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opencc-by-4.0Dec 2021View details →

Fig. 2 in Genetic Differentiation Of Ukrainian Populations Of Eusomus Ovulum (Coleoptera, Curculionidae): Evidence Of Multiple Hybrid Speciation

Fig. 2. The electrophoretic spectra of the esterases in the Eusomus ovulum specimens.

opencc-by-4.0Dec 2021View details →

Fig. 1 in Genetic Differentiation Of Ukrainian Populations Of Eusomus Ovulum (Coleoptera, Curculionidae): Evidence Of Multiple Hybrid Speciation

Fig. 1. Geographic localization of Eusomus ovulum samples.

opencc-by-4.0Mar 2020View details →

Fig. 3 in Winter Diet Of The Common Genet, Genetta Genetta (Carnivora, Viverridae), And The African Golden Wolf, Canis Anthus (Carnivora, Canidae), In Altitudinal Locality Of The Edough Forest (Northeastern Algeria)

Fig. 3. Occurrence frequency of different food categories for both species.

opencc-by-4.0Mar 2020View details →

Fig. 4 in Winter Diet Of The Common Genet, Genetta Genetta (Carnivora, Viverridae), And The African Golden Wolf, Canis Anthus (Carnivora, Canidae), In Altitudinal Locality Of The Edough Forest (Northeastern Algeria)

Fig. 4. Diets of the African golden wolf (left) and the common genet (right) in the study area.

opencc-by-4.0Mar 2020View details →

Fig. 2 in Winter Diet Of The Common Genet, Genetta Genetta (Carnivora, Viverridae), And The African Golden Wolf, Canis Anthus (Carnivora, Canidae), In Altitudinal Locality Of The Edough Forest (Northeastern Algeria)

Fig. 2. All food categories consumed by the two predators (©: M. Boukheroufa).

Genetic covariance in immune measures and pathogen resistance in decorated crickets (Gryllodes sigillatus) is sex and pathogen specific

Insects are important models for studying immunity in an ecological and evolutionary context. Yet, most empirical work on the insect immune system has come from phenotypic studies meaning we have a limited understanding of the genetic architecture of immune function in the sexes. We use nine highly inbred lines to thoroughly examine the genetic relationships between a suite of commonly used immune assays (haemocyte count, implant encapsulation, total phenoloxidase activity, antibacterial zone of inhibition, pathogen clearance) and resistance to infection by three generalist insect pathogens (the gram-negative bacterium Serratia marcescens, the gram-positive bacterium Bacillus cereus and the fungus Metarhizium robertsii) in male and female Gryllodes sigillatus. There were consistent positive genetic correlations between haemocyte count, antibacterial and phenoloxidase activity and resistance to S. marcescens in both sexes, but these relationships were less consistent for resistance to B. cereus and M. robertsii. In addition, the clearance of S. marcescens was genetically correlated with the resistance to all three pathogens in both sexes. Genetic correlations between resistances to the different pathogen species were inconsistent, indicating that resistance to one pathogen does not necessarily mean resistance to another. Finally, while there is ample genetic (co)variance in immune assays and pathogen resistance, these genetic estimates differed across the sexes and many of these measures were not genetically correlated across the sexes suggesting that these measures could evolve independently in the sexes. Our finding that the genetic architecture of immune function is sex and pathogen specific suggests that the evolution of immune function in male and female G. sigillatus is likely to be complex. Similar quantitative genetic studies that measure a large number of assays and resistance to multiple pathogens in both sexes are needed to ascertain if this complexity extends to other species.

Genetic differentiation and signatures of local adaptation revealed by RADseq for a highly-dispersive mud crab Scylla olivacea in the Sulu Sea

Connectivity of marine populations is shaped by complex interactions of biological and physical processes across the seascape. The influence of environmental features on the genetic structure of populations has key implications to the dynamics and persistence of populations, and an understanding of spatial scales and patterns of connectivity is crucial for management and conservation. This study employed a seascape genomics approach combining larval dispersal modeling and population genomic analysis using single nucleotide polymorphisms (SNPs) obtained from RADseq to examine environmental factors influencing patterns of genetic structure and connectivity for a highly-dispersive mud crab, Scylla olivacea (Herbst, 1796) in the Sulu Sea. Dispersal simulations reveal widespread but asymmetric larval dispersal influenced by persistent southward and westward surface circulation features in the Sulu Sea. Despite potential for widespread dispersal across the Sulu Sea, significant genetic differentiation was detected among eight populations based on 1,655 SNPs (FST = 0.0057, p < 0.001) and a subset of 1,643 putatively neutral SNP markers (FST = 0.0042, p < 0.001). Oceanography influences genetic structure, with redundancy analysis (RDA) indicating significant contribution of asymmetric ocean currents to neutral genetic variation (R2adj = 0.133; p = 0.035). Genetic structure may also reflect demographic factors, with divergent populations characterized by low effective population sizes (Ne < 50). Pronounced latitudinal genetic structure was recovered for loci putatively under selection (FST = 0.2390, p < 0.001), significantly correlated with sea surface temperature variabilities during peak spawning months for S. olivacea (R2adj = 0.692-0.763; p < 0.050), suggesting putative signatures of selection and local adaptation to thermal clines. While oceanography and dispersal ability likely shape patterns of gene flow and genetic structure of S. olivacea across the Sulu Sea, the impacts of genetic drift and natural selection influenced by sea surface temperature also appear as likely drivers of population genetic structure. This study contributes to the growing body of literature documenting population genetic structure and local adaptation for highly-dispersive marine species, and provides information useful for spatial management of the fishery resource.

Lack of spatial and temporal genetic structure of Japanese eel (Anguilla japonica) populations

Japanese eel (Anguilla japonica) is an important food source in East Asia whose population has dramatically declined since the 1970s. Despite past analysis with DNA sequencing, microsatellite and isozyme methods, management decisions remain hampered by contradictory findings. For example, it remains unresolved whether Japanese eels are a single panmictic population or whether they harbor significant substructure. Accurate assessment of population genetic substructure, both spatial and temporal, is essential for determining the relevant number of distinct management units appropriate for this species. In the present study, we assayed genetic variation genome-wide using Restriction Site Associated DNA Sequencing (RAD-seq) technology to analyze the population genetic structure of Japanese eels. For analysis of temporal isolation, five "cohort" samples were collected yearly from 2005 to 2009 in the Yangtze River Estuary. For analysis of spatial structure, five "arrival wave" samples were collected in China in 2009, and two arrival wave samples were collected in Japan in 2001. In each cohort of each arrival wave, five individuals were collected for a total of 55 eels sampled. In total, 214,210 loci were identified from these individuals, 106,652 of which satisfied quality checks and were retained for further analysis. There was relatively little population differentiation between arrival waves and cohorts collected either at different locations during the same year (Fst = 0.077) or at the same location collected over subsequent years (Fst = 0.082), and locations displayed no consistent isolation-by-distance.

Transitioning from environmental genetics to genomics using mitogenome reference databases

Species detection using eDNA is revolutionizing the global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information—especially sequence information that includes intraspecific variation—creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of complete mitogenomic sequence information to evaluate the effectiveness of such data to differentiate, identify and detect taxa. We created the Oregon Biodiversity Genome Project working group to utilize recent advances in sequencing technology to create a database of complete, near error-free mitogenomic sequences for all of Oregon's resident freshwater fishes. So far, we have successfully assembled the complete mitogenomes of 313 specimens of freshwater fish representing 7 families, 55 genera, and 129 (88%) of the 146 resident species and lineages. Our comparative analyses of these sequences illustrate that the short (~150 bp) mitochondrial "barcode" regions typically used for eDNA assays are not consistently diagnostic for species-level identification and that no single region is best for metabarcoding Oregon's fishes. However, often-overlooked intergenic regions of the mitogenome such as the D-loop have the potential to reliably diagnose and differentiate species. This project provides a blueprint for other researchers to follow as they build regional databases. It also illustrates the taxonomic value and limits of complete mitogenomic sequences, and how current eDNA assays and the "PCR-free" environmental genomics methods of the future can best leverage this information.

Data from: Sustained positive consequences of genetic rescue of fitness and behavioural traits in inbred populations of Drosophila melanogaster

One solution to alleviate the detrimental genetic effects associated with reductions in population size and fragmentation is to introduce immigrants from other populations. While the effects of this genetic rescue on fitness traits are fairly well known, it is less clear to what extent inbreeding depression and subsequent genetic rescue affects behavioural traits. In this study, replicated crosses between inbred lines of Drosophila melanogaster were performed in order to investigate the effects of inbreeding and genetic rescue on egg-to-adult viability and negative geotaxis behaviour - a locomotor response used to measure e.g. the effects of physiological ageing. Transgenerational effects of outcrossing were investigated by examining the fitness consequences in both the F1 and F4 generation. The majority of inbred lines showed evidence for inbreeding depression for both egg-to-adult viability and behavioural performance (95% and 66% of lines, respectively), with inbreeding depression being more pronounced for viability compared to locomotor response. Subsequent outcrossing with immigrants led to an alleviation of the negative effects for both viability and geotaxis response resulting in inbred lines being similar to the outbred controls, with beneficial effects persisting from F1 to F4. Overall, the results clearly show that genetic rescue can provide transgenerational rescue of small, inbred populations by rapidly improving population fitness components. Thus, we show that even the negative effects of inbreeding on behaviour, similar to that of neurodegeneration associated with physiological ageing, can be reversed by genetic rescue.

opencc-zeroMar 2022View details →

Genetic basis for the evolution of pelvic-fin brooding, a new mode of reproduction, in a Sulawesian fish

Modes of reproduction in animals are diverse, with different modes having evolved independently in multiple lineages across a variety of taxa. However, an understanding of the genomic change driving the transition between different modes of reproduction is limited. Several ricefishes (Adrianichthyidae) on the island of Sulawesi have a unique mode of reproduction called "pelvic-fin brooding," wherein females carry externally fertilized eggs until hatching using their pelvic fins. Phylogenomic analysis demonstrated pelvic-fin brooders to have evolved at least twice in two distant clades of the Adrianichthyidae. We investigated the genetic architecture of the evolution of this unique mode of reproduction. Morphological analyses and laboratory observations revealed that females of pelvic-fin brooders have longer pelvic fins and a deeper abdominal concavity, and that they can carry an egg clutch for longer than non-brooding adrianichthyids, suggesting that these traits play important roles in this reproductive mode. Quantitative trait locus mapping using a cross between a pelvic-fin brooder Oryzias eversi and a non-brooding O. dopingdopingensis reveals different traits involved in pelvic-fin brooding to be controlled by different loci on different chromosomes. Genomic analyses of admixture detected no signatures of introgression between two lineages with pelvic-fin brooders, indicating that introgression is unlikely to be responsible for repeated evolution of pelvic-fin brooding. These findings suggest that multiple independent mutations may have contributed to the convergent evolution of this novel mode of reproduction.

Data from: Tracking population genetic signatures of local extinction with herbarium specimens

Background and Aims Habitat degradation and landscape fragmentation dramatically lower population sizes of rare plant species. Decreasing population sizes may, in turn, negatively affect genetic diversity and reproductive fitness which can ultimately lead to local extinction of populations. Although such extinction vortex dynamics have been postulated in theory and modelling for decades, empirical evidence from local extinctions of plant populations is scarce. In particular, comparisons between current vs. historical genetic diversity and differentiation are lacking despite their potential to guide conservation management. Methods We studied the population genetic signatures of the local extinction of Biscutella laevigata subsp. gracilis populations in Central Germany. We used microsatellites to genotype individuals from 15 current populations, one ex-situ population, and 81 herbarium samples from five extant and 22 extinct populations. In the current populations, we recorded population size and fitness proxies, collected seeds for a germination trial and conducted a vegetation survey. The latter served as surrogate for habitat conditions to study how habitat dissimilarity affects functional connectivity among the current populations. Key Results Bayesian clustering revealed similar gene pool distribution in current and historical samples but also indicated that a distinct genetic cluster was significantly associated with extinction probability. Gene flow was affected by both spatial distance and floristic composition of population sites, highlighting the potential of floristic composition as powerful predictor of functional connectivity which may promote decision making for reintroduction measures. For an extinct population, we found a negative relationship between sampling year and heterozygosity. Inbreeding negatively affected germination. Conclusions Our study illustrates the usefulness of historical DNA to study extinction vortices in threatened species. Our novel combination of classical population genetics together with data from herbarium specimens, an ex-situ population and a germination trial underscores the need for genetic rescue measures to prevent extinction of B. laevigata in Central Germany.

Concordant patterns of morphological, stable isotope, and genetic variation in a recent ecological radiation (Salmonidae:Coregonus spp.)

Groups of sympatric taxa with low inter-specific genetic differentiation, but considerable ecological differences, offer great opportunities to study the dynamics of divergence and speciation. This is the case of ciscoes (Coregonus spp.) in the Laurentian Great Lakes, which are characterized by a complex evolutionary history and are commonly described as having undergone an adaptive radiation. In this study, morphometrics, stable isotopes and transcriptome sequencing were used to study the relationships within the Coregonus artedi complex in western Lake Superior. We observed general concordance for morphological, ecological and genomic variation, but the latter was more taxonomically informative as it showed less overlap among species in multivariate space. Low levels of genetic differentiation were observed between individuals morphologically identified as C. hoyi and C. zenithicus, which could be evidence of incomplete lineage sorting or recent hybridization between the two groups. Transcriptome-based single nucleotide polymorphisms exhibited significant divergence for genes associated with vision, development, metabolism and immunity among species that occupy different habitats. This study highlights the importance of using an integrative approach when studying groups of taxa with a complex evolutionary history, as individual-level analyses of multiple independent datasets can provide a clearer picture of the patterns and processes associated with the origins of biodiversity.

opencc-by-4.0Jan 2022View details →

The combined impact of persistent infections and human genetic variation on C-reactive protein levels

GWAS summary statistics for high-sensitive C-reactive protein (hsCRP) levels, and list of the 1809 SNPs included in the hsCRP polygenic risk score (CRP-PRS) calculation.

Database of non-target invertebrates recorded in field experiments of genetically engineered Bt maize and corresponding non-Bt maize: data files

This database represents a comprehensive collection of experimental field data from all over the world on non-target invertebrates recorded in genetically engineered/modified Bt and non-Bt maize. The three data files deposited here are described by Meissle et al. (2022), BMC Research Notes, <a href="https://doi.org/10.1186/s13104-022-06021-3">https://doi.org/10.1186/s13104-022-06021-3</a> . The database was created for a systematic review with the question if growing Bt maize changes abundance or ecological function of non-target animals compared to growing of non-GM maize, published by Meissle et al. (2022), Environmental Evidence, <a href="https://doi.org/10.1186/s13750-022-00272-0">https://doi.org/10.1186/s13750-022-00272-0</a>. Data file 1 contains the database with 7279 records of non-target invertebrate abundance, activity density, or predation or parasitism in Bt and non-Bt maize, extracted from 120 publications. Data file 2 includes the list and definitions of variables in the database, and data file 3 represents the critical appraisal questions and answer options.

opencc-by-4.0May 2022View details →

Additional data for "Tissue-specific impacts of aging and genetics on gene expression patterns in humans"

Additional files for paper "Tissue-specific impacts of aging and genetics on gene expression patterns in humans" by Yamamoto and Chung et al. 2021. Contains file of results from joint age and genetics model.

Genomic evidence that a sexually selected trait captures genome-wide variation and facilitates the purging of genetic load

The evolution of costly traits like deer antlers and peacock trains, which drove the formation of Darwinian sexual selection theory, has been hypothesised to both reflect and affect patterns of genetic variance across the genome, but direct tests are missing. Here, we used an evolve and re-sequence approach to reveal patterns of genome-wide diversity associated with the expression of a sexually-selected weapon that is dimorphic among males of the bulb mite, Rhizoglyphus robini. Populations selected for the weapon showed reduced genome-wide diversity compared to populations selected against the weapon, particularly in terms of the number of segregating non-synonymous positions, indicating enhanced purifying selection. This increased purifying selection reduced inbreeding depression, but outbred female fitness did not improve, possibly because any benefits were offset by increased sexual antagonism. The majority of single nucleotide polymorphisms (SNPs) that consistently diverged in response to selection were initially rare and overrepresented in exons, and enriched in regions under balancing or relaxed selection, suggesting they are likely moderately deleterious variants. These diverged SNPs were scattered across the genome, further demonstrating that selection for or against the weapon and the associated changes to the mating system can both capture and influence genome-wide variation.

Population changes in a whale breeding ground revealed by citizen science noninvasive genetics unique microsatellite profiles of southern right whales

Historical exploitation, and a combination of current anthropogenic impacts, such as climate change and habitat degradation, impact the population dynamics of marine mammalian megafauna. Right whales (Eubalaena spp.) are large cetaceans recovering from hunting, whose reproductive and population growth rate appear to be impacted by climate change. We apply noninvasive genetic methods to monitor southern right whale (E. australis, SRW) and test the application of noninvasive genetics to minimise the observer effects on the population. Our aim is to describe population structure, and interdecadal and interannual changes to assess species status in the Great Acceleration period of Anthropocene. As a basis for population genetic analyses, we collected samples from sloughed skin during post-migration epidermal moult. Considering the exploration-exploitation dilemma, we collaborated with whale-watching companies, as part of a citizen science approach and to reduce ad hoc logistic operations and biopsy equipment. We used mitochondrial and microsatellite data and population genetic tools. We report for the first time the genetic composition and differentiation of the Namibian portion of the range. Population genetic parameters suggest that South Africa hosts the largest population. This corresponds with higher estimates of current gene flow from Africa compared to older samples. We have observed considerable interannual variation in population density at the breeding ground and an interdecadal shift in genetic variability, evidenced by an increase in the point estimate inbreeding. Clustering analyses confirmed differentiation between the Atlantic and Indo-Pacific, presumably originating during the ice ages. We show that population monitoring of large whales, essential for their conservation management, is feasible using noninvasive sampling within non-scientific platforms. Observed patterns are concurrent to changes of movement ecology and decline in reproductive success of the South African population, probably reflecting a large-scale restructuring of pelagic marine food webs.

Population genetics and biogeography of the lungwort lichen in North America support distinct Eastern and Western gene pools

Populations of species with large spatial distributions are shaped by complex forces that differ throughout their ranges. To maintain the genetic diversity of species, genepool-based subsets of widespread species must be considered in conservation assessments. In this study, the population genetics of the lichenized fungus Lobaria pulmonaria and its algal partner, Symbiochloris reticulata , were investigated to determine population structure, genetic diversity, and degree of congruency in eastern and western North America. Data loggers measuring temperature and humidity were deployed at selected populations in eastern North America to test for climatic adaptation. To better understand the role Pleistocene glaciations played in shaping population patterns, a North American, range-wide species distribution model was constructed and hindcast to 22,000 years before present and at 500-year time slices from then to the present. The presence of two gene pools with minimal admixture was supported, one in the Pacific Northwest and one in eastern North America. Western populations were significantly more genetically diverse than eastern populations. There was no evidence for climatic adaptation among eastern populations, though there was evidence for range-wide adaptation to evapotranspiration rates. Hindcast distribution models suggest that observed genetic diversity may be due to a drastic Pleistocene range restriction in eastern North America, whereas a substantial coastal refugial area is inferred in the west. Taken together the results show different, complex population histories of L. pulmonaria in eastern and western North America, and suggest that conservation planning for each gene pool should be considered separately.

Genetic diversity and lifespan of transplanted colonies

Selection may favour traits throughout an individuals lifetime or at a particular life stage. In many species of social insects, established colonies that are more genetically diverse outperform less diverse colonies with respect to a variety of traits that contribute to fitness, but whether selection favours high diversity in small colonies is unknown. We tested the hypothesis that selection favours genetically diverse colonies during the juvenile period using a multi-year field experiment with the harvester ant, Pogonomyrmex occidentalis. We used controlled matings to generate colonies that varied in genetic diversity and transplanted them into the field. We monitored their survival for seven (the 2015 cohort, N = 149) and six (the 2016 cohort, N = 157) years. Genetically more diverse colonies had greater survival, resulting in significant viability selection. However, in both cohorts survival was not influenced by genetic diversity until colonies were three years old. We suggest that changes in their internal organization enabled colonies to use the benefits of multiple genotypes, and discuss possible mechanisms that can generate this pattern. The accompanying data give the number of patrilines, the date of transplant and the number of years that the colony survived.