Number Of Unique Genotypes Research Articles

Inferred pseudo-cryptic speciation in the coccolithophore species Braarudosphaera bigelowii (Gran and Braarud) during the Early Paleocene (Danian)

Abstract Pseudo-cryptic speciation occurs commonly in living oceanic plankton. In the coccolithophores, recent genetic studies have revealed that Braarudosphaera bigelowii has a number of unique genotypes that correlate well with pentalith size, indicating that this coccolithophore “species” actually contains multiple pseudo-cryptic taxa. In order to look for evidence of pseudo-cryptic speciation in the past, we measured the radii of 2800 B. bigelowii pentaliths from the Braarudosphaera-rich limestones that contain the GSSP for the Lower/Middle Paleocene (Danian/Selandian) boundary at Zumaia, Spain. Analysis of the radius measurements using the Expectation-Maximization algorithm yielded two size groups, herein termed form X (

Use of non-invasive techniques to determine population size of the marine otter in two regions of Peru

The marine otter (Lontra felina) can be found on rocky shores from the northern coast of Peru (9°S) to the extreme south of Argentina (56°S). This species is currently classified as endangered but there is little information on population size because marine otters are very difficult to observe and count. Between June and August 2012 we collected 240 samples of marine otter feces from seven localities in Peru. All locations were visited four times. One-hundred and thirty-three samples (55%) were successfully amplified at five to seven microsatellite loci and a sex-linked marker. We identified a minimum of 80 individuals (41 males and 39 females) across all locations for a density estimate of 4.4 otters per km, a value about 2X higher than estimates based on previous visual counts. Estimates using the program CAPWIRE averaged 12.6 otters/km, a value six times higher than estimates based on previous visual counts, although confidence limits were large due to the low number of recaptures. There was a strong positive relationship between the number of fresh scats and the number of unique genotypes, suggesting scat counts might be used to estimate the minimum number of otters at a site. Non-invasive genotyping of marine otter feces and scat counts will be valuable tools for estimating population sizes and monitoring movements of this secretive species.

Reproductive mode and fine-scale population genetic structure of grape phylloxera (Daktulosphaira vitifoliae) in a viticultural area in California

BackgroundGrape phylloxera (Daktulosphaira vitifoliae) is one of the world’s most important viticultural pests. However, the reproductive mode, genetic structure and host adaptation of phylloxera in various viticultural environments remains unclear. We examined reproductive mode and genetic structure of phylloxera by analyzing microsatellite makers across the samples from four vineyard-sites in California.ResultThe phylloxera populations in California are believed to have predominantly parthenogenetic reproduction. Therefore, genetic diversity of phylloxera is expected to be limited. However, this study showed relatively high levels of diversity in Napa and Yolo county populations with a large number of unique genotypes, average number of alleles (2.1 to 2.9) and observed heterozygosities (0.330 to 0.388) per vineyard-sites. Reproduction diversity index (G: N—unique genotypes versus number of samples) ranged from 0.500 to 0.656 among vineyard-sites. Both significant and non-significant Psex (probability of sexual reproduction) were observed among different repeated genotypes within each vineyard. Moreover, high variation of FIS was observed among different loci in each vineyard-site. Genetic structure analysis (UPGMA) and various measures of population differentiations (FST, PCA, and gene flow estimates) consistently separated AXR#1 (Vitis vinifera x V. rupestris—widely planted in California during the 1960s and 1970s) associated populations from the populations associated with other different rootstocks.ConclusionGenetic diversity, G: N ratio, Psex and FIS consistently suggested the occurrence of both parthenogenetic and sexual reproduction in California populations. This study clearly identified two major groups of phylloxera obtained from various rootstocks, with one group exclusively associated with only AXR#1 rootstock, defined as “biotype B”, and another group associated with vinifera-based rootstocks, known as “biotype A”.

GENETIC DIVERSITY OF INTENSIVELY AND EXTENSIVELY MANAGED CHESTNUT (CASTANEA SATIVA) ORCHARDS IN GREECE

Chestnut (Castanea sativa) orchards in Greece can be broadly classified in two categories: intensively managed (commercial cultivars grafted on selected rootstock established on agricultural land in the vicinity of rural communities) and extensively managed (local scions grafted on wild trees demarcating areas within natural forests, away from rural communities). The genetic diversity and multilocus genetic structure of two intensively and two extensively managed orchards is reported and compared based on 17 isoenzyme loci. Results indicated that intensively managed orchards present a high number of unique genotypes (85% of the total number of individuals), while extensively managed orchards have a rather low-number of unique genotypes (21% of the total number of individuals). In one intensively managed orchard, interspecific C. sativa × C. crenata hybrids were identified in 22% of the individuals studied. Genetic diversity parameters were higher in the intensively managed orchards evidently as a result of the higher number of alleles present (mean average number of alleles per locus in the intensively and the extensively managed orchards was 2.31 versus 1.50 respectively). The genetic diversity of intensively managed orchards is comparable to that of adjacent natural populations and higher than the diversity reported in western European orchards. It is postulated that the greater number of unique genotypes in intensively managed orchards may reflect the traditional arboricultural practices of the local growers. It can present an obstacle regarding the nut uniformity for industrial processing; nevertheless it may be beneficial under climatic change scenarios. The implementation of the above results for further selection and breeding is discussed.

Field surveys of capercaillie (Tetrao urogallus) in the Swiss Alps underestimated local abundance of the species as revealed by genetic analyses of non-invasive samples

An increasing number of species are becoming threatened by habitat loss and fragmentation. Therefore, solid estimates of the species’ abundance in the remaining populations are required to develop suitable conservation measures and to monitor their effectiveness. The capercaillie (Tetrao urogallus L.) has experienced a dramatic decline in central Europe and has disappeared from large areas of its former natural range. In Switzerland, the species’ distribution, habitat requirements and demographic status were studied and evaluated in an attempt to support appropriate management decisions to conserve the species. National surveys of the capercaillie in Switzerland have traditionally been obtained from male counts at leks. However, individual attendance to the lek is sex- and age-specific. Thus, male counts at leks may provide a biased estimate of local population sizes. In the present study, we compared two alternative indirect methods to estimate the sizes of local populations at eight study sites situated in the Alps and Prealps of Switzerland. We first assessed the sizes of local populations from the observed density and distribution of direct and indirect evidence of the species’ presence during field surveys. Feather and faeces samples collected during field surveys were genotyped at twelve nuclear microsatellite loci and a sex-specific nuclear gene fragment. Individual genotypes were used as genetic tags to estimate the sizes of the eight local populations using an urn model developed for small populations. The index of local population sizes assessed from field surveys was lower than the number of unique genotypes at each study site, which itself underestimated the abundances of populations in most cases. Based on our results, the genetic tagging method appeared to be less biased than the field survey method. However, an alternative faeces sampling scheme, resulting in 2–3 genotypings per individual, could further improve the accuracy of the size estimates of local populations. Our study confirms that genetic tagging methods are a valuable tool to estimate the sizes of local populations and to monitor the response of rare and elusive species to management actions.

Genetic diversity of poplar leaf rust populations in the north-central United States

Uredinia of poplar leaf rust, Melampsora medusae Thüm f.sp. deltoides, appeared in late July 1998, June 1999, and August 2000 in a cottonwood (Populus deltoides Bartr.) stand in Ames, Iowa. Seedlings of the alternate host (eastern larch, Larix laricina (Du Roi) K. Koch) set out at the site in spring 2000 formed aecia 3 months before uredinia appeared. Using three PCR-based microsatellite markers, the aecial population was genetically diverse and in Hardy–Weinberg equilibrium, typical of a population that had gone through sexual reproduction. Uredinia populations in 1998–2000 had lower levels of gene diversities (from 0.58 to 0.71) and were not in Hardy–Weinberg equilibrium. Of nine populations in Minnesota, Iowa, and Missouri during the early stage of the 1999 epidemic, the two populations with the highest gene diversity, the highest level of heterozygosity, and the greatest number of unique genotypes were within the natural geographic range of larch. However, the southernmost population in Missouri was also in Hardy–Weinberg equilibrium. Epidemics started sooner in Iowa than in Minnesota, which contradicts the hypothesis that epidemics begin in northern regions where the alternate hosts naturally overlap. Epidemics appeared to commence independently in the various locations, perhaps focused around areas where ornamental larch is in proximity to P. deltoides.

Genetic connectivity of the scleractinian coral Goniastrea aspera around the Okinawa Islands

Genetic variation and gene flow in the scleractinian coral Goniastrea aspera (Verrill), found around the north–south Okinawa Islands, were studied using allozyme and starch gel electrophoresis. The relative contribution of sexual and asexual reproduction to recruitment was determined. Analysis of multilocus genotypes of samples, collected at least 3 m apart, identified a high number of unique genotypes (NG) relative to the number of individuals sampled (N) (mean NG: N=0.97±0.03 [SD]), and also highly observed genotypic diversity (GO) relative to expected genotypic diversity under Hardy–Weinberg equilibrium (GE) (mean GO: GE=0.95±0.06 [SD]). These results suggest that the collected G. aspera propagated predominantly by sexual reproduction in Okinawan populations. The UPGMA grouping of five populations in the Okinawa, based on Nei’s unbiased genetic distance, showed two clusters that were south and north Okinawa populations. AMOVA analyses that incorporated the data of populations from the Kerama and the Ishigaki Islands detected significant FSC values among the populations within groups in analyses distinguishing north–south Okinawa, Okinawa–Kerama, and Okinawa–Kerama–Ishigaki. Significant FCT values were neither detected between north–south Okinawa nor between the Okinawa–Kerama groups. The “local-recruits” hypothesis, which assumes that a substantial proportion of recruits is produced locally, appears to be applicable to coral populations in the Ryukyu Archipelago. On the other hand, detection of nonsignificant FCT values indicated the presence of genetic connectivity between north–south Okinawa and Kerama–Okinawa groups.