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opencc-by-4.0Jun 2022View details →

Characterization data for the manuscript: "Using genetic algorithms to systematically improve the synthesis conditions of Al-PMOF"

This entry contains characterization data for the manuscript "Using genetic algorithms to systematically improve the synthesis conditions of Al-PMOF", which we exported from the electronic lab notebook (ELN). To visualize the data in this dataset: <a href="https://www.cheminfo.org/flavor/zenodo/index.html?id=6620502">open entry</a>

opencc-zeroJun 2022View details →

Deep-sequencing of viral genomes from treatment-naive HIV-infected persons shows positive association between intrahost genetic diversity and viral load

Background: Infection with human immunodeficiency virus type 1 (HIV) typically results from transmission of a small and genetically uniform viral population. Following transmission, the virus population becomes more diverse because of recombination and acquired mutations through genetic drift and selection. Viral intrahost genetic diversity remains a major obstacle to the cure of HIV; however, there is a disagreement whether intrahost viral genetic diversification associates positively or negatively with disease progression and progression markers. Viral load is a key progression marker and understanding its relationship to viral intrahost genetic diversity could help design future strategies for HIV monitoring and treatment. Methods: We analyzed deep-sequenced viral genomes from 2,650 treatment-naive HIV-infected persons to measure the intrahost genetic diversity of 2,447 genomic codon positions as calculated by Shannon entropy. We tested for associations between viral load (VL) and amino acid (AA) entropy accounting for sex, age, race, duration of infection, and HIV population structure. Results: We confirmed that the intrahost genetic diversity is highest in the env gene. Furthermore, we showed that mean Shannon entropy is significantly associated with VL, especially in infections of >24 months duration. We identified 16 significant associations between VL (p-value<2.0x10-5) and Shannon entropy at AA positions which in our association analysis explained 13% of the variance in VL. Conclusions: Our results elucidate that viral intrahost genetic diversity is associated with VL and could be used as a better disease progression marker than HIV consensus sequence variants, especially in infections of longer duration. We emphasize that viral intrahost diversity should be considered when studying viral genomes and infection outcomes.

opencc-zeroJun 2022View details →

Population connectivity and genetic offset in the spawning coral Acropora digitifera in Western Australia

Anthropogenic climate change has caused widespread loss of species biodiversity and ecosystem productivity across the globe, particularly on tropical coral reefs. Predicting the future vulnerability of reef-building corals, the foundation species of coral reef ecosystems, is crucial for cost-effective conservation planning in the Anthropocene. In this study, we combine regional population genetic connectivity and seascape analyses to explore patterns of genetic offset (the mismatch of gene-environmental associations under future climate conditions) in Acropora digitifera across 12 degrees of latitude in Western Australia. Our data revealed a pattern of restricted gene flow and limited genetic connectivity among geographically distant reef systems. Environmental association analyses identified a suite of loci strongly associated with the regional temperature variation. These loci helped forecasting future genetic offset in random forest and generalised dissimilarity models. These analyses predicted pronounced differences in the response of different reef systems in Western Australia to rising temperatures. Under the most optimistic future warming predictions (RCP 2.6), we observed a general pattern of increasing genetic offset with latitude. Under the most extreme climate scenario (RCP 8.5 in 2090-2100), coral populations at the Ningaloo World Heritage Area were predicted to experience a higher mismatch in genetic composition, compared to populations in the inshore Kimberley region. The study suggest complex and spatially heterogeneous patterns of climate-change vulnerability in coral populations across Western Australia, reinforcing the notion that regionally tailored conservation efforts will be most effective at managing coral reef resilience into the future.

opencc-by-4.0Aug 2021View details →

CONTENT -- Multi-context genetic modeling TWAS and eAssociation summary statistics

We provide the summary statistics of running CONTENT, the context-by-context approach, and UTMOST on over 22 phenotypes. The phenotypes are listed in the manuscript, and their respective studies and sample size can be found in a table under the supplementary section of the manuscript. All 3 methods were trained on GTEx v7 as well as CLUES, a single-cell RNA sequencing dataset of PBMCs. The data include the gene name, model, cross-validated R^2, prediction pvalue, TWAS p value, TWAS Z score, and a column titled "hFDR" indicating whether the association was statistically significant while employing hierarchical FDR. The benefits of employing such an approach for all methods can be found in the manuscript.   We also include the eAssociations that we obtain by training prediction models on GTEx and CLUES alone. For the CxC and UTMOST approaches, these files contain the gene, context, pvalue and adjusted R^2. For CONTENT, these include the gene, context and pvalue and adjusted R^2 for each CONTENT model--the column names are described like a regression of y~x, rsq_y_x, so rsq_observed_full is the adjusted R^2 from regressing the observed expression onto the cross-validated full model predictions. In cases where the R^2 is higher from the specific or shared models, it's best to use either of those rather than the full model for out of sample prediction.

opencc-zeroJun 2022View details →

Additive genetic variation, but not temperature, influences warning signal expression in Amata nigriceps moths (Lepidoptera: Arctiinae)

Many aposematic species show variation in their colour patterns even though selection by predators is expected to stabilise warning signals towards a common phenotype. Warning signal variability can be explained by trade-offs with other functions of colouration, such as thermoregulation, that may constrain warning signal expression by favouring darker individuals. Here, we investigated the effect of temperature on warning signal expression in aposematic Amata nigriceps moths that vary in their black and orange wing patterns. We sampled moths from two flight seasons that differed in the environmental temperatures and also reared different families under controlled conditions at three different temperatures. Against our prediction that lower developmental temperatures would reduce the warning signal size of the adult moths, we found no effect of temperature on warning signal expression in either wild or laboratory-reared moths. Instead, we found sex- and population-level differences in wing patterns. Our rearing experiment indicated that ~70% of the variability in the trait is genetic but understanding what signalling and non-signalling functions of wing colouration maintain the genetic variation requires further work. Our results emphasise the importance of considering both genetic and plastic components of warning signal expression when studying intraspecific variation in aposematic species.

opencc-zeroJul 2022View details →

Can disease resistance evolve independently at different ages? Genetic variation in age-dependent resistance to disease in three wild plant species

1. Juveniles are typically less resistant (more susceptible) to infectious disease than adults, and this difference in susceptibility can help fuel the spread of pathogens in age-structured populations. However evolutionary explanations for this variation in resistance across age remain to be tested. 2. One hypothesis is that natural selection has optimized resistance to peak at ages where disease exposure is greatest. A central assumption of this hypothesis is that hosts have the capacity to evolve resistance independently at different ages. This would mean that hosts populations have a) standing genetic variation in resistance at both juvenile and adult stages, and b) that this variation is not strongly correlated between age-classes so that selection acting at one age does not produce a correlated response at the other age 3. Here we evaluated the capacity of three wild plant species (Silene latifolia, S. vulgaris, and Dianthus pavonius) to evolve resistance to their anther-smut pathogens (Microbotryum fungi), independently at different ages. The pathogen is pollinator-transmitted, and thus exposure risk is considered to be highest at the adult flowering stage. 4. Within each species we grew families to different ages, inoculated individuals with anther smut, and evaluated the effects of age, family and their interaction on infection. 5. In two of the plant species, S. latifolia and D. pavonius, resistance to smut at the juvenile stage was not correlated with resistance to smut at the adult stage. In all three species, we show there are significant age*family interaction effects, indicating that age-specificity of resistance varies among the plant families. 6. Synthesis: These results indicate that different mechanisms likely underlie resistance at juvenile and adult stages and support the hypothesis that resistance can evolve independently in response to differing selection pressures as hosts age. Taken together our results provide new insight into the structure of genetic variation in age-dependent resistance in three well-studied wild host-pathogen systems.

opencc-by-4.0Jul 2022View details →

data for "Plant genetic effects on microbial hubs impact host fitness in repeated field trials"

These are data tables required for the analysis of the paper "Plant genetic effects on microbial hubs impact host fitness in repeated field trials".  All scripts are available at https://forgemia.inra.fr/bbrachi/microbiota_paper.git The folder architecture in the zip files is the same as in the repository: https://forgemia.inra.fr/bbrachi/microbiota_paper.git The dataset includes:  - OTU count tables for 16S and ITS - taxonomic assignation - plant seed-set estimates - plant growth data from the B38 experiment.  - Metabolomics datasets

opencc-zeroJul 2022View details →

Data from: Genetic, maternal, and environmental influences on sociality in a pedigreed primate population

Various aspects of sociality in mammals (e.g., dyadic connectedness) are linked with measures of biological fitness (e.g., longevity). How within- and between-individual variation in relevant social traits arises in uncontrolled wild populations is challenging to determine but is crucial for understanding constraints on the evolution of sociality. We use an advanced statistical method, known as the 'animal model', which incorporates pedigree information, to look at social, genetic, and environmental influences on sociality in a long-lived wild primate. We leverage a longitudinal database spanning 20 years of observation on individually recognized white-faced capuchin monkeys (Cebus capucinus imitator), with a multi-generational pedigree. We analyze two measures of spatial association, using repeat sampling of 376 individuals (mean: 53.5 months per subject, range: 6-185 months per subject). Conditioned on the effects of age, sex, group size, seasonality , and El Niño–Southern Oscillation phases, we show low to moderate long-term repeatability (across years) of the proportion of time spent social (posterior mode [95% Highest Posterior Density interval]: 0.207 [0.169, 0.265]) and of average number of partners (0.144 [0.113, 0.181]) (latent scale). Most of this long-term repeatability could be explained by modest heritability (h2social: 0.152 [0.094, 0.207]; h2partners: 0.113 [0.076, 0.149]) with small long-term maternal effects (m2social: 0.000 [0.000, 0.045]; m2partners: 0.000 [0.000, 0.041]). Our models capture the majority of variance in our behavioral traits, with much of the variance explained by temporally changing factors, such as group of residence, highlighting potential limits to the evolvability of our trait due to social and environmental constraints.

opencc-by-4.0Dec 2021View details →

Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and East Asian ancestries

Colorectal cancer (CRC) is a leading cause of mortality worldwide. We conducted a genome-wide association study meta-analysis of 100,204 CRC cases and 154,587 controls of European and Asian ancestry, identifying 205 independent risk associations, of which 50 were unreported. We performed integrative genomic, transcriptomic and methylomic analyses across large bowel mucosa and other tissues. Transcriptome- and methylome-wide association studies revealed an additional 53 risk associations. We identified 155 high confidence effector genes functionally linked to CRC risk, many of which had no previously established role in CRC. These have multiple different functions, and specifically indicate that variation in normal colorectal homeostasis, proliferation, cell adhesion, migration, immunity and microbial interactions determines CRC risk. Cross-tissue analyses indicated that over a third of effector genes most likely act outside the colonic mucosa. Our findings provide insights into colorectal oncogenesis, and highlight potential targets across tissues for new CRC treatment and chemoprevention strategies. The data submitted here are expression and methylation models with LD reference data for the transcriptome-wide (TWAS), methylome-wide (MWAS) and transcript isoform-wide association study (TIsWAS) as described in the manuscript "Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and East Asian ancestries". Details of the methods are presented in the method section and supplementary information file.  TWAS analysis  Gene expression models for the six in-house expression datasets were generated using the PredictDB v7 pipeline for a total of 1,077 participants. Elastic net model building with 10-fold cross-validation was performed independently for each dataset. The elastic net models for GTEx v8 Colon Transverse were obtained from the PredictDB data repository (<a href="http://predictdb.org/">http://predictdb.org/</a>) and had been generated using the same pipeline. Models were computed using HapMap2 SNPs ±1Mb from each gene, together with covariate factors estimated using PEER32, clinical covariates when appropriate (age, sex and, where appropriate, case-control status, type of polyp and anatomic location in the colorectum), and three PCs from the individual dataset’s SNP genotype data. Transcript-based TWAS analyses (TIsWAS) were likewise performed by using transcript-level data from the SOCCS, BarcUVa-Seq and GTEx Colon Transverse datasets. MWAS analysis  Methylation beta values were calculated based on the manufacturer’s standard, ranging from 0 to 1. Quality control and data normalization were performed in R using the ChAMP software pipeline for the EPIC and 450K arrays. Briefly, we filtered out failed probes with detection P > 0.02 in >5% of samples, probes with <3 reads in >5% of samples per probe and all non-CpG probes. Samples with failed probes >0.1 were also excluded from downstream analyses. We discarded all probes with SNPs within 10bp of the interrogated CpG (from 1,000 Genomes Project, CEU population)34, and probes that ambiguously mapped to multiple locations in the human genome with up to two mismatches33. We only considered probes mapping to autosomes and those overlapping between the EPIC and the 450K arrays. Normalization was achieved using the Beta MIxture Quantile (BMIQ) method. Per probe methylation models were created using the PredictDB pipeline on the normalized methylation matrix and the genotypes as per TWAS eQTL analysis. To optimize power, we restricted our analysis to 263,341-238,443 (for the 450K array) and 377,678 (for the EPIC array) probes annotated to Islands, Shores and Shelves, and discarded “Open Sea” regions.

opencc-zeroAug 2022View details →

Attempting genetic inference from directional asymmetry during convergent hindlimb reduction in squamates

Loss and reduction of paired appendages is common in vertebrate evolution. How often does such convergent evolution depend on similar developmental and genetic pathways? For example, many populations of the Threespine Stickleback and Ninespine Stickleback (Gasterosteidae) have independently evolved pelvic reduction, usually based on independent mutations that caused reduced Pitx1 expression. Reduced Pitx1 expression has also been implicated in pelvic reduction in manatees. Thus, hind limb reduction stemming from reduced Pitx1 expression has arisen independently in groups that diverged tens to hundreds of millions of years ago, suggesting a potential for repeated use of Pitx1 across vertebrates. Notably, hindlimb reduction based on reduction of Pitx1 expression produces left-larger directional asymmetry in the vestiges. We used this phenotypic signature as a genetic proxy, testing for hindlimb directional asymmetry in six genera of squamate reptiles that independently evolved hindlimb reduction and for which genetic and developmental tools are not yet developed: Agamodon anguliceps, Bachia intermedia, Chalcides sepsoides, Indotyphlops braminus, Ophisaurus attenuatuas and O. ventralis, and Teius teyou. Significant asymmetry occurred in one taxon, Chalcides sepsoides, whose left-side pelvis and femur vestiges were 18% and 64% larger than right-side vestiges, respectively, suggesting modification of Pitx1 expression in that species. However, there was either right-larger asymmetry or no directional asymmetry in the other five taxa, suggesting multiple developmental genetic pathways to hindlimb reduction in squamates and vertebrates more generally.

opencc-zeroAug 2022View details →

On the impermanence of species: The collapse of genetic incompatibilities in hybridizing populations

Species pairs often become genetically incompatible during divergence, which is an important source of reproductive isolation. An idealized picture is often painted where incompatibility alleles accumulate and fix between diverging species. However, recent studies have shown both that incompatibilities can collapse with ongoing hybridization, and that incompatibility loci can be polymorphic within species. This paper suggests some general rules for the behavior of incompatibilities under hybridization. In particular, we argue that redundancy of genetic pathways can strongly affect the dynamics of intrinsic incompatibilities. Since fitness in genetically redundant systems is unaffected by introducing a few foreign alleles, higher redundancy decreases the stability of incompatibilities during hybridization, but also increases tolerance of incompatibility polymorphism within species. We use simulations and theories to show that this principle leads to two types of collapse: in redundant systems, exemplified by classical Dobzhansky-Muller incompatibilities, collapse is continuous and approaches a quasi-neutral polymorphism between broadly sympatric species, often as a result of isolation-by-distance. In non-redundant systems, exemplified by coevolution among genetic elements, incompatibilities are often stable, but can collapse abruptly with spatial traveling waves. As both types are common, the proposed principle may be useful in understanding the abundance of genetic incompatibilities in natural populations.

opencc-by-4.0Aug 2022View details →

Supplemental datasets for: Carlson et al. 2022. Genetics.

Supplemental datasets S1 (phenotypes) and S2 (images), R code, and corresponding metadata from GENETICS research article: Carlson et al. 2022. Archetypes of inflorescence: Genome-wide association networks of panicle morphometric, growth, and disease variables in a multiparent oat population. GENETICS. (in press)

opencc-by-4.0May 2022View details →

Data to accompany the publication "Combined biophysical and genetic modelling approaches reveal complementary information about population connectivity of New Zealand green-lipped mussels"

Data to accompany the publication "Combined biophysical and genetic modelling approaches reveal complementary information about population connectivity of New Zealand green-lipped mussels".  migrationmatrix14.txt contains the particle tracking matrix, with the total number of particles that migrated from row i to column j (out of a total of 2217864 particles released per population). mussel_microsat_Genepop.txt contains the microsatellite data for each population in Genepop format.

opencc-zeroAug 2022View details →

Over the hills and through the farms: Land use and topography influence genetic connectivity of northern leopard frog (Rana pipiens) in the Prairie Pothole Region

Context Agricultural land-use conversion has fragmented prairie wetland habitats in the Prairie Pothole Region (PPR), an area with one of the most wetland-dense regions in the world. This fragmentation can lead to negative consequences for wetland obligate organisms, heightening risk of local extinction and reducing evolutionary potential for populations to adapt to changing environments. Objectives This study models biotic connectivity of prairie-pothole wetlands using landscape genetic analyses of the northern leopard frog (Rana pipiens) to: (1) identify population structure and (2) determine landscape factors driving genetic differentiation and possibly leading to population fragmentation. Methods Frogs from 22 sites in the James River and Lake Oahe river basins in North Dakota were genotyped using Best-RAD sequencing at 2868 bi-allelic single nucleotide polymorphisms (SNPs). Population structure was assessed using STRUCTURE, DAPC, and fineSTRUCTURE. Circuitscape was used to model resistance values for ten landscape variables that could affect habitat connectivity. Results STRUCTURE results suggested a panmictic population, but other more sensitive clustering methods identified six spatially organized clusters. Circuit theory-based landscape resistance analysis suggested land use, including cultivated crop agriculture, and topography were the primary influences on genetic differentiation. Conclusions While the R. pipiens populations appear to have high gene flow, we found a difference in the patterns of connectivity between the eastern portion of our study area which was dominated by cultivated crop agriculture, versus the western portion where topographic roughness played a greater role. This information can help identify amphibian dispersal corridors and prioritize lands for conservation or restoration.

A baseline for the genetic stock identification of Atlantic herring, Clupea harengus, in ICES Divisions 6.a, 7.b-c

Atlantic herring in ICES Divisions 6.a, 7.b-c comprises at least three populations, distinguished by temporal and spatial differences in spawning, which have until recently been managed as two stocks defined by geographic delineators. Outside of spawning the populations form mixed aggregations, which are the subject of acoustic surveys. The inability to distinguish the populations has prevented the development of separate survey indices and separate stock assessments. A panel of 45 SNPs, derived from whole genome sequencing, were used to genotype 3,480 baseline spawning samples (2014-2021). A temporally stable baseline comprising 2,316 herring from populations known to inhabit Division 6.a was used to develop a genetic assignment method, with a self-assignment accuracy >90%. The long-term temporal stability of the assignment model was validated by assigning archive (2003-2004) baseline samples (270 individuals) with a high level of accuracy. Assignment of non-baseline samples (1,514 individuals) from Division 6.a, 7.b-c indicated previously unrecognised levels of mixing of populations outside of the spawning season. The genetic markers and assignment models presented constitute a 'toolbox' that can be used for the assignment of herring caught in mixed survey and commercial catches in Division 6.a into their population of origin with a high level of accuracy.

Relationship between genome-wide and MHC class I and II genetic diversity and complementarity in a nonhuman primate

Although mate choice is expected to favor partners with advantageous genetic properties, the relative importance of genome-wide characteristics, such as overall heterozygosity or kinship, versus specific loci, is unknown. To disentangle genome-wide and locus-specific targets of mate choice, we must first understand congruence in global and local variation within the same individual. This study compares genetic diversity, both absolute and relative to other individuals (e.g., complementarity), assessed across the genome to that found at the major histocompatibility complex (MHC), a hyper-variable gene family integral to immune system function and implicated in mate choice across species. Using DNA from 22 captive olive baboons (Papio anubis), we conducted double digest restriction-site associated DNA sequencing to estimate genome-wide heterozygosity and kinship and sequenced two class I and two class II MHC loci. We found that genome-wide diversity was not associated with MHC diversity, and that diversity at class I MHC loci was not correlated with diversity at class II loci. Additionally, kinship was a significant predictor of the number of MHC alleles shared between dyads at class II loci. Our results provide further evidence of the strong selective pressures maintaining genetic diversity at the MHC in comparison to other randomly selected sites throughout the genome. Furthermore, our results indicate that class II MHC disassortative mate choice may mediate inbreeding avoidance in this population. Our study suggests that mate choice favoring genome-wide genetic diversity is not always synonymous with mate choice favoring MHC diversity, and highlights the importance of controlling for kinship when investigating MHC-associated mate choice.

Seascape genetics in a polychaete worm: Disentangling the roles of a biogeographic barrier and environmental factors

Aim: Seascape genomics studies aim to understand how environmental variables shape species diversity through genotype-environment associations. Identifying these effects on lecithotrophic larval species that live in intertidal zones is particularly challenging because they are subject to environmental heterogeneity and anthropogenic events. Here, we evaluate how biotic and abiotic features in the Southwest Atlantic littoral zone can affect a high dispersal species' present and historical demographic. Taxon: Perinereis ponteni. Methods: We investigated population genetic diversity, connectivity, and past dynamics using 23,300 SNPs generated using Genotyping by sequencing. We tested whether environmental abiotic variables could explain the variance found in genotype frequencies using isolation-by-environment (IBE) and landscape association approaches. These data, combined with paleodistribution simulations and oceanic circulation modeling, were used to infer species demographic history and connectivity patterns. Results: Along with high levels of connectivity detected, we found a genetic boundary in the southeastern region of Brazil around Cabo Frio (Rio de Janeiro) and a cline trend for some loci. The paleodistribution simulations reveal a spatial refuge in the southeast during the Last Glacial Maximum (21 kya), with the expansion of the northern region. We identified 1,421 SNPs with frequencies associated with eight environmental variables, most of which were related to temperature - the main environmental factor determining IBE. Main conclusions: Perinereis ponteni, a polychaete with high gene flow capability responds to biogeographic barriers, highlighting the importance of biotic and abiotic factors in shaping population connectivity. Furthermore, the effect of temperature indicates that future climate change and ocean warming can hugely impact this species.

Epidendrum radicans - genetic data of 4 regional populations

Colonization is a fundamental ecological process that is important for the persistence of species, particularly when a changing environment necessitates range shifts. Vacant habitats available for colonization often arise from landscape disturbance. Colonization and population expansion processes can be inferred by examining the levels and spatial distribution of genetic variation of plant populations with known disturbance histories. Samples (N = 690) of the terrestrial orchid, Epidendrum radicans, were collected from five lava flow sites on the slopes of Volcán Arenal in Costa Rica that last experienced major eruptions in 1968 and 1992. Individuals were also sampled (N = 188) from four regional populations. Samples were characterized using 15 nuclear genetic markers and analyzed using population genetics statistics. Genetic diversity within sites was moderate (He = 0.092 – 0.192). Contrary to expectation, diversity tended to be lower on the older lava flows (0.131 versus 0.172) which may reflect their more sheltered topography that restricted pollen/seed immigration, and/or greater intra- and interspecific competition. Genetic diversity measures indicate that the lava flows were colonized by numerous individuals that likely originated from multiple sources while spatial genetic structure (SGS) statistics indicate that most recruitment in the study sites subsequent to colonization resulted from in situ reproduction and localized seed deposition. Younger sites had significantly greater SGS over larger distances which reflects fewer reproductive events, and less spatial and temporal overlap of seed shadows relative to the older sites. Clones were also generally larger on the older sites (≤ 8m versus ≤ 3m).

opencc-by-4.0Feb 2022View details →

Alternative splicing and genetic variation of MHC-E: Implications for rhesus cytomegalovirus-based vaccines

We used long-read sequencing to interrogate rhesus macaque (RM) MHC-E (Mamu-E) alternative splicing and genetic variations. Full-length Mamu-E RNA isoforms were recovered using the PacBio Iso-Seq method. Incomplete 5' ends of Mamu-E isoforms were confirmed using Sanger sequencing, where we identified three additional isoforms. Full-length human MHC-E (HLA-E) isoforms were also recovered using the PacBio Iso-Seq method. Isoform sequences and annotations are provided for both Mamu-E and HLA-E in addition to Mamu-E Sanger sequencing data. HLA-E annotations are reported using the hg38 reference, while Mamu-E annotations are shown using rhesus MHC Class I and II assemblies previously generated using Bacterial Artificial Cloning (BAC) technology (https://www.ncbi.nlm.nih.gov/nuccore/AC148696.1). Using PacBio Long Amplicon Analysis, we sequenced complete Mamu-E coding regions of 59 RMs and additionally captured 3' UTR polymorphism using mRNA-seq haplotype phasing analysis. The complete genotyping data for these animals are provided as well as animal metadata. Genotyping data is shown using the Mamu-E canonical isoform (Mamu-E1 from Iso-Seq analysis) as reference.

Epidendrum radicans – x, y coordinates and genetic data of individuals within 5 focal populations

Colonization is a fundamental ecological process that is important for the persistence of species, particularly when a changing environment necessitates range shifts. Vacant habitats available for colonization often arise from landscape disturbance. Colonization and population expansion processes can be inferred by examining the levels and spatial distribution of genetic variation of plant populations with known disturbance histories. Samples (N = 690) of the terrestrial orchid, Epidendrum radicans, were collected from five lava flow sites on the slopes of Volcán Arenal in Costa Rica that last experienced major eruptions in 1968 and 1992. Individuals were also sampled (N = 188) from four regional populations. Samples were characterized using 15 nuclear genetic markers and analyzed using population genetics statistics. Genetic diversity within sites was moderate (He = 0.092–0.192). Contrary to expectation, diversity tended to be lower on the older lava flows (0.131 versus 0.172) which may reflect their more sheltered topography that restricted pollen/seed immigration, and/or greater intra- and interspecific competition. Genetic diversity measures indicate that the lava flows were colonized by numerous individuals that likely originated from multiple sources while spatial genetic structure (SGS) statistics indicate that most recruitment in the study sites subsequent to colonization resulted from in situ reproduction and localized seed deposition. Younger sites had significantly greater SGS over larger distances which reflects fewer reproductive events, and less spatial and temporal overlap of seed shadows relative to the older sites. Clones were also generally larger on the older sites (≤ 8m versus ≤ 3m).