Extensive Gene Flow Research Articles

Phylogeography of Quercus aquifolioides provides novel insights into the Neogene history of a major global hotspot of plant diversity in south‐west China

AbstractAimHotspots of biodiversity are often associated with areas that have undergone orogenic activity during recent geological history. Mountain uplifts are known to catalyse species radiation but their impact on evolutionarily stable taxa such as many trees remains little understood. The oak Quercus aquifolioides is endemic to yet widely distributed across the Hengduanshan Biodiversity Hotspot in the Eastern Himalayas. Here, we investigate how the region's Neogene and Quaternary history has driven the species' past population dynamics and the resulting extant patterns of intraspecific diversity.LocationHengduanshan Biodiversity Hotspot in SW China.MethodsWe sampled 58 populations throughout the species range and genotyped a total of 959 individuals at four chloroplast DNA fragments and 11 nuclear microsatellite loci. Phylogenetic reconstructions, molecular dating techniques and ancestral area reconstructions were used in combination with population genetic statistics to infer the biogeographical history of Q. aquifolioides. The phylogeographical study was complemented by a survey of fossil records and a niche modelling exercise.ResultsCombined molecular and fossil evidence indicates that Q. aquifolioides descended during the late Miocene from the central Qinghai‐Tibet Plateau into Tibet and the western Sichuan Plateau, and from there, into the area of highest endemism in the Hengduan Mountains sensu lato. Great apparent population stability and a haplotype ‘radiation’ in this area contrasted with marked extinction–recolonization dynamics and reduced population diversity in Tibet. We found evidence for extremely limited seed gene flow but extensive pollen gene flow (global FST: cpDNA = 0.98, nSSR = 0.07) with signals of asymmetric pollen dispersal from the Hengduan Mountains into Tibet.Main conclusionOur results provide insights of unprecedented detail into the ancient biogeographical history of the Hengduanshan Biodiversity Hotspot, suggesting that past environmental changes in the region may have catalysed radiative diversifications within species much in the same way as among species.

Genetic analyses reveal high levels of seed and pollen flow in hawthorn (Crataegus monogyna Jacq.), a key component of hedgerows

Hedgerows represent important components of agri-environment landscapes that are increasingly coming under threat from climate change, emergent diseases, invasive species and land use change. Given that population genetic data can be used to inform best-practice management strategies for woodland and hedgerow tree species, we carried out a study on hawthorn (Crataegus monogyna Jacq.), a key component of hedgerows, on a regional basis using a combination of nuclear and chloroplast microsatellite markers. We found that levels of genetic diversity were high and comparable to, or slightly higher than, other tree species from the same region. Levels of population differentiation for both sets of markers, however, were extremely low, suggesting extensive gene flow via both seed and pollen. These findings suggest that a holistic approach to woodland management, one which does not necessarily rely on the concept of “seed zones” previously suggested, but which also takes into account populations with high and/or rare chloroplast (i.e. seed-specific) genetic variation, might be the best approach to restocking and replanting.

Genetic structure of winter populations of the endangered Indiana bat (Myotis sodalis) prior to the white nose syndrome epidemic: implications for the risk of disease spread

The spread of white nose syndrome raises serious concerns about the long-term viability of affected bat species. Here we examine the geographic distribution of genetic variation, levels of population connectivity that may influence the spatial spread of WNS, and the likelihood that recent population declines in regions affected by WNS have led to the loss of unique genetic variation for the endangered Indiana bat (Myotis sodalis). We amplified a fragment of the mitochondrial control region for 375 individuals and genotyped 445 individuals at 10 microsatellite loci from 18 sampling sites distributed across the majority of the species' range. Analysis of mitochondrial DNA indicated the presence of at least five distinct matrilineal clusters, with the most pronounced differences between northeastern sites and those in the rest of the range. The majority of individuals in the Ozark- Central, Midwest, and Appalachian recovery units fell into a single cluster. Significant differentiation also was observed between one Appalachian and one Midwestern site and the majority of other sites. However, using nuclear microsatellites we observed the absence of differentiation and widespread gene flow among all hibernacula, suggesting the occurrence of extensive gene flow through dispersal and mating. The absence of genetically distinct populations within the range of Indiana bats indicates a lack of barriers to WNS transmission, and it is unlikely that significant portions of the hibernating population of Indiana bats will remain disease free into the future. Further, while matrilineal gene flow was restricted among some sites and regions, we found no genetic evidence to support the division of Indiana bats into separate recovery units.

Genetic homogeneity of the geoduck clam Panopea generosa in the northeast Pacific

Geoduck clams are a valuable natural resource along the northeast Pacific, which makes the assessment of the biological and genetic status of their populations a key element to provide a basis for their proper management and conservation. In the present study, we assess the genetic variability and connectivity of Panopea generosa Gould, 1850 among four localities in the northeast Pacific using mitochondrial (DNA sequences from COI and COIII) and nuclear (five microsatellite loci) data. We found no evidence of genetic differentiation among localities encompassing scales of 100s to 1000s of kilometers along the northeast Pacific, which is consistent with a large effective population size and extensive gene flow in the absence of significant barriers acting on the larval stages. Our genetic findings and phenotypic evidence are consistent with the existence of a single management unit shared by Canada, the United States and Mexico, but further studies with increased geographic and genetic sampling are warranted to better estimate the extent and direction of gene flow to help in international management and conservation measures of this valuable resource.

Long‐distance dispersal and barriers shape genetic structure of peatmosses (Sphagnum) across the Northern Hemisphere

AbstractAimDisjunctly distributed peatmosses (Sphagnum) have been found to exhibit little genetic structure over regional and intercontinental scales, mainly caused by high ability for transoceanic long‐distance dispersal. Although, most Northern Hemisphere peatmoss species have wide circumboreal/nemoral ranges, little is known about the magnitude and effects of long‐distance dispersal and barriers in shaping the genetic structure of such species. We investigate whether high dispersal capacity has caused genetic homogeneity across broad areas of the Northern Hemisphere, or whether barriers act to shape genetic structure across different species with similar distributional ranges.LocationNorthern Hemisphere.MethodsWe studied genetic variation and structure in six Sphagnum species using 19 microsatellite loci.ResultsFour out of six species were genetically structured in similar ways; with mainly one Beringian and one Atlantic group. Overall, both the North American and Eurasian continents seemed to act as a barrier to gene flow in several species. However, the most abrupt breakpoint between genetic groups was found in south‐east Alaska.Main conclusionsWe found evidence for extensive gene flow between regions across the Northern Hemisphere among peatmosses, with oceans seemingly acting as weaker barriers to gene flow than landmasses. Plants from the amphi‐Atlantic and amphi‐Beringian regions of several species were genetically differentiated. Similar genetic structuring across several species, indicate that spore‐producing species do not disperse freely across their entire distributional range, but are likely limited by wind directions, landmass barriers and/or habitat availability.

Reconstruction of the Evolutionary History and Dispersal of Usutu Virus, a Neglected Emerging Arbovirus in Europe and Africa.

ABSTRACTUsutu virus (USUV), one of the most neglected Old World encephalitic flaviviruses, causes epizootics among wild and captive birds and sporadic infection in humans. The dynamics of USUV spread and evolution in its natural hosts are unknown. Here, we present the phylogeny and evolutionary history of all available USUV strains, including 77 newly sequenced complete genomes from a variety of host species at a temporal and spatial scaled resolution. The results showed that USUV can be classified into six distinct lineages and that the most recent common ancestor of the recent European epizootics emerged in Africa at least 500 years ago. We demonstrated that USUV was introduced regularly from Africa into Europe in the last 50 years, and the genetic diversity of European lineages is shaped primarily by in situ evolution, while the African lineages have been driven by extensive gene flow. Most of the amino acid changes are deleterious polymorphisms removed by purifying selection, with adaptive evolution restricted to the NS5 gene and several others evolving under episodic directional selection, indicating that the ecological or immunological factors were mostly the key determinants of USUV dispersal and outbreaks. Host-specific mutations have been detected, while the host transition analysis identified mosquitoes as the most likely origin of the common ancestor and birds as the source of the recent European USUV lineages. Our results suggest that the major migratory bird flyways could predict the continental and intercontinental dispersal patterns of USUV and that migratory birds might act as potential long-distance dispersal vehicles.

Signatures of natural selection on Pinus cembra and P. mugo along elevational gradients in the Alps

Alpine regions represent an interesting biome for studying local adaptation in forest trees. Strong genetic differentiation is expected along elevational gradients in spite of extensive gene flow. We sampled 18 and 20 natural populations of Pinus cembra and Pinus mugo, in two subregions and four elevational gradients. To investigate the effects of elevation on genetic diversity and adaptation, 768 and 1152 single nucleotide polymorphisms (SNPs) were genotyped in P. cembra and P. mugo. We found low but significant genetic differentiation among populations in both species. To discover outliers, we applied Bayesian simulation and hierarchical island model analyses. A larger number of outliers were found using the first method. Some SNPs were detected with both analyses: one SNP in P. cembra and three in P. mugo when using two subregions and four SNPs in P. cembra and one in P. mugo when using four elevational gradients. The association between environmental and genetic variation was tested with Bayesian simulation (Bayenv) and a latent factor mixed model (LFMM). The first method, using all populations, detected 6 and 20 SNPs associated to temperature in P. cembra and in P. mugo, respectively, 3 SNPs associated to precipitation in P. cembra, and 14 SNPs to elevation in P. mugo. The LFMM found a higher number of SNPs associated to temperature in P. mugo than in P. cembra (37 vs. 27), with a stronger association with maximum temperature (April–June). In P. cembra, the majority of associations (51 SNPs) were found with precipitation (January–March). Five SNPs in common between species were found on genes potentially involved in plant response to abiotic stress. Using these results, we confirmed that temperature was an important driver of adaptive potential for each species so that continued changes to global temperatures will likely involve continued adaptation as ranges shift upwards.

Population Structure of a Widespread Species under Balancing Selection: The Case of Arbutus unedo L.

Arbutus unedo L. is an evergreen shrub with a circum-Mediterranean distribution that also reaches the Eurosiberian region in northern Iberia, Atlantic France, and a disjunct population in southern Ireland. Due to the variety of climatic conditions across its distribution range, the populations of A. unedo were expected to display local adaptation. Conversely, common garden experiments revealed that diverse genotypes from a range of provenances produce similar phenotypes through adaptive plasticity, suggesting the action of stabilizing selection across its climatically heterogeneous range. Nonetheless, since a uniform response might also result from extensive gene flow, we have inferred the population structure of A. unedo and assessed whether its extended and largely one-dimensional range influences gene flow with the help of AFLP genotypes for 491 individuals from 19 populations covering the whole range of the species. As we had anticipated, gene flow is restricted in A. unedo, providing further support to the hypothesis that stabilizing selection is the most likely explanation for the homogeneous phenotypes along the range. The Euro-Siberian populations were not particularly isolated from the Mediterranean. Instead, there was a distinct genetic divide between the populations around the Mediterranean Sea and those sampled along Atlantic coasts from northern Africa up to Ireland. This genetic structure suggests the action of historic rather than biogeographic factors as it seems consistent with a scenario of independent glacial refugia in the Atlantic and Mediterranean portions of the range of A. unedo. Genetic exchange was likewise restricted within each set of populations. Nevertheless, isolation-by-distance (IBD) was stronger, and FST increased faster with distance, along the Atlantic, suggesting that gene flow might be larger among Mediterranean populations. Genetic diversity was significantly lower in NW Iberia and Ireland than in other populations whereas Ireland was more closely related to populations in NW Iberia than to a population in Atlantic France, suggesting a postglacial stepping-stone colonization of the Atlantic coast. Altogether, our results show that stabilizing selection is able to homogenize the phenotypic response even when population structure is strong, gene flow is constrained, and the phylogeographic past is complex.

The Historical Speciation of Mauremys Sensu Lato: Ancestral Area Reconstruction and Interspecific Gene Flow Level Assessment Provide New Insights.

Mauremys sensu lato was divided into Mauremys, Chinemys, Ocadia, and Annamemys based on earlier research on morphology. Phylogenetic research on this group has been controversial because of disagreements regarding taxonomy, and the historical speciation is still poorly understood. In this study, 32 individuals of eight species that are widely distributed in Eurasia were collected. The complete mitochondrial (mt) sequences of 14 individuals of eight species were sequenced. Phylogenetic relationships, interspecific divergence times, and ancestral area reconstructions were explored using mt genome data (10,854 bp). Subsequent interspecific gene flow level assessment was performed using five unlinked polymorphic microsatellite loci. The Bayesian and maximum likelihood analyses revealed a paraphyletic relationship among four old genera (Mauremys, Annamemys, Chinemys, and Ocadia) and suggested the four old genera should be merged into the genus (Mauremys). Ancestral area reconstruction and divergence time estimation suggested Southeast Asia may be the area of origin for the common ancestral species of this genus and genetic drift may have played a decisive role in species divergence due to the isolated event of a glacial age. However, M. japonica may have been speciated due to the creation of the island of Japan. The detection of extensive gene flow suggested no vicariance occurred between Asia and Southeast Asia. Inconsistent results between gene flow assessment and phylogenetic analysis revealed the hybrid origin of M. mutica (Southeast Asian). Here ancestral area reconstruction and interspecific gene flow level assessment were first used to explore species origins and evolution of Mauremys sensu lato, which provided new insights on this genus.

The Southwestern fringe of Europe as an important reservoir of caprine biodiversity.

BackgroundPortugal and Spain, with six and 22 officially recognized caprine breeds, encompass 25 % of the European Union goat census. Many of these populations have suffered strong demographic declines because of competition with exotic breeds and the phasing-out of low income rural activities. In this study, we have investigated the consequences of these and other demographic processes on the genetic diversity, population structure and inbreeding levels of Iberian and Atlantic goats.MethodsA sample of 975 individuals representing 25 officially recognized breeds from Portugal and Spain, two small populations not officially recognized (Formentera and Ajuí goats) and two ecotypes of the Tinerfeña and Blanca Celtibérica breeds were genotyped with a panel of 20 microsatellite markers. A wide array of population genetics methods was applied to make inferences about the genetic relationships and demography of these caprine populations.ResultsGenetic differentiation among Portuguese and Spanish breeds was weak but significant (FST = 0.07; P < 0.001), which is probably the consequence of their short splitting times and extensive gene flow due to transhumance. In contrast, Canarian goats were strongly differentiated because of prolonged geographic isolation. Most populations displayed considerable levels of diversity (mean He = 0.65).ConclusionsHigh diversity levels and weak population structures are distinctive features of Portuguese and Spanish breeds. In general, these local breeds have a reduced census, but are still important reservoirs of genetic diversity. These findings reinforce the need for the implementation of management and breeding programs based on genetic data in order to minimize inbreeding, maintain overall genetic and allelic diversities and breed identities, while at the same time taking into account the within-breed genetic structure.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-015-0167-8) contains supplementary material, which is available to authorized users.

Protected areas of Spain preserve the neutral genetic diversity of Quercus ilex L. irrespective of glacial refugia

Quercus ilex L. (holm oak) is a wind-pollinated, sclerophyllous tree that copes with the environmental variability of the Mediterranean climate and that displays flexible ecophysiological adaptability in relation to hydric and thermic stresses. The holm oak dominates Mediterranean woodlands on both acidic and calcareous soils and has been exposed to management (dehesas) for thousands of years. Both protected areas and glacial refugia are supposed to preserve a substantial fraction of the genetic diversity of Iberian species. Genetic diversity was examined for 68 populations sampled throughout Spain using ptDNA SNPs, ptDNA microsatellites, and primarily nuclear AFLPs. Protected populations did not significantly differ from nonprotected populations by any of the measures of levels of genetic diversity. The three-level hierarchical AMOVA indicated that a low number of protected populations harbor most of the species’ genetic diversity. In addition, we found no evidence from either ptDNA or AFLP variation to support that populations from putative glacial refugia are divergent genetic groups as expected during isolation. Outcrossing, anemophilous long-distance pollen dispersal, acorn transport by animals, tree reliance, and habitat availability in Spain probably played a primarily role in homogenizing allele frequency among populations. This result leads us to suggest that extensive gene flow has been prevalent across Spanish populations. We conclude that glacial refugia have not been essential to maintain the neutral genetic makeup of Q. ilex. Nevertheless, conservation of the holm oak in protected areas ensures protection of the species’ genetic diversity, the most widespread woodland ecosystem in Iberia and indirectly the four iconic, endangered animal species (black stork, cinereous vulture, Iberian lynx, western imperial eagle).

Genetic Differentiation among Nigerian Indigenous Goat Populations

A total of 200 goats and 25 microsatellite markers proposed by the Food and Agricultural Organization and the International Society for Animal Genetics (FAO-ISAG) were used to determine the genetic diversity of three breeds of the Nigerian indigenous goats, namely Sahel (60), Red Sokoto (60), West African Dwarf (60) and one strain; Kano Brown (20). Genetic differentiation between the breeds and strain ranged from 0.011 to 0.037, and the least genetically differentiated populations were Kano Brown and Red Sokoto. Molecular variations were observed to be higher within populations (96%) than among populations (4%), which suggest higher heterozygosity within populations. This study showed that the Nigerian goats are admixed due to extensive cross-breeding and high gene flow amongst the breeds, and that the goats are geographically distributed in two major locations. Measures to conserve the uniqueness/distinctiveness of the Nigerian goat breeds should be sought, and gene flow between populations should be controlled by adopting effective breeding and management practices.

Development and characterization of 10 microsatellite markers in the Cape horseshoe bat, Rhinolophus capensis (Chiroptera, Rhinolophidae) and cross-amplification in southern African Rhinolophus species.

BackgroundThe Cape horseshoe bat, Rhinolophus capensis, is endemic to the Cape region of South Africa. Coalescent analysis of mitochondrial DNA sequence data suggests extensive historical gene flow between populations despite strong geographic variation of their echolocation call phenotype. Nevertheless the fine-scale genetic structure and evolutionary ecology of R. capensis remains poorly understood. Here we describe the development of 10 novel polymorphic microsatellite loci to investigate of the dispersal ecology of R. capensis and to facilitate taxonomic studies of Rhinolophus species in southern Africa.FindingsWe report 10 microsatellite primer pairs that consistently amplify scorable and polymorphic loci across 12 African rhinolophid species. Initial analysis of two populations of R. capensis from South Africa revealed moderate to high levels of allelic variation with 4–14 alleles per locus and observed heterozygosities of 0.450–0.900. No evidence of linkage disequilibrium was observed and eight of the loci showed no departure from Hardy–Weinberg equilibrium. Cross-species utility of these markers revealed consistently amplifiable polymorphic loci in eleven additional rhinolophid species.ConclusionsThe cross-amplification success of the microsatellites developed here provides a cost-effective set of population genetic marker for the study of rhinolophid evolutionary ecology and conservation in southern Africa.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-015-1465-5) contains supplementary material, which is available to authorized users.

Population Variation in the Life History of a Land Fish, Alticus arnoldorum, and the Effects of Predation and Density.

Life history variation can often reflect differences in age-specific mortality within populations, with the general expectation that reproduction should be shifted away from ages experiencing increased mortality. Investigators of life history in vertebrates frequently focus on the impact of predation, but there is increasing evidence that predation may have unexpected impacts on population density that in turn prompt unexpected changes in life history. There are also other reasons why density might impact life history independently of predation or mortality more generally. We investigated the consequences of predation and density on life history variation among populations of the Pacific leaping blenny, Alticus arnoldorum. This fish from the island of Guam spends its adult life out of the water on rocks in the splash zone, where it is vulnerable to predation and can be expected to be sensitive to changes in population density that impact resource availability. We found populations invested more in reproduction as predation decreased, while growth rate varied primarily in response to population density. These differences in life history among populations are likely plastic given the extensive gene flow among populations revealed by a previous study. The influence of predation and density on life history was unlikely to have operated independently of each other, with predation rate tending to be associated with reduced population densities. Taken together, our results suggest predation and density can have complex influences on life history, and that plastic life history traits could allow populations to persist in new or rapidly changing environments.

High-resolution genetic analysis reveals extensive gene flow within the jellyfishPelagia noctiluca(Scyphozoa) in the North Atlantic and Mediterranean Sea

Despite the importance of gelatinous zooplankton as components of marine ecosystems, both ecologically and socio-economically, relatively little information is known about population persistence or connectivity in jellyfish. In the present study, we employed a combination of nuclear microsatellite markers and sequence data from the mitochondrial cytochrome oxidase I (COI) gene to determine levels and patterns of population genetic structuring in the holoplanktonic jellyfish Pelagia noctiluca across the northeast Atlantic Ocean and Mediterranean Sea. Our results indicate a high degree of connectivity in P. noctiluca, with little evidence of geographical structuring of genetic variation. A small but significant differentiation of Atlantic Ocean and Mediterranean stocks was detected based on the microsatellite data, but no evidence of differentiation was observed with the mtDNA, probably due to the higher power of the microsatellites to detect low levels of genetic structuring. Two clearly distinct groups of genotypes were observed within the mtDNA COI, which probably diverged in the early Pleistocene, but with no evidence of geographical structuring. Palaeodistribution modelling of P. noctiluca at the Last Glacial Maximum (LGM; c. 21 Kya) indicated large areas of suitable habitat south of the species’ current-day distribution, with little reduction in area. The congruent evidence for minimal genetic differentiation from the nuclear microsatellites and the mtDNA, coupled with the results of the palaeodistribution modelling, supports the idea of long-term population stability and connectivity, thus providing key insights into the population dynamics and demography of this important species.

Origins, admixture and founder lineages in European Roma.

The Roma, also known as 'Gypsies', represent the largest and the most widespread ethnic minority of Europe. There is increasing evidence, based on linguistic, anthropological and genetic data, to suggest that they originated from the Indian subcontinent, with subsequent bottlenecks and undetermined gene flow from/to hosting populations during their diaspora. Further support comes from the presence of Indian uniparentally inherited lineages, such as mitochondrial DNA M and Y-chromosome H haplogroups, in a significant number of Roma individuals. However, the limited resolution of most genetic studies so far, together with the restriction of the samples used, have prevented the detection of other non-Indian founder lineages that might have been present in the proto-Roma population. We performed a high-resolution study of the uniparental genomes of 753 Roma and 984 non-Roma hosting European individuals. Roma groups show lower genetic diversity and high heterogeneity compared with non-Roma samples as a result of lower effective population size and extensive drift, consistent with a series of bottlenecks during their diaspora. We found a set of founder lineages, present in the Roma and virtually absent in the non-Roma, for the maternal (H7, J1b3, J1c1, M18, M35b, M5a1, U3, and X2d) and paternal (I-P259, J-M92, and J-M67) genomes. This lineage classification allows us to identify extensive gene flow from non-Roma to Roma groups, whereas the opposite pattern, although not negligible, is substantially lower (up to 6.3%). Finally, the exact haplotype matching analysis of both uniparental lineages consistently points to a Northwestern origin of the proto-Roma population within the Indian subcontinent.

Mitochondrial DNA variations in Korean Apis cerana (Hymenoptera: Apidae) and development of another potential marker

The geographic relationships and biogeography of Apis cerana have been studied extensively, but Korean populations have not been investigated thoroughly. We sequenced the non-coding region between the tRNALeu and COII mitochondrial (mt) genes (herein named NC2) of Korean samples, along with the samples from seven Asian localities (China, Vietnam, and Thailand). Four undiscovered haplotypes were found in Korea and China, respectively. A phylogenetic analysis confirmed that Korean A. cerana belonged to the Mainland Asian group. Dominance of Japan1 haplotype in Mainland Asia including Korea suggests extensive gene flow and a common genetic origin. A newly developed non-coding region between the tRNAMet and tRNAGln mt genes (named NC1) provided nine haplotypes with twice the number of variable positions compared to those in NC2. A NC1-based phylogenetic analysis revealed the presence of two phylogenetic groups in Apis cerana from Korea suggesting two different sources.

A population genetic assessment of coral recovery on highly disturbed reefs of the Keppel Island archipelago in the southern Great Barrier Reef.

Coral reefs surrounding the islands lying close to the coast are unique to the Great Barrier Reef (GBR) in that they are frequently exposed to disturbance events including floods caused by cyclonic rainfall, strong winds and occasional periods of prolonged above-average temperatures during summer. In one such group of islands in the southern GBR, the Keppel Island archipelago, climate-driven disturbances frequently result in major coral mortality. Whilst these island reefs have clearly survived such dramatic disturbances in the past, the consequences of extreme mortality events may include the loss of genetic diversity, and hence adaptive potential, and a reduction in fitness due to inbreeding, especially if new recruitment from external sources is limited. Here we examined the level of isolation of the Keppel Island group as well as patterns of gene flow within the Keppel Islands using 10 microsatellite markers in nine populations of the coral, Acropora millepora. Bayesian cluster analysis and assignment tests indicated gene flow is restricted, but not absent, between the outer and inner Keppel Island groups, and that extensive gene flow exists within each of these island groups. Comparison of the Keppel Island data with results from a previous GBR-wide study that included a single Keppel Island population, confirmed that A. millepora in the Keppel Islands is genetically distinct from populations elsewhere on the GBR, with exception of the nearby inshore High Peak Reef just north of the Keppel Islands. We compared patterns of genetic diversity in the Keppel Island populations with those from other GBR populations and found them to be slightly, but significantly lower, consistent with the archipelago being geographically isolated, but there was no evidence for recent bottlenecks or deviation from mutation-drift equilibrium. A high incidence of private alleles in the Keppel Islands, particularly in the outer islands, supports their relative isolation and contributes to the conservation value of the archipelago. The lack of evidence for genetic erosion, in combination with our observation that the North Keppel Island population samples collected in 2002 and 2008, respectively, exhibited a pairwise genetic distance of zero, supports previous published work indicating that, following bleaching, Acropora corals in the Keppel Islands predominantly recover from regrowth of small amounts of remaining live tissue in apparently dead coral colonies. This is likely supplemented by recruitment of larvae from genetically similar, less disturbed populations at nearby reefs, particularly following extreme flood events.

Discordance between nuclear and mitochondrial DNA analyses of population structure in closely related triplefin fishes (Forsterygion lapillum and F. capito, F. Tripterygiidae) supports speciation with gene flow

Unusually for a marine fish clade, most New Zealand triplefin species display broad, sympatric geographic distributions. Explaining diversification in this species flock therefore requires a detailed understanding of patterns of gene flow. Here, we test the patterns reported in previous studies by examining population structure over a range of spatial scales in Forsterygion lapillum and at regional scales in F. capito using microsatellites. Samples were collected between 2000 and 2009, and between 35°56′S and 46°36′S. The microsatellite findings differ from previous mtDNA results in several key respects. First, there is no support for a genetically distinct population at Banks Peninsula, as was seen with mtDNA. Second, in contrast to mtDNA, the two triplefin species exhibited very similar patterns of population structuring at regional scales (102–103 km), suggesting that year-round spawning only in F. lapillum does not have a significant effect on population connectivity. Third, while there is evidence of isolation by distance in both species, there are no clear phylogeographic breaks, and far less structure is evident than in the mtDNA data. Further, we found a lack of structure over local scales in F. lapillum, suggesting extensive gene flow over tens of kilometres. Our findings suggest a pattern of stepping-stone dispersal and contiguous gene flow, sometimes over large distances, supporting the hypothesis that factors other than geographic isolation, such as ecological speciation with gene flow, have been important in the evolution of this group.

Population genetic study of Plasmodium falciparum parasites pertaining to dhps gene sequence in malaria endemic areas of Assam

Plasmodium falciparum malaria parasite had developed resistance to almost all the currently used antimalarial drugs. The purpose of the study was to come across the genetic distances in P. falciparum dhps gene sequences circulating in Assam. A partial fragment of P. falciparum dhps gene containing major single nucleotide polymorphisms associated with sulphadoxine resistance were amplified and sequenced. Thereafter specific bioinformatics tools like BioEdit v7.0.9, ClustalW in Mega 5, DnaSP version v.5.10.01 etc were used for the analysis. A total of 100 P. falciparum positive cases in different malaria endemic areas of Assam were included for the study. Based upon the mutation analysis, a total of seven different P. falciparum dhps genotypes were observed with five variable sites. Maximum five haplotypes were found in the P. falciparum isolates from Jorhat district of Assam. Four polymorphic sites were observed in the P. falciparum dhps gene sequences in Karbi Anglong, NC Hills, Chirang and Jorhat whereas the isolates from other study areas had three polymorphic sites. A statistically significant positive value of Tajima’s D were observed among the P. falciparum field isolates in Assam indicating that there is an excess of intermediate frequency alleles and can result from population bottlenecks, structure and/or balancing selection. Extensive gene flow took place among the P. falciparum population of Jorhat with Sivasagar, Chirang with Sivasagar and Chirang with Karbi Anglong. However, large genetic differentiation was observed among the P. falciparum isolates of NC Hills with Lakhimpur, Tinsukia, Dibrugarh and Golaghat and also the parasite population of Karbi Anglong with Lakhimpur and Tinsukia signifying little gene flow among the population. This finding has shown that mutant Pfdhps gene associated with sulphadoxine resistance is circulating in Assam. It is believed that, the parasite population may have undergone high level of breeding.