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1,467 results for “Genetic structure”
Data from: Limited gene dispersal and spatial genetic structure as stabilizing factors in an ant-plant mutualism
Comparative studies of the population genetics of closely associated species are necessary to properly understand the evolution of these relationships because gene flow between populations affects the partners' evolutionary potential at the local scale. As a consequence (at least for antagonistic interactions), asymmetries in the strength of the genetic structures of the partner populations can result in one partner having a co-evolutionary advantage. Here, we assess the population genetic structure of partners engaged in a species-specific and obligatory mutualism: the Neotropical ant-plant, Hirtella physophora, and its ant associate, Allomerus decemarticulatus. Although the ant cannot complete its life cycle elsewhere than on H. physophora and the plant cannot live for long without the protection provided by A. decemarticulatus, these species also have antagonistic interactions: the ants have been shown to benefit from castrating their host plant and the plant is able to retaliate against too virulent ant colonies. We found similar short dispersal distances for both partners, resulting in the local transmission of the association and, thus, inbred populations in which too virulent castrating ants face the risk of local extinction due to the absence of H. physophora offspring. On the other hand, we show that the plant populations probably experienced greater gene flow than did the ant populations, thus enhancing the evolutionary potential of the plants. We conclude that such levels of spatial structure in the partners' populations can increase the stability of the mutualistic relationship. Indeed, the local transmission of the association enables partial alignments of the partners' interests, and population connectivity allows the plant retaliation mechanisms to be locally adapted to the castration behaviour of their symbionts.
Data from: Genetic structure of Omani goats reveals admixture among populations from geographically proximal sites
The genetic diversity of most global goat populations has been assessed in recent decades using nuclear markers but remains unstudied in the south Arabian Peninsula, particularly in Sultanate of Oman, despite the importance of these animals for the local economy and food supply. Therefore, the present study provides a comparative analysis of the genetic diversity of five native Omani goat populations and evaluates possible admixture rates with the four most frequently imported goat populations from geographically proximal countries. Quality control of 15 loci was conducted and molecular characterization of nine populations was performed with 11 microsatellite markers. Accordingly, a data set based on 11 high informative microsatellites loci genotypes from nine populations was used to estimate the population genetic parameters. The summary statistics for the parameters depicted relatively highly diverse populations (Ho = 0.667, He = 0.663) with relatively low and mostly non-significant levels of inbreeding (FIS). Furthermore, the population substructure estimators (AMOVA) and population differentiation coefficient (FST) were indicated weak genetic differentiation among populations (P < 0.001).A finer analysis of the population substructure and differentiation using STRUCTURE, discriminant analyses of principal components (DAPCs) and a neighbor-joining (NJ) tree were supported a scenario that a high level of gene flow between populations from close geographical locations are the main evolutionary driving force. Thus, any future conservation strategy and breeding programs should include to preserve unique alleles that might be contributing to with stand the limited feed and requirement in desert ecosystems as well as economic traits.
Data from: The interplay of dispersal limitation, rivers, and historical events shapes the genetic structure of an Amazonian frog
Disentangling the impact of landscape features such as rivers and historical events on dispersal is a challenging but necessary task to gain a comprehensive picture of the evolution of diverse biota such as that found in Amazonia. Adenomera andreae, a small, territorial, terrestrial frog species of the Amazonian forest represents a good model for such studies. We combined Cytochrome b sequences with 12 microsatellites to investigate the genetic structure at two contrasted spatial scales in French Guiana: along a ~6 km transect to evaluate dispersal ability and between paired bank populations along a ~65 km stretch of the Approuague river to test the effect of rivers as barriers to dispersal. We observed significant spatial genetic structure between individuals at a remarkably small geographical scale and conclude that the species has a restricted dispersal ability likely tied to its life history traits. Mitochondrial and microsatellite data also indicate a high level of differentiation among populations on opposite banks of the river and, in some cases, among populations on the same riverbank. These results suggest that the observed population structure in A. andreae is due to restricted dispersal abilities combined with the action of rivers and Quaternary population isolation. Given that Amazonia hosts a great portion of anurans, as well as other small vertebrates, that display life history traits comparable to Adenomera andreae, we argue that our analyses provide new insights into the complex interactions among evolutionary processes shaping Amazonian biodiversity.
Data from: Noninvasive sampling reveals population genetic structure in the Royle's pika, Ochotona roylei, in the western Himalaya
Understanding population genetic structure of climate-sensitive herbivore species is important as it provides useful insights on how shifts in environmental conditions can alter their distribution and abundance. Herbivore responses to the environment can have a strong indirect cascading effect on community structure. This is particularly important for Royle's pika (Lagomorpha: Ochotona roylei), a herbivorous talus-dwelling species in alpine ecosystem, which forms a major prey base for many carnivores in the Himalayan arc. In this study, we used seven polymorphic microsatellite loci to detect evidence for recent changes in genetic diversity and population structure in Royle's pika across five locations sampled between 8 km to 160 km apart in the western Himalaya. Using four clustering approaches, we found the presence of significant contemporary genetic structure in Royle's pika populations. The detected genetic structure could be primarily attributed to the landscape features in alpine habitat (e.g. wide lowland valleys, rivers) that may act as semi-permeable barriers to gene flow and distribution of food plants, which are key determinants in spatial distribution of herbivores. Pika showed low inbreeding coefficients (FIS) and a high level of pairwise relatedness for individuals within 1km suggesting low dispersal abilities of talus-dwelling pikas. We have found evidence of a recent population bottleneck, possibly due to effects of environmental disturbances (e.g. snow melting patterns or thermal stress). Our results reveal significant evidence of isolation by distance in genetic differentiation (FST range = 0.04−0.19). This is the first population genetics study on Royle's pika, which helps to address evolutionary consequences of climate change which are expected to significantly affect the distribution and population dynamics in this talus dwelling species.
Data from: Genetic population structure of the blister beetle Gnathium minimum: core and peripheral populations
Populations on the periphery of a species' range tend to contain lower genetic variation and increased genetic differentiation compared to populations at the core of a species range, although some exceptions to this generalization occur. The blister beetle Gnathium minimum (Say) exhibits a wide-ranging distribution in the western United States but has peripheral or disjunct populations in Mexico, Florida, and Wisconsin. We used amplified fragment length polymorphism (AFLP) to compare the genetic variation and magnitude of genetic differentiation of the Wisconsin peripheral population to western core populations (Colorado, Kansas, New Mexico, and Texas). The proportion of polymorphic loci was 53.6 and 54.3, and expected heterozygosity 0.1864 and 0.1933 for the Kansas/Colorado (n = 87) and New Mexico/Texas (n = 35) regions, respectively. Specimens from Wisconsin (n = 121) had a lower proportion of polymorphic loci (38.4) and expected heterozygosity (0.1475). Genetic cluster estimation with GENELAND and F ST values showed greater genetic differentiation among the sampling locations within Wisconsin compared to core regions. Significant isolation-by-distance (IBD) was also observed in Wisconsin but not within the core regions. Lower genetic variation and increased isolation may reduce the Wisconsin population's ability to respond to change, thereby increasing their susceptibility to extinction.
Data from: Fine-scale genetic structure in a wild bird population: the role of limited dispersal and environmentally-based selection as causal factors
Individuals are typically not randomly distributed in space; consequently ecological and evolutionary theory depends heavily on understanding the spatial structure of populations. The central challenge of landscape genetics is therefore to link spatial heterogeneity of environments to population genetic structure. Here, we employ multivariate spatial analyses to identify environmentally induced genetic structures in a single breeding population of 1174 great tits Parus major genotyped at 4701 single-nucleotide polymorphism (SNP) loci. Despite the small spatial scale of the study relative to natal dispersal we found multiple axes of genetic structure. We built distance-based Moran's eigenvector maps to identify axes of pure spatial variation, which we used for spatial correction of regressions between SNPs and various external traits known to be related to fitness components (avian malaria infection risk, local density of conspecifics, oak tree density and altitude). We found clear evidence of fine-scale genetic structure, with 21, 7 and 9 significant SNPs respectively associated with infection risk by two species of avian malaria (Plasmodium circumflexum and P. relictum) and local conspecific density. Such fine-scale genetic structure relative to dispersal capabilities suggests ecological and evolutionary mechanisms maintain within-population genetic diversity in this population with the potential to drive micro-evolutionary change.
Data from: Population genetic structure of the tree-hole tick Ixodes arboricola (Acari: Ixodidae) at different spatial scales
The endophilic tick Ixodes arboricola infests cavity-nesting birds, and its dispersal strongly depends on the movements of its host. Population genetic structure of I. arboricola was studied with seven polymorphic microsatellite markers. We collected 268 ticks from 76 nest boxes in four woodlots near Antwerp, Belgium. These nest boxes are mainly used by the principal hosts of I. arboricola, the great tit Parus major and the blue tit Cyanistes caeruleus. As these birds typically return to the same cavity for roosting or breeding, ticks within nest boxes were expected to be highly related, and tick populations were expected to be spatially structured among woodlots and among nest boxes within woodlots. In line with the expectations, genetic population structure was found among woodlots and among nest boxes within woodlots. Surprisingly, there was considerable genetic variation among ticks within nest boxes. This could be explained by continuous gene flow from ticks from nearby tree holes, yet this remains to be tested. A pairwise relatedness analysis conducted for all pairs of ticks within nest boxes showed that relatedness among larvae was much higher than among later instars, which suggests that larvae are the most important instar for tick dispersal. Overall, tick populations at the studied spatial scale are not as differentiated as predicted, which may influence the scale at which host–parasite evolution occurs.
Data from: Influence of northern limit range on genetic diversity and structure in a widespread North American tree, sugar maple (Acer saccharum Marshall)
Due to climate change, the ranges of many North-American tree species are expected to shift northward. Sugar maple (Acer saccharum Marshall) reaches its northern continuous distributional limit in north-eastern North America at the transition between boreal mixed-wood and temperate deciduous forests. We hypothesized that marginal fragmented northern populations from the boreal mixed-wood would have a distinct pattern of genetic structure and diversity. We analyzed 18 microsatellite loci variation in 23 populations distributed along three latitudinal transects (west, central and east) that encompass the continuous-discontinuous species range. Each transect was divided into two zones, continuous (temperate deciduous) and discontinuous (boreal mixed-wood), based on sugar maple stand abundance. Respective positive and negative relationships were found between the distance of each population to the northern limit (D north), and allelic richness (AR) and population differentiation (FST). These relations were tested for each transect separately; the pattern (discontinuous/continuous) remained significant only for the western transect. structure analysis revealed the presence of four clusters. The most northern populations of each transect were assigned to a distinct group. Asymmetrical gene flow occurred from the southern into the four northernmost populations. Southern populations in Québec may have originated from two different postglacial migration routes. No evidence was found to validate the hypothesis that northern populations were remnants of a larger population that had migrated further north of the species range after the retreat of the ice sheet. The northernmost sugar maple populations possibly originated from long distance dispersal.
Data from: Geographically structured genetic variation in the Medicago lupulina – Ensifer mutualism
Gene flow between genetically differentiated populations can maintain variation in species interactions, especially when population structure is congruent between interacting species. However, large-scale empirical comparisons of the population structure of interacting species are rare, particularly in positive interspecific interactions (mutualisms). One agriculturally and ecologically important mutualism is the partnership between legume plants and rhizobia. Through characterizing and comparing the population genomic structure of the legume Medicago lupulina and two rhizobial species (Ensifer medicae and E. meliloti), we explored the spatial scale of population differentiation between interacting partners in their introduced range in North America. We found high proportions of E. meliloti in southeastern populations and high proportions of E. medicae in northwestern populations. Medicago lupulina and the Ensifer genus showed similar patterns of spatial genetic structure (isolation by distance). However, we detected no evidence of isolation by distance or population structure within either species of bacteria. Genome-wide nucleotide diversity within each of the two Ensifer species was low, suggesting limited introduction of strains, founder events, or severe bottlenecks. Our results suggest that there is potential for geographically structured coevolution between M. lupulina and the Ensifer genus, but not between M. lupulina and either Ensifer species.
Data from: Genetic population structure of the round whitefish (Prosopium cylindraceum) in North America: multiple markers reveal glacial refugia and regional subdivision.
Round whitefish (Prosopium cylindraceum) have a broad, disjunct range across northern North America and Eurasia, and little is known about their genetic population structure. We performed genetic analyses of round whitefish from 17 sites across its range using nine microsatellites, two mitochondrial DNA (mtDNA) loci, and 4918 to 8835 single-nucleotide polymorphism (SNP) loci. Our analyses identified deep phylogenetic division between eastern and western portions of the range, likely indicative of origins from at least two separate Pleistocene glacial refugia. Regionally, microsatellites and SNPs identified congruent patterns in subdivision, and population structure was consistent with expectations based on hydrologic connectivity. Within the Laurentian Great Lakes, Lake Huron and Lake Ontario were identified as key areas of interest. Lake Huron appears to be a contemporary source population for several other Great Lakes, and Lake Ontario contains a genetically discrete group of round whitefish. In all cases, multiple genetic markers yielded similar patterns, but SNPs offered substantially enhanced resolution. We conclude that round whitefish have population subdivision on several scales important for understanding their evolutionary history and conservation planning.
Genetic structure and mating patterns in sessile oak (Quercus petraea (Matt.) Liebl.)
<p>Oaks (<em>Quercus</em>) are major components of temperate forest ecosystems in the Northern Hemisphere where they form intermediate or climax communities. Sessile oak (<em>Quercus petraea</em>) forests represent the climax vegetation in eastern Germany and western Poland. Here, sessile oak forms pure stands or occurs intermixed with Scots Pine (<em>Pinus sylvestris</em>). A large body of research is available on gene flow, reproduction dynamics, and genetic structure in fragmented landscapes and mixed populations. At the same time, our knowledge regarding large, contiguous and monospecific populations is considerably less well developed. Our study is an attempt to further develop our understanding of the reproduction ecology of sessile oak as an ecologically and economically important forest tree by analyzing mating patterns and genetic structure within adult trees and seedlings originating from one or two reproduction events in an extensive, naturally regenerating sessile oak forest. We detected positive spatial genetic structure up to 30 meters between adult trees and up to 40 meters between seedlings. Seed dispersal distances averaged 8.4 meters. Pollen dispersal distances averaged 22.6 meters. In both cases, the largest proportion of the dispersal occurred over short distances. Dispersal over longer distances was more common for pollen but also appeared regularly for seeds. The reproductive success of individual trees was highly skewed. Only 41 percent of all adult trees produced any offspring while the majority did not participate in reproduction. Among those trees that contributed to the analyzed seedling sample, 80 percent contributed 1-3 gametes. Only 20 percent of all parent trees contributed four or more gametes. However, these relatively few most fertile trees contributed 51 percent of all gametes within the seedling sample. Our study demonstrates that extensive, apparently homogenous oak forests are far from uniform on the genetic level. On the contrary, they form highly complex mosaics of remarkably small local neighborhoods. This counterbalances the levelling effect of long-distance dispersal and may increase the species' adaptive potential. Incorporating these dynamics in the management, conservation and restoration of oak forests can support the conservation of forest genetic diversity and assist those forests in coping with environmental change.</p>
FIGURE 1 in Genetic structure of Ipomoea imperati (Convolvulaceae) in the Mediterranean region and implications for its conservation
FIGURE 1. Geographical distribution of chloroplast haplotypes. Further locality details are provided in Table 1.
FIGURE 3 in Genetic structure of Ipomoea imperati (Convolvulaceae) in the Mediterranean region and implications for its conservation
FIGURE 3. Single most parsimonious (MP) tree /Maximum Clade Credibility (MCC) tree for ITS sequences of the organisms in study. Topology of the MP tree is identical to that of MCC tree from the Bayesian analyses (see text for details). Numbers below branches are, left to right, bootstrap percentages (Felsenstein 1985) out of 1000 replicates, the clade decay index (Bremer 1994) computed out of trees up to 10 steps longer and the posterior probability of the maximum clade credibility tree (branches with p.p. <0.5 were collapsed, with the exception of the Israel/Honduras/Valencia clade, which was present in the MP tree). Estimated divergence times are provided above nodes. Nodes numbers refer to Table 3.
FIGURE 2 in Genetic structure of Ipomoea imperati (Convolvulaceae) in the Mediterranean region and implications for its conservation
FIGURE 2. Median-joining network for plastid DNA haplotypes in Mediterranean, Mexican and Honduran samples of Ipomoea imperati. Haplotypes are represented by the circles, the size of each being proportional to the observed frequency of each haplotype. Median vectors are labelled mv1 and mv2; these represent possible unsampled or extinct haplotypes. Information on the geographic locations where each haplotype is found is provided in Table 1.
Data from: Harvest is associated with the disruption of social and fine-scale genetic structure among matrilines of a solitary large carnivore
<p>Harvest can disrupt wildlife populations by removing adults with naturally high survival. This can reshape sociospatial structure, genetic composition, fitness, and potentially affect evolution. Genetic tools can detect changes in local, fine-scale genetic structure (FGS) and assess the interplay between harvest-caused social and FGS in populations. We used data on 1,614 brown bears, <i>Ursus arctos</i>, genotyped with 16 microsatellites, to investigate whether harvest intensity (mean low: 0.13 from 1990-2005, mean high: 0.28 from 2006-2011) caused changes in FGS among matrilines (8 matrilines; 109 females ≥ 4 years of age), sex-specific survival and putative dispersal distances, female spatial genetic autocorrelation, matriline persistence, and male mating patterns. Increased harvest decreased FGS of matrilines. Female dispersal distances decreased and male reproductive success was redistributed more evenly. Adult males had lower survival during high harvest, suggesting that higher male turnover caused this redistribution and helped explain decreased structure among matrilines, despite shorter female dispersal distances. Adult female survival and survival probability of both mother and daughter were lower during high harvest, indicating that matriline persistence was also lower. Our findings indicate a crucial role of regulated harvest in shaping populations, decreasing differences among 'groups', even for solitary-living species, and potentially altering the evolutionary trajectory of wild populations.</p>
Oceanographic features and limited dispersal shape the population genetic structure of the vase sponge Ircinia campana in the Greater Caribbean
<p>Understanding population genetic structure can help us to infer dispersal patterns, predict population resilience and design effective management strategies. For sessile species with limited dispersal, this is especially pertinent because genetic diversity and connectivity are key aspects of their resilience to environmental stressors. Here, we describe the population structure of <i>Ircinia campana</i>, a common Caribbean sponge subject to mass mortalities and disease. Microsatellites were used to genotype 440 individuals from 19 sites throughout the Greater Caribbean. We found strong genetic structure across the region, and significant isolation by distance across the Lesser Antilles, highlighting the influence of limited larval dispersal. We also observed spatial genetic structure patterns congruent with oceanography. This includes evidence of connectivity between sponges in the Florida Keys and the southeast coast of the United States (>700 km away) where the oceanographic environment is dominated by the strong Florida Current. Conversely, the population in southern Belize was strongly differentiated from all other sites, consistent with the presence of dispersal-limiting oceanographic features, including the Gulf of Honduras gyre. At smaller spatial scales (<100 km), sites showed heterogeneous patterns of low-level but significant genetic differentiation (chaotic genetic patchiness), indicative of temporal variability in recruitment or local selective pressures. Genetic diversity was similar across sites, but there was evidence of a genetic bottleneck at one site in Florida where past mass mortalities have occurred. These findings underscore the relationship between regional oceanography and weak larval dispersal in explaining population genetic patterns, and could inform conservation management of the species.</p>
Data from: Genetic structuring among colonies of a pantropical seabird: Implication for subspecies validation and conservation
Appendix S1 <table> <tbody> <tr> <td>Table S1</td> <td>Details of field researchers and licences under which they took blood samples from white-tailed tropicbirds from populations in the years of study</td> </tr> <tr> <td>Table S2</td> <td>Morphometrics of 616 individual white-tailed tropicbirds from 11 populations. Population codes are as described in Table 1.</td> </tr> <tr> <td>Table S3</td> <td>Raw microsatellite genotypes for 382 individual White-tailed tropicbird from 13 populations. Population codes are as described in Table 1</td> </tr> <tr> <td>Table S4</td> <td>Details of mtDNA sequences </td> </tr> <tr> <td>Table S5</td> <td>Tests of bottleneck (P-values for one-tailed Wilcoxon's signed rank test for heterozygosity excess) based on 10 microsatellites in 13 populations of Phaethon lepturus</td> </tr> <tr> <td>Table S6</td> <td>Pairwise FST estimates based on nuclear microsatellite variation (above diagonal), and ΦST estimates based on mtDNA sequence (below diagonal) for 11 populations with sample sizes >5 ('Pop's) of Phaethon lepturus (see Table 1 for population codes)</td> </tr> </tbody> </table>
Context-dependent dispersal determines relatedness and genetic structure in a patchy amphibian population
<p>Dispersal is a central process in ecology and evolution with far reaching consequences for the dynamics and genetics of spatially structured populations (SSPs). Individuals can adjust their decisions to disperse according to local fitness prospects, resulting in context-dependent dispersal. By determining dispersal rate, distance, and direction, these individual-level decisions further modulate the demography, relatedness, and genetic structure of SSPs. Here, we examined how context-dependent dispersal influences the dynamics and genetics of a Great Crested Newt (<i>Triturus cristatus</i>) SSP. We collected capture-recapture data of 5564 individuals and genetic data of 950 individuals across a SSP in northern Germany. We added genetic data from six sites outside this SSP to assess genetic structure and gene flow at a regional level. Dispersal rates within the SSP were high but dispersal distances were short. Dispersal was context-dependent: individuals preferentially immigrated into high-quality ponds where breeding probabilities were higher. The studied SSP behaved like a patchy population, where subpopulations at each pond were demographically interdependent. High context-dependent dispersal led to weak but significant spatial genetic structure and relatedness within the SSP. At the regional level, a strong hierarchical genetic structure with very few first-generation migrants as well as low effective dispersal rates suggest the presence of independent demographic units. Overall, our study highlights the importance of habitat quality for driving context-dependent dispersal and therefore demography and genetic structure in SSPs. Limited capacity for long-distance dispersal seems to increase genetic structure within a population and leads to demographic isolation in anthropogenic landscapes.</p>
Figure 4 in Complete mitogenome of Chinese shrew mole Uropsilus soricipes (Milne- Edwards, 1871) (Mammalia: Talpidae) and genetic structure of the species in the Jiajin Mountains (China)
Figure 4. Expected (solid line) and observed (broken lines) mismatch distribution of Uropsilus soricipes based on cyt b. The x-axis represents the numbers of pairwise differences among sequences and the y-axis represents the relative frequencies of pairwise comparisons. (A) All individuals; (B) Jiajin Mountains population.
Figure 3. Bayesian 50 in Complete mitogenome of Chinese shrew mole Uropsilus soricipes (Milne- Edwards, 1871) (Mammalia: Talpidae) and genetic structure of the species in the Jiajin Mountains (China)
Figure 3. Bayesian 50% majority rule consensus phylogenetic tree of Eulipotyphla species from a phylogenetic analysis by the concatenated nucleotide sequences of 12 heavy strand proteincoding genes. Rattus rattus and Tupaia belangeri used as outgroup. The numbers on the internode branche is bootstrap percentages for ML analyses.
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