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1,598 results for “genetic diversity”
Figure 10a. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 10a. - Habitat of Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan.Figure 10a.small pond where the present leeches were found. Photo taken by Dr Atsushi Tominaga.Figure 10b.landscape of the Suygaty Valley (Ili River Depression). Photo taken by KN. <br> small pond where the present leeches were found. Photo taken by Dr Atsushi Tominaga.
Figure 7a. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 7a. - Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan, KUZ Z702. Abbreviations: at, atrium; ed, ejaculatory duct; ep, epididymis; mg, male gonopore; pes, penis sheet.Figure 7a.dorsal view of male median reproductive system including positions of ganglia XI and XII. Scale bar: 0.25 mm.Figure 7b.left lateral view of schematic drawing of male median reproductive system. <br> dorsal view of male median reproductive system including positions of ganglia XI and XII. Scale bar: 0.25 mm.
Figure 7b. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 7b. - Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan, KUZ Z702. Abbreviations: at, atrium; ed, ejaculatory duct; ep, epididymis; mg, male gonopore; pes, penis sheet.Figure 7a.dorsal view of male median reproductive system including positions of ganglia XI and XII. Scale bar: 0.25 mm.Figure 7b.left lateral view of schematic drawing of male median reproductive system. <br> left lateral view of schematic drawing of male median reproductive system.
Figure 4. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 4. - Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan, KUZ Z702. Ventral view of somites XI and XII. Abbreviations: fp, female gonopore; mp, male gonopore; np, nephridiopore. Scale bar: 0.5 mm.
Figure 2b. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 2b. - Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan, KUZ Z702. Scale bars: 5 mm.Figure 2a.dorsal view.Figure 2b.ventral view. <br> ventral view.
Figure 6. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 6. - Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan, KUZ Z702. Dorsal view of reproductive system including ventral nervous system. Abbreviations: at, atrium; ep, epididymis; ov, ovisac; ts, testisac; vg, vagina. Scale bar: 1 mm.
Figure 2a. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 2a. - Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan, KUZ Z702. Scale bars: 5 mm.Figure 2a.dorsal view.Figure 2b.ventral view. <br> dorsal view.
Figure 9. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 9. - Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan. Dorsal view of a live animal, one of the leeches examined in this study, in the field. Photo taken by KN.
Figure 1. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 1. - Localities where Limnatispaluda (Tennent 1859) has been recorded. Open circles indicate collection localities in previous studies. Sources: aBoye and Joshi (1994); bKinzelbach and Rückert (1985); cKuntz and Myers (1968); dMoore (1927a).
Figure 8a. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 8a. - Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan, KUZ Z702. Abbreviations: cod, common oviduct; fg, female gonopore; od, oviduct; ov, ovisac; vg, vagina.Figure 8a.dorsal view of female reproductive system including positions of ganglia XII and XIII. Scale bar: 0.25 mm.Figure 8b.left lateral view of schematic drawing of female reproductive system. <br> dorsal view of female reproductive system including positions of ganglia XII and XIII. Scale bar: 0.25 mm.
Figure 3b. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 3b. - Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan, KUZ Z702. Abbreviations: np, nephridiopore. Scale bars: 0.5 mm.Figure 3a.dorsal view of somites I–VIII.Figure 3b.left lateral view of somites I–VIII.Figure 3c.ventral view of somites I–VIII. <br> left lateral view of somites I–VIII.
Figure 8b. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 8b. - Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan, KUZ Z702. Abbreviations: cod, common oviduct; fg, female gonopore; od, oviduct; ov, ovisac; vg, vagina.Figure 8a.dorsal view of female reproductive system including positions of ganglia XII and XIII. Scale bar: 0.25 mm.Figure 8b.left lateral view of schematic drawing of female reproductive system. <br> left lateral view of schematic drawing of female reproductive system.
Figure 3a. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 3a. - Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan, KUZ Z702. Abbreviations: np, nephridiopore. Scale bars: 0.5 mm.Figure 3a.dorsal view of somites I–VIII.Figure 3b.left lateral view of somites I–VIII.Figure 3c.ventral view of somites I–VIII. <br> dorsal view of somites I–VIII.
Figure 5a. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 5a. - Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan, KUZ Z702. Abbreviations: an, anus; np, nephridiopore. Scale bars: 1 mm.Figure 5a.dorsal view of somites XXIII–XXVII and caudal sucker.Figure 5b.ventral view of somites XXIII and caudal sucker. <br> dorsal view of somites XXIII–XXVII and caudal sucker.
Figure 5b. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 5b. - Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan, KUZ Z702. Abbreviations: an, anus; np, nephridiopore. Scale bars: 1 mm.Figure 5a.dorsal view of somites XXIII–XXVII and caudal sucker.Figure 5b.ventral view of somites XXIII and caudal sucker. <br> ventral view of somites XXIII and caudal sucker.
Figure 3c. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 3c. - Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan, KUZ Z702. Abbreviations: np, nephridiopore. Scale bars: 0.5 mm.Figure 3a.dorsal view of somites I–VIII.Figure 3b.left lateral view of somites I–VIII.Figure 3c.ventral view of somites I–VIII. <br> ventral view of somites I–VIII.
Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels
<pre>This repository contains data related to: Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels Amanda J. Lea, Julie Peng, Julien F. Ayroles A preprint of this work can be found here: https://www.biorxiv.org/content/10.1101/2021.11.04.467311v2 Specifically, the filtered, normalized, and batch corrected gene expression data file (31Mar21_all_runs_voom_resid.txt) is provided along with the metadata. We also provide the output from matrix eQTL that was used as input for mashR. Scripts used to generate and analyze these data are provided here: https://github.com/AmandaJLea/LCLs_gene_exp</pre>
Genetic diversity, genetic differentiation and demographic history of Cryptomeria (Cupressaceae), a Tertiary relict plant in East Asia based on RAD sequencing
<p>Genetic structure and distribution patterns of modern floras are strongly affected by climatic change and geographical isolation. In the present study, we applied restriction-site-associated DNA sequencing (RAD-seq) to analyze the genetic structure and to simulate the demographic history of two extant <em>Cryptomeria</em> species in Japan (<em>C. japonica</em>) and Southeastern China (<em>C</em>. <em>japonica</em> var. <em>sinensis</em>). Thirteen natural populations representing the entire species distributed in East Asia were collected from Japan and China. At the species level, the genetic diversity of <em>Cryptomeria</em> was moderate (<em>H<sub>o</sub></em> = 0.217, <em>H<sub>e</sub></em> = 0.203) with a significant genetic differentiation among populations (85.30%, P < 0.001), especially between Japan and China lineages (<em>F</em><sub>ST</sub> = 0.147). Except for the Lushan (LS) population in China, all populations were clustered into two lineages (Japanese and Chinese), which was consistent with their geographical distribution. Approximate Bayesian computations (ABC) model indicated that the current two geographical lineages diverged from a common ancestral lineage and that their divergence time was about 0.417 ~ 0.139 million years ago (Mya). Geographical isolation, climate change in the Quaternary, and human disturbance played important roles in genetic variation and distribution patterns of <em>Cryptomeria</em> in East Asia. Our results shed light on the speciation processes of <em>Cryptomeria</em> and provide a reference for the conservation of this species.</p>
Data and code for: Species-specific effects of production practices on genetic diversity in plant reintroduction programs
<p class="MsoNormal"><span>Plant production practices can influence the genetic diversity of cultivated plant materials and, ultimately, their potential to adapt to a reintroduction site. A common step in the plant production process is the application of seed pre-treatment to alleviate physiological seed dormancy and successfully germinate seeds. In production settings, the seeds that germinate more rapidly may be favored in order to fill plant quotas. In this study, we investigated how the application of cold-moist stratification treatments with different durations can lead to differences in the genetic diversity of the propagated plant materials. Specifically, we exposed seeds of three <em>Viola</em> species to two different cold stratification durations, and then we analyzed the genetic diversity of the resulting subpopulations through </span><span>double-digestion restriction site-associated sequencing (ddRADseq). Our results show that, in two out of three species, utilizing a short stratification period will decrease the genetic diversity of neutral and expressed loci, likely due to the imposition of a genetic bottleneck and artificial selection. We conclude that, in some species, the use of minimal stratification practices in production may jeopardize the adaptive potential and long-term persistence of reintroduced populations and suggest that practitioners carefully consider the evolutionary implications of their production protocols. We highlight the need to consider the germination ecology of target species when selecting the length of dormancy-breaking pre-treatments.</span></p>
Original FASTQ files of: Global genetic diversity and historical demography of the Bull Shark
<p><strong>Aim</strong></p> <p>Biogeographic boundaries and genetic structuring have important effects on the inferences and interpretation of effective population size (N<sub>e</sub>) temporal variations, a key genetics parameter. We reconstructed the historical demography and divergence history of a vulnerable coastal high-trophic shark using population genomics and assessed our ability to detect recent bottlenecks events.</p> <p><strong>Location</strong></p> <p>Western and Central Indo-Pacific (IPA), Western Tropical Atlantic (WTA), Eastern Tropical Pacific (EPA)</p> <p><strong>Taxon</strong></p> <p>Carcharhinus leucas (Müller & Henle, 1839)</p> <p><strong>Methods</strong></p> <p>A <a>DArTcap</a><sup>TM</sup> approach was used to sequence 475 samples and assess global genetic structuring. Three demographic models were tested on each population, using an ABC-RF framework coupled with coalescent simulations, to investigate within-cluster structure. Divergence times between clusters were computed, testing multiple scenarios, with <em>fastsimcoal</em>. N<sub>e</sub> temporal variations were reconstructed with STAIRWAYPLOT. Coalescent simulations were performed to determine the detectability of recent bottleneck under the estimated historical trend for datasets of this size.</p> <p><strong>Results</strong></p> <p>Three genetic clusters corresponding to the IPA, WTA and EPA regions were identified, agreeing with previous studies. The IPA presented the highest genetic diversity and was consistently identified as the oldest. No significant within-cluster structuring was detected. N<sub>e </sub>increased globally, with an earlier onset in the IPA, during the last glacial period. Coalescent simulations showed that weak and recent bottlenecks could not be detected with our dataset, while old and/or strong bottlenecks would erase the observed ancestral expansion.</p> <p><strong>Main conclusions</strong></p> <p>This study further confirms the role of marine biogeographic breaks in shaping the genetic history of large mobile marine predator. N<sub>e </sub>Historical increases of N<sub>e</sub> are potentially linked to extended coastal habitat availability. The limited within-cluster population structuring suggests that Ne can be monitored over ocean basins. Due to insufficient amount of available genetic data, it cannot be concluded whether overfishing is impacting Bull Shark genetic diversity, calling for whole genome sequencing.</p>
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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