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1,598 results for “genetic diversity”
Data from: The making of a rapid plant invader: genetic diversity and differentiation in the native and invaded range of Senecio inaequidens
To become invasive, exotic species have to succeed in the consecutive phases of introduction, naturalization and invasion. Each of these phases leaves traces in genetic structure, which may affect the species' success in subsequent phases. We examine this interplay of genetic structure and invasion dynamics in the South African Ragwort (Senecio inaequidens), one of Europe's fastest plant invaders. We used AFLP and microsatellite markers to analyze 19 native African and 32 invasive European populations. In combination with historic data, we distinguished invasion routes and traced them back to the native source areas. This revealed that different introduction sites had markedly different success in the three invasion phases. Notably, an observed lag-phase in Northern Germany was evidently not terminated by factors increasing the invasiveness of the resident population but by invasive spread from another introduction centre. The lineage invading Central Europe was introduced to sites in which winters are more benign than in the native source region. Subsequently, this lineage spread into areas in which winter temperatures match the native climate more closely. Genetic diversity clearly increases with population age in Europe and less clearly decreases with spread rate up to population establishment. This indicates that gene flow along well-connected invasion routes counteracted losses of genetic diversity during rapid spread. In summary, this study suggests that multiple introductions, environmental preadaptation and high gene flow along invasion routes contributed to the success of this rapid invader. More generally, it demonstrates the benefit of combining genetic, historical and climatic data for understanding biological invasions.
Data from: Genetic diversity and population structure of Trypanosoma brucei in Uganda: implications for the epidemiology of sleeping sickness and Nagana
Background: While Human African Trypanosomiasis (HAT) is in decline on the continent of Africa, the disease still remains a major health problem in Uganda. There are recurrent sporadic outbreaks in the traditionally endemic areas in south-east Uganda, and continued spread to new unaffected areas in central Uganda. We evaluated the evolutionary dynamics underpinning the origin of new foci and the impact of host species on parasite genetic diversity in Uganda. We genotyped 269 Trypanosoma brucei isolates collected from different regions in Uganda and southwestern Kenya at 17 microsatellite loci, and checked for the presence of the SRA gene that confers human infectivity to T. b. rhodesiense. Results: Both Bayesian clustering methods and Discriminant Analysis of Principal Components partition Trypanosoma brucei isolates obtained from Uganda and southwestern Kenya into three distinct genetic clusters. Clusters 1 and 3 include isolates from central and southern Uganda, while cluster 2 contains mostly isolates from southwestern Kenya. These three clusters are not sorted by subspecies designation (T. b. brucei vs T. b. rhodesiense), host or date of collection. The analyses also show evidence of genetic admixture among the three genetic clusters and long-range dispersal, suggesting recent and possibly on-going gene flow between them. Conclusions: Our results show that the expansion of the disease to the new foci in central Uganda occurred from the northward spread of T. b. rhodesiense (Tbr). They also confirm the emergence of the human infective strains (Tbr) from non-infective T. b. brucei (Tbb) strains of different genetic backgrounds, and the importance of cattle as Tbr reservoir, as confounders that shape the epidemiology of sleeping sickness in the region.
Data from: Paleo-islands as refugia and sources of genetic diversity within volcanic archipelagos: The case of the widespread endemic Canarina canariensis (Campanulaceae)
Geographical isolation by oceanic barriers and climatic stability has been postulated as some of the main factors driving diversification within volcanic archipelagos. However, few studies have focused on the effect that catastrophic volcanic events have had on patterns of within-island differentiation in geological time. This study employed data from the chloroplast (cpDNA haplotypes) and the nuclear (AFLPs) genomes to examine the patterns of genetic variation in Canarina canariensis, an iconic plant species associated with the endemic laurel forest of the Canary Islands. We found a strong geographical population structure, with a first divergence around 0.8 Ma that has Tenerife as its central axis and divides Canarian populations into eastern and western clades. Genetic diversity was greatest in the geologically stable 'palaeo-islands' of Anaga, Teno and Roque del Conde; these areas were also inferred as the ancestral location of migrant alleles towards other disturbed areas within Tenerife or the nearby islands using a Bayesian approach to phylogeographical clustering. Oceanic barriers, in contrast, appear to have played a lesser role in structuring genetic variation, with intra-island levels of genetic diversity larger than those between-islands. We argue that volcanic eruptions and landslides after the merging of the palaeo-islands 3.5 Ma played key roles in generating genetic boundaries within Tenerife, with the palaeo-islands acting as refugia against extinction, and as cradles and sources of genetic diversity to other areas within the archipelago.
FIGURE 1. Map showing collection localities for L in Morphological diversity and genetic structure within Lerista kalumburu Storr, 1976 (Squamata: Scincomorpha: Sphenomorphidae) — taxonomic implications
FIGURE 1. Map showing collection localities for L. kalumburu. Type locality (Kalumburu) in red, collection locality for twotoed specimens (Theda Station) in yellow. Locality lacking tissue sample (Doongan Station) indicated with hollow symbol. (Google © 2010; Image NASA © 2012 Cnes/Spot Image Data S10, NOAA, U.S. Navy, NGA, CEBCO).
FIGURE 2 in Morphological diversity and genetic structure within Lerista kalumburu Storr, 1976 (Squamata: Scincomorpha: Sphenomorphidae) — taxonomic implications
FIGURE 2. Majority-rule consensus tree of L. kalumburu and outgroup taxa based on four independent runs of the concatenated dataset combining four genetic loci (12S, 16S, ND4 and ATPsβ). Posterior probabilities are detailed above the branches. Branches with <60% support were collapsed. Modal digit configurations (forelimb, hindlimb) follow L. kalumburu specimen labels.
Phylogenetically under‐dispersed gut microbiomes are not correlated with host genomic heterozygosity in a genetically diverse reptile community
<p>We are providing semi-processed datasets relevant to the paper "Phylogenetically under-dispersed gut microbiomes across a range of host genetic diversity in a reptile community point to structuring by conserved host genes." Specifically, we include VCF files of RADseq data from host individuals, which are processed versions of the raw reads available at NCBI's Short Read Archive under PRJA744273. These data were processed for heterozygosity calculation using an adapted of the pipeline presented in Singhal et al. 2017, "Genetic diversity is largely unpredictable but scales with museum occurrences in a species-rich clade of Australian lizards."</p> <p>In addition, we include a database of 16S sequences from gut microbiome amplicon sequencing from the same host animals. The raw reads are available at NCBI's Short Read Archive under PRJNA746253. The sequences accessioned here are a curated, cleaned set of reference reads to which we realigned reads from each individual host.</p>
Data Source file for manuscript: Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long-term colonized patients
<p>ABSTRACT</p><p>Infections caused by extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (ESBL-PE) are associated with excess morbidity and mortality. Despite recognition of this immediate impact on human health, essential aspects of their molecular epidemiology remain under-investigated. This includes knowledge on the potential of a particular strain to persist in a host, mutational events during colonization, and the genetic diversity in individual patients over time. To investigate long-term genetic diversity of colonizing and infecting ESBL-producing <i>Klebsiella pneumoniae </i>species complex and ESBL-<i>Escherichia coli</i> in individual patients over time, we conducted performed a ten-year longitudinal retrospective study and extracted clinical and microbiological data from electronic health records. In this investigation, 76 ESBL-<i>K. pneumoniae</i> species complex and 284 ESBL-<i>E. coli</i> isolates were recovered from 19 and 61 patients. Strain persistence was detected in all patients colonized with ESBL-<i>K. pneumoniae </i>species complex, and 83.6% of patients colonized with ES BL-<i>E. coli</i>. Antimicrobial resistance genes, plasmid replicons, and whole ESBL-plasmids were shared between isolates regardless of chromosomal relatedness. Our study suggests that patients colonized with ESBL-producers may act as durable reservoirs for ongoing transmission of ESBLs, and that they are at a prolonged risk of recurrent infection with colonizing strains.</p><p>DATA SOURCE FILE</p><p>In this Data Source file, you will find access to the raw data, metadata and results obtained during the study: "Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long-term colonized patients". Data is organized following the structure of Figures/Tables of the manuscript and Supplementary Material. Additional figures not included in the main manuscript nor in the Supplementary Material are also available.</p><p>All sequencing and sample data from this study can be accessed at the NCBI database under the BioProject number PRJNA910977: <a href="http://dataview.ncbi.nlm.nih.gov/object/PRJNA910977">http://dataview.ncbi.nlm.nih.gov/object/PRJNA910977. </a>No new software was developed during this study. Standard bioinformatics software was used and the commands used can be accessed at the Supplementary Information file.</p>
Fig. 10 in Taxonomy, genetic diversity, and phylogeny of the Antarctic mud dragon, Polacanthoderes (Kinorhyncha: Echinorhagata: Echinoderidae)
Fig. 10. Maximum-likelihood tree of Kinorhyncha based on 18S (1353 bp) + 28S (2750 bp) dataset. Numbers near nodes are the maximum-likelihood bootstrap (BS) and Bayesian posterior probability (PP) values, respectively; asterisks indicate the node with the full support values (BS = 100% and PP = 1.00); BS values lower than 50% indicate as polytomy; PP values lower than 0.95 are indicated by dashes. The scale bar indicates branch length in substitutions per site.
Fig. 9 in Taxonomy, genetic diversity, and phylogeny of the Antarctic mud dragon, Polacanthoderes (Kinorhyncha: Echinorhagata: Echinoderidae)
Fig. 9. Polacanthoderes shiraseae sp. nov., scanning electron micrographs of females (A, C–E) and a male (B and F). A, segments 5–7, ventral view; B, segments 6–8, ventral view; C, segments 7–9, lateral view; D, close-up of sieve plate on segment 9; E, segments 8–11, laterodorsal view; F, segments 9–11, ventral view. Black arrows and black arrowhead indicate sensory spot and type-2 glandular cell outlet, respectively. Abbreviations (ac), acicular spine; LA, lateral accessory; LD, laterodorsal; ltas, lateral terminal accessory spine; lts lateral terminal spine; LV, lateroventral; MD, middorsal; pa, papilla; pe, penile spine; (sac), small acicular spine; SD, subdorsal; se, seta; si, sieve plate; SL, sublateral; (tu), tube; VL, ventrolateral; VM, ventromedial. Digits after abbreviations indicate the corresponding segment number.
Fig. 7 in Taxonomy, genetic diversity, and phylogeny of the Antarctic mud dragon, Polacanthoderes (Kinorhyncha: Echinorhagata: Echinoderidae)
Fig. 7. Polacanthoderes shiraseae sp. nov., scanning electron micrographs of females (A–E) and a male (F). A, overview from lateroventral side; B, head (right side); C, segments 1–4, lateral view; D, segments 1–5, ventral view; E, segments 4–7, lateral view; F, segments 4–6, laterodorsal view. Black arrows and black arrowhead indicate sensory spot and type-2 glandular cell outlet, respectively. Abbreviations (ac), acicular spine; LA, lateral accessory; LD, laterodorsal; LV, lateroventral; MD, middorsal; ML, midlateral; oos, outer oral style; phc, pharynx crown; psps, primary spinoscalid; (sac), small acicular spine; SD, subdorsal; sec, sector number; SL, sublateral; sps, spinoscalid followed by the corresponding ring number (tu), tube; VM, ventromedial. Digits after abbreviations (except for sec and sps) indicate the corresponding segment number.
Fig. 5 in Taxonomy, genetic diversity, and phylogeny of the Antarctic mud dragon, Polacanthoderes (Kinorhyncha: Echinorhagata: Echinoderidae)
Fig. 5. Polacanthoderes shiraseae sp. nov., camera lucida drawings. A, B, holotype female (ICHUM 8348), segments 1–11, dorsal view (A) and ventral view (B); C, D, paratype male (ICHUM 8371), segments 10 and 11, dorsal view (C) and ventral view (D). Abbreviations (ac), acicular spine; gco1/2, type- 1/2 glandular cell outlet; LA, lateral accessory; LD, laterodorsal; ltas, lateral terminal accessory spine; lts, lateral terminal spine; LV, lateroventral; MD, middorsal; mdp, middorsal placid; ML, midlateral; mvp, midventral placid; pa, papilla; pe, penile spine; (sac), small acicular spine; SD, subdorsal; se, seta; si, sieve plate; SL, sublateral; ss, sensory spots (tu), tube; VL, ventrolateral; VM, ventromedial. Digits in the abbreviations (except for gco1/2) indicate the corresponding segment number.
Fig. 4 in Taxonomy, genetic diversity, and phylogeny of the Antarctic mud dragon, Polacanthoderes (Kinorhyncha: Echinorhagata: Echinoderidae)
Fig. 4. Polacanthoderes martinezi, scanning electron micrographs of females. A, segments 2–5, lateroventral view; B, segments 5–7, lateral view; C, segments 6–8, lateroventral view; D, segment 7, lateroventral view. Black arrows and a black arrowhead indicate sensory spot and type-2 glandular cell outlet, respectively. Abbreviations (ac), acicular spine; LA, lateral accessory; LD, laterodorsal; LV, lateroventral; ML, midlateral; pa, papilla; (sac), small acicular spine; SD, subdorsal; (tu), tube; VM, ventromedial; VL, ventrolateral. Digits in abbreviations indicate the corresponding segment number.
Fig. 6 in Taxonomy, genetic diversity, and phylogeny of the Antarctic mud dragon, Polacanthoderes (Kinorhyncha: Echinorhagata: Echinoderidae)
Fig. 6. Polacanthoderes shiraseae sp. nov., DIC photomicrographs. A–F, the holotypic female (ICHUM 8348), neck and segments 1–6, dorsal view (A) and ventral view (B), segments 7–11, dorsal view (C) and ventral view (D), segments 6 and 7, ventral view, focused at cuticle surface (E) and focused at deeper layer (F); G and H, paratype male (ICHUM 8371), segments 6–8, ventral view (G), segments 10 and 11, dorsal view (H). Black arrows, white arrowheads, and black arrowheads indicate sensory spot, type-1 glandular cell outlet, and type-2 glandular cell outlet, respectively. Abbreviations (ac), acicular spine; LA, lateral accessory; LD, laterodorsal; ltas, lateral terminal accessory spine; lts, lateral terminal spine; LV, lateroventral; MD, middorsal; ML, midlateral; pa, papilla; pe, penile spine; (sac), small acicular spine; SD, subdorsal; si, sieve plate; SL, sublateral; (tu), tube; VL, ventrolateral; VM, ventromedial. Digits in the abbreviations indicate the corresponding segment number.
Fig. 3. Polacanthoderes martinezi, DIC photomicrographs. A, B, D, E in Taxonomy, genetic diversity, and phylogeny of the Antarctic mud dragon, Polacanthoderes (Kinorhyncha: Echinorhagata: Echinoderidae)
Fig. 3. Polacanthoderes martinezi, DIC photomicrographs. A, B, D, E, the holotypic female (ZMB 11237), head, neck, and segments 1–5, dorsal view (A) and ventral view (B), segments 6–11, dorsal view (D) and ventral view (E); C, the allotype male (ZMB 11238a), neck and segments 1–6, dorsal view; F, paratype male (ZMB 11238d), segments 7–11, ventral view. Black arrows, white arrowheads, and black arrowheads indicate sensory spot, type-1 glandular cell outlet, and type-2 glandular cell outlet, respectively. Abbreviations (ac), acicular spine; LA, lateral accessory; LD, laterodorsal; LV, lateroventral; MD, middorsal; ML, midlateral; pa, papilla; pe, penile spine; (sac), small acicular spine; SD, subdorsal; (tu), tube; VL, ventrolateral; VM, ventromedial. Digits in the abbreviations indicate the corresponding segment number.
Fig. 1 in Taxonomy, genetic diversity, and phylogeny of the Antarctic mud dragon, Polacanthoderes (Kinorhyncha: Echinorhagata: Echinoderidae)
Fig. 1. Map of Antarctica indicating the type localities of P. martinezi and the sampling stations of P. shiraseae sp. nov. in Lützow-Holm Bay, off Cape Darnley, and off Totten Glacier.
Fig. 2. Polacanthoderes martinezi, camera lucida drawings. A, B in Taxonomy, genetic diversity, and phylogeny of the Antarctic mud dragon, Polacanthoderes (Kinorhyncha: Echinorhagata: Echinoderidae)
Fig. 2. Polacanthoderes martinezi, camera lucida drawings. A, B, holotype female (ZMB 11237), segments 1–11, dorsal view (A) and ventral view (B); C, D, allotype male (ZMB 11238a), segments 10 and 11, dorsal view (C) and ventral view (D). Abbreviations (ac), acicular spine; gco1/2, type-1/2 glandular cell outlet; LA, lateral accessory; LD, laterodorsal; ltas, lateral terminal accessory spine; lts, lateral terminal spine; LV, lateroventral; MD, middorsal; mdp, middorsal placid; ML, midlateral; mvp, midventral placid; pa, papilla; pe, penile spine; (sac), small acicular spine; SD, subdorsal; se, seta; si, sieve plate; ss, sensory spots (tu), tube; VL, ventrolateral; VM, ventromedial. Digits in the abbreviations (except for gco1/2) indicate the corresponding segment number.
Supplementary material 1 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Supplementary material 1 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Supplementary material 2 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Supplementary material 2 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
The genetic diversity, phylogeography, and population structure of Pacific harbor seals reveal isolation at the southern end of their distribution
<p>The Pacific harbor seal (<em>Phoca vitulina richardii</em>) occurs in the Mexican Pacific region at the southernmost edge of the subspecies' distribution, along 700 km of coastline and on nine islands west of the Baja California peninsula. Its abundance corresponds to 3% of its total abundance in the north Pacific Ocean. The species is considered relatively sedentary and highly philopatric, which make it vulnerable to stochastic processes; thus, reproductive and genetic isolation of the Mexican Pacific colonies is expected. This study aimed to genetically characterize the harbor seal in the Mexican Pacific to inform conservation efforts. We estimated the levels of genetic diversity for five colonies, using a 572-base pair mitochondrial DNA control region fragment and nine microsatellite loci. We examined the population genetic structure and its phylogeographic patterns. We found 15 variable sites that defined 18 mitochondrial DNA haplotypes. Results show one of the lowest levels of diversity reported for the species (overall haplotype diversity <em>h</em> = 0.626 ± SD 0.041; overall nucleotide diversity π = 0.0018 ± SD 0.0013; mean expected heterozygosity H<sub>E</sub> = 0.537). We found a stronger genetic structure with both markers than in the larger regions of the north Pacific, from Alaska to California. The Pacific harbor seal colonies found in Mexico may have their origins in northern colonies, via a founder event. We found only four haplotypes in common with those observed (451) along the rest of the Pacific colonies, while nine of the 14 haplotypes exclusive to the Mexican Pacific are private.</p>
Stoneflies of Medvednica Nature Park: genetic diversity and morphological variability
<p>Stoneflies of Medvednica Nature Park: genetic diversity and morphological variability</p> <p>Version 2: corrected the sequence lengths</p>
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