Inferring seed exchange between farmers from population genetic structure of barley landrace Arabi Aswad from Northern Syria

Apart from their significance in genetic conservation, barley landraces are still favoured by local farmers in low-input farming systems. They often perform more predictably under adverse conditions than modern cultivars due to local adaptation. Increased seed exchange between farmers may put adaptation of local populations of barley landraces at risk. Isozyme markers were used to investigate differentiation and infer gene flow between local populations of barley landrace Arabi Aswad in Northern Syria. Inferred gene flow decreased exponentially with geographic distance and may imply that seed exchange between farmers is limited to a regional scale and diminishes over longer distance. Gene flow seems to be a suitable index for estimating seed exchange in highly inbreeding crop species such as barley. In the future, improved mobility of farmers and extension work may facilitate seed exchange over longer distances, and consequently jeopardise preservation of locally adapted landraces in barley.     

Genetic insights into population recovery following experimental perturbation in a fragmented landscape

We investigated the mechanism of population recovery in the Australian bush rat, Rattus fuscipes, following experimental perturbation in a fragmented landscape. Our study involved genetic monitoring over 24 months following the removal of animals from seven sites by intense trapping. A total of 171 bush rats was removed and statistical analysis confirmed a significant knockdown. At one site, local extinction followed the perturbation, while population sizes at 24 months varied from 37% to 90% of the original population size at the remaining sites. The outcomes of genetic analysis at 11 microsatellite loci and mtDNA indicated that population recovery was achieved predominantly by residual animals: recovery populations were genetically more similar to their respective pre-treatment population than near neighbours; assignment tests detected few immigrants; there was no influx of new immigrant alleles and haplotypes. This finding is consistent with emerging evidence for restricted gene flow in bush rats. The local extinction observed at one site indicate that, under severe perturbation restricted dispersal limits opportunities for, and the rate of, population recovery. Thus, while the bush rat appears resilient to substantial population size perturbation, once a critical minimum population size threshold has been reached, this species may be susceptible to local extinction. We concluded that some widespread species currently predicted to be extinction-resilient may, in fact, be at risk if localized extinctions occur and dispersal limitations prevent recolonisation.     

Ecological and genetic measurements of dispersal in a threatened dragonfly

Leucorrhinia caudalis is a rare dragonfly, threatened throughout its European distribution. The species was formerly widespread in the Swiss lowlands, but only a single population remained in the 1980s. However, a spread has recently been observed, with additional ponds being colonised, sometimes at considerable distance. Despite this evidence of recent long-distance dispersal, it is unknown whether L. caudalis regularly moves among ponds or whether this is a rather rare event. A combination of an ecological mark-resight and a population genetic study was applied to investigate contemporary dispersal and the genetic footprint of the recent population history of L. caudalis in Switzerland. DNA for genetic microsatellite analysis was extracted from exuviae. The mark-resight study and the genetic analysis gave congruent results. They showed that L. caudalis is mostly a sedentary species, with only a few contemporary dispersal events over distances up to 5 km being observed. The genetic analysis was in agreement with the recent population history of the Swiss populations. The oldest and largest population showed large genetic diversity and acted as source population for the recent spread of L. caudalis in Switzerland. Recurrent gene flow among this source population and close populations caused substantial local genetic variation in the latter, as well as low population differentiation. The two recently founded distant populations (?30 km distance) were genetically less diverse and highly differentiated. These distant populations and another recently colonised population also expressed signatures of genetic bottlenecks.     

Spatial genetic variation of a riparian wolf spider Pardosa agricola (Thorell, 1856) on lowland river banks: The importance of functional connectivity in linear spatial systems

Habitat patches along river systems are often highly isolated and characterised by a high degree of heterogeneity at different spatio-temporal scales. The connectivity between river bank arthropod populations directly adjoining the river channel is often greatly disturbed due to river regulation. While flight-active arthropods easily disperse upstream, less mobile species are expected to show predominant downstream dispersal unless specific upward movements are prevalent. In linear river ecosystems, downstream drift of organisms may therefore prevail with subsequently strong asymmetrical gene flow. We analysed patterns of genetic variation within and among nine spatially structured populations of the highly stenotopic riparian wolf spider (Lycosidae) Pardosa agricola (Thorell, 1856) using Amplified Fragment Length Polymorphism (AFLP) markers. No evidence was found for downstream accumulation of genetic diversity. The high genetic diversity is hypothesised to be the result of historical drift processes. Nearby populations on the same river shore were less genetically differentiated compared with populations further away and/or on the opposite shore. This indicates that short-distance dispersal still occurs on river banks during low water flow levels, but at the same time that the river channel constitutes a physical barrier for species exchange between opposite shores. The rehabilitation of the riparian corridor will increase the amount of suitable habitat, the functional connectivity during periods of low flow-discharges and eventually riparian spider population persistence.     

AFLP analysis of genetic diversity in leafy kale (<Emphasis Type="Italic">Brassica oleracea</Emphasis> L. convar. <Emphasis Type="Italic">acephala</Emphasis> (DC.) Alef.) landraces,cultivars and wild populations in Europe

AFLP markers were used to characterize diversity and asses the genetic structure among 17 accessions of kale landraces, cultivars and wild populations from Europe. The range of average gene diversity in accessions was 0.11–0.27. Several landraces showed higher levels of diversity than the wild populations and one cultivar had the lowest diversity measures. The landraces that were most genetically diverse were from areas where kales are known to be extensively grown, suggesting in situ conservation in these areas as a supplement to storage of seeds in gene banks. An analysis of molecular variance (AMOVA) showed that 62% of the total variation was found within accessions. For most accessions, genetic distance was not related to geographic distance. Similarities among accessions were probably not caused by recent gene flow since they were widely separated geographically; more likely the relationship among them is due to seed dispersal through human interactions. Our results indicate that a kale population found in a natural habitat in Denmark was probably not truly wild but most likely an escape from a cultivated Danish kale that had subsequently become naturalized.     

Habitat quality, conspecific density, and habitat pre-use affect the dispersal behaviour of two earthworm species, Aporrectodea icterica and Dendrobaena veneta, in a mesocosm experiment

Dispersal capacity is a life-history trait that may have profound consequences for earthworm populations: it influences population dynamics, species persistence and distribution and community structure. It also determines the level of gene flow between populations and affects processes such as local adaptation, speciation and the evolution of life-history traits. It may play a great role in soil functioning by determining the spatial distribution of ecosystem engineers such as earthworms. Dispersal is an evolutionary outcome of the behaviour in response to the ecological constraints of the species. Hence different dispersal behaviour is expected from the different ecological types of earthworms. Nevertheless the dispersal behaviour of earthworms has been little documented.In this work we test a series of basic mechanisms that are fundamental and complementary to understand earthworms dispersal behaviour. We focus on the dispersal triggered by environmental conditions, a fundamental process usually termed “conditional dependent dispersal”. We show experimentally in mesocosms that in one week: 1) earthworm dispersal can be triggered by low habitat quality, either through soil quality or the presence/absence of litter. 2) Earthworms can be subject to positive density dependent dispersal, that is the rate of dispersal increases when density increases; and 3) earthworm dispersal can be reduced by the pre-use of the soil by conspecific individuals that are no longer present.Our results suggest that earthworms may be more mobile than expected from previous estimations, and that they present high capacities of habitat selection. In the light of our findings we elaborate a behavioural scenario of earthworm foraging, and propose several priority working directions.     

Barrier analysis detected genetic discontinuity among Ethiopian barley (Hordeum vulgare L.) landraces due to landscape and human mobility on gene flow

The rate of gene flow is greatly affected by the ability of a species to move from one location to another. In Ethiopia the presence of diverse agro-ecological zones, climatic features, rugged mountains and isolated valleys affected the seed-mediated gene flow among regions. Hence, this study was aimed at investigating and detecting presence of any gene barriers and genetic differentiation among regions. Thus, the study was proposed to test whether the high genetic diversity of barley in Ethiopia was due to a reduced gene flow resulting from geographic barriers and/or effects of human activities. A total of 199 barley landraces collected from 10 different geographic regions and altitudes of Ethiopia were analyzed for 15 molecular markers. A barrier analysis was conducted to identify any geographic areas with pronounced genetic discontinuity between the regions that can be interpreted as barriers to gene flow. The result obtained from analysis of molecular variances indicated high genetic variation within regions rather than between regions. Despite high gene flow among regions, we were able to detect genetic discontinuity due to landscape and human mobility for certain barley growing areas. Hence, it was postulated that these barriers have to be considered in genetic resource sampling strategies.     

Does seed dispersal by sheep affect the population genetic structure of the calcareous grassland species Bromus erectus?

This study investigates the contribution of the traditional land-use system “sheep herding” (transhumance) to the gene flow among populations. Three sheep trails with altogether 12 calcareous grassland sites were chosen for the analysis of the tussock grass Bromus erectus, which is known to be the species with the highest rate of dispersal via sheep fleece. Each trail links two to four isolated populations. Allozymes were chosen as genetic markers. Six loci were used, five of which were polymorphic. While genetic variability within populations was found to be quite high (averaged h=0.352), only little between-population differentiation was measured (G_ST=5.5%). Despite this, the UPGMA-dendrogram of Nei's genetic distance shows genetic similarity relations largely congruent with the sheep herding trails. However, a (more) detailed comparison reveals several differences between genetic patterns and trail system. Hence, additional factors other than dispersal by sheep are regarded as being responsible for exchange of genes, and sheep herding is considered to have only minor importance for the genetic patterns of the investigated species. The comparison of Bromus erectus to species with the same life history traits (i.e. pollination by wind, a perennial life cycle, and autopolyploid constitution) shows similar values, thus providing further evidence for the relatively small contribution of dispersal via sheep fleece.     

Population structure of the primary gene pool of Oryza sativa in Thailand

The gene pool of cultivated Asian rice consists of wild rice (Oryza rufipogon Griff.), cultivated rice (O. sativa L.) and a weedy form (O. sativa f. spontanea). All three components are widespread in Thailand, frequently co-occurring within fields and providing the opportunity for gene flow and introgression. The purpose to this study is to understand the on-going evolutionary processes that affect the gene pool of rice by analysis of microsatellite variation. Results indicate that O. rufipogon, the wild ancestor of rice, has high levels of genetic variation both within and among populations. Moreover, the variation is structured predominantly by annual and perennial life history. High levels of variation are detected among cultivars indicating Thai cultivated rice has a broad genetic base with only a 20 % reduction in diversity from its wild ancestor. The weedy rice populations reveal varying levels of genetic variation, from nearly as high as wild rice to near zero. Weedy rice is genetically structured into 2 groups. Some populations of invasive weedy rice are the result of hybridization and gene flow between local wild rice and local cultivated rice in the regions of co-occurrence. Other populations of weedy rice are genetically nearly identical to the local cultivated rice. The diversity analysis indicates that the rice gene pool in Thailand is a dynamic genetic system. Gene flow is ongoing among its three main components, first between cultivated and wild rice resulting in weedy rice. Weedy rice in turn crosses with both cultivated varieties and wild rice.     

Using SSR markers to determine the population genetic structure of wild apricot (<Emphasis Type="Italic">Prunus armeniaca</Emphasis> L.) in the Ily Valley of West China

Genetic structure of three wild populations (Xinyuan, Gongliu and Daxigou) of apricot in the Ily Valley, Xinjiang Uygur Autonomous Region of China, was investigated with microsatellite (simple sequence repeat, SSR) markers. The higher polymorphism and greater transportability of these markers between Prunus species proved SSR markers were much efficient for conducting genetic diversity studies in wild apricot. Nei's gene diversity (He) and Shannon's index of diversity (I) were 0.287 and 0.458, respectively. This indicated that the wild apricot in the Ily Valley still maintained a relatively high level of diversity. The Gst of 0.137 and Fst of 0.164 revealed that genetic variation mainly resided among individuals within populations (83.6–86.3%). Population differentiation could also be found according to the distribution of SSR alleles between the populations. Mantel test showed the genetic distance between populations was significantly correlated to the geographical distance. The modest amount of gene flow (2.684) would reduce the disjunction between wild apricots. The long-distance dispersal of pollen by insects was probably the main way of gene flow between populations. Based on the study of population genetic structure, an effective conservation strategy of the species was discussed.     

Restricted gene flow in the clonal hepatic Trichocolea tomentella in fragmented landscapes

We studied the genetic diversity, gene flow and population structure among 18 populations of the clonal bryophyte Trichocolea tomentella located in Finland, Lithuania, the UK and Canada using DNA fingerprinting methods. T. tomentella is a habitat-limited, unisexual hepatic, which occupies spring and mesic habitats in woodland. The relatively small populations are increasingly fragmented with a high risk for extinction for extrinsic reasons. The presence of relatively high levels of genetic diversity regardless of population size highlights the role of even small remnant populations as important sources of genetic diversity in T. tomentella. The long-term accumulation of genotypes and somatic mutations may explain the observed levels of diversity. Gene flow among populations seems to be infrequent indicating dispersal limitation also on the relatively small spatial scale. Colonization within populations is not affected by isolation by distance suggesting the occurrence of random short-range dispersal of detached vegetative fragments. The population structure study confirmed the low mortality rates of shoots indicating a long life span of the clones in favourable conditions. Efficient ramet production by branching is likely to operate against interspecific competition. To conclude, T. tomentella appears to persist well in undisturbed habitats due to clonal regeneration, although restricted dispersal capacity is likely to prevent successful (re-)colonization in the potential habitat patches of recovering forest landscapes. The implications of the results for conservation are introduced.     

Genetic diversity in sweetpotato [Ipomoea batatas (L.) Lam.] in relationship to geographic sources as assessed with RAPD markers

Available evidence shows that sweetpotato originated from either Central or South American lowlands with subsequent dispersal to North America, Europe, Africa, Asia and the pacific islands. A total of 71 polymorphic RAPD molecular markers were used to assess the genetic relationships amongst 74 sweetpotato varieties originating from a total of 23 sweetpotato producing countries within six geographical regions, namely, South America, Central America/Caribbean, United States of America (USA), East Africa, Asia and Oceania. An Analysis of Molecular Variance (AMOVA) indicated that 93.4% of the total variance was due to the differences between genotypes within regions. The difference between regions was significant (P < 0.001) but only contributed 6.6% to the variance. Genetic distance (PhiST) calculated with AMOVA and multidimensional scaling (MDS) revealed that the South American and the Central American/Caribbean genotypes formed two separate clusters. East African varieties, which have unique characteristics from other traditional varieties, were distinct from other traditional varieties from South America and Oceania. These results support the reported hypothesis of the origin and dispersal of the sweetpotato and indicate that the primary centre of diversity probably has two distinct genepools. It is proposed that the dispersal of the sweetpotato from its origin may have mainly involved varieties from Central America/Caribbean as opposed to varieties from South America. There is an indication that new genepools may be evolving in Africa and Asia due to hybridisation and adaptation to the local environments.     

Ecogeographic adaptation and genetic variation in wild barley, Application of molecular markers targeted to environmentally regulated genes

Long primer PCR (LP-PCR) markers specifically targeted to sequences involved in the response to abiotic stress were utilised to analyse genetic variation within and among wild barley populations from Israel.Populations were sampled in locations reflecting a wide range of habitats and the potential correlation between genetic variation and ecogeographic parameters was examined. A high level of polymorphism was observed. Most of the variability was due to differences within populations, however a substantial portion of genetic variation (36%) could be attributed to differences among populations, indicating local adaptation of genotypes to microclimatic conditions. Moreover, clustering and ordination techniques showed that genotypes grouped together according to their area of origin and were separated on thebasis of ecogeography, chiefly by a combination of temperature, altitude and rainfall variables. Finally, 28% of the polymorphic PCR fragments were significantly correlated with ecogeographic parameters. Our results demonstrate the effectiveness of PCR-based molecular markers targeted to environmentally regulated genes in detecting useful variation andthus in monitoring the impact exerted by adaptation to the environment ongenetic differentiation.     

Relative effects of road mortality and decreased connectivity on population genetic diversity

Roads can have two important effects on populations that impact genetic variation: reduced gene flow and reduced abundance. Reduced gene flow (“barrier effects”) due to road avoidance behavior or road mortality can lead to reduced genetic diversity because genetic drift is enhanced in fragmented populations. Road mortality can also reduce population abundance (“depletion effects”) whenever road-caused mortality outpaces recruitment, also lowering diversity even when barrier effects are inconsequential. Although roads are expected to affect both genetic diversity and fragmentation, most research focuses only on fragmentation. Furthermore, in studies that do investigate road effects on genetic diversity, correlations are usually attributed to barrier effects and little attention is paid to the potentially confounding influence of mortality-caused depletion effects. Here we investigate the relative importance of barrier and depletion effects on genetic diversity of populations separated by a road by performing coalescent simulations wherein these two road effects are varied independently. By simulating wide ranging rates of migration and population decline, we also determine how the importance of these forces changes depending on their relative magnitude. We show that the vast majority of potential variation in genetic diversity is governed by depletion (mortality) rather than barrier effects. We also show that unless migration is sufficiently high and population decline due to mortality is sufficiently low, increasing migration across roads will generally not recoup genetic variation lost due to road mortality. We argue that the genetic effects of road-mediated mortality have been underappreciated and should be more often considered before prioritizing road-mitigation measures.     

Genetic diversity and local population structure of fragmented populations of Trillium camschatcense (Trilliaceae)

Trillium camschatcense, a long-lived common woodland herb, has been experiencing intensive habitat fragmentation over the last century in eastern Hokkaido, Japan. We examined the genetic diversity and population genetic structure of 12 fragmented populations with different population sizes using allozyme electrophoresis. The percentage of polymorphic loci and mean number of alleles per locus were positively related to population size, probably due to the stochastic loss of rare alleles (frequency of q<0.1) in small populations. Populations with 350 flowering plants or fewer had lost almost all of their rare alleles. While the heterozygosity and inbreeding coefficient were not related to population size, some small populations showed relatively high inbreeding coefficients. In spite of the low genetic differentiation among overall populations (F_ST=0.130), local population structuring was recognized between the two geographically discontinuous population groups. Within groups, sufficient historical gene flow was inferred, whereas a low dispersal ability of this species and geographical separation could produce apparent differentiation between groups.     

Genetic diversity and population structure of Chinese Cherry revealed by chloroplast DNA trnQ-rps16 intergenic spacers variation

Chinese Cherry, generally referring to Prunus pseudocerasus Lindl. species, is one of the most economically important domestic fruit tree in China. To effectively preserve and sustainably utilize this species, a study in genetic diversity and population structure was carried out by the sequence variation of chloroplast DNA trnQ-rps16 intergenic spacers. Polymorphism was calculated among the 200 individuals from 7 local and 10 wild populations across its geographical range in China. The results showed that (1) Total genetic variation in species level was poor (h = 0.478, π = 0.0018). But in the wild populations, it was much higher than that in the local populations (h = 0.565, π = 0.0021 vs. h = 0.152, π = 0.0006). (2) Low levels of genetic differentiation (F_SC = 0.19595, P = 0.000), genetic distance (0.00000–0.00297), as well as pairwise Fst value among populations were detected. These results, combined with the insignificant gene genealogy pattern and neutrality tests indicate that Chinese Cherry has relatively low levels of genetic diversity and insignificant population structure. Coancestry might be a combined effect of the reduction in effective population size with the recent demographic bottlenecks and mating systems. The pronounced seed dispersal abilities and relatively high rates of gene exchange are supported by the limited genetic differentiation among populations.     

Quantitative variation as a tool for detecting human-induced impacts on genetic diversity

We propose quantitative genetic variation as a useful tool complementary to molecular variation in order to detect changes in biodiversity caused by different human-induced activities. We simulated a metapopulation setting under a number of realistic scenarios caused by anthropogenic activities (population isolation, reduced carrying capacity or reproductive rates, shifts in the local optima, and enhanced environmental variation or mutational rates). The effects on diversity of these scenarios were assessed for neutral variation estimated from molecular markers and for an additive quantitative trait that represents a typical morphological characteristic subject to stabilising selection promoting local adaptation to environmental conditions. The results show that monitoring quantitative genetic variation can be more informative than neutral variation to detect some human-induced environmental or genetic impacts on diversity, both at intra and interpopulation levels. We also compared the precision of diversity estimates obtained from molecular markers and quantitative traits. Under low migration rates and typical selection intensities for the quantitative trait, the precision of estimates can be substantially larger for a quantitative trait than for a single molecular marker. Thus, about 10-20 (2-4) independent markers are necessary for the precision of estimates of heterozygosity (population differentiation) from molecular markers to reach that of genetic variances (differentiation) from quantitative traits.     

Population genetic structure in polar bears (Ursus maritimus) from Hudson Bay, Canada: Implications of future climate change

The primary habitat for polar bears is sea ice, yet unlike most of the high Arctic, Hudson Bay undergoes a summer ice-free period that forces all bears ashore until ice forms again in fall. Polar bear populations in the greater Hudson Bay region have been placed in four management units based primarily on data from tag returns from harvested animals, capture-recapture studies, and conventional and satellite telemetry. Our results indicate that there is a high level of gene flow among management units observed using 26 microsatellite loci and analysis of genetic profiles of 377 polar bears. However, individual-based Bayesian analysis identified population genetic structuring into three clusters and significant F_ST differentiation. Specifically, our data suggest differentiation of polar bears sampled from islands in James Bay. These results were in spite of the extensive dispersal capabilities of polar bears that could homogenize the population. Mapping of high-ancestry individuals suggests that two of the three clusters have foci in southern Hudson Bay and may be a result of predictable annual freeze-thaw patterns that are maintaining breeding ‘groups’. Predicted changes in the distribution and duration of sea ice in Hudson Bay suggest that gene flow among these clusters may be reduced in the future.     

Genetic diversity in wild Tunisian populations of Mentha pulegium L. (Lamiaceae)

The allozyme variation of 15 Tunisian wild populations of Mentha pulegium L. threatened by human activities (clearing, hard-grazing, ploughing, traditional uses) was surveyed by the analysis of 14 isozyme loci using horizontal gel starch electrophoresis. The species exhibited a high level of genetic variation within populations (the mean Ap = 2.20, P = 72%, Ho = 0.349 and He = 0.229), which indicates a predominately outcrossing mating system and the recruitment of new genotypes via dispersal seeds. The genetic structure analysis of the populations using F statistics indicates no inbreeding, and showed an excess of heterozygosity for few loci. The moderate differentiation of populations (F_ST = 0.110) and the low rate of gene flow between them (Nm = 2.02) might been caused by recent isolation of the populations through biotope disturbances. The value of Nei's genetic identity varied from 0.839 to 0.999 reflecting a relatively low genetic divergence between populations. Cluster analysis using UPGMA method and Nei's genetic identity values, showed that populations geographically close didn't always cluster together. However, populations within the same bioclimatic stage generally subclustered together indicating that differentiation between bioclimatic regions occurred.     

Current genetic isolation and fragmentation contrasts with historical connectivity in an alpine lizard (Cyclodomorphus praealtus) threatened by climate change

Assessing levels of genetic diversity, connectivity and historical demography for threatened species provides important information for conservation management. We used a combination of the mitochondrial ND4 gene and seven microsatellite markers to examine both historical and recent population genetic structure and demography of the threatened alpine she-oak skink, Cyclodomorphus praealtus. This species is restricted to the “sky islands” of the Australian alpine region. Based on mtDNA, the New South Wales and Victorian regions are reciprocally monophyletic and highly divergent, with among population variation of 0.9 and net sequence divergence of 4.28%, which suggests that they should be considered separate Evolutionary Significant Units for management purposes. The mtDNA data also indicate historical connectivity between the three Victorian populations. However, a model-based clustering analysis of microsatellite genotypes identified strong population structure in Victoria, with three distinct populations that have no current inter-population gene flow. This suggests that the Victorian populations are effectively isolated from each other, and is indicative of very low dispersal capacity and a high degree of habitat specialisation. This is reinforced by the substantially lower genetic diversity within the lowest elevation population compared to the other higher elevation populations. We found no genetic signature of major changes in effective population size. These data provide a baseline for assessing future impacts of climate change on the genetic structure of this alpine endemic species.