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opencc-zeroJun 2021View details →

Scripts in C for simulating the wave of gene advance under diverse systems of mating

This dataset includes 4 programs coded in C for simulating the wave of gene advance under diverse systems of mating. Program 1 was used for simulation under unifor density based on Equations (1) and (2) in the main text. Program 2 was used for simulation under uniform density based on Equations (5)-(11). Program 3 was used for Monte Carlo (MC) simulation under uniform density. Program 4 was used for MC simulation under logistic growth model. Variable and parameter symbols within these programs are self-explanatory. You may simulate different cases by changing parameter settings.

opencc-zeroDec 2017View details →

Data from: Standing genetic diversity and selection at functional gene loci are associated with differential invasion success in two non-native fish species

Invasive species are expected to experience a unique combination of high genetic drift due to demographic factors while also experiencing strong selective pressures. The paradigm that reduced genetic diversity should limit the evolutionary potential of invasive species and thus their potential for range expansion has received little empirical support, possibly due to the choice of genetic markers. Our goal was to test for effects of genetic drift and selection at functional genetic markers as they relate to the invasion success of two paired invasive goby species, one widespread (successful) and one with limited range expansion (less successful). We genotyped fish using two marker types: single nucleotide polymorphisms (SNPs) in known-function, protein-coding genes and microsatellites to contrast the effects of neutral genetic processes. We identified reduced allelic variation in the invaded range for the less-successful tubenose goby. SNPs putatively under selection were responsible for the observed differences in population structure between marker types for round goby (successful) but not tubenose goby (less successful). A higher proportion of functional loci experienced divergent selection for round goby, suggesting increased evolutionary potential in invaded ranges may be associated with round goby's greater invasion success. Genes involved in thermal tolerance were divergent for round goby populations but not tubenose goby, consistent with the hypothesis that invasion success for fish in temperate regions is influenced by capacity for thermal tolerance. Our results highlight the need to incorporate functional genetic markers in studies to better assess evolutionary potential for the improved conservation and management of species.

opencc-zeroOct 2019View details →

Urbanization impacts apex predator gene flow but not genetic diversity across an urban-rural divide

Apex predators are important indicators of intact natural ecosystems. They are also sensitive to urbanization because they require broad home ranges and extensive contiguous habitat to support their prey base. Pumas (Puma concolor) can persist near human developed areas, but urbanization may be detrimental to their movement ecology, population structure, and genetic diversity. To investigate potential effects of urbanization in population connectivity of pumas, we performed a landscape genomics study of 130 pumas on the rural Western Slope and more urbanized Front Range of Colorado, USA. Over 12,000 single nucleotide polymorphisms were genotyped using double-digest, restriction site-associated DNA sequencing (ddRADseq). We investigated patterns of gene flow and genetic diversity, and tested for correlations between key landscape variables and genetic distance to assess the effects of urbanization and other landscape factors on gene flow. Levels of genetic diversity were similar for the Western Slope and Front Range, but effective population sizes were smaller, genetic distances were higher, and there was more admixture in the more urbanized Front Range. Forest cover was strongly positively associated with puma gene flow on the Western Slope, while impervious surfaces restricted gene flow and more open, natural habitats enhanced gene flow on the Front Range. Landscape genomic analyses revealed differences in puma movement and gene flow patterns in rural versus urban settings. Our results highlight the utility of dense, genome-scale markers to document subtle impacts of urbanization on a wide-ranging carnivore living near a large urban center.

opencc-zeroJul 2021View details →

Genomic time-series data show that gene flow maintains high genetic diversity despite substantial genetic drift in a butterfly species

Effective population size affects the efficacy of selection, rate of evolution by drift, and neutral diversity levels. When species are subdivided into multiple populations connected by gene flow, evolutionary processes can depend on global or local effective population sizes. Theory predicts that high levels of diversity might be maintained by gene flow, even very low levels of gene flow, consistent with species long-term effective population size, but tests of this idea are mostly lacking. Here, we show that Lycaeides butterfly populations maintain low contemporary (variance) effective population sizes (e.g., ~200 individuals) and thus evolve rapidly by genetic drift. In contrast, populations harbored high levels of genetic diversity consistent with an effective population size several orders of magnitude larger. We hypothesized that the differences in the magnitude and variability of contemporary versus long-term effective population sizes were caused by gene flow of sufficient magnitude to maintain diversity but only subtly affect evolution on generational time scales. Consistent with this hypothesis, we detected low but non-trivial gene flow among populations. Furthermore, using short-term population-genomic time-series data, we documented patterns consistent with predictions from this hypothesis, including a weak but detectable excess of evolutionary change in the direction of the mean (migrant gene pool) allele frequencies across populations, and consistency in the direction of allele frequency change over time. The documented decoupling of diversity levels and short-term change by drift in Lycaeides has implications for our understanding of contemporary evolution and the maintenance of genetic variation in the wild.

opencc-zeroJul 2021View details →

Evidence for reduced immune gene diversity and activity during the evolution of termites

This dataset contains data from a termite immunity related study described in the paper: "He Shulin, Sieksmeyer Thorben, Che Yanli, Mora M. Alejandra Esparza, Stiblik Petr, Banasiak Ronald, Harrison Mark C., Šobotník Jan, Wang Zongqing, Johnston Paul R. and McMahon Dino P. 2021Evidence for reduced immune gene diversity and activity during the evolution of termitesProc. R. Soc. B.288:20203168.http://doi.org/10.1098/rspb.2020.3168". The study investigates the evolution of termite molecular immune system: evolution of immune gene family along a constructed phylogeny, different individual immune response between three termite castes, a subsocial cockroach and a non-social cockroach, the caste specific expression of immune genes, different social immune response between a social termite species and a non-social cockroach species. In the first experiment, we de novo sequenced 18 cockroach and termite species, spanning the full spectrum of solitary and social lifestyles, including two solitary cockroach species, two species of subsocial Cryptocercus wood-feeding cockroaches and 14 termite species. We exploited a transcriptomic approach to compare the immune gene repertoire of these sequenced species. In the second experiment, we compared individual immune responses in a solitary cockroach, B. orientalis, a subsocial wood-feeding roach, Cryptocercus meridianus, and each caste of a social termite, Neotermes castaneus, following direct injection with heat-killed microbes. In the third experiment, we explored total gene expression differences between castes without immune challenge. In the fourth experiment, we studied gene expression changes in each caste of N. castaneus following colony exposure to immune-challenged nestmates, and compared these with gene expression changes in the solitary cockroach, B. orientalis, following group exposure to immune-challenged conspecifics. Main results of the experiments are that (1) immune gene families show contractions and expansions during temite evolution; (2) compared with cockroaches, termites showed weak individual immune response; (3) termites have caste-specific constitutive immunity; (4) Compared with cockroach, termite showed a stronger gene expression changes in response to a social immune challenge.

opencc-zeroAug 2021View details →

Oxytenanthera abyssinica (A. Rich.) Munro; lowland bamboo (Poaceae, Bambusinea) in Ethiopia: Genetic diversity, population structure and gene flow analysis

As one of the most important non-timber forest resources, a potential alternative to wood and wood product and fastest-growing plant in the world (91 cm (35 in) per day), bamboo is a member of the grass family (Poaceae) and constitutes a single subfamily Bambusoideae. 67% of total area of bamboo in Africa and 7% of world total is contributed by Ethiopia giving more than 1.44 million hectares. Silica gel dried young fresh leaves from 130 individuals of O. abyssinica were collected for DNA extraction and PCR amplification. Each of the PCR amplified ISSR fragments using 19 ISSR primers were used to study band pattern and heterozigosity, level of polymorphism, calculating marker efficiency, Nei`s (H) and Shannon (I) genetic diversity, analysis of molecular variance (AMOVA), analysis for cluster, principal coordinates (PCoA) and admixture results. High genetic variation at species level was observed with the percentage of the polymorphic loci (PPL) = 84.48%. The H, I, observed number of alleles (Na) and effective number of alleles (Ne) at species level was 0.2702, 0.4061, 1.8448, and 1.4744, respectively, showing a relatively high level of genetic diversity. However, the genetic differentiation at the population level was relatively low. AMOVA using grouped populations revealed that, most of the diversity was distributed within the populations (61.05%) with FST = 0.38949, FSC = 0.10486 and FCT = 0.31797. Cluster analysis grouped the populations into sharply distinct clusters, which could be attributed to cross pollination nature of the plant and long lived to the area. STRUCTURE analyses for all population and excluding Gambella population gives different result K = 2 and K = 11. Using these markers, we find strong evidence linking geographic origin of diversity and samples from Gambella Region found different from others and might tell the availability of additional bamboo species in the country.

opennotspecifiedMar 2021View details →

Figure 1 in Mitogenomics of the endangered Mediterranean monk seal (Monachus monachus) reveals dramatic loss of diversity and supports historical gene-flow between Atlantic and eastern Mediterranean populations

Figure 1. Sampling sites (number of specimens per location in brackets) with the current Mediterranean monk seal distribution range in green.

opennotspecifiedMar 2021View details →

Figure 3 in Mitogenomics of the endangered Mediterranean monk seal (Monachus monachus) reveals dramatic loss of diversity and supports historical gene-flow between Atlantic and eastern Mediterranean populations

Figure 3. Mitochondrial genome clades sequenced in our study. A, female monk seal with its pup on Desertas Islands (Madeira); photo credit: Rosa Pires. B, Bayesian phylogeny using the complete mtDNA. Black dots indicate posterior probability values ≥ 0.95. (*) indicates historical specimens. The colours of the bars match the colours used on the network analyses and maps in Figure 2.

Figure 3 in An underground burst of diversity - a new look at the phylogeny and taxonomy of the genus Talpa Linnaeus, 1758 (Mammalia: Talpidae) as revealed by nuclear and mitochondrial genes

Figure 3. The Bayesian phylogeny of the genus Talpa as inferred from the complete cytb gene sequence. The designations are as in Figure 3. The outgroup (representatives of the genera Euroscaptor, Mogera, Parascaptor, Scaptochirus and tribes Desmanini, Scalopini and Condylurini) is not shown.

Figure 4 in An underground burst of diversity - a new look at the phylogeny and taxonomy of the genus Talpa Linnaeus, 1758 (Mammalia: Talpidae) as revealed by nuclear and mitochondrial genes

Figure 4. Species tree of Talpa produced by the *BEAST algorithm using the Bayesian multispecies coalescent approach. Values above the branches correspond to Bayesian posterior probabilities.

Figure 2 in An underground burst of diversity - a new look at the phylogeny and taxonomy of the genus Talpa Linnaeus, 1758 (Mammalia: Talpidae) as revealed by nuclear and mitochondrial genes

Figure 2. The Bayesian phylogeny of the genus Talpa as inferred from a concatenated alignment of four nuclear genes. Values above the branches correspond to Bayesian posterior probabilities (BPP) in MrBayes and bootstrap support (1000 pseudoreplicates) in ML and MP analyses, correspondingly. Representatives of the genera Euroscaptor, Mogera, Parascaptor, Scaptochirus and tribes Desmanini, Scalopini and Condylurini are used as outgroups.

Figure 1 in An underground burst of diversity - a new look at the phylogeny and taxonomy of the genus Talpa Linnaeus, 1758 (Mammalia: Talpidae) as revealed by nuclear and mitochondrial genes

Figure 1. Map of sampling localities for specimens of the genus Talpa used in this study. Localities 1–37 are listed in Table 1 (original material), localities 38–57 correspond to the sequences retrieved from GenBank and are listed in Supporting Information 1.

Figure 5 in An underground burst of diversity - a new look at the phylogeny and taxonomy of the genus Talpa Linnaeus, 1758 (Mammalia: Talpidae) as revealed by nuclear and mitochondrial genes

Figure 5. Timescale of major divergence events among Talpa based on nuclear concatenation (BEAST). The divergence times correspond to the mean posterior estimate of their age in Myr. The grey bars represent the 95% HPD interval. Numbers above the branches correspond to posterior probabilities for each node.

opencc-by-4.0Jun 2021View details →

Dimensional reduction of phenotypes from 53,000 mouse models reveals a diverse landscape of gene function - data bundle

This bundle is an archive of data files, configuration files, and scripts related to the manuscript "Dimensional reduction of phenotypes from 53,000 mouse models reveals a diverse landscape of gene function".

Fig. 7 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice

Fig. 7. Expression profiles analysis of OsFBNs under different temperature stresses. Eleven OsFBN genes in rice were detected for their transcript levels in leave tissues of seedlings at the three-leaf stage with different time intervals after the 35 ̊C (heat stress) and 6 ̊C (cold stress) stresses in the growth chamber, separately. The OsUBQ gene was used as a normalization control; data was measured as the mean values ± SD of three replicates, respectively.

Fig. 4 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice

Fig. 4. Phylogenetic and exon-intron structure analysis of FBN family genes in rice and Arabidopsis. The phylogenetic analysis was performed using the amino acid sequences of 25 FBN family proteins in rice and Arabidopsis (Left). The unrooted phylogenetic tree was generated by the neighbor-joining method and displayed using MEGA7 software. Numbers above or below branches of the evolution tree indicated the bootstrap values; The exon-intron structures of 25 FBN family genes in rice and Arabidopsis were analyzed (Right), the exons were represented by yellow boxes, the UTR by blue, black lines connecting two exons were introns. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 6 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice

Fig. 6. The in vitro lipid binding assays of PAP-domains. A and C, schematic representations of the mutant residues in OsFBN2 and OsFBN4 proteins in the in vitro lipid binding assays. B and D, the in vitro lipid-binding activity assays were performed by a fluorescence lipid probe P-96 (1 mM), fatty acids with C12:0, C14:0, C16:0, C18:0, C20:0, C22:0, with each (0.5 mM) of wild type (Wt) and mutant fusion protein (Mut) of PAP domains in OsFBN2 and OsFBN4 proteins, respectively. Detection experiments were performed with three biological replicates. * and ** symbols indicated the significant difference levels of P <0.05 or P <0.01 between mutant and wild type, respectively.

Fig. 5 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice

Fig. 5. Subcellular localization of CTP domains-fused GFP proteins. These constructs of p35S-FBN1-11-CTP-GFP or p35S-Trxm5-GFP, separately, were transiently expressed in Nicotiana benthamiana mesophyll cells. The co-localizations of fluorescence patterns of CTP domains of ten OsFBN proteins except OsFBN8 fused GFP were observed with the autofluorescence of chlorophyll in chloroplasts in protoplasts. The Trxm5-GFP was used as a chloroplast marker.

Fig. 3 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice

Fig. 3. PKC domain analysis of FBN11 clade in plants. A, Homology analysis of PKC domain sequences in FBN11 clades; B, evolutionary tree analysis of PKC domain in five plant species (Oryza sativa (Os), Selaginella moellendorffii (Smo), Arabidopsis thaliana (At), Glycine max (Gm), and Zea mays (Zm)) and algae (Monoraphidium neglectum (Mon), Chlorella sorokiniana (Chlo), Chlamydomonas sp. UWO 241 (Chla), and Haemato coccus lacustris (Hae); C, the conserved motif analysis of PKC domain in FBN11 protein clades in higher plants.

Fig. 2 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice

Fig. 2. Box-plot graphs and motif analysis of CTP and PAP-domain in plants. The protein sequences of CTP domains and PAP domains were analyzed in six plant species: Selaginella moellendorffii (Smo), Physcomitrella patens (Ppa), Arabidopsis thaliana (At), Glycine max (Gm), Oryza sativa (Os), and Zea mays (Zm), The grand average of hydropathicity (GRAVY) and isoelectric point (pI) of CTP domains of FBN1-11 protein clades were showed in A and B, respectively; The GRAVY and pI of PAP domains in FBN1-11 protein clades were showed in C and D, respectively; The dotted line represented the average values of GRAVY and pI, respectively; The conserved motif sequence of PAP domains in these plants were showed in E.