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opencc-by-nc-4.0Feb 2017View details →

Raw Genotyping data from: Variation in recombination rate and its genetic determinism in sheep populations from combining multiple genomewide datasets

Data supporting : Variation in recombination rate and its genetic determinism in sheep populations from combining multiple genomewide datasets Morgane Petit, Jean-Michel Astruc, Julien Sarry, Laurence Drouilhet, Stephane Fabre, Carole Moreno, Bertrand Servin http://doi.org/10.1534/genetics.117.300123 Abstract Recombination is a complex biological process that results from a cascade of multiple events during meiosis. Understanding the genetic determinism of recombination can help to understand if and how these events are interacting. To tackle this question, we studied the patterns of recombination in sheep, using multiple approaches and datasets. We constructed male recombination maps in a dairy breed from the south of France (the Lacaune breed) at a fine scale by combining meiotic recombination rates from a large pedigree genotyped with a 50K SNP array and historical recombination rates from a sample of unrelated individuals genotyped with a 600K SNP array. This analysis revealed recombination patterns in sheep similar to other mammals but also genome regions that have likely been affected by directional and diversifying selection. We estimated the average recombination rate of Lacaune sheep at 1.5 cM/Mb, identified about 50,000 crossover hotspots on the genome and found a high correlation between historical and meiotic recombination rate estimates. A genome-wide association study revealed two major loci affecting inter-individual variation in recombination rate in Lacaune, including the RNF212 and HEI10 genes and possibly 2 other loci of smaller effects including  the KCNJ15  and FSHR genes. Finally, we compared our results to those obtained previously in a distantly related population of domestic sheep, the Soay. This comparison revealed that Soay and Lacaune males have a very similar distribution of recombination along the genome and that the two datasets can be combined to create more precise male meiotic recombination maps in sheep. Despite their similar recombination maps, we show that Soay and Lacaune males exhibit different heritabilities and QTL effects for inter-individual variation in genome-wide recombination rates.   Data files are provided in Plink format ( https://www.cog-genomics.org/plink2 ).

opencc-zeroDec 2023View details →

Variation in personality shaped by evolutionary history, genotype, and developmental plasticity in response to feeding modalities in the Arctic charr

Animal personality has been shown to be influenced by both genetic and environmental factors and shaped by natural selection. Currently, little is known about mechanisms influencing the development of personality traits. This study examines the extent to which personality development is genetically influenced and/or environmentally responsive (plastic). We also investigated the role of evolutionary history, assessing whether personality traits could be canalized along a genetic and ecological divergence gradient. We tested the plastic potential of boldness in juveniles of five Icelandic Arctic charr morphs (Salvelinus alpinus), including two pairs of sympatric morphs, displaying various degrees of genetic and ecological divergence from the ancestral anadromous charr, split between treatments mimicking benthic vs. pelagic feeding modalities. We show that differences in mean boldness are mostly affected by genetics. While the benthic treatment led to bolder individuals overall, the environmental effect was rather weak, suggesting that boldness lies under strong genetic influence with reduced plastic potential. Finally, we found hints of differences by morphs in boldness canalization through reduced variance and plasticity, and higher consistency in boldness within morphs. These findings provide new insights into how behavioural development may impact adaptive diversification.

opencc-by-4.0Mar 2022View details →

CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data

To date, ancient genome analyses have been largely confined to the study of single nucleotide polymorphisms (SNPs). Copy number variants (CNVs) are a major contributor of disease and of evolutionary adaptation, but identifying CNVs in ancient shotgun-sequenced genomes is hampered by (i) most published genomes being <1x coverage, (ii) ancient DNA fragments being typically <80 bps. These characteristics preclude state-of-the-art CNV detection software to be effectively applied to ancient genomes. Here we present CONGA, an algorithm tailored for genotyping deletion and duplication events in genomes with low depths of coverage. Simulations and down-sampling experiments show that CONGA can genotype deletions >1 kbps with F-scores >0.75 at >=1x, and distinguish between heterozygous and homozygous states. Using CONGA, we analyse deletion events at 10,018 loci in 56 ancient human genomes spanning the last 50,000 years, with coverages 0.4x-26x. We show that inter-individual genetic diversity measured using deletions and SNPs are highly correlated, as in modern-day genomes, confirming that deletion frequencies broadly reflect demographic history. We also identify signatures of strong purifying selection on deletions in ancient-genomes, such as an excess of singletons compared to those in SNPs. CONGA paves the way for systematic studies of drift, mutation load, and adaptation in ancient and modern-day gene pools through the lens of CNVs.

opencc-by-4.0Aug 2012View details →

Fig. 4 in Among-Genotype Variation For Sediment Rejection In The Reef-Building Coral Diploastrea Heliopora (Lamarck, 1816)

Fig. 4. Percentage area cleared of sediment over the five-hour duration of the experiment calculated from 12 fragments (four replicates × three treatment) per genotype. Significantly more sediment was cleared under the 'low' sediment load compared to the 'medium' and 'high' loads (Table 2).

opencc-by-4.0Aug 2012View details →

Fig. 5 in Among-Genotype Variation For Sediment Rejection In The Reef-Building Coral Diploastrea Heliopora (Lamarck, 1816)

Fig. 5. Percentage of sediment mass cleared after five hours (the duration of the experiment) calculated from 12 fragments (four replicates × three treatment) per genotype.

opencc-by-4.0Aug 2012View details →

Fig. 2 in Among-Genotype Variation For Sediment Rejection In The Reef-Building Coral Diploastrea Heliopora (Lamarck, 1816)

Fig. 2. Profiles of natural sediments retrieved from sediment traps positioned at Pulau Hantu (solid line) and the artificial silicon carbide mixture (dotted line).

Fig. 14 in Congruent Patterns of Genetic and Morphological Variation in the Parthenogenetic Lizard Aspidoscelis tesselata (Squamata: Teiidae) and the Origins of Color Pattern Classes and Genotypic Clones in Eastern New Mexico

Fig. 14. Additive tree (phenogram), based on Mahalanobis D2 distances (table 13), depicting meristic resemblance among nine groups of Aspidoscelis tesselata. Distances (similarities) between groups are computed by adding lengths of nodes between groups of interest. Terminal nodes represent the nine groups, and internal nodes represent horizontal distances between clusters. As an interpretation example, the resemblance between Conchas 6CE and Conchas 1CE is 7.2 + 3.2 + 2.2 + 2.8 + 5.6 = 21.0, while the resemblance between Conchas 6CE and Macho EC is 7.2 + 1.0 + 1.9 + 3.1 = 13.2.

Fig. 3 in Congruent Patterns of Genetic and Morphological Variation in the Parthenogenetic Lizard Aspidoscelis tesselata (Squamata: Teiidae) and the Origins of Color Pattern Classes and Genotypic Clones in Eastern New Mexico

Fig. 3. Electrophoretic phenotypes of sACOH, a monomeric enzyme, from liver homogenates of nine specimens of A. tesselata of pattern class CE from Conchas Lake State Park, New Mexico. Letters below gel identify allozymes based on alleles present (table 3), and the genotype of each lizard is listed on the right. Lanes for individual lizards are labeled beside their patterns on the gel. Anode is to the right.

Fig. 11 in Congruent Patterns of Genetic and Morphological Variation in the Parthenogenetic Lizard Aspidoscelis tesselata (Squamata: Teiidae) and the Origins of Color Pattern Classes and Genotypic Clones in Eastern New Mexico

Fig. 11. Pattern of multivariate morphological variation among Aspidoscelis tesselata of pattern classes C (N = 44), E (N = 32), and New Mexico D (N = 5) from the vicinity of Sumner Lake State Park, De Baca County, New Mexico. Canonical variate scores were derived from a canonical variate analysis using meristic characters identified in table 10.

Fig. 2 in Congruent Patterns of Genetic and Morphological Variation in the Parthenogenetic Lizard Aspidoscelis tesselata (Squamata: Teiidae) and the Origins of Color Pattern Classes and Genotypic Clones in Eastern New Mexico

Fig. 2. Electrophoretic phenotypes of GPI, a dimeric enzyme, from erythrocyte hemolysates of six specimens of Aspidoscelis. Letters below gel identify allozymes based on alleles present (table 3), and the genotype of each lizard is listed on the right. Note the very slight difference in migration between the products of the ballele versus callele. Lanes for individual lizards are labeled beside their patterns on the gel as follows: TESC, A. tesselata of pattern class CE from Conchas Lake State Park, New Mexico; and TESE, A. tesselata of pattern class E from Sandoval County, New Mexico. Anode is to the right.

Fig. 1 in Congruent Patterns of Genetic and Morphological Variation in the Parthenogenetic Lizard Aspidoscelis tesselata (Squamata: Teiidae) and the Origins of Color Pattern Classes and Genotypic Clones in Eastern New Mexico

Fig. 1. Geographic relationships among four northern collecting localities of Aspidoscelis tesselata of color pattern classes C, New Mexico D, and E and convenience classes CE and EC. Color patterns found at the four sites are (1) Conchas Lake State Park: CE and New Mexico D; (2) Sumner Lake State Park: C, New Mexico D, and E; (3) Puerto de Luna: E; and (4) Arroyo del Macho: EC.

Fig. 7 in Congruent Patterns of Genetic and Morphological Variation in the Parthenogenetic Lizard Aspidoscelis tesselata (Squamata: Teiidae) and the Origins of Color Pattern Classes and Genotypic Clones in Eastern New Mexico

Fig. 7. Color pattern variation in Aspidoscelis tesselata of pattern class CE from the vicinity of Conchas Lake State Park, San Miguel County, New Mexico. Morphological subgroup 6CE: A (RU 0002, 93 mm SVL); B (RU 0029, 96 mm SVL); morphological subgroup 1CE: C (RU 0013, 95 mm SVL); D (RU 0030, 89 mm SVL); E (RU 0021, 95 mm SVL); morphological subgroup 8CE: F (RU 0027, 86 mm SVL).

Fig. 4 in Congruent Patterns of Genetic and Morphological Variation in the Parthenogenetic Lizard Aspidoscelis tesselata (Squamata: Teiidae) and the Origins of Color Pattern Classes and Genotypic Clones in Eastern New Mexico

Fig. 4. Electrophoretic phenotypes of MPI, a monomeric enzyme, from liver homogenates of 11 specimens of Aspidoscelis. Letters below gel identify allozymes based on alleles present (table 3), and the genotype of each lizard is listed on the right. Lanes for individual lizards are labeled beside their patterns on the gel (with genotype) as follows: NEOTESA, B, and C, different pattern classes of the triploid A. neotesselata from Colorado; TESC and D, A. tesselata of pattern classes CE and D from Conchas Lake State Park, New Mexico; TESE, A. tesselata of pattern class EC from Arroyo del Macho, New Mexico; TESF, A. dixoni from New Mexico; TESF × PUN, triploid hybrid of A. dixoni × A. tigris punctilinealis from New Mexico; and TESG and H, A. dixoni of two pattern classes from Texas. Anode is to the right.

opencc-zeroApr 2023View details →

Genotype and genetic diversity data for: Contrasts in riverscape patterns of intraspecific genetic variation in a diverse Neotropical fish community of high conservation value

Spatial patterns in genetic variation compared across species provide information about the predictability of genetic diversity of natural populations and areas requiring conservation measures. Due to their remarkable fish diversity, rivers in Neotropical regions are ideal systems to confront theory with observations and would benefit greatly from such approaches given their increasing vulnerability to anthropogenic pressures. We used SNP data from 18 fish species with contrasting life-history traits, co-sampled across 12 sites in the Maroni – a major river system from the Guiana Shield – to compare patterns of intraspecific genetic variation and identify their underlying drivers. Analyses of covariance revealed a decrease in genetic diversity as distance from the river outlet increased for 5 of the 18 species, illustrating a pattern commonly observed in riverscapes for species with low-to-medium dispersal abilities. However, mean within-site genetic diversity was lowest in the two easternmost tributaries of the Upper Maroni and around an urbanized location downstream, indicating the need to address the potential influence of local pressures in these areas, such as goldmining or fishing. Finally, the relative influence of isolation by stream distance, isolation by discontinuous river flow and isolation by spatial heterogeneity in effective size on pairwise genetic differentiation varied across species. Species with similar dispersal and reproductive guilds did not necessarily display shared patterns of population structure. Increasing the knowledge of specific life history traits and ecological requirements of fish species in these remote areas should help further understand factors that influence their current patterns of genetic variation.

publicDec 2023View details →

Variation in personality shaped by evolutionary history, genotype, and developmental plasticity in response to feeding modalities in the Arctic charr

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