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2,785 results for “genotyping”
Taxus genotype data for "Trunk perimeter correlates with genetic bottleneck intensity and the level of genetic diversity in populations of Taxus baccata L."
<p>The data set contains microsatellite genotypes (18 loci) of Taxus baccata trees, together with the information about sampling sites.</p>
Data from: Spontaneous hybridization and introgression between walleye (Sander vitreus) and sauger (S. canadensis) in two large reservoirs: insights from genotyping-by-sequencing
<p>Anthropogenic activities may facilitate undesirable hybridization and genomic introgression between fish species. Walleye (<i>Sander vitreus</i>) and sauger (<i>Sander canadensis</i>) are economically valuable freshwater species that can spontaneously hybridize in areas of sympatry. Levels of genomic introgression between walleye and sauger may be increased by modifications to waterbodies (e.g., reservoir development) and inadvertent propagation of hybrids in stocking programs. We used genotyping by sequencing (GBS) to examine 217 fish from two large reservoirs with mixed populations of walleye and sauger in Saskatchewan, Canada (Lake Diefenbaker, Tobin Lake). Analyses with 20,038 (r90) and 478 (r100) SNPs clearly resolved walleye and sauger, and classified hybrids with high confidence. F<sub>1</sub>, F<sub>2</sub>, and multi-generation hybrids were detected in Lake Diefenbaker, indicating potentially high levels of genomic introgression. In contrast, only F<sub>1</sub> hybrids were detected in Tobin Lake. Field classification of fish was unreliable; 7% of fish were misidentified based on broad species categories. Important for activities such as brood stock selection, 12/173 (7%) fish field-identified as pure walleye, and 1/24 (4%) identified as pure sauger were actually hybrids. In addition, 2/15 (13%) field-identified hybrids were actually pure walleye or sauger. We conclude that hybridization and introgression are occurring in Saskatchewan reservoirs, and that caution is warranted when using these populations in stocking programs. GBS offers a powerful and flexible tool for examining hybridization without pre-identification of informative loci, eliminating some of the key challenges associated with other marker types.</p>
Effect of maternal infection on progeny growth and resistance mediated by maternal genotype and nutrient availability
<div class="_3U2q6dcdZCrTrR_42Nxby JWNdg1hee9_Rz6bIGvG1c allowTextSelection"> <div> <div class="BodyFragment"> <div class="PlainText">1. Maternal effects of pathogen infection on progeny development and disease resistance may be adaptive and have important consequences for population dynamics. However, these effects are often context dependent and examples of adaptive transgenerational responses from perennials are scarce, although they may be a particularly important mechanism generating variation in the offspring of long-lived species.</div> <div class="PlainText"> <br> 2. Here, we studied the effect of maternal infection of Plantago lanceolata by Podosphaera plantaginis, a fungal parasite, on the growth, flower production and resistance of the progeny of six maternal genotypes in nutrient rich and poor environments. For this purpose, we combined a common garden study with automated phenotyping measurements of early life-stages, and an inoculation experiment.</div> <div class="PlainText"> <br> 3. Our results show that the effects of infection on the mother plants transcend to impact their progeny. Although maternal infection decreased total leaf and flower production of the progeny by the end of the growing season, it accelerated early growth and enhanced resistance to the pathogen P. plantaginis.</div> <div class="PlainText"> <br> 4. We also discovered that the effects of maternal infection affected progeny development and resistance both directly, and through a three way-interaction between maternal genotype, maternal infection status and nutrient availability.</div> <div class="PlainText"> </div> <div class="PlainText">5. Synthesis: Our results emphasize the importance of maternal effects mediated through genotypic and environmental factors in long living perennials and suggest that maternal infection can create a layer of phenotypic diversity in resistance. These results may have important implications for both epidemiological and evolutionary dynamics of host–parasite interactions in the wild.</div> </div> </div> </div>
Supplementary material 1 from: Sun Y, Beuchat C, Müller-Schärer H (2020) Is biocontrol efficacy rather driven by the plant or the antagonist genotypes? A conceptual bioassay approach. NeoBiota 63: 81-100. https://doi.org/10.3897/neobiota.63.54962
Figure S1–S8
Microsatellite genotype data from seven loci for a phylogeographic/population genetic study of the South African endemic freshwater crab Potamonautes lividus sampled from eight localities in the KwaZulu-Natal and Eastern Cape provinces in South Africa
<ol> <li>During the present study, the phylogeography of the only southern African IUCN Red Listed vulnerable (VU) freshwater crab, <i>Potamonautes lividus</i> was investigated by surveying several localities in the Eastern Cape and KwaZulu-Natal provinces in South Africa. Both nuclear and mitochondrial DNA markers were used, and it was hypothesized, that marked genetic differentiation should be present, while niche modeling was undertaken to explore the distribution of the species along the east coast of South Africa. <span><span>Further, the shortfalls in the present approach to IUCN Red Listing, as illustrated by a vulnerable species of crabs are discussed</span></span>.</li> <li>Results from the mtDNA revealed the presence of two haploclades confined to specimens from the two provinces respectively and the general absence of maternal dispersal; a fact that was further validated by the marked <i>F</i><sub>ST</sub> data and high F<sub>ST</sub>. Within the Eastern Cape haploclade, low frequency maternal dispersal occurred, corroborated by the low F<sub>ST</sub>. In contrast, no haplotypes were shared in the KwaZulu-Natal haploclade a fact corroborated by marked F<sub>ST</sub> differences. </li> <li>The microsatellite data demonstrated the presence of higher frequency, possibly paternally biased dispersal of specimens between the Eastern Cape and KwaZulu-Natal provinces. Our results suggest that presence of two distinct management units within <i>P. lividus</i>. Divergence time estimation suggest a late Pleistocene cladogenesis between the Eastern Cape and KwaZulu-Natal haploclades. </li> <li>Considering the presence of <i>P. lividus</i> in several newly collected nature conservation areas in both provinces, and its potential presence in the intermediary area based on the MAXENT niche modeling, our data suggest the species IUCN Red Listing status should be downgraded to LC.</li> <li>A comparison of all the EN, VU and CR IUCN Red Listed freshwater crabs for the entire Afrotropical region reveals the lack of recent sampling in the three biodiversity hotspots in West, Central and East Africa, with mountainous areas containing a disproportionate number of species with most species being devoid of phylogeographic study. </li> </ol>
Genotype, spatial and morphological data of adults and progeny in a natural population of Leucadendron rubrum
<p>We provide a dataset containing data on both female and male plants measured in a natural population of <em>Leucadendron rubrum</em> about plant architecture, and leaf morphology, thus informing about sexual dimorphism in this species. Genotypes of these males and females on eight microsatellites combined with corresponding genotype data in their progeny permits to undertake parentage analyses. Finally, the spatial distribution of both parents and juveniles allows to account for potential spatial biases in sampling juveniles in parentage analyses.</p>
Data from: What drives selection on flowering time? An experimental manipulation of the inherent correlation between genotype and environment
The optimal timing of the seasonal switch from somatic growth to reproduction can depend on an individual's condition at reproduction, the quality of the environment in which it will reproduce, or both. In annual plants, vegetative size (a function of age at flowering) affects resources available for seed production, while exposure to mutualists, antagonists, and abiotic stresses in the environment (functions of Julian date of flowering), influences success in converting resources into offspring. The inherent tight correlation between age, size, and environment obscures their independent fitness contributions. We isolated the fitness effects of these factors by experimentally manipulating the correlation between age at flowering and date of flowering in Brassica rapa. We staggered the planting dates of families with differing ages at flowering to produce experimental populations in which age at flowering and date of flowering were positively-, negatively-, or uncorrelated. In all populations, plants with an early date of flowering produced more seed than those flowering late, regardless of age or size at flowering onset. The temporal environment was thus the principal driver of selection on flowering time, but its importance relative to that of age and size varied with the presence/absence of herbivores and seed predators.
Data from: Estimations of linkage disequilibrium, effective population size and ROH-based inbreeding coefficients in Spanish Churra sheep using imputed high-density SNP genotypes
In this study, the availability of the Ovine HD SNP BeadChip (HD-chip) and the development of an imputation strategy provided an opportunity to further investigate the extent of linkage disequilibrium (LD) at short distances in the genome of the Spanish Churra dairy sheep breed. A population of 1686 animals, including 16 rams and their half-sib daughters, previously genotyped for the 50K-chip, was imputed to the HD-chip density based on a reference population of 335 individuals. After assessing the imputation accuracy for beagle v4.0 (0.922) and fimpute v2.2 (0.921) using a cross-validation approach, the imputed HD-chip genotypes obtained with beagle were used to update the estimates of LD and effective population size for the studied population. The imputed genotypes were also used to assess the degree of homozygosity by calculating runs of homozygosity and to obtain genomic-based inbreeding coefficients. The updated LD estimations provided evidence that the extent of LD in Churra sheep is even shorter than that reported based on the 50K-chip and is one of the shortest extents compared with other sheep breeds. Through different comparisons we have also assessed the impact of imputation on LD and effective population size estimates. The inbreeding coefficient, considering the total length of the run of homozygosity, showed an average estimate (0.0404) lower than the critical level. Overall, the improved accuracy of the updated LD estimates suggests that the HD-chip, combined with an imputation strategy, offers a powerful tool that will increase the opportunities to identify genuine marker-phenotype associations and to successfully implement genomic selection in Churra sheep.
Data from: Quantifying genotype x environment effects in long-term common wheat yield trials from an agroecologically diverse production region
Multienvironment trials (METs) are used to investigate the performance of crop genotypes. To efficiently generate reliable performance estimates, the magnitude and patterns of genotype × environment interaction (G×E) in MET data must be known. We quantified G×E in fall-planted common wheat (Triticum aestivum L.) in California, with the goal of increasing the reliability and efficiency of statewide variety testing activities. Linear mixed models and the genotype main effects plus G×E interaction effects (GGE) biplot method were used to analyze MET data for 211 common wheat genotypes, the MET consisted of 9 locations and 14 seasons. The representativeness and discriminating power of the MET locations were tested, and estimates of the optimum number of test locations were made. The analyses did not find evidence for significant, repeatable, crossover G×E. The genotype and G×E effects were of a similar magnitude, and the G×E effects were relatively strong compared with other sources of variance but were dominated by seasonal effects, with potentially repeatable genotype-by-location (G×L) effects being relatively weak. The GGE analyses did not detect repeatable G×L patterns across seasons. As a result, we conclude that the cereal production regions of California consist of a single, but unstable, mega-environment for common wheat grain yield. The test location evaluation found few significant differences between test locations in terms of how well they represent the target production environment. We estimate that the number of test locations could be reduced while maintaining trial accuracy, which would improve the resource use efficiency of statewide trial activities without sacrificing information about variety-specific common wheat yield performance.
Data from: The architecture of an empirical genotype-phenotype map
Recent advances in high-throughput technologies are bringing the study of empirical genotype-phenotype (GP) maps to the fore. Here, we use data from protein binding microarrays to study an empirical GP map of transcription factor (TF) binding preferences. In this map, each genotype is a DNA sequence. The phenotype of this DNA sequence is its ability to bind one or more TFs. We study this GP map using genotype networks, in which nodes represent genotypes with the same phenotype, and edges connect nodes if their genotypes differ by a single small mutation. We describe the structure and arrangement of genotype networks within the space of all possible binding sites for 525 TFs from three eukaryotic species encompassing three kingdoms of life (animal, plant, and fungi). We thus provide a high-resolution depiction of the architecture of an empirical GP map. Among a number of findings, we show that these genotype networks are "small-world" and assortative, and that they ubiquitously overlap and interface with one another. We also use polymorphism data from Arabidopsis thaliana to show how genotype network structure influences the evolution of TF binding sites in vivo. We discuss our findings in the context of regulatory evolution.
Data from: Susceptibility of Macrosiphum euphorbiae to the parasitoid Aphidius ervi: larval development depends on host aphid genotype
The potato aphid, Macrosiphum euphorbiae Thomas (Hemiptera: Aphididae: Macrosiphini), is a common polyphagous aphid in Europe and North America. However, the factors influencing potato aphid dynamics and susceptibility to natural enemies are largely undescribed, particularly in relation to facultative endosymbiotic bacteria, which can provide protection against parasitism and disease in some aphid species. This study investigated whether potato aphid susceptibility to one of its principal natural enemies, the parasitoid Aphidius ervi Haliday (Hymenoptera: Braconidae: Aphidiinae), varied in relation to aphid genotype and/or endosymbiont presence. Parasitism and aphid fitness assays were conducted on clonal lineages of aphids, harbouring their natural endosymbiont infections, collected over 3 years from separate geographic locations. Parasitized aphids were dissected to quantify parasitoid oviposition, larval development, and mummification. Amongst the 19 clonal lines of M. euphorbiae tested, seven aphid genotypes were identified, and 11 lines harboured one or both of the facultative endosymbionts Hamiltonella defensa Moran et al. and Regiella insecticola Moran et al.; H. defensa infections were associated exclusively with two of the seven M. euphorbiae genotypes. Parasitism resistance was detected in clonal lines belonging to a single aphid genotype and resulted from failure of parasitoid eggs to develop into larvae rather than failure of the parasitoid to oviposit. Contrary with studies of several other aphid species, there was little evidence that H. defensa provided strong protection to M. euphorbiae from parasitism by A. ervi. Furthermore, there were no clear fitness costs to the aphid associated with parasitism resistance or with H. defensa infection. The two M. euphorbiae genotypes in which H. defensa occurred, which included the resistant genotype, exhibited faster development, higher survival, and greater fecundity than the other five aphid genotypes. These findings suggest that biological control of M. euphorbiae using A. ervi alone could exacerbate pest problems by selecting for the fittest parasitism-resistant genotypes.
Data from: Phenotypic but not genotypic selection for earlier flowering in a perennial herb
1. Timing of reproduction affects the outcome of interactions between plants and their pollinators, grazers and seed predators, as well as with their local abiotic environment. In seasonal environments, phenotypic selection has often been shown to favor early flowering. Yet, we still know little about the agents driving selection in natural populations and whether observed phenotypic selection corresponds to genotypic selection – a prerequisite for evolutionary change. 2. In this study, we experimentally assessed phenotypic and genotypic selection for flowering time in a natural population of the perennial herb Lathyrus vernus. We transplanted sibling individuals, obtained through controlled crosses, to their source population and found net phenotypic selection for earlier flowering in the field. 3. Despite a higher susceptibility to roe deer grazing, early-flowering plants had higher fruit set and more seeds per fruit than late-flowering plants. We found no support for genotypic selection on flowering time, and heritability for first flowering day was very low. 4. Synthesis: Our results suggest that commonly observed patterns of higher fitness in early-flowering plants do not always correspond to selection on genotypic values and are thus not necessarily expected to result in evolutionary change even if the relationship between flowering time and fitness is causal. This finding should be important to understand how species phenology might respond to changing environmental conditions.
Data from: Identifying and reducing AFLP genotyping error: an example of tradeoffs when comparing population structure in broadcast spawning versus brooding oysters
Phylogeographic inferences about gene flow are strengthened through comparison of co-distributed taxa, but also depend on adequate genomic sampling. Amplified Fragment Length Polymorphisms (AFLP) provide a rapid and inexpensive source of multilocus allele frequency data for making genomically robust inferences. Every AFLP study initially generates markers with a range of locus-specific genotyping error rates and applies criteria to select a subset for analysis. However, there has been very little empirical evaluation of the best tradeoff between culling all but the lowest-error loci to minimize overall genotyping error versus the potential for increasing population genetic signal by retaining more loci. Here, we used AFLPs to compare population structure in co-distributed broadcast spawning (Crassostrea virginica) and brooding (Ostrea equestris) oyster species. Using existing methods for almost entirely automated marker selection and scoring, genotyping error tradeoffs were evaluated by comparing results across a nested series of datasets with mean mismatch errors of 0, 1, 2, 3, 4 and >4%. Artifactual population structure was diagnosed in high-error datasets and we assessed the low-error point at which expected population substructure signal was lost. In both species we identified substructure patterns deemed to be inaccurate at error rates {less than or equal to}2% and >4%. In the species comparison, the optimum datasets showed higher gene flow for the brooding oyster with more oceanic salinity tolerances. AFLP tradeoffs may differ among studies, but our results suggest that important signal may be lost in the pursuit of 'acceptable' error levels and our procedures provide a general method for empirically exploring these tradeoffs.
Data from: Interactions among bacterial strains and fluke genotypes shape virulence of co-infection
Most studies of virulence of infection focus on pairwise host-parasite interactions. However, hosts are almost universally co-infected by several parasite strains and/or genotypes of the same or different species. While theory predicts that co infection favours more virulent parasite genotypes through intensified competition for host resources, knowledge of effects of genotype by genotype (G×G) interactions between unrelated parasite species on virulence of co infection is limited. Here we tested such relationship by challenging rainbow trout with replicated bacterial strains and fluke genotypes both singly and in all possible pairwise combinations. We found that virulence (host mortality) was higher in co infections compared to single-infections. Importantly, we also found that the overall virulence was dependent on the genetic identity of the co-infecting partners so that the outcome of co infection could not be predicted from the respective virulence of single infections. Our results imply that G×G interactions among co infecting parasites may significantly affect host health, add to variance in parasite fitness and thus influence evolutionary dynamics and ecology of disease in unexpected ways.
Data from: Dietary choices are influenced by genotype, mating status, and sex in Drosophila melanogaster
Mating causes many changes in physiology, behaviour and gene expression in a wide range of organisms. These changes are predicted to be sex-specific, influenced by the divergent reproductive roles of the sexes. In female insects, mating is associated with an increase in egg production which requires high levels of nutritional input with direct consequences for the physiological needs of individual females. Consequently, females alter their nutritional acquisition in line with the physiological demands imposed by mating. Although much is known about the female mating-induced nutritional response, far less is known about changes in males. In addition, it is unknown whether variation between genotypes translates into variation in dietary behavioral responses. Here we examine mating-induced shifts in male and female dietary preferences across genotypes of Drosophila melanogaster. We find sex- and genotype-specific effects on both the quantity and quality of the chosen diet. These results contribute to our understanding of sex-specific metabolism and reveal genotypic variation that influences responses to physiological demands.
Data from: Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)
Background: The majority of the subspecies of Daucus carota have not yet been discriminated clearly by various molecular or morphological methods and hence their phylogeny and classification remains unresolved. Recent studies using 94 nuclear orthologs and morphological characters, and studies employing other molecular approaches were unable to distinguish clearly many of the subspecies. Fertile intercrosses among traditionally recognized subspecies are well documented. We here explore the utility of single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS) to serve as an effective molecular method to discriminate the subspecies of the D. carota complex. Results: We used GBS to obtain SNPs covering all nine Daucus carota chromosomes from 162 accessions of Daucus and two related genera. To study Daucus phylogeny, we scored a total of 10,814 or 38,920 SNPs with a maximum of 10 or 30 % missing data, respectively. To investigate the subspecies of D. carota, we employed two data sets including 150 accessions: (i) rate of missing data 10 % with a total of 18,565 SNPs, and (ii) rate of missing data 30 %, totaling 43,713 SNPs. Consistent with prior results, the topology of both data sets separated species with 2n = 18 chromosome from all other species. Our results place all cultivated carrots (D. carota subsp. sativus) in a single clade. The wild members of D. carota from central Asia were on a clade with eastern members of subsp. sativus. The other subspecies of D. carota were in four clades associated with geographic groups: (1) the Balkan Peninsula and the Middle East, (2) North America and Europe, (3) North Africa exclusive of Morocco, and (4) the Iberian Peninsula and Morocco. Daucus carota subsp. maximus was discriminated, but neither it, nor subsp. gummifer (defined in a broad sense) are monophyletic. Conclusions: Our study suggests that (1) the morphotypes identified as D. carota subspecies gummifer (as currently broadly circumscribed), all confined to areas near the Atlantic Ocean and the western Mediterranean Sea, have separate origins from sympatric members of other subspecies of D. carota, (2) D. carota subsp. maximus, on two clades with some accessions of subsp. carota, can be distinguished from each other but only with poor morphological support, (3) D. carota subsp. capillifolius, well distinguished morphologically, is an apospecies relative to North African populations of D. carota subsp. carota, (4) the eastern cultivated carrots have origins closer to wild carrots from central Asia than to western cultivated carrots, and (5) large SNP data sets are suitable for species-level phylogenetic studies in Daucus.
Data from: Degenerate adaptor sequences for detecting PCR duplicates in reduced representation sequencing data improve genotype calling accuracy
RAD-tag is a powerful tool for high-throughput genotyping. It relies on PCR amplification of the starting material, following enzymatic digestion and sequencing adaptor ligation. Amplification introduces duplicate reads into the data, which arise from the same template molecule and are statistically nonindependent, potentially introducing errors into genotype calling. In shotgun sequencing, data duplicates are removed by filtering reads starting at the same position in the alignment. However, restriction enzymes target specific locations within the genome, causing reads to start in the same place, and making it difficult to estimate the extent of PCR duplication. Here, we introduce a slight change to the Illumina sequencing adaptor chemistry, appending a unique four-base tag to the first index read, which allows duplicate discrimination in aligned data. This approach was validated on the Illumina MiSeq platform, using double-digest libraries of ants (Wasmannia auropunctata) and yeast (Saccharomyces cerevisiae) with known genotypes, producing modest though statistically significant gains in the odds of calling a genotype accurately. More importantly, removing duplicates also corrected for strong sample-to-sample variability of genotype calling accuracy seen in the ant samples. For libraries prepared from low-input degraded museum bird samples (Mixornis gularis), which had low complexity, having been generated from relatively few starting molecules, adaptor tags show that virtually all of the genotypes were called with inflated confidence as a result of PCR duplicates. Quantification of library complexity by adaptor tagging does not significantly increase the difficulty of the overall workflow or its cost, but corrects for differences in quality between samples and permits analysis of low-input material.
Data from: Leaf photosynthetic, economics and hydraulic traits are decoupled among genotypes of a widespread species of eucalypt grown under ambient and elevated CO2
Leaf economics and hydraulic traits strongly influence photosynthesis. While the level of coordination among these traits can differ between sets of species, leaf functional trait coordination within species remains poorly understood. Furthermore, elevated concentrations of atmospheric CO2 commonly influence the expression of leaf photosynthetic, economics and hydraulic traits in contrasting ways, yet the effect of variable concentrations of atmospheric CO2 on patterns of trait coordination within species remains largely untested. We examined the relationships among key leaf photosynthetic (e.g. net photosynthesis and photosynthetic biochemistry), economics and water-use (e.g. leaf mass per unit area and stomatal conductance) and hydraulic traits (e.g. vein density) in 14 genotypes of Eucalyptus camaldulensis grown in ambient (aCO2) and elevated (eCO2) [CO2]. We examined the level of coordination among leaf traits in aCO2 and then assessed whether growth in eCO2 altered that coordination. We found that leaf traits related to photosynthetic capacity, economics and water-use, and hydraulics were decoupled among genotypes grown in aCO2, yet strong relationships were generally observed among suites of traits within each 'functional group'. Significant responses to growth in eCO2 were observed for most leaf photosynthetic and economics and water-use traits, with the magnitude and direction of the response varying among traits. In contrast, leaf hydraulics traits were unaffected by variable growth CO2. Despite this, growth in eCO2 did not substantially alter patterns of leaf trait coordination observed in aCO2. These results suggest suites of leaf traits associated with photosynthetic capacity, economics and water-use and hydraulics, respectively, can form independent axes of variation among genotypes of a single species, regardless of growth CO2. Although growth in eCO2 did not substantially alter patterns of trait coordination, decoupling of leaf functional traits among genotypes may allow genetically distinct populations to produce novel combinations of traits that may be adaptive in response to changes in their local environment.
Data from: Gene flow between nascent species: geographic, genotypic and phenotypic differentiation within and between Aquilegia formosa and A. pubescens.
Speciation can be described as a reduction, and the eventual cessation, in the ability to interbreed. Thus, determining how gene flow differs within and between nascent species can illuminate the relative stage the taxa have attained in the speciation process. Aquilegia formosa and A. pubescens are fully intercompatible yet occur in different habitats and have flowers specialized for pollination by hummingbirds and hawkmoths respectively. Using 79 SNP loci we genotyped nearly 1,000 individuals from populations of both species in close proximity to each other and from putative hybrid zones. The species shared all but one SNP polymorphism and on average, allele frequencies differed by only 0.14. However, the species were clearly differentiated using Structure and admixed individuals were primarily identified at putative hybrid zones. PopGraph identified a highly integrated network among all populations but populations of each species and hybrid zones occupied distinct regions in the network. Using either conditional graph distance (cGD) or Fst/(1-Fst) we found significant isolation by distance (IBD) among populations. Within species, IBD was strong, indicating high historic gene flow. IBD extended approximately 100 km in A. pubescens and 30 km in A. formosa. However, IBD between the species was very weak and extended only a few km beyond hybrid zones, suggesting little recent gene flow. The extensive sharing of SNP polymorphisms between these species suggests that they are very early in the speciation process while the low signal of IBD suggests that they have largely ceased gene exchange.
Genotyping by sequencing data of five legume tree species widespread in the rainforests of West and Central Africa
<p>Although today the forest cover is continuous in Central Africa this may have not always been the case, as the scarce fossil record in this region suggests that arid conditions might have significantly reduced tree density during the Ice Ages. Our aim was to investigate whether the dry ice-age periods left a genetic signature on tree species that can be used to infer the date of the past fragmentation of the rainforest. We sequenced reduced representation libraries of 182 samples representing five widespread Legume trees and seven outgroups. Phylogenetic analyses identified an early divergent lineage for all species in West Africa (Upper Guinea), and two clades in Central Africa: Lower Guinea-North and Lower Guinea-South. As the structure separating the Northern and Southern clades -congruent across species- cannot be explained by geographic barriers, we tested other hypotheses with demographic model testing using ∂a∂I. The best estimates indicate that the two clades split between the Upper Pliocene and the Pleistocene, a date compatible with forest fragmentation driven by ice-age climatic oscillations. Furthermore, we found remarkably older split dates for the shade-tolerant tree species with non-assisted seed dispersal than for light-demanding species with long-distance wind dispersal. Different recolonisation abilities after recurrent cycles of forest fragmentation seem to explain why species with long-distance dispersal show more recent genetic admixture between the two clades than species with limited seed dispersal. Despite their old history, our results depict the African rainforests as a dynamic biome where tree species have expanded relatively recently after the last glaciation.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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