Characterisation of the genetic diversity of <Emphasis Type="Italic">Brucella</Emphasis> by multilocus sequencing

Background  

Brucella species include economically important zoonotic pathogens that can infect a wide range of animals. There are currently six classically recognised species of Brucella although, as yet unnamed, isolates from various marine mammal species have been reported. In order to investigate genetic relationships within the group and identify potential diagnostic markers we have sequenced multiple genetic loci from a large sample of Brucella isolates representing the known diversity of the genus.     

Congruent phylogeographic patterns in a young radiation of live‐bearing marine snakes: Pleistocene vicariance and the conservation implications of cryptic genetic diversity

Aim

To investigate phylogeographic patterns among and within co‐occurring sea snake species from Australia's endemic viviparous Aipysurus lineage, which includes critically endangered species, and evaluate the conservation implications of geographically structured patterns of genetic divergence and diversity.

Location

Australia's tropical shallow water marine environments spanning four regions: Great Barrier Reef (GBR), Gulf of Carpentaria (GoC), Timor Sea (TS) and coastal WA (WAC).

Methods

Samples from >550 snakes representing all nine nominal Aipysurus group species were obtained from throughout their known Australian ranges. Coalescent phylogenetic analyses and Bayesian molecular dating of mitochondrial DNA, combined with Bayesian and traditional population genetic analyses of 11 microsatellite loci, were used to evaluate genetic divergence and diversity.

Results

Mitochondrial DNA revealed highly congruent phylogeographic breaks among co‐occurring species, largely supported by nuclear microsatellites. For each species, each region was characterized by a unique suite of haplotypes (phylogroups). Divergences between the TS, GoC and/or GBR were invariably shallow and dated as occurring 50,000–130,000 years ago, coinciding with the cyclic Pleistocene emergence of the Torres Strait land bridge. By contrast, sea snakes from coastal WA were consistently highly divergent from other regions and dated as diverging 178,000–526,000 years ago, which was not associated with any known vicariant events.

Main Conclusions

Previously unappreciated highly divergent sea snake lineages in coastal WA potentially represent cryptic species, highlighting this region as a high‐priority area for conservation. The cyclic emergence of the Torres Strait land bridge is consisted with observed divergences between the TS, GoC and/or GBR; however, processes involved in the earlier divergences involving the WAC remain to be determined. The observed strong population genetic structures (as surrogates for dispersal) indicate that sea snakes have limited potential to reverse population declines via replenishment from other sources over time frames relevant to conservation.

     

Construction of nested genetic core collections to optimize the exploitation of natural diversity in <Emphasis Type="Italic">Vitis vinifera</Emphasis> L. subsp. <Emphasis Type="Italic">sativa</Emphasis>

Background  

The first high quality draft of the grape genome sequence has just been published. This is a critical step in accessing all the genes of this species and increases the chances of exploiting the natural genetic diversity through association genetics. However, our basic knowledge of the extent of allelic variation within the species is still not sufficient. Towards this goal, we constructed nested genetic core collections (G-cores) to capture the simple sequence repeat (SSR) diversity of the grape cultivated compartment (Vitis vinifera L. subsp. sativa) from the world's largest germplasm collection (Domaine de Vassal, INRA Hérault, France), containing 2262 unique genotypes.     

Adaptation and diversity along an altitudinal gradient in Ethiopian barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L.) landraces revealed by molecular analysis

Background  

Among the cereal crops, barley is the species with the greatest adaptability to a wide range of environments. To determine the level and structure of genetic diversity in barley (Hordeum vulgare L.) landraces from the central highlands of Ethiopia, we have examined the molecular variation at seven nuclear microsatellite loci.     

Comparative phylogeography of two co‐distributed but ecologically distinct rainbowfishes of far‐northern Australia

Aim

To test the influence of historical and contemporary environment in shaping the genetic diversity of freshwater fauna we contrast genetic structure in two co‐distributed, but ecologically distinct, rainbowfish; a habitat generalist (Melanotaenia splendida) and a habitat specialist (M. trifasciata).

Location

Fishes were sampled from far northern Australia (Queensland and Northern Territory).

Methods

We used sequence data from one mitochondrial gene and one nuclear gene to investigate patterns of genetic diversity in M. splendida and M. trifasciata to determine how differences in habitat preference and historical changes in drainage boundaries affected patterns of connectivity.

Results

Melanotaenia splendida showed high levels of genetic diversity and little population structure across its range. In contrast, M. trifasciata showed high levels of population structure. Whereas phylogeographic patterns differed, both species showed a strong relationship between geographical distance and genetic differentiation between populations. Melanotaenia splendida showed a shallower relationship with geographical distance, and genetic differentiation was best explained by stream length and a lower scaled ocean distance (11.98 times coast length). For M. trifasciata, genetic differentiation was best explained by overwater distance between catchments and ocean distance scaled at 1.16 × 10⁶ times coast length.

Main conclusions

Connectivity of freshwater populations inhabiting regions periodically interconnected during glacial periods appears to have been affected by ecological differences between species. Species‐specific differences are epitomized here by the contrast between co‐distributed congeners with different habitat requirements: for the habitat generalist, M. splendida, there was evidence for greater historical genetic connectivity with oceans as a weaker barrier to gene exchange in contrast with the habitat specialist, M. trifasciata.     

Phylogeography and sexual macrocyst formation in the social amoeba <Emphasis Type="Italic">Dictyostelium giganteum</Emphasis>

Background  

Microorganisms are ubiquitous, yet we are only beginning to understand their diversity and population structure. Social amoebae (Dictyostelia) are a diverse group of unicellular eukaryotic microbes that display a unique social behaviour upon starvation in which cells congregate and then some die to help others survive and disperse. The genetic relationships among co-occurring cells have a major influence on the evolution of social traits and recent population genetic analysis found extensive genetic variation and possible cryptic speciation in one dictyostelid species (Dictyostelium purpureum). To further characterize the interplay among genetic variation, species boundaries, social behaviour, and reproductive isolation in the Dictyostelia, we conducted phylogenetic analyses and mating experiments with the geographically widespread social amoeba Dictyostelium giganteum.     

Identification and characterization of bovine regulator of telomere length elongation helicase gene (<Emphasis Type="Italic">RTEL</Emphasis>): molecular cloning,expression distribution,splice variants and DNA methylation profile

Background  

The genetic basis of telomere length heterogeneity among mammalian species is still not well understood. Recently, a gene named regulator of telomere length elongation helicase (RTEL) was identified and predicted to be an essential participant in species-specific telomere length regulation in two murine species. To obtain broader insights into its structure and biological functions and to ascertain whether RTEL is also a candidate gene in the regulation of telomere length diversity in other mammalian species, data from other mammals may be helpful.     

Genetic diversity and colony structure of Tapinoma melanocephalum on the islands and mainland of South China

Aim

Tapinoma melanocephalum is listed as one of the most important invasive pest species in China. Information regarding the patterns of invasion and effects of geographic isolation on the population genetics of this species is largely lacking.

Location

South China.

Methods

To address this problem, we genotyped 39 colonies (two colonies were collapsed due to genetic similarity) using microsatellite markers and mitochondrial DNA sequencing to compare colony genetic structure of T. melanocephalum on the mainland and islands of South China.

Results

An analysis of the colony genotypes showed that the genetic diversity of the mainland population was slightly higher than that of the island populations but not significantly so. However, the observed heterozygosity on Shangchuan Island (SCD) was significantly lower than that of the other colonies. We also found six haplotypes in 111 mitochondrial DNA COI sequences. The relatedness (r) value between colonies of SCD was 0.410, higher than that of the other populations. The genetic clusters among colonies were not related to geographic locations and exhibited admixture likely due to frequent human‐mediated dispersal associated with trade between the mainland population and the islands. Pairwise F_STs between populations showed differentiation among mainland populations, while SCD displayed high levels of divergence (F_ST > 0.15) from most mainland populations. There was no significant isolation by distance among colonies. Most populations showed signs of a bottleneck effect.

Main conclusions

Our study suggests that there was no significant difference in the genetic diversity among the islands and the mainland; however, the lower genetic diversity, the higher degree of genetic divergence from other colonies, and the higher relatedness among nestmates made the SCD population stand out from all the others.     

Comparative phylogeography of two related plant species with overlapping ranges in Europe, and the potential effects of climate change on their intraspecific genetic diversity

Background  

The aim of the present study was to use a combined phylogeographic and species distribution modelling approach to compare the glacial histories of two plant species with overlapping distributions, Orthilia secunda (one-sided wintergreen) and Monotropa hypopitys (yellow bird's nest). Phylogeographic analysis was carried out to determine the distribution of genetic variation across the range of each species and to test whether both correspond to the "classic" model of high diversity in the south, with decreasing diversity at higher latitudes, or whether the cold-adapted O. secunda might retain more genetic variation in northern populations. In addition, projected species distributions based on a future climate scenario were modelled to assess how changes in the species ranges might impact on total intraspecific diversity in both cases.     

Unexpected species diversity of Malagasy primates (<Emphasis Type="Italic">Lepilemur</Emphasis> spp.) in the same biogeographical zone: a morphological and molecular approach with the description of two new species

Background  

The lemurs of Madagascar provide an excellent mammalian radiation to explore mechanisms and processes favouring species diversity and evolution. Species diversity, in particular of nocturnal species, increased considerably during the last decade. However, the factors contributing to this high diversity are not well understood. We tested predictions derived from two existing biogeographic models by exploring the genetic and morphological divergence among populations of a widely distributed lemur genus, the sportive lemur (Lepilemur ssp.) along a 560 km long transect from western to northern Madagascar.     

Construction of a consensus linkage map for red clover (Trifolium pratense L.)

Background  

Red clover (Trifolium pratense L.) is a major forage legume that has a strong self-incompatibility system and exhibits high genetic diversity within populations. For several crop species, integrated consensus linkage maps that combine information from multiple mapping populations have been developed. For red clover, three genetic linkage maps have been published, but the information in these existing maps has not been integrated.     

<Emphasis Type="Italic">Helicobacter pylori</Emphasis> genome variability in a framework of familial transmission

Background  

Helicobacter pylori infection is exceptionally prevalent and is considered to be acquired primarily early in life through person-to-person transmission within the family. H. pylori is a genetically diverse bacterial species, which may facilitate adaptation to new hosts and persistence for decades. The present study aimed to explore the genetic diversity of clonal isolates from a mother and her three children in order to shed light on H. pylori transmission and host adaptation.     

Microsatellite analysis of the natterjack toad (Bufo calamita) in Denmark: populations are islands in a fragmented landscape

The European natterjack toad (Bufo calamita) has declined rapidly in recent years, primarily due to loss of habitat, and in Denmark it is estimated that 50% of the isolated populations are lost each decade. To efficiently manage and conserve this species and its genetic diversity, knowledge of the genetic structure is crucial. Based on nine polymorphic microsatellite loci, the genetic diversity, genetic structure and gene flow were investigated at 12 sites representing 5–10% of the natterjack toad localities presently known in Denmark. The expected heterozygosity (H _E) within each locality was generally low (range: 0.18–0.43). Further analyses failed to significantly correlate genetic diversity with population size, degree of isolation and increasing northern latitude, indicating a more complex combination of factors in determining the present genetic profile. Genetic differentiation was high (overall θ = 0.29) and analyses based on a Bayesian clustering method revealed that the dataset constituted 11 genetic clusters, defining nearly all sampling sites as distinct populations. Contemporary gene flow among populations was undetectable in nearly all cases, and the failure to detect a pattern of isolation by distance within major regions supported this apparent lack of a gene flow continuum. Indications of a genetic bottleneck were found in three populations. The analyses suggest that the remaining Bufo calamita populations in Denmark are genetically isolated, and represent independent units in a highly fragmented gene pool. Future conservation management of this species is discussed in light of these results. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Rapid linkage disequilibrium decay in the <Emphasis Type="Italic">Lr10</Emphasis> gene in wild emmer wheat (<Emphasis Type="Italic">Triticum dicoccoides</Emphasis>) populations

Introduction  

Recombination is a key evolutionary factor enhancing diversity. However, the effect of recombination on diversity in inbreeding species is expected to be low. To estimate this effect, recombination and diversity patterns of Lr10 gene were studied in natural populations of the inbreeder species, wild emmer wheat (Triticum dicoccoides). Wild emmer wheat is the progenitor of most cultivated wheats and it harbors rich genetic resources for disease resistance. Lr10 is a leaf rust resistance gene encoding three domains: a coiled-coil, nucleotide-binding site, and leucine-rich repeat (CC-NBS-LRR).     

Surviving historical Patagonian landscapes and climate: molecular insights from <Emphasis Type="Italic">Galaxias maculatus</Emphasis>

Background  

The dynamic geological and climatic histories of temperate South America have played important roles in shaping the contemporary distributions and genetic diversity of endemic freshwater species. We use mitochondria and nuclear sequence variation to investigate the consequences of mountain barriers and Quaternary glacial cycles for patterns of genetic diversity in the diadromous fish Galaxias maculatus in Patagonia (~300 individuals from 36 locations).     

Genetic diversity and relationships in mulberry (genusMorus) as revealed by RAPD and ISSR marker assays

Background  

The genus Morus, known as mulberry, is a dioecious and cross-pollinating plant that is the sole food for the domesticated silkworm, Bombyx mori. Traditional methods using morphological traits for classification are largely unsuccessful in establishing the diversity and relationships among different mulberry species because of environmental influence on traits of interest. As a more robust alternative, PCR based marker assays including RAPD and ISSR were employed to study the genetic diversity and interrelationships among twelve domesticated and three wild mulberry species.     

Genetic diversity of Ophiocordyceps sinensis, a medicinal fungus endemic to the Tibetan Plateau: Implications for its evolution and conservation

Background  

Ophiocordyceps sinensis (syn. Cordyceps sinensis), endemic to alpine regions on the Tibetan plateau, is one of the most valuable medicinal fungi in the world. Huge commercial demand has led to excessive harvest and a dramatic decline in its numbers. The diversity of terrains and climates on the Tibetan Plateau and the broad insect host range (more than 50 species in the family Hepialidae) may have resulted in substantial intraspecific genetic diversity for this fungus. The objective of this study was to evaluate the population distribution of O. sinensis from geographically diverse regions of the Tibetan Plateau based on nrDNA ITS and MAT1-2-1 gene sequences. Understanding of the genetic diversity and genesis of O. sinensis will provide important information for the evolution and conservation of this fungus.     

Global isolation by distance despite strong regional phylogeography in a small metazoan

Background  

Small vagile eukaryotic organisms, which comprise a large proportion of the Earth's biodiversity, have traditionally been thought to lack the extent of population structuring and geographic speciation observed in larger taxa. Here we investigate the patterns of genetic diversity, amongst populations of the salt lake microscopic metazoan Brachionus plicatilis s. s. (sensu stricto) (Rotifera: Monogononta) on a global scale. We examine the phylogenetic relationships of geographic isolates from four continents using a 603 bp fragment of the mitochondrial COI gene to investigate patterns of phylogeographic subdivision in this species. In addition we investigate the relationship between genetic and geographic distances on a global scale to try and reconcile the paradox between the high vagility of this species and the previously reported patterns of restricted gene flow, even over local spatial scales.     

Pleistocene glacial cycle effects on the phylogeography of the Chinese endemic bat species, <Emphasis Type="Italic">Myotis davidii</Emphasis>

Background  

Global climatic oscillations, glaciation cycles and the unique geographic topology of China have profoundly influenced species population distributions. In most species, contemporary distributions of populations cannot be fully understood, except in a historical context. Complex patterns of Pleistocene glaciations, as well as other physiographic changes have influenced the distribution of bat species in China. Until this study, there had been no phylogeographical research on Myotis davidii, an endemic Chinese bat. We used a combination of nuclear and mitochondrial DNA markers to investigate genetic diversity, population structure, and the demographic history of M. davidii. In particular, we compared patterns of genetic variation to glacial oscillations, topography, and environmental variation during the Pleistocene in an effort to explain current distributions in light of these historical processes.