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Population Genetic Analyses (population + genetic_analysis)

Distribution by Scientific Domains

Life Sciences	97%

Distribution within Life Sciences

Evolution	59%
Conservation Science	5%
7 Other Subdomains	36%

Selected Abstracts

COMPARATIVE GENOMIC AND POPULATION GENETIC ANALYSES INDICATE HIGHLY POROUS GENOMES AND HIGH LEVELS OF GENE FLOW BETWEEN DIVERGENT HELIANTHUS SPECIES

EVOLUTION, Issue 8 2009
Nolan C. Kane
While speciation can be found in the presence of gene flow, it is not clear what impact this gene flow has on genome- and range-wide patterns of differentiation. Here we examine gene flow across the entire range of the common sunflower, H. annuus, its historically allopatric sister species H. argophyllus and a more distantly related, sympatric relative H. petiolaris. Analysis of genotypes at 26 microsatellite loci in 1015 individuals from across the range of the three species showed substantial introgression between geographically proximal populations of H. annuus and H. petiolaris, limited introgression between H. annuus and H. argophyllus, and essentially no gene flow between the allopatric pair, H. argophyllus and H. petiolaris. Analysis of sequence divergence levels among the three species in 1420 orthologs identified from EST databases identified a subset of loci showing extremely low divergence between H. annuus and H. petiolaris and extremely high divergence between the sister species H. annuus and H. argophyllus, consistent with introgression between H. annuus and H. petiolaris at these loci. Thus, at many loci, the allopatric sister species are more genetically divergent than the more distantly related sympatric species, which have exchanged genes across much of the genome while remaining morphologically and ecologically distinct. [source]

RAPID ADAPTIVE DIVERGENCE IN NEW WORLD ACHILLEA, AN AUTOPOLYPLOID COMPLEX OF ECOLOGICAL RACES

EVOLUTION, Issue 3 2008
Justin Ramsey
Adaptive evolution is often associated with speciation. In plants, however, ecotypic differentiation is common within widespread species, suggesting that climatic and edaphic specialization can outpace cladogenesis and the evolution of postzygotic reproductive isolation. We used cpDNA sequence (5 noncoding regions, 3.5 kb) and amplified fragment length polymorphisms (AFLPs: 4 primer pairs, 1013 loci) to evaluate the history of ecological differentiation in the North American Achillea millefolium, an autopolyploid complex of "ecological races" exhibiting morphological, physiological, and life-history adaptations to diverse environments. Phylogenetic analyses reveal North American A. millefolium to be a monophyletic group distinct from its European and Asian relatives. Based on patterns of sequence divergence, as well as fossil and paleoecological data, colonization of North America appears to have occurred via the Bering Land Bridge during the Pleistocene (1.8 MYA to 11,500 years ago). Population genetic analyses indicate negligible structure within North American A. millefolium associated with varietal identity, geographic distribution, or ploidy level. North American populations, moreover, exhibit the signature of demographic expansion. These results affirm the "ecotype" concept of the North American Achillea advocated by classical research and demonstrate the rapid rate of ecological differentiation that sometimes occurs in plants. [source]

Pleistocene glaciation events shape genetic structure across the range of the American lobster, Homarus americanus

MOLECULAR ECOLOGY, Issue 8 2009
ELLEN L. KENCHINGTON
Abstract A north/south discontinuity along the northeastern coast of North America in the genetic structure of the American lobster (Homarus americanus) was detected using a suite of 13 microsatellite loci assessed using spatial analyses. Population genetic data laid over existing data on physiographic changes and sea-surface temperatures were used to reconstruct the Pleistocene distribution of this species. A postglacial northern-edge colonization model best explains the relative genetic homogeneity of the northern region compared to the southern region centred in the Gulf of Maine. Population genetic analyses identified significant structure (range of standardized theta 0,0.02) but no significant evidence for isolation by distance. The novel application of spatial genetic analyses to a marine species allowed us to interpret these results by providing a greater insight into the evolutionary factors responsible for shaping the genetic structure of this species throughout is natural range. [source]

Estimation of dispersal distances of the obligately plant-associated ant Crematogaster decamera

ECOLOGICAL ENTOMOLOGY, Issue 5 2010
MANFRED TÜRKE
1. In obligate symbioses with horizontal transmission, the population dynamics of the partner organisms are highly interdependent. Host population size limits symbiont number, and distribution of partners is restricted by the presence and thus dispersal abilities of their respective partner. The Crematogaster decamera,Macaranga hypoleuca ant,plant symbiosis is obligate for both partners. Host survival depends on colonisation by its ant partner while foundress queens require hosts for colony establishment. 2. An experimental approach and population genetic analyses were combined to estimate dispersal distances of foundresses in their natural habitat in a Bornean primary rainforest. 3. Colonisation frequency was significantly negatively correlated with distance to potential reproductive colonies. Results were similar for seedlings at natural densities as well as for seedlings brought out in the area experimentally. Population genetic analysis revealed significant population differentiation with an FST of 0.041 among foundresses (n = 157) located at maximum 2280 m apart. In genetic spatial autocorrelation, genotypes of foundresses were significantly more similar than expected at random below 550 m and less similar above 620 m. Direct estimation of dispersal distances by pedigree analysis yielded an average dispersal distance of 468 m (maximum 1103 m). 4. For ants that disperse on the wing, genetic differentiation at such small spatial scales is unusual. The specific nesting requirements of the queens and the necessity for queens to find a host quickly could lead to colonisation of the first suitable seedling encountered, promoting short dispersal distances. Nonetheless, dispersal distances of C. decamera queens may vary with habitat or host spatial distribution. [source]

Population genetic analysis of the Brahman cattle (Bos indicus) in Colombia with microsatellite markers

JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 2 2010
M.A. Novoa
Summary The Brahman is one of the most popular breeds for meat production in the Neotropics. However, genetic studies of the breed in Latin American countries have only recently begun. In total, 178 animals of the Brahman breed from 20 Colombian provinces were genotyped at 11 microsatellite markers with the aim of studying the genetic diversity of this population and its genetic relationships with zebuine and taurine breeds. The outcomes of multivariate analyses, Bayesian inferences and inter-individual genetic distances suggested that there is no genetic sub-structure in the population, because of the high rate of animal migration among provinces. The population shows a high degree of heterozygosity and allelic diversity compared with other breeds, reflecting its multibreed origin. The study of the genetic relationships among the breeds reveals that the Brahman breed belongs to the zebuine group. However, it is the population nearest to taurine breeds with high frequencies of taurine alleles. Intensive artificial selection may have favoured the taurine alleles after the breed was formed. There has also been some degree of mixture with local taurine breeds while the Brahman breed has evolved in Colombia. [source]

Gastrointestinal Bacterial Transmission among Humans, Mountain Gorillas, and Livestock in Bwindi Impenetrable National Park, Uganda

CONSERVATION BIOLOGY, Issue 6 2008
INNOCENT B. RWEGO
ecología de enfermedades; Escherichia coli; primates; salud del ecosistema; zoonosis Abstract:,Habitat overlap can increase the risks of anthroponotic and zoonotic pathogen transmission between humans, livestock, and wild apes. We collected Escherichia coli bacteria from humans, livestock, and mountain gorillas (Gorilla gorilla beringei) in Bwindi Impenetrable National Park, Uganda, from May to August 2005 to examine whether habitat overlap influences rates and patterns of pathogen transmission between humans and apes and whether livestock might facilitate transmission. We genotyped 496 E. coli isolates with repetitive extragenic palindromic polymerase chain reaction fingerprinting and measured susceptibility to 11 antibiotics with the disc-diffusion method. We conducted population genetic analyses to examine genetic differences among populations of bacteria from different hosts and locations. Gorilla populations that overlapped in their use of habitat at high rates with people and livestock harbored E. coli that were genetically similar to E. coli from those people and livestock, whereas E. coli from gorillas that did not overlap in their use of habitats with people and livestock were more distantly related to human or livestock bacteria. Thirty-five percent of isolates from humans, 27% of isolates from livestock, and 17% of isolates from gorillas were clinically resistant to at least one antibiotic used by local people, and the proportion of individual gorillas harboring resistant isolates declined across populations in proportion to decreasing degrees of habitat overlap with humans. These patterns of genetic similarity and antibiotic resistance among E. coli from populations of apes, humans, and livestock indicate that habitat overlap between species affects the dynamics of gastrointestinal bacterial transmission, perhaps through domestic animal intermediates and the physical environment. Limiting such transmission would benefit human and domestic animal health and ape conservation. Resumen:,El traslape de hábitats puede incrementar los riesgos de transmisión de patógenos antroponótica y zoonótica entre humanos, ganado y simios silvestres. Recolectamos bacterias Escherichia coli de humanos, ganado y gorilas de montaña (Gorilla gorilla beringei) en el Parque Nacional Bwindi Impenetrable, Uganda, de mayo a agosto 2005 para examinar sí el traslape de hábitat influye en las tasas y patrones de transmisión de patógenos entre humanos y simios y sí el ganado facilita esa transmisión. Determinamos el genotipo de 496 aislados de E. coli con marcaje de reacción en cadena de polimerasa palindrómica extragénica (rep-PCR) y medimos la susceptibilidad a 11 antibióticos con el método de difusión de disco. Realizamos análisis de genética poblacional para examinar las diferencias genéticas entre poblaciones de bacterias de huéspedes y localidades diferentes. Las poblaciones de gorilas con alto grado de traslape en el uso de hábitat con humanos y ganado presentaron E. coli genéticamente similar a E. coli de humanos y ganado, mientras que E. coli de gorilas sin traslape en el uso hábitat con humanos y ganado tuvo relación lejana con las bacterias de humanos y ganado. Treinta y cinco porciento de los aislados de humanos, 27% de los aislados de ganado y 17% de los aislados de gorilas fueron clínicamente resistentes a por lo menos un antibiótico utilizado por habitantes locales, y la proporción de gorilas individuales con presencia de aislados resistentes declinó en las poblaciones proporcionalmente con la disminución en el grado de traslape con humanos. Estos de patrones de similitud genética y resistencia a antibióticos entre E. coli de poblaciones de simios, humanos y ganado indican que el traslape de hábitat entre especies afecta la dinámica de transmisión de bacterias gastrointestinales, probablemente a través de animales domésticos intermediarios y el ambiente físico. La limitación de esa transmisión beneficiaría a la salud de humanos y animales domésticos y a la conservación de simios. [source]

Estimation of dispersal distances of the obligately plant-associated ant Crematogaster decamera

Integration of genotoxicity and population genetic analyses in kangaroo rats (Dipodomys merriami) exposed to radionuclide contamination at the Nevada Test Site, USA

ENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 2 2001
Christopher W. Theodorakis
Abstract We examined effects of radionuclide exposure at two atomic blast sites on kangaroo rats (Dipodomys merriami) at the Nevada Test Site, Nevada, USA, using genotoxicity and population genetic analyses. We assessed chromosome damage by micronucleus and flow cytometric assays and genetic variation by randomly amplified polymorphic DNA (RAPD) and mitochondrial DNA (mtDNA) analyses. The RAPD analysis showed no population structure, but mtDNA exhibited differentiation among and within populations. Genotoxicity effects were not observed when all individuals were analyzed. However, individuals with mtDNA haplotypes unique to the contaminated sites had greater chromosomal damage than contaminated-site individuals with haplotypes shared with reference sites. When interpopulation comparisons used individuals with unique haplotypes, one contaminated site had greater levels of chromosome damage than one or both of the reference sites. We hypothesize that shared-haplotype individuals are potential migrants and that unique-haplotype individuals are potential long-term residents. A parsimony approach was used to estimate the minimum number of migration events necessary to explain the haplotype distributions on a phylogenetic tree. The observed predominance of migration events into the contaminated sites supported our migration hypothesis. We conclude the atomic blast sites are ecological sinks and that immigration masks the genotoxic effects of radiation on the resident populations. [source]

TESTING THE ROLE OF INTERSPECIFIC COMPETITION IN THE EVOLUTIONARY ORIGIN OF ELEVATIONAL ZONATION: AN EXAMPLE WITH BUARREMON BRUSH-FINCHES (AVES, EMBERIZIDAE) IN THE NEOTROPICAL MOUNTAINS

EVOLUTION, Issue 5 2007
Carlos Daniel Cadena
Interspecific competition might drive the evolution of ecological niches and result in pairs of formerly competing species segregating along ecological gradients following a process of character displacement. This mechanism has been proposed to account for replacement of related species along gradients of elevation in many areas of the world, but the fundamental issue of whether competition is responsible for the origin of elevational replacements has not been tested. To test hypotheses about the role of interspecific competition in the origin of complementary elevational ranges, I combined molecular phylogenetics, phylogeography, and population genetic analyses on Buarremon torquatus and B. brunneinucha (Aves, Emberizidae), whose patterns of elevational distribution suggest character displacement or ecological release. The hypothesis that elevational distributions in these species changed in opposite directions as a result of competition is untenable because: (1) a historical expansion of the range of B. brunneinucha into areas occupied by B. torquatus was not accompanied by a shift in the elevational range of the former species; (2) when B. brunneinucha colonized the range of B. torquatus, lineages of the latter distributions had already diverged; and (3) historical trends in effective population size do not suggest populations with elevational ranges abutting those of putative competitors have declined as would be expected if competition caused range contractions. However, owing to uncertainty in coalescent estimates of historical population sizes, the hypothesis that some populations of B. torquatus have declined cannot be confidently rejected, which suggests asymmetric character displacement might have occurred. I suggest that the main role of competition in elevational zonation may be to act as a sorting mechanism that allows the coexistence along mountain slopes only of ecologically similar species that differ in elevational distributions prior to attaining sympatry. The contrasting biogeographic histories of B. brunneinucha and B. torquatus illustrate how present-day ecological interactions can have recent origins, and highlights important challenges for testing the hypothesis of character displacement in the absence of data on population history and robust reconstructions of the evolution of traits and geographic ranges. [source]

Massive parallel MHC genotyping: titanium that shines

MOLECULAR ECOLOGY, Issue 9 2009
K. MATHIAS WEGNER
The power of population genetic analyses is often limited by sample size resulting from constraints in financial resources and time to genotype large numbers of individuals. This particularly applies to nonmodel species where detailed genomic knowledge is lacking. Next-generation sequencing technology using primers ,tagged' with an individual barcode of a few nucleotides offers the opportunity to genotype hundreds of individuals at several loci in parallel (Binladen et al. 2007; Meyer et al. 2008). The large number of sequence reads can also be used to identify artefacts by frequency distribution thresholds intrinsically determined for each run and data set. In Babik et al. (2009), next-generation deep sequencing was used to genotype several major histocompatibility complex (MHC) class IIB loci of the European bank vole (Fig. 1). Their approach can be useful for many researchers working with complex multiallelic templates and large sample sizes. Figure 1. Hypothetical example of parallel genotyping of two individuals using individually bar-coded primers. Polymerase chain reactions (PCRs) are performed separately for each individual using a forward primer with a unique Tag -sequence of four nucleotides. After sequencing of pooled PCR products, sequences can be sorted by their forward primer Tag (Tag -sorting error rate was estimated < 0.1%). Rare sequences most likely represent artefacts and due to the large amount of sequences obtained (up to 106) the artefact threshold can be determined intrinsically for each data set and was estimated to be around 3% in the case of bank vole MHC class IIB genes (Babik et al. 2009). Photos by Gabriela Bydlon. [source]

Revealing the hidden complexities of mtDNA inheritance

MOLECULAR ECOLOGY, Issue 23 2008
DANIEL JAMES WHITE
Abstract Mitochondrial DNA (mtDNA) is a pivotal tool in molecular ecology, evolutionary and population genetics. The power of mtDNA analyses derives from a relatively high mutation rate and the apparent simplicity of mitochondrial inheritance (maternal, without recombination), which has simplified modelling population history compared to the analysis of nuclear DNA. However, in biology things are seldom simple, and advances in DNA sequencing and polymorphism detection technology have documented a growing list of exceptions to the central tenets of mitochondrial inheritance, with paternal leakage, heteroplasmy and recombination now all documented in multiple systems. The presence of paternal leakage, recombination and heteroplasmy can have substantial impact on analyses based on mtDNA, affecting phylogenetic and population genetic analyses, estimates of the coalescent and the myriad of other parameters that are dependent on such estimates. Here, we review our understanding of mtDNA inheritance, discuss how recent findings mean that established ideas may need to be re-evaluated, and we assess the implications of these new-found complications for molecular ecologists who have relied for decades on the assumption of a simpler mode of inheritance. We show how it is possible to account for recombination and heteroplasmy in evolutionary and population analyses, but that accurate estimates of the frequencies of biparental inheritance and recombination are needed. We also suggest how nonclonal inheritance of mtDNA could be exploited, to increase the ways in which mtDNA can be used in analyses. [source]

Living on the edge: demographic and phylogeographical patterns in the woodlouse-hunter spider Dysdera lancerotensis Simon, 1907 on the eastern volcanic ridge of the Canary Islands

MOLECULAR ECOLOGY, Issue 15 2007
LETICIA BIDEGARAY-BATISTA
Abstract The Eastern Canary Islands are the emerged tips of a continuous volcanic ridge running parallel to the northeastern African coast, originated by episodic volcanic eruptions that can be traced back to the Miocene and that, following a major period of quiescence and erosion, continued from the Pliocene to the present day. The islands have been periodically connected by eustatic sea-level changes resulting from Pleistocene glacial cycles. The ground-dwelling spider Dysdera lancerotensis Simon, 1907 occurs along the entire ridge, except on recent barren lavas and sand dunes, and is therefore an ideal model for studying the effect of episodic geological processes on terrestrial organisms. Nested clade and population genetic analyses using 39 haplotypes from 605 base pairs of mitochondrial DNA cytochrome c oxidase I sequence data, along with phylogenetic analyses including two additional mitochondrial genes, uncover complex phylogeographical and demographic patterns. Our results indicate that D. lancerotensis colonized the ridge from north to south, in contrast to what had been expected given the SSW-NNE trend of volcanism and to what had been reported for other terrestrial arthropods. The occurrence of several episodes of extinction, recolonization and expansion are hypothesized for this species, and areas that act as refugia during volcanic cycles are identified. Relaxed molecular clock methods reveal divergence times between main haplotype lineages that suggest an older origin of the northern islets than anticipated based on geological evidence. This study supports the key role of volcanism in shaping the distribution of terrestrial organisms on oceanic islands and generates phylogeographical predictions that warrant further research into other terrestrial endemisms of this fascinating region. [source]

Power for detecting genetic divergence: differences between statistical methods and marker loci

MOLECULAR ECOLOGY, Issue 8 2006
NILS RYMAN
Abstract Information on statistical power is critical when planning investigations and evaluating empirical data, but actual power estimates are rarely presented in population genetic studies. We used computer simulations to assess and evaluate power when testing for genetic differentiation at multiple loci through combining test statistics or P values obtained by four different statistical approaches, viz. Pearson's chi-square, the log-likelihood ratio G -test, Fisher's exact test, and an FST -based permutation test. Factors considered in the comparisons include the number of samples, their size, and the number and type of genetic marker loci. It is shown that power for detecting divergence may be substantial for frequently used sample sizes and sets of markers, also at quite low levels of differentiation. The choice of statistical method may be critical, though. For multi-allelic loci such as microsatellites, combining exact P values using Fisher's method is robust and generally provides a high resolving power. In contrast, for few-allele loci (e.g. allozymes and single nucleotide polymorphisms) and when making pairwise sample comparisons, this approach may yield a remarkably low power. In such situations chi-square typically represents a better alternative. The G -test without Williams's correction frequently tends to provide an unduly high proportion of false significances, and results from this test should be interpreted with great care. Our results are not confined to population genetic analyses but applicable to contingency testing in general. [source]

Evolutionary genetics and biogeographic structure of Rhizobium gallicum sensu lato, a widely distributed bacterial symbiont of diverse legumes

MOLECULAR ECOLOGY, Issue 13 2005
CLAUDIA SILVA
Abstract We used phylogenetic and population genetics approaches to evaluate the importance of the evolutionary forces on shaping the genetic structure of Rhizobium gallicum and related species. We analysed 54 strains from several populations distributed in the Northern Hemisphere, using nucleotide sequences of three ,core' chromosomal genes (rrs, glnII and atpD) and two ,auxiliary' symbiotic genes (nifH and nodB) to elucidate the biogeographic history of the species and symbiotic ecotypes (biovarieties) within species. The analyses revealed that strains classified as Rhizobium mongolense and Rhizobium yanglingense belong to the chromosomal evolutionary lineage of R. gallicum and harbour symbiotic genes corresponding to a new biovar; we propose their reclassification as R. gallicum bv. orientale. The comparison of the chromosomal and symbiotic genes revealed evidence of lateral transfer of symbiotic information within and across species. Genetic differentiation analyses based on the chromosomal protein-coding genes revealed a biogeographic pattern with three main populations, whereas the 16S rDNA sequences did not resolve that biogeographic pattern. Both the phylogenetic and population genetic analyses showed evidence of recombination at the rrs locus. We discuss our results in the light of the contrasting views of bacterial species expressed by microbial taxonomist and evolutionary biologists. [source]

Genetic variation within and among fragmented populations of lesser prairie-chickens (Tympanuchus pallidicinctus)

MOLECULAR ECOLOGY, Issue 3 2003
Ronald A. Van Den Bussche
Abstract As a result of recurrent droughts and anthropogenic factors, the range of the lesser prairie-chicken (Tympanuchus pallidicinctus) has contracted by 92% and the population has been reduced by approximately 97% in the past century, resulting in the smallest population size and most restricted geographical distribution of any North American grouse. We examined genetic variation through DNA sequence analysis of 478 base pairs of the mitochondrial genome and by assaying allelic variation at five microsatellite loci from lesser prairie-chickens collected on 20 leks in western Oklahoma and east-central New Mexico. Traditional population genetic analyses indicate that lesser prairie-chickens maintain high levels of genetic variation at both nuclear and mitochondrial loci. Although some genetic structuring among lesser prairie-chicken leks was detected within Oklahoma and New Mexico for both nuclear and mitochondrial loci, high levels of differentiation were detected between Oklahoma and New Mexico populations. Nested-clade analysis of mitochondrial haplotypes revealed that both historic and contemporary processes have influenced patterns of haplotype distributions and that historic processes have most likely led to the level of differentiation found between the Oklahoma and New Mexico populations. [source]

The linkage disequilibrium between chloroplast DNA and mitochondrial DNA haplotypes in Beta vulgaris ssp. maritima (L.): the usefulness of both genomes for population genetic studies

MOLECULAR ECOLOGY, Issue 2 2000
B. Desplanque
Abstract The structure and evolution of the plant mitochondrial genome may allow recurrent appearance of the same mitochondrial variants in different populations. Whether the same mitochondrial variant is distributed by migration or appears recurrently by mutation (creating homoplasy) in different populations is an important question with regard to the use of these markers for population genetic analyses. The genetic association observed between chloroplasts and mitochondria (i.e. two maternally inherited cytoplasmic genomes) may indicate whether or not homoplasy occurs in the mitochondrial genome. Four-hundred and fourteen individuals sampled in wild populations of beets from France and Spain were screened for their mitochondrial and chloroplast polymorphisms. Mitochondrial DNA (mtDNA) polymorphism was investigated with restriction fragment length polymorphism (RFLP) and chloroplast DNA (cpDNA) polymorphism was investigated with polymerase chain reaction PCR,RFLP, using universal primers for the amplification. Twenty and 13 variants for mtDNA and cpDNA were observed, respectively. Most exhibited a widespread geographical distribution. As a very strong linkage disequilibrium was estimated between mtDNA and cpDNA haplotypes, a high rate of recurrent mutation was excluded for the mitochondrial genome of beets. Identical mitochondrial variants found in populations of different regions probably occurred as a result of migration. We concluded from this study that mtDNA is a tool as valuable as cpDNA when a maternal marker is needed for population genetics analyses in beet on a large regional scale. [source]

New chloroplast primers for intraspecific variation in Dicranum scoparium Hedw. (Dicranaceae) and amplification success in other bryophyte species

MOLECULAR ECOLOGY RESOURCES, Issue 4 2010
A. LANG
Abstract Primers for four loci that amplify cpDNA regions have been designed for population genetic analyses in Dicranum scoparium Hedw. and compared with trnL(UAA)5,exon- trnF. All loci showed intraspecific variation with a number of haplotypes ranging between two and six. trnH- psbADic showed an intercontinental disjunction, but no variability within the four Swiss populations surveyed, whereas the three remaining loci displayed intrapopulation variability in at least one population (rps19- rpl2, rpoB, trnT- rps4). These primers were additionally tested on 22 bryophytes and three fern species. The primers amplified mostly in mosses and liverworts, but less well in ferns, pointing to their evolutionary distance from the bryophytes. [source]

Twenty-one novel microsatellite DNA loci isolated from the Puget Sound white-crowned sparrow, Zonotrichia leucophrys pugetensis

MOLECULAR ECOLOGY RESOURCES, Issue 3 2009
ANGELIKA POESEL
Abstract The white-crowned sparrow, Zonotrichia leucophrys, has served as a model species for studies of song and reproductive physiology. Here, we describe primers for 21 novel microsatellite loci isolated from the Puget Sound subspecies, Zonotrichia leucophrys pugetensis, which will be useful for parentage and population genetic analyses. Based on genotypes from seven to 22 adult birds from one population, the average number of alleles per locus was 10.9 (four to 21 alleles) and observed heterozygosity varied from 0.50 to 1.00. All loci also amplified products in at least one of three other passerine species tested. [source]

New polymorphic microsatellite loci for the Macedonian crested newt, Triturus macedonicus, and cross-priming testing in four other crested newt species

MOLECULAR ECOLOGY RESOURCES, Issue 6 2008
K. SOTIROPOULOS
Abstract Eleven microsatellites have been characterized for Triturus macedonicus. Nine loci showed different variation patterns in a sample of 40 individuals from a single breeding pond in Zagori province (Greece), with an average number of 4.2 alleles per locus and an expected heterozygosity ranging from 0.1199 to 0.8079. Distinct cross-priming amplification rates were recovered on four additional crested newt species. Two monomorphic T. macedonicus loci were polymorphic in other Triturus species. The microsatellites developed herein could be a useful intraspecific genetic tool to undertake fine-scale population genetic analyses as well as in the study of contact zones between crested newt species. [source]

Development of 16 microsatellite markers for the European cockchafer, Melolontha melolontha

MOLECULAR ECOLOGY RESOURCES, Issue 1 2008
JÜRG ENKERLI
Abstract Sixteen polymorphic microsatellite markers were isolated from the European cockchafer, Melolontha melolontha L., based on enriched genomic libraries. Allelic variability was assessed in a collection of 30 individuals obtained from a field in eastern Switzerland. The number of detected alleles ranged from three to 13 with a mean of 6.69 and average observed and expected heterozygosities were 0.52 and 0.66, respectively. The 16 highly polymorphic microsatellite markers represent a powerful molecular tool, which will allow for detailed population genetic analyses on this important pest insect. [source]

Characterization of population structure from the mitochondrial DNA vis-à-vis language and geography in Papua New Guinea

AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 4 2010
Esther J. Lee
Abstract Situated along a corridor linking the Asian continent with the outer islands of the Pacific, Papua New Guinea has long played a key role in understanding the initial peopling of Oceania. The vast diversity in languages and unique geographical environments in the region have been central to the debates on human migration and the degree of interaction between the Pleistocene settlers and newer migrants. To better understand the role of Papua New Guinea in shaping the region's prehistory, we sequenced the mitochondrial DNA (mtDNA) control region of three populations, a total of 94 individuals, located in the East Sepik Province of Papua New Guinea. We analyzed these samples with a large data set of Oceania populations to examine the role of geography and language in shaping population structure within New Guinea and between the region and Island Melanesia. Our results from median-joining networks, star-cluster age estimates, and population genetic analyses show that while highland New Guinea populations seem to be the oldest settlers, there has been significant gene flow within New Guinea with little influence from geography or language. The highest genetic division is between Papuan speakers of New Guinea versus East Papuan speakers located outside of mainland New Guinea. Our study supports the weak language barriers to genetic structuring among populations in close contact and highlights the complexity of understanding the genetic histories of Papua New Guinea in association with language and geography. Am J Phys Anthropol 142:613,624, 2010. © 2010 Wiley-Liss, Inc. [source]

Spanish colonial effects on Native American mating structure and genetic variability in northern and central Florida: Evidence from Apalachee and western Timucua

AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 2 2005
Christopher M. Stojanowski
Abstract Standard population genetic analyses are implemented for a series of precontact and contact period samples from central and northern Florida to investigate changes in genetic variability and population affinity coincident with the establishment of Spanish missions during the 17th century. Estimates of FST based on odontometric data indicate limited heterogeneity for the Apalachee samples, suggestive of some degree of within-group endogamy for this ethnic group prior to contact. This corresponds well with ethnohistoric reconstructions indicating that Apalachee were populous, partially linguistically isolated from its neighbors, and involved in persistent cycles of warfare with neighboring groups. Estimates of extralocal gene flow for the Apalachee samples indicate limited initial changes in the mating structure of these populations. After 1650, however, extralocal gene flow increases, consistent with evidence for dramatic population movements throughout northern Florida and increased Spanish presence in the province, particularly at the mission of San Luis. Inclusion of non-Apalachee outgroups does not increase estimates of genetic heterogeneity, as was expected based on ethnohistoric data. The pattern of genetic distances suggests a biological division between north and south Florida population groups, consistent with archaeological and ethnohistoric data, and similarly indicates some distinction between precontact and postcontact local groups. Differential extralocal gene flow experienced by pre-1650 Apalachee and Timucua populations suggests localized mission experience. The Apalachee, with large, dense populations, experienced limited initial changes in genetic diversity or mating structure. However, after 1650 they were apparently involved in a much more expansive mating network that may have included Spaniards and immigrant Native American groups to the region. These results are in contrast to the mission experience of the Guale Indians of the Georgia coast. Am J Phys Anthropol, 2005. © 2005 Wiley-Liss, Inc. [source]

Evidence for bias in estimates of local genetic structure due to sampling scheme

ANIMAL CONSERVATION, Issue 3 2006
E. K. Latch
Abstract Traditional population genetic analyses typically seek to characterize the genetic substructure caused by the nonrandom distribution of individuals. However, the genetic structuring of adult populations often does not remain constant over time, and may vary relative to season or life-history stages. Estimates of genetic structure may be biased if samples are collected at a single point in time, and will reflect the social organization of the species at the time the samples were collected. The complex population structures exhibited by many migratory species, where temporal shifts in social organization correspond to a large-scale shift in geographic distribution, serve as examples of the importance that time of sampling can have on estimates of genetic structure. However, it is often fine-scale genetic structure that is crucial for defining practical units for conservation and management and it is at this scale that distributional shifts of organisms relative to the timing of sampling may have a profound yet unrecognized impact on our ability to interpret genetic data. In this study, we used the wild turkey to investigate the effects of sampling regime on estimates of genetic structure at local scales. Using mitochondrial sequence data, nuclear microsatellite data and allozyme data, we found significant genetic structuring among localized winter flocks of wild turkeys. Conversely, we found no evidence for genetic structure among sampling locations during the spring, when wild turkeys exist in mixed assemblages of genetically differentiated winter flocks. If the lack of detectable genetic structure among individuals is due to an admixture of social units as in the case of wild turkeys during the spring, then the FIS value rather than the FST value may be the more informative statistic in regard to the levels of genetic structure among population subunits. [source]

Genetic structure of Eurasian cattle (Bos taurus) based on microsatellites: clarification for their breed classification,

ANIMAL GENETICS, Issue 2 2010
M.-H. Li
Summary We pool three previously published data sets and present population genetic analyses of microsatellite variation in 48 Bos taurus cattle breeds from a wide range of geographical origins in Eurasia, mostly its northern territory. Bayesian model-based clustering reveals six distinct clusters: besides a single-population cluster of the Yakutian Cattle from Far Eastern Siberia and a cluster of breeds characteristic of an early origin, the other four major clusters largely correspond to previously defined morphological subgroups of Red Lowland, Lowland Black-Pied, Longhorned Dairy and North European Polled cattle breeds. The results highlighted past expansion events of the productive breeds such as Danish Red, Angeln, Holstein-Friesian and Ayrshire in northern and Eastern Europe. Based on genetic assignment of the breeds and the availability of breed information, we provide a preliminary classification of the five breeds that were to date undefined. Furthermore, in the analysis of molecular variance, despite some correspondence between geographical proximity and genetic similarity, the breed classification appears to be a better predictor of genetic structure in the cattle populations (the among-group variance component: breed classification, 2.47%, P < 0.001; geographical division, 0.77%, P < 0.001). [source]

Sex ratio, reproductive mode and genetic diversity in Triops cancriformis

FRESHWATER BIOLOGY, Issue 7 2009
THORID ZIEROLD
Summary 1. Aquatic invertebrates display a wide array of alternative reproductive modes from apomixis to hermaphroditism and cyclical parthenogenesis. These have important effects on genetic diversity and population structure. Populations of the ,living fossil'Triops cancriformis display a range of sex ratios, and various reproductive modes are thought to underlie this variation. Using sex ratio information and histological analyses European populations have been inferred to be gonochoric (with separate males and females), selfing hermaphroditic and androdioecious, a rare reproductive mode in which selfing hermaphrodites coexist with variable proportions of males. In addition, some populations have been described as meiotic parthenogens. 2. Here we use population genetic analysis using microsatellite loci in populations with a range of sex ratios including a gonochoric population, and marker segregation patterns in heterozygote individuals reared in isolation, to clarify the reproductive mode in this species. 3. Our data show that populations in general have very low levels of genetic diversity. Non-gonochoric populations show lower genetic diversity, more heterozygote deficiencies, higher inbreeding coefficients and stronger linkage disequilibria than the gonochoric population. The maintenance of some heterozygosity in populations is consistent with some male influence in T. cancriformis populations, as would be expected from an androdioecious reproductive system. Results of marker segregation in eggs produced in isolation from non-gonochoric populations indicate that meiosis occurs and are consistent with two reproductive modes: selfing hermaphroditism and a type of ameiotic parthenogenesis. 4. Overall, our data indicate that androdioecy and selfing hermaphroditism are the most likely reproductive modes of non-gonochoric European Triops populations. Triops populations are strongly structured, suggesting high genetic drift and low levels of gene flow. [source]

Kin structure and queen execution in the Argentine ant Linepithema humile

JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 6 2001
M. Reuter
Every spring, workers of the Argentine Ant Linepithema humile kill a large proportion of queens within their nests. Although this behaviour inflicts a high energetic cost on the colonies, its biological significance has remained elusive so far. An earlier study showed that the probability of a queen being executed is not related to her weight, fecundity, or age. Here we test the hypothesis that workers collectively eliminate queens to which they are less related, thereby increasing their inclusive fitness. We found no evidence for this hypothesis. Workers of a nest were on average not significantly less related to executed queens than to surviving ones. Moreover, a population genetic analysis revealed that workers were not genetically differentiated between nests. This means that workers of a given nest are equally related to any queen in the population and that there can be no increase in average worker,queen relatedness by selective elimination of queens. Finally, our genetic analyses also showed that, in contrast to workers, queens were significantly genetically differentiated between nests and that there was significant isolation by distance for queens. [source]

Functional and geographical differentiation of candidate balanced polymorphisms in Arabidopsis thaliana

MOLECULAR ECOLOGY, Issue 13 2009
JENNIFER M. REININGA
Abstract Molecular population genetic analysis of three chromosomal regions in Arabidopsis thaliana suggested that balancing selection might operate to maintain variation at three novel candidate adaptive trait genes, including SOLUBLE STARCH SYNTHASE I (SSI), PLASTID TRANSCRIPTIONALLY ACTIVE 7(PTAC7), and BELL-LIKE HOMEODOMAIN 10 (BLH10). If balanced polymorphisms are indeed maintained at these loci, then we would expect to observe functional variation underlying the previously detected signatures of selection. We observe multiple replacement polymorphisms within and in the 32 amino acids just upstream of the protein,protein interacting BELL domain at the BLH10 locus. While no clear protein sequence differences are found between allele types in SSI and PTAC7, these two genes show evidence for allele-specific variation in expression levels. Geographical patterns of allelic differentiation seem consistent with population stratification in this species and a significant longitudinal cline was observed at all three candidate loci. These data support a hypothesis of balancing selection at all three candidate loci and provide a basis for more detailed functional work by identifying possible functional differences that might be selectively maintained. [source]

Microsatellite DNA markers for three toad-headed lizard species (Phrynocephalus vlangalii, P. przewalskii and P. guttatus)

MOLECULAR ECOLOGY RESOURCES, Issue 2 2009
AIBIN ZHAN
Abstract To assess the impact of natural landscapes on the population structure of lizards, 10 polymorphic microsatellite DNA markers were developed for the Qinghai toad-headed lizard, Phrynocephalus vlangalii. The number of alleles at these informative loci ranged from four to 28. The novel markers and those previously developed for Phrynocephalus przewalskii were cross-tested among three toad-headed lizard species P. vlangalii, P. przewalskii and P. guttatus. A high cross-utility rate of more than 58% was observed among these three species. These markers are expected to be useful tools for taxonomic considerations as well as population genetic analysis and future conservation management. [source]

Characterization of 11 microsatellite loci derived from genomic sequences of polychaete Capitella capitata complex

MOLECULAR ECOLOGY RESOURCES, Issue 6 2007
HONGWEI DU
Abstract Eleven microsatellite loci derived from the genomic sequence data of Capitella capitata were characterized using 30 samples. The observed number of alleles per locus ranged from four to 36. The levels of observed and expected heterozygosities for polymorphic loci were from 0.10 to 0.87 and from 0.37 to 0.98, averaging 0.52 and 0.77, respectively. Analyses of Hardy,Weinberg equilibrium and genotypic linkage disequilibrium suggest the possible presence of both null alleles and Wahlund effect. One of the 11 loci was difficult to amplify for genotyping. Therefore, the rest 10 loci are good molecular markers for population genetic analysis. [source]

formatomatic: a program for converting diploid allelic data between common formats for population genetic analysis

MOLECULAR ECOLOGY RESOURCES, Issue 4 2007
NICHOLAS C. MANOUKIS
Abstract There has been a great increase in both the number of population genetic analysis programs and the size of data sets being studied with them. Since the file formats required by the most popular and useful programs are variable, automated reformatting or conversion between them is desirable. formatomatic is an easy to use program that can read allelic data files in genepop, raw (csv) or convert formats and create data files in nine formats: raw (csv), arlequin, genepop, immanc/bayesass+, migrate, newhybrids, msvar, baps and structure. Use of formatomatic should greatly reduce time spent reformatting data sets and avoid unnecessary errors. [source]