Find research datasets worth reusing

opencc-by-4.0Dec 2024View details →

Aligned DNA sequence matrix for phylogenetic analyses in the article "Three new species of Torrent Treefrogs (Anura: Hylidae) of the Hyloscirtus bogotensis group from the eastern Andean slopes and the biogeographic history of the genus"

<p>Aligned DNA sequence matrix for phylogenetic analyses of the article "Three new species of Torrent Treefrogs (Anura: Hylidae) of the Hyloscirtus bogotensis group from the Amazon foothills and the biogeographic history of the genus"</p> <p>The matrix is in NEXUS format and has 3259 bp and 25 terminals.</p> <p>Partitions are as follows:</p> <div>charset 12S = 1-955;</div> <div>charset ND1_nonCoding1 = 956-1279;</div> <div>charset ND1_Pos1 = 1280-2240\3;</div> <div>charset ND1_Pos2 = 1281-2241\3;</div> <div>charset ND1_Pos3 = 1282-2242\3;</div> <div>charset ND1_nonCoding2 = 2243-2361;</div> <div>charset cmyc_Pos1 = 2362-2779\3;</div> <div>charset cmyc_Pos2 = 2363-2780\3;</div> <div>charset cmyc_Pos3 = 2364-2781\3;</div> <div>charset Rag1_Pos1 = 2782-3415\3;</div> <div>charset Rag1_Pos2 = 2783-3416\3;</div> <div>charset Rag1_Pos3 = 2784-3417\3;</div>

opencc-by-4.0Apr 2024View details →

Aligned DNA sequence matrix for phylogenetic analyses in the article "A new glassfrog of the genus Centrolene (Amphibia: Centrolenidae) from the Subandean Kutukú Cordillera, eastern Ecuador"

<p>Aligned DNA sequence matrix for phylogenetic analyses of the article "A new glassfrog of the genus Centrolene (Amphibia: Centrolenidae) from the Subandean Kutukú Cordillera, eastern Ecuador"</p> <p>The matrix is in NEXUS format and has 6626 bp and 239 terminals.</p> <p>Partitions are as follows:</p> <div> <div>charset 12S = 1-967;</div> <div>charset 16S = 968-2130;</div> <div> </div> <div>charset BNDFcodonPos1 =  2133-2829\3;</div> <div>charset BNDFcodonPos2 =  2131-2830\3;</div> <div>charset BNDFcodonPos3 =  2132-2828\3;</div> <div> </div> <div> </div> <div>charset ND1codonPos1 =  2832-3786\3;</div> <div>charset ND1codonPos2 =  2833-3787\3;</div> <div>charset ND1codonPos3 =  2831-3788\3;</div> <div> </div> <div> </div> <div>charset CXCR4codonPos1 =  3790-4144\3;</div> <div>charset CXCR4codonPos2 =  3791-4142\3;</div> <div>charset CXCR4codonPos3 =  3789-4143\3;</div> <div> </div> <div> </div> <div>charset cmyccodonPos1 =  4145-4547\3;</div> <div>charset cmyccodonPos2 =  4146-4548\3;</div> <div>charset cmyccodonPos3 =  4147-4549\3;</div> <div> </div> <div> </div> <div>charset POMCcodonPos1 =  4551-5160\3;</div> <div>charset POMCcodonPos2 =  4552-5161\3;</div> <div>charset POMCcodonPos3 =  4550-5162\3;</div> <div> </div> <div> </div> <div>charset RAG1codonPos1 =  5163-5616\3;</div> <div>charset RAG1codonPos2 =  5164-5617\3;</div> <div>charset RAG1codonPos3 =  5165-5618\3;</div> <div> </div> <div> </div> <div>charset SLC8A1codonPos1 =  5620-6160\3;</div> <div>charset SLC8A1codonPos2 =  5621-6158\3;</div> <div>charset SLC8A1codonPos3 =  5619-6159\3;</div> <div> </div> <div> </div> <div> </div> <div>charset SLC8A3codonPos1 =  6162-6627\3;</div> <div>charset SLC8A3codonPos2 =  6163-6625\3;</div> <div>charset SLC8A3codonPos3 =  6161-6626\3;</div> </div> <p> </p>

opencc-by-4.0Sep 2023View details →

Coat protein (CP) and trimmed replication-associated protein (Rep) amino acid alignments, phylogenetic analyses, and associated metadata for ICTV-approved begomovirus RefSeq species exemplars

<p>DATA RETRIEVAL</p> <p>Annotated begomovirus coding sequences corresponding to each begomovirus species exemplar with a RefSeq accession number listed in the ICTV Virus Metadata Resource (VMR #18, 2021-10-19, <a href="https://ictv.global/vmr">https://ictv.global/vmr</a>) were downloaded from GenBank in protein FASTA file format. CP and Rep amino acid sequences were extracted and split into separate data sets for analysis. We confirmed the identity of misannotated ORF products by performing a BLAST search. For exemplar sequences missing ORF annotations (listed in metadata spreadsheet), ORFfinder (<a href="https://www.ncbi.nlm.nih.gov/orffinder/">https://www.ncbi.nlm.nih.gov/orffinder/</a>) was used to identify CP and Rep ORFs that were subsequently translated and added to each corresponding data set after BLAST confirmation.</p> <p>ALIGNMENTS</p> <p>Multiple sequence alignments were constructed using the MUSCLE method (Edgar, 2004) as implemented in MEGA 11 (Tamura et al., 2021) and manually corrected using AliView v1.26<strong> </strong>(Larsson, 2014). After an initial alignment inspection, exemplars with either severely truncated (i.e., length < 50% of the average length of the protein) or very divergent (i.e., causing us to doubt protein homology) CP or Rep sequences were excluded from the data set. Due to the difficulties in aligning the Rep sequences at the N- and C- terminal ends, the Rep alignment was trimmed to eliminate all residues prior to the iteron related domain (i.e., the known Rep functional region closest to the Rep start (Arguello-Astorga & Ruiz-Medrano, 2001)) in the N-terminus and after a conserved geminivirus motif found near the C-terminus, which corresponds to where other circular, Rep-encoding single-stranded DNA viruses possess an arginine finger motif (Kazlauskas et al., 2019; Krupovic et al., 2020). In total, our CP and Rep data sets contained amino acid sequences from 432 begomovirus species exemplars that met our inclusion criteria.</p> <p>PHYLOGENETIC ANALYSIS</p> <p>Maximum likelihood (ML) trees were inferred with IQ-Tree v2.0.7 (Minh et al., 2020) using the best fitting substitution model identified by the built-in ModelFinder feature (Kalyaanamoorthy et al., 2017). Tree inference was performed with 3000 ultrafast bootstrap (UFBoot) replicates, a perturbation strength of 0.2 and a stopping rule requiring an iteration interval of 500 iterations between unsuccessful improvements to the local optimum. The -bnni flag was enabled to reduce the risk of overestimating branch supports with UFBoot due to severe model violations. The provided phylogenies in NEXUS format are midpoint-rooted and branches are colored based on traditional begomovirus geographic groupings: exemplars sampled in the Americas in orange and exemplars sampled in the 'Africa, Asia, Europe and Oceania' (AAEO) region in blue. </p> <p>METADATA</p> <p>Metadata associated with each ICTV-approved species exemplar (n=445) – including country of isolation, geographic designation (i.e., AAEO/Americas), genome segmentation (i.e., monopartite/bipartite), presence/absence of V2/AV2 gene and length of genome/DNA-A segments – are included. Exemplars not incorporated into the other analyses are highlighted in red on the spreadsheet.</p> <p> </p>

opencc-by-4.0Sep 2021View details →

Nicobarese 100 item wordlist for phylogenetic analyses

<p>The data set is based on a modified Swadesh 100 list, intended to provide indications of the internal branching of the Nicobarese languages. To date little work has been done on the classification of the small Nicobarese group, which appears to consisted of approximately seven distinct languages spoken across an island chain. Only two of the languages are have extensive dictionaries and grammatical descriptions, while the others are only partially documented, and the materials can be highly problematic to work with. The excel includes the author's nexus file used for input to phylogentic software, such as SplitsTree.<br> The data supports the author's paper for the 9th ICAAL meeting, Novemer 2021, Lund, Sweden and subsequent published versions.</p>

opencc-by-4.0May 2023View details →

Phylogenetic analyses of hub genes accompanying the study "Environmental gradients reveal stress hubs predating plant terrestrialization"

<p>135 ML phylogenies of hub genes identified in the study "Environmental gradients reveal stress hubs predating plant terrestrialization"</p>

opencc-by-4.0Apr 2019View details →

Fig. 1 in Multiloci analyses suggest synonymy among Rhomboplites, Ocyurus and Lutjanus and reveal the phylogenetic position of Lutjanus alexandrei (Lutjanidae: Perciformes)

Fig. 1. Phylogenetic relationships in Lutjaninae species from the Western Atlantic estimated by Bayesian (BI), maximum likelihood (ML) and a Species Tre analyses inferences based on a data matrix (4.4 kb) comprising mitochondrial (16S rRNA, COI, cyt b, and ND-4) and nuclear (Rhodopsin, TMO4C4 and RAG-1) markers. The BI topology is presented with the posterior probability (BI and Species Tree) and bootstrap (ML) values. The letters in the nodes refer to the clades discussed in the text.

dryad40/100

Anatomical partitioning has little influence in topologies from Bayesian phylogenetic analyses of morphological data

<p>Morphological data is a fundamental source of evidence to reconstruct the Tree of Life, and Bayesian phylogenetic methods are increasingly being used for this task, along with, or instead of, traditional parsimony approaches. Bayesian phylogenetic analyses require the use of proper evolutionary models and their performance have been intensively studied in the past few years, with significant improvements to our knowledge regarding their performance. Notwithstanding, it was only recently that partitioned models for morphology received attention in studies of empirical data, but a systematic evaluation of its performances using simulations was never performed. Here we evaluate the influence of partitioned models defined by anatomical criterion in the precision and accuracy of consensus tree topologies, evaluating the possible negative effects of under and overpartitioning. For that, we analysed datasets simulated using parameters and properties of two empirical datasets, using Bayesian phylogenetic analyses in MrBayes. Additionally, we reanalysed 32 empirical datasets for diverse groups of vertebrates, applying unpartitioned and partitioned models. We found that in general, partitioning by anatomy has little to no influences in the performance of Bayesian phylogenetic methods in respect to the metrics studied here, with analyses under alternative partitioning schemes presenting very similar tree precision and accuracy. We discuss the possible reasons for the disagreement between the results obtained here and previous studies for empirical morphological data, and with empirical and simulation studies of molecular data, discussing the adequacy of anatomical partitioning relative to alternative methods to partition morphological datasets and how morphological and molecular partitioning are related.</p>

opencc-zeroDec 2020View details →

Fig. 40. Schaffneropsallus oaxacensis. A in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)

Fig. 40. Schaffneropsallus oaxacensis. A. Lateral view of head. B. Mesothoracic spiracle and metathoracic scent-efferent system. C. Detail of metathoracic scent-efferent evaporatory area. D. Frontolateral view of pretarsus. E. Lateral view of pygophore, tubercle at upper left. F. Detail of setae on tubercle of pygophore.

Fig. 43 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)

Fig. 43. Paralogy-free trees portraying biogeographic relationships of Phymatopsallus-group taxa (see text for explanation).

Fig. 32 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)

Fig. 32. Phymatopsallus patagoniae: Male genitalia (male 1, AMNH_PBI 00068597; male 2, 00068661; male 3, 00068652).

Fig. 30 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)

Fig. 30. Phymatopsallus acaciae: Male genitalia (male 1, AMNH_PBI 00062324; male 2, 00071888); female genitalia (AMNH_PBI 00097049).

Fig. 27. Knightopsallus portalensis. A in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)

Fig. 27. Knightopsallus portalensis. A. Lateral view of head. B. Mesothoracic spiracle and metathoracic scent-efferent system. C. Frontal view of pretarsus. D. Antennal segments 1 and 2. E. Lateral view of male abdomen, showing extruded vesica. F. Dorsal view of male pygophore (right paramere missing).

Fig. 22 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)

Fig. 22. Ceratopsallus septentrionalis: Male genitalia (upper, AMNH_PBI 00062810; lower, AMNH_PBI 00077235; vesicae drawn at 50% of scale of other structures).

Fig. 42 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)

Fig. 42. Phylogenetic relationships of Phymatopsallus-group taxa. Characters showing no homoplasy are indicated by filled circles; characters showing homoplasy are indicated by open circles (See text for explanation of methods).

Fig. 24. Cercocarpopsallus bispinosus. A in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)

Fig. 24. Cercocarpopsallus bispinosus. A. Lateral view of head. B. Mesothoracic spiracle and metathoracic scent-efferent system. C. Setae on hemelytron. D. Detail of patch of specialized setae on left side of male pygophore (arrow indicates low tubercle and setal patch on pygophore). E. Frontoventral view of pretarsus. F. Dorsal view of male pygophore.

Fig. 17 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)

Fig. 17. Ceratopsallus pintoi: Male genitalia (male 1, AMNH_PBI 00082262, vesica drawn at 50% scale of other structures; male 2, AMNH_PBI 00063239;); female genitalia (AMNH_PBI 00082902).

Fig. 18 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)

Fig. 18. Ceratopsallus plautus: Male genitalia (AMNH_PBI 00071806, vesica only; 00071801, other genitalic structures); female genitalia (AMNH_PBI 00071815).

Fig. 41 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)

Fig. 41. Schaffneropsallus oaxacensis: Male genitalia (AMNH_PBI 00058288; 00058287, right paramere only); female genitalia (AMNH_PBI 00058289).

Fig. 39 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)

Fig. 39. Stictopsallus aspersus: Male genitalia (male 1 [left hand], AMNH_PBI 00062641; male 2 [right hand], AMNH_PBI 00063197); female genitalia (AMNH_PBI 00062622).