Recent Demographic Expansion Research Articles

Genetic Diversity and Distribution Patterns of Host Insects of Caterpillar Fungus Ophiocordyceps sinensis in the Qinghai-Tibet Plateau

The caterpillar fungus Ophiocordyceps sinensis is one of the most valuable medicinal fungi in the world, and it requires host insects in family Hepialidae (Lepidoptera) to complete its life cycle. However, the genetic diversity and phylogeographic structures of the host insects remain to be explored. We analyzed the genetic diversity and temporal and spatial distribution patterns of genetic variation of the host insects throughout the O. sinensis distribution. Abundant haplotype and nucleotide diversity mainly existed in the areas of Nyingchi, ShangriLa, and around the edge of the Qinghai-Tibet Plateau, where are considered as the diversity center or micro-refuges of the host insects of O. sinensis. However, there was little genetic variation among host insects from 72.1% of all populations, indicating that the host species composition might be relatively simple in large-scale O. sinensis populations. All host insects are monophyletic except for those from four O. sinensis populations around Qinghai Lake. Significant phylogeographic structure (NST>GST, P<0.05) was revealed for the monophyletic host insects, and the three major phylogenetic groups corresponded with specific geographical areas. The divergence of most host insects was estimated to have occurred at ca. 3.7 Ma, shortly before the rapid uplift of the QTP. The geographical distribution and star-like network of the haplotypes implied that most host insects were derived from the relicts of a once-widespread host that subsequently became fragmented. Neutrality tests, mismatch distribution analysis, and expansion time estimation confirmed that most host insects presented recent demographic expansions that began ca. 0.118 Ma in the late Pleistocene. Therefore, the genetic diversity and distribution of the present-day insects should be attributed to effects of the Qinghai-Tibet Plateau uplift and glacial advance/retreat cycles during the Quaternary ice age. These results provide valuable information to guide the protection and sustainable use of these host insects as well as O. sinensis.

Genetic Structure and Demographic History of Endemic Micronesian Blue Riffle Goby,Stiphodon caeruleus(Gobiidae) Inferred from Mitochondrial DNA Sequence Analysis

The Blue Riffle Goby, Stiphodon caeruleus (Gobiidae: Sicydiinae), is an amphidromous species endemic to the volcanic islands of Kosrae and Pohnpei, Federated States of Micronesia, in the eastern Caroline Islands. This study evaluated the population genetic structure and demographic history of S. caeruleus using mitochondrial NADH subunits 4 (ND4) and 4L (ND4L) DNA sequences. A total of 876 base pairs were successfully sequenced for 208 specimens from 15 localities. Twenty-three haplotypes were recovered with diversity indices of h = 0.489±0.043 and π = 0.097±0.012% that are lower than many other marine species. The median-joining network of haplotypes is star-like in formation and displayed no genetic structure. AMOVA results show that 99% of the genetic variation is found within populations, rather than between streams or islands. Mismatch distribution analysis and associated statistical tests indicate that a very recent demographic expansion has occurred for the species. Bayesian skyline plot confirms a gradual demographic expansion over the past 5000 years. This expansion is coincident with a reduction in sea level that produced coastal plains and shallow coastal waters, and human settlement of the islands. Our analyses suggest that populations of S. caeruleus among streams are historically unstructured for ND4 and ND4L haplotypes, that larvae may be presently recruited among streams of both islands, and that further nuclear DNA investigations are warranted to resolve potential genetic divergence of populations.

Microsatellite data show recent demographic expansions in sedentary but not in nomadic human populations in Africa and Eurasia

The transition from hunting and gathering to plant and animal domestication was one of the most important cultural and technological revolutions in human history. According to archeologists and paleoanthropologists, this transition triggered major demographic expansions. However, few genetic studies have found traces of Neolithic expansions in the current repartition of genetic polymorphism, pointing rather toward Paleolithic expansions. Here, we used microsatellite autosomal data to investigate the past demographic history of 87 African and Eurasian human populations with contrasted lifestyles (nomadic hunter-gatherers, semi-nomadic herders and sedentary farmers). Likely due to the combination of a higher mutation rate and the possibility to analyze several loci as independent replicates of the coalescent process, the analysis of microsatellite data allowed us to infer more recent expansions than previous genetic studies, potentially resulting from the Neolithic transition. Despite the variability in their location and environment, we found consistent expansions for all sedentary farmers, while we inferred constant population sizes for all hunter-gatherers and most herders that could result from constraints linked to a nomadic or semi-nomadic lifestyle and/or competition for land between herders and farmers. As an exception, we inferred expansions for Central Asian herders. This might be linked with the arid environment of this area that may have been more favorable to nomadic herders than to sedentary farmers. Alternatively, current Central Asian herders may descent from populations who have first experienced a transition from hunter-gathering to sedentary agropastoralism, and then a second transition to nomadic herding.

Phylogeography and population history of Leopardus guigna, the smallest American felid

The guigna (Leopardus guigna) is the smallest and most-restricted New World cat species, inhabiting only around 160,000 km2 of temperate rain forests in southern South America and is currently threatened by habitat loss, fragmentation and human persecution. We investigated phylogeographic patterns of genetic diversity, demographic history and barriers to gene flow with 116 individuals sampled across the species geographic range by analyzing 1,798 base pairs of the mtDNA (496 bp HVSI region, 720 bp NADH-5 gene, 364 bp from 16S gene and 218 bp from ATP-8 gene) and 15 microsatellite loci. Mitochondrial DNA data revealed a clear phylogeographic pattern with moderate separation between northern and southern Chilean populations supporting recognized subspecific partitions based on morphology. A recent demographic expansion was inferred for the southern-most group (San Rafael Lake), presumably due to the complete coverage of this area during the last glacial period, 28000–16000 years BP. Geographical barriers such as the Andes Mountains and the Chacao Channel have partially restricted historic and more-recent gene flow and the Chiloe Island population has diverged genetically since being separated from the mainland 7000 years BP. This is the first study of the genetic structure of this threatened species throughout its whole geographic range.

Concordance between Phylogeographical and Biogeographical Patterns in the Brazilian Cerrado: Diversification of the Endemic Tree Dalbergia miscolobium (Fabaceae)

Few studies have addressed the phylogeography of species of the Cerrado, the largest savanna biome of South America. Here we aimed to investigate the phylogeographical structure of Dalbergia miscolobium, a widespread tree from the Cerrado, and to verify its concordance with plant phylogeographical and biogeographical patterns so far described. A total of 287 individuals from 32 populations were analyzed by sequencing the trnL intron of the chloroplast DNA and the internal transcribed spacer of the nuclear ribosomal DNA. Analysis of population structure and tests of population expansion were performed and the time of divergence of haplotypes was estimated. Twelve and 27 haplotypes were identified in the cpDNA and nrDNA data, respectively. The star-like network configuration and the mismatch distributions indicated a recent spatial and demographic expansion of the species. Consistent with previous tree phylogeographical studies of Cerrado trees, the cpDNA also suggested a recent expansion towards the southern Cerrado. The diversity of D. miscolobium was widespread but high levels of genetic diversity were found in the Central Eastern and in the southern portion of Central Western Cerrado. The combined analysis of cpDNA and nrDNA supported a phylogeographic structure into seven groups. The phylogeographical pattern showed many concordances with biogeographical and phylogeographical studies in the Cerrado, mainly with the Cerrado phytogeographic provinces superimposed to our sampling area. The data reinforced the uniqueness of Northeastern and Southeastern Cerrados and the differentiation between Eastern and Western Central Cerrados. The recent diversification of the species (estimated between the Pliocene and the Pleistocene) and the ‘genealogical concordances’ suggest that a shared and persistent pattern of species diversification might have been present in the Cerrado over time. This is the first time that an extensive ‘genealogical concordance’ between phylogeographic and phytogeographic patterns is shown for the Cerrado biome.

Phylogeographic analyses of Sarcocheilichthys nigripinnis(Teleostei: Cyprinidae)based on mitochondrial DNA Cyt b gene sequences

Sarcocheilichthys nigripinnis is a small cyprinid fish widely distributed in East Asia, and it has been widely used in biogeographic analyses of freshwater fishes in China. In the present study, 142 S. nigripinnis individuals from 20 sampling sites in eight river systems were collected to investigate its phylogeography and genetic variations.. Populations from the Yellow River represent northern clade and all others represent southern clade. The results showed that 56 haplotypes were identified as mitochondrial DNA (mtDNA) Cyt b gene of 1 140 bp length. Relatively high haplotype diversity (h=0.971) and low nucleotide diversity (π=0.0212) were detected, and the estimated average genetic distance was 2.2%. Moreover, a neighbor-joining(NJ)tree revealed seven strongly supported lineages. Populations from the Yellow River were located at the basal position, whereas the remaining populations were more derived. Our results indicate that S. czerskii might have been evolved from S. nigripinnis in the Yellow River ~1.03 Ma. Based on the phylogeographical analysis of S. nigripinnis, we also suggest that vicariance, following mountain uplift and drainage isolation, plays an important role in producing evolutionary lineage differentiations. Moreover, molecular dating estimated that the divergence time of S. czerskii could be dated back to 0.95~3.92 Ma. Mismatch distribution analysis and neutrality tests also suggested the recent demographic expansions of S. nigripinnis populations, and that the effects of Pleistocene climatic changes could be a vital factor of the population dynamics of S. nigripinnis.

Genetic diversity and demographic evolution of baobab (Adansonia digitata L., Bombacoideae, Malvaceae) populations in Senegalese Sahelian areas

This study evaluated the spatial genetic structure of baobab (Adansonia digitata L.) populations from three agroecological sites located in sahelian zone of Senegal usingITS1, 5.8S rDNA and ITS2 gene sequences. To determine the extent of isolation, gene sequences were analyzed between and among three sahelian baobab populations. At least 25 haplotypes of baobab (A. digitata L.) were revealed in Senegal (6, 9 and 10, respectively in Dakar, Bandia and Widou Thiengoly). Private haplotypes found in each locality show that there is an adaptation of the plant to environmental conditions prevailing in each site. Indeed, nucleotide diversity was more important in Dakar (0.00527); it ranges from 0.00483 to 0.00060 for Bandia and Widou populations, respectively. Curves of mismatch distribution show that the population of Ferlo has undergone a recent demographic expansion. Although Bandia and Dakar populations were polyphyletic; each shows a balanced expansion. Fst values ranging from 0.62946 to 0.90712 correlates a strong genetic differentiation between sites. A correlation between geographic and genetic distances was not highlighted by the Mantel’s test but phylogenetic trees of maximum likelihood and Bayesian inference have assigned two clades demonstrating that population of Ferlo (Widou) form a different ecotype from those of Bandia and Dakar. Key words: ITS1, 5.8S, ITS2, Adansonia digitata, haplotype, genetic diversity, demographic evolution.

Spotted stream frog diversification at the Australasian faunal zone interface, mainland versus island comparisons, and a test of the Philippine ‘dual‐umbilicus’ hypothesis

AbstractAimTo utilize comprehensive geographical sampling and a new, multilocus dataset to re‐examine the biogeography of spotted stream frogs (Hylarana signata complex) throughout Southeast Asia. To compare patterns of diversification among stream frog populations on land‐bridge islands and oceanic islands and to re‐evaluate a previous ‘dual‐invasion’ hypothesis for the origins of endemic Philippine taxa.LocationSoutheast Asia, Sundaland, and the Philippines.MethodsWe sequenced two mitochondrial and two nuclear gene regions for members of the Hylarana signata complex. We used summary statistics and phylogenetic networks to characterize genetic variation; phylogenetic relationships and ancestral ranges were estimated using Bayesian and likelihood methods. We used the preferred topology and Bayesian methods to evaluate a previous biogeographical ‘dual‐invasion’ hypothesis.ResultsIn contrast to expectations, we found highly divergent, demographically stable and geographically regionalized lineages on the mainland and on land‐bridge islands, but minimally divergent, widespread and clinally distributed populations, with evidence of recent demographic expansion, in adjacent oceanic island populations. Novel phylogenetic relationships depart from previous studies and our data strongly reject the previously published ‘dual‐invasion’ hypothesis.Main conclusionsOur results join new literature demonstrating that species on mainland and continental shelf islands may harbour high levels of unrecognized diversity, whereas adjacent oceanic island archipelagos can and do support naturally occurring widespread species. Although our data indicate that the individual identities of species previously hypothesized to be involved in the ‘dual‐invasion’ scenario may have been incorrect, this mechanism for faunal exchange between the archipelago and adjacent mainland undoubtedly has contributed substantially to the accumulation of endemic vertebrate diversity in the Philippines.

Who is moving where? Molecular evidence reveals patterns of range shift in the acorn barnacle Hexechamaesipho pilsbryi in Asia

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 488:187-200 (2013) - DOI: https://doi.org/10.3354/meps10385 Who is moving where? Molecular evidence reveals patterns of range shift in the acorn barnacle Hexechamaesipho pilsbryi in Asia Ling Ming Tsang1, Benny K. K. Chan2, Gray A. Williams3, Ka Hou Chu1,* 1Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 2Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan, ROC 3The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR *Corresponding author. Email: kahouchu@cuhk.edu.hk ABSTRACT: Global warming is predicted to cause a shift in the geographic ranges of marine organisms. Such shifts have already been observed with the polar retreat of temperate species and northern expansion of more tropical species. Hexechamaesipho pilsbryi is an intertidal acorn barnacle first identified by Hiro in 1936. Hiro reported the southern limit of H. pilsbryi as southern Kyushu Island, Japan. However, H. pilsbryi has recently been recorded in Taiwan as well as Maritime Southeast Asia—suggesting a recent southward range extension into tropical waters that would be contrary to general predictions. To test this hypothesis, we compared the mitochondrial COI gene sequences of 200 individuals sampled from two sites in the previously reported range, and nine sites in the newly reported localities. Two highly diverged lineages were found: a northern lineage, predominantly in Japan and Okinawa, and a southern lineage, primarily in Taiwan and Southeast Asia. The unimodal mismatch distribution and the star-like shaped haplotype network suggest recent demographic expansion in the southern lineage. The molecular data, therefore, rejected the southward extension hypothesis, and instead supported an alternative scenario of a northward range shift of the southern lineage from Southeast Asia to Taiwan. Our results reveal that range shifts in cryptic or poorly studied marine taxa may confound the identification of species’ distributions and consequent interpretation of possible changes in ranges and sources of invasion. The application of molecular data to identify and monitor such changes can address these problems and permits a rapid and sensitive confirmation of such events. KEY WORDS: Global warming · Intertidal · Biogeography · Cryptic species · Population genetics · Chthamalidae Full text in pdf format PreviousNextCite this article as: Tsang LM, Chan BKK, Williams GA, Chu KH (2013) Who is moving where? Molecular evidence reveals patterns of range shift in the acorn barnacle Hexechamaesipho pilsbryi in Asia. Mar Ecol Prog Ser 488:187-200. https://doi.org/10.3354/meps10385 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 488. Online publication date: August 15, 2013 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2013 Inter-Research.

Northern origin and diversification in the central lowlands? – Complex phylogeography and taxonomy of widespread day geckos (Phelsuma) from Madagascar

Day geckos of the Phelsuma lineata group are widespread in Madagascar and have been historically split into numerous species and subspecies based almost exclusively on differences in coloration and body size. We apply phylogenetic and phylogeographic methods to examine the biogeography and taxonomy of these lizards, including explicit tests of various biogeographic predictions and based on a molecular data set covering much of the distribution ranges of all species and subspecies of P. lineata, P. dorsivittata, P. comorensis, P. hoeschi, P. kely, and P. pusilla in Madagascar (and the Comoros archipelago for P. comorensis). Sequences of the mitochondrial 16S rRNA and the nuclear RAG-1 gene fragment were determined from 376 samples, and a multigene mtDNA phylogeny of the species group was constructed for the main phylogroups identified in the 16S haplotype network. We used the 16S sequences to estimate the geographic location of the ancestor of each major mtDNA clade and to infer their demographic history using a variety of statistical tools. Our phylogeny separates the taxa analyzed into two well-supported major subclades mainly occurring in the north respectively east of the island. Mismatch distribution of samples together with rejection of neutrality, the results of Bayesian Skyline Plots analysis, and a star-like network suggests a recent demographic expansion for the P. l. lineata lineage into the eastern lowlands, while the highland (P. l. elanthana) and northern clades (P. dorsivittata and P. l. punctulata) show signatures of rather stable populations. A major genetic discontinuity observed coincided with a northern lowland stretch that separates mid-altitude rainforests in the north from those in the center and south. Our analysis points to numerous unsolved taxonomic problems in this group of geckos, especially in the small-sized taxa (P. hoeschi, P. kely, P. pusilla), and provides a basis for a future comprehensive taxonomic revision, which will require integrative analysis of molecular, morphological and chromatic data as well as careful examination of type specimens.

Phylogeography and population genetic structure of the Talas tuco-tuco (Ctenomys talarum): integrating demographic and habitat histories

We examined the phylogeography of the South American subterranean rodent Ctenomys talarum (Talas tucotuco) using mitochondrial DNA control region (D-loop) sequences. This species is an herbivorous rodent endemic to the province of Buenos Aires, Argentina, that lives in natural grasslands in coastal sand dune habitats and in some fragmented inland populations. In this study we assessed the genetic relationship among populations of C. talarum across its entire distributional range and analyzed how the geological history of the habitat has affected the genetic structure and demographic history of these populations. A complex network of haplotypes in conjunction with analysis of molecular variance results showed high genetic subdivision and a strong phylogeographic pattern among populations of C. talarum .P airwiseFST-values showed significant differentiation among all populations studied. The overall pattern was similar to that expected under the isolation-by-distance model, suggesting equilibrium between gene flow and local genetic drift. Major geographical barriers (e.g., rivers and unsuitable habitat) in the area, in conjunction with population isolation, appeared to be associated with strong genetic differentiation among the different geographical groups. Local mismatch distributions and tests of neutrality suggest contrasting histories for different groups of populations; although some populations appeared to be characterized by demographic stability and no significant departures from neutrality, others showed departures from strict neutrality consistent with a recent demographic expansion. Finally, a close association seems to exist between the major climatic changes that occurred during the late Pleistocene and Holocene in the central region of Argentina and the main historical demographic changes inferred from C. talarum. Current populations of C. talarum appear to be relicts of a more extended historical distribution along the Argentinean Pampas. These historical extinctions, however, have not erased the signature of long-term stability and geographical structure in this species along the coastal and inland distribution ranges.

Genetic differentiation of Trachurus japonicus from the Northwestern Pacific based on the mitochondrial DNA control region

Trachurus japonicus is a pelagic fish widely distributed from China, Korea to Japan. To examine the gene flow of T. japonicus between Chinese and Japanese coastal waters, eight populations were collected for the present study. Eighty-seven variable sites defined 168 haplotypes. The populations of T. japonicus showed high haplotype diversity (h) with a range from 0.964 ± 0.027 to 1.000 ± 0.016 and low nucleotide diversity with a range from 0.011 ± 0.006 to 0.015 ± 0.008. The topology of the neighbour-joining tree showed no significant genealogical branches or clusters corresponding to sampling localities. The starburst structure of the minimum spanning tree suggested a very recent origin for most haplotypes. Both pairwise Fst and analysis of molecular variance revealed no significant genetic differentiation throughout the range examined. The results of neutrality tests and mismatch distributions indicated that T. japonicus may experience a recent population demographic expansion.

Annual use of man-made wetlands by the mute swan (Cygnus olor)

This is essential to understand habitat selection by wildlife to manage habitats and populations. Studying the annual use of aquatic habitats provides information on how to manage wetlands for waterfowl, and to predict possible detrimental effects associated with extended usage by these birds. This is particularly important for species like the mute swan (Cygnus olor Gmelin), given its recent dramatic demographic expansion, causing concern in both Europe and America. We studied the extent of usage (swan.days.ha−1) of habitat patches by mute swans in a heterogeneous and fluctuating fishpond landscape. We assessed seasonal differences of swan usage of fishponds, annual variation for a given fishpond, and determined which habitat factors drive swan usage over the year. The seasonal use pattern was regular: a similar proportion of fishponds was used heavily, moderately or lightly in all seasons. Flocking throughout the year and breeding during summer were associated with heavy use of fishponds, i.e. large number of swan.days.ha−1. Flocking on some fishponds during several successive seasons demonstrated that some waterbody provide valuable habitats over time for swans. However, swans did not use individual fishponds to the same extent each season, mostly depending on the fluctuating ecological requirements of swans and variation in habitat properties. Agricultural practices on fishponds drastically affected swan usage during autumn and winter: formerly dried fishponds were used preferentially once reflooded. The specific agricultural crops used during the drought period had no influence though. The large-sized fishponds and fishponds within a dense network of waterbody were the most heavily used by swans throughout the year. Our results may thus be helpful to predict and prevent possible habitat damage by swans. They also provide information on habitats that are valuable for waterfowl species in general, by using mute swans as a proxy for waterfowl requirements.

Rapid Divergent Evolution of Male Genitalia Among Populations of Drosophila buzzatii

Fil: Soto, Ignacio Maria. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Oficina de Coordinacion Administrativa Ciudad Universitaria. Instituto de Ecologia, Genetica y Evolucion de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecologia, Genetica y Evolucion de Buenos Aires; Argentina

Spatiotemporal behavioral plasticity of wild boar (Sus scrofa) under contrasting conditions of human pressure: primeval forest and metropolitan area

The aim of this study was to examine the effects of sex and age of individuals, season, and human pressure (both human presence and habitat structure) on spatiotemporal behavior of wild boar (Sus scrofa). Specifically, we compared wild boar behavior under contrasting conditions of human pressure, within the primeval temperate forest of Biaoowieu (eastern Poland) and the metropolitan area of Cracow (Poland). It was predicted that, compared with the forest, wild boar within the urban area will have smaller home ranges due to restricted space, will show longer daily movements due to patchy resources, and will exhibit increased nocturnal activity and ranging behavior in an attempt to avoid human interference. We used radiotracking data from 35 wild boar. Animals inhabiting the urban area had smaller home ranges, yet covered almost twice as much distance on a daily basis than individuals inhabiting primeval forest. Daily duration of activity was similar in the 2 study areas. However, distribution of activity throughout the day differed considerably. In the urban area wild boar were almost exclusively nocturnal, whereas in the primeval forest wild boar activity was evenly distributed throughout the day. Additionally, in the urban area, activity was strongly associated with traveling speed, whereas in the primeval forest active wild boar moved about to little extent. Seasonal effects were stronger in the primeval forest and affected daily distance traveled, duration of activity, and level of diurnality. This study showed that wild boar can adjust their spatiotemporal behavior to local conditions and this may be one factor explaining recent rapid demographic expansion in Europe.

Cryptic speciation and genetic structure of widely distributed brittle stars (Ophiuroidea) in Europe

Pérez‐Portela, R., Almada, V. &amp; Turon, X. (2012). Cryptic speciation and genetic structure of widely distributed brittle stars (Ophiuroidea) in Europe. —Zoologica Scripta, 00, 000–000.The development of molecular techniques has led to the detection of numerous cases of cryptic speciation within widely distributed marine invertebrate species and important taxonomic revisions in all the major marine taxa. In this study, we analysed a controversial marine species complex in the genus Ophiothrix, a widespread taxon in European waters traditionally assigned to two nominal species, Ophiothrix fragilis and O. quinquemaculata. These species are important components of the rocky shores and deep marine benthos along the North Atlantic and Mediterranean littoral. Their status (including variants of both species) has remained contentious due to overlapping variability in morphological characters. In this study, we analysed the genetic and morphological differences of Ophiothrix lineages along the Atlantic and Mediterranean coasts. We also assessed population genetic structure in the Atlantic and Mediterranean basins by sequencing two mitochondrial genes, the 16S rRNA gene and COI gene, of 221 specimens from 13 locations. Phylogenetic analyses demonstrated the existence of two genetically distinct lineages, attributable to two different species although unrelated to previous taxonomic distinctions. Morphological differences could also be detected between these lineages. Samples from the Northeast Atlantic and one from the deep Mediterranean grouped within Lineage I, whereas Lineage II pooled together the southern Atlantic and rocky shallow Mediterranean samples. In the northern region of the Iberian Peninsula and at a deep locality in the Mediterranean, both lineages overlap. Speciation processes likely happened during the Mio–Pliocene transition (about 4.8–7.5 million years ago), when marine‐level oscillations led to the blockage of major marine corridors in Europe and promoted genetic isolation by vicariance. Secondary contact between lineages following sea‐level increases and recolonization during the refilling of the Mediterranean after the Miocene salinity crisis could explain the present‐day distribution of genetic variability. No barriers to gene flow along the Atlanto‐Mediterranean area were detected for Lineage II, and the lack of genetic structure could be caused by a mixture of several factors, such as wide dispersal potential, recent demographic expansion and large population size.

Natural or naturalized? Phylogeography suggests that the abundant sea urchin Arbacia lixula is a recent colonizer of the Mediterranean.

We present the global phylogeography of the black sea urchin Arbacia lixula, an amphi-Atlantic echinoid with potential to strongly impact shallow rocky ecosystems. Sequences of the mitochondrial cytochrome c oxidase gene of 604 specimens from 24 localities were obtained, covering most of the distribution area of the species, including the Mediterranean and both shores of the Atlantic. Genetic diversity measures, phylogeographic patterns, demographic parameters and population differentiation were analysed. We found high haplotype diversity but relatively low nucleotide diversity, with 176 haplotypes grouped within three haplogroups: one is shared between Eastern Atlantic (including Mediterranean) and Brazilian populations, the second is found in Eastern Atlantic and the Mediterranean and the third is exclusively from Brazil. Significant genetic differentiation was found between Brazilian, Eastern Atlantic and Mediterranean regions, but no differentiation was found among Mediterranean sub-basins or among Eastern Atlantic sub-regions. The star-shaped topology of the haplotype network and the unimodal mismatch distributions of Mediterranean and Eastern Atlantic samples suggest that these populations have suffered very recent demographic expansions. These expansions could be dated 94–205 kya in the Mediterranean, and 31–67 kya in the Eastern Atlantic. In contrast, Brazilian populations did not show any signature of population expansion. Our results indicate that all populations of A. lixula constitute a single species. The Brazilian populations probably diverged from an Eastern Atlantic stock. The present-day genetic structure of the species in Eastern Atlantic and the Mediterranean is shaped by very recent demographic processes. Our results support the view (backed by the lack of fossil record) that A. lixula is a recent thermophilous colonizer which spread throughout the Mediterranean during a warm period of the Pleistocene, probably during the last interglacial. Implications for the possible future impact of A. lixula on shallow Mediterranean ecosystems in the context of global warming trends must be considered.

Population genetics of the malaria vector Anopheles aconitus in China and Southeast Asia

Anopheles aconitus is a well-known vector of malaria and is broadly distributed in the Oriental Region, yet there is no information on its population genetic characteristics. In this study, the genetic differentiation among populations was examined using 140 mtDNA COII sequences from 21 sites throughout Southern China, Myanmar, Vietnam, Thailand, Laos and Sri Lanka. The population in Sri Lanka has characteristic rDNA D3 and ITS2, mtDNA COII and ND5 haplotypes, and may be considered a distinct subspecies. Clear genetic structure was observed with highly significant genetic variation present among population groups in Southeast Asia. The greatest genetic diversity exists in Yunnan and Myanmar population groups. All population groups are significantly different from one another in pairwise Fst values, except Northern Thailand with Central Thailand. Mismatch distributions and extremely significant Fs values suggest that the populations passed through a recent demographic expansion. These patterns are discussed in relation to the likely biogeographic history of the region and compared to other Anopheles species.

Phylogeography of Cyananthus delavayi (Campanulaceae) in Hengduan Mountains inferred from variation in nuclear and chloroplast DNA sequences

Abstract Phylogeographic studies on alpine plants endemic to the Hengduan Mountains of the southeastern Qinghai–Tibet Plateau are still limited in number. In this study, we used sequence variation of one nuclear gene (ncpGS, which encodes the chloroplastic glutamine synthetase) and in two chloroplast DNA segments to investigate the phylogeographic structure and population demographic history of Cyananthus delavayi, a narrow‐range species endemic to this region. We identified eight chlorotypes and 16 nuclear genotypes in a survey of 10 populations sampled throughout the range of the species. The results of both phylogenetic and network analyses suggested that the genealogical relationships of both chlorotypes and nuclear genotypes showed a clear geographical correlation. High total genetic diversity, low levels of within‐population diversity, and strong population differentiation (chloroplast DNA: hT= 0.827, hS= 0.087, NST= 0.899, GST= 0.895; nuclear DNA: hT= 0.910, hS= 0.348, NST= 0719, GST= 0.618) were identified. Based on the mismatch distribution analyses, no evidence of recent demographic population expansion was found for this species. Nested clade analyses of both chlorotypes and nuclear genotypes indicated that restricted gene flow resulting from isolation by distance and allopatric fragmentation were likely to have been the major processes that shaped their present‐day spatial distribution. Our dating of the genetic divergences between three major geographic lineages suggested that the largest glaciation of the early Quaternary developed in the Qinghai–Tibet Plateau and mountainous isolation may have together led to deep intraspecific vicariance within this species.

Genetic and morphological differentiation of the Indo-West Pacific intertidal barnacle Chthamalus malayensis.

Chthamalus malayensis is a common intertidal acorn barnacle widely distributed in the Indo-West Pacific. Analysis of sequences of mitochondrial cytochrome c oxidase subunit I reveals four genetically differentiated clades with almost allopatric distribution in this region. The four clades exhibit morphological differences in arthropodal characters, including the number of conical spines and number of setules of the basal guard setae on the cirri. These characters are, however, highly variable within each clade; such that the absolute range of the number of conical spines and setules overlaps between clades, and therefore, these are not diagnostic characters for taxonomic identification. The geographic distribution of the four clades displays a strong relationship between surface temperatures of the sea and ocean-current realms. The Indo-Malay (IM) clade is widespread in the tropical, equatorial region, including the Indian Ocean, Malay Peninsula, and North Borneo. The South China (SC) and Taiwan (TW) clades are found in tropical to subtropical regions, with the former distributed along the coasts of southern China, Vietnam, Thailand, and the western Philippines under the influence of the South China Warm Current. The TW clade is endemic to Taiwan, while the Christmas Island (CI) clade is confined to CI. There was weak or no population subdivision observed within these clades, suggesting high gene flow within the range of the clades. The clades demonstrate clear signatures of recent demographic expansion that predated the Last Glacial Maximum (LGM), but they have maintained a relatively stable effective population in the past 100,000 years. The persistence of intertidal fauna through the LGM may, therefore, be a common biogeographic pattern. The lack of genetic subdivision in the IM clade across the Indian and Pacific Oceans may be attributed to recent expansion of ranges and the fact that a mutation-drift equilibrium has not been reached, or the relaxed habitat requirements of C. malayensis that facilitates high concurrent gene flow. Further studies are needed to determine between these alternative hypotheses.