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opencc-zeroJul 2021View details →

Weak spatial-genetic structure in a native invasive, the southern pine beetle (Dendroctonus frontalis), across the eastern United States

The southern pine beetle, Dendroctonus frontalis, is a native pest of pine trees that has recently expanded its range into the northeastern United States. Understanding its colonization, dispersal, and connectivity will be critical for mitigating negative economic and ecological impacts in the newly invaded areas. Characterization of spatial-genetic structure can contribute to this; however, previous studies have reached different conclusions about regional population genetic structure, with one study reporting a weak east-west pattern, and the most recent reporting absence of structure. Here we systematically assessed several explanations for the absence of spatial-genetic structure. To do this, we developed nine new microsatellite markers and combined them with an existing 24-locus data matrix for the same individuals. We then reanalyzed this full dataset alongside datasets in which certain loci were omitted with the goal of creating more favorable signal to noise ratios. We also partitioned the data based on the sex of D. frontalis individuals, and then employed a broad suite of genotypic clustering and isolation-by-distance (IBD) analyses. We found that neither inadequate information content in the molecular marker set, nor unfavorable signal-to-noise ratio, nor insensitivity of the analytical approaches could explain the absence of structure. Regardless of dataset composition, there was little evidence for clusters (i.e., distinct geo-genetic groups) or clines (i.e., gradients of increasing allele frequency differences over larger geographic distances), with one exception: significant IBD was repeatedly detected using an individual-based measure of relatedness whenever datasets included males (but not for female-only datasets). This is strongly indicative of broad-scale female-biased dispersal, which has not previously been reported for D. frontalis, in part owing to logistical limitations of direct approaches (e.g., capture-mark-recapture). Weak spatial-genetic structure suggests long-distance connectivity and that gene flow is high, but additional research is needed to understand range expansion dynamics in this species using alternate approaches.

opencc-by-4.0Jul 2021View details →

Reproduction Package for A Partial Reproduction of A Guided Genetic Algorithm for Crash Reproduction

A reproduction package for "A Partial Reproduction of A Guided Genetic Algorithm for Crash Reproduction" Includes datasets and source code for reproducing our results

opencc-zeroJul 2021View details →

Phenotypic architecture of sociality and its associated genetic polymorphisms in zebrafish

Sociality is often seen as a single phenotypic trait, but it relies on motivational and cognitive components implemented by specific causal mechanisms. Hence, these components may have evolved independently, or may have been linked by phenotypic correlations driven by a shared selective pressure for increased social competence. Furthermore, these components may be domain-specific or of general domain across social and non-social contexts. Here we have characterized the phenotypic architecture of sociality in zebrafish, which has been increasingly used as a model organism in social neuroscience. For this purpose, we have behaviorally phenotyped zebrafish from different wild type lines in four tests: social tendency, social and non-social recognition, and open-field test. Our results indicate that: (1) sociality has two main components that are independent from each other (social tendency and social recognition), hence not supporting the occurrence of a sociality syndrome; (2) both social traits are phenotypically linked to non-social traits (non-social exploration and non-social memory, respectively), forming two general behavioral modules, general inspection and general recognition, and suggesting that sociality traits have been co-opted from general-domain motivational and cognitive traits. Moreover, the study of the association between genetic polymorphisms (i.e. single nucleotide polymorphisms, SNPs) and each behavioral module further supports this view, since several SNPs from a list of candidate "social" genes, are statistically associated with the general inspection (motivational), but not with a general recognition (cognitive), behavioral module. The SNPs associated with general inspection are widespread across different chromosomes and include neurotransmitters, neuromodulators, and synaptic plasticity genes, suggesting that this behavioral module is regulated by multiple genes, each of them with small effects. Together, these results support the occurrence of general domain motivational and cognitive behavioral modules in zebrafish, which have been co-opted for the social domain.

opencc-by-4.0Aug 2021View details →

RNA-seq data and results from in-vitro experiments for "Genetic control of fetal placental genomics contributes to development of health and disease" (Bhattacharya et al 2021)

This dataset includes data and results from RNA-seq data collected from in-vitro experiments presented in "Genetic control of fetal placental genomics contributes to development of health and disease" (Bhattacharya et al 2021). Please check the README.txt file for more details.

Evidence for genetic isolation and local adaptation in the field cricket Gryllus campestris

Understanding how species can thrive in a range of environments is a central challenge for evolutionary ecology. There is strong evidence for local adaptation along large-scale ecological clines in insects. However, potential adaptation among neighbouring populations differing in their environment has been studied much less. We used RAD-sequencing to quantify genetic divergence and clustering of ten populations of the field cricket Gryllus campestris in the Cantabrian Mountains of northern Spain, and an outgroup on the coastal plain. Our populations were chosen to represent replicate high and low altitude habitats. We identified genetic clusters that include both high and low altitude populations indicating that the two habitat types do not hold ancestrally distinct lineages. Using common-garden rearing experiments to remove environmental effects, we found evidence for differences between high and low altitude populations in physiological and life-history traits. As predicted by the local adaptation hypothesis, crickets with parents from cooler (high altitude) populations recovered from periods of extreme cooling more rapidly than those with parents from warmer (low altitude) populations. Growth rates also differed between offspring from high and low altitude populations. However, contrary to our prediction that crickets from high altitudes would grow faster, the most striking difference was that at high temperatures, growth was fastest in individuals from low altitudes. Our findings reveal that populations a few tens of kilometres apart have independently evolved adaptations to their environment. This suggests that local adaptation in a range of traits may be commonplace even in mobile invertebrates at scales of a small fraction of species' distributions.

Temporally-balanced selection during development of larval Pacific oysters (Crassostrea gigas) inherently preserves genetic diversity within offspring

Balancing selection is one of the mechanisms which has been proposed to explain the maintenance of genetic diversity in species across generations. For species with large populations and complex life histories, however, heterogeneous selection pressures may create a scenario in which the net effects of selection are balanced across developmental stages. With replicated cultures and a pooled sequencing approach, we show that genotype-dependent mortality in larvae of the Pacific oyster (Crassostrea gigas) is largely temporally dynamic and inconsistently in favor of a single genotype or allelic variant at each locus. Overall, the patterns of genetic change we observe to be taking place are more complex than what would be expected under classical examples of additive or dominant genetic interactions. They are also not easily explained by our current understanding of the effects of genetic load. Collectively, temporally heterogeneous selection pressures across different larval developmental stages may act to maintain genetic diversity in oysters, while also inherently sheltering genetic load within populations.

opencc-by-4.0Dec 2020View details →

Genetic variation influencing DNA methylation provides new insights into the molecular pathways regulating genomic function - Selected Supplementary Tables

Selected Supplementary Tables - ST5, 7, 8 and 9 Supplementary Table 5. Cosmopolitan results. Cosmopolitan SNP-CpG associations identified through genome-wide association amongst Europeans and South Asians. Supplementary Table 7. Cross-tissue replication. Results for further testing of the 11,165,559 cosmopolitan SNP-CpG associations identified (by genome-wide association in blood), in 4 isolated white cell subsets (CD4+ lymphocytes, CD8+ lymphocytes, monocytes and neutrophils), in adipocytes isolated from subcutaneous adipose tissue or visceral adipose tissue, and in whole adipose tissue. Supplementary Table 8. Conditional analysis. Results of conditional analysis to identify SNPs independently associated with each of the ~360K CpG sites tested.  Supplementary Table 9. Sentinel SNPs and CpGs. Results of R2 pruning and locus merging to identify discrete genetic and methylation loci that are associated, and their respective sentinel SNPs and sentinel CpG sites.  Other files (e.g. annotation files and 'intermediate' processing files) referenced in our code are also provided.

Genetic variation for upper thermal tolerance diminishes within and between populations with increasing acclimation temperature in Atlantic salmon

Populations may counteract lasting temperature changes or recurrent extremes through plasticity or adaptation. However, it remains underexplored how outbreeding, either naturally, unintentionally, or facilitated, may modify a local response potential and whether genotype-by-environment interactions or between-trait correlations can restrict this potential. We quantified population differences and outbreeding effects, within-population genetic variation, and plasticity of these, for thermal performance proxy traits using 32 pedigreed wild, domesticated, and wild-domesticated Atlantic salmon families reared under common-garden conditions. Following exposure to ambient cold (11.6°C) or ~4- and ~8-degree warmer summer temperatures, populations differed notably for body length and critical thermal maximum (CTmax) and for thermal plasticity of length, condition, and CTmax, but not for haematocrit. Line-cross analysis suggested mostly additive and some dominant outbreeding effects on means and solely additive outbreeding effects on plasticity. Heritability was detected for all traits. However, with increasing acclimation temperature, differences in CTmax between populations and CTmax heritability diminished, and CTmax breeding values re-ranked. Furthermore, CTmax and body size were negatively correlated at the genetic and phenotypic levels, and there was indirect evidence for a positive correlation between growth potential and thermal performance breadth for growth. Thus, population differences (including those between wild and domesticated populations) in thermal performance and plasticity may present a genetic resource in addition to the within-population genetic variance to facilitate, or impede, thermal adaptation. However, unfavourable genotype-by-environment interactions and negative between-trait correlations may generally hamper joint evolution in response to increase in average temperature and temporary extremes.

Sea ice reduction drives genetic differentiation among Barents Sea polar bears

Loss of Arctic sea ice due to climate change is predicted to reduce both genetic diversity and gene flow in ice-dependent species, with potential negative consequences for their long-term viability. Here, we tested for the population-genetic impacts of reduced sea ice cover on the polar bear (Ursus maritimus) sampled across two decades (1995–2016) from the Svalbard Archipelago, Norway, an area that is affected by rapid sea ice loss in the Arctic Barents Sea. We analysed genetic variation at 22 microsatellite loci for 626 polar bears from four sampling areas within the archipelago. Our results revealed a 3-10% loss of genetic diversity across the study period, accompanied by a near 200% in genetic differentiation across regions. These effects may best be explained by a decrease in gene flow caused by habitat fragmentation due to loss of sea ice coverage, resulting in increased inbreeding of local polar bears within the focal sampling areas in the Svalbard Archipelago. This study illustrates the importance of genetic monitoring for developing adaptive management strategies for polar bears and other ice-dependent species.

opencc-by-4.0Aug 2016View details →

Fig. 1 in New record of Rhinolophus chiewkweeae (Chiroptera: Rhinolophidae) from the east coast of Peninsular Malaysia with new information on their echolocation calls, genetics and their taxonomy

Fig. 1. Latero-ventral view of Rhinolophus chiewkweeae, from Sungai Buweh, Lawit

opencc-by-4.0Feb 2013View details →

Fig. 6 in Genetically Determined Colour Polymorphism In Larvae Of Ceriagrion Chaoi (Insecta: Odonata: Coenagrionidae)

Fig. 6. Ceriagrion chaoi male emerged from dark larva.

opencc-by-4.0Feb 2013View details →

Fig. 5 in Genetically Determined Colour Polymorphism In Larvae Of Ceriagrion Chaoi (Insecta: Odonata: Coenagrionidae)

Fig. 5. Female Ceriagrion chaoi emerging from brown larva.

opencc-by-4.0Feb 2013View details →

Fig. 1 in Genetically Determined Colour Polymorphism In Larvae Of Ceriagrion Chaoi (Insecta: Odonata: Coenagrionidae)

Fig. 1. Exuviae of brown (left) and dark (right) colour larvae of Ceriagrion chaoi.

opencc-by-4.0Aug 2012View details →

Fig. 1 in Low Genetic Variability In The Recovering Urban Banded Leaf Monkey Population Of Singapore

Fig. 1. Distribution of Presbytis femoralis.

opencc-by-4.0Jan 2000View details →

Fig. 35 in Hybridization Among Western Whiptail Lizards (Cnemidophorus Tigris) In Southwestern New Mexico: Population Genetics, Morphology, And Ecology In Three Contact Zones

Fig. 35. Ventral views of the same lizards arranged in the same sequence as in figure 34.

opencc-by-4.0Jan 2000View details →

Fig. 3. The contact region. Numbers designate collecting sites. Compare with figure 49 in Hybridization Among Western Whiptail Lizards (Cnemidophorus Tigris) In Southwestern New Mexico: Population Genetics, Morphology, And Ecology In Three Contact Zones

Fig. 3. The contact region. Numbers designate collecting sites. Compare with figure 49.

Genome-wide SNP analysis elucidates the evolution of Prunus takesimensis in Ulleung Island: Genetic consequences of anagenetic speciation

Of two major speciation modes of endemic plants on oceanic islands, cladogenesis and anagenesis, the latter has been recently emphasized as an effective mechanism for increasing plant diversity in isolated, ecologically homogeneous insular setting. As a single flowering cherry occurring on Ulleung Island in East Sea, Prunus takesimensis Nakai has been presumed as derived through anagenetic speciation on the Island. Based on morphological similarities, P. sargentii distributed in adjacent continental areas and islands has been suggested as its purported continental progenitor. However, the overall genetic complexity and resultant non-monophylies of closely related flowering cherries have hindered determining their phylogenetic relationships as well as establishing concrete continental progenitor and insular derivative relationship. Based on extensive sampling of wild flowering cherries including P. takesimensis and P. sargentii from Ulleung Island and its adjacent areas, this study inferred the origin and evolution of P. takesimensis using multiple different molecular markers. As the result of phylogeny and population genetic structure analyses based on SNPs detected by MIG-Seq and complementary cpDNA haplotypes, we could provide the extensive and convincing evidence for (1) the monophyly of P. takesimensis, (2) clear genetic differentiation between P. takesimensis (insular derivative) and P. sargentii (continental progenitor), (3) the geographic origin of P. takesimensis via single introduction from source population of P. sargentii in Korean Peninsula, (4) no significant genetic reduction in anagenetically derived insular species P. takesimsnsis compared to continental progenitor P. sargentii, (5) no strong population genetic structuring or geographical patters in the insular derived species, and (6) Mig-seq method as an effective tool to unravel complex evolutionary history of plant groups.

opencc-by-4.0Dec 2016View details →

Figure 4 in Population genetic structure and demographic history of the Chinese endemic Mongoloniscus sinensis (Dollfus, 1901) (Isopoda: Oniscidea)

Figure 4. Pairwise mismatch distributions for six derived clades.

opencc-by-4.0Dec 2021View details →

Figure 1 in Genetic diversity, population structure and demographic history of Dugesia japonica in Taihang Mountains

Figure 1. Geographical distribution of Dugesia japonica populations sampled in Taihang Mountains.

pgHMA: Application of the Heteroduplex mobility assay analysis in phylogenetics and population genetics

The Heteroduplex mobility assay (HMA) has proven to be a robust tool for the detection of genetic variation. Here, we describe a simple and rapid application of the HMA by microfluidic capillary electrophoresis, for phylogenetics and population genetic analyses (pgHMA). We show how commonly applied techniques in phylogenetics and population genetics have equivalents with pgHMA: phylogenetic reconstruction with bootstrapping, skyline plots, and mismatch distribution analysis. We assess the performance and accuracy of pgHMA by comparing the results obtained against those obtained using standard methods of analyses applied to sequencing data. The resulting comparisons demonstrate that: (1) there is a significant linear relationship (R = 0.992) between heteroduplex mobility and genetic distance; (2) phylogenetic trees obtained by HMA and nucleotide sequences present nearly identical topologies; (3) clades with high pgHMA parametric bootstrap support also have high bootstrap support on nucleotide phylogenies; (4) skyline plots estimated from the UPGMA trees of HMA and Bayesian trees of nucleotide data reveal similar trends, especially for the median trend estimate of effective population size; and (5) optimized mismatch distributions of HMA are closely fitted to the mismatch distributions of nucleotide sequences. In summary, pgHMA is an easily-applied method for approximating phylogenetic diversity and population trends.