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32 results for “genetic species identification”
Datasets for phylogenetic analyses and phylogenetic trees for: Genetic barcodes for species identification and phylogenetic estimation in ghost spiders (Araneae: Anyphaenidae: Amaurobioidinae). Invertebrate Systematics, 2024
<p>We combined the COI sequence data with legacy multigene sequence data to create a new, taxon-rich phylogeny for the Amaurobioidinae. We used sequences for four loci that have been used in previous studies on the subfamily: two mitochondrial loci, COI (658bp) and ribosomal subunit 16S (16S, 410bp); and two nuclear loci, Histone H3 (H3, 327bp) and ribosomal subunit 28S (28S, 839bp). We complemented the Amaurobioidinae data with sequences from several non-amaurobioidine anyphaenids and two clubionids as outgroups. Sequence alignment was performed using the MAFFT (ver. 7.308) plugin in Geneious, allowing MAFFT to automatically select an appropriate alignment strategy based on the properties of each locus, or with the online MAFFT server (https://mafft.cbrc.jp), which consistently selected the L-INS-i algorithm. Finally, alignments of the four loci were concatenated to construct a 2234 bp multigene sequence matrix containing 692 taxa, with about 55% missing/gap data (“full” matrix henceforth). To ensure that excessive missing data did not affect the resulting topology, we also constructed a reduced matrix by removing additional COI-only specimens so that each species and morphotype was represented by just one or two specimens for which all loci were available (where possible). After realignment, this reduced matrix was 2235 bp long, included 167 taxa, and had about 22% missing/gap data (“reduced” matrix henceforth). Phylogenetic analyses under maximum likelihood, including model selection, were then conducted with IQ-TREE 2. We performed phylogenetic analyses on both concatenated matrices (the full matrix and the reduced matrix) and on each individual locus. For model selection, we provided an initial scheme that partitioned the matrix by locus, and further partitioned the protein-coding loci (COI and H3) by codon position. We used ModelFinder and searched for the best partition scheme, all in IQ-TREE. The best models (partitions) for the full dataset were: GTR+F+I+G4 (16S), GTR+F+I+I+R4 (28S), TVM+F+I+I+R2 (COI-1), TIM2+F+R4 (COI-2), GTR+F+R5 (COI-3), TVMe+G4 (H3-1-H3-2), SYM+G4 (H3-3); and for the reduced dataset: GTR+F+I+G4 (16S), GTR+F+I+G4: (28S), GTR+F+I+G4: (COI-2), GTR+F+I+G4: (COI-3), TVM+F+I+G4: (COI-1, H3-2), GTR+F+I+G4: (H3-1), GTR+F+I+G4: (H3-3). For each dataset, once the best models and partitions were defined, we executed 10 independent replicates of tree calculations followed by 1000 ultrafast bootstrap replicates, and the replicate reaching the maximum likelihood was chosen. Phylogenetic analyses under parsimony were made with TNT, under equal weights, using the “new technology” search with default values, asking for 10 independent hits to the minimal length, and submitting the resulting trees to a round of TBR branch swapping. </p>
Fig. 1 in Genetic identification of interspecific hybrid of Neotropical catfish species (Pseudoplatystoma corruscans vs. Pseudoplatystoma reticulatum) in rivers of Mato Grosso do Sul State, Brazil
Fig. 1. Map of collection sites of the biological material. Upper Paraná River basin: Dourados River (1 to 16), Brilhante River (17), and Ivinhema River (18 to 20). Paraguay River basin: Miranda River (21), Aquidauana River (22), Negro River (23), and Paraguay River (24).
Data for: Species identification and population genetics of the Antarctic fish genera Lepidonotothen and Nototheniops (Perciformes, Notothenioidei)
<p>Accurate species identification is essential to assess biodiversity and species richness in ecosystems threatened by rapid and recent environmental changes, such as warming in most Antarctic waters. The <em>Lepidonotothen</em> species complex comprises demersal notothenioid fishes which inhabit the shelf areas of the Antarctic Peninsula, the Scotia Arc and sub-Antarctic islands with a circum-Antarctic distribution. Species determination in this group has often been problematic. In particular, whether <em>Lepidonotothen squamifrons</em> and <em>Lepidonotothen kempi </em>are valid as separate species has been questioned. In this study, we analysed the genetic variation among four nominal southern polar species within this complex (<em>L. kempi</em>, <em>L. squamifrons</em>, <em>Nototheniops larseni</em>, <em>Nototheniops nudifrons</em>) by means of three different markers (ND2 and tRNA mitochondrial genes and a panel of 16 nuclear microsatellites). We tested whether individuals morphologically assigned to <em>L. kempi</em> showed genetic separation from <em>L. squamifrons</em>. Our analyses indicated a lack of differentiation between <em>L. kempi</em> and <em>L. squamifrons</em>. However, a genetically distinct population was found for <em>L. squamifrons</em> at the Shag Rocks islands near South Georgia. Antarctic and sub-Antarctic islands are known to be home to many cryptic species and further studies will elucidate if the genetically differentiated population we found potentially originated from this context and can be considered as an incipient species. Our analysis contributes to further characterize the species composition of the most abundant fish suborder in the Southern Ocean, which is amongst the regions most threatened by climate change.</p>
Multiplexing PCR allows the identification of within-species genetic diversity in ancient eDNA
<p><span>Sedimentary ancient DNA (<em>seda</em>DNA) has rarely been used to obtain population-level data due to either a lack of taxonomic resolution for the molecular method used, limitations in the reference material or inefficient methods. Here, we present the potential of multiplexing different PCR primers to retrieve population-level genetic data from <em>seda</em>DNA samples. <em>Vaccinium</em> <em>uliginosum</em> (Ericaceae) is a widespread species with a circumpolar distribution and three lineages for present-day populations. We searched 18 plastid genomes for intraspecific variable regions and developed 61 primers to target these. Initial multiplex PCR testing resulted in a final set of 38 primers. These primers were used to analyse 20 lake <em>seda</em>DNA samples (11,200 cal. yr BP to present) from five different localities in northern Norway, the Alps and the Polar Urals. All known V<em>. uliginosum</em> lineages in these regions and all primers could be recovered from the <em>seda</em>DNA data, where for each sample 28.1 primers containing 34.15 variant sequences were obtained on average. All sediment samples were dominated by a single lineage, except three alpine samples which had co-occurrence of two different lineages. Furthermore, lineage turnover was observed in the Alps and northern Norway, suggesting that present-day phylogeographical studies may overlook past genetic patterns. Multiplexing primers is a promising tool for generating population-level genetic information from <em>seda</em>DNA. The relatively simple method, combined with high sensitivity, provides a scalable method that will allow researchers to track populations through time and space using environmental DNA.</span></p>
Multiplexing PCR allows the identification of within-species genetic diversity in ancient eDNA
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Data for: Species identification and population genetics of the Antarctic fish genera Lepidonotothen and Nototheniops (Perciformes, Notothenioidei)
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FIGURE 6. Genetic relationships between Munidopsis myojinensis and M in A new species of vent associated Munidopsis (Crustacea: Decapoda: Anomura: Galatheidae) from the Western Pacific, with notes on its genetic identification
FIGURE 6. Genetic relationships between Munidopsis myojinensis and M. lauensis based on DNA sequences. Munida taenia is the outgroup.
FIGURE 4 in A new species of vent associated Munidopsis (Crustacea: Decapoda: Anomura: Galatheidae) from the Western Pacific, with notes on its genetic identification
FIGURE 4. Munidopsis myojinensis paratype male (LACM CR 2004-019.1); a, carapace, frontal region, dorsal; b, right anterior part of carapace, lateral; c, right P1, dorsal; d, left P1, dorsal, with details of merus, ventral; e, thoracic sternum; f, right P2, lateral; g, right P5, lateral. Scales = 3 mm.
FIGURE 2 in A new species of vent associated Munidopsis (Crustacea: Decapoda: Anomura: Galatheidae) from the Western Pacific, with notes on its genetic identification
FIGURE 2. Munidopsis myojinensis holotype female (NSMT-Cr16877), a, carapace, lateral; b, right P1, dorsal; c, right P2, lateral; d, dactylus of P2, lateral e, thoracic sternum, f, endopod of right third maxilliped; g, posterior part of abdomen and telson; h, left antennal peduncle, ventral view; i, left antennular basal article, ventral. Scales: a, b, c = 3 mm; e, g = 3mm; d, f, h, i = 1 mm.
FIGURE 5 in A new species of vent associated Munidopsis (Crustacea: Decapoda: Anomura: Galatheidae) from the Western Pacific, with notes on its genetic identification
FIGURE 5. Munidopsis myojinensis paratype male (LACM CR 2004-019.1); a, right antennal peduncle, dorsal (right) and ventral (left) views; b, left third maxilliped, ventral, and dorsal view of merus; c, left antennular basal article, ventral; d, telson, dorsal. Scales: a–c = 1 mm; d = 3 mm.
FIGURE 3 in A new species of vent associated Munidopsis (Crustacea: Decapoda: Anomura: Galatheidae) from the Western Pacific, with notes on its genetic identification
FIGURE 3. Munidopsis myojinensis holotype female (NSMT-Cr16877), a, dorsal view, b, lateral view, c, in-situ photograph of Myojin Knoll sampling site; d, in–situ photograph of Northwest Eifuku Seamount sampling site.
Systematic Identification of Needlefish (Belonidae) Species using Molecular Genetic and Morphological Markers in the Mediterranean and Black Seas
<p><span>In this study, we aimed to clarify the taxonomic status of Belonidae species distributed in the Mediterranean Sea and the Black Sea by conducting detailed genetic and morphological markers. A total of 550 needlefish samples were caught between January 2022 and January 2024.<span> </span>The data set used in the study contains a total of 171 sequences for the <em>COI</em> gene and 120 sequences for the <em>12s rRNA</em> gene from different Belonidae species, including data from GenBank. Systematic analysis of needlefish species was investigated by using sequencing of mtDNA <em>COI</em> and <em>12s rRNA</em> gene regions and morphological characters in the Turkish Marine Waters. A separate analysis of the two mitochondrial genes supported by morphological characters revealed that each species is grouped within itself. The genetic and morphological analyses showed that <em>Belone belone acus</em> and <em>Belone belone euxini</em> which are considered as the subspecies of <em>Belone belone</em> are not subspecies of the genus <em>Belone</em> and should be considered at the species level, <em>Belone belone</em>.<span> </span><em>Belone svetovidovi</em> is also considerably different from <em>Belone belone</em> and should be considered as a different species. <em>T. acus imperialis</em>, which is thought to be distributed in the Mediterranean Sea, is not a subspecies of <em>Tylosorus acus and should be revised as Tylosorus imperialis </em><span>which genetically </span>differs from<em> Tylosorus acus </em>and also other<em> Tylosorus </em><span>species</span><em> </em>at the species level<em>. </em></span></p>
Six genome assemblies of Drosophila species for: Identification and genetic analysis of a pervasive "needle-eye" sperm phenotype in Drosophila sterile hybrid males
<p>Interspecies hybrid sterility has been extensively studied, especially in the genus <em>Drosophila</em>. Hybrid sterility is more often found in the heterogametic (XX or ZW) sex, a trend called Haldane's rule. Although this phenomenon is pervasive, identification of a common genetic mechanism remains elusive, with modest support found for a range of potential theories. Here, we identify a single precise morphological phenotype, which we call "needle-eye sperm," that is associated with hybrid sterility in three separate species pairs that span the <em>Drosophila</em> genus. The nature of the phenotype indicates a common point of meiotic failure in sterile hybrid males. We used ten generations of backcross selection paired with whole-genome pooled sequencing to genetically map the regions underlying the needle-eye sperm phenotype. Surprisingly, the sterility phenotype was present in ~50% of males even after ten generations of backcrossing, yet the genetic map showed multiple regions associated with sterility, indicating multiple regions may have the capacity to be sufficient to induce sterility in the F1. Due to the common phenotype among sterile male hybrids and the strong effect of individual loci, further exploration of the genes uncovered here may identify a universal mechanism for the evolution of hybrid sterility. </p>
Six genome assemblies of Drosophila species for: Identification and genetic analysis of a pervasive “needle-eye” sperm phenotype in Drosophila sterile hybrid males
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Genetic dataset of Systematic Identification of Needlefish (Belonidae) Species using Molecular Genetic and Morphological Markers in the Mediterranean and Black Seas
<p>The sequences used in the study from NCBI and BOLD databases.</p>
Supplementary material 2 from: Hernández-Triana LM, Brugman VA, Nikolova NI, Ruiz-Arrondo I, Barrero E, Thorne T, de Marco MF, Krüger A, Lumley S, Johnson N, Fooks AR (2019) DNA barcoding of British mosquitoes (Diptera, Culicidae) to support species identification, discovery of cryptic genetic diversity and monitoring invasive species. ZooKeys 832: 57-76. https://doi.org/10.3897/zookeys.832.32257
: Data type: molecular data
Supplementary material 1 from: Hernández-Triana LM, Brugman VA, Nikolova NI, Ruiz-Arrondo I, Barrero E, Thorne T, de Marco MF, Krüger A, Lumley S, Johnson N, Fooks AR (2019) DNA barcoding of British mosquitoes (Diptera, Culicidae) to support species identification, discovery of cryptic genetic diversity and monitoring invasive species. ZooKeys 832: 57-76. https://doi.org/10.3897/zookeys.832.32257
: Data type: molecular data
Figure 2 from: Hernández-Triana LM, Brugman VA, Nikolova NI, Ruiz-Arrondo I, Barrero E, Thorne T, de Marco MF, Krüger A, Lumley S, Johnson N, Fooks AR (2019) DNA barcoding of British mosquitoes (Diptera, Culicidae) to support species identification, discovery of cryptic genetic diversity and monitoring invasive species. ZooKeys 832: 57-76. https://doi.org/10.3897/zookeys.832.32257
Figure 2 Neighbor joining tree of COI DNA barcodes (658 bp) for mosquito species. A divergence of > 2% may be indicative of separate operational taxonomic units. Only bootstrap values higher than 70% are shown.
Figure 1 from: Hernández-Triana LM, Brugman VA, Nikolova NI, Ruiz-Arrondo I, Barrero E, Thorne T, de Marco MF, Krüger A, Lumley S, Johnson N, Fooks AR (2019) DNA barcoding of British mosquitoes (Diptera, Culicidae) to support species identification, discovery of cryptic genetic diversity and monitoring invasive species. ZooKeys 832: 57-76. https://doi.org/10.3897/zookeys.832.32257
Figure 1 Location of study sites in the United Kingdom. Key: 1 ADAS Arthur Rickwood; 2 Church Farm; 3 Coombelands Farms; 4 Elmley Nature Reserve; 5 Glendell Livery, Mill Lane; 6 Frimley; 7 Mudchute Farm; 8 Northney Farm, Hayling Island; 9 White Lodge, Bisley; 10 Bartley Heath; 11 Dee Marsh.
Supplementary material 1 from: Li Y, Li H, Motokawa M, Wu Y, Harada M, Sun H, Mo X, Wang J, Li Y (2019) A revision of the geographical distributions of the shrews Crocidura tanakae and C. attenuata based on genetic species identification in the mainland of China. ZooKeys 869: 147-160. https://doi.org/10.3897/zookeys.869.33858
: Data type: species data
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Allen Brain Atlas
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OpenNeuro
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