Nested Clade Analysis Research Articles

Contribution of small rodent communities (Muridae) to the history of West Central African savannas (case of Gabonese savannas): diversity, biogeographic affinities, phylogeography and paleoenvironmental analyses

Savannas of West Central Africa stand around or inside the large rainforest block. They result from paleo-climatic fluctuations, but the details of their history remain poorly known. The aim of the present study is to explain the present distribution of savannas in West Central Africa, considering the two classic anthropic or paleoclimatic hypotheses about their origin. The study was focused on Gabonese savannas and based on small terrestrial mammal patterns. The phylogeography of small species of strictly savanicolous rodents was compared using nested clade analysis of haplotype networks based on cytochrome b mitochondrial DNA, coupled with other approaches. The data were also compared with literature data on vegetation changes in tropical West Africa over the last 150,000 years to test scenarios on the origin and history of Gabonese savannas. The results showed several fragmentation events of small rodent populations and revealed redundant biogeographic relationships. These events were dated, and the results about the history of rodent species were congruent with palaeobiological data about the successive phases of savanna expansion and fragmentation: the results support the hypothesis of a paleoclimatic origin of the Western Congolian forest-savanna mosaic. These rodent population fragmentation events occurred more than 50,000 years ago.

Phylogeographic patterns in the Philippine archipelago influence symbiont diversity in the bobtail squid-Vibrio mutualism.

Marine microbes encounter a myriad of biotic and abiotic factors that can impact fitness by limiting their range and capacity to move between habitats. This is especially true for environmentally transmitted bacteria that cycle between their hosts and the surrounding habitat. As geologic history, biogeography, and other factors such as water temperature, salinity, and physical barriers can inhibit bacterial movement to novel environments, we chose to examine the genetic architecture of Euprymna albatrossae (Mollusca: Cephalopoda) and their Vibrio fischeri symbionts in the Philippine archipelago using a combined phylogeographic approach. Eleven separate sites in the Philippine islands were examined using haplotype estimates that were examined via nested clade analysis to determine the relationship between E. albatrossae and V. fischeri populations and their geographic location. Identical analyses of molecular variance (AMOVA) were used to estimate variation within and between populations for host and symbiont genetic data. Host animals demonstrated a significant amount of variation within island groups, while symbiont variation was found within individual populations. Nested clade phylogenetic analysis revealed that hosts and symbionts may have colonized this area at different times, with a sudden change in habitat. Additionally, host data indicate restricted gene flow, whereas symbionts show range expansion, followed by periodic restriction to genetic flow. These differences between host and symbiont networks indicate that factors “outside the squid” influence distribution of Philippine V. fischeri. Our results shed light on how geography and changing environmental factors can impact marine symbiotic associations at both local and global scales.

Repeated expansions and fragmentations linked to Pleistocene climate changes shaped the genetic structure of a woody climber,Actinidia arguta(Actinidiaceae)

The genetic structure of temperate plants was extremely affected by climate changes during the Pleistocene. In East Asia, however, there are a limited number of phylogeography studies of widely distributed species. Actinidia arguta (Sieb. & Zucc.) Planch. ex Miq. (Actinidiaceae), a widely distributed woody climber, was chosen for this study. Twelve haplotypes were obtained using five chloroplast fragments. No haplotypes were shared on two sides of the Qinling–Dabie mountain ranges, indicating a phylogeographic break. The break was further revealed by analysis of molecular variance, spatial analysis of molecular variance, and ecological niche modelling. The most recent common ancestor of all haplotypes showed that global cooling and aridity of the Asian interior at the Pliocene–Pleistocene boundary may triggered this divergence. Two monophyletic lineages (north and south lineage) were revealed by Bayesian phylogeny and the maximum parsimony network. In the north lineage, mismatch analysis indicated an ancient spatial expansion. Distant distribution of closely related haplotypes indicated subsequent allopatric fragmentation. The widespread haplotype H2 implied another significant range expansion. In the south lineage, a considerable rise in sea level of the East China Sea may have triggered population fragmentation. The nested clade analysis also indicated that expansion and allopatric fragmentation were the main processes shaping the haplotype distributions. So, repeated range expansions and fragmentations have shaped the present genetic structure of A. arguta.

Phylogeography of the purple snail Plicopurpura pansa along the Mexican Pacific coast

The purple snail Plicopurpura pansa is a common member of the rocky intertidal community of the Tropical Eastern Pacific. It has a free-living larva that is dispersed by marine currents. We analyzed the demographic (historic), genetic, and phylogeographic structure of P. pansa using a fragment of the cytochrome b gene (687 bp). Data were analyzed by analysis of molecular variance, nested clade analysis (NCA), and a mismatch distribution analysis under the expanding population hypothesis. A total of 219 organisms were collected from 16 localities along the Mexican Pacific coast and one in Costa Rica. We obtained a total of 92 haplotypes. Genetic differences among Mexican populations were low. The Clarión Island population was significantly different from 6 of the Mexican populations studied. This result was attributed to the fact that Clarión is an oceanic island and the currents veer offshore most of the year. Haplotype network and mismatch distribution analyses indicated that the Mexican populations are undergoing expansion. The NCA confirmed a contiguous range expansion of haplotypes and this result may be related to the time that larvae spend in marine currents and to the effect of natural barriers, such as gyres, in Central America and the Isthmus of Tehuantepec.

Impacts of forest fragmentation and post-glacial colonization on the distribution of genetic diversity in the Polish population of the hazel grouse Terastes bonasia

While the hazel grouse Tetrastes bonasia declined in the twentieth century to the point where certain local subpopulations in Poland disappeared altogether, the overall population of the species in the country now seems to be back on the increase. To consider the remaining genetic diversity in that population, analyses of a fragment of the hypervariable domain I of the mitochondrial control region were performed on faecal samples from 251 of the birds. This work provided confirmation of conclusions drawn from previous observations that birds in the populations present in smaller and more isolated forests were characterised by more limited genetic diversity than those occurring in continuous, less-fragmented forests. The level of genetic diversity among birds from central Poland is also found to be high, most likely because recent recolonisation there has involved individuals from both the north and south of the country, as is also suggested when migration rates are estimated. Analysis further indicated a pronounced genetic structure, with a range of processes seen to affect genetic differentiation from one region of Poland to another. Analysis of molecular variance (AMOVA) provided for an assignment of populations to groups corresponding well with the geographical distribution of forests in Poland. Gene flow among the populations is shown to be very low, with no more than 1.5 female migrants per generation coming in. Both high nucleotide diversity and mismatch distribution, and the AMOVA and nested clade analysis (NCA) suggest that birds following at least two different post-glacial recolonisation routes encountered one another in north-eastern Poland. Equally, there are clear indications that the north-eastern and southern parts of the country were recolonised in different periods. The genetic results presented here underline the importance of gene flow in maintaining genetic variability within populations of the hazel grouse, at the same time suggesting that the country’s southern and north-eastern populations should be managed independently where conservation efforts are concerned.

Phylogeography and palaeodistribution modelling of Nassauvia subgenus Strongyloma (Asteraceae): exploring phylogeographical scenarios in the Patagonian steppe.

The Patagonian steppe is an immense, cold, arid region, yet phylogeographically understudied. Nassauvia subgen. Strongyloma is a characteristic element of the steppe, exhibiting a continuum of morphological variation. This taxon provides a relevant phylogeographical model not only to understand how past environmental changes shaped the genetic structure of its populations, but also to explore phylogeographical scenarios at the large geographical scale of the Patagonian steppe. Here, we (1) assess demographic processes and historical events that shaped current geographic patterns of haplotypic diversity; (2) analyze hypotheses of isolation in refugia, fragmentation of populations, and/or colonization of available areas during Pleistocene glaciations; and (3) model extant and palaeoclimatic distributions to support inferred phylogeographical patterns. Chloroplast intergenic spacers, rpl32–trnL and trnQ–5′rps16, were sequenced for 372 individuals from 63 populations. Nested clade analysis, analyses of molecular variance, and neutrality tests were performed to assess genetic structure and range expansion. The present potential distribution was modelled and projected onto a last glacial maximum (LGM) model. Of 41 haplotypes observed, ten were shared among populations associated with different morphological variants. Populations with highest haplotype diversity and private haplotypes were found in central-western and south-eastern Patagonia, consistent with long-term persistence in refugia during Pleistocene. Palaeomodelling suggested a shift toward the palaeoseashore during LGM; new available areas over the exposed Atlantic submarine platform were colonized during glaciations with postglacial retraction of populations. A scenario of fragmentation and posterior range expansion may explain the observed patterns in the center of the steppe, which is supported by palaeomodelling. Northern Patagonian populations were isolated from southern populations by the Chubut and the Deseado river basins during glaciations. Pleistocene glaciations indirectly impacted the distribution, demography, and diversification of subgen. Strongyloma through decreased winter temperatures and water availability in different areas of its range.

Phylogeography of Cephalotaxus oliveri (Cephalotaxaceae) in relation to habitat heterogeneity, physical barriers and the uplift of the Yungui Plateau

Habitat heterogeneity, physical barriers, and the uplift of the Yungui Plateau were found to deeply affect the phylogeographic pattern and evolutionary history of Cephalotaxus oliveri, a perennial conifer endemic to China. In this study, we explored the phylogeography using three chloroplast sequences (trnL–trnF, trnT–trnD and atpB–rbcL) in 22 natural populations of C. oliveri distributed throughout its range. The Yungui Plateau populations of C. oliveri were revealed to origin ca. 9.15Ma by molecular clock estimation, which is consistent with rapid uplift of the Qinghai–Tibetan Plateau (QTP) ca. 8–10Ma. Additionally, geological effects of the Yungui Plateau were suggested to promote the rapid intra-specific differentiation of C. oliveri in the Pliocene and Early Pleistocene. The relatively low level of genetic diversity (h=0.719, θ=1.17×10−3) and high population differentiation (NST=0.771 and GST=0.642) implied restricted gene flow among populations, which was confirmed by the Nested Clade Analysis (NCA). Mismatch distribution and haplotypes network provided evidences of recent demographic population expansion. Furthermore, the statistical dispersal–vicariance analysis indicated that the center of origin was in Central China. The comparison of haplotype distribution patterns indicated that the regions of HNHPS and HBLD were the potential refugia during the Pleistocene ice ages. Our results highlighted that habitat heterogeneity and physical barriers presenting in a species range can predict genetic patterns.

Phylogeography of northern Dolly VardenSalvelinus malma malmabased on analysis of mitochondrial DNA

The northern Dolly Varden, Salvelinus malma malma, is a typical representative of arctic fauna distributed in northeastern Asia and northwestern North America. Because its spawning habitats were affected by Pleistocene glacial advances over most of its natural range, S. m. malma is among the most interesting objects of phylogeographic and microevolutionary studies. We reconstructed the genealogy of mtDNA haplotypes from 27 Alaskan and Asian populations to study the influence of glacial and geological vicariance events on the contemporary population genetic structure, phylogeographic subdivision and distribution of the northern Dolly Varden. Analysis of restriction site states in three PCR-amplified mtDNA regions (ND1/ND2, ND5/ND6, Cytb/D-loop; 47% of the mitochondrial genome) resolved 75 haplotypes in 436 fish. Similar patterns of subspecific variation apparent from hierarchical diversity and nested clade analyses of mtDNA haplotypes identify weak spatial differentiation and low levels of divergence. Our results suggest that (1) demographic history has been influenced by historical range expansions and recent isolation by distance, (2) present populations from Asia and North America were colonized from one main Beringian Refugium, and (3) that this taxon's ancestral population probably experienced a bottleneck in the Beringian Refugium during the late Pleistocene (Wisconsin) glacial period.

Phylogeography of the Brackish Water ClamCorbicula japonicaAround the Japanese Archipelago Inferred from Mitochondrial COII Gene Sequences

We investigated the phylogeography of the Asian brackish water clam, Corbicula japonica, to clarify its demographic history using partial mitochondrial COII gene sequences (990 bp) from 283 individuals collected from around the Japanese archipelago and adjacent areas. Phylogenetic analyses revealed the presence of two major groups within our samples: monophyletic Group I comprising Lineages A-E of C. japonica and paraphyletic Group II consisting of Corbicula sp. Lineages A-C were distributed in Japan and Sakhalin Island, and Lineages D, E, and Corbicula sp. were distributed in the Korean Peninsula. Nested clade analysis (NCA) revealed that Lineage A-the dominant lineage in Japan-consisted of Pacific and Japan Sea lineages, the latter comprising southern and northern Japan Sea groups. Genetic diversity indices of the southern group were higher than those of the northern group, suggesting historical range expansion in the Sea of Japan from southwest to northeast. Geographical distribution of these genetic groups appears to have been influenced by major ocean currents around the Japanese archipelago. Dominant haplotypes in the star-shaped haplotype network of Lineage A were distributed throughout the entire distribution range of each genetic group, implying rapid range expansion of this species. The results of mismatch distribution analysis and molecular clock estimation suggest that expansion of lineage A occurred during the late Middle or Late Pleistocene. In contrast, restricted or past gene flow suggested by NCA and the many unique haplotypes (110/123; 89.4%) present in Lineage A suggest that gene flow among extant populations is rather limited.

Origin area and migration route: Chloroplast DNA diversity in the arctic-alpine plant Koenigia islandica

The Hengduan Mountains (henceforth H-D Mountains) on the Tibet Plateau are a distribution and diversity center for many alpine genera. We examine patterns of genetic variation in an arctic-alpine plant to evaluate the possibility that the H-D Mountains constitute the area of origin of the species as well as to uncover postglacial migration routes. 220 individuals of the arctic-alpine plant Koenigia islandica were sampled from 26 populations distributed in western China and northern Finland. DNA haplotypes were identified using restriction site analysis of two chloroplast DNA intergene spacer regions, atpB-rbcL and trnL-trnF. We examined the geographical distribution of haplotype diversity in relation to latitude, and also compared various indices of diversity in putatively glaciated and unglaciated regions. Patterns of migration were inferred using nested clade analysis. A total of 25 haplotypes were detected. High haplotype diversity was found in the H-D Mountains. H3 and its radiated haplotypes were distributed in the Himalayas. Two haplotypes were fixed concurrently in the H-D Mountains and northern Finland. High genetic diversity of K. islandica and high species diversity of K. islandica are expected in the origin area. Our observations suggest that the H-D Mountains are not only the place of origin of K. islandica, but also the refugia for K. islandica on the Tibet Plateau. What is more, the migration route for the arctic-alpine plant K. islandica must have originated in the region defined by the H-D Mountains in western China extending northward to the Arctic circumpolar, and moved westward along the Himalayas, then northward across the Altay Mountains and the Central Siberian Plateau at different time periods.

Genetic population structure in Siniperca scherzeri (Perciformes: Siniperca) in China inferred from mitochondrial DNA sequences and microsatellite loci

This study aims to improve the estimates of fine-scale genetic diversity and to compare the population structure of Siniperca scherzeri with nuclear and mitochondrial DNA (mtDNA) markers. We first combined mtDNA sequences and seven microsatellite loci to examine the genetic diversity of S. scherzeri in China. Phylogenetic and nested clade analyses revealed two major mtDNA lineages and four subclades. Bayesian multilocus genotype clustering from the microsatellite loci revealed that regional divergence estimates were quantitatively congruent between marker classes. These lineages should be recognized as the basic evolutionary significant units for S. scherzeri in China. Contradict to the previous studies on Coreoperca whiteheadi and Siniperca chuatsi, neither the Nanling–Wuyi Mountain range nor the Qingling–Dabie Mountain range represented a major phylogeographic barrier for S. scherzeri. Our fine-scale analyses of the genetic population structure of S. scherzeri provided insights into the evolutionary processes that shaped the genetic heterogeneity of this fish. This study may serve as a basis for the protection, monitoring and breeding improvement of germplasm resources of this commercially important fish.

Variacion genetica de Procambarus llamasi (Decapoda: Cambaridae) en la peninsula de Yucatan: evidencia de conectividad en un paisaje fragmentado

Within the family Cambaridae, the genus Procambarus is especially important due to the number of species it contains and its wide distribution in the American Continent. Procambarus ( Austrocambarus ) llamasi is endemic to the Yucatan Peninsula, distributed in epicontinental water bodies, including lakes, marshes and flood plains, which may be relatively isolated. Due to the fragmented nature of its habitat, it might be expected to find highly structured populations with unique haplotypes. To describe the genetic variation of the different populations of P. llamasi and their distribution pattern, a phylogeographic analysis was performed using the mitochondrial COI gene. A 643 base pair fragment was sequenced from 53 individuals of ten populations. Different haplotypes were identified and a haplotype network was built using statistical parsimony for nested clade analysis. A total of 14 variable sites were found, 12 of which were informative; all nucleotide changes were transitions and nucleotide diversity was π = 0.0045. Ten haplotypes were found with a diversity of HD = 0.532, with one of them widely distributed. The nested clade analysis shows that current haplotypes are the result of a contiguous range expansion, suggesting that the source of the expansion was at the southern portion of the peninsula. This may occur due to the seasonal floodings in the region, which can create temporary connections between populations.

Phylogeography of Coreoperca whiteheadi (Perciformes: Coreoperca) in China based on mitochondrial and nuclear gene sequences

The phylogeography of Coreoperca whiteheadi was studied using sequences from the mitochondrial cytochrome b (cytb) gene and first intron of the S7 ribosomal protein gene. The reciprocal monophyly mitochondrial cytb and nuclear sequences strongly suggest that C. whiteheadi has significantly reduced gene flow between populations and may be in the process of speciation. Phylogenetic analysis revealed phylogeographical structuring into two major clades (highly supported by bootstrap analysis) corresponding to the two regions divided by Nanling-Wuyi Mountain Range. Subsequent nested clade analysis confirmed this structure. The results suggest that Nanling-Wuyi Mountain Range represents a major phylogeographic barrier for C. whiteheadi. Six evolutionarily significant units of C. whiteheadi were designated from the genetic analysis for conservation and management.

Genetic structure of Curculio elephas Gyll. (Coleoptera, Curculionidae) in Greece: an important pest of sweet chestnut

The weevil, Curculio elephas (Coleoptera, Curculionidae), is one of the most abundant and widespread chestnut feeding pests in Greece. Together with the tortricid moths Cydia splendana and C. fagiglandana (Lepidoptera, Tortricidae), C. elephas greatly affect chestnut production. This weevil occurs in a continuous range throughout Greece; however, its population structure is unknown. Information concerning its population structure could help in the future control of this pest. A 790 bp portion of the mitochondrial Cytochrome Oxidase I gene was sequenced for 160 C. elephas larvae from ten populations. Compared to other Curculio species haplotype diversity with 31 haplotypes and nucleotide diversity with six nucleotide substitutions was low. The Bayesian inference of phylogeography in concert with nested clade analysis revealed a loose geographic distribution of genetic diversity that was likely the joint effect of isolation by distance and gene flow. In addition, population indices and Bayesian-based calculations showed that the populations of C. elephas in Greece are at the phase of expansion. Dating the phylogeny suggests about 300,000 years before present as the start of divergence among the populations of C. elephas in Greece.

Phylogeographic analysis of a temperate-deciduous forest restricted plant (Bupleurum longiradiatum Turcz.) reveals two refuge areas in China with subsequent refugial isolation promoting speciation

This study investigates the influence of climate-induced oscillations and complicated geological conditions on the evolutionary processes responsible for species formation in presently fragmented temperate forest habitats, located in continental East Asia. In addition to this, we also investigate the heavily debated issue of whether temperate forests migrated southwards during such glacial periods or, alternatively, whether there existed refugia within north China, enabling localized survival of temperate forests within this region. In order to achieve these, we surveyed the phylogeography of Bupleurum longiradiatum Turcz. (a herbaceous plant solely confined to temperate forests) constructed from sequence variation in three chloroplast (cp) DNA fragments: trnL–trnF, psbA–trnH and rps16. Our analyses show high genetic diversity within species (hT=0.948) and pronounced genetic differentiation among groups (yellow and purple flowers) with a significant phylogeographical pattern (NST>GST, P<0.05). Forty-three haplotypes were identified and clustered into two lineages (the purple-flowered lineage and the yellow-flowered lineage). Two corresponding refuge areas, one in Qinling and its adjacent regions and one in the Changbai Mountains/eastern China, were revealed across the entire distribution ranges of Bupleurum longiradiatum. These results provide evidence for the hypothesis that independent refugia were maintained across the range of temperate forests in northern China during the last glacial maximum or earlier cold periods. Bupleurum longiradiatum var. porphyranthum formed a single taxon based on molecular data. This specific formation process suggests that the historical vicariance factors, i.e. climate-induced eco-geographic isolation through the biotic displacement of temperate-deciduous forest habitats, enhanced the divergence of the yellow and purple flower lineages at different spatial–temporal scales and over glacial and interglacial periods. Additionally, geological conditions that restricted gene flow might also be responsible for the observed high genetic and geographic differentiation. A nested clade analysis (NCA) revealed that allopatric fragmentation was a major factor responsible for the phylogeographic pattern observed, and also supported a role for historical vicariance factors. Our results therefore support the inference that Quaternary refugial isolation promoted allopatric speciation of temperate plants in East Asia. This may help to explain the existence of high diversity and endemism of plant species in East Asia.

Colour polymorphism in common primrose (Primula vulgaris Huds.): many colours–many species?

Primula vulgaris exhibits flower colour polymorphism in the eastern part of its range, especially pronounced on the NE coast of the Black Sea. This polymorphism in the Caucasian populations has been taxonomically described and some segregated species are listed as rare and endangered. We used sequence variation in two chloroplast noncoding regions (trnL–trnF and rpll32–trnL) and the complete nuclear internal transcribed spacer (ITS) of ribosomal DNA region to investigate correspondence between flower colour and geographical distribution of both nuclear and chloroplast haplotypes. It appears that variability in these DNA regions does not correlate with flower colour, being, however, clearly structured geographically. We used nested clade analysis to explore this geographical structure. It seems that the territory of the Colchis refugium on the E coast of the Black Sea contains both the highest flower colour and haplotype diversities. The results suggest that common primroses colonized the NE coast of the Black Sea from this refugium, spreading along the coast westward. At the same time, the analysis of ITS haplotypes indicates that P. vulgaris colonized the Crimea from NW Anatolia. This makes it clear that no segregated species can be recognized within flower colour polymorphic P. vulgaris in the Caucasus region. However, its phylogeography needs further detailed study on a broader scale.

Population genetic structure and phylogenetic origin of Triops longicaudatus (Branchiopoda: Notostraca) on the Korean Peninsula

The small notostracan crustacean Triops longicaudatus (LeConte, 1846) is considered a living fossil, with a geological record that reaches back to the Carboniferous Period, and is widespread in North America. This species has been found since 1986 on the Korean Peninsula and was officially designated by the Korean government as an endangered species. No taxonomic survey has yet been performed for the samples of Triops found in Korea. Here, we examined the population genetic structure from 79 individuals of T. longicaudatus throughout the species’ geographical range in Korea and to elucidate the phylogenetic relationships among T. longicaudatus-long, T. logicaudatus-short, and T. newberryi, using the nucleotide sequences of COI (643 bp) and ND1 (444 bp). A total of eight haplotypes in COI and nine haplotypes in ND1 were found, and 15 haplotypes (H1-H15) from the combined data of the two genes were also observed. The nested clade analysis and phylogenetic analyses unambiguously corroborate that the Korean populations are subdivided into three distinct genetic lineages. It is highly likely that the Korean populations of T. longicaudatus belong to T. longicaudatus-short. Additionally, T. longicaudatus-long and T. longicaudatus-short may be different, independent species, based on the present phylogeny, the number of legless abdominal rings (LAR), posterior marginal carapace teeth (PMCT), sexual mode, and egg colour. This work is the first comprehensive population genetic and phylogenetic approach for studying T. longicaudatus from East Asia.

MtDNA and AFLP markers demonstrate limited genetic differentiation within thePyganodon cataracta–Pyganodon fragilisfreshwater mussel complex in Atlantic Canada

Two nominal species of freshwater mussels, Pyganodon cataracta (Say, 1817) (eastern floater) and Pyganodon fragilis (Lamarck, 1819) (Newfoundland floater), occur in Atlantic Canada, but their taxonomic status has been controversial. We analyzed the female-transmitted mitochondrial cytochrome c oxidase subunit I (i.e., FCOI) and nuclear internal transcribed spacer region (ITS-1) gene sequences, as well as multilocus amplified fragment length polymorphism (AFLP) markers, to evaluate genetic variation in Pyganodon specimens from Atlantic Canada. We found that Pyganodon samples from this region displayed no or extremely low (i.e., &lt;0.5%) genetic divergence for ITS-1 and FCOI sequence data, respectively. Inferences from nested clade analysis of FCOI haplotypes suggest restricted gene flow with isolation by distance and contiguous range expansion. Analysis of molecular variance inferred from presence or absence of nuclear-encoded AFLP bands showed moderate geographic structuring among provinces but no correspondence between mtDNA haplotypes and AFLP profiles. Similarly, there was no correspondence between presence of a single or a double loop on the umbo and FCOI haplotype. These mtDNA and AFLP markers demonstrate limited genetic differentiation within the Pyganodon cataracta–Pyganodon fragilis freshwater mussel complex in Atlantic Canada and question the species-level distinctness of these putative taxa.

The phylogeography ofLemniscomys striatus(Rodentia: Muridae) Confirms a Remarkable Vicariant Event in Neighbouring Savanna Populations in Central Gabon

Our recent phylogeographic study on the strictly savanna small rodent Nannomys minutoides revealed an unexpected pattern of divergence between populations occupying neighbouring savanna islands in Central Gabon, suggesting the historical and continuing fragmentation of these savanna habitats. In this study, we test this hypothesis using comparative phylogeography with another species of savanna rodent, Lemnhcomys striatus, using nested clade analysis (NCA) on cytochrome b sequences of 53 individuals, particularly checking for vicariance patterns in the Lope National Park region. Lemniscomys striatus is characterized by a local structured pattern similar to that of N. minutoides. These new results further support the scenario of historical and ongoing fragmentation of the local savanna landscape which commenced in the upper Pleistocene, despite the repetitive savanna expansion episodes as documented by the landscape history. Geographic barriers most likely comprising forested areas, which prevent the mixin...

Genetic structure and phylogeography of Pyrus pashia L. (Rosaceae) in Yunnan Province, China, revealed by chloroplast DNA analyses

In this study, we investigated two chloroplast intergenic spacers (accD-psaI and trnL-trnF) for a total of 266 individuals over 22 populations of Pyrus pashia to detect the genetic diversity, genetic, and phylogeographic structure and provide needed information for the development of conservation strategies. Thirteen haplotypes (H1–H13) were recognized. A high level of total diversity was detected (H T = 0.746). Analysis of molecular variance indicated that the genetic variation mainly existed within populations, representing 59.61 % of the total variation. Genetic differentiation among populations was high (F st = 0.404). A Mantel test did not show a correlation between the genetic and geographic distances (r = 0.139, P = 0.09, 1,000 permutations), implying that geographic distance was not critical to gene flow among populations. A significantly higher N st than G st (N st = 0.420, G st = 0.402, P < 0.05) reflected the phylogeographic structure in P. pashia. While nested clade analyses of clade 2-2 showed that restricted gene flow existed among populations, clades 1-2 and 2-1, and the total cladogram exhibited contiguous range expansion events in P. pashia. Both sum of square deviations and the raggedness index failed to reject the sudden demographic expansion model. The overall population expansion of P. pashia was estimated to occur between 621,000 and 209,000 years ago.