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Data from: Conservation and convergence of genetic architecture in the adaptive radiation of anolis lizards

The G matrix, which quantifies the genetic architecture of traits, is often viewed as an evolutionary constraint. However, G can evolve in response to selection and may also be viewed as a product of adaptive evolution. Convergent evolution of G in similar environments would suggest that G evolves adaptively, but it is difficult to disentangle such effects from phylogeny. Here, we use the adaptive radiation of Anolis lizards to ask whether convergence of G accompanies the repeated evolution of habitat specialists, or ecomorphs, across the Greater Antilles. We measured G in seven species representing three ecomorphs (trunk-crown, trunk-ground, and grass-bush). We found that the overall structure of G does not converge. Instead, the structure of G is well conserved and displays a phylogenetic signal consistent with Brownian motion. However, several elements of G showed signatures of convergence, indicating that some aspects of genetic architecture have been shaped by selection. Most notably, genetic correlations between limb traits and body traits were weaker in long-legged trunk-ground species, suggesting effects of recurrent selection on limb length. Our results demonstrate that common selection pressures may have subtle but consistent effects on the evolution of G, even as its overall structure remains conserved.

opencc-by-4.0Aug 2022View details →

Genetic parentage reconstruction as a practical tool applied to aquaculture and restoration programs for the European flat oyster, Ostrea edulis

Preserving and maximizing genetic diversity in conservation programs, including for restocking, are of high importance. The threatened European flat oyster (Ostrea edulis) is currently the subject of several applied conservation and restocking programs, but concerns have been raised over potential negative side effects of these programs, for example due to our limited knowledge about the genetic effects in natural populations of releasing offspring of hatchery origin. Here, we developed a cost-effective, easily applicable and highly reliable method to assess the genetic diversity and parental contributions in flat oyster hatchery production based on analyses of 17 microsatellite loci. We analyzed broodstock and hatchery-produced spat (total n = 289) and compared diversity to that in wild samples of adults and spat from the broodstock source in the Limfjorden (total n = 190). Based on four hatchery tank experiments, we found that five swarming events (larval releases) were characterized by a single maternal and multiple paternal contributions, and that the number of contributing parents varied greatly both among individual tanks, and between swarming events within tank. On average, the effective number of breeders was only one third of the actual broodstock size. Although the broodstock exhibited high genetic variation, the high reproductive skew resulted in produced seed representing only a relatively small subset of this variation. The work demonstrates potential impact of hatchery reared offspring on decreasing genetic diversity in wild populations, but also that genetic monitoring can be integrated in conservation programs to minimize negative effects on restoration and supplementary restocking programs that utilize hatchery reared spats to support natural populations.

Genetic diversity and differentiation of populations of Anthyllis vulneraria along elevational and latitudinal gradients

The abundant centre model (ACM) predicts that the suitability of environmental conditions for a species decreases from the centre of its distribution towards its range periphery and consequently its populations will become scarcer, smaller and more isolated, resulting in lower genetic diversity and increased differentiation. However, little is known about whether genetic diversity shows similar patterns along elevational and latitudinal gradients with similar changes in important environmental conditions. Using microsatellite markers we studied the genetic diversity and structure of 20 populations each of Anthyllis vulneraria along elevational gradients in the Alps from the valleys to the elevational limit (2500 m), and along a latitudinal gradient (2500 km) from Central Europe to the range margin in northern Scandinavia. Both types of gradients corresponded to a 11.5 °C difference in mean annual temperature. Genetic diversity strongly declined and differentiation increased with latitude in line with the predictions of the ACM. However, as population size did not decline with latitude and genetic diversity was not related to population size in A. vulneraria, this pattern is not likely to be due to less favourable conditions in the North, but due to serial founder effects during the post-glacial recolonization process. Genetic diversity was not related to elevation, but we found significant isolation by distance along both gradients, although the elevational gradient was shorter by orders of magnitude. Subarctic populations differed genetically from alpine populations indicating that the northern populations did not originate from high elevational Alpine ones. Our results support the notion that postglacial latitudinal colonization over large distances resulted in a larger loss of genetic diversity than elevational range shifts. The lack of genetic diversity in subarctic populations may threaten their long-term persistence in the face of climate change, whereas alpine populations could benefit from gene flow from low-elevation populations.

The Atlas of mitochondrial genetic diversity for Western Palearctic butterflies

Abstract: Motivation Butterflies represent a model in biology and a flagship group for invertebrate conservation. We provide four new resources for the Western-Palearctic butterflies: 1) An updated checklist comprising 552 species; 2) a curated dataset of 32,129 mitochondrial COI sequences for 532 species, including a de novo reference library for the Maghreb (Morocco and northern Algeria and Tunisia) and Macaronesia (Azores, Madeira and Canary Islands); 3) seven indexes of intraspecific genetic variation (IGV): observed and expected number of haplotypes, haplotype and nucleotide diversity, two fixation indexes, and maximum p-distance; 4) species-level maps illustrating the distribution of COI variability and haplotype networks. The updated checklist will be fundamental for any application dealing with butterfly diversity in Western Palearctic. IGV indexes provide measures for genetic polymorphism and spatial structure and represent proxies for dispersal capacity. These resources will facilitate comparative studies of macrogenetics, will foster integrative taxonomy, and will aid conservation strategies. Main types of variables contained A complete species checklist in table format, 32,129 mitochondrial DNA-barcodes provided with metadata (species membership, WGS84 coordinates, sequence length), and a book in PDF format including the IGV atlas and indexes. Spatial location and grain The checklist encompasses Europe up to Urals in the east, north Macaronesia (Azores, Madeira and Canary Islands), as well as the Maghreb (Morocco and northern Algeria and Tunisia). DNA-barcodes have been retained in the geographic interval of -31.3–67.5 degrees of longitude and 27.5–71.2 degrees of latitude. Time period and grain DNA-barcodes originate from studies published between 1998-2022 and from de novo sequencing of 2,608 specimens done between 2007-2022. Major taxa and level of measurement Butterflies (Lepidoptera, Papilionoidea), analysed from individual to species level. Software format Data and functions to manage the dataset are provided in the iodatabase R package (<a href="https://github.com/leondap/iodatabase" rel="noopener noreferrer">https://github.com/leondap/iodatabase</a>) and in Dryad

Fine-scale spatial genetic structure in a locally abundant native bunchgrass (Achnatherum thurberianum) including distinct lineages revealed within seed transfer zones

Analyses of the factors shaping genetic variation in widespread plant species are important for understanding evolutionary history and local adaptation and have applied significance for guiding conservation and restoration decisions. Thurber's needlegrass (Achnatherum thurberianum) is a widespread, locally abundant grass that inhabits heterogeneous arid environments of western North America and is of restoration significance. It is a common component of shrubland steppe communities in the Great Basin Desert, where drought, fire, and invasive grasses have degraded natural communities. Using a reduced representation sequencing approach, we generated SNP data at 5,677 loci across 246 individuals from 17 A. thurberianum populations spanning five previously delineated seed zones from the western Great Basin. Analyses revealed pronounced population genetic structure, with individuals forming consistent geographical clusters across a variety of population genetic analyses and spatial scales. Low levels of genetic diversity within populations, as well as high population estimates of linkage disequilibrium and relatedness, were consistent with self-fertilization as a contributor to population differentiation. Variance partitioning and partial redundancy analysis (pRDA) indicated local adaptation to environment as additionally influencing the spatial distribution of genetic variation. The environmental variables driving these results were similar to those implicated in recent genecological work which inferred local adaptation for seed zone delineation. Our analyses also revealed a complex evolutionary history of A. thurberianum in the Great Basin, where previously delineated seed zones contain distantly related populations. Our results indicate evolutionary history, mating system, and differentiation across distinct geographic and environmental scales have shaped genetic variation in A. thurberianum and illustrate how numerous aspects of population genetic variation might require consideration for restoration planning.

Microscopy data from: Identification of genetic interactions with priB links the PriA/PriB DNA replication restart pathway to double-strand DNA break repair in Escherichia coli

Collisions between DNA replication complexes (replisomes) and impediments such as damaged DNA or proteins tightly bound to the chromosome lead to premature dissociation of replisomes at least once per cell cycle in Escherichia coli. Left unrepaired, these events produce incompletely replicated chromosomes that cannot be properly partitioned into daughter cells. DNA replication restart, the process that reloads replisomes at prematurely terminated sites, is therefore essential in E. coli and other bacteria. Three replication restart pathways have been identified in E. coli: PriA/PriB, PriA/PriC, and PriC/Rep. A limited number of genetic interactions between replication restart and other genome maintenance pathways have been defined, but a systematic study placing replication restart reactions in a broader cellular context has not been performed. We have utilized transposon insertion sequencing to identify new genetic interactions between DNA replication restart pathways and other cellular systems. Known genetic interactors with the priB replication restart gene (uniquely involved in the PriA/PriB pathway) were confirmed and several novel priB interactions were discovered. Far fewer connections were found with the PriA/PriC or PriC/Rep pathways, suggesting a primacy role for the PriA/PriB pathway in E. coli. Targeted genetic and imaging-based experiments with priB and its genetic partners revealed significant double-strand DNA break (DSB) accumulation in strains with mutations in dam, rep, rdgC, lexA, or polA. Modulating the activity of the RecA recombinase partially suppressed the detrimental effects of rdgC or lexA mutations in ΔpriB cells. Taken together, our results highlight roles for several genes in DSB homeostasis and define a genetic network that facilitates DNA repair/processing upstream of PriA/PriB-mediated DNA replication restart in E. coli.

Phenotypic plasticity contributes more to the variations in nutrient resorption than genetic differentiation in a grassland dominant

1. Phenotypic plasticity and genetic differentiation are the two important processes determining the leaf nutrient resorption among and within plant species, which is critical for understanding the adaptability of plants. However, relative contributions of these two processes have never been quantified at a large geographical scale. 2. Here, we investigated intraspecific variations in nutrient resorption among 14 Stipa breviflora populations along a latitude gradient in 2018 and 2019. Furthermore, we sow seeds from these populations in two common gardens at different latitudes, and examined the variations in nutrient resorption. 3. Our results showed that nitrogen and phosphorus resorption efficiency (NRE and PRE) among S. breviflora populations in nature were positively related to latitude, while this trend disappeared in the common gardens. The heritability of NRE and PRE was 11.45 % and 16.78 %, respectively. These results suggested that phenotypic plasticity contributed much more than genetic variation to nutrient resorption of S. breviflora. Moreover, the structural equation modeling (SEM) suggested that latitude indirectly affected nutrient resorption mainly by altering soil nutrients. With the increasing of latitude, soil nutrients decreased while nutrient resorption increased. This suggested <a name="_Hlk78556987"></a>the main process regulating nutrient resorption is negative feedback to soil nutrient availability. 4. Our study provides new insights into the role of nutrient resorption in plant adaptations to geographic variations.

opencc-by-4.0Jul 2022View details →

Data for The genetics monopolistic industry, as expected, is missing information two inches beyond their nose: in this case, transcripts

De novo transcriptome assembly is one of the many fundamental pieces of new research in genomics. It is, for example, the preferred method for studying non-model organisms, since it is easier and cheaper than building a genome, and reference methods are not possible without an existing genome. The transcriptomes of these organisms can thus reveal novel proteins and their isoforms that are implicated in such unique biological phenomena. This technique is also useful in cancer research as it makes possible to detect potentially significant chimeric transcripts in cancer and normal somatic tissues. Given that the genetics industry is organized in the form of a monopoly controlled by hidden lobbies who also control Academia, all the available software for de novo transcriptome assembly is being developed by academic researchers under the open-source paradigm. We report here, that as anyone could have very easily deduced from past experiences in other industries, this unethical form of organization in the industry is resulting in incompetence whose effects include missing a significant portion of the available information that could be obtained from some genomics studies. In this case, missing transcripts in transcriptome studies. We won't deep in on the consequences, but these could include overpricing, over costs, and failing to achieve the goals of some studies.

Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution

Chromosomal inversions have been shown to play a major role in local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence.

Nuclear genetic diversity and structure of Anastrepha ludens wild populations evidenced by microsatellite markers

The Mexican fruit fly, Anastrepha ludens is an important pest that causes widespread damage to a number of fruit crops in Mexico. The Sterile Insect Technique (SIT) is commonly used for its control. However, the existence of natural barriers can give rise to a population structure in neutral loci and possibly behavioral or adaptive traits that interfere with SIT. For this reason, it is important to understand the genetic diversity and structure of A. ludens populations and to better understand the evolutionary ecology and population processes in view of possible expansions and possible host shifts due to climate change. We genotyped nine nuclear DNA (nDNA) microsatellite loci among fruit fly populations collected from five biogeographic areas within Mexico, Mexican Plateau, the Northeastern Coastal Plain, the Pacific Coast, the Gulf Coast of Mexico, the Soconusco and a laboratory strain. The nuclear genetic diversity was moderate (from He = 0.34 to He = 0.39) within the wild mexfly population. We found that populations were clustered in three genetic groups (K=3). The diversity and genetic structure of A. ludens are produced by environmental and geological conditions as well as local conditions like anthropogenic perturbation which would produce population expansion and the existence of possible predators that would affect the population density. Gene flow showed recent migration among populations. The laboratory strain showed less diversity than the wild samples. Large values of current and ancestral population size suggest high resistance to climatic changes, probably due to biological attributes, such as its polyphagous, multivoltine and high dispersal characteristics. In particular ecosystem fragmentation and perturbation as well as the existence of new plant hosts all of which would probably increase the abundance of flies.

opencc-by-4.0Dec 2021View details →

Plasmid Sequences for Brophy et al., 2022: Synthetic genetic circuits as a means of reprogramming plant roots

Plasmid Sequences for Brophy et. al. 2022: Synthetic genetic circuits as a means of reprogramming plant roots

opencc-by-4.0Sep 2019View details →

T a b l e 2 in Genetic Diversity And Place In The General Phylogeographic Structure Of Capercaillie,Tetrao Urogallus (Galliformes, Phasianidae), From Belarus

T a b l e 2. The number of the capercaillie in Belarus

Genetic confirmation of a hybrid between two highly divergent cardinalid species: A Rose-breasted Grosbeak (Pheucticus ludovicianus) and a Scarlet Tanager (Piranga olivacea)

Using low-coverage whole-genome sequencing, analysis of vocalizations, and inferences from natural history, we document a first-generation hybrid between a rose-breasted grosbeak (Pheucticus ludovicianus) and a scarlet tanager (Piranga olivacea). These two species occur sympatrically throughout much of eastern North America, although were not previously known to interbreed. Following the field identification of a putative hybrid, we use genetic and bioacoustic data to show that a rose-breasted grosbeak was the maternal parent and a scarlet tanager was the paternal parent of the hybrid, whose song was similar to the latter species. These two species diverged >10 million years ago, and thus it is surprising to find a hybrid formed under natural conditions in the wild. Notably, the hybrid has an exceptionally heterozygous genome, with a conservative estimate of a heterozygous base every 100 bp. The observation that this hybrid of such highly divergent parental taxa has survived until adulthood serves as another example of the capacity for hybrid birds to survive with an exceptionally divergent genomic composition.

Genetic and transcriptomic datasets characterizing gene drive mosquitoes expressing antimicrobial peptides that retard Plasmodium sporogonic development

Gene drives hold promise for the genetic control of malaria vectors. The development of vector population modification strategies hinges on the availability of effector mechanisms impeding parasite development in transgenic mosquitoes. We augmented a midgut gene of the malaria mosquito Anopheles gambiae to secrete two exogenous antimicrobial peptides, Magainin 2 and Melittin. This small genetic modification, capable of efficient non-autonomous gene drive, hampers oocyst development in both Plasmodium falciparum and Plasmodium berghei. It delays the release of infectious sporozoites while it simultaneously reduces the lifespan of homozygous female transgenic mosquitoes. Modeling the spread of this modification using a large-scale agent-based model of malaria epidemiology reveals that it can break the cycle of disease transmission across a range of transmission intensities.

Determinants of genetic diversity and species richness of North American amphibians

Aim: Ecological limits on population sizes and the number of species a region can sustain are thought to simultaneously produce spatial patterns in population genetic diversity and species richness due to the effects of random drift operating in parallel across population and community levels. Here, we test the extent to which resource-based environmental limits jointly determine these patterns of biodiversity in amphibians. Location: North America. Taxon: Amphibians. Methods: We repurposed open, raw microsatellite data from 19 species sampled at 554 sites in North America and mapped nuclear genetic diversity at the continental scale. We then tested whether ecological limits defined by resource availability and environmental heterogeneity could simultaneously shape biogeographic patterns in genetic diversity and species richness with structural equation modeling. Results: Spatial patterns of population genetic diversity run opposite patterns of species richness and genetic differentiation. However, while measures of resource availability and niche heterogeneity predict 89% of the variation in species richness, these landscape metrics were poor predictors of genetic diversity. Main conclusions: Although heterogeneity appears to be an important driver of genetic and species biodiversity patterns in amphibians, variation in genetic diversity both within and across species makes it difficult to infer general processes producing spatial patterns of amphibian genetic diversity. This result differs from those found in endotherms and may be due to the considerable life history variation found across amphibians.

Simulated data for: The evolution of mating preferences for genetic attractiveness and quality in the presence of sensory bias

This repository contains simulated datasets relating to the publication: Henshaw JM, Fromhage L, Jones AG (2022) The evolution of mating preferences for genetic attractiveness and quality in the presence of sensory bias. Proc. Natl. Acad. Sci. USA (doi:10.1073/pnas.2206262119) In this paper, we simulate the evolution of female preferences for multiple male ornament types (e.g., 'Fisherian', 'handicap' and 'indicator' ornaments) that differ in their associations with genes for attractiveness and for general 'quality' (operationalized as the ability to acquire resources). We allowed for ornaments to differ in their saliency to females. We also analyze the causal mechanisms generating sexual selection (e.g., 'good genes' and 'sexy sons') using causal inference. Datasets are organised into ZIP files named after the corresponding figure in the publication. For further information see the publication and the file README.txt in this repository.

Population dynamics of Amazonian floodplain forest species support spatial variation on genetic diversity but not range expansions through time

Aim: We tested if historical demographic changes of populations occurring on the floodplains of a major Amazon Basin tributary could be associated with range expansions from upper and middle sections of the river, following the establishment of widespread river-created environments during the Late Pleistocene and Holocene. Location: Solimões River, Western Amazon, South America. Taxon: Myrmoborus lugubris, Thamnophilus cryptoleucus and Myrmotherula assimilis. Methods: We explored spatial patterns of genetic diversity and connectivity among sampled localities using thousands of Ultra-Conserved Elements. Range expansions were tested with alternative methods. We quantified habitat preference for the analyzed species to test whether the occupation of dynamic habitats could predict spatial patterns of genetic diversity. Results: Our study did not support shared population range expansions related to historical regionalized changes in habitat availability. We found considerable variation in the spatial distribution of the genetic diversity between studied taxa, and that species with higher levels of specialization to dynamic environments have a more heterogeneous distribution of genetic diversity and reduced levels of gene flow across space. Main conclusions: Our results suggest that demographic expansions along the Solimões River might be linked to spatially homogeneous oscillation in the distribution of floodplain environments, promoting effective population size changes but not range expansion. We found that habitat specificity might be a good predictor of population connectivity along the Amazonian floodplains.

Give and take: Effects of genetic admixture on mutation load in endangered Florida panthers

Genetic admixture is a biological event inherent to genetic rescue programs aimed at the long-term conservation of endangered wildlife. Although the success of such programs can be measured by the increase in genetic diversity and fitness of subsequent admixed individuals, predictions supporting admixture costs to fitness due to the introduction of novel deleterious alleles are necessary. Here, we analyzed nonsynonymous variation from conserved genes to quantify and compare levels of mutation load (i.e., proportion of deleterious alleles and genotypes carrying these alleles) among endangered Florida panthers and non-endangered Texas pumas. Specifically, we used canonical (i.e., non-admixed) Florida panthers, Texas pumas, and F1 (canonical Florida x Texas) panthers dating from a genetic rescue program and Everglades National Park panthers with Central American ancestry resulting from an earlier admixture event. We found neither genetic drift nor selection significantly reduced overall proportions of deleterious alleles in the severely bottlenecked canonical Florida panthers. Nevertheless, the deleterious alleles identified were distributed into a disproportionately high number of homozygous genotypes due to close inbreeding in this group. Conversely, admixed Florida panthers (either with Texas or Central American ancestry) presented reduced levels of homozygous genotypes carrying deleterious alleles but increased levels of heterozygous genotypes carrying these variants relative to canonical Florida panthers. Although admixture is likely to alleviate the load of standing deleterious variation present in homozygous genotypes, our results suggest introduced novel deleterious alleles (temporarily present in heterozygous state) in genetically rescued populations could potentially be expressed in subsequent generations if their effective sizes remain small.

Population genetic structure and demographic history of Rhodeus atremius suigensis, an endangered bitterling in Japan

Demographic events can shape genetic diversity through genetic drift, often leaving a persistent signal in the genetic characteristics of species. Rhodeus atremius suigensis is an endangered bitterling fish endemic to the Okayama Plain, Japan. In this study, we inferred its demographic history and genetic structure using a comprehensive analysis of the mtDNA ND1 gene, microsatellite markers (MS) and MHC class IIB gene. Based on mtDNA, R. a. suigensis included two sublineages; A and B. While <a name="OLE_LINK85"></a><a name="OLE_LINK88"></a>the former was widely distributed, the latter was restricted to eastern populations<a name="OLE_LINK11"></a><a name="OLE_LINK12"></a> that were monomorphic in MHC. Phylogenetic analysis revealed that R. a. suigensis, together with R. a. atremius, experienced a substantial bottleneck in the middle Pleistocene. In MS and MHC, genetic diversity was low in all populations; ranked as the lowest among bitterling species. Bayesian clustering suggested that two clusters of MS had been widely introgressed in the centre of its distribution. These clusters seem to have been formed by the disruption of the distribution in the last Pleistocene, and later admixed by a large-scale reclamation in the Okayama Plain since the 16th century, which triggered a decline in effective population size (Ne) in many populations. Based on coalescence analysis, all populations reached their lowest Ne around the middle of the 20th century. Accordingly, R. a. suigensis seems to have experienced two large bottlenecks in the past. While the first bottleneck was probably due to climatic changes in the middle Pleistocene, the second is due to anthropogenic degradation and fragmentation of habitats in recent years.