Search

Climatic changes during the Pleistocene were responsible for dramatic redistributions of plant species worldwide. On the rugged southern hemisphere island of Tasmania, temperature increases following the last glaciation saw upslope migration of climatically suitable species from lowland refugia and the expansion of eucalypt-dominated forests and woodlands in the Central Highlands. We integrate multiple lines of evidence (chloroplast and nuclear DNA markers, seedling morphology, and survival in common garden experiments) from a group of closely related endemic eucalypts (the alpine white gums) to argue that (i) the Central Highlands of the island were colonised by multiple glacial refugia with hybridisation among species and previously separated populations, and (ii) natural selection has filtered the admixed populations, resulting in local adaptation to the harsh sub-alpine environment. Chloroplast haplotype diversity decreased and nuclear microsatellite diversity increased with altitude, chloroplast sharing among taxa was common, and nuclear DNA differentiation of morphologically distinct taxa was lower in the Central Highlands compared with lowland regions. Local adaptation in the highlands was signalled by evidence from (i) a glasshouse trial in which directional selection (QST > FST) had shaped seedling morphological trait variation and (ii) population survival differences in 35-year-old reciprocal plantings along the major environmental gradients. We conclude that the evolutionary response of these island endemic trees to past climate change has involved the interplay of both hybridisation and natural selection, highlighting the importance of maintaining species interactions under future climate change. [ABSTRACT FROM AUTHOR]

The water hyacinth grasshopper Cornops aquaticum (Bruner 1906) constitutes an appropriate model to assess phenotypic and karyotypic variability in the context of differentiation and adaptation of insect populations because it occurs over a wide latitudinal range. This study represents a general analysis of phenotype, karyotype and molecular variation in native populations of C. aquaticum in South America. This is also relevant because this insect is considered a promising biological control agent of water hyacinth, a native South American aquatic plant but a pest in South Africa. Along Paraná and Uruguay River Basins, body size correlated negatively with latitude, and positively so with temperature and rainfall in both sexes. To test whether the chromosomal and phenotypic patterns were adaptive, we compared them with neutral microsatellite loci variation in populations from the medium and lower course of the Paraná River. Firstly, the lack of pairwise association between karyotype and phenotype distance matrixes with that of neutral loci suggested non-neutrality. Secondly, phenotypic differentiation for all morphometric traits (PST) was significantly larger than molecular differentiation (FST), indicating a prevailing divergence selection effect on the observed phenotypic patterns. Finally, the phenotypic and genotypic spatial structures – inferred from Bayesian approaches – were discordant: neutral genetic structure clustered together most populations except for the two southernmost, downstream ones, whereas phenotypic spatial structure groups together all the deltaic populations and singles out the two northernmost ones. The results suggest directional selection leading to higher centric fusion frequencies in the downstream populations and favouring morphometric optimal differences in relation to the environment. [ABSTRACT FROM AUTHOR]

• Ottelia acuminata var. jingxiensis is confined to several Karst rivers. • Genetic connectivity and genetic variation were assessed based on 11 microsatellites. • Both water flow and zoochory (or mankind) were major contributors for gene exchange. • Recent habitat fragmentation resulted in decreased gene flow. • Separate conservation among rivers and watercourse dredging were suggested. Dispersal is a key evolutionary force affecting gene flow and genetic diversity. Therefore, analysis of population connectivity plays an important role in protecting endangered species. Ottelia acuminata var. jingxiensis is a perennial endangered aquatic plant, and present in several karst rivers of Yunnan–Guizhou Plateau. We estimated the genetic variation and population connectivity by nuclear microsatellites in 11 populations mainly from three rivers. The plant showed low genetic diversity (H E = 0.205–0.367), which was mainly explained by its critically restricted geographical range. Meanwhile, relatively low genetic differentiation (F ST = 0.186; G" ST = 0.242) was found compared with that of other studies about varieties of O. acuminata in isolated habitats. Cluster analyses based on different approaches consistently showed populations from the same river clustered together, suggesting water flow acting as corridors for dispersal; additionally, bidirectional gene flows within and among rivers indicated that zoochory or mankind were also major contributors to gene exchange. The results showed that contemporary gene flow was much lower than historical gene flow, suggesting that recent habitat fragmentation resulted in decreased gene flow. We recommend watercourse dredging within rivers to enhance habitat stability and to improve connectivity among populations. In addition, the different populations from different rivers or isolated habitats should be protected to maintain the genetic diversity. [ABSTRACT FROM AUTHOR]

Spatial genetic variation of river-dwelling freshwater fishes is typically affected by the historical and contemporary river landscape as well as life-history traits. Tropical river and stream landscapes have endured extended geological change, shaping the existing pattern of genetic diversity, but were not directly affected by glaciation. Thus, spatial genetic variation of tropical fish populations should look very different from the pattern observed in temperate fish populations. These data are becoming important for designing appropriate management and conservation plans, as these aquatic systems are undergoing intense development and exploitation. This study evaluated the effects of landscape features on population genetic diversity of Garra cambodgiensis, a stream cyprinid, in eight tributary streams in the upper Nan River drainage basin (n = 30–100 individuals/location), Nan Province, Thailand. These populations are under intense fishing pressure from local communities. Based on 11 microsatellite loci, we detected moderate genetic diversity within eight population samples (average number of alleles per locus = 10.99 ± 3.00; allelic richness = 10.12 ± 2.44). Allelic richness within samples and stream order of the sampling location were negatively correlated (P

The population genetics of two seagrasses, Syringodium isoetifolium and Thalassia hemprichii were assessed throughout the Indonesian Archipelago. We genotyped 257 blades of S. isoetifolium at 15 microsatellite loci collected from 14 sampling sites and 406 blades of T. hemprichii at 17 microsatellite loci from 16 sampling sites. Once clones were removed, 165 individuals of S. isoetifolium and 389 of T. hemprichii were used in downstream analyses. Bayesian clustering methods revealed two genetically distinguishable clusters in each species, although the geographic boundaries of these clusters differed. Syringodium isoetifolium has a cluster that is located exclusively on the shallow Sunda Shelf and appears to follow the demarcation defined by Wallace's line. Thalassia hemprichii, however, has a genetically distinguishable cluster located within the Banda Sea. The Banda Sea has unique physical oceanographic conditions, which may be driving the observed differentiation in T. hemprichii. We speculate that historical sea level changes exposing the Sunda Shelf, and the unique oceanographic conditions of the Banda Sea are contributing to the observed population differentiation. The observed genetic differentiation in both species is a possible starting point for speciation. [ABSTRACT FROM AUTHOR]

Abstract: The loss of variability in farmed populations and the risks of interactions with wild populations support the need for the genetic monitoring of species farmed throughout the world. In Brazil, the tambaqui is the most widely farmed native fish species. Despite this, there are no data on the pedigree of the farmed stocks, and the potential for interactions with wild populations in the Amazon basin has raised concerns with regard to the genetic variability of these stocks. The present study analysed sequences of the mitochondrial Control Region and 12 microsatellites to characterize the genetic variability of seven historically important commercial tambaqui breeding centres located in four different regions of Brazil, and compared these sequences with those obtained from individuals collected from a wild population. High levels of genetic diversity were found in the wild population, whereas genetic diversity was reduced in both markers in most captive populations, except for the broodstock located near the Amazon River. High FST and DEST indices were recorded between the wild population and most of the captive stocks analysed. The drastic reduction in genetic diversity found in most captive stocks and the difference between these stocks and the wild population may have been the result of the small size of the founding populations and the absence of breeding management. The renewal of the broodstocks and the application of breeding management techniques are recommended. In the Amazon region, in addition, the use of broodstocks that are genetically very different from local wild populations should be avoided. [ABSTRACT FROM AUTHOR]

Spatial genetic variation of river-dwelling freshwater fishes is typically affected by the historical and contemporary river landscape as well as life-history traits. Tropical river and stream landscapes have endured extended geological change, shaping the existing pattern of genetic diversity, but were not directly affected by glaciation. Thus, spatial genetic variation of tropical fish populations should look very different from the pattern observed in temperate fish populations. These data are becoming important for designing appropriate management and conservation plans, as these aquatic systems are undergoing intense development and exploitation. This study evaluated the effects of landscape features on population genetic diversity of Garra cambodgiensis, a stream cyprinid, in eight tributary streams in the upper Nan River drainage basin (nD30-100 individuals/location), Nan Province, Thailand. These populations are under intense fishing pressure from local communities. Based on 11 microsatellite loci, we detected moderate genetic diversity within eight population samples (average number of alleles per locusD10.993.00; allelic richnessD10.122.44). Allelic richness within samples and stream order of the sampling location were negatively correlated (P < 0:05). We did not detect recent bottleneck events in these populations, but we did detect genetic divergence among populations (Global FST = 0.022, P <0:01). The Bayesian clustering algorithms (TESS and STRUCTURE) suggested that four to five genetic clusters roughly coincide with sub-basins: (1) headwater streams/main stem of the Nan River, (2) a middle tributary, (3) a southeastern tributary and (4) a southwestern tributary. We observed positive correlation between geographic distance and linearized FST (P < 0:05), and the genetic differentiation pattern can be moderately explained by the contemporary stream network (STREAMTREE analysis, R2 = 0.75). The MEMGENE analysis suggested genetic division between northern (genetic clusters 1 and 2) and southern (clusters 3 and 4) sub-basins. We observed a high degree of genetic admixture in each location, highlighting the importance of natural flooding patterns and possible genetic impacts of supplementary stocking. Insights obtained from this research advance our knowledge of the complexity of a tropical stream system, and guide current conservation and restoration efforts for this species in Thailand. [ABSTRACT FROM AUTHOR]

Seven microsatellite markers were used to investigate the population structure of the offshore ecotype of the European anchovy (Engraulis encrasicolus) by comparing 12 marine samples collected off the Moroccan coast with an inshore sample taken as a reference for the lagoonal ecotype.F-statistics, correspondence analysis and Bayesian assignment all concurred to cluster the European anchovy in this region into three groups: (i) one reference lagoonal sample, (ii) samples north of the 25°N latitude and (iii) samples south of it. Moreover, the Bayesian cluster analysis pointed toward the existence of an admixture between the group north of 25°N and the lagoonal ecotype, while this was not detectable with the group south of 25°N. Differential introgression between the two ecotypes could be one of the plausible explanations for the observed genetic structure and reveals the possible existence of a phylogeographic break around the 25th parallel North. Our study illustrates the fact that, for those species that encompass several incompletely isolated ecotypes, the level of gene flow among them may vary in space and serve as a tool for stock identification. This information may be useful to improve fishery management of this important harvested species along the Moroccan coast. [ABSTRACT FROM AUTHOR]

Allohexaploid wheat was derived from interspecific hybridization, followed by spontaneous chromosome doubling. Newly synthesized hexaploid wheat by crossing Triticum turgidum and Aegilops tauschii provides a classical model to understand the mechanisms of allohexaploidization in wheat. However, immediate chromosome level variation and microsatellite level variation of newly synthesized hexaploid wheat have been rarely reported. Here, unreduced gametes were applied to develop synthesized hexaploid wheat, NA0928, population by crossing T. turgidum ssp. dicoccum MY3478 and Ae. tauschii SY41, and further S0-S3 generations of NA0928 were assayed by sequential cytological and microsatellite techniques. We demonstrated that plentiful chromosomal structural changes and microsatellite variations emerged in the early generations of newly synthesized hexaploid wheat population NA0928, including aneuploidy with whole-chromosome loss or gain, aneuploidy with telosome formation, chromosome-specific repeated sequence elimination (indicated by fluorescence in situ hybridization) and microsatellite sequence elimination (indicated by sequencing), and many kinds of variations have not been previously reported. Additionally, we reported a new germplasm, T. turgidum accession MY3478 with excellent unreduced gametes trait, and then succeeded to transfer powdery mildew resistance from Ae. tauschii SY41 to synthesized allohexaploid wheat population NA0928, which would be valuable resistance resources for wheat improvement. [ABSTRACT FROM AUTHOR]

The past studies of postglacial recolonization patterns in high latitude regions have revealed a significant role of dispersal capacity in shaping the genetic diversity and population structure of temperate trees. However, most of these studies have focused on species with long-distance dispersal followed by exponential population growth and were therefore unable to reveal the patterns in the case of a gradual expansion. Here we studied the impacts of postglacial range expansions on the distribution of genetic diversity in the Manchurian walnut ( Juglans mandshurica ), a common tree of East Asian cool-temperate deciduous forests that apparently lacks long-distance seed dispersal ability. The genetic diversity and structure of 19 natural walnut populations in Northeast China and the Korean Peninsula were examined using 17 nuclear simple sequence repeat (SSR) loci. Potential habitats under current and past climatic conditions were predicted using the ecological niche modelling (ENM) method. Bayesian clustering analysis revealed three groups, which were inferred to have diverged through multiple glacial-interglacial cycles in multiple refugia during the Quaternary Period. ENM estimated a southward range shift at the LGM, but high suitability scores still occurred in the western parts of the Changbai Mountains (Northeast China), the Korean peninsula and the exposed seafloor of the Yellow Sea. In contrast to most other cool-temperate trees co-occurring in the same region, the Manchurian walnut did not show any evidence of a population bottleneck, loss of genetic diversity or isolation by distance during the postglacial expansion. Our study clearly indicates that current northern populations originated from one glacial lineage and recolonization via a gradually advancing front due to the lack of a long-distance seed dispersal mechanism led to no latitudinal decrease in genetic diversity. [ABSTRACT FROM AUTHOR]

After more than 20 years of hatchery production of Asian seabass in Thailand, genetic information is still lacking for effective genetic management and a selective breeding programme. This study aimed to evaluate genetic status of existing hatchery populations and genetic consequences of a selective breeding attempt. We examined genetic relatedness in seven hatchery samples, including a selectively bred population ( RACF-F1), compared with three wild samples using 11 microsatellite loci. Genetic diversity and relatedness values within most hatchery samples, except for RACF-F1, did not differ from those of wild populations ( P > 0.05). RACF-F1 had the lowest allelic diversity and effective population size ( Ar = 6.99; Ne = 7.8) and highest relatedness values (mean r xy = 0.075-0.204). Pairwise ΦST values, principal component analysis and model-based cluster analyses revealed three genetically distinct hatchery groups: Eastern Thailand ( CHN, RACF, NSCF and SKCF), Southern Thailand ( NICA) and the Andaman Sea ( STCF). Results suggest that exiting domestic populations capture reasonable amount of genetic variation and can be useful for a base population for genetic improvement programmes. In addition, given the rapid increase in relatedness that we observed in one selectively bred population, we recommend using selection methods and hatchery practices that reduce variability in family contribution in the subsequent generations. [ABSTRACT FROM AUTHOR]

Donkey domestication drastically changed ancient transport systems in Africa and Asia, enabling overland circulation of people and goods and influencing the organization of early cities and pastoral societies. Genetic studies based on mt DNA have pointed to the African wild ass as the most probable ancestor of the domestic donkey, but questions regarding its center of origin remain unanswered. Endeavoring to pinpoint the geographical origin of domestic donkey, we assessed levels and patterns of genetic diversity at 15 microsatellite loci from eight populations, representing its three hypothesized centers of origin: northeast Africa, the Near East and the Arabian Peninsula. Additionally, we compared the donkey genotypes with those from their wild relative, the African wild ass ( Equus africanus somaliensis) to visualize patterns of differentiation among wild and domestic individuals. Obtained results revealed limited variation in levels of unbiased expected heterozygosity across populations in studied geographic regions (ranging from 0.637 in northeast Africa to 0.679 in the Near East). Both allelic richness (Ar) and private allelic richness presented considerably higher values in northeast Africa and in the Arabian Peninsula. By looking at variation at the country level, for each region, we were able to identify Sudan and Yemen as the countries possessing higher allelic richness and, cumulatively, Yemen also presented higher values for private allelic richness. Our results support previously proposed northeast Africa as a putative center of origin, but the high levels of unique diversity in Yemen opens the possibility of considering this region as yet another center of origin for this species. [ABSTRACT FROM AUTHOR]

Despite numerous studies on the taxonomy of a highly complex group of schizothoracine (snow trouts), with over five recognized species from Kashmir, India ( Schizothorax niger, Schizothorax esocinus, Schizothorax plagiostomus, Schizothorax curvifrons and Schizothorax labiatus) based on traditional morphological data, the relationships between these species is poorly understood and the taxonomic validity is still under debate. To resolve the evolutionary relationships among these species, we sequenced mitochondrial fragments, including 16Sr RNA, Cytb and the D-loop. Separate analyses of 16S and Cytb showed intermixing of the species and 16S was found more conserved than Cytb. The D-loop was found highly variable and showed length variation between and within species. Length variation was observed in di-nucleotide (TA) microsatellite repeats with a variable number of repeat units ( n = 7-14) that did not show heteroplasmy. Central conserved sequence blocks (CSBs) in D-loop sequences were found comparable to other vertebrate species. All phylogenetic reconstructions recovered the focal taxa as a monophyletic clade within the schizothoracines. Analyses with combined mitochondrial data sets showed close genetic relationships of all the five species. In addition to a close relationship between S. niger and S. curvifrons, two distinct groupings of S. ecoscinus and S. plagiostomus were supported by all the analyses. This study gives an insight into molecular phylogeny of the species and improves our understanding of historical and taxonomic relationships derived from morphological and ecological studies. [ABSTRACT FROM AUTHOR]

Genomic instability at microsatellite loci is a hallmark of many cancers, including breast cancer. However, much of the genomic variation and many of the hereditary components responsible for breast cancer remain undetected. We hypothesized that variation at microsatellites could provide additional genomic markers for breast cancer risk assessment. A total of 1,345 germline and tumor DNA samples from individuals diagnosed with breast cancer, exome sequenced as part of The Cancer Genome Atlas, were analyzed for microsatellite variation. The comparison group for our analysis, representing healthy individuals, consisted of 249 females which were exome sequenced as part of the 1,000 Genomes Project. We applied our microsatellite-based genotyping pipeline to identify 55 microsatellite loci that can distinguish between the germline of individuals diagnosed with breast cancer and healthy individuals with a sensitivity of 88.4 % and a specificity of 77.1 %. Further, we identified additional microsatellite loci that are potentially useful for distinguishing between breast cancer subtypes, revealing a possible fifth subtype. These findings are of clinical interest as possible risk diagnostics and reveal genes that may be of potential therapeutic value, including genes previously not associated with breast cancer. [ABSTRACT FROM AUTHOR]

In this study, 64 498 ESTs of Melampsora spp. was assembled into 1 998 contigs, and 604 SSR loci were detected on these contigs, with 736.6 bp containing one SSR on average. Among these SSRs, trinucleotide repeats were the most abundant repeats (44.70% ). As for the composition of microsatellites, AC and AT repeats were the richest motif in dinucleotide repeats, and AGT and AAG repeats were the most frequent motifs in trinucleotide repeats, whereas ( AAAN)n and (AAAAN)n repeats were dominant in tetranucleotide and pentanucleotide repeats, respectively. All the dominant repeat motifs of different types of SSRs were rich in A and T. In EST sequences of Melampsora spp. genome, microsatellites longer than 20 bp accounted for about 15.07%. It was noticeable that microsatellites were highly rich in the expressed sequences of Melampsora spp. genome, which implied that SSRs played a significant role in triggering the gene mutation in Melampsora spp. genome. A total of 455 SSR primers were designed according to the detected microsatellites using Primer 5.0 and Oligo 6.0, and 30 primer pairs were randomly selected for amplification test. Among these primer pairs, 27 primer pairs succeed in amplification, with a successful rate of 90%. Eight primer pairs generated polymorphic fingerprints in Melampsora spp. collected from different poplar genotypes, accounting for 26.7% of the total primer pairs. The EST-SSR markers developed from Melampsora spp. EST sequences provided important marker resources for studying Melampsora spp. from the aspects of pathogen identification and survey of genetic variation. [ABSTRACT FROM AUTHOR]

Microsatellites are some of the most highly variable repetitive DNA tracts in genomes. Few studies focus on whether the characteristic instability of microsatellites is linked to phenotypic effects in plants. We summarise recent data to investigate how microsatellite variations affect gene expression and hence phenotype. We discuss how the basic characteristics of microsatellites may contribute to phenotypic effects. In summary, microsatellites in plants are universal and highly mutable, they coexist and coevolve with transposable elements, and are under selective pressure. The number of motif nucleotides, the type of motif and transposon activity all contribute to the nonrandom generation and decay of microsatellites, and to conservation and distribution biases. Although microsatellites are generated by accident, they mature through responses to environmental change before final decay. This process is mediated by organism adjustment mechanisms, which maintain a balance between birth versus death and growth versus decay in microsatellites. Close relationships also exist between the physical structure, variation and functionality of microsatellites: in most plant species, sequences containing microsatellites are associated with catalytic activity and binding functions, are expressed in the membrane and organelles, and participate in the developmental and metabolic processes. Microsatellites contribute to genome structure and functional plasticity, and may be considered to promote species evolution in plants in response to environmental changes. In conclusion, the generation, loss, functionality and evolution of microsatellites can be related to plant gene expression and functional alterations. The effect of microsatellites on phenotypic variation may be as significant in plants as it is in animals. Microsatellites (also called simple repeat sequences) are not 'junk' DNA with no function but a 'jewel' in plant genomes. We investigated the regularity of generation, evolution and decay of microsatellites, and the relationships among physical structure, variation and functionality of microsatellites. The phenotypic effects of plant microsatellites will increase our understanding of the functionality of repetitive sequences. [ABSTRACT FROM AUTHOR]

To estimate the genetic variability of two subspecies of cynomolgus monkeys ( Macaca fascicularis fascicularis and M. f. aurea) using microsatellite markers, 26 microsatellite markers were selected from previous reports. Seventeen markers showed high polymorphism in a subset of monkeys and were used for the assessment of genetic diversity in the larger sample. The effective number of alleles, the polymorphism information content (PIC) and the expected heterozygosity of M. f. aurea monkeys were all statistically significantly higher than those of M. f. fascicularis monkeys ( P < 0.05), suggesting the M. f. aurea monkeys had a higher degree of genetic variation than the M. f. fascicularis monkeys. Substantial differences in allele distribution were also detected between the two subspecies of cynomolgus monkeys. Private alleles restricted to the M. f. fascicularis or the M. f. aurea monkeys were found throughout the selected 17 loci. These private alleles may allow the discrimination of the two subspecies of cynomolgus monkeys. The selected markers could also be used to estimate the genetic variation for other subspecies of cynomolgus monkeys. Further work using additional animals obtained from native or independent sources will be important for a more complete understanding of the genetic differences between these two subgroups. Am. J. Primatol. 74:561-568, 2012. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The growing number of grey seals in the Baltic Sea has led to a dramatic increase in interactions between seals and fisheries. The conflict has become such a problem that hunting was introduced in Finland in 1998 and the Swedish Environment Protection Agency recommended a cull of grey seals starting in 2001. Culling has been implemented despite the lack of data on population structure. Low levels of migration between regions would mean that intensive culling in specific geographic areas would have disproportionate effects on local population structure and genetic diversity. We used eight microsatellite loci and a 489 bp section of the mtDNA control region to examine the genetic variability and differentiation between three breeding sites in the Baltic Sea and two in the UK. We found high levels of genetic variability in all sampled Baltic groups for both the microsatellites and the control region. There were highly significant differences in microsatellite allele frequencies between all three Baltic breeding sites and between the Baltic sites and the UK sites. However, there were no significant differences in mtDNA control region haplotypes between the Baltic sites. This genetic substructure of the Baltic grey seal populations should be taken into consideration when managing the seal population to prevent the hunting regime from having an adverse effect on genetic diversity by setting hunting quotas separately for the different subpopulations. [ABSTRACT FROM AUTHOR]

Two hundred years of elephant hunting for ivory, peaking in 1970–1980s, caused local extirpations and massive population declines across Africa. The resulting genetic impacts on surviving populations have not been studied, despite the importance of understanding the evolutionary repercussions of such human-mediated events on this keystone species. Using Bayesian coalescent-based genetic methods to evaluate time-specific changes in effective population size, we analysed genetic variation in 20 highly polymorphic microsatellite loci from 400 elephants inhabiting the greater Samburu-Laikipia region of northern Kenya. This area experienced a decline of between 80% and 90% in the last few decades when ivory harvesting was rampant. The most significant change in effective population size, however, occurred approximately 2500 years ago during a mid–Holocene period of climatic drying in tropical Africa. Contrary to expectations, detailed analyses of four contemporary age-based cohorts showed that the peak poaching epidemic in the 1970s caused detectable temporary genetic impacts, with genetic diversity rebounding as juveniles surviving the poaching era became reproductively mature. This study demonstrates the importance of climatic history in shaping the distribution and genetic history of a keystone species and highlights the utility of coalescent-based demographic approaches in unravelling ancestral demographic events despite a lack of ancient samples. Unique insights into the genetic signature of mid-Holocene climatic change in Africa and effects of recent poaching pressure on elephants are discussed. [ABSTRACT FROM AUTHOR]

To analyze the contribution of the Czech population to the Y-chromosome diversity landscape of Europe and to reconstruct past demographic events, we typed 257 males from five locations for 21 UEPs. Moreover, 141 carriers of the three most common haplogroups were typed for 10 microsatellites and coalescent analyses applied. Sixteen Hg's characterized by derived alleles were identified, the most common being R1a-SRY10831 and P-DYS257*(xR1a). The pool of haplogroups within I-M170 represented the third most common clade. Over-all, the degree of population structure was low. The ages for Hg I-M170, P-DYS257*(xR1a), and R1a-SRY10831 appeared to be comparable and compatible with their presence during or soon after the LGM. A signal of population growth beginning in the first millennium B.C. was detected. Its similarity among the three most common Hg's indicated that growth was characteristic for a gene pool that already contained all of them. The Czech population appears to be influenced, to a very moderate extent, by genetic inputs from outside Europe in the post-Neolithic and historical times. Population growth post-dated the archaeologically documented introduction of Neolithic technology and the estimated central value coincides with a period of repeated changes driven by the development of metal technologies and the associated social and trade organization. [ABSTRACT FROM AUTHOR]

The genetic structure of eulachon ( Thaleichthys pacificus) populations was examined in an analysis of variation of 14 microsatellite loci representing approximately 1900 fish from 9 sites between the Columbia River and Cook Inlet, Alaska. Significant genetic differentiation occurred among the putative populations. The mean FST for all loci was 0.0046, and there was a significant correlation between population genetic differentiation ( FST) and geographic distance. Simulated mixed-stock samples comprising populations from different regions suggested that variation at microsatellite loci provided reasonably accurate estimates of stock composition for potential fishery samples. Marine sampling indicated that immature eulachons from different rivers, during the 2 to 3 years of prespawning life in offshore marine waters, do not mix thoroughly. For eulachons captured incidentally in offshore trawl fisheries, there was a clear geographic cline in relative abundance of eulachons from different geographic areas. The sample from northern British Columbia was dominated by northern and central coastal populations of British Columbia, the sample from central British Columbia was composed of eulachons from all regions, and the sample from southern British Columbia was dominated by Columbia River and Fraser River populations. These results have implications for the management of trawl fisheries and conservation of spawning populations in some rivers where abundance is at historically low levels. [ABSTRACT FROM AUTHOR]

One hundred and ninety three parental lines obtained from 26 countries for an international rice molecular breeding program were evaluated using 101 well-distributed simple sequence repeat (SSR) markers. An overall genetic diversity of 0.68 and an average of 6.3 alleles per locus were revealed, indicating a high level of genetic variation in these lines. Cluster analysis of the 193 accessions showed three major groups and nine subgroups. Group I corresponded to the classical indica subspecies, whereas groups II and III belong to the japonica subspecies. Indica and japonica differentiation accounted for only 6.5% of the total variation in the entire sample and 93.5% was due to within-subspecies diversity. Differentiation among eco-geographic regions accounted for 24% of the diversity within the subspecies. Larger amounts of the eco-geographical differentiation were resolved within japonica than within indica. The largest indica-japonica differentiation based on the single locus level was detected by markers on chromosomes 9 and 12, while the smallest differentiation was detected by markers on chromosomes 4 and 8. Furthermore, genetic differences at the single-locus and two-locus levels, as well as components due to allelic and gametic differentiation, were revealed between indica and japonica and among the main geographic regions. The multilocus analysis in genetic diversity showed a higher proportion of variation caused by predominant non-random associations of different loci within and among the classified subspecies and geographic subdivisions. The results suggest that selection for eco-geographical adaptation on multilocus associations was largely responsible for the maintenance of the extensive variation in the primary gene pool of rice. [ABSTRACT FROM AUTHOR]

The genetic structure of five natural populations of common wild rice Oryza rufipogon Griff. from China, was investigated with 21 microsatellite loci and compared to estimates of genetic diversity and genetic differentiation detected by 22 allozyme loci. Microsatellite loci, as expected, have much higher levels of genetic diversity (mean values of A = 3.1, P = 73.3%, Ho = 0.358 and He = 0.345) than allozyme loci (mean values of A = 1.2, P = 12.7%, Ho = 0.020 and He = 0.030). Genetic differentiation detected by microsatellite loci (FST = 0.468, mean I = 0.472) was higher than that for allozyme loci (FST =0.388, mean I = 0.976). However, microsatellite markers showed less deviation from Hardy-Weinberg expectation (Wright's inbreeding coefficient FIS = –0.069) than do allozymes (FIS = 0.337). These results suggest that microsatellite markers are powerful high-resolution tools for the accurate assessment of important parameters in population biology and conservation genetics of O. rufipogon, and offer advantages over allozyme markers. [ABSTRACT FROM AUTHOR]

Abstract Variation at mitochondrial and microsatellite loci was used to study the breeding and dispersal structure of Glossina morsitans centralis, in six natural populations from Botswana, the Caprivi Strip (Namibia), Zambia, and in a laboratory culture derived from Singida, Tanzania. Only seven mitochondrial haplotypes were found. Mean diversity averaged over the six natural populations was 0.216 ± 0.085. The fixation index FST = 0.866 indicated a high degree of genetic differentiation among populations. Fifty-three alleles were detected among six microsatellite loci and six natural populations. Mean microsatellite diversity was 0.702 ± 0.091. Depending on the estimating model used, fixation indices varied from 0.15 to 0.225 confirming that G. m. centralis populations are strongly subdivided. For all FST estimates, positive correlations were detected between pair-wise genetic distance measures and geographical distances. The difference in fixation indices estimated from mitochondrial or nuclear loci was explained by the greater sensitivity of mitochondrial genomes to genetic drift. Population differentiation can be explained by genetic drift and the subsequent recovery of extant populations from small, discontinuous populations. These data confirm genetically the collapse and retreat of G. m. centralis populations caused by the rinderpest epizootic of the late 19th and early 20th centuries. [ABSTRACT FROM AUTHOR]

Eight highly variable microsatellite loci were used to examine the genetic variability and differentiation of grey seals (Halichoerus grypus) at two widely spaced British breeding colonies. Samples were collected from adults and pups on the island of North Rona, off the north-west coast of Scotland, and on the Isle of May, situated at the mouth of the Firth of Forth on the east coast. Highly significant differences in allele frequencies between these two sites were found for all eight loci, indicating considerable genetic differentiation. Thus, although grey seals are known to range over very large areas outside the breeding season, site fidelity of adults and philopatry of pups for these breeding colonies must be sufficiently common to have effects, through genetic drift, at the sub-population level. Migration rate was estimated using Wright's fixation index (FST), Slatkin's private alleles model and the new statistic, RST, which is analogous to FST but which takes into account the process of microsatellite mutation. An almost 8-fold discrepancy between the values we obtained provides cautionary evidence that microsatellite loci may contravene one or more of the assumptions on which these methods are based. [ABSTRACT FROM AUTHOR]

We describe genetic variation at three microsatellite single loci and six allozyme loci of seven natural Atlantic salmon populations from Ireland and Spain. A comparison of genetic variability detected at both types of loci is performed. Also, the relative value of microsatellite single locus variability with regard to the identification of individual salmon populations is assessed. Microsatellite loci are shown to display higher levels of variation than allozyme loci. Mean number of alleles (6±1.53) and heterozygosity (0.46±0.04) at microsatellite loci are greater than those found for allozymes (1.85±0.05 and 0.21±0.03, respectively), and some microsatellite alleles appear to be specific for a location or geographical area. Allozyme and microsatellite variation show the same pattern of differentiation between populations with Irish and Spanish populations grouped into different clusters. However, greater values of genetic distance were found among microsatellite (D = 0.0747±0.011) rather than among allozyme loci (D = 0.0449±0.008). These results provide evidence that microsatellite-based analysis of genetic variation will be useful in the identification of individual populations of Atlantic salmon. [ABSTRACT FROM AUTHOR]

C57BL/6 laboratory mice usually show black coat color. We observed a dilute (gray) coat color phenotype in progenies of two C57BL/6 mice. This phenotype is inherited in an autosomal recessive mode. To uncover the molecular mechanism underlying this naturally occurring phenotypic variation, we performed whole-genome sequencing (25×) on 10 offspring of the two founder mice. The whole-genome DNA sequencing and additional RNA-Seq data reveal that Myo5a is the gene responsible for the coat color dilution in C57BL/6 mice, and novel mutations in the Myo5a gene are likely causal. We further performed reverse transcription-quantitative PCR, and showed increased expression of truncated Myo5a transcripts encoding dysfunctional proteins and decreased expression of Myo5a full-length transcripts encoding functional proteins in mutant individuals. The decrease in full-length messenger RNA abundance was accompanied by reduced Myo5a protein level and deficient melanosome transport, a potential mechanistic link between the Myo5a mutations and the dilute color phenotype. This study not only advances our understanding of the molecular mechanisms of pigmentation in mice, but also provides a typical case of deciphering the molecular basis of phenotypic variation in mice by genomic analyses and subsequent functional work. [ABSTRACT FROM AUTHOR]

The population genetics of the banded coral shrimp, Stenopus hispidus (Olivier, 1811) from the Indonesian Archipelago were investigated. We genotyped 387 individuals collected from 11 sampling locations throughout Indonesia at 15 microsatellite loci. Bayesian clustering methods revealed evidence of three genetically distinct clusters. F' ST and F ST values are generally low, but significant. This was unexpected given the comparatively small geographic scale over which this survey was performed, approximately 2000km in an East to West orientation, even more so when accounting for the pan tropical distribution and long pelagic larval duration (210 days) of S. hispidus. Factors other than larval dispersal must be promoting population differentiation. In this case, genetic partitions appear to correspond to differing habitat types, possibly allowing selection to augment any oceanographic, geographic or biological barriers to gene flow, the resulting genetic differentiation is a source of evolutionary novelty and could facilitate reproductive isolation ultimately resulting in parapatric speciation. [ABSTRACT FROM AUTHOR]

• By SSRs, gene flow patterns were revealed in Nelumbo nucifera along Yangtze River. • The genetic depauperation and obvious genetic differentiation were found. • Genetic discontinuities were revealed between any adjacent populations. • Abundant historical gene flow and limited recent gene flow were found. Wild populations of Nelumbo nucifera are valuable genetic resources and provide significant ecological functions for aquatic ecosystems. However, they have suffered from habitat fragmentation and degradation. Here, the genetic connectivity and variation of N. nucifera wild populations were analysed based on 22 microsatellite markers and 10 populations along the Yangtze River. Abundant historical gene flows were found among populations (Nm : 1.806–3.735). In contrast, low levels of recent migration rates were revealed and only two migrants were detected in the first generation among populations. The results indicated that habitat deteriorations have resulted in dramatically reduced gene flow, and the seasonal floods failed to act as a valid path for migration. The bidirectional gene flows, combined with the lack of accumulation effects in downstream populations, suggested that both river flow and zoochory (or human activity) contributed to gene exchange. High levels of genetic differentiation were found in all pairs of populations (F ST : 0.208 - 0.666; G" ST : 0.306 - 0.866) and in the global estimate across all populations (F ST = 0.403, G" ST = 0.593), indicating genetic discontinuities among populations. The genetic depauperation (H E = 0.273) and obvious genetic structure in N. nucifera populations were explained by reduced gene flow and accentuated genetic drift, combined with the inbreeding and repeated genetic bottlenecks. Based on these results, a conservation strategy for protecting all isolated populations to maintain genetic diversity of wild lotus is proposed, and hydrological connectivity should be facilitated across the aquatic system. [ABSTRACT FROM AUTHOR]

The population genetics of the economically important collector urchin, Tripneustes gratilla, were examined in 353 individuals collected from 16 sampling sites throughout Indonesia at 12 microsatellite loci. Bayesian clustering methods over all sampling locations revealed evidence of two genetically distinct clusters, one located predominantly on the shallow Sunda Shelf and the second in the deep waters associated with the biogeographic region known as Wallacea; further analysis revealed additional genetic structure around the island of Halmahera and the Islands of Nias and Mentawai. We propose that the observed genetic differentiation is the result of habitat loss during periods of glacial maxima and differences in physical oceanographic properties throughout the Archipelago. The subsequent recolonization of this habitat as glaciers retreat and sea levels return to present‐day levels creates an unparalleled opportunity for colonists to exploit new habitat. The documentation of cryptic diversity will aid in the identification of hot spots of biodiversity and ultimately its conservation. These data indicate that genetic structure can be detected in a species that has a relatively high dispersal potential, and this differentiation is a potential source of evolutionary novelty. [ABSTRACT FROM AUTHOR]

Eight accessions of olive trees from three common varieties in Palestine, Nabali Baladi, Nabali Mohassan and Surri, were genetically evaluated using five simple sequence repeat (SSR) markers. A total of 17 alleles from 5 loci were observed in which 15 (88.2%) were polymorphic and 2 (11.8%) were monomorphic. An average of 3.4 alleles per locus was found ranging from 2.0 alleles with the primers GAPU-103 and DCA-9 to 5.0 alleles with U9932 and DCA-16. The smallest amplicon size observed was 50 bp with the primer DCA-16, whereas the largest one (450 bp) with the primer U9932. Cluster analysis with the unweighted pair group method with arithmetic average (UPGMA) showed three clusters: a cluster with four accessions from the 'Nabali Baladi' cultivar, another cluster with three accessions that represents the 'Nabali Mohassen' cultivar and finally the 'Surri' cultivar. The similarity coefficient for the eight olive tree samples ranged from a maximum of 100% between two accessions from Nabali Baladi and also in two other samples from Nabali Mohassan, to a minimum similarity coefficient (0.315) between the Surri and two Nabali Baladi accessions. The results in this investigation clearly highlight the genetic dissimilarity between the three main olive cultivars that have been misidentified and mixed up in the past, based on conventional morphological characters.