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Fixation Index (fixation + index)
Selected AbstractsInbreeding and inbreeding depression in a threatened endemic plant, the African violet (Saintpaulia ionantha ssp. grotei), of the East Usambara Mountains, TanzaniaAFRICAN JOURNAL OF ECOLOGY, Issue 3 2010Johanna Kolehmainen Abstract Mating among closely-related individuals in small and isolated plant populations may result in reduced vigour of the inbred offspring, i.e. inbreeding depression, especially in naturally outbreeding plants. Occurrence of inbreeding and inbreeding depression was studied in Saintpaulia ionantha ssp. grotei, a threatened endemic plant species with a narrow ecological amplitude from the East Usambara Mountains. The level of inbreeding (measured as the fixation index, F) was investigated in twelve populations by analyzing variation at one microsatellite marker locus. The effect of one generation of selfing and outcrossing on the progeny fitness was studied by controlled crosses in two small patches that differ in the level isolation. The fixation index (F) across the populations was on the average 0.21 and varied among the populations from substantial inbreeding (F = 0.58) to surplus heterozygosity (F = ,0.29). High inbreeding depression (,) was observed at early and late stages of the life-cycle. The isolated patch exhibited lower inbreeding depression than did the non-isolated patch. The results of this study suggest that inbreeding and subsequent inbreeding depression are potential threats to the survival of Saintpaulia populations. Résumé L'accouplement d'individus étroitement liés, dans des petites populations végétales isolées, peut aboutir à une vigueur moindre de la progéniture de même souche, c'est-à-dire une dépression due à l'endogamie, spécialement chez des plantes qui sont naturellement exogames. L'occurrence de l'endogamie et de la dépression qui y est liée a étéétudiée chez le Saintpaulia ionantha spp. grotei, une plante endémique menacée qui n'a qu'une faible amplitude écologique dans l'est des Usambara Mountains. On a recherché le taux d'endogamie (mesuré par l'indice de fixation F) dans 12 populations en analysant la variation d'un locus microsatellite marqueur. L'effet d'une génération d'auto- et d'allofécondation sur l'aptitude (fitness) de la progéniture a étéétudié par des croisements contrôlés dans deux petites parcelles dont le degré d'isolement différait. L'indice de fixation F dans les populations était en moyenne de 0,21 et il variait d'une autofécondation substantielle (F = 0,58) à une hétérozygosité en surplus (F = ,0,29). Une forte dépression due à l'endogamie (,) a été observée aux stades précoce et tardif du cycle vital. La parcelle isolée a présenté une dépression liée à l'endogamie moins forte que celle de la parcelle non isolée. Les résultats de cette étude suggèrent que l'auto-fécondation et la dépression qui en résulte sont des menaces potentielles pour la survie des populations de Saintpaulia. [source] The mean measure of divergence: Its utility in model-free and model-bound analyses relative to the Mahalanobis D2 distance for nonmetric traitsAMERICAN JOURNAL OF HUMAN BIOLOGY, Issue 3 2010Joel D. Irish The mean measure of divergence (MMD) distance statistic has been used by researchers for nearly 50 years to assess inter-sample phenetic affinity. Its widespread and often successful use is well documented, especially in the study of cranial and dental nonmetric traits. However, the statistic has accumulated some undesired mathematical baggage through the years from various workers in their attempts to improve or alter its performance. Others may not fully understand how to apply the MMD or interpret its output, whereas some described a number of perceived shortcomings. As a result, the statistic and its sometimes flawed application(s) have taken several well-aimed hits; a few researchers even argued that it should no longer be utilized or, at least, that its use be reevaluated. The objective of this report is to support the MMD, and in the process: (1) provide a brief history of the statistic, (2) review its attributes and applicability relative to the often-used Mahalanobis D2 statistic for nonmetric traits, (3) compare results from MMD and D2 model-free analyses of previously-recorded sub-Saharan African dental samples, and (4) investigate its utility for model-bound analyses. In the latter instance, the ability of the D2 and other squared Euclidean-based statistics to approximate a genetic relationship matrix and Sewall Wright's fixation index using phenotypic data, and the inability of the MMD to do so, is addressed. Three methods for obtaining such results with nonlinear MMD distances, as well as an assessment of the fit of the isolation-by-distance model, are presented. Am. J. Hum. Biol., 2010. © 2009 Wiley-Liss, Inc. [source] Genetic differentiation analysis of African cassava (Manihot esculenta) landraces and elite germplasm using amplified fragment length polymorphism and simple sequence repeat markersANNALS OF APPLIED BIOLOGY, Issue 2 2009A.A.J. Raji Abstract Molecular-marker-aided evaluation of germplasm plays an important role in defining the genetic diversity of plant genotypes for genetic and population improvement studies. A collection of African cassava landraces and elite cultivars was analysed for genetic diversity using 20 amplified fragment length polymorphic (AFLP) DNA primer combinations and 50 simple sequence repeat (SSR) markers. Within-population diversity estimates obtained with both markers were correlated, showing little variation in their fixation index. The amount of within-population variation was higher for landraces as illustrated by both markers, allowing discrimination among accessions along their geographical origins, with some overlap indicating the pattern of germplasm movement between countries. Elite cultivars were grouped in most cases in agreement with their pedigree and showed a narrow genetic variation. Both SSR and AFLP markers showed some similarity in results for the landraces, although SSR provided better genetic differentiation estimates. Genetic differentiation (Fst) in the landrace population was 0.746 for SSR and 0.656 for AFLP. The molecular variance among cultivars in both populations accounted for up to 83% of the overall variation, while 17% was found within populations. Gene diversity (He) estimated within each population varied with an average value of 0.607 for the landraces and 0.594 for the elite lines. Analyses of SSR data using ordination techniques identified additional cluster groups not detected by AFLP and also captured maximum variation within and between both populations. Our results indicate the importance of SSR and AFLP as efficient markers for the analysis of genetic diversity and population structure in cassava. Genetic differentiation analysis of the evaluated populations provides high prospects for identifying diverse parental combinations for the development of segregating populations for genetic studies and the introgression of desirable genes from diverse sources into the existing genetic base. [source] Reproductive biology of a mycoheterotrophic species, Burmannia wallichii (Burmanniaceae)BOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2000DIANXIANG ZHANG The breeding system of a mycoheterotrophic species, Bumannia wallichii (Miers) Hook. f. (Burmanniaceae), is assessed using field observations, floral anatomy, pollen histochemistry and isozyme electrophoresis. The structure of the flower effectively prevents pollinators from accessing the stamens, and no pollinators were observed visiting natural populations in Hong Kong. The pollen is starch-rich but lipid-poor. Analysis of isozyme variation revealed a small proportion of polymorphic loci, a low level of total heterozygosity (HT= 0.1972), and a very high overall fixation index of populations (FIT= 0.6602). These results strongly suggest that B. wallichii is predominantly self-pollinated. The coefficient of gene differentiation (GST) is low (0.05), although it is suggested that this is due to genetic homogenization of populations consonant with the formation of numerous tiny ,diaspora' seeds that are wind dispersed. [source] Population genetics of the European trout (Salmo trutta L.) migration system in the river Rhine: recolonisation by sea troutECOLOGY OF FRESHWATER FISH, Issue 1 2005A. Schreiber Abstract , Allozyme genetics (34 loci) is studied in up to 1010 European trout (Salmo trutta) from the Rhine, Meuse, Weser, Elbe and Danube river systems in Central Europe. Population samples from single collection sites, chiefly small streams (GCG = 0.2126), rather than the divergence of the trout from Atlantic and Danubian drainages (GSG = 0.0711), contributed to the overall gene diversity of GST = 0.2824. Sea trout (n = 164) and brown trout (n = 767) in Atlantic rivers adhere to the same biogeographical stock, but anadromous trout from the Rhine and the Elbe display more genetic cohesion than resident brown trout from the Rhine system alone. Strayers from the Elbe could have founded the recently re-established sea trout population of the Rhine, after a few decades of absence or precarious rarity. Migrants may even connect the Rhine and Elbe stocks by ongoing gene flow. A release,recapture study confirms that all trout in the Rhine belong to one partly migratory population network: Six of 2400 juvenile sea trout released into a tributary of the Rhine were later recorded as emigrants to the Rhine delta, against three of 1600 released brown trout. One migrant had entered the open North Sea, but the other dispersers were recorded in fresh waters of the Rhine delta (Ijsselmeer, Amstelmeer). Stocking presumably elevated both heterozygosity and fixation indices of brown trout, but this effect is subtle within the range of the Atlantic population group. Improved sea trout management in the Rhine, and modifications to brown trout stocking in the upper Danubian area are recommended. [source] World phylogeography and male-mediated gene flow in the sandbar shark, Carcharhinus plumbeusMOLECULAR ECOLOGY, Issue 10 2010DAVID S. PORTNOY Abstract The sandbar shark, Carcharhinus plumbeus, is a large, cosmopolitan, coastal species. Females are thought to show philopatry to nursery grounds while males potentially migrate long distances, creating an opportunity for male-mediated gene flow that may lead to discordance in patterns revealed by mitochondrial DNA (mtDNA) and nuclear markers. While this dynamic has been investigated in elasmobranchs over small spatial scales, it has not been examined at a global level. We examined patterns of historical phylogeography and contemporary gene flow by genotyping 329 individuals from nine locations throughout the species' range at eight nuclear microsatellite markers and sequencing the complete mtDNA control region. Pairwise comparisons often resulted in fixation indices and divergence estimates of greater magnitude using mtDNA sequence data than microsatellite data. In addition, multiple methods of estimation suggested fewer populations based on microsatellite loci than on mtDNA sequence data. Coalescent analyses suggest divergence and restricted migration among Hawaii, Taiwan, eastern and western Australia using mtDNA sequence data and no divergence and high migration rates, between Taiwan and both Australian sites using microsatellite data. Evidence of secondary contact was detected between several localities and appears to be discreet in time rather than continuous. Collectively, these data suggest complex spatial/temporal relationships between shark populations that may feature pulses of female dispersal and more continuous male-mediated gene flow. [source] The Garífuna (Black Carib) people of the Atlantic coasts of Honduras: Population dynamics, structure, and phylogenetic relations inferred from genetic data, migration matrices, and isonymyAMERICAN JOURNAL OF HUMAN BIOLOGY, Issue 1 2010Edwin-Francisco Herrera-Paz The aim of this study is to assess population dynamics, structure, and phylogenetic relations of the populations that inhabit the Caribbean coasts of Honduras: the Garífuna (or Black Carib) people, an admixture of Black Africans and Red Carib Native Amerindians. Thirteen autosomal tetranucleotide microsatellite markers of the DNA (namely short tandem repeats) were genotyped in samples from the Garifuna communities of Bajamar, in the Department of Cortés; Corozal, in the Department of Atlántida; and Iriona, in the Department of Gracias a Dios. Each subject in the study filled a questionnaire with the following information: complete name and surname of participant, and places of birth of the participant, his/her parents, and grandparents. We performed analyses that included determination of migration rates and residence patterns from information of places of birth, fixation indices from genetic data, and analysis of surnames of the sampled subjects (isonymy). Migration matrices showed a migration wave from east to west in the parents and grandparents of the subjects. A raise in migration rates and a shift in predominating residence pattern from neolocality to matrilocality from grandparents to parents were observed. Analysis of isonymy conjunctly with values for FIS in each community showed high endogamy in Bajamar, and recent, high immigration in Iriona. A dendrogram constructed with allele frequencies of the Garifuna and other populations from the Americas, Africa, and Europe revealed the close relationships of this ethnic group with Afro-Caribbean and African Populations. Am. J. Hum. Biol. 2010. © 2009 Wiley-Liss, Inc. [source] | ||||||||||||||||||||||