads, and further between populations within phylad I. Hence, a bona species status was assigned to two new, cryptic species: Zaprionus africanus and Zaprionus gabonicus, and both were encompassed along with Z. indianus and Zaprionus megalorchis into the indianus complex. The ecology of these two species reveals that they are forest dwellers, which explains their restricted endemic distribution, in contrast to their relative cosmopolitan Z. indianus, known to be a human-commensal. Our results reconfirm the great utility of mtDNA at both inter- and intraspecific analyses within the frame of an integrated taxonomical project. [source] Genetic structure of Euclea schimperi (Ebenaceae) populations in monsoonal fog oases of the southern Arabian PeninsulaNORDIC JOURNAL OF BOTANY, Issue 3-4 2007Jörg Meister Euclea schimperi, a widespread Afromontane shrub or tree, occurs in the Arabian Peninsula in fragmented, semi-evergreen or evergreen woodland refugia in wet escarpment localities of the western and southern mountain chains. In the southern coastal mountains, the (semi-) evergreen woodland with E. schimperi is close to its ecological limit and consequently today very rare, with the exception of the monsoonal fog oases of east Yemen and south Oman in the central south coast of the Arabian Peninsula. Due to the steep precipitation gradient from the centre to the western edge in this monsoon affected area, E. schimperi is found in two different habitat types: in continuous woodland belts in the Hawf and Dhofar mountains, and in isolated, scattered woodland patches in the Fartak Mountains. Ten populations (138 individuals) from across the southern Arabian distribution area of the species were analysed using chloroplast microsatellites and AFLP fingerprinting to a) reconstruct the phylogeographical pattern of E. schimperi on the southern Arabian Peninsula and b) to evaluate the consequences of population fragmentation on the genetic diversity harboured in isolated patches vs cohering stands. Phylogeographical reconstructions show that the distribution area of E. schimperi in the southern Arabian Peninsula is characterised by a geographical split that separates the southwestern populations (representated by material from Jabal Eraf and Jabal Uthmar), from the southcentral populations, which themselves are split from each other into a western (Ras Fartak) and an eastern refugium (Hawf/Dhofar). The analysis of the within-population genetic diversity in E. schimperi populations resulted in a slightly, but not significantly higher genetic variation in small and isolated woodland patches (HS=0.302) compared to larger, cohering stands (HS=0.291). [source] Genetic structure of Anogeissus dhofarica (Combretaceae) populations endemic to the monsoonal fog oases of the southern Arabian PeninsulaBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2009CHRISTOPH OBERPRIELER Anogeissus dhofarica (Combretaceae) is an endemic tree of the monsoon affected coastal mountains of the southern Arabian Peninsula, being the character species of the Hybantho durae,Anogeissetum dhofaricae association, a drought deciduous, monsoon forest community found only in the Dhofar region of southern Oman and the eastern Al-Mahra region of south-east Yemen. Due to the steep precipitation gradient from the centre to the edges in this monsoon affected area, A. dhofarica is found in two different habitat types: in continuous woodland belts of the Hawf and Dhofar mountains, and in isolated, scattered woodland patches, as found especially in the Fartak Mts (south-east Yemen). Fifteen populations (212 individuals) from across the whole distribution area of the species were analysed using amplified fragment length polymorphism fingerprinting to: (1) evaluate the consequences of population fragmentation on the genetic diversity harboured in isolated patches versus cohering stands of the species and (2) to reconstruct the phylogeographical pattern of A. dhofarica as a consequence of oscillations in the monsoon activity during the Pleistocene and Holocene. The analysis of among-population genetic differentiation and within-population genetic diversity in A. dhofarica populations resulted in a lack of genetic pauperization and genetic differentiation of populations of the distinctly isolated patches of the Fartak Mts compared to the more luxurious forests of the Hawf and Dhofar regions. This is considered to be due to the high buffer capacity against the loss of genetic diversity caused by the long-lived life-form of the species combined with the capability to propagate clonally and the relatively recent fragmentation of Anogeissus forests into the described patches rather than due to high values of gene flow among remnant populations caused by bee pollination and anemochorical and hydrochorical diaspore dispersal. The phylogeographical pattern of the species argues for a quite recent fragmentation of a once continuous forest belt of A. dhofarica that is rather connected with climate changes in the Holocene than triggered by aridity,humidity oscillations reported for the Pleistocene. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 40,51. [source] Phylogeography of Pulsatilla vernalis (L.) Mill. (Ranunculaceae): chloroplast DNA reveals two evolutionary lineages across central Europe and ScandinaviaJOURNAL OF BIOGEOGRAPHY, Issue 9 2008Micha, Ronikier Abstract Aim, The aim of this study was to test hypotheses regarding some of the main phylogeographical patterns proposed for European plants, in particular the locations of glacial refugia, the post-glacial colonization routes, and genetic affinities between southern (alpine) and northern (boreal) populations. Location, The mountains of Europe (Alps, Balkans, Carpathians, Central Massif, Pyrenees, Scandinavian chain, Sudetes), and central European/southern Scandinavian lowlands. Methods, As our model system we used Pulsatilla vernalis, a widely distributed European herbaceous plant occurring both in the high-mountain environments of the Alps and other European ranges and in lowlands north of these ranges up to Scandinavia. Based on a distribution-wide sampling of 61 populations, we estimated chloroplast DNA (cpDNA) variation along six regions using polymerase chain reaction,restriction fragment-length polymorphisms (PCR,RFLPs) (trnH,trnK, trnK,trnK, trnC,trnD, psbC,trnS, psaA,trnS, trnL,trnF) and further sequencing of trnL,trnF and trnH,psbA. In addition, 11 samples of other European species of Pulsatilla were sequenced to survey the genus-scale cpDNA variation. Results, Eleven PCR,RFLP polymorphisms were detected in P. vernalis, revealing seven haplotypes. They formed two distinct genetic groups. Three haplotypes representing both groups dominated and were widely distributed across Europe, whereas the others were restricted to localized regions (central Alps, Tatras/Sudetes mountains) or single populations. Sequencing analysis confirmed the reliability of PCR,RFLPs and homology of haplotypes across their distribution. The chloroplast DNA variation across the section Pulsatilla was low, but P. vernalis did not share haplotypes with other species. Main conclusions, The genetic distinctiveness of P. vernalis populations from the south-western Alps with respect to other Alpine populations, as well as the affinities between the former populations and those from the eastern Pyrenees, is demonstrated, thus providing support for the conclusions of previous studies. Glacial refugia in the Dolomites are also suggested. Isolation is inferred for the high-mountain populations from the Tatras and Sudetes; this is in contrast to the case for the Balkans, which harboured the common haplotype. Specific microsatellite variation indicates the occurrence of periglacial lowland refugia north of the Alps, acting as a source for the post-glacial colonization of Scandinavia. The presence of different fixed haplotypes in eastern and western Scandinavia, however, suggests independent post-glacial colonization of these two areas, with possible founder effects. [source] Genetic divergences pre-date Pleistocene glacial cycles in the New Zealand speckled skink, Oligosoma infrapunctatumJOURNAL OF BIOGEOGRAPHY, Issue 5 2008Stephanie N. J. Greaves Abstract Aim, To examine the hypothesis raised by Graham S. Hardy that Pleistocene glacial cycles suffice to explain divergence among lineages within the endemic New Zealand speckled skink, Oligosoma infrapunctatum Boulenger. Location, Populations were sampled from across the entire range of the species, on the North and South Islands of New Zealand. Methods, We sequenced the mitochondrial genes ND2 (550 bp), ND4 + tRNAs (773 bp) and cytochrome b (610 bp) of 45 individuals from 21 locations. Maximum likelihood, maximum parsimony and Bayesian methods were used for phylogenetic reconstruction. The Shimodaira,Hasegawa test was used to examine hypotheses about the taxonomic status of morphologically distinctive populations. Results, Our analysis revealed four strongly supported clades within O. infrapunctatum. Clades were largely allopatric, except on the west coast of the South Island, where representatives from all four clades were found. Divergences among lineages within the species were extremely deep, reaching over 5%. Two contrasting phylogeographical patterns are evident within O. infrapunctatum. Main conclusions, The deep genetic divisions we found suggest that O. infrapunctatum is a complex of cryptic species which diverged in the Pliocene, contrary to the existing Pleistocene-based hypothesis. Although Pleistocene glacial cycles do not underlie major divergences within this species, they may be responsible for the shallower phylogeographical patterns that are found within O. infrapunctatum, which include a radiation of haplotypes in the Nelson and Westland regions. [source] Glacial survival or late glacial colonization?JOURNAL OF BIOGEOGRAPHY, Issue 12 2006Phylogeography of the root vole (Microtus oeconomus) in north-west Norway Abstract Aim, It has been proposed that the root vole subspecies, Microtus oeconomus finmarchicus, survived the last glacial period on islands on the north-west coast of Norway. The Norwegian island of Andøya may have constituted the only site with permanent ice-free conditions. Geological surveys and fossil finds from Andøya demonstrate that survival throughout the last glacial maximum was probably possible for some plants and animals. In this study we aim to infer the recent evolutionary history of Norwegian root vole populations and to evaluate the glacial survival hypothesis. Methods, DNA sequence variation in the mitochondrial cytochrome b gene was studied in 46 root voles from 19 localities. Location, Northern Fennoscandia and north-west Russia with a focus on islands on the north-west coast of Norway. Results The phylogeographical analyses revealed two North European phylogroups labelled ,Andøya' and ,Fennoscandia'. The Andøya phylogroup contained root voles from the Norwegian islands of Andøya, Ringvassøya and Reinøya and two localities in north-west Russia. The Fennoscandian phylogroup encompassed root voles from the three Norwegian islands of Kvaløya, Håkøya and Arnøya and the remaining specimens from Norway, northern Sweden and Finland. Nucleotide diversity within the Andøya and Fennoscandian phylogroups was similar, ranging from 0.5% to 0.7%. Main conclusions Both our genetic data and previously published morphological data are consistent with in situ glacial survival of root voles on Andøya during the last glacial maximum. However, the level of genetic diversity observed in the extant island populations, the past periods of severe climatic conditions on Andøya and the ecology of the root vole are somewhat difficult to reconcile with this model. A biogeographical scenario involving late glacial recolonization along the northern coasts of Russia and Norway therefore represents a viable alternative. Our results demonstrate that complex recolonization and extinction histories can generate intricate phylogeographical patterns and relatively high levels of genetic variation in northern populations. [source] Nested areas of endemism analysisJOURNAL OF BIOGEOGRAPHY, Issue 9 2006Anthony J. Deo Abstract Aim, To develop and evaluate a nested clade approach to aid in the determination of areas of endemism (AoE) in biogeographical studies. Methods, We adapted the nested clade analysis (NCA) to studies of areas of endemism. For this purpose we adapted several of the programs currently in use. Two data sets were examined using this approach , one involving Sciobius in southern Africa and the other involving terrestrial mammals in Mexico. Results, Nested clade analysis as applied to areas of endemism produced results similar to those of previous analyses of Sciobus in southern Africa. An analysis of terrestrial mammals in Mexico supports the designation of some biogeographical provinces as areas of endemism while suggesting that other provinces may comprise composite distributions that should be subdivided. Main conclusions, The nested clade analysis approach utilized primarily in genetic analysis of phylogeographical patterns in population biology studies can be adapted to understanding AoE in the realm of biogeography. This approach offers a statistical paradigm to evaluate AoE suggested by parsimony analysis of endemicity (PAE) trees. [source] Contrasting phylogeographical patterns of two closely related species, Machilus thunbergii and Machilus kusanoi (Lauraceae), in TaiwanJOURNAL OF BIOGEOGRAPHY, Issue 5 2006Su-Hwa Wu Abstract Aim, The purpose of this paper was to study the patterns of genetic variation, demographic history, haplotype relationships and potential location of diversity centres of two closely related species, Machilus thunbergii and Machilus kusanoi. Location, The phylogeography of M. thunbergii and M. kusanoi was examined by sampling 110 and 106 individuals from 25 and 16 sampling sites, respectively, across their distributional range in Taiwan. Machilus thunbergii is distributed on the Asian mainland, South Korea, southern Japan, the Ryukyus, Taiwan and the Philippines, whereas M. kusanoi is endemic to Taiwan. These two species are closely related, and both are widely distributed in Taiwan but occupy different altitudinal zones and habitats. Methods, The range-wide variation of M. thunbergii and M. kusanoi in Taiwan was studied using chloroplast DNA (cpDNA) variations. A haplotype network was constructed with the computer program tcs. Nested clade analysis was conducted with the computer program ceodis, and various parameters of genetic diversity were calculated and neutrality tested by the computer program DnaSP. Population differentiation was estimated using the programs arlequin and hapstep. The contribution of the populations to gene diversity and to allelic richness was calculated using the software contrib. The level of divergence for each population from the remaining populations was calculated as the mean value of pairwise FST for each population against the rest of the populations. Results, Extremely low levels of genetic differentiation were found for both species. This result suggested that these two species probably survived in multiple relict refugia with different population sizes throughout the island during low-temperature periods of the Pleistocene. In addition, nested clade analysis (NCA) of cpDNA haplotypes indicated that restricted gene flow with isolation-by-distance characterized the recolonization after the Pleistocene by Tashueshan and Shiouhluan populations of M. thunbergii in the north-central area west of the Central Mountain Range (CMR). In contrast, NCA analysis indicated that a major diversity centre on the southern tip of the island (Kending population) and contiguous range expansion characterized the recolonization by M. kusanoi of northern areas along the east side of the CMR. The major diversity centres found for the two species examined were further supported by the results of the mean FST for individual populations in comparison with other populations, and of the contribution of the divergence component to the total diversity. Main conclusions, This research supports the multiple relict refugia hypothesis for both species investigated. Populations of M. thunbergii at Shiouhluan and Tashueshan in the north-central area west of the CMR represent a diversity centre currently expanding its size. A diversity centre at the southern-edge population of M. kusanoi, and a contiguous range expansion from Kending, were found. These results indicate that the M. thunbergii populations at Tashueshan and Shiouhluan and the M. kusanoi population at Kending, and even Soukar, are evolutionarily significant units for conservation programmes. [source] Biogeographical patterns of genetic differentiation in dung beetles of the genus Trypocopris (Coleoptera, Geotrupidae) inferred from mtDNA and AFLP analysesJOURNAL OF BIOGEOGRAPHY, Issue 7 2004Loredana Carisio Abstract Aim, To examine the phylogeography and population structure of three dung beetle species of the genus Trypocopris (Coleoptera, Geotrupidae). We wanted to test whether genetic differences and genealogies among populations were in accordance with morphologically described subspecies and we aimed to establish times of divergence among subspecies to depict the appropriate temporal framework of their phylogeographical differentiation. We also wished to investigate the historical demographic events and the relative influences of gene flow and drift on the distribution of genetic variability of the different populations. Location, Europe (mostly Italy). Methods, We collected adult males from dung pats from 15 Italian localities over the period 2000,2002. For sequence analysis, some dried specimens from Albania, Croatia, Slovakia and Spain were also used. We applied cytochrome oxidase I mitochondrial DNA sequencing and the amplified fragment length polymorphism (AFLP) technique to determine whether phylogeographical patterns within the three species support the proposed hypotheses of subspecies designations, and to detect further structure among populations that might mediate diversification. Results and main conclusions, The results show a high concordance between the distribution of mtDNA variation and the main morphological groups recognized as subspecies, which thus may represent independent evolutionary units. The degree of mitochondrial divergence suggests that speciation events occurred during the Pliocene, while diversification of the main subspecific lineages took place in the Pleistocene, from c. 0.3 to 1.5 Ma. Mitochondrial and nuclear data also reveal that there is phylogeographical structuring among populations within each of the main groups and that both contemporary and historical processes determined this pattern of genetic structure. Geographical populations form monophyletic clades in both phylogenetic and network reconstructions. Despite the high levels of intrapopulational diversity, FST values indicate moderate but significant genetic differentiation among populations, and a Bayesian clustering analysis of the AFLP data clearly separates the geographical populations. Nucleotide and gene diversity estimates reveal interspecific differences in the degree of diversification among populations that may be related to the different ecological requirements of the three species. [source] Comparative phylogeography of five avian species: implications for Pleistocene evolutionary history in the Qinghai-Tibetan plateauMOLECULAR ECOLOGY, Issue 2 2010Y. QU Abstract Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. In contrast to Europe and North America where the effects of recent glacial cycles on genetic diversity have been well studied, the genetic legacy of the Pleistocene for the Qinghai-Tibetan (Tibetan) plateau, a region where glaciation was not synchronous with the North Hemisphere ice sheet maxima, remains poorly understood. Here, we compared the phylogeographical patterns of five avian species on the Qinghai-Tibetan plateau by three mitochondrial DNA fragments: the Tibetan snow finch (Montifringilla adamsi), the Blanford's snow finch (Pyrgilauda blanfordi), the horned lark (Eremophila alpestris), the twite (Carduelis flavirostris) and the black redstart (Phoenicurus ochruros). Our results revealed the three species mostly distributed on the platform region of the plateau that experienced population expansion following the retreat of the extensive glaciation period (0.5,0.175 Ma). These results are at odds with the results from avian species of Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023,0.018 Ma). A single refugium was identified in a restricted semi-continuous area around the eastern margin of the plateau, instead of multiple independent refugia for European and North American species. For the other two species distributed on the edges of the plateau (the twite and black redstart), populations were maintained at stable levels. Edge areas are located on the eastern margin, which might have had little or no ice cover during the glaciation period. Thus, milder climate may have mitigated demographic stresses for edge species relative to the extremes experienced by platform counterparts, the present-day ranges of which were heavily ice covered during the glaciation period. Finally, various behavioural and ecological characteristics, including dispersal capacities, habitat preference and altitude specificity along with evolutionary history might have helped to shape different phylogeographical structures appearing in these five species. [source] Pleistocene phylogeography and phylogenetic concordance in cold-adapted spring snails (Bythinella spp.)MOLECULAR ECOLOGY, Issue 5 2009M. BENKE Abstract Previous studies on Pleistocene phylogeography of European taxa are biased towards (i) vertebrates, (ii) terrestrial taxa, (iii) single species, and (iv) taxa that survived the Pleistocene in southern refugia. Relatively little is known about whether evolutionary patterns of vertebrate and terrestrial taxa are also applicable to freshwater invertebrates, whether cold-adapted freshwater species could survive in extensive permafrost areas without retreating into refugia, and whether Pleistocene phylogeographical patterns are influenced by phylogeny. Here, the widespread and species-rich European spring snail genus Bythinella Moquin-Tandon, 1856 is utilized in an attempt to mitigate this bias. These strongly cold-adapted freshwater animals mostly occur in springs , highly isolated habitats that are relatively unaffected by anthropogenic influences. Phylogenetic and phylogeographical analyses based on mitochondrial DNA and nuclear DNA sequence data were conducted in 458 specimens from 142 populations occurring throughout Europe. The study provides evidence that most Bythinella spp. survived the Pleistocene in restricted northern glacial refugia that largely correspond to refugia previously recognized for other European biota. However, survival of Bythinella spp. in extensive permafrost areas outside of refugia can likely be rejected. Low dispersal ability and the isolation and fragmentation of spring habitats, as well as the distribution of perennial springs within permafrost regions, may account for this result. Tests involving a total of 29 nominal species showed that phylogenetically closely related Bythinella species did not occupy similar refugia. This lack of phylogenetic concordance could possibly be explained by the stochasticity of survival and dispersal in spring snails. [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] 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] Living on the edge: demographic and phylogeographical patterns in the woodlouse-hunter spider Dysdera lancerotensis Simon, 1907 on the eastern volcanic ridge of the Canary IslandsMOLECULAR ECOLOGY, Issue 15 2007LETICIA BIDEGARAY-BATISTA Abstract The Eastern Canary Islands are the emerged tips of a continuous volcanic ridge running parallel to the northeastern African coast, originated by episodic volcanic eruptions that can be traced back to the Miocene and that, following a major period of quiescence and erosion, continued from the Pliocene to the present day. The islands have been periodically connected by eustatic sea-level changes resulting from Pleistocene glacial cycles. The ground-dwelling spider Dysdera lancerotensis Simon, 1907 occurs along the entire ridge, except on recent barren lavas and sand dunes, and is therefore an ideal model for studying the effect of episodic geological processes on terrestrial organisms. Nested clade and population genetic analyses using 39 haplotypes from 605 base pairs of mitochondrial DNA cytochrome c oxidase I sequence data, along with phylogenetic analyses including two additional mitochondrial genes, uncover complex phylogeographical and demographic patterns. Our results indicate that D. lancerotensis colonized the ridge from north to south, in contrast to what had been expected given the SSW-NNE trend of volcanism and to what had been reported for other terrestrial arthropods. The occurrence of several episodes of extinction, recolonization and expansion are hypothesized for this species, and areas that act as refugia during volcanic cycles are identified. Relaxed molecular clock methods reveal divergence times between main haplotype lineages that suggest an older origin of the northern islets than anticipated based on geological evidence. This study supports the key role of volcanism in shaping the distribution of terrestrial organisms on oceanic islands and generates phylogeographical predictions that warrant further research into other terrestrial endemisms of this fascinating region. [source] Comparative phylogeography of unglaciated eastern North AmericaMOLECULAR ECOLOGY, Issue 14 2006DOUGLAS E. SOLTIS Abstract Regional phylogeographical studies involving co-distributed animal and plant species have been conducted for several areas, most notably for Europe and the Pacific Northwest of North America. Until recently, phylogeographical studies in unglaciated eastern North America have been largely limited to animals. As more studies emerge for diverse lineages (including plants), it seems timely to assess the phylogeography across this region: (i) comparing and contrasting the patterns seen in plants and animals; (ii) assessing the extent of pseudocongruence; and (iii) discussing the potential applications of regional phylogeography to issues in ecology, such as response to climatic change. Unglaciated eastern North America is a large, geologically and topographically complex area with the species examined having diverse distributions. Nonetheless, some recurrent patterns emerge: (i) maritime , Atlantic vs. Gulf Coast; (ii) Apalachicola River discontinuity; (iii) Tombigbee River discontinuity; (iv) the Appalachian Mountain discontinuity; (v) the Mississippi River discontinuity; and (vi) the Apalachicola River and Mississippi River discontinuities. Although initially documented in animals, most of these patterns are also apparent in plants, providing support for phylogeographical generalizations. These patterns may generally be attributable to isolation and differentiation during Pleistocene glaciation, but in some cases may be older (Pliocene). Molecular studies sometimes agree with longstanding hypotheses of glacial refugia, but also suggest additional possible refugia, such as the southern Appalachian Mountains and areas close to the Laurentide Ice Sheet. Many species exhibit distinct patterns that reflect the unique, rather than the shared, aspects of species' phylogeographical histories. Furthermore, similar modern phylogeographical patterns can result from different underlying causal factors operating at different times (i.e. pseudocongruence). One underemphasized component of pseudocongruence may result from the efforts of researchers to categorize patterns visually , similar patterns may, in fact, not fully coincide, and inferring agreement may obscure the actual patterns and lead to erroneous conclusions. Our modelling analyses indicate no clear spatial patterning and support the hypothesis that phylogeographical structure in diverse temperate taxa is complex and was not shaped by just a few barriers. [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] Complex phylogeographical patterns, introgression and cryptic species in a lineage of Malagasy dung beetles (Coleoptera: Scarabaeidae)BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2009H. WIRTA Many taxa, including dung beetles, exhibit small-scale microendemism in Madagascar, which has contributed to the high level of species' diversity on the island. Species in the genus Nanos are numerically dominant in the dung beetle communities in rainforests in eastern Madagascar, but typically just one species occurs in any one locality. The two northern species, N. clypeatus and N. dubitatus, cannot be distinguished by either a mitochondrial or a nuclear genetic marker (cytochrome oxidase subunit I and internal transcription spacer 2). One population of the southern N. viettei is genetically highly divergent, although morphologically indistinguishable. Genetic data indicate that introgression occurred from N. dubitatus to N. viettei 1,2 Mya, and these species may continue to hybridize. Complex genetic patterns have mostly evolved within the last 2 Myr. During this time, the glacial cycles in the northern hemisphere were reflected in the oscillating climatic conditions in Africa, which repeatedly fragmented and re-united the rainforests in eastern Madagascar, possibly leading to the observed complex phylogeographical patterns in Nanos. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 96, 942,955. [source] | ||||||||||