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Data from: Transgenerational genetic effects help explain latitudinal variation in seed mass and germination timing in Plantago lanceolata

We know little about the underlying genetic control of phenotypic patterns of seed traits across large-scale geographic and environmental gradients. Such knowledge is important for understanding the evolution of populations within species and for improving species conservation. Therefore, to test for genetic variation in P. lanceolata, we made reciprocal crosses between northern and southern genotypes that span the species' range in Europe. Results provide evidence of transgenerational genetic effects on seed mass and germination timing. Northern mothers produced larger seeds with delayed germination, in contrast to southern mothers, which produced smaller seeds with accelerated germination. Maternal latitude affected both the seed coat, solely maternal tissue, and embryo/endosperm tissues. Thus, latitudinal variation in seed size and germination timing can be explained, in part, by the direct influence of maternal genotype, independent of zygotic genes that parents pass directly to the embryo and endosperm. Data suggest that researchers exploring the existence and evolution of large-scale geographic variation within species test for transgenerational genetic effects. Also, data suggest that transgenerational control of seed traits should be considered when developing procedures designed to facilitate species conservation and restoration.

The genetic and social contributions to sex differences in lifespan in Drosophila serrata

Sex differences in lifespan remain an intriguing puzzle in evolutionary biology. While explanations range from sex differences in selection to sex differences in the expression of recessive lifespan-altering mutations (via X-linkage), little consensus has been reached. One unresolved issue is the extent to which genetic influences on lifespan dimorphism are modulated by the environment. For example, studies have shown that sex-differences in lifespan can either increase or decrease depending upon the social environment. Here we took an experimental approach, manipulating multiple axes of social environment across inbred long- and short-lived genotypes and their reciprocal F1s in the fly Drosophila serrata. Our results reveal strong genetic effects and subtle yet significant genotype-by-environment interactions for male and female lifespan, specifically due to both population density and mating status. Further, our data do not support the idea that unconditional expression of deleterious X-linked recessive alleles in heterogametic males accounts for lower male lifespan.

opencc-by-4.0Mar 2022View details →

Genetic and immunological evaluation of children with inborn errors of immunity and hypoxemic COVID-19 pneumonia

Background: SARS-CoV-2 has infected more than 450 million people around the world. In about 10% of cases, the infection leads to hypoxemic pneumonia, which is much rarer in children, while multisystem inflammation is seen almost only in children. Methods: We evluated 31 young patients (0.5-19 years) who had both pre-existing inborn errors of immunity (IEI) and were later diagnosed with COVID-19 complications. Whole-exome sequencing was performed, SARS-CoV-2 specific antibodies and autoantibody against type I interferons were measured and plasma inflammatory factors were profiled. We also reviewed COVID-19 disease severity and outcome in IEI patients in the literature. Results:  A potential genetic cause of the IEI was identified in 28 patients (90.3%). The IgM and IgG-specific antibody response against the spike protein of the virus was positive in 14 (66.6%) of the IEI patients tested. Autoantibodies neutralizing type I interferons were identified in the plasma of two patients (6.8% of tested samples). Five patients fulfilled the diagnostic criteria of multisystem inflammatory syndrome in children (MIS-C). Eleven patients (35.4%) died due to COVID-19 complications showing a 3000 fold higher mortality rate compared to normal COVID-19 death rate in children (0.01%). For the additional 696 IEI patients reported till date, severe presentation of COVID-19 was observed in 23.3% of cases. Furthermore, a 5-fold higher mortality rate was observed, when compared with global infection-fatality reports. Conclusions: Elucidating the genetic basis of IEI patients with severe/critical COVID-19 may help to better understand the human innate and adaptive immune response against SARS-CoV-2, which may assist to develop better preventive and therapeutic strategies.

opennotspecifiedMar 2022View details →

FIGURE 4 in Comparative study and genetic diversity of Salicornia persica (Chenopodiaceae) using SCOT molecular markers

FIGURE 4. PCA plot of Salicornia persica populations based on morphological characters. Numbers are according to Table 1.

opennotspecifiedMar 2022View details →

FIGURE 3 in Comparative study and genetic diversity of Salicornia persica (Chenopodiaceae) using SCOT molecular markers

FIGURE 3. PCoA plot of populations in Salicornia persica based on SCoT molecular markers, (Population numbers are according to Table 1.)

opennotspecifiedMar 2022View details →

FIGURE 2 in Comparative study and genetic diversity of Salicornia persica (Chenopodiaceae) using SCOT molecular markers

FIGURE 2. WARD tree of populations in Salicornia persica based on SCoT molecular markers, (Population numbers are according to Table 1.)

opencc-by-4.0Apr 2022View details →

Genetic insights into the range expansion of the cattle egret (Pelecaniformes: Ardeidae) in Brazil and population differentiation between the native and colonized areas

Gnotypes of Cattle Egrets (Bubulcus ibis) at 14 microsatellite loci amplified using the primers in Table S1 of the article. The protocols are described in Appendix S1 of the Supplementary Material of Miño et al. 2022. Bubulcus ibis ibis naturally expanded its range by flying over the Atlantic Ocean from Africa or Europe (native range) to South America, being first reported in Suriname towards the end of the 19th century. However, the source populations of the birds colonising South America still remains unclear. Here, to o gain insights into the possible source and routes of colonisation, we characterize the levels of diversity at nuclear microsatellites and assessed the genetic structure of populations from central and southern Africa (n = 129, 13 sites, five countries) and from different latitudes along Brazil (n = 166, six sites). We found overall high levels of genetic diversity in the colonised range, which fit the expectations for organisms with long-distance dispersal potential, rapid growth rates and feeding plasticity. Noteworthy, the results from population-genetic analyses based on different assumptions concurrently agree in indicating that cattle egrets from Brazil harbour a genetic pool distinct from populations from Africa, suggesting restricted contemporary gene flow between these ranges. The lack of genetic differentiation among the African populations did not enable us to identify the source of Brazilian cattle egrets. Fernando de Noronha Archipelago, off the Brazilian northeastern coast, had the highest proportion of the African allelic ancestry. Approximate Bayesian computation analyses supported a scenario of population growth in Africa with subsequent expansion to Brazil and migration from Africa to Brazil at the time of colonisation. We discuss our findings in light of the anthropogenic changes that may have promoted the range expansion of this egret into Brazil.

Population differences in Chinook salmon (Oncorhynchus tshawytscha) DNA methylation: genetic drift and environmental factors

Local adaptation and phenotypic differences among populations have been reported in many species, though most studies focus on either neutral or adaptive genetic differentiation. With the discovery of DNA methylation, questions have arisen about its contribution to individual variation in and among natural populations. Previous studies have identified differences in methylation among populations of organisms, although most to date have been in plants and model animal species. Here we obtained eyed eggs from eight populations of Chinook salmon (Oncorhynchus tshawytscha) and assayed DNA methylation at 23 genes involved in development, immune function, stress response, and metabolism using a gene-targeted PCR-based assay for next-generation sequencing. Evidence for population differences in methylation was found at eight out of 23 gene loci after controlling for developmental timing in each individual. However, we found no correlation between freshwater environmental parameters and methylation variation among populations at those eight genes. A weak correlation was identified between pairwise DNA methylation dissimilarity among populations and pairwise FST based on 15 microsatellite loci, indicating weak effects of genetic drift or geographic distance on methylation. The weak correlation was primarily driven by two genes, GTIIBS and Nkef. However, single-gene Mantel tests comparing methylation and pairwise FST were not significant after Bonferroni correction. Thus, population differences in DNA methylation are more likely related to unmeasured oceanic environmental conditions, local adaptation, and/or genetic drift. DNA methylation is an additional mechanism that contributes to among population variation, with potential influences on organism phenotype, adaptive potential, and population resilience.

Phylogeny and disparate selection signatures suggest two genetically independent domestication events of pea (Pisum L.)

Domestication is considered a model of adaptation that can be used to draw conclusions about the modus operandi of selection in natural systems. Investigating domestication may give insights into how plants react to different intensities of human manipulation, which has direct implication for the continuing efforts of crop improvement. Therefore, scientists of various disciplines study domestication-related questions to understand the biological and cultural bases of the domestication process. We employed restriction site-associated DNA sequencing (RAD-seq) of 494 Pisum sativum (pea) samples from all wild and domesticated groups to analyze the genetic structure of the collection. Patterns of ancient admixture were investigated by analysis of admixture graphs. We used two complementary approaches, one diversity based and one based on differentiation, to detect the selection signatures putatively associated with domestication. An analysis of the subpopulation structure of wild P. sativum revealed five distinct groups with a notable geographic pattern. Pisum abyssinicum clustered unequivocally within the P. sativum complex, without any indication of hybrid origin. We detected 32 genomic regions putatively subjected to selection: 29 in P. sativum ssp. sativum and three in P. abyssinicum. The two domesticated groups did not share regions under selection and did not display similar haplotype patterns within those regions. Wild P. sativum is structured into well-diverged subgroups. Although Pisum sativum ssp. humile is not supported as a taxonomic entity, the so-called 'southern humile' is a genuine wild group. Introgression did not shape the variation observed within the sampled germplasm. The two domesticated pea groups display distinct genetic bases of domestication, suggesting two genetically independent domestication events.

Data from: Landscape genetics reveals contrasting patterns of connectivity in two newt species (Lissotriton montandoni and L. vulgaris)

Ecologically distinct species may respond to landscape changes in different ways. In addition to basic ecological data, the extent of the geographic range has been successfully used as an indicator of species sensitivity to anthropogenic landscapes, with widespread species usually found to be less sensitive compared to range-restricted species. In this study, we investigate connectivity patterns of two closely related but ecologically distinct newt species – the range-restricted, Lissotriton montandoni and the widespread, L. vulgaris – using genomic data, a highly replicated setting (six geographic regions per species), and tools from landscape genetics. Our results show the importance of forest for connectivity in both species, but at the same time suggest differential use of forested habitat, with L. montandoni and L. vulgaris showing the highest connectivity at forest-core and forest-edges, respectively. Anthropogenic landscapes (i.e., higher crop- or urban-cover) increased resistance in both species, but the effect was one to three orders of magnitude stronger in L. montandoni than in L. vulgaris. This result is consistent with a view of L. vulgaris as an ecological generalist. Even so, currently, the negative impact of anthropogenic landscapes is mainly seen in connectivity among L. vulgaris populations, which show significantly stronger isolation and lower effective sizes relative to L. montandoni. Overall, this study emphasizes how habitat destruction is compromising genetic connectivity not only in endemic, range-restricted species of conservation concern but also in widespread generalist species, despite their comparatively lower sensitivity to anthropogenic landscape changes.

opennotspecifiedOct 2019View details →

One of the first cryptic mammal species discovered, when it was separated from the morphologically similar R. tumida (= R. bickhami) based on karyological studies. Karyotype of 2n = 42 of R. genowaysi is identical to that observed in R. velilla, but these species are genetically distinct; their ranges do not overlap. R. genowaysi is morphologically very similar to other species within the R. tumida complex and is sympatric with R. bickhami (2n = 34). Monotypic. Distribution. Two nearby localities in Pacific lowlands of S Chiapas, S Mexico. in Vespertilionidae

One of the first cryptic mammal species discovered, when it was separated from the morphologically similar R. tumida (= R. bickhami) based on karyological studies. Karyotype of 2n = 42 of R. genowaysi is identical to that observed in R. velilla, but these species are genetically distinct; their ranges do not overlap. R. genowaysi is morphologically very similar to other species within the R. tumida complex and is sympatric with R. bickhami (2n = 34). Monotypic. Distribution. Two nearby localities in Pacific lowlands of S Chiapas, S Mexico.

openMar 2022View details →

Data from: Traces of Genetic but Not Epigenetic Adaptation in the Invasive Goldenrod Solidago canadensis Despite the Absence of Population Structure

General information This deposition contains the datasets that were used in the statistical analysis of the manuscript entitled Traces of genetic but not epigenetic adaptation in the invasive goldenrod Solidago canadensis despite the absence of population structure published in Frontiers in Ecology and Evolution (doi: <a href="https://doi.org/10.3389/fevo.2022.856453">10.3389/fevo.2022.856453</a>). Uploaded files <ul> <li>README file to explain the datasets</li> <li>AFLP/MSAP metadata called EckertHerdenStiftDurkavanKleunenJoshi_2022_FrontEcolEvol_AFLPMSAP_meta_data.txt</li> <li>AFLP scoring dataset called EckertHerdenStiftDurkavanKleunenJoshi_2022_FrontEcolEvol_AFLP_scoring_data.txt</li> <li>MSAP scoring dataset called EckertHerdenStiftDurkavanKleunenJoshi_2022_FrontEcolEvol_MSAP_scoring_data.txt</li> <li>MSAP mix1-scoring dataset called EckertHerdenStiftDurkavanKleunenJoshi_2022_FrontEcolEvol_MSAP_scoring_data_mix1.txt</li> <li>All files were combined in a .zip file</li> </ul>

Data from: Do genetic drift and gene flow affect the geographic distribution of female plants in gynodioecious Lobelia siphilitica?

Variation in population sex ratio is particularly pronounced in gynodioecious angiosperms. Extremely high female frequencies in gynodioecious populations cannot be readily explained by selective forces alone. To assess the contributions of drift and gene flow to extreme sex-ratio variation, we documented sex ratio and population size in 92 populations of Lobelia siphilitica across its range and genotyped plants using plastid and nuclear genetic markers. Similarity in spatial patterns of genetic and demographic variables may suggest that drift and/or gene flow have contributed to population sex-ratio variation in L. siphilitica. We found strong spatial structuring of extremely high female frequencies: populations with >50% female plants are restricted to the south–central portion of the range. However, we did not detect any spatial structuring in population size nor metrics of genetic diversity, suggesting that extreme variation in female frequency is not strongly affected by drift or gene flow. Extreme sex-ratio variation is frequently observed in gynodioecious plants, but its causes are difficult to identify. Further investigation into mechanisms that create or maintain spatial structure of sex ratios in gynodioecious species will provide much needed insight.

opencc-zeroApr 2022View details →

Genetic diversity and relatedness among African Painted dogs in North America

African painted dogs (Lycaon pictus, APD) are highly endangered, with fewer than 7,000 remaining in nature. Captive breeding programs can preserve a genetically diverse population and provide a source of individuals for re-introductions. However, most programs are initiated from few founders and suffer from low genetic diversity and inbreeding. The aims of this study were to use molecular markers to assess genetic variation, inbreeding, and relatedness among APDs in the North American captive population, to use these data to realign studbook records, and to compare these data to wild populations and to the European captive population to facilitate development of a global management plan. We sequenced mitochondrial and major histocompatibility (MHC) class II loci, and genotyped 14 microsatellite loci from 109 APDs from 34 institutions in North America. We identified three likely studbook errors and resolved ten cases of uncertain paternity. Overall, microsatellite heterozygosity was higher than reported in Europe, but effective population size estimates were lower. Mitochondrial sequence variation was extremely limited, and there were fewer MHC haplotypes than in Europe or the wild. Although the population did not show evidence of significant inbreeding overall, several individuals shared high relatedness values, which should be incorporated into future breeding programs.

opencc-zeroApr 2022View details →

Data from: Competitive consequences determined by phenotypic but not genetic distance: a study with asexual Daphnia genotypes

1. How evolutionary relatedness influences the strength of competitive interactions among genetically isolated populations has been a long-standing interest in ecology. Darwin's "Competition Relatedness Hypothesis (CRH)" states that, since closely related species should compete more strongly, they are less likely to coexist, while Herbert's "Bimodal Competition Hypothesis (BCH)" predicts that competitive exclusion is less likely to occur when the competing species are genetically close or distant. 2. To test these hypotheses, we experimentally examined the difference in the competitive ability and life tables of fecundity and survivorship among four different genotypes of asexual Daphnia cf. pulex that diverged from a single ancestral genotype. 3. The experiments showed that the competitive consequences differed depending on the pairing of the competing genotypes, and that the degree of the competitive exclusion was lower when the competing genotypes were genetically closer to each other. These results partially supported the BCH but not the CRH at all. More importantly, the degree of competitive exclusion was better predicted by the phenotypic rather than genetic distances between the competing genotypes. 4. The life table experiments revealed that competitively inferior genotypes had higher early reproduction rates, but survival rates decreased with age and thus body size, probably a result of selection by predation pressures found in nature. 5. These results indicate that competitive superiority is highly dependent on selection pressures that given organisms have been evolutionally subjected to, and, that genetic similarity is not necessarily an appropriate measure for predicting the completive exclusion on an ecological time scale. To predict competitive relationships among the organisms, it is essential to comprehend their phenotypic differences rather than simply knowing their genetic or phylogenetic relationships.

opencc-zeroApr 2022View details →

History and environment shape spatial genetic variation and predict climate maladaptation in a narrowly distributed serotinous pine, Pinus muricata

Understanding the distribution of genetic diversity and differentiation in species with disjunct and isolated populations is critical for assessing how environment shapes genetic variation and the potential response to climate change. In contrast to the large distributions and population sizes of most pine species, Pinus muricata (Bishop pine) occurs in a small number of isolated and disjunct populations occupying a narrow band of environmental conditions along the coast of western North America. We used genotyping by sequencing to generate population genomic data for trees sampled from nearly all existing populations of P. muricata (12 populations, 213 individuals, 7,828 loci) to describe the spatial arrangement of genetic differentiation and diversity. We used genetic-environment association (GEA) analyses to quantify the contribution of environmental variables to local adaptation and spatial genetic structure. Based on these results, we quantified relative levels of potential maladaptation given future climate projections at 2041 – 2060 and 2081 – 2100. Our analyses reveal pronounced spatial genetic structure across the distribution, with most populations forming genetically identifiable groups across a latitudinal gradient, and remarkable evidence for differentiation among three proximally distributed stands on Santa Cruz Island. Despite occurring in small, isolated populations, P. muricata do not exhibit strongly reduced diversity. GEA analyses suggested that specific soil and climate variables have contributed to local adaptation. Genomic offset analyses suggest geographic variation in potential maladaptation, with northern populations experiencing higher levels under projected climate change. Overall, our results suggest that isolation and local adaptation have shaped genetic variation among disjunct populations, and illustrate the consequences of this variation for P. muricata under projected climate change.

opencc-by-4.0Apr 2022View details →

Genetic Control of Reproductive Traits under Different Temperature Regimes in Inbred Line Populations Derived from Crosses between S. pimpinellifolium and S. lycopersicum Accessions

Marker genotypes, linkage map and phenotypic data used for QTL analysis included in the manuscript  by Gonzalo et al. in press "Genetic Control of Reproductive Traits under Different Temperature Regimes in Inbred Line Populations Derived from Crosses between S. pimpinellifolium and S. lycopersicum Accessions".

opennotspecifiedJul 2021View details →

Figure 9 in Is mimicry a diversification-driver in ants? Biogeography, ecology, ethology, genetics and morphology define a second West-Palaearctic Colobopsis species (Hymenoptera: Formicidae)

Figure 9. Above: distribution map of Colobopsis samples examined – countries where Colobopsis presence is known from the literature are highlighted in grey. Below: approximate distributions of other Camponotini (Camponotus barbaricus, of C. micans and of C. ruber) which resemble that of CSL Colobopsis.

opennotspecifiedJul 2021View details →

Figure 10. Colobopsis imitans. A, B, E in Is mimicry a diversification-driver in ants? Biogeography, ecology, ethology, genetics and morphology define a second West-Palaearctic Colobopsis species (Hymenoptera: Formicidae)

Figure 10. Colobopsis imitans. A, B, E, worker (holotypus); C, D, F, G, soldier (specimen from the type locality). Scale bars: 0.5 mm. Pictures also available on AntWeb.org database, specimen codes: ANTWEB1041481 and ANTWEB1041482.