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424 results for “ecological genetics”
Genomics of extreme ecological specialists: multiple convergent evolution but no genetic divergence between ecotypes of Maculinea alcon butterflies
<p>Biotic interactions are often acknowledged as catalysers of genetic divergence and eventual explanation of processes driving species richness. We address the question, whether extreme ecological specialization is always associated with lineage sorting, by analysing polymorphisms in morphologically similar ecotypes of the myrmecophilous butterfly <em>Maculinea alcon</em>. The ecotypes occur in either hygric or xeric habitats, use different larval host plants and ant species, but no significant distinctive molecular traits have been revealed so far. We apply genome-wide RAD-sequencing to specimens originating from both habitats across Europe in order to get a view of the potential evolutionary processes at work. Our results confirm that genetic variation is mainly structured geographically but not ecologically — specimens from close localities are more related to each other than populations of each ecotype from distant localities. However, we found two loci for which the association with xeric versus hygric habitats is supported by segregating alleles, suggesting convergent evolution of habitat preference. Thus, ecological divergence between the forms probably does not represent an early stage of speciation, but may result from independent recurring adaptations involving few genes. We discuss the implications of these results for conservation and suggest preserving biotic interactions and main genetic clusters.</p>
FIGURE 17. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURE 17. Hungarosoma bokori Verhoeff, 1928, female, vulvae (Driny Cave). Vulvae in posterior-ventral view (o = opercula) Not scaled.
FIGURE 19 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURE 19. Distribution of the genus Hungarosoma Verhoeff, 1928. Empty dot: H. inexpectatum, solid dots: H. bokori. Distribution of H. bokori in Slovak-Aggtelek Karst drawn in higher scale.
FIGURE 18. A in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURE 18. A Maximum-Likelihood tree (GTR + G + I model) based on the COI gene and rooted with Polyxenus lagurus. All data—except from H. bokori — were obtained from Genbank. Numbers refer to bootstrap values (1000 replicates). Scale bar = 0.02 substitutions / site. For origin of the H. bokori material, see Table 1.
FIGURES 12 – 14. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURES 12 – 14. Hungarosoma bokori Verhoeff, 1928, male (Abaliget Cave). 12: Antenna. 13: Gonopod complex, anterior view. The right side of pair structures is slightly turned laterally. 14: Gonopods in right lateral view. Abbreviations: Letters a – h signal equivalent structures in both views. Anterior gonopods (legs 8): a = cheirite, b = brush-like arm, c = additive divided arm, d = hyaline process. Posterior gonopods (legs 9): e = gonopod, f = ventral hyaline prominence, g = claw shape process with long seta. Not scaled. Photos: Andrej Mock.
FIGURES 6 – 9. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURES 6 – 9. Hungarosoma bokori Verhoeff, 1928, specimens from the Abaliget Cave, preserved in alcohol (not scaled). 6: Habitus of adult male in lateral view; the cheirites of anterior gonopods are visible. 7: Details of the dorsal part of the male trunk. 8: Ventral side of mid-body segments in detail. 9: Dorsal side of a juvenile of stadium III with the shape of the pleurotergites typical for the genus (all material from the Abaliget Cave, Hungary). Photos: Andrej Mock.
FIGURES 10 – 11. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURES 10 – 11. Hungarosoma bokori Verhoeff, 1928, female from the Driny Cave, scanning electronic microscopy of details of the shape and surface of mid-body segments. 10: Dorsolateral view (left side). 11: A pleurotergite, dorsolateral view in detail. Photos: Andrej Mock & Karel Tajovský.
FIGURE 16. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURE 16. Hungarosoma bokori Verhoeff, 1928, male, gonopods (Abaliget Cave). Right lateral view. Letters a – h signal equivalent structures in both views. Abbreviations: Letters a – h signal equivalent structures in both views. Anterior gonopods (legs 8): a = cheirite, b = brush-like arm, c = additive divided arm, d = hyaline process. Posterior gonopods (legs 9): e = gonopod, f = ventral hyaline prominence, g = claw shape process with long seta.
FIGURES 2 – 5. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURES 2 – 5. Hungarosoma bokori Verhoeff, 1928, female, holotype (Abaliget Cave). 2: Head end of the body, right lateral view. 3: Tergite 15, dorsal view. 4: Antenna, lateral view. 5: Discernable vulvae in situ (v), right lateral view. Photos: Jörg Spelda.
FIGURE 15. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURE 15. Hungarosoma bokori Verhoeff, 1928, male, gonopods (Abaliget Cave). Anterior view (right side of pair structures is slightly turned laterally). Abbreviations: Letters a – h signal equivalent structures in both views. Anterior gonopods (legs 8): a = cheirite, b = brush-like arm, c = additive divided arm, d = hyaline process. Posterior gonopods (legs 9): e = gonopod, f = ventral hyaline prominence, g = claw shape process with long seta.
FIGURE 1. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURE 1. Hungarosoma bokori Verhoeff, 1928, female, sampled at the entrance of the Baradla Cave, Hungary, 21. iii. 2013. Photo: Ľubomír Kováč & Andrej Mock.
Indirect genetic effects are shaped by demographic history and ecology in Arabidopsis thaliana
<p><em>This folder contains data & code used for the study "Indirect genetic effects are shaped by demographic history and ecology in Arabidopsis thaliana"</em></p> <p>All data analyzed in the study are stored in the folder "data":</p> <ul> <li>"pheno_file.csv": the main phenotypic file corresponding to the experiment with paired plants used to estimate Indirect Genetic Effects.</li> <li>"pheno_file_single_plants.csv": phenotypic file with measurements of plant biomasses in the absence of competition (single plants)</li> <li>"call_method_75_TAIR9.csv": genomic data (SNPs) for each accession from the RegMap panel (ref [1])</li> <li>"Data_geo_RegMap_accessions.csv": geographic localization of each accession from the RegMap panel (ref [2])</li> <li>"igeGWAS_scores.csv": Genome-Wide Association Study (GWAS) results reporting for each SNP from the RegMap panel the p-value and estimated effect sizes of their direct and indirect genetic effects</li> <li>"1001_accessions_info.csv": geographic localization and admixture group for each accession from the 1001 genomes project (ref [3])</li> <li>"snp_data_all_samples.txt": allelic value of each accession from the 1001 genomes project at the eleven top SNPs associated with IGE</li> <li>"sample_names.txt": names of accessions listed in the file "snp_data_all_samples.txt"</li> <li>"climatic_data.csv": climatic data for each accessions from the 1001 genomes project (ref [4])</li> <li>"candidate_genes_all.csv": list of all genes (and associated GO terms) with a non-synonymous, nonsense, or frameshift mutation in close proximity (distance < half LD decay distance) and high linkage (r2>0.5) with a SNP significantly associated with IGE</li> <li>"genes.coord.bed": list of all genes in a +- 500 kb around top IGE SNPs and their coordinates</li> <li>"AllGenes_fst.GeneID.txt": pairwise Fst computed between each pair of admixture groups, for all genes annotated in the genome of A. thaliana</li> </ul> <p>"ABBA_BABA" subfolder contains ABBA_BABA statistics computed for each individual chromosome (Chr1-Chr5) using genomic windows of 20 kb with at least 250 SNPs per windows. ABBA-BABA statistics were computed using custom python scripts from https://github.com/simonhmartin/genomics_general</p> <p><br> "GEA" subfolder contains Genome-Environment Association results, with one file per chromosome x climatic variable. Climatique variable are indexed, following the order listed in the file "Climatic_variables.txt" within the subfolder "GEA". GEA analysis were run with the gemma program: https://github.com/genetics-statistics/GEMMA.</p> <p><br> "LD_IGE_SNPs" subfolders contains the list of SNPs located at +- 2Mb of a significant IGE SNP (one file per IGE SNP, named "SNPalias_LDSimplified.csv") and their linkage (r2) with the IGE SNP. It also contains the file "LD_windows_sizes.csv" with the half LD decay distances for all significant IGE SNP.</p> <p>All analysis performed to produce the tables and figures presented in the study (main manuscript & supplementary information) were done with the R script "Arabidopsis_IGE_analysis.R", which uses "manhattan_custom.R" as a source function to produce custom manhattan plots.</p> <p> </p> <p><strong>REFERENCES:</strong></p> <p>[1] Horton MW, Hancock AM, Huang YS, Toomajian C, Atwell S, Auton A, Muliyati NW, Platt A, Sperone FG, Vilhjálmsson BJ, et al. 2012. Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nature Genetics 44: 212–216.</p> <p>[2] Anastasio AE, Platt A, Horton M, Grotewold E, Scholl R, Borevitz JO, Nordborg M, Bergelson J. 2011. Source verification of mis-identified Arabidopsis thaliana accessions. The Plant Journal 67: 554–566.</p> <p>[3] 1001 Genomes Consortium. 2016. 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166: 481–491.</p> <p>[4] Ferrero-Serrano Á, Assmann SM. 2019. Phenotypic and genome-wide association with the local environment of Arabidopsis. Nature Ecology & Evolution 3: 274–285.</p>
Data from: Female-biased population sex ratios caused by genetic rather than ecological mechanisms in dwarf willow (Salix herbacea L.)
<p>Biased sex ratios among reproductive individuals are common in plants, but the underlying mechanisms, as well as the evolutionary consequences, are not well understood. The classical theory of Düsing and Fisher predicts an equal primary sex ratio at seed production, based on the selective advantage of the rare sex. Biased sex ratios among reproductive plants can arise from sexual dimorphism in survival and flowering. Sex ratio biases can also be present from the seed stage; in these cases, assumptions of Düsing's and Fisher's theory, for example, random mating or demographic equilibrium, are thought to be violated.</p> <p>We investigated mechanisms leading to female-biased sex ratios in the arctic-alpine dwarf willow <em>Salix herbacea</em> L. We studied sex ratios in three natural populations over three years as well as in 29 crosses (full-sib families) under controlled conditions over four growth periods. We tested whether sex ratio was associated with habitat parameters (elevation and snowmelt time), or with germination, survival or flowering, and whether females and males differed in size or flowering that may cause observation bias.</p> <p>We detected a strong and consistent female bias, both in natural populations (sex ratio [proportion of females]: 0.71-0.82) and in our controlled experiment (overall sex ratio: 0.70-0-72). Female bias became more pronounced with increasing elevation. Our data did not support sexual dimorphism in size or flowering. Family sex ratios varied largely (from 0.25 to 1), including many female-biased families, unbiased families and two male-biased families. Families with lower germination, seedling establishment, survival or flowering did not have stronger female bias, indicating that intrinsically higher survival or flowering in females does not explain overall female bias. </p> <p>Synthesis: Our results suggest that sex ratio bias in <em>S. herbacea</em> is already present in seeds and does not arise through intrinsic differences between sexes. Candidate mechanisms that can lead to both overall female bias and variation in sex ratio among families are meiotic drive or cyto-nuclear interactions. The pioneer habit of <em>Salix</em> may lead to non-equilibrium population dynamics that allow for the long-term persistence of variable genetic sex ratio distortion systems that arise from genetic conflict.</p>
Data from: Dispersal in a house sparrow metapopulation: an integrative case study of genetic assignment calibrated with ecological data and pedigree information
<p class="western">Dispersal has a crucial role determining eco-evolutionary dynamics through both gene flow and population size regulation. However, to study dispersal and its consequences, one must distinguish immigrants from residents. Dispersers can be identified using telemetry, capture-mark-recapture (CMR) methods, or genetic assignment methods. All of these methods have disadvantages, such as, high costs and substantial field efforts needed for telemetry and CMR surveys, and adequate genetic distance required in genetic assignment. In this study, we used genome-wide 200K Single Nucleotide Polymorphism data and two different genetic assignment approaches (GSI_SIM, Bayesian framework; BONE, network-based estimation) to identify the dispersers in a house sparrow (<i>Passer domesticus</i>) metapopulation sampled over 16 years. Our results showed higher assignment accuracy with BONE. Hence, we proceeded to diagnose potential sources of errors in the assignment results from the BONE method due to variation in levels of inter-population genetic differentiation, intra-population genetic variation and sample size. We show that assignment accuracy is high even at low levels of genetic differentiation and that it increases with the proportion of a population that has been sampled. Finally, we highlight that dispersal studies integrating both ecological and genetic data provide robust assessments of the dispersal patterns in natural populations.</p>
Fig. 51 in Hybridization Among Western Whiptail Lizards (Cnemidophorus Tigris) In Southwestern New Mexico: Population Genetics, Morphology, And Ecology In Three Contact Zones
Fig. 51. Electrophoretic phenotypes of proteins of several subspecies of C. tigris. Left. ESTD polymorphism in C. t. septentrionalis. The fluorescent patterns were photographed in ultraviolet light. Right. Banding patterns of PGM2 that distinguish septentrionalis (SEP, genotype cc) from punctilinealis (PUN genotype dd), marmoratus (MAR, genotype dd), and aethiops (genotype dd, not illustrated). Arrows indicate sites of sample application; anode is to the right.
Fig. 49 in Hybridization Among Western Whiptail Lizards (Cnemidophorus Tigris) In Southwestern New Mexico: Population Genetics, Morphology, And Ecology In Three Contact Zones
Fig. 49. The contact region. Horizontal lines represent range of pure punctilinealis (coloration indices of 0–0.1; table 24), and vertical lines pure marmoratus (coloration indices of 0.8–1.0). Sites in between (2–5, 18, 19, 26, and 41–44) represent primarily hybrids (coloration indices of 0.11–0.79).
Fig. 52 in Hybridization Among Western Whiptail Lizards (Cnemidophorus Tigris) In Southwestern New Mexico: Population Genetics, Morphology, And Ecology In Three Contact Zones
Fig. 52. Differences in the tissue distribution of lactate dehydrogenase, a tetramer. Top (six lanes) LDH1 predominates in heart. Bottom (five lanes). Both LDH1 and LDH2 are active in liver and the banding patterns include numerous isozymes composed of subunits of both. Note the fivebanded patterns for LDH1 for heterozygous diploid C. neomexicanus (NEO) and a triploid hybrid (HYB) of neomexicanus × tigris. In the heart tissue, LDH1 genotype ab for neomexicanus, the isozymes approximate activities of 1:4:6:4:1. For the triploid hybrid with genotype aab, the faster migrating isozymes stain most intensely (activities approximate the theoretically expected ratio of 16:32:24:8:1). These patterns are consistent with the origin of the hybrid from a mating between C. neomexicanus (NEO) and C. t. punctilinealis (PUN). Other abbreviations are: UNI, C. uniparens; MAR, C. t. marmoratus. Arrow indicates sites of sample application; anode is to the right.
Fig. 47 in Hybridization Among Western Whiptail Lizards (Cnemidophorus Tigris) In Southwestern New Mexico: Population Genetics, Morphology, And Ecology In Three Contact Zones
Fig. 47. Relationship between body length and number of eggs per clutch in specimens of C. tigris from the contact region. MAR, pure marmoratus; PUN, pure punctilinealis; HYB, hybrids. Data are summarized in table 30 and figure 48.
Fig. 48 in Hybridization Among Western Whiptail Lizards (Cnemidophorus Tigris) In Southwestern New Mexico: Population Genetics, Morphology, And Ecology In Three Contact Zones
Fig. 48. Relationship between body length and number of eggs per clutch (same data as table 30 and fig. 47), showing 95% confidence intervals (broken lines) for each plot. M, pure marmoratus P, pure punctilinealis; H, hybrids.
Fig. 46 in Hybridization Among Western Whiptail Lizards (Cnemidophorus Tigris) In Southwestern New Mexico: Population Genetics, Morphology, And Ecology In Three Contact Zones
Fig. 46. Polygons and letters representing the scores of 27 specimens of C. tigris on the first two principal components extracted from the correlation matrix of nine morphological characters observed in the southern transect (table 28). P represents 9 punctilinealis from site 36; M, 9 marmoratus from site 48; and H, 9 hybrids from site 42, the center of the southern hybrid zone (fig. 5).
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.