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Allelic Richness (allelic + richness)
Selected AbstractsDevelopment of microsatellite markers for noninvasive DNA samples of the eastern green lizard Lacerta viridisMOLECULAR ECOLOGY RESOURCES, Issue 3 2006MAREN LAUBE Abstract We report the isolation and characterization of microsatellite markers for the eastern green lizard (Lacerta viridis) usable for noninvasive samples. Ten polymorphic loci were obtained by screening 3000 recombinant clones and tested on 39 noninvasive DNA samples of individuals from different locations of the Danube area, Germany. Allelic richness ranged from three to nine alleles, the observed heterozygosity from 0.33 to 0.80, and the expected heterozygosity from 0.36 to 0.85. Our 10 loci, along with another 12 loci previously described, deliver effective analytical tools to analyse the genetic variability and to assess the social structure of eastern green lizard populations. [source] Eight microsatellite markers for the neotropical tree Luehea seemannii (Tiliaceae)MOLECULAR ECOLOGY RESOURCES, Issue 1 2004F. A. Jones Abstract We isolated eight polymorphic microsatellites from the neotropical tree Luehea seemannii for gene flow and genetic structure studies. We used a streptavidin subtractive enrichment technique to develop a library of CA/GT repeats. Eight loci were screened for diversity from 96 individuals from Barro Colorado Island (BCI) and neighbouring Gigante peninsula in Panama. Luehea seemannii shows moderate levels of genetic diversity within these two populations. Allelic richness ranged from four to nine alleles and averaged 6.44 alleles per locus. Average expected heterozygosity was 0.65 on BCI and 0.60 on Gigante. Results are compared to microsatellite data from another wind-dispersed gap colonizing species common in Panama. [source] Susceptibility of Common and Rare Plant Species to the Genetic Consequences of Habitat FragmentationCONSERVATION BIOLOGY, Issue 3 2007OLIVIER HONNAY diversidad genética; endogamia; fragmentación de hábitat; sistema reproductivo; tamaño poblacional Abstract:,Small plant populations are more prone to extinction due to the loss of genetic variation through random genetic drift, increased selfing, and mating among related individuals. To date, most researchers dealing with genetic erosion in fragmented plant populations have focused on threatened or rare species. We raise the question whether common plant species are as susceptible to habitat fragmentation as rare species. We conducted a formal meta-analysis of habitat fragmentation studies that reported both population size and population genetic diversity. We estimated the overall weighted mean and variance of the correlation coefficients among four different measures of genetic diversity and plant population size. We then tested whether rarity, mating system, and plant longevity are potential moderators of the relationship between population size and genetic diversity. Mean gene diversity, percent polymorphic loci, and allelic richness across studies were positively and highly significantly correlated with population size, whereas no significant relationship was found between population size and the inbreeding coefficient. Genetic diversity of self-compatible species was less affected by decreasing population size than that of obligate outcrossing and self-compatible but mainly outcrossing species. Longevity did not affect the population genetic response to fragmentation. Our most important finding, however, was that common species were as, or more, susceptible to the population genetic consequences of habitat fragmentation than rare species, even when historically or naturally rare species were excluded from the analysis. These results are dramatic in that many more plant species than previously assumed may be vulnerable to genetic erosion and loss of genetic diversity as a result of ongoing fragmentation processes. This implies that many fragmented habitats have become unable to support plant populations that are large enough to maintain a mutation-drift balance and that occupied habitat fragments have become too isolated to allow sufficient gene flow to enable replenishment of lost alleles. Resumen:,Las poblaciones pequeñas de plantas son más propensas a la extinción debido a la pérdida de variación genética por medio de la deriva génica aleatoria, el incremento de autogamia y la reproducción entre individuos emparentados. A la fecha, la mayoría de los investigadores que trabajan con erosión genética en poblaciones fragmentadas de plantas se han enfocado en las especies amenazadas o raras. Cuestionamos si las especies de plantas comunes son tan susceptibles a la fragmentación del hábitat como las especies raras. Realizamos un meta análisis formal de estudios de fragmentación que reportaron tanto tamaño poblacional como diversidad genética. Estimamos la media general ponderada y la varianza de los coeficientes de correlación entre cuatro medidas de diversidad genética y de tamaño poblacional de las plantas. Posteriormente probamos si la rareza, el sistema reproductivo y la longevidad de la planta son moderadores potenciales de la relación entre el tamaño poblacional y la diversidad genética. La diversidad genética promedio, el porcentaje de loci polimórficos y la riqueza alélica en los estudios tuvieron una correlación positiva y altamente significativa con el tamaño poblacional, mientras que no encontramos relación significativa entre el tamaño poblacional y el coeficiente de endogamia. La diversidad genética de especies auto compatibles fue menos afectada por la reducción en el tamaño poblacional que la de especies exogámicas obligadas y especies auto compatibles, pero principalmente exogámicas. La longevidad no afectó la respuesta genética de la población a la fragmentación. Sin embargo, nuestro hallazgo más importante fue que las especies comunes fueron tan, o más, susceptibles a las consecuencias genéticas de la fragmentación del hábitat que las especies raras, aun cuando las especies histórica o naturalmente raras fueron excluidas del análisis. Estos resultados son dramáticos porque muchas especies más pueden ser vulnerables a la erosión genética y a la pérdida de diversidad genética como consecuencia de los procesos de fragmentación que lo se asumía previamente. Esto implica que muchos hábitats fragmentados han perdido la capacidad para soportar poblaciones de plantas lo suficientemente grandes para mantener un equilibrio mutación-deriva y que los fragmentos de hábitat ocupados están tan aislados que el flujo génico es insuficiente para permitir la reposición de alelos perdidos. [source] Effects of environmental pollution on microsatellite DNA diversity in wood mouse (Apodemus sylvaticus) populationsENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 11 2005Veerle Berckmoes Abstract Ten microsatellite DNA loci were surveyed to investigate the effects of heavy metal pollution on the genetic diversity and population genetic structure of seven wood mouse (Apodemus sylvaticus) populations along a heavy metal pollution gradient away from a nonferrous smelter in the south of Antwerp (Flanders, Belgium). Analysis of soil heavy metal concentrations showed that soil Ag, As, Cd, Cu, and Pb decreased with increasing distance from the smelter. Genetic analyses revealed high levels of genetic variation in all populations, but populations from the most polluted sites in the gradient did not differ from those of less-polluted sites in terms of mean observed and expected heterozygosity level and mean allelic richness. No correlation was found between measures of genetic diversity and the degree of heavy metal pollution. However, an analysis of molecular variance and a neighbor-joining tree suggested a contamination-related pattern of genetic structuring between the most polluted and less polluted sites. Pairwise FST values indicated that populations were significantly genetically differentiated, and assignment tests and direct estimates of recent migration rates suggested restricted gene flow among populations. Additionally, genetic differentiation increased significantly with geographical distance, which is consistent with an isolation-by-distance model. We conclude that, at least for our microsatellite DNA markers, genetic diversity in the studied wood mouse populations is not affected greatly by the heavy metal pollution. [source] ANTHROPOGENIC EFFECTS ON POPULATION GENETICS OF PHYTOPHAGOUS INSECTS ASSOCIATED WITH DOMESTICATED PLANTSEVOLUTION, Issue 12 2007Nadir Alvarez The hypothesis of isolation by distance (IBD) predicts that genetic differentiation between populations increases with geographic distance. However, gene flow is governed by numerous factors and the correlation between genetic differentiation and geographic distance is never simply linear. In this study, we analyze the interaction between the effects of geographic distance and of wild or domesticated status of the host plant on genetic differentiation in the bean beetle Acanthoscelides obvelatus. Geographic distance explained most of the among-population genetic differentiation. However, IBD varied depending on the kind of population pairs for which the correlation between genetic differentiation and geographic distance was examined. Whereas pairs of beetle populations associated with wild beans showed significant IBD (P < 10,4), no IBD was found when pairs of beetle populations on domesticated beans were examined (P= 0.2992). This latter result can be explained by long-distance migrations of beetles on domesticated plants resulting from human exchanges of bean seeds. Beetle populations associated with wild beans were also significantly more likely than those on domesticated plants to contain rare alleles. However, at the population level, beetles on cultivated beans were similar in allelic richness to those on wild beans. This similarity in allelic richness combined with differences in other aspects of the genetic diversity (i.e., IBD, allelic diversity) is compatible with strongly contrasting effects of migration and drift. This novel indirect effect of human actions on gene flow of a serious pest of a domesticated plant has important implications for the spread of new adaptations such as resistance to pesticides. [source] BALANCING SELECTION, RANDOM GENETIC DRIFT, AND GENETIC VARIATION AT THE MAJOR HISTOCOMPATIBILITY COMPLEX IN TWO WILD POPULATIONS OF GUPPIES (POECILIA RETICULATA)EVOLUTION, Issue 12 2006Cock van Oosterhout Abstract Our understanding of the evolution of genes of the major histocompatibility complex (MHC) is rapidly increasing, but there are still enigmatic questions remaining, particularly regarding the maintenance of high levels of MHC polymorphisms in small, isolated populations. Here, we analyze the genetic variation at eight microsatellite loci and sequence variation at exon 2 of the MHC class IIB (DAB) genes in two wild populations of the Trinidadian guppy, Poecilia reticulata. We compare the genetic variation of a small (Ne, 100) and relatively isolated upland population to that of its much larger (Ne, 2400) downstream counterpart. As predicted, microsatellite diversity in the upland population is significantly lower and highly differentiated from the population further downstream. Surprisingly, however, these guppy populations are not differentiated by MHC genetic variation and show very similar levels of allelic richness. Computer simulations indicate that the observed level of genetic variation can be maintained with overdominant selection acting at three DAB loci. The selection coefficients differ dramatically between the upland (s 0.2) and lowland (s, 0.01) populations. Parasitological analysis on wild-caught fish shows that parasite load is significantly higher on upland than on lowland fish, which suggests that large differences in selection intensity may indeed exist between populations. Based on the infection intensity, a substantial proportion of the upland fish would have suffered direct or indirect fitness consequences as a result of their high parasite loads. Selection by parasites plays a particularly important role in the evolution of guppies in the upland habitat, which has resulted in high levels of MHC diversity being maintained in this population despite considerable genetic drift. [source] Genetic diversity and structure of the West Balkan Pramenka sheep types as revealed by microsatellite and mitochondrial DNA analysisJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 6 2008inkulov Summary Several different phenotypes of the native Pramenka sheep have been developed in the Balkan region for different environmental and socio-cultural conditions. Animals from seven West Balkan Pramenka sheep types were analysed for 15 microsatellite markers and for mitochondrial DNA (mtDNA) and the results were used to assess genetic variation within and among the types and to infer the genetic population structure of the Pramenka sheep. Mean expected heterozygosity and allelic richness over the microsatellite loci and sheep types were 0.78 and 7.9, respectively. A Bayesian statistical method for estimating hidden genetic structure suggested that a core of the largest panmictic population was formed by Serbian, Kosovan, Bosnian, Montenegrin and Albanian types, while Croatian and Macedonian types comprised two other main populations, respectively. Mitochondrial DNA analysis revealed two mtDNA haplogroups in the Pramenka sheep, B and A, with a frequency of 93.7% and 6.3%, respectively. A total of 60 mtDNA haplotypes were found in 64 animals sequenced, and the mean nucleotide and haplotypic diversities over the types were 0.013 and 0.945, respectively. Molecular analysis suggests that the West Balkan Pramenka sheep types have their origins in two distinct maternal lineages of domestic sheep and different Pramenka phenotypes tend to form few panmictic populations. The Pramenka sheep represents a valuable resource of genetic diversity in sheep. [source] Contrasting patterns of nuclear microsatellite genetic structure of Fraxinus mandshurica var. japonica between northern and southern populations in JapanJOURNAL OF BIOGEOGRAPHY, Issue 6 2010Li-Jiang Hu Abstract Aim, The aim of this study is to detect extant patterns of population genetic structure of Fraxinus mandshurica var. japonica in Japan, and to provide insights into the post-glacial history of this species during the Holocene. Location, Hokkaido and Honshu islands, Japan (including the Oshima and Shimokita peninsulas). Methods, We examined nine polymorphic nuclear microsatellite loci to assess genetic variation within and among 15 populations across almost the entire range of the species in Japan. Extant patterns of geographical structure were analysed using Bayesian clustering, Monmonier's algorithm, analysis of molecular variance, Mantel tests and principal coordinates analysis. Recent bottlenecks within populations and regional genetic variation were also assessed. Results, Northern populations (Hokkaido Island and the Shimokita Peninsula) formed a single homogeneous deme, maintaining the highest level of allelic diversity on the Oshima Peninsula. By contrast, southern populations (Honshu Island) demonstrated strong substructure on both coasts. Specifically, populations on the Pacific side of Honshu exhibited significant bottlenecks and erosion of allelic diversity but preserved distinct subclusters diverging from widespread subclusters on the Japan Sea side of this island. Main conclusions, Genetic evidence and life history traits suggest that F. mandshurica occupied cryptic northern refugia on the Oshima Peninsula during the Last Glacial Maximum, which is reflected in the species' extant northern distribution. Strong geographical structure in southern populations, in agreement with fossil pollen records, suggests geographical isolation by mountain ranges running north,south along Honshu. Given that this tree species is cold-adapted and found in riparian habitats, populations on the Pacific side of Honshu probably contracted into higher-elevation swamps during warm post-glacial periods, leading to a reduction of effective population sizes and rare allelic richness. [source] Range-wide genetic structure in a north-east Asian spruce (Picea jezoensis) determined using nuclear microsatellite markersJOURNAL OF BIOGEOGRAPHY, Issue 5 2009Mineaki Aizawa Abstract Aim, We used microsatellite markers to determine the range-wide genetic structure of Picea jezoensis and to test the hypothesis that the past population history of this widespread cold-temperate spruce has resulted in a low level of genetic variation and in imprints of inbreeding and bottlenecks in isolated marginal populations. Location, The natural range of the three infraspecific taxa of P. jezoensis throughout north-east Asia, including isolated marginal populations. Methods, We analysed a total of 990 individuals across 33 natural populations using four nuclear microsatellite loci. Population genetic structure was assessed by analysing genetic diversity indices for each population, examining clustering (model-based and distance-based) among populations, evaluating signals of recent bottlenecks, and testing for isolation by distance (IBD). Results, The 33 populations were clustered into five groups. The isolated marginal groups of populations (in Kamchatka, Kii in Japan and South Korea) exhibited low levels of allelic richness and gene diversity and a complete or almost complete loss of rare alleles. A recent bottleneck was detected in the populations in Hokkaido across to mid-Sakhalin. The IBD analysis revealed that genetic divergence between populations was higher for populations separated by straits. Main conclusions,Picea jezoensis showed a higher level of genetic differentiation among populations (FST = 0.101) than that observed in the genus Picea in general. This might be attributable to the fact that historically the straits around Japan acted as barriers to the movement of seeds and pollen. The low levels of genetic diversity in the isolated marginal population groups may reflect genetic drift that has occurred after isolation. Evidence of a significant bottleneck between the Hokkaido and mid-Sakhalin populations implies that the cold, dry climate in the late Pleistocene resulted in the decline and contraction of populations, and that there was a subsequent expansion followed by a founder effect when conditions improved. The high polymorphism observed in P. jezoensis nuclear microsatellites revealed cryptic genetic structure that organellar DNA markers failed to identify in a previous study. [source] Contrasting phylogeographical patterns of two closely related species, Machilus thunbergii and Machilus kusanoi (Lauraceae), in TaiwanJOURNAL OF BIOGEOGRAPHY, Issue 5 2006Su-Hwa Wu Abstract Aim, The purpose of this paper was to study the patterns of genetic variation, demographic history, haplotype relationships and potential location of diversity centres of two closely related species, Machilus thunbergii and Machilus kusanoi. Location, The phylogeography of M. thunbergii and M. kusanoi was examined by sampling 110 and 106 individuals from 25 and 16 sampling sites, respectively, across their distributional range in Taiwan. Machilus thunbergii is distributed on the Asian mainland, South Korea, southern Japan, the Ryukyus, Taiwan and the Philippines, whereas M. kusanoi is endemic to Taiwan. These two species are closely related, and both are widely distributed in Taiwan but occupy different altitudinal zones and habitats. Methods, The range-wide variation of M. thunbergii and M. kusanoi in Taiwan was studied using chloroplast DNA (cpDNA) variations. A haplotype network was constructed with the computer program tcs. Nested clade analysis was conducted with the computer program ceodis, and various parameters of genetic diversity were calculated and neutrality tested by the computer program DnaSP. Population differentiation was estimated using the programs arlequin and hapstep. The contribution of the populations to gene diversity and to allelic richness was calculated using the software contrib. The level of divergence for each population from the remaining populations was calculated as the mean value of pairwise FST for each population against the rest of the populations. Results, Extremely low levels of genetic differentiation were found for both species. This result suggested that these two species probably survived in multiple relict refugia with different population sizes throughout the island during low-temperature periods of the Pleistocene. In addition, nested clade analysis (NCA) of cpDNA haplotypes indicated that restricted gene flow with isolation-by-distance characterized the recolonization after the Pleistocene by Tashueshan and Shiouhluan populations of M. thunbergii in the north-central area west of the Central Mountain Range (CMR). In contrast, NCA analysis indicated that a major diversity centre on the southern tip of the island (Kending population) and contiguous range expansion characterized the recolonization by M. kusanoi of northern areas along the east side of the CMR. The major diversity centres found for the two species examined were further supported by the results of the mean FST for individual populations in comparison with other populations, and of the contribution of the divergence component to the total diversity. Main conclusions, This research supports the multiple relict refugia hypothesis for both species investigated. Populations of M. thunbergii at Shiouhluan and Tashueshan in the north-central area west of the CMR represent a diversity centre currently expanding its size. A diversity centre at the southern-edge population of M. kusanoi, and a contiguous range expansion from Kending, were found. These results indicate that the M. thunbergii populations at Tashueshan and Shiouhluan and the M. kusanoi population at Kending, and even Soukar, are evolutionarily significant units for conservation programmes. [source] Development of a Core Set from a Large Rice Collection using a Modified Heuristic Algorithm to Retain Maximum DiversityJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 12 2009Hun-Ki Chung Abstract A new heuristic approach was undertaken for the establishment of a core set for the diversity research of rice. As a result, 107 entries were selected from the 10 368 characterized accessions. The core set derived using this new approach provided a good representation of the characterized accessions present in the entire collection. No significant differences for the mean, range, standard deviation and coefficient of variation of each trait were observed between the core and existing collections. We also compared the diversity of core sets established using this Heuristic Core Collection (HCC) approach with those of core sets established using the conventional clustering methods. This modified heuristic algorithm can also be used to select genotype data with allelic richness and reduced redundancy, and to facilitate management and use of large collections of plant genetic resources in a more efficient way. [source] Genetic structure of the European polecat (Mustela putorius) and its implication for conservation strategiesJOURNAL OF ZOOLOGY, Issue 1 2006C. Pertoldi Abstract During the last century, the European polecat Mustela putorius populations in most of Europe declined and survived in fragmented patches, because of habitat alterations and direct persecution. To assess the genetic consequences of the demographic decline and to describe the spatial pattern of genetic diversity, 250 polecats sampled at seven localities from five European countries , Poland, Denmark (southern Denmark and northern Denmark), Spain, Belgium (eastern and western) and the Netherlands , were screened by means of nine microsatellite loci. Genetic diversity estimated by mean expected heterozygosity (HE) and allelic richness (AR) were moderately high within populations [range: 0.50 (northern Denmark) ,HE,0.64 (Poland) and 1.33,AR,7.80] as compared with other carnivores and mustelids. Bottleneck tests suggested that polecat populations in southern Denmark and Poland have declined recently and populations from northern Denmark and the Netherlands have expanded recently, whereas the remaining populations did not show any sign of demographic change. Recent demographic changes could suggest that some of the populations are still not in equilibrium, which could partly explain the relatively high genetic variability observed in polecat populations despite the drastic decline in population size observed in several European countries. A significant heterozygote deficiency [FIS=0.19; 0.01,95% confidence interval (CI),0.32] suggests substructuring within the total European sample. Partitioning of the genetic variation among sampling locations (FST=0.14; 0.06,95% CI,0.23) and pairwise FST between localities (range: 0.01,FST,0.37) without any correlation with the geographic distances between localities were found, suggesting a recent divergence and a restriction of gene flow between populations and the action of genetic drift. An assignment test showed that the Polish and the northern Danish populations were the most unique, whereas the other populations were partially admixed. Factorial component analysis tests indicate a subdivision of the total sample into two distinct groups: one including the samples from Poland and the two Danish localities and the second group comprising the remaining localities investigated. The observed pattern of genetic differentiation is suggested to be due to two main routes of recolonization after the last glacial period. To compare the results obtained with microsatellite data, the most variable region of the mitochondrial DNA (d-loop) was sequenced and different phylogenetic reconstructions and genetic diversity analyses based on nucleotide (,) and haplotype diversity (h) measures within populations were performed using a subsample of populations. The lack of well-defined geographical structure, as well as the reduced level of mitochondrial DNA variability (,: 0.00274±0.00038; h: 0.876±0.028) that was found, has been previously reported in several studies on different carnivores and supports the hypothesis of post-glacial recolonization from southern or eastern refugees of Europe as suggested by the microsatellite data. Implications for conservation strategies of the polecat at the European level are discussed. [source] Seasonal effects and fine-scale population dynamics of Aedes taeniorhynchus, a major disease vector in the Galapagos IslandsMOLECULAR ECOLOGY, Issue 20 2010ARNAUD BATAILLE Abstract Characterization of the fine-scale population dynamics of the mosquito Aedes taeniorhynchus is needed to improve our understanding of its role as a disease vector in the Galapagos Islands. We used microsatellite data to assess the genetic structure of coastal and highland mosquito populations and patterns of gene flow between the two habitats through time on Santa Cruz Island. In addition, we assessed possible associations of mosquito abundance and genetic diversity with environmental variables. The coastal and highland mosquito populations were highly differentiated from each other all year round, with some gene flow detected only during periods of increased precipitation. The results support the hypothesis that selection arising from ecological differences between habitats is driving adaptation and divergence in A. taeniorhynchus, and maintaining long-term genetic differentiation of the populations against gene flow. The highland and lowland populations may constitute an example of incipient speciation in progress. Highland populations were characterized by lower observed heterozygosity and allelic richness, suggesting a founder effect and/or lower breeding site availability in the highlands. A lack of reduction in genetic diversity over time in highland populations suggests that they survive dry periods as dormant eggs. Association between mosquito abundance and precipitation was strong in the highlands, whereas tide height was the main factor affecting mosquito abundance on the coast. Our findings suggests differences in the infection dynamics of mosquito-borne parasites in the highlands compared to the coast, and a higher risk of mosquito-driven disease spread across these habitats during periods of increased precipitation. [source] Genetic effective size, Ne, tracks density in a small freshwater cyprinid, Pecos bluntnose shiner (Notropis simus pecosensis)MOLECULAR ECOLOGY, Issue 14 2010MEGAN J. OSBORNE Abstract Genetic monitoring tracks changes in measures of diversity including allelic richness, heterozygosity and genetic effective size over time, and has emerged as an important tool for understanding evolutionary consequences of population management. One proposed application of genetic monitoring has been to estimate abundance and its trajectory through time. Here, genetic monitoring was conducted across five consecutive year for the Pecos bluntnose shiner, a federally threatened minnow. Temporal changes in allele frequencies at seven microsatellite DNA loci were used to estimate variance effective size (NeV) across adjacent years in the time series. Likewise, effective size was computed using the linkage disequilibrium method (NeD) for each sample. Estimates of Ne were then compared to estimates of adult fish density obtained from traditional demographic monitoring. For Pecos bluntnose shiner, density (catch-per-unit-effort), NeV and NeD were positively associated across this time series. Results for Pecos bluntnose shiner were compared to a related and ecologically similar species, the Rio Grande silvery minnow. In this species, density and NeV were negatively associated, which suggested decoupling of abundance and effective size trajectories. Conversely, density and NeD were positively associated. For Rio Grande silvery minnow, discrepancies among estimates of Ne and their relationships with adult fish density could be related to effects of high variance in reproductive success in the wild and/or effects of supplementation of the wild population with captive-bred and reared fish. The efficacy of Ne as a predictor of density and abundance may depend on intrinsic population dynamics of the species and how these dynamics are influenced by the landscape features, management protocols and other factors. [source] Inferring ancient Agave cultivation practices from contemporary genetic patternsMOLECULAR ECOLOGY, Issue 8 2010KATHLEEN C. PARKER Abstract Several Agave species have played an important ethnobotanical role since prehistory in Mesoamerica and semiarid areas to the north, including central Arizona. We examined genetic variation in relict Agave parryi populations northeast of the Mogollon Rim in Arizona, remnants from anthropogenic manipulation over 600 years ago. We used both allozymes and microsatellites to compare genetic variability and structure in anthropogenically manipulated populations with putative wild populations, to assess whether they were actively cultivated or the result of inadvertent manipulation, and to determine probable source locations for anthropogenic populations. Wild populations were more genetically diverse than anthropogenic populations, with greater expected heterozygosity, polymorphic loci, effective number of alleles and allelic richness. Anthropogenic populations exhibited many traits indicative of past active cultivation: fixed heterozygosity for several loci in all populations (nonexistent in wild populations); fewer multilocus genotypes, which differed by fewer alleles; and greater differentiation among populations than was characteristic of wild populations. Furthermore, manipulated populations date from a period when changes in the cultural context may have favoured active cultivation near dwellings. Patterns of genetic similarity among populations suggest a complex anthropogenic history. Anthropogenic populations were not simply derived from the closest wild A. parryi stock; instead they evidently came from more distant, often more diverse, wild populations, perhaps obtained through trade networks in existence at the time of cultivation. [source] Origin and genetic diversity of Western European populations of the potato cyst nematode (Globodera pallida) inferred from mitochondrial sequences and microsatellite lociMOLECULAR ECOLOGY, Issue 9 2008O. PLANTARD Abstract Native to South America, the potato cyst nematode Globodera pallida is one of the principal pests of Andean potato crops and is also an important global pest following its introduction to Europe, Africa, North America, Asia and Oceania. Building on earlier work showing a clear south to north phylogeographic pattern in Peruvian populations, we have been able to identify the origin of Western European populations with high accuracy. They are all derived from a single restricted area in the extreme south of Peru, located between the north shore of the Lake Titicaca and Cusco. Only four cytochrome b haplotypes are found in Western Europe, one of them being also found in some populations of this area of southern Peru. The allelic richness at seven microsatellite loci observed in the Western European populations, although only one-third of that observed in this part of southern Peru, is comparable to the allelic richness observed in the northern region of Peru. This result could be explained by the fact that most of the genetic variability observed at the scale of a field or even of a region is already observed at the scale of a single plant within a field. Thus, even introduction via a single infected potato plant could result in the relatively high genetic variability observed in Western Europe. This finding has important consequences for the control of this pest and the development of quarantine measures. [source] Conserving the evolutionary potential of California valley oak (Quercus lobata Née): a multivariate genetic approach to conservation planningMOLECULAR ECOLOGY, Issue 1 2008DELPHINE GRIVET Abstract California valley oak (Quercus lobata Née) is a seriously threatened endemic oak species in California and a keystone species for foothill oak ecosystems. Urban and agricultural development affects a significant fraction of the species' range and predicted climate change is likely to dislocate many current populations. Here, we explore spatial patterns of multivariate genotypes and genetic diversity throughout the range of valley oak to determine whether ongoing and future patterns of habitat loss could threaten the evolutionary potential of the species by eradicating populations of distinctive genetic composition. This manuscript will address three specific questions: (i) What is the spatial genetic structure of the chloroplast and nuclear genetic markers? (ii) What are the geographical trends in the distribution of chloroplast and nuclear genotypes? (iii) Is there any part of the species' range where allelic diversity in either the chloroplast or nuclear genomes is particularly high? We analysed six chloroplast and seven nuclear microsatellite genetic markers of individuals widespread across the valley oak range. We then used a multivariate approach correlating genetic markers and geographical variables through a canonical trend surface analysis, followed by GIS mapping of the significant axes. We visualized population allelic richness spatially with GIS tools to identify regions of high diversity. Our findings, based on the distribution of multivariate genotypes and allelic richness, identify areas with distinctive histories and genetic composition that should be given priority in reserve network design, especially because these areas also overlap with landscape change and little degree of protection. Thus, without a careful preservation plan, valuable evolutionary information will be lost for valley oak. [source] Genetic diversity and population size: island populations of the common shrew, Sorex araneusMOLECULAR ECOLOGY, Issue 10 2007THOMAS A. WHITE Abstract Populations of many species are currently being fragmented and reduced by human interactions. These processes will tend to reduce genetic diversity within populations and reduce individual heterozygosities because of genetic drift, inbreeding and reduced migration. Conservation biologists need to know the effect of population size on genetic diversity, as this is likely to influence a population's ability to persist. Island populations represent an ideal natural experiment with which to study this problem. In a study of common shrews (Sorex araneus) on offshore Scottish islands, 497 individuals from 13 islands of different sizes and 6 regions on the mainland were trapped and genotyped at eight microsatellite loci. Previous genetic work had revealed that most of the islands in this study were highly genetically divergent from one another and the mainland. We found that most of the islands exhibited lower genetic diversity than the mainland populations. In the island populations, mean expected heterozygosity, mean observed heterozygosity and mean allelic richness were significantly positively correlated with log island size and log population size, which were estimated using habitat population density data and application of a Geographic Information System. [source] Molecular evidence for a founder effect in invasive house finch (Carpodacus mexicanus) populations experiencing an emergent disease epidemicMOLECULAR ECOLOGY, Issue 1 2006DANA M. HAWLEY Abstract The impact of founder events on levels of genetic variation in natural populations remains a topic of significant interest. Well-documented introductions provide a valuable opportunity to examine how founder events influence genetic diversity in invasive species. House finches (Carpodacus mexicanus) are passerine birds native to western North America, with the large eastern North American population derived from a small number of captive individuals released in the 1940s. Previous comparisons using amplified fragment length polymorphism (AFLP) markers found equivalent levels of diversity in eastern and western populations, suggesting that any genetic effects of the founder event were ameliorated by the rapid growth of the newly established population. We used an alternative marker system, 10 highly polymorphic microsatellites, to compare levels of genetic diversity between four native and five introduced house finch populations. In contrast to the AFLP comparisons, we found significantly lower allelic richness and heterozygosity in introduced populations across all loci. Three out of five introduced populations showed significant reductions in the ratio of the number of alleles to the allele size range, a within-population characteristic of recent bottlenecks. Finally, native and introduced populations showed significant pairwise differences in allele frequencies in every case, with stronger isolation by distance within the introduced than native range. Overall, our results provide compelling molecular evidence for a founder effect during the introduction of eastern house finches that reduced diversity levels at polymorphic microsatellite loci and may have contributed to the emergence of the Mycoplasma epidemic which recently swept the eastern range of this species. [source] Low gene flow but high genetic diversity in the threatened Mallorcan midwife toad Alytes muletensisMOLECULAR ECOLOGY, Issue 11 2005F. J. L. KRAAIJEVELD-SMIT Abstract We investigated fine-scale genetic structuring in the rare and vulnerable Mallorcan midwife toad Alytes muletensis using eight polymorphic microsatellite markers. The current range of this amphibian is restricted to some 19 sites of which six are derived from reintroductions, all located in the mountain ranges of Mallorca. We sampled tadpoles from 14 pools covering 10 natural sites and two reintroduction sites for microsatellite DNA analyses. Relatively high levels of genetic variation were found in most pools (HE = 0.38,0.71, allelic richness = 2.6,6.2). Only at one pool has the population recently gone through a bottleneck. Dispersal between pools in different torrents does not occur whereas downstream dispersal between pools within the same torrent does happen at low frequencies. This occasional exchange of individuals does not lead to neighbouring pools in the same torrent being panmictic. This can be concluded because all FST values (0.12,0.53) differ significantly from zero and structure analyses identified neighbouring pools as separate populations. Furthermore, assignment and migration tests showed little exchange between neighbouring pools. If upstream locations or complete torrents go extinct, they are unlikely to be recolonized naturally. For conservation purposes, reintroductions of tadpoles to sites where local extinctions have occurred may therefore be advisable. [source] SHORT COMMUNICATION: Do farmers reduce genetic diversity when they domesticate tropical trees?MOLECULAR ECOLOGY, Issue 2 2005A case study from Amazonia Abstract Agroforestry ecosystems may be an important resource for conservation and sustainable use of tropical trees, but little is known of the genetic diversity they contain. Inga edulis, a widespread indigenous fruit tree in South America, is used as a model to assess the maintenance of genetic diversity in five planted vs. five natural stands in the Peruvian Amazon. Analysis of five SSR (simple sequence repeat) loci indicated lower allelic variation in planted stands [mean corrected allelic richness 31.3 (planted) and 39.3 (natural), P = 0.009]. Concerns regarding genetic erosion in planted Amazonian tree stands appear valid, although allelic variation on-farm is still relatively high. [source] Genetic and morphological evolution following a founder event in the dark-eyed junco, Junco hyemalis thurberiMOLECULAR ECOLOGY, Issue 3 2004C. A. Rasner Abstract An isolated population of dark-eyed juncos, Junco hyemalis, became established on the campus of the University of California at San Diego (UCSD), probably in the early 1980s. It now numbers about 70 breeding pairs. Populations across the entire natural range of the subspecies J. h. thurberi are weakly differentiated from each other at five microsatellite loci (FST = 0.01). The UCSD population is significantly different from these populations, the closest of which is 70 km away. It has 88% of the genetic heterozygosity and 63% of the allelic richness of populations in the montane range of the subspecies, consistent with a harmonic mean effective population size of 32 (but with 95% confidence limits from four to > 70) over the eight generations since founding. Results suggest a moderate bottleneck in the early establishment phase but with more than seven effective founders. Individuals in the UCSD population have shorter wings and tails than those in the nearby mountains and a common garden experiment indicates that the morphological differences are genetically based. The moderate effective population size is not sufficient for the observed morphological differences to have evolved as a consequence of genetic drift, indicating a major role for selection subsequent to the founding of the UCSD population. [source] Population genetic structure of male black grouse (Tetrao tetrix L.) in fragmented vs. continuous landscapesMOLECULAR ECOLOGY, Issue 9 2003Alain Caizergues Abstract We investigated the association of habitat fragmentation with genetic structure of male black grouse Tetrao tetrix. Using 14 microsatellites, we compared the genetic differentiation of males among nine localities in continuous lowland habitats in Finland to the genetic differentiation among 14 localities in fragmented habitats in the Alps (France, Switzerland and Italy). In both areas, we found significant genetic differentiation. However, the average differentiation, measured as ,, was more than three times higher in the Alps than in Finland. The greater differentiation found in the Alps is probably due to the presence of mountain ridges rising above natural habitats of the species, which form barriers to gene flow, and to a higher influence of genetic drift resulting from lower effective sizes in highly fragmented habitats. The detection of isolation by distance in the Alps suggests that gene flow among populations does occur. The genetic variability measured as gene diversity HE and allelic richness A was lower in the Alps than in Finland. This could result from the higher fragmentation and/or from the fact that populations in the Alps are isolated from the main species range and have a lower effective size than in Finland. This study suggests that habitat fragmentation can affect genetic structure of avian species with relatively high dispersal propensities. [source] Genetic variation in BoLA microsatellite loci in Portuguese cattle breedsANIMAL GENETICS, Issue 1 2009C. Bastos-Silveira Summary Major histocompatibility complex (MHC) typing based on microsatellites can be a valuable approach to understanding the selective processes occurring at linked or physically close MHC genes and can provide important information on variability and relationships of populations. Using microsatellites within or in close proximity with bovine lymphocyte antigen (BoLA) genes, we investigated the polymorphisms in the bovine MHC, known as the BoLA, in eight Portuguese cattle breeds. Additional data from non-BoLA microsatellite loci were also used to compare the variability between these regions. Diversity was higher in BoLA than in non-BoLA microsatellites, as could be observed by the number of alleles, allelic richness and observed heterozygosity. Brava de Lide, a breed selected for aggressiveness and nobility, presented the lowest values of observed heterozygosity and allelic richness in both markers. Results from neutrality tests showed few statistically significant differences between the observed Hardy,Weinberg homozygosity (F) and the expected homozygosity (FE), indicating the apparent neutrality of the BoLA microsatellites within the analysed breeds. Nevertheless, we detected a trend of lower values of observed homozygosity compared with the expected one. We also detected some differences in the levels of allelic variability among the four BoLA microsatellites. Our data showed a higher number of alleles at the BoLA-DRB3 locus than at the BoLA-DRBP1 locus. These differences could be related to their physical position in the chromosome and may reflect functional requirements for diversity. [source] Population structure, genetic variation and morphological diversity in indigenous sheep of EthiopiaANIMAL GENETICS, Issue 6 2007S. Gizaw Summary We investigated genetic and morphological diversity and population structure of 14 traditional sheep populations originating from four ecological zones in Ethiopia (sub-alpine, wet highland, sub-humid lowland and arid lowland). All animals (n = 672) were genotyped for 17 microsatellite markers and scored for 12 morphological characters. The sheep were initially classified as fat-tailed (11 populations), thin-tailed (one population) and fat-rumped sheep (two populations). These classifications are thought to correspond to three consecutive introduction events of sheep from the Near-East into East Africa. For the 14 populations, allelic richness ranged from 5.87 to 7.51 and expected heterozygosity (HE) from 0.66 to 0.75. Genetic differentiations (FST values) between all pairs of populations, except between sub-alpine populations, were significantly different from zero (P < 0.001). Cluster analysis of morphological characters and a dendrogram constructed from genetic distances were broadly consistent with the classification into fat-tailed, thin-tailed and fat-rumped sheep. Bayesian cluster analysis using microsatellite markers indicated that there has been further genetic differentiation after the initial introduction of sheep into Ethiopia. Investigation of factors associated with genetic variation showed that an isolation-by-distance model, independently of other factors, explained most of the observed genetic variation. We also obtained a strong indication of adaptive divergence in morphological characters, patterns of morphological variation being highly associated with ecology even when the effect of neutral genetic divergence (FST) was parcelled out in partial Mantel tests. Using a combination of FST values, Bayesian clustering analysis and morphological divergence, we propose a classification of Ethiopian sheep into six breed groups and nine breeds. [source] Genome-wide genetic diversity of Holstein Friesian cattle reveals new insights into Australian and global population variability, including impact of selectionANIMAL GENETICS, Issue 1 2007K. R. Zenger Summary Past breeding strategies for dairy cattle have been very effective in producing rapid genetic gain to achieve industry targets and raise profitability. Such gains have been largely facilitated by intense selection of sires combined with the use of artificial insemination. However, this practice can potentially limit the level of genetic diversity through inbreeding and selection plateaus. The rate of inbreeding in Australia is increasing, primarily as a result of semen importation from a small number of prominent bulls from the USA. The effect of this genetic influx in the Australian dairy cattle population is poorly understood both in terms of diversity and local adaptation/divergence. This study uses 845 genome-wide SNP genetic markers and 431 bulls to characterize the level of genetic diversity and genetic divergence within the Australian and international Holstein Friesian dairy population. No significant differences in genetic diversity (as measured by heterozygosity [Ho] and allelic richness [A]) were observed over the 25-year time period (1975,1999) for bulls used in Australia. The importation of foreign semen into Australia has increased the effective population size until it was in effect a sub-sample of the global population. Our data indicate that most individuals are equally closely related to one another, regardless of country of origin and year of birth. In effect, the global population can be considered as one single population unit. These results indicate that inbreeding, genetic drift and selection has had little effect at reducing genetic diversity and differentiating the Australian Holstein Friesian population at a genome-wide level. [source] Genetic variability revealed with microsatellite markers in an introduced population of the abalone Haliotis discus hannai InoAQUACULTURE RESEARCH, Issue 3 2009S Marchant Abstract One of the challenges for the culture of any species is to control the loss of genetic variability, which may result in a decrease in the quality of commercially important traits. The goal of this study is to assess the genetic diversity of a hatchery population of the Pacific abalone (Haliotis discus hannai) from the Center for Abalone Production of the Universidad Católica del Norte (CAP-UCN) that is maintained under a breeding programme. We used six polymorphic microsatellite markers within the cultivated population. The loci Awb033 and Awb079 had the highest number of alleles (11 and 10 respectively) and the loci Awb022 and Awb026 the lowest (two and four respectively). The mean number of alleles per locus was 6.83. The average observed and expected heterozygosities were 0.71 and 0.70, respectively, and the average FIS (f) index was ,0.023. We compared the population genetic parameters of the CAP-UCN population with previously published data of wild and hatchery populations of the same species. Results indicate lower genetic diversity estimated as allelic richness in the introduced population with a loss of 11,58% alleles per locus. Despite the high allelic loss, the estimated inbreeding coefficient suggests that the breeding programme carried out in the CAP-UCN has controlled and maintained heterozygosity levels successfully. A temporal study is necessary to determine whether the genetic diversity loss detected was caused during the initial introduction of breeders or to the breeding programme actually implemented. [source] Genetic variability in the European bison (Bison bonasus) population from Bia,owie,a forest over 50 yearsBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2009GORZATA TOKARSKA The aim of this study was to assess potential post-bottleneck temporal genetic differentiation following the reintroduction of the species into the Bia,owie,a Forest. Variability of 12 polymorphic microsatellite markers was analysed for 178 individuals born between 1955 and 2005, divided by birth year into five temporal groups. Low overall allelic richness (AR) per locus (AR = 2.0) and a low overall expected heterozygosity (HE = 0.28) were observed. The overall FIS was not significantly different from zero. The mean FIS values were, however, significantly different from zero for individuals born between 1955 and 1965 (FIS = 0.19). A Bayesian computation was used to estimate effective population size (Ne) for each temporal group. We observed relatively small values of Ne ranging from 7.9 to 28.4. The low Ne values confirm that, despite a rapid growth of the bison population following the founder event, Ne increased only slowly. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 801,809. [source] | ||||||||||