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133 results for “genetic lineages”
Exploring the Pocillopora cryptic diversity: a new genetic lineage in the western Indian Ocean or remnants from an ancient one?
<p>Cryptic species and lineages have been widely reported during the last decades, particularly in the marine realm. Misidentifications and ignoring species complexes imply many consequences, notably biasing biodiversity and connectivity assessments, which in turn mislead our understanding of ecosystems and impact the effective design and management of conservation plans. Focusing on the Indo-Pacific coral genus <em>Pocillopora</em>, playing key roles in reef ecosystems as one of the main bio-constructors, we report the first <em>Pocillopora</em> PSH16 (ORF53; <em>sensu</em> Gélin et al. 2017, Mol Phylogenet Evol 109:430–446) colonies (<em>N</em> = 19) in the western Indian Ocean (Nosy Tanikely, Madagascar), 6,000 km further from its current distribution. Colonies were identified according to their mitochondrial Open Reading Frame (ORF) haplotype and Bayesian assignment tests based on 13-microsatellite genotypes. Additionally, we performed genetic structure and diversity analyses with sympatric colonies from other <em>Pocillopora</em> species and <em>Pocillopora</em> PSH16 colonies from the tropical southwestern Pacific, revealing (1) a weak clonal richness, (2) a weak genetic diversity and (3) a relative isolation for the newly reported PSH16 colonies. These colonies thus represent either a new, distinct and uncommon, genetic lineage, or isolated remnants of a wider one. In any case, unless specific management measures are implemented, their long-term maintenance seems compromised due to restricted gene flow within a restricted pool of genes.</p> <p> </p> <p>This dataset contains the microsatellite genotypes analysed (98 <em>Pocillopora</em> colonies × 13 loci + ORF). Missing data are encoded as "?". The sampling marine province and the population are indicated for each individual.</p>
Figure 4 in Phenotypic Convergence in Genetically Distinct Lineages of a Rhinolophus Species Complex (Mammalia, Chiroptera)
Figure 4. The bacula of five species of Rhinolophidae. Dorsal (row D), ventral (V) and lateral (L) views. Row Bis the dorsal view of the base of each baculum. a) R. damarensis (Orange River), b) R. damarensis (Taung, TM 48040), c) R. darlingi (TM 47947), d) R. capensis (TM 40574), e) R. blasii (TM 7080), f) R. clivosus (TM46882). All figures are to the same scale and the scale line (bottom right) = 1 mm.
Figure 8 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 8. Daphnia tanakai sp. nov., male from Lake Midori-ga-ike, Japan. A, lateral view. B, caudal spine. C, head. D, E, armature of antero-ventral and posterior portion of valve. F, G, postabdomen and postabdominal claw. H, male antenna I. I, tip of male seta ('flagellum') on antenna I. J, K, limb I and its distal portion. L–O, distal-most endite of limb II.
Figure 7 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 7. Daphnia tanakai sp. nov., thoracic limbs of parthenogenetic female from Lake Midori-ga-ike, Japan. A, B, limb I. C, D, anterior seta on its endite 3 and 2. E, limb II. F, G, stiff seta on its inner-distal end. H, gnathobase II. I, J, limb III and its inner-distal portion. K, L, limb IV and its inner-distal portion. M, N, limb V and distal portion of its exopodite.
Figure 6 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 6. Daphnia tanakai sp. nov. from Lake Midori-ga-ike, collected on August 30, 2004 by S. Tanaka (A–F, K–O) and Lake Kagami-ike, collected on September 01, 2004 by S. Tanaka (G–J, P–R); both lakes are in Hida Mountain Range, Honshu Island, Japan. A, parthenogenetic female, lateral view. B, head of parthenogenetic female. C, D, armature of postero-ventral and posterior region of valve. E, postabdomen. F–I, postabdominal claws of adults. J, postabdominal claw of juvenile. K, L, antenna I in lateral and distal view. M, N, distal portion of basal segment in posterior and anterior view. O, swimming seta. P, Q, ephippial female and postero-dorsal portion of its carapace. R, ephippium.
Figure 3 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 3. Daphnia curvirostris, large parthenogenetic female from Lake Glubokoe, Moscow area, European Russia, collected on August 9, 2004 by AAK. A, lateral view. B, caudal spine. C–E, head. F, G, armature of postero-ventral and posterior region of valve. H, postabdomen. I, J, postabdominal claw. K, L, antenna I in lateral and posterior view.
Figure 5 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 5. Daphnia curvirostris from Lake Glubokoe, Moscow area, European Russia, collected on September 9, 2004 by N. N. Smirnov. A, B, ephippial female and its postero-dorsal region. C, fresh ephippium. D, adult male. E, male head. F, G, armature of ventral margin of valve. H, armature of posterior portion of valve. I, J, postabdomen and abdomen. K, antenna I. L, antenna II. M, N, limb I and its distal portion. O, armature of distal portion of largest seta of outer distal lobe. P, innerdistal portion of limb II.
Figure 2 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 2. Mapping the characters of chromosome number and postabdominal claw morphology onto the Daphnia ND2 consensus tree (Fig. 1). A, the left cladogram shows the evolution of chromosome number. Black line denotes 2n = 22, white line denotes 2n = 20 and dot line denotes 2n = 24. B, the right cladogram shows the evolution of postabdominal claw morphology. Black line denotes variable phenotype between the longispina-claw and pulex-claw types, white line denotes the longispina- claw type, dot line denotes the pulex-claw type and grey line denotes equivocal.
Figure 4 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 4. Daphnia curvirostris, appendages of parthenogenetic female from Lake Glubokoe, European Russia. A, coxal part of antenna II. B, distal portion of basal segment and basal portion of branches. C, distal portion of endopod. D, swimming seta. E, maxilla I. F, limb I: ODL indicates outer distal lobe; IDL indicates inner distal lobe. G–I, limb II, second seta on its inner-distal end, and gnathobase II. J–L, limb III, its inner-distal portion and filtering seta of gnathobase. M, N, limb IV and its inner-distal portion. O, limb V.
Figure 1 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 1. ME bootstrap consensus tree of Daphnia ND2 sequences. The numbers on each branch show support values of the branch. Upper numbers indicate ME, and ML bootstrap support values for nucleotide sequences. Middle numbers indicate MP bootstrap support values and Bayesian clade credibility values for nucleotide sequences. Lower numbers indicate MP bootstrap support values and Bayesian clade credibility values for amino acid sequences. Asterisks indicate no support values.
Figure 4 in Genetic lineages of Parisotoma notabilis sensu lato (Collembola) in Eastern Europe and the Caucasus
Figure 4. Sites of lineage findings in the Caucasus region and in southern Eastern Europe (L0, L1, L2, L3, L4-Hebert, L-Hyrcan, L-Crimea, L-Cheget, L-Georgia, L-Khosta).
Figure 1 in Genetic lineages of Parisotoma notabilis sensu lato (Collembola) in Eastern Europe and the Caucasus
Figure 1. Maximum Likelihood genetic tree of 10 lineages of P. notabilis based on the COI gene fragment.
Inferred genetic architecture underlying evolution in a fossil stickleback lineage
<p>Inferring the genetic architecture of evolution in the fossil record is difficult because genetic crosses are impossible, the acquisition of DNA is usually impossible, and phenotype-genotype maps are rarely obvious. However, such inference is valuable because it reveals the genetic basis of microevolutionary change across many more generations than is possible in studies of extant taxa, thereby integrating microevolutionary process and macroevolutionary pattern. Here, we infer the genetic basis of pelvic skeleton reduction in <i>Gasterosteus doryssus</i>, a Miocene stickleback fish from a finely resolved stratigraphic sequence that spans nearly 17,000 years. Reduction in pelvic score, a categorical measure of pelvic structure, resulted primarily from reciprocal frequency changes of two discrete phenotypic classes. Pelvic vestiges also showed left-side-larger asymmetry. These patterns implicate <i>Pitx1</i>, a large-effect gene whose deletion generates left-larger asymmetry of pelvic vestiges in extant, closely-related <i>Gasterosteus aculeatus. </i>In contrast, reductions in lengths of the pelvic girdle and pelvic spines resulted from directional shifts of unimodal, continuous trait distributions, suggesting an additional suite of genes with minor, additive pelvic effects, again like <i>G. aculeatus</i>. Similar genetic architectures explain shared but phyletically independent patterns across 10 million years of stickleback evolution.</p>
Figure 4. - Intralineage and interlineage uncorrected genetic distance values for the "ivonicus/yuna" and "carteri" lineages.
Figure 4. - Intralineage and interlineage uncorrected genetic distance values for the "ivonicus/yuna" and "carteri" lineages.
Data from: Genetic signatures of lineage fusion closely resemble population decline
<p>Accurate interpretation of the genetic signatures of past demographic events is crucial for reconstructing evolutionary history. Lineage fusion (complete merging, resulting in a single panmictic population) is a special case of secondary contact that is seldom considered. Here, the circumstances under which lineage fusion can be distinguished from population size constancy, growth, bottleneck, and decline were investigated. Multi-locus haplotype data were simulated under models of lineage fusion with different divergence versus sampling lag times (D:L ratios). These pseudo-observed datasets also differed in their allocation of a fixed amount of sequencing resources (number of sampled alleles, haplotype length, number of loci). Distinguishability of lineage fusion versus each of 10 untrue non-fusion scenarios was quantified based on six summary statistics (neutrality tests). Some datasets were also analyzed using extended Bayesian skyline plots. Results showed that signatures of lineage fusion very closely resemble those of decline—high distinguishability was generally limited to the most favorable scenario (D:L = 9), using the most sensitive summary statistics (<em>F</em><sub>S</sub> and <em>Z</em><sub>nS</sub>), coupled with the optimal sequencing resource allocation (maximizing number of loci). Also, extended Bayesian skyline plots often erroneously inferred population decline. Awareness of the potential for lineage fusion to carry the hallmarks of population decline is critical.</p>
Genetic data and niche differences suggest that disjunct populations of Diglossa brunneiventris are not sister lineages
<p>Disjunct distributions within a species are of great interest in systematics and biogeography. This separation can function as a barrier to gene flow when the distance among populations exceeds the dispersal capacity of individuals, and depending on the duration of the barrier, it may eventually lead to speciation. Here we describe patterns of geographic differentiation of two disjunct populations of <em>Diglossa brunneiventris</em> separated by approximately 1000 km along the Andes. <em>Diglossa brunneiventris vuilleumieri </em>is isolated in northern Colombia, while <em>Diglossa brunneiventris brunneiventris</em> has a seemingly continuous distribution across Peru, Bolivia, and Chile. We sequenced mitochondrial and nuclear DNA of the two <em>Diglossa brunneiventris</em> subspecies to evaluate whether they form a monophyletic clade, while including the other three species within the carbonaria complex (<em>D. gloriosa</em>, <em>D. humeralis</em> and <em>D. carbonaria</em>). We also constructed ecological niche models for each <em>Diglossa brunneiventris </em>subspecies to compare their climatic niches. We found that when using all available molecular data, the two <em>D. brunneiventris</em> subspecies are not sister lineages. In fact, each subspecies is more closely related to other species in the carbonaria complex. Our niche modeling analyses showed that the subspecies are occupying almost entirely different climatic niches. An additional, and not expected result was that the carbonaria complex might encompass more cryptic species than previously considered. We suggest reevaluating the taxonomic status of these brunneiventris populations, especially the northern subspecies, given its highly restricted range and potential threatened status.</p>
Molecular Genetic Analysis of SARS-CoV-2 Lineages in Armenia - additional data
<p>Sequencing of SARS-CoV-2 provides essential information on viral evolution, transmission, and epidemiology. In this study, we performed whole-genome sequencing of SARS-CoV-2 using nanopore and Illumina short-read sequencing to describe the circulation of the virus lineage in Armenia.</p> <p>This dataset contains Nextstrain configuration files, the auspice JSON file, BEAST output logs, and trees files, and resulting log and tree files as well as R scripts and data files used in phylogenetic and functional analyses. </p> <p> </p>
Fine-scale spatial genetic structure in a locally abundant native bunchgrass (Achnatherum thurberianum) including distinct lineages revealed within seed transfer zones
<p>Analyses of the factors shaping genetic variation in widespread plant species are important for understanding evolutionary history and local adaptation and have applied significance for guiding conservation and restoration decisions. Thurber's needlegrass (<em>Achnatherum</em> <em>thurberianum</em>) is a widespread, locally abundant grass that inhabits heterogeneous arid environments of western North America and is of restoration significance. It is a common component of shrubland steppe communities in the Great Basin Desert, where drought, fire, and invasive grasses have degraded natural communities. Using a reduced representation sequencing approach, we generated SNP data at 5,677 loci across 246 individuals from 17 <em>A. thurberianum</em> populations spanning five previously delineated seed zones from the western Great Basin. Analyses revealed pronounced population genetic structure, with individuals forming consistent geographical clusters across a variety of population genetic analyses and spatial scales. Low levels of genetic diversity within populations, as well as high population estimates of linkage disequilibrium and relatedness, were consistent with self-fertilization as a contributor to population differentiation. Variance partitioning and partial redundancy analysis (pRDA) indicated local adaptation to environment as additionally influencing the spatial distribution of genetic variation. The environmental variables driving these results were similar to those implicated in recent genecological work which inferred local adaptation for seed zone delineation. Our analyses also revealed a complex evolutionary history of <em>A. thurberianum</em> in the Great Basin, where previously delineated seed zones contain distantly related populations. Our results indicate evolutionary history, mating system, and differentiation across distinct geographic and environmental scales have shaped genetic variation in <em>A. thurberianum</em> and illustrate how numerous aspects of population genetic variation might require consideration for restoration planning.</p>
Supplementary Materials for Respiratory Syncytial Virus Genetic Diversity and Lineage Changes in Ireland pre- and post-COVID-19 pandemic
<p><span>The datasets presented here are the list of publicly available reference sequences used in NextClade (</span><a href="https://github.com/rsv-lineages"><span>https://github.com/rsv-lineages</span></a><span>) to provide the lineage classification of samples and used as reference for analysis of Irish RSV sequences (Supplementary Table 1), the list of sequenced Human respiratory syncytial viruses (RSV) in the Republic of Ireland during the period 2015-2024 (Supplementary Table 2) and the details of sequences downloaded from GISAID corresponding to European RSV sequences for the same period of time.</span></p> <p><span> </span></p> <p><span>Description of the data and file structure</span></p> <p><span>The files in this dataset were formatted in Microsoft Excel 2019 to allow easy access and manipulation of the data. The data corresponds to details on the sequences used in the analysis of RSV in Europe during the 2015-2024 period. The contents of the files are described below: -<strong>Supplementary Table 1</strong>: NextClade Reference Sequences publicly available at </span><a href="https://github.com/rsv-lineages"><span>https://github.com/rsv-lineages</span></a><span>. -<strong>Supplementary Table 2</strong>: Irish RSV Sequence Details contains details on the sequences generated in our study with the GenBank accession number, the GISAID accession number, reported collection RSV season, Nextclade assigned taxonomical clade. -<strong><span>Supplementary Table 3</span></strong>: European RSV Sequence Details contains a list of European RSV sequences downloaded from GISAID (</span><a href="https://gisaid.org/"><span>https://gisaid.org/</span></a><span>) with details on the sampling RSV season, the accession number, country of collection, and lineage assigned by NextClade.</span></p> <p><span> </span></p> <p><span>Sharing/Access information</span></p> <p><span>The databases used to extract and deposit the data were:</span></p> <p><span>-GenBank: the North American repository of sequences and publicly available at: </span><a href="https://www.ncbi.nlm.nih.gov/genbank/"><strong><span>https://www.ncbi.nlm.nih.gov/genbank/</span></strong></a><span> </span></p> <p><span>-GISAID:International consortium of sequences with some metadata and clinical data. It is a semi-public repository with easy access requiring only to create an account. Available at: </span><a href="https://gisaid.org/"><strong><span>https://gisaid.org/</span></strong></a></p> <p><span>-Github: reference sequences of RSV are available at the repository </span><a href="https://github.com/"><strong><span>https://github.com/</span></strong></a></p>
Figure 3. L1, L2 in Genetic lineages of Parisotoma notabilis sensu lato (Collembola) in Eastern Europe and the Caucasus
Figure 3. L1, L2, and L4-Hebert lineage finds in Eastern Europe.
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OpenNeuro
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