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opencc-zeroAug 2020View details →

Reconciling seascape genetics and fisheries science in three co-distributed flatfishes

Uncertainty hampers innovative mixed-fisheries management by the scales at which connectivity dynamics are relevant to management objectives. The spatial scale of sustainable stock management is species-specific and depends on ecology, life history and population connectivity. One valuable approach to understand these spatial scales is to determine to what extent population genetic structure correlates with the oceanographic environment. Here we compare the level of genetic connectivity in three co-distributed and commercially exploited demersal flatfish species living in the North East Atlantic Ocean. Population genetic structure was analysed based on 14, 14 and 10 neutral DNA microsatellite markers for turbot, brill and sole respectively. We then used redundancy analysis (RDA) to attribute the genetic variation to spatial (geographic location), temporal (sampling year) and oceanographic (water column characteristics) components.

opencc-zeroAug 2020View details →

Comparative population genetics of the federally endangered Relict Darter, and its sister taxon the Clarks Darter (Teleostei: Percidae)

The southeastern United States harbors one of the most diverse temperate freshwater fish faunas of the world. Unfortunately, due to improper land use practices and habitat degradation, many of the species in this region are imperiled and may become extinct without appropriate conservation efforts. This study examined the population dynamics of an endangered endemic darter of southwest Kentucky, the Relict Darter (Etheostoma chienense) and its sister taxon, the undescribed Clarks Darter (Etheostoma cf. oophylax). Mitochondrial sequence data coupled with SNP data were used to infer population structure, gene flow, genetic variation, and effective population sizes of both species. The results from this study, based on 160 individuals from nine localities, indicate that the endangered Relict Darter possesses limited genetic variation based on mitochondrial DNA haplotypes (N=4). In addition, SNP data (6.8k markers) further indicates limited genetic structure (K=1), as well as a low effective population size (143-918), suggesting that the Relict Darter can be managed as a single, panmictic conservation unit. It is suggested that conservation efforts be taken to protect remaining habitats, augment the system with artificial spawning substrates, and, as a last resort (if needed), supplement the natural population with captive reared individuals. Ethesotoma cf. oophylax showed some genetic variation among distant sites, but more samples are needed throughout the range in order to fully understand the population dynamics of this species.

opencc-zeroAug 2020View details →

Data from: Riverscape genetics in brook lamprey: genetic diversity is less influenced by river fragmentation than by gene flow with the anadromous ecotype

Understanding the effect of human induced landscape fragmentation on gene flow and evolutionary potential of wild populations has become a major concern. Here, we investigated the effect of riverscape fragmentation on patterns of genetic diversity in the freshwater resident European brook lamprey (Lampetra planeri) that has a low ability to pass obstacles to migration. We also tested the hypotheses of i) asymmetric gene flow following water current and ii) a positive effect of admixture with the closely related anadromous river lamprey (L. fluviatilis) ecotype on L. planeri genetic diversity. We genotyped 2472 individuals, including 225 L. fluviatilis, sampled from 81 sites upstream and downstream barriers to migration, in 29 western European rivers. Linear modelling revealed a strong positive relationship between genetic diversity and the distance from the river source, consistent with expected patterns of decreased gene flow into upstream populations. However, the presence of anthropogenic barriers had a moderate effect on spatial genetic structure. Accordingly, we found evidence for downstream-directed gene flow, supporting the hypothesis that barriers do not limit dispersal mediated by water flow. Downstream L. planeri populations in sympatry with L. fluviatilis displayed consistently higher genetic diversity. We conclude that genetic drift and slight downstream gene flow drive the genetic make-up of upstream L. planeri populations whereas admixture between ecotypes maintains higher levels of genetic diversity in L. planeri populations sympatric with L. fluviatilis. We discuss the implications of these results for the design of conservation strategies of lamprey, and other freshwater organisms with several ecotypes, in fragmented dendritic river networks.

opencc-zeroAug 2021View details →

Data from: Topography, more than land cover, explains genetic diversity in a Neotropical savanna treefrog

Aim: Effective conservation policies rely on information about population genetic structure and the connectivity of remnants of suitable habitat. The interaction between natural and anthropogenic discontinuities across landscapes can uncover the relative contributions of different barriers to gene flow, with direct consequences for decision-making in conservation. Therefore, we aimed to quantify the relative roles of land cover and topographic variables on the population genetic differentiation and diversity of a stream-breeding savanna treefrog (Bokermannohyla ibitiguara) across its range. Location: Serra da Canastra mountain range, Cerrado of Minas Gerais State, Brazil. Methods: We collected and extracted DNA samples from 12 populations within and outside a strictly protected park, and used 17 microsatellite markers to assess genetic structure, among-population differentiation, and within-population diversity measures. We incorporated landscape data derived from digital models and satellite images to create connectivity matrices to correlate with genetic differentiation using Mantel tests. We used generalized linear models and path analyses to assess the roles of each landscape variable in shaping genetic diversity in this species. Results: Populations within and outside the park boundaries belonged to four genetic clusters. Most populations showed evidence of limited gene flow, with significant genetic differentiation, except for those within the park, which also had higher levels of allelic richness and heterozygosity. However, genetic differentiation among populations in this landscape was primarily explained by topographic complexity. Likewise, within-population genetic measures were best explained by models including elevation and topographic complexity, and not the amount of natural habitat or gallery forests. Main conclusions: Our results underscore that topography may be a strong historical factor shaping genetic structure among amphibian populations. Therefore, effective conservation strategies for endangered amphibians should avoid focusing exclusively on habitat suitability, and incorporate topographic complexity, which seems to be a key factor for the fauna of the extremely threatened Brazilian savanna.

Genetic analysis of Bromus tectorum in the eastern and western Mediterranean regions

Genetic diversity within and among 42 native populations of Bromus tectorum (cheatgrass) was characterized within two regions, the eastern Mediterranean and the western Mediterranean. Two hypotheses were tested for the genetic diversity of these populations: 1) populations from the eastern Mediterranean are more genetically diverse compared with populations to the west, a potential consequence of the species' westward dispersal with the spread of agriculture and 2) populations across the Mediterranean contain comparable genetic diversity but display high genetic differentiation, a potential consequence of both regions having served as refugia during glacial advances in the late Quaternary Period. Populations in the eastern Mediterranean possess 16 polymorphic loci and 37 multilocus genotypes. In contrast, populations from the western Mediterranean include a subset of these polymorphic loci (9) and fewer multilocus genotypes (19), consistent with the dispersal of B. tectorum with the east-west Holocene spread of agriculture. Among the 19 multilocus genotypes identified in populations from the western Mediterranean, 13 are undetected among eastern Mediterranean populations. Average genetic diversity within populations from the eastern Mediterranean is nonetheless comparable to the genetic diversity in populations from the Iberian Peninsula, whereas diversity is lowest in the populations from southern France. Our results suggest a prominent role for agriculture in the grass's western spread, although glacial history and environmental heterogeneity also could have influenced the grass's genetic diversity. The exceptionally high level of self-pollination (> 99%) in B. tectorum has contributed to preserving the genetic signature associated with the species' biogeographical history across the Mediterranean Region.

Contact zone of two different chloroplast lineages and genetic guidelines for seed transfer in Quercus serrata and Q. crispula

Within their natural distribution ranges, plant species exhibit genetic structure which has been created by global climate change and natural selection over long periods. To conserve local forests with different genetic structures, genetic guidelines for seed and seedling transfer in individual species are therefore necessary. Genetic guidelines have been published for 43 Japanese tree species using population genetic data; however, for practical use, more detailed genetic borders between important genetic lineages should be clarified to inform seed collection and planting. Thus, we investigated in detail the genetic borders between two important Japanese oak species, Quercus serrata and Q. crispula, in the Chubu region of Japan using chloroplast and nuclear DNA markers, and we discuss the factors that influenced border creation using the results of species distribution modelling (SDM). Two distinct cpDNA haplotypes were found for each species (northern and southern haplotype) within the Chubu region of Japan but the difference in nuclear DNA between northern and southern haplotype populations was very small both in Q. serrata and Q. crispula. The results of SDM showed that during the LGM Q. serrata was distributed mostly along the coastline but Q. crispula was distributed not only along the coast but also in mountainous areas further inland. The cpDNA genetic borders of these two oak species are complex and seem to have been influenced by topography and their distribution during the LGM. We propose and discuss genetic guidelines for these two oak species based on the results of this study.

The Influence of Environmental Variation on the Genetic Structure of a Poison Frog Distributed Across Continuous Amazonian Rainforest

Biogeographic barriers such as rivers have been shown to shape spatial patterns of biodiversity in the Amazon basin, yet relatively little is known about the distribution of genetic variation across continuous rainforest. Here, we characterize the genetic structure of the brilliant-thighed poison frog (Allobates femoralis) across an 880-km-long transect along the Purus-Madeira interfluve south of the Amazon river, based on 64 individuals genotyped at 7609 single-nucleotide polymorphism loci. A population tree and clustering analyses revealed 4 distinct genetic groups, one of which was strongly divergent. These genetic groups were concomitant with femoral spot coloration differences, which was intermediate within a zone of admixture between two of the groups. The location of these genetic groups did not consistently correspond to current ecological transitions between major forest types. A multimodel approach to quantify the relative influence of isolation-by-geographic distance (IBD) and isolation-by-environmental resistance (IBR) nevertheless revealed that, in addition to a strong signal of IBD, spatial genetic differentiation was explained by IBR primarily linked to dry season intensity (r2 = 8.4%) and canopy cover (r2 = 6.4%). We show significant phylogenetic divergence in the absence of obvious biogeographical barriers and that finer-scaled measures of genetic structure show patterns that are associated with environmental variables also known to predict the density of A. femoralis.

Symbiotic efficiency and genetic characterization of bacteria associated with cowpea genotypes grown in semiarid tropics of Kenya

Cowpea (Vigna unguiculata (L.) Walp) is an important multipurpose legume crop grown in arid semiarid areas of sub-Saharan Africa. The crop associates with a wide diversity of high ecological value rhizobia bacteria, improving biological soil fertility and crop production. Here, we evaluated the symbiotic efficiency (SE) and genetic diversity of native rhizobia isolated from root nodules of cowpea genotypes cultivated in semiarid areas of Kenya. Rhizobia trapping and SE experiments were done in the greenhouse while genetic diversity was evaluated based on 16S rRNA gene sequencing. Ninety four bacterial nodule isolates were purified from root nodules and placed into 20 groups based on morphological characteristics. SE of the native isolates varied (p<0.0001) significantly. Remarkably, two isolates, M2 and M3 recorded higher SE of 82.49 % and 72.76 % respectively compared to the commercial strain Bradyrhizobia sp. USDA 3456 (67.68 %). The isolates closely resembled bacteria belonging to the genus Rhizobium and non-rhizobial endophytes Enterobacter, Strenotrophomonas, Pseudomonas, and Paraburkholderia. For the first time, we report the presence of an efficient native nodule isolate Paraburkholderia phenoliruptrix BR3459a in Kenya. Our results form an important step towards the development of efficient microbial inocula which are pertinent for sustainable food production in African agriecosystems.

Unique genetic signatures of local adaptation over space and time for diapause, an ecologically relevant complex trait, in Drosophila melanogaster

Organisms living in seasonally variable environments utilize cues such as light and temperature to induce plastic responses, enabling them to exploit favorable seasons and avoid unfavorable ones. Local adapation can result in variation in seasonal responses, but the genetic basis and evolutionary history of this variation remains elusive. Many insects, including Drosophila melanogaster, are able to undergo an arrest of reproductive development (diapause) in response to unfavorable conditions. In D. melanogaster, the ability to diapause is more common in high latitude populations, where flies endure harsher winters, and in the spring, reflecting differential survivorship of overwintering populations. Using a novel hybrid swarm-based genome wide association study, we examined the genetic basis and evolutionary history of ovarian diapause. We exposed outbred females to different temperatures and day lengths, characterized ovarian development for over 2800 flies, and reconstructed their full phased genomes. We found that diapause scored at two different developmental cutoffs has modest heritability, and we identified hundreds of SNPs associated with each of the two phenotypes. Alleles associated with one of the diapause phenotypes tend to be more common at higher latitudes, but these alleles do not show predictable seasonal variation. The collective signal of many small-effect, clinally varying SNPs can plausibly explain latitudinal phenotypic variation seen in North America. SNPs associated with diapause do not exhibit signs of recent selective sweeps, but most are segregating at relatively high frequencies in Africa, suggesting that variation in diapause relies on ancestral polymorphisms. Finally, we utilized outdoor mesocosms to track diapause under natural conditions. We found that hybrid swarms reared outdoors evolved increased propensity for diapause in late fall, whereas indoor control populations experienced no such change. Our results indicate that diapause is a complex, quantitative trait with different evolutionary patterns across time and space.

Efficient weighting methods for genomic best linear unbiased prediction (BLUP) adaption to the genetic architectures of quantitative traits

<a name="_Hlk19877414"></a>Genomic best linear unbiased prediction (GBLUP) assumes equal variance for all marker effects, which is suitable for traits that conform to the infinitesimal model. For traits controlled by major genes, Bayesian methods with shrinkage priors or genome-wide association study (GWAS) methods can be used to identify <a name="_Hlk24974556">causal variants</a> effectively. The information from Bayesian/GWAS methods can be used to construct the weighted genomic relationship matrix (G). However, it remains unclear which methods perform best for traits varying in genetic architecture. Therefore, we developed several methods to <a name="_Hlk23592218">optimize</a> the performance of weighted GBLUP and compare them with other available methods using simulated and real datasets. First, two types of methods (marker effects with local-shrinkage or normal prior) were used to obtain test statistics and estimates for each marker effect. Second, three weighted G matrices were constructed based on the marker information from the first step: (1) the genomic-feature weighted G (GFWG), (2) the estimated marker-variance weighted G (EVWG), and (3) the absolute value of estimated marker-effect weighted G (AEWG). Following the above process, six different weighted GBLUP methods (local-shrinkage/normal prior GF/EV/AE-WGBLUP) were proposed for genomic prediction. Analyses with both simulated and real data demonstrated that these options offer flexibility for optimizing the weighted GBLUP for traits with a broad spectrum of genetic architectures. The advantage of weighting methods over GBLUP in terms of accuracy were trait dependent, ranging from 14.8% to marginal for simulated traits and from 44% to marginal for real traits. Local-shrinkage prior EVWGBLUP is superior for traits mainly controlled by loci of large effect. Normal prior AEWGBLUP performs well for traits mainly controlled by loci of moderate effect. For traits controlled by some loci with large effects (<a name="_Hlk49869847">explain 25%~50% genetic variance</a>) and a range of loci with small effects, GFWGBLUP has advantages. In conclusion, the optimal weighted GBLUP method for genomic selection should take both the genetic architecture and number of QTLs of traits into consideration carefully.

Whole genome sequence analysis of porcine astroviruses reveals novel genetically diverse genotypes circulating in East African smallholder pig farms

Supplementary materials for the porcine astrovirus study in East Africa. Table S1: Pairwise comparison of nucleotide sequence identities of the complete (near complete, U460) genomes of the seven (7) astrovirus field strains (bold) and with sequences of other astroviruses available in GenBank  Table S2. Summary of nucleotide sequence identity matrix of the capsid protein (ORF2) among the seven (7) astroviruses field strains (bold) and the known reference strains in the GenBank using Clustal Omega Table S3. Summary of amino acid sequence identity matrix of the capsid protein (ORF2) among the 7 astroviruses field strains (bold) and the known reference strains in the GenBank using Clustal Omega Table S4: Estimates of evolutionary divergence between the East African PoAstVs and selected known AstV in the GenBank based on the amino acid sequences of complete ORF2 protein. The number of amino acid differences per site from between sequences is shown. Standard error estimate(s) are shown above the diagonal for our strains. Table S5. Recommended potential linear antigenic epitopes predicted inside capsid protein (ORF2) of our field strains by SVMTriP web-based tool and corresponding antigenicity predicted by VaxiJen software

opencc-by-4.0Nov 2019View details →

Berbers and Arabs: tracing the genetic diversity and history of Southern Tunisia through genome wide analysis

SNP data of 79 individuals from 3 ethnolinguistic groups from Tunisia

Data from Koch et al. 2020 Evolution: Genetic variance in fitness and its cross-sex covariance predict adaptation during experimental evolution.

Abstract In presence of rapid environmental changes, it is of particular importance to assess the adaptive potential of populations, which is mostly determined by the additive genetic variation (VA) in fitness. In this study we used Tribolium castaneum (red flour beetles) to investigate its adaptive potential in three new environmental conditions (Dry, Hot, Hot-Dry). We tested for potential constraints that might limit adaptation, including negative genetic covariance between female and male fitness.  Based on VA estimates for fitness, we expected the highest relative fitness increase in the most stressful condition Hot-Dry and similar increases in single stress conditions Dry and Hot. High adaptive potential in females in Hot was reduced by a negative covariance with male fitness. We tested adaptation to the three conditions after 20 generations of experimental evolution and found that observed adaptation mainly matched our predictions. Given that body size is commonly used as a proxy for fitness, we also tested how this trait and its genetic variance (including non-additive genetic variance) were impacted by environmental stress. In both traits, variances were sex and condition dependent, but they differed in their variance composition, cross-sex and cross-environment genetic covariances, as well as in the environmental impact on VA.   Method Strain and environmental conditions We used the Tribolium castaneum Cro1 strain collected from a wild population in 2010 and adapted to lab standard conditions (33°C, 70% relative humidity) for more than 20 generations. Beetles were kept in 24h darkness on organic wheat flour mixed with 10% organic baker's yeast. We sterilized flour and yeast by heating them for 12h at 80°C before use. To test for adaptation to new environmental conditions we used replicate lines and exposed them to three treatments and Control conditions. The conditions in the treatments were: Dry: 33°C and 30% relative humidity; Hot: 37°C and 70% r. h.; Hot-Dry: 37°C and 30% r. h.   Crossing, fitness assay and measurement of body size In order to be able to estimate genetic variances, we applied a split-brood paternal half-sib breeding design.  We produced 147 half-sib families by mating virgin males to three virgin females. Half- as well as full-sib families were split across all conditions. Male and female offspring (four females and two males per full-sib family and condition) were separated at the pupal stage and transferred to 10 mL tubes with 1 g of medium and remained there until they were used for the fitness assay eight weeks later. To estimate fitness, we mated each virgin male with two unrelated virgin females from the same condition in 15mL tube with 1g medium. The male was removed after 24h and females transferred into two separate tubes. Females were removed from the tubes after one week of egg laying, and 9g medium was added to provide food for the developing offspring. After five weeks the number of adult offspring was counted. While we conducted the matings for the fitness assay, we followed a specific crossing design and always crossed two pairs of full-sib families. Individuals resulting from these crosses (the F2 genaration) were double first cousins. Body size was measured in the F2, i.e. in the offspring of beetles that were used for the fitness assay. To estimate body size, we used the centroid size of the abdominal segment IV as proxy for total size since it can be measured more accurately than dry weight in very small insects and shows a high correlation with body mass.   Experimental evolution We used ten replicate lines per condition originating from the same ancestral population (Cro1) and let them adapt for 20 generations. Each new generation was set up by randomly selecting 120 pupae and placing them into a new vial with 70g medium. One selection line in Dry became extinct. Adult beetles of generation 20 from all selection lines were transferred to control conditions, in which they stayed for one week to mate and lay eggs. After removal of the adults, we waited until their offspring had reached the pupal stage and separated males and females. These individuals (generation 21) developed completely in control conditions. When they had reached the adult stage, each virgin male was mated with a virgin female of the same selection line and their offspring was transferred to all four conditions in the egg stage, resulting in full-sib families split across all conditions . As soon as these offspring (generation 22) had reached the pupal stage, males and females were separated. To compare fitness of different selection lines and test for adaptation, a virgin male and a virgin female of the same selection line in the same condition, but from different families were mated and the number of adult offspring produced within four days of mating and egg laying was used as a fitness estimate.     Files This data publication contains the following files: Fitness_data.txt: Fitness data (offspring number) of the first generation in new environmental conditions. ANIMAL: ID of female individuals; male: ID of mating partner, father of the offspring; fitness: number of adult offspring per female produced within one week of egg laying; condition: condition under which the individuals grew up, mated, reproduced (CTL: control, D: dry, H: hot, HD: hot-dry, see Methods for details); MOTHER: mother of the female; Batch: samples where fitness assay was started on the same day   Size_data.txt: Centroid size of abdominal segment IV. ANIMAL: ID of measured individuals; condition: condition under which the individuals grew up (CT: control, D: dry, H: hot, HD: hot-dry, see Methods for details); sex: sex of individuals (f: female, m: male); AS: centroid size [Pixel] of abdominal segment IV; Mother: ID of their mother; batch: Batches represent individuals that grew up at the same time, and thus accounts for variations in the medium or lab temperature   Pedigree.txt: Pedigree of measured individuals. ANIMAL: individual ID ; MOTHER: mother ID; FATHER: father ID   Transplant_data.txt: Offspring number of different selection lines under different conditions after 20 generations of experimental evolution. Line: Selection-line ID; Selection: condition, in which the selection-line spent 20 generations (CT: Control; D: Dry; Hot; HD: Hot-Dry); Fam: each selection line consisted of several families; Treatment: condition, in which offspring number was measured; offspring: number of adult offspring that a female produced within four days of egg-laying

Approximation of a marine ecosystem model by artificial neural networks designed using a genetic algorithm

Data from the Paper: Approximation of a marine ecosystem model by artificial neural networks designed using a genetic algorithm. Abstract:  Marine ecosystem models are important to identify the  processes that affects for example the global carbon cycle. Computation of an annually periodic solution (i.e., a steady annual cycle) for these models requires a high computational effort. To reduce this effort, we approximated an exemplary marine ecosystem model by different artificial neural networks. We used a fully connected network, then applied the sparse evolutionary training  (SET) procedure, and finally applied a genetic algorithm (GA) to optimize both the   network topology. With all three approaches, a direct approximation of the  steady annual cycle  was not sufficiently accurate. However, using the mass-corrected prediction of the ANN as initial concentration for additional model runs, the results were in very good agreement.   In this way, we achieved a runtime reduction by about 15 \%. The result from the SET algorithm were comparable to those of the full network. Further application of the GA may lead to an even higher reduction. Content: Database sqlite <a href="https://zenodo.org/api/files/669d208b-7304-4d31-a6cc-3ad78e3544e9/ANN_Database.db">ANN_Database.db</a> zip-files with data:  <a href="https://zenodo.org/api/files/669d208b-7304-4d31-a6cc-3ad78e3544e9/ANN-Data.zip">ANN-Data.zip</a> structure and weights of used networks <a href="https://zenodo.org/api/files/669d208b-7304-4d31-a6cc-3ad78e3544e9/ANN-Results.zip">ANN-Results.zip</a> results obtained with networks <a href="https://zenodo.org/api/files/669d208b-7304-4d31-a6cc-3ad78e3544e9/Reference-Results.zip">Reference-Results.zip</a> reference results and training data

Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent Trichogramma evanescens - Data table and code for data analysis

We provide data and code needed to re-do the analyses and figures presented in our preprint Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent Trichogramma evanescens (DOI : 10.1101/2020.08.21.257881 ): - data table : data_repetition01.xls, with informations about each column in the file data_repetition_info.pdf - data table : data_individual01.xls, with informations about each column in the file data_indivdual_info.pdf - The R code used to do the analyses : Rscript-Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent Trichogramma evanescens.R

Data from: The impact of anthropogenic disturbances on the genetic diversity of terrestrial species: a global meta-analysis

Duplicate of 10.5061/dryad.6hdr7sqxq Human activities are primarily responsible for habitat loss and changes in natural environments around the world. It has been suggested that populations inhabiting human-modified landscapes experience reduced gene flow, inbreeding depression, and loss of alleles due to genetic drift. However, the empirical evidence shows contrasting effects of anthropogenic disturbances on the genetic diversity of species. We performed a meta-analysis of 61 studies that compared the genetic diversity of plant and/or animal populations in disturbed and more preserved areas (316 paired comparisons) to investigate the genetic responses to different disturbance types. There is a negative effect (effect size: -0.45; 95% CI: -0.61, -0.29) of disturbances on genetic diversity, in which the most detrimental effects are caused by the loss of connectivity and forest cover. The methodological approach can explain part of the heterogeneity among the genetic responses detected by primary studies: (i) studies using the number of effective alleles did not detect genetic erosion, while all other indices, revealed negative responses to disturbances; and (ii) only studies performed with transferred or a combination of transferred and specific microsatellites detected negative responses. The effects on animal populations are more detrimental than in plant populations. Only plant species with shrub life form, self-incompatible reproductive systems, and biotic pollination and seed dispersal, showed negative responses to disturbances. Despite all heterogeneity among studies, there is an overall negative effect of disturbances on the genetic diversity, which indicates that remaining populations inhabiting human-modified landscapes have reduced evolutionary potential and are prone to local extinction.

Parasite turnover zone at secondary contact: a new pattern in host-parasite population genetics

We introduce a new pattern of population genetic structure in a host-parasite system that can arise after secondary contact of previously isolated populations. Due to different generation time and therefore different tempo of molecular evolution the host and parasite populations reach different degrees of genetic differentiation during their separation (e.g. in refugia). Consequently, during the secondary contact the host populations are able to re-establish a single panmictic population across the area of contact, while the parasite populations stop their dispersal at the secondary contact zone and create a narrow hybrid zone. From the host's perspective, the parasite's hybrid zone functions on a microevolutionary scale as a "parasite turnover zone": while the hosts are passing from area A to area B, their parasites turn genetically from the area A genotypes to the area B genotypes. We demonstrate this novel pattern on a model composed of Apodemus mice and Polyplax lice by comparing maternally inherited markers (complete mitochondrial genomes, and complete genomes of vertically transmitted symbiont Legionella polyplacis) with SNPs derived from the louse genomic data. We discuss circumstances that may lead to this pattern and possible reasons why it has been overlooked in the studies on host parasite population genetics.

Clinical and genomic evaluation of 207 genetic myopathies in the Indian subcontinent

Objective Inherited myopathies comprise more than 200 different individually rare disease-subtypes but when combined together have a high prevalence of 1 in 6000 individuals across the world. Our goal was to determine for the first time the clinical- and gene-variant spectrum of genetic myopathies in a substantial cohort study of the Indian subcontinent. Methods In this cohort-study, we performed the first large clinical exome sequencing (ES) study with phenotype correlation on 207 clinically well-characterized inherited myopathy-suspected patients from the Indian subcontinent with diverse ethnicities. Results Clinical-correlation driven definitive molecular diagnosis was established in 49% (101 cases; 95% CI, 42%-56%) of patients with the major contributing pathogenicity in either of three genes, GNE (28%; GNE-myopathy), DYSF (25%; Dysferlinopathy) and CAPN3 (19%; Calpainopathy). We identified 65 variant alleles comprising 37 unique variants in these three major genes. 78% of the DYSF patients were homozygous for the detected pathogenic variant suggesting the need for carrier-testing for autosomal-recessive disorders like Dysferlinopathy that are common in India. We describe the observed clinical spectrum of myopathies including uncommon and rare subtypes in India: Sarcoglycanopathies (SGCA/B/D/G), Collagenopathy (COL6A1/2/3), Anoctaminopathy (ANO5), telethoninopathy (TCAP), Pompe-disease (GAA), Myoadenylate-deaminase-deficiency-myopathy (AMPD1), myotilinopathy (MYOT), laminopathy (LMNA), HSP40-proteinopathy (DNAJB6), Emery-Dreifuss-muscular-dystrophy (EMD), Filaminopathy (FLNC), TRIM32-proteinopathy (TRIM32), POMT1-proteinopathy (POMT1), and Merosin-deficiency-congenital-muscular-dystrophy-type-1 (LAMA2). 13 Patients harbored pathogenic variants in >1 gene and had unusual clinical features suggesting a possible role of synergistic-heterozygosity / digenic-contribution to disease presentation and progression. Conclusions Application of clinically-correlated ES to myopathy diagnosis has improved our understanding of the clinical and genetic spectrum of different subtypes and their overlaps in Indian patients. This, in turn, will enhance the global gene-variant-disease databases by including data from developing countries/continents for more efficient clinically-driven molecular diagnostics.

Data from: Genetic structure in Orkney island mice: isolation promotes morphological diversification

Following human occupation, the house mouse has colonized numerous islands, exposing the species to a wide variety of environments. Such a colonization process, involving successive founder events and bottlenecks, may either promote random evolution or facilitate adaptation, making the relative importance of adaptive and stochastic processes in insular evolution difficult to assess. Here, we jointly analyse genetic and morphometric variation in the house mice (Mus musculus domesticus) from the Orkney archipelago. Genetic analyses, based on mitochondrial DNA and microsatellites, revealed considerable genetic structure within the archipelago, suggestive of a high degree of isolation and long-lasting stability of the insular populations. Morphometric analyses, based on a quantification of the shape of the first upper molar, revealed considerable differentiation compared to Western European populations, and significant geographic structure in Orkney, largely congruent with the pattern of genetic divergence. Morphological diversification in Orkney followed a Brownian motion model of evolution, suggesting a primary role for random drift over adaptation to local environments. Substantial structuring of human populations in Orkney has recently been demonstrated, mirroring the situation found here in house mice. This synanthropic species may thus constitute a bio-proxy of human structure and practices even at a very local scale.

Data from: Navigating the southern seas with small fins: Genetic connectivity of seahorses (Hippocampus abdominalis) across the Tasman Sea

Aim Historical patterns of ocean circulation in the Southern Hemisphere have been well studied, but the effects of coastal oceanography on marine biogeography in this region remain poorly understood relative to northern latitudes. Our study investigates historical and contemporary patterns of migration and dispersal across the Tasman Sea. Location Coastal regions of the Tasman Sea including southeastern Australia, Tasmania and New Zealand. Taxon Hippocampus abdominalis, the pot-bellied seahorse, one of the most broadly distributed seahorse species, and the only seahorse to have successfully colonized New Zealand from Australia across 2,000 km of open ocean. Methods We used a multilocus genetic dataset to measure population diversity and differentiation from seahorses across the full species range to investigate contemporary and historical demography, and to reconstruct colonization routes across the Tasman Sea. Results Genetic data indicate that seahorses colonized New Zealand from Australia during the previous interglacial-glacial cycle (12,000-120,000 ybp), and have evolved in relative isolation since the initial establishment event. Contemporary effective population sizes in the newly colonized range are substantially larger than those inferred in Australia, and both appear to be reduced relative to ancestral levels. Australian seahorses are genetically diverse and show high levels of population connectivity, while the distribution of genetic variation in New Zealand suggests an initial colonization of the South Island following by northward migration. Importantly, despite clear evidence that New Zealand seahorses are descendent from Australian ancestors, patterns of contemporary genetic diversity are consistent with trans-Tasman migration from New Zealand to Australia, suggesting that genetic variation accumulated in the newly colonized range is contributing to the genetic diversity of Australian seahorses. Main conclusions Despite a largely independent evolutionary trajectory of seahorses separated by the Tasman Sea, haplotype sharing between populations in Australia and New Zealand suggests that secondary genetic exchange is contributing to the contemporary phylogeography of the species. Patterns of genetic structure in H. abdominalis mirror those found in other rafting species, suggesting that adult dispersal via rafting has been an important vector of marine dispersal in this species.