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1,598 results for “genetic diversity”
Using multiple seedlots in restoration planting enhances genetic diversity compared to natural regeneration in fragmented tropical forests
<p>Catastrophic degradation of forests is ongoing worldwide and leads to severe forest fragmentation. Restoration plantings are often necessary to restore fragmented forests, complementing the limited natural regeneration. High genetic diversity is critical for the long-term viability of restored forests. However, there is limited knowledge of whether planted populations capture a genetic variation comparable to natural populations. We measured the efficiency of two forest restoration strategies using the common tropical oak <em>Quercus bambusifolia</em>. The multi-seedlot planting was established over ten years by collecting seeds from several locations in fragmented secondary forests of Hong Kong, while the single seedlot planting was established in just one year with seeds from a single natural location. We analysed the genetic diversity and genetic structure from both plantings and compared them with natural populations. The multi-seedlot planting exhibited a higher rate of genetic recovery, greater genetic diversity (He = 0.69), and higher effective population size (Ne_p = 86.5) compared to natural populations (He = 0.66, Ne_p = 64.3, on average) and the single seedlot planting (He = 0.50, Ne_p = 30.8). The multi-seedlot planting erased the effect of seed shadows which was detected in natural populations while the single seedlot planting strengthened the effect. We conclude that capturing high levels of genetic diversity in the collection of propagules is a standard requirement to ensure the long-term viability of forest restoration. Propagule collection over multiple years is required when only a few parental trees are available to avoid founder effects.</p>
Genetic diversity within and between British and Irish breeds: the maternal and paternal history of native ponies
The UK and Ireland have many native pony breeds, yet there is a lack of comprehensive research investigating their genetic diversity and phylogenetic interrelationships. Many studies contain a limited number of pony breeds, or small sample sizes for these breeds. This may result in erroneous grouping of pony breeds that otherwise have intricate interrelationships with each other and are not evaluated correctly when placed as a token subset of a larger dataset. This is the first study that specifically investigates the genetic diversity within and between British and Irish native pony breeds using large sample numbers from locations of their native origin. This study used a panel of microsatellite markers and sequence analysis of the mitochondrial control region to analyse the genetic diversity within and between 11 pony breeds from Britain and Ireland. A large dataset was collected and previously published data were used to place the British and Irish ponies in a global context. The native ponies of Britain and Ireland were found to have had a complex history and the interrelationships between the breeds were revealed. Overall, high levels of genetic diversity were present, including maintenance of rare ancient matrilines in the Welsh and Fell breeds. In contrast the Dartmoor showed limited maternal diversity. A number of unexpected shared ancestral origins were elucidated between some breeds. The data generated herein provides valuable information to guide and implement the conservation of increasingly rare native genetic resources.
Data from: Conserving the genetic diversity of condemned populations: optimizing collections and translocation
<p>We generated SNP genotype data from two endangered plant species, <em>Pimelea spicata</em> and <em>Eucalyptus</em> sp. Cattai. For each, we genotyped plants from a population that was 'condemned,' or that would soon be destoyed. We used the genotype data to design ex situ germplasm collections that preserved the diversity in the condemned populations, in ways that were optimized. Here, we provide an archive of these SNP genotype data, and the code that was used to analyse these data, including the optimizations.</p>
Cryptic genetic diversity and cytonuclear discordance characterize contact among Canada jay (Perisoreus canadensis) morphotypes in western North America
<p>Three distinct Canada jay (<em>Perisoreus canadensis</em>) morphotypes with easily recognizable plumage traits come into contact in western North America. Recent work demonstrated high genetic structure across the species' range; however, patterns of genetic variation in these contact zones remain unknown. We categorized 605 individuals into one of three morphotypes (Pacific, Rocky Mountain, and Boreal) based on plumage, and genotyped individuals at the mtDNA control region and 12 microsatellite loci to assess the extent of hybridization between morphotypes. Our data showed cryptic genetic diversity and high cytonuclear discordance among morphotypes within contact zones, which is likely the result of recent and historical admixture. The distributions of the Boreal and Pacific morphotypes each showed a strong association with a single, distinct genetic group, whereas the Rocky Mountain morphotype exhibited higher genetic diversity and was associated with multiple genotypes. Our analyses show the importance of considering both plumage and genetic traits when examining contact zones between closely related taxa. Finally, the data presented in this study reaffirm that the Pacific morphotype is distinct from the Boreal and Rocky Mountain morphotypes based on genetic, phenotypic, and ecological data, indicating that the Pacific morphotype should be re-elevated to a full species.</p>
Data from: Functional genetic diversity in an exploited marine species and its relevance to fisheries management
<p>The timing of reproduction influences key evolutionary and ecological processes in wild populations. Variation in reproductive timing may be an especially important evolutionary driver in the marine environment, where the high mobility of many species and few physical barriers to migration provide limited opportunities for spatial divergence to arise, and where many species synchronize their reproduction to seasonal cycles of planktonic productivity. Using genomic data collected from spawning aggregations of Pacific herring (<i>Clupea pallasii</i>) across 1,600 km of coastline, we show that reproductive timing drives population structure in these pelagic fish. Within a specific spawning season we observed isolation by distance, indicating that gene flow is limited over our study area. These results emphasize the importance of considering both seasonal and spatial variation in reproductive timing when delineating management units for Pacific herring. On several chromosomes we detected linkage disequilibrium extending over millions of base pairs, suggesting the presence of chromosomal rearrangements. The frequencies of putative chromosomal rearrangements differed between populations spawning at different times of year. Spawning phenology was highly correlated with polymorphisms in several genes, in particular <i>SYNE2</i>, which influences the development of retinal photoreceptors in vertebrates. <i>SYNE2 </i>is likely within a chromosomal rearrangement in Pacific herring and is also associated with spawn timing in Atlantic herring (<i>Clupea harengus</i>). The observed genetic diversity likely underlies resource waves provided by spawning herring and demonstrates how population-level genetic diversity can influence ecosystem processes. Given the ecological, economic, and cultural significance of herring, our results support that conserving intraspecific genetic diversity is important for maintaining current and future ecosystem processes.</p>
Data from: The evolution of hominoid cranial diversity: a quantitative genetic approach
Hominoid cranial evolution is characterized by substantial phenotypic diversity, yet the cause of this variability has rarely been explored. Quantitative genetic techniques for investigating evolutionary processes underlying morphological divergence are dependent on the availability of good ancestral models, a problem in hominoids where the fossil record is fragmentary and poorly understood. Here, we use a maximum likelihood approach based on a Brownian motion model of evolutionary change to estimate nested hypothetical ancestral forms from 15 extant hominoid taxa. These ancestors were then used to calculate rates of evolution along each branch of a phylogenetic tree using Lande's generalized genetic distance. Our results show that hominoid cranial evolution is characterized by strong stabilizing selection. Only two instances of directional selection were detected; the divergence of Homo from its last common ancestor with Pan, and the divergence of the lesser apes from their last common ancestor with the great apes. In these two cases, selection gradients reconstructed to identify the specific traits undergoing selection indicated that selection on basicranial flexion, cranial vault expansion and facial retraction characterizes the divergence of Homo, whereas the divergence of the lesser apes was defined by selection on neurocranial size reduction.
Data from: Low genetic diversity but strong population structure reflects multiple introductions of western flower thrips (Thysanoptera: Thripidae) into China followed by human-mediated spread
Historical invasion scenarios based on observational records are usually incomplete and biased, but these can be supplemented by population genetic data. The western flower thrips (WFT), Frankliniella occidentalis, invaded China in the last 13 years and has rapidly become one of the most serious pests in the country. To assess whether this invasion involved a single event or multiple events, we examined patterns of genetic diversity and population structure of WFT across 12 Chinese populations and a native US population based on mitochondrial DNA and/or 18 microsatellite loci. The average allelic richness and haplotype diversity in Chinese populations were significantly lower than in a population from its native range. The distribution of mitochondrial haplotypes suggested multiple independent invasions of WFT into China, including two invasions into the Beijing region. Based on microsatellite data, two distinct clusters were identified, with both of them splitting further into two clusters; in the Beijing region, the microsatellite data also provided evidence for two introductions. Both the absence of isolation by distance and the fact that distant populations were similar genetically suggest patterns of WFT movement linked to human activities. Our study therefore suggests multiple introductions of WFT into China and human-assisted spread.
Data from: Extreme genetic diversity in asexual grass thrips populations
The continuous generation of genetic variation has been proposed as one of the main factors explaining the maintenance of sexual reproduction in nature. However, populations of asexual individuals may attain high levels of genetic diversity through within-lineage diversification, replicate transitions to asexuality from sexual ancestors and migration. How these mechanisms affect genetic variation in populations of closely related sexual and asexual taxa can therefore provide insights into the role of genetic diversity for the maintenance of sexual reproduction. Here, we evaluate patterns of intra- and interpopulation genetic diversity in sexual and asexual populations of Aptinothrips rufus grass thrips. Asexual A. rufus populations are found throughout the world, whereas sexual populations appear to be confined to few locations in the Mediterranean region. We found that asexual A. rufus populations are characterized by extremely high levels of genetic diversity, both in comparison with their sexual relatives and in comparison with other asexual species. Migration is extensive among asexual populations over large geographic distances, whereas close sexual populations are strongly isolated from each other. The combination of extensive migration with replicate evolution of asexual lineages, and a past demographic expansion in at least one of them, generated high local clone diversities in A. rufus. These high clone diversities in asexual populations may mimic certain benefits conferred by sex via genetic diversity and could help explain the extreme success of asexual A. rufus populations.
Data from: Higher genetic diversity in recolonized areas than in refugia of Alnus glutinosa triggered by continent-wide lineage admixture
Genetic admixture is supposed to be an important trigger of species expansions because it can create the potential for selection of genotypes suitable for new climatic conditions. Up until now, however, no continent-wide population genetic study has performed a detailed reconstruction of admixture events during natural species expansions. To fill this gap, we analysed the postglacial history of Alnus glutinosa, a keystone species of European swamp habitats, across its entire distribution range using two molecular markers, cpDNA and nuclear microsatellites. CpDNA revealed multiple southern refugia located in the Iberian, Apennine, Balkan and Anatolian Peninsulas, Corsica and North Africa. Analysis of microsatellites variation revealed three main directions of postglacial expansion: (i) from the northern part of the Iberian Peninsula to Western and Central Europe and subsequently to the British Isles, (ii) from the Apennine Peninsula to the Alps and (iii) from the eastern part of the Balkan Peninsula to the Carpathians followed by expansion towards the Northern European plains. This challenges the classical paradigm that most European populations originated from refugial areas in the Carpathians. It has been shown that colonizing lineages have met several times and formed secondary contact zones with unexpectedly high population genetic diversity in Central Europe and Scandinavia. On the contrary, limited genetic admixture in southern refugial areas of A. glutinosa renders rear-edge populations in the Mediterranean region more vulnerable to extinction due to climate change.
Data from: Genetic diversity and population structure in contemporary house sparrow populations along an urbanization gradient.
House sparrow (Passer domesticus) populations have suffered major declines in urban as well as rural areas, while remaining relatively stable in suburban ones. Yet, to date no exhaustive attempt has been made to examine how, and to what extent, spatial variation in population demography is reflected in genetic population structuring along contemporary urbanization gradients. Here we use putatively neutral microsatellite loci to study if and how genetic variation can be partitioned in a hierarchical way among different urbanization classes. Principal coordinate analyses did not support the hypothesis that urban/suburban and rural populations comprise two distinct genetic clusters. Comparison of FST values at different hierarchical scales revealed drift as an important force of population differentiation. Redundancy analyses revealed that genetic structure was strongly affected by both spatial variation and level of urbanization. The results shown here can be used as baseline information for future genetic monitoring programmes and provide additional insights into contemporary house sparrow dynamics along urbanization gradients.
Data from: Genetic diversity of Bartonella quintana in macaques suggests zoonotic origin of trench fever
Bartonella quintana is a bacterium that causes a broad spectrum of diseases in humans including trench fever. Humans were previously considered to be the primary, if not the only, reservoir hosts for B. quintana. To identify the animal reservoir and extend our understanding of the ecological and evolutionary history of B. quintana, we examined blood samples from macaques and performed multilocus sequence typing (MLST) analysis. We demonstrated the prevalence of B. quintana infection was common in macaques from main primate centres in mainland China. Overall, 18.0% (59/328) of rhesus macaques and 12.7% (39/308) of cynomolgus macaques were found to be infected with B. quintana by blood culture and/or polymerase chain reaction. The infection was more frequently identified in juvenile and young monkeys compared with adult animals. In contrast with the relatively low level of sequence divergence of B. quintana reported in humans, our investigation revealed much higher genetic diversity in nonhuman primates. We identified 44 new nucleotide variable sites and 14 novel sequence types (STs) among the B. quintana isolates by MLST analysis. Some STs were found only in cynomolgus macaques, while some others were detected only in rhesus macaques, suggesting evidence of host-cospeciation, which were further confirmed by phylogenetic analysis and Splits decomposition analysis. Our findings suggest that trench fever may primarily be a zoonotic disease with macaques as the natural hosts.
Data from: High genetic diversity and stable Pleistocene distributional ranges in the widespread Mexican red oak Quercus castanea Née (1801) (Fagaceae)
<p>The Mexican highlands are areas of high biological complexity where taxa of Nearctic and Neotropical origin and different population histories are found. To gain a more detailed view of the evolution of the biota in these regions, it is necessary to evaluate the effects of historical tectonic and climate events on species. Here, we analyzed the phylogeographic structure, historical demographic processes, and the contemporary period, Last Glacial Maximum (LGM) and Last Interglacial (LIG) ecological niche models of Quercus castanea, to infer the historical population dynamics of this oak distributed in the Mexican highlands. A total of 36 populations of Q. castanea were genotyped with seven chloroplast microsatellite loci in four recognized biogeographic provinces of Mexico: the Sierra Madre Occidental (western mountain range), the Central Plateau, the Trans-Mexican Volcanic Belt (TMVB, mountain range crossing central Mexico from west to east) and the Sierra Madre del Sur (SMS, southern mountain range). We obtained standard statistics of genetic diversity and structure and tested for signals of historical demographic expansions. A total of 90 haplotypes were identified and 29 of these haplotypes were restricted to sngle populations. The within-population genetic diversity was high (mean hS = 0.72), and among-population genetic differentiation showed a strong phylogeographic structure (NST = 0.630 > GST = 0.266; P < 0.001). Signals of demographic expansion were identified in the TMVB and the SMS. The ecological niche models suggested a considerable percentage of stable distribution area for the species during the LGM and connectivity between the TMVB and the SMS. High genetic diversity, strong phylogeographic structure and potential distribution models suggest in situ permanence of Q. castanea populations with large effective population sizes. The complex geological and climatic histories of the TMVB help to explain the origin and maintenance of a large proportion of the genetic diversity in this oak species.</p>
Data from: Clonal genetic structure and diversity in populations of an aquatic plant with combined versus separate sexes
Clonality is often implicated in models of the evolution of dioecy, but few studies have explicitly compared clonal structure between plant sexual systems, or between the sexes in dioecious populations. Here, we exploit the occurrence of monoecy and dioecy in clonal Sagittaria latifola (Alismataceae) to evaluate two main hypotheses: (1) clone sizes are smaller in monoecious than dioecious populations, because of constraints imposed on clone size by costs associated with geitonogamy; (2) in dioecious populations, male clones are larger and flower more often than female clones because of sex-differential reproductive costs. Differences in clone size and flowering could result in discordance between ramet- and genet-based sex ratios. We used spatially explicit sampling to address these hypotheses in 10 monoecious and 11 dioecious populations of S. latifolia at the northern range limit in eastern N. America. In contrast to our predictions, monoecious clones were significantly larger than dioecious clones, probably due to their higher rates of vegetative growth and corm production, and in dioecious populations there was no difference in clone size between females and males; ramet- and genet-based sex ratios were therefore highly correlated. Genotypic diversity declined with latitude for both sexual systems, but monoecious populations exhibited lower genotypic richness. Differences in life history between the sexual systems of S. latifolia appear to be the most important determinants of clonal structure and diversity.
Data from: Genetic diversity does not explain variation in extra-pair paternity in multiple populations of a songbird
Many songbirds are socially monogamous but genetically polyandrous, mating with individuals outside their pair bonds. Extra-pair paternity (EPP) varies within and across species, but reasons for this variation remain unclear. One possible source of variation is population genetic diversity, which has been shown in interspecific meta-analyses to correlate with EPP but which has limited support from intraspecific tests. Using eight populations of the genetically polyandrous red-winged blackbird (Agelaius phoeniceus), including an island population, we investigated whether population-level differences in genetic diversity led to differences in EPP. We first measured genetic diversity over ten microsatellite loci and found, as predicted, low genetic diversity in the island population. Additional structure analyses with multilocus genotypes and mtDNA showed the island population to be distinct from the continental populations. However, the island population's EPP rate fell in the middle of the continental populations' distribution, while the continental populations themselves showed significant variation in EPP. This result suggests that genetic diversity by itself is not a predictor of EPP rate. We discuss reasons for the departure from previous results, including hypotheses for EPP that do not solely implicate female-driven behavior.
Data from: Dendritic connectivity shapes spatial patterns of genetic diversity: a simulation-based study
Landscape features notoriously affect spatial patterns of biodiversity. For instance, in dendritic ecological networks (such as river basins), dendritic connectivity has been proposed to create unique spatial patterns of biodiversity. Here, we compared genetic datasets simulated under a lattice-like, a dendritic and a circular landscape to test the influence of dendritic connectivity on neutral genetic diversity. The circular landscape had a level of connectivity similar to that of the dendritic landscape, so as to isolate the influence of dendricity on genetic diversity. We found that genetic diversity and differentiation varied strikingly among the three landscapes. For instance, the dendritic landscape generated higher total number of alleles and higher global Fst than the lattice-like landscape, and these indices also varied between the dendritic and the circular landscape, suggesting an effect of dendricity. Furthermore, in the dendritic landscape, allelic richness was higher in highly connected demes (e.g. confluences in rivers) than in low connected demes (e.g. upstream and downstream populations), which was not the case in the circular landscape, hence confirming the major role of dendricity. This led to bell-shaped distributions of allelic richness along an upstream-downstream gradient. Conversely, genetic differentiation (Fst) was lower in highly than in low connected demes (which was not observed in circular landscape), and significant patterns of isolation-by-distance (IBD) were also observed in the dendritic landscape. We conclude that in dendritic networks, the combined influence of dendricity and connectivity generates unique spatial patterns of neutral genetic diversity, which has implications for population geneticists and conservationists.
Data from: Microsatellite analysis of genetic diversity and population structure of Arabian horse populations
The Arabian horse ignites imagination throughout the world. Populations of this breed exist in many countries, and recent genetic work has examined the diversity and ancestry of a few of these populations in isolation. Here we explore seven different populations of Arabians represented by 682 horses. Three of these are Middle Eastern populations from near the historical origin of the breed, including Syrian, Persian, and Saudi Arabian. The remaining Western populations are found in Europe (the Shagya-Arabian and Polish-Arabian) and America (American-Arabian). Analysis of genetic structure was carried out using 15 microsatellite loci. Genetic distances, AMOVA, factorial correspondence analysis and a Bayesian method were applied. The results consistently show higher level of diversity within the Middle Eastern populations than the Western populations. The Western Arabian populations were the main source of among populations variation. Genetic differentiation was not strong among all Middle Eastern populations, but all American-Arabians showed differentiation from Middle Eastern populations and were somewhat uniform among themselves. Here, we explore the diversities of many different populations of Arabian horses, and find that populations not from the Middle East have noticeably lower levels of diversity, which may adversely affect the health of these populations.
Data from: Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants
Detailed information about the geographic distribution of genetic and genomic variation is necessary to better understand the organization and structure of biological diversity. In particular, spatial isolation within species and hybridization between them can blur species boundaries and create evolutionary relationships that are inconsistent with a strictly bifurcating tree model. Here we analyze genome-wide DNA sequence and genetic ancestry variation in Lycaeides butterflies to quantify the effects of admixture and spatial isolation on how biological diversity is organized in this group. We document geographically widespread and pervasive historic admixture, with more restricted recent hybridization. This includes evidence supporting previously known and unknown instances of admixture. The genome composition of admixed individuals varies much more among than within populations, and tree- and genetic ancestry-based analyses indicate that multiple distinct admixed lineages or populations exist. We find that most genetic variants in Lycaeides are rare (minor allele frequency < 0.5%). Because the spatial and taxonomic distributions of alleles reflect demographic and selective processes since mutation, rare alleles, which are presumably younger than common alleles, were spatially and taxonomically restricted compared to common variants. Thus, we show patterns of genetic variation in this group are multifaceted, and we argue that this complexity challenges simplistic notions concerning the organization of biological diversity into discrete, easily delineated, and hierarchically structured entities.
Data from: Genetic basis of amphibian larval development along a latitudinal gradient: gene diversity, selection and links with phenotypic variation in transcription factor C/EBP-1
Ectotherm development rates often show adaptive divergence along climatic gradients, but the genetic basis for this variation is rarely studied. Here, we investigated the genetic basis for phenotypic variation in larval development in the moor frog Rana arvalis from five regions along a latitudinal gradient from Germany to northern Sweden. We focused on the C/EBP-1 gene, a transcription factor associated with larval development time. Allele frequencies at C/EBP-1 varied strongly among geographic regions. Overall, the distribution of alleles along the gradient was in concordance with the dual postglacial colonization routes into Scandinavia, with a large number of alleles exclusively present along the southern colonization route. Only three of 38 alleles were shared between the routes. Analysis of contemporary selection on C/EBP-1 showed divergent selection among the regions, likely reflecting adaptation to the local environmental conditions, although this was especially strong between southern and northern regions coinciding also with lineages from different colonization routes. Overall, the C/EBP-1 gene has historically been under purifying selection, however, two specific amino acid positions showed significant signals of positive selection. These positions showed divergence between southern and northern regions, and we suggest that they are functionally involved in the climatic adaptation of larval development. Using phenotypic data from a common garden experiment, we found evidence for specific C/EBP-1 alleles being correlated with larval development time, suggesting a functional role in adaptation of larval development to large-scale climatic variation.
Data from: Fire increases genetic diversity of populations of Six-lined Racerunner
Wildfires are highly variable and can disturb habitats, leading to direct and indirect effects on the genetic characteristics of local populations. Florida scrub is a fire-dependent, highly fragmented, and severely threatened habitat. Understanding the effect of fire on genetic characteristics of the species that use this habitat is critically important. We investigated one such lizard, the Six-lined Racerunner (Aspidoscelis sexlineata), which has a strong preference for open areas. We collected Six-lined Racerunners (n=154) from 11 sites in Highlands County Florida and defined two time-since-last-fire categories: recently burned and long unburned. We screened genetic variation at six microsatellites to estimate genetic differentiation and compare genetic diversity among sites to determine the relationship with time-since-last-fire. A clear pattern exists between genetic diversity and time-since-last-fire in the absence of strong genetic differentiation. Genetic diversity was greater and inbreeding was lower in sites with more recent time-since-last-fire, and genetic characteristics had significantly larger variance in long unburned sites compared to more recently burned sites. Our results suggest that fire suppression increases variance in genetic characteristics of the Six-lined Racerunner. More generally, fire may benefit genetic characteristics of some species that use fire dependent habitats and management efforts for such severely fragmented habitat will be challenged by the presence of multiple species with incompatible fire preferences.
Data from: Genetic diversity confers colony-level benefits due to individual immunity
Several costs and benefits arise as a consequence of eusociality and group-living. With increasing group size, spread of disease among nest-mates poses selective pressure on both individual immunity and group-level mechanisms of disease resistance (social immunity). Another factor known to influence colony-level expression of disease is intracolony genetic diversity, which in honeybees (Apis mellifera) is a direct function of the number of mates of the queen. Colonies headed by queens with higher mating numbers have less variable infections of decreased intensity, though the underlying mechanisms remain unclear. By pathogen-challenging larvae in vitro, we decoupled larval immune response from mechanisms of social immunity. Our results show that baseline immunity and degree of immune response do not vary with genetic diversity. However, intracolony variance in antimicrobial peptide production after pathogen challenge decreases with increasing genetic diversity. This reduction in variability of the larval immune response could drive the mitigation of disease observed in genetically diverse colonies.
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