Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
194
datasets available to search
ShareScore release 0.7.1
Dataset results
194 results for “Reticulation”
Figure 2 in A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change
Figure 2 The NeighborNet of 273 accessions based on 27 concatenated nuclear gene fragments. Numbers indicate the series to which species have been recognized 1: Aestivales (Planchon); 2: Cinerascentes (Planchon); 3: Cordifoliae (Munson); 4: Labruscae (Planchon); 5: Ripariae (Munson); 6: Occidentales (Munson); 7: Viniferae (Planchon); 8: Flexuosae (Galet); 9: Spinosae (Galet). See also Additional file 15.
River drainage reorganization and reticulate evolution in the Two-Lined Salamander (Eurycea bislineata) species complex
<p>The origin and eventual loss of biogeographic barriers can create alternating periods of allopatry and secondary contact, facilitating gene flow among distinct metapopulations and generating reticulate evolutionary histories that are not adequately described by a bifurcating evolutionary tree. One such example may exist in the two-lined salamander (<em>Eurycea bislineata</em>) species complex, where discordance among morphological and molecular datasets has created a "vexing taxonomic challenge". Previous phylogeographic analyses of mitochondrial DNA (mtDNA) suggested that the reorganization of Miocene paleodrainages drove vicariance and dispersal, but the inherent limitations of a single-locus dataset precluded the evaluation of subsequent gene flow. Here, we generate triple-enzyme restriction site-associated DNA sequencing (3RAD) data for >100 individuals representing all major mtDNA lineages and use a suite of complementary methods to demonstrate that discordance among earlier datasets is best explained by a reticulate evolutionary history influenced by river drainage reorganization. Systematics of such groups should acknowledge these complex histories and relationships that are not strictly hierarchical.</p>
Data from: Phylogenomics, reticulation, and biogeographical history of Elaeagnaceae
Open the record for dataset details and reuse information.
Data from: Rapid radiations outweigh reticulations during the evolution of a 750-million-year-old lineage of cyanobacteria
Open the record for dataset details and reuse information.
River drainage reorganization and reticulate evolution in the Two-Lined Salamander (Eurycea bislineata) species complex
Open the record for dataset details and reuse information.
Widespread reticulate evolution in an adaptive radiation
Open the record for dataset details and reuse information.
Data from: Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus)
<p>Gene flow between evolutionarily distinct lineages is increasingly recognized as a common occurrence. Such processes distort our ability to diagnose and delimit species, as well as confound attempts to estimate phylogenetic relationships. A conspicuous example is Dusky Salamanders (<i>Desmognathus</i>), a common model-system for ecology, evolution, and behavior. Only 22 species are described; 7 in the last 40 years. However, mitochondrial datasets indicate the presence of up to 45 "candidate species" presenting a complex history of reticulation. Some authors have even suggested that the search for species boundaries in the group may be in vain. Here, we analyze nuclear and mitochondrial data containing 161 individuals from at least 49 distinct evolutionary lineages that we treat as candidate species. Concatenated and species-tree methods fail to provide satisfactory resolution for relationships among these taxa. Comparing topologies and applying methods for estimating phylogenetic networks, we find strong support for numerous instances of hybridization throughout the history of the group. We suggest that these processes may be more common than previously thought across the phylogeography-phylogenetics continuum, and that while the search for species boundaries in <i>Desmognathus</i> may not be in vain, it will be complicated by factors such as crypsis, parallelism, and gene-flow.</p>
Data from: Phylogenetic comparative methods on phylogenetic networks with reticulations
The goal of Phylogenetic Comparative Methods (PCMs) is to study the distribution of quantitative traits among related species. The observed traits are often seen as the result of a Brownian Motion (BM) along the branches of a phylogenetic tree. Reticulation events such as hybridization, gene flow or horizontal gene transfer, can substantially affect a species' traits, but are not modeled by a tree. Phylogenetic networks have been designed to represent reticulate evolution. As they become available for downstream analyses, new models of trait evolution are needed, applicable to networks. One natural extension of the BM is to use a weighted average model for the trait of a hybrid, at a reticulation point. We develop here an efficient recursive algorithm to compute the phylogenetic variance matrix of a trait on a network, in only one preorder traversal of the network. We then extend the standard PCM tools to this new framework, including phylogenetic regression with covariates (or phylogenetic ANOVA), ancestral trait reconstruction, and Pagel's λ test of phylogenetic signal. The trait of a hybrid is sometimes outside of the range of its two parents, for instance because of hybrid vigor or hybrid depression. These two phenomena are rather commonly observed in present-day hybrids. Transgressive evolution can be modeled as a shift in the trait value following a reticulation point. We develop a general framework to handle such shifts, and take advantage of the phylogenetic regression view of the problem to design statistical tests for ancestral transgressive evolution in the evolutionary history of a group of species. We study the power of these tests in several scenarios, and show that recent events have indeed the strongest impact on the trait distribution of present-day taxa. We apply those methods to a dataset of Xiphophorus fishes, to confirm and complete previous analysis in this group. All the methods developed here are available in the Julia package PhyloNetworks.
Data from: A multilocus phylogeny of the fish genus Poeciliopsis: solving taxonomic uncertainties and preliminary evidence of reticulation
The fish genus Poeciliopsis constitutes a valuable research system for evolutionary ecology, whose phylogenetic relationships have not been fully elucidated. We conducted a multilocus phylogenetic study of the genus based on seven nuclear and two mitochondrial loci with a thorough set of analytical approaches, i.e., concatenated (also known as super-matrix), species trees, and phylogenetic networks. Although several relationships remain unresolved, the overall results uncovered phylogenetic affinities among several members of this genus. A population previously considered of undetermined taxonomic status could be unequivocally assigned to P. scarlli; revealing a relatively recent dispersal event across the Trans Mexican Volcanic Belt (TMVB) or Pacific Ocean, which constitute a strong barrier to north-south dispersal of many terrestrial and freshwater taxa. The closest relatives of P. balsas, a species distributed south of the TMVB, are distributed in the north; representing an additional north–south split in the genus. An undescribed species of Poeciliopsis, with a highly restricted distribution (i.e., a short stretch of the Rio Concepcion; just south of the US-Mexico border), falls within the Leptorhaphis species complex. Our results are inconsistent with the hypothesis that this species originated by "breakdown" of an asexual-hybrid lineage. On the other hand, network analyses suggest one or more possible cases of reticulation within the genus that require further evaluation with genome-wide marker representation and additional analytical tools. The most strongly supported case of reticulation occurred within the subgenus Aulophallus (restricted to Central America), and implies a hybrid origin for P. retropinna (i.e., between P. paucimaculata and P. elongata). We consider that P. balsas and P. new species are of conservation concern.
Data from: Phylogeny and evolution of the neotropical radiation of Lachemilla (Rosaceae): uncovering a history of reticulate evolution and implications for infrageneric classification
Reticulate evolution often leads to incongruence between nuclear and plastid phylogenies and comparisons between them have been used as a first approximation to disentangle patterns of hybridization. Because other processes like incomplete lineage sorting and phylogenetic error also produce similar incongruence patterns, additional sources of evidence must be incorporated. Here we focus on reconstructing the phylogeny of genus Lachemilla using nuclear ribosomal ITS and plastid trnL-F DNA sequences, and explore widespread patterns of cytonuclear discordance in this group. Lachemilla is a highly morphologically variable group of perennial herbs and shrubs, and a nearly ubiquitous member of the diverse Neotropical high-altitude grasslands. Our analyses identified four major clades within Lachemilla that are in part congruent with previous morphological classifications of the group. Furthermore, using multiple sources of evidence, including a procrustean approach to cophylogeny estimation, coalescent-based simulations, phylogenetic networks, chromosome counts, and genome size estimations, we also revealed a large-scale pattern of incongruence between the plastid and nuclear phylogenies in Lachemilla, which is mainly the result of widespread hybridization and polyploidy. We also estimated that the origin of Lachemilla in South America (~14.5 mya) predates the "rapid-uplift" diversification model that has been suggested for other high species-richness Andean plant clades, but following the formation of the high-elevation Andean grasslands during the last 5 mya, a rapid accumulation of particular nested lineages occurred has contributed to the ubiquitous presence of Lachemilla in these biomes.
Data from: Reticulate evolution within a spruce (Picea) species complex revealed by population genomic analysis
The role of reticulation in the rapid diversification of organisms is attracting greater attention in evolutionary biology. Here, we report a population genomics approach to test the role of hybridization and introgression in the evolution of the Picea likiangensis species complex. Based on 84,793 SNPs detected in transcriptomes of 82 trees collected from 35 localities, we identified 18 hybrids (including backcrosses) distributed within the range boundaries of the four taxa. Coalescent simulations, for each pair of taxa and for all taxa taken together, rejected several tree-like divergence models and supported instead a reticulate evolution model with secondary contacts occurring during Pleistocene glacial cycles after initial divergence in the late Pliocene. Significant gene flow occurred among some taxa after secondary contact according to an analysis based on modified ABBA-BABA statistics that accommodated a rapid diversification scenario. A novel finding was that introgression between certain taxa can contribute to increasing divergence (and possibly reproductive isolation) between those taxa and other taxa within a complex at some loci. These results illuminate the reticulate nature of evolution within the P. likiangensis complex and highlight the value of population genomic data in detecting the effects of introgression in the rapid diversification of related taxa.
Data from: Reticulate evolution in nuclear Middle America causes discordance in the phylogeny of palm‐pitvipers (Viperidae: Bothriechis)
Aim: A number of processes can lead to weak or conflicting phylogenetic signals, especially in geographically dynamic regions where unstable landscapes and climates promote complex evolutionary histories. The Middle American pitviper genus Bothriechis has a complex biogeographic distribution and previous phylogenetic analyses have recovered conflicting topologies based on the data type used. Here, we tested whether historic conflicts in the phylogeny were the result of reticulate evolution and whether the inferred biogeographic history of the group would enable contact among reticulate lineages. Location: Middle America Taxon: Palm-Pitvipers (genus Bothriechis) Methods: We generated a phylogenomic dataset using an anchored phylogenomics approach and inferred a genomics-based species tree and mitochondrial tree to assess incongruence among datasets. We then generated a dated phylogeny and conducted ancestral area reconstruction to examine the biogeographic history surrounding the diversification of these species. We additionally tested whether the discordance among trees is better explained by lineage sorting or reticulate evolution by testing models of reticulate evolution inferred through multiple methods. Results: We found strong support for discordance in the phylogeny of <i>Bothriechis</i> and corresponding evidence for reticulate evolution among lineages with incongruent placement. Ancestral area reconstruction placed these taxa in adjacent regions during the time period when reticulation was projected to take place and suggested a biogeographic history heavily influenced by vicariant processes. Main conclusions: Reticulation among geographically proximate lineages has driven apparent genomic discordance in Bothriechis and is responsible for historical incongruence in the phylogeny. Inference of the order of events suggests that reticulation in Nuclear Middle American occurred during a time of geologic upheaval, promoting lineage divergence and secondary contact. Reticulate evolution and similar processes can have substantial impacts on the evolutionary trajectory of taxa and are important to explicitly test for in biogeographically complex regions. Main conclusions: Reticulation among geographically proximate lineages has driven apparent genomic discordance in Bothriechis and is responsible for historical incongruence in the phylogeny. Inference of the order of events suggests that reticulation in Nuclear Middle American occurred during a time of geologic upheaval, promoting lineage divergence and secondary contact. Reticulate evolution and similar processes can have substantial impacts on the evolutionary trajectory of taxa and are important to explicitly test for in biogeographically complex regions.
Figure 1. - Mitotic metaphases, karyograms and idiogram of Euterpe species with 2n=36 chromosomes. Euterpeedulis (A–B), Euterpeoleracea (C-D) and Euterpeprecatoria (E–F). Arrows indicate secondary constrictions. Semi-reticulate interphase nuclei of Euterpeedulis (G), Euterpeoleracea (H) and Euterpeprecatoria (I). Bar: 10 µm.
Figure 1. - Mitotic metaphases, karyograms and idiogram of Euterpe species with 2n=36 chromosomes. Euterpeedulis (A–B), Euterpeoleracea (C-D) and Euterpeprecatoria (E–F). Arrows indicate secondary constrictions. Semi-reticulate interphase nuclei of Euterpeedulis (G), Euterpeoleracea (H) and Euterpeprecatoria (I). Bar: 10 µm.
The original figure plates and associated images for "A new fossil species of the reticulated beetle genus Cupes (Coleoptera: Archostemata: Cupedidae) from Eocene Baltic amber"
<p>The original figure plates and associated images for "<strong>A new fossil species of the reticulated beetle genus <em>Cupes</em> (Coleoptera: Archostemata: Cupedidae) from Eocene Baltic amber</strong>" in Zootaxa.</p> <p> </p> <h3>Abstract</h3> <p>The single extant species of the reticulated beetle genus <em>Cupes</em> Fabricius is confined to North America. In contrast, a diverse and abundant fossil record of the genus has been documented in Cenozoic deposits in Europe, especially in Eocene Baltic amber. This paper describes another species, <em>Cupes balticus</em> <strong>sp. n.</strong>, as the eighth named species of the genus from Baltic amber. The discovery of an additional <em>Cupes</em> species further evidences the hidden paleodiversity of reticulated beetles in European Eocene forests.</p> <p> </p> <p>Yamamoto, S. (2024) A new fossil species of the reticulated beetle genus <em>Cupes</em> (Coleoptera: Archostemata: Cupedidae) from Eocene Baltic amber. Zootaxa, 5432(4), 451–460. DOI: 10.11646/ZOOTAXA.5432.4.1</p>
Dataset from: Incomplete lineage sorting and reticulate evolution mask species relationships in Brunelliaceae, an Andean family with rapid, recent diversification
<p><strong>Premise</strong>: To date, phylogenetic relationships within the monogeneric Brunelliaceae have been based on morphological evidence, which does not provide sufficient phylogenetic resolution. Here we use target-enriched nuclear data to improve our understanding of phylogenetic relationships in the family. </p> <p><strong>Methods</strong>: We used the Angiosperms353 toolkit for targeted recovery of exonic regions and supercontigs (exons + introns) from low copy nuclear genes from 53 of 70 species in <em>Brunellia</em>, and several outgroup taxa. We removed loci that indicated biased relationships and applied concatenated and coalescent methods to infer <em>Brunellia</em> phylogeny. We identified conflicts among gene trees that may reflect hybridization or incomplete lineage-sorting events and assessed their impact on the phylogeny. Finally, we performed ancestral-state reconstructions of morphological traits and assessed the homology of character states used to define sections and subsections in <em>Brunellia</em>.</p> <p><strong>Results</strong>: <em>Brunellia</em> comprises two major clades and several subclades. Most of these clades/subclades do not correspond to previous infrageneric taxa. There is high topological incongruence among the subclades across analyses.</p> <p><strong>Conclusions</strong>: Phylogenetic reconstructions point to rapid species diversification in Brunelliaceae, reflected in very short branches between successive species splits. The removal of putatively biased loci slightly improves phylogenetic support for individual clades. Reticulate evolution due to hybridization and/or incomplete lineage sorting likely both contribute to gene-tree discordance. Morphological characters used to define taxa in current classification schemes are homoplastic in the ancestral character state reconstructions. While target enrichment data allows us to broaden our understanding of diversification in <em>Brunellia</em>, the relationships among subclades remain incompletely understood.</p>
Whole genome analyses disentangle reticulate evolution of primroses in a biodiversity hotspot
<p>1. Biodiversity hotspots<span>, such as the Caucasus mountains,</span> provide unprecedented opportunities for understanding the evolutionary processes that shape species diversity and richness. <span>Therefore, w</span>e investigate<span>d</span> the evolution of <em>Primula</em> sect. <em>Primula</em>, a clade with a high degree of endemism in the Caucasus.</p> <p>2. We performed phylogenetic and network analyses of whole-genome resequencing data from the entire nuclear genome, the entire chloroplast genome, and the entire heterostyly supergene. The different characteristics of the genomic partitions and the resulting phylogenetic incongruences enabled us to disentangle evolutionary histories resulting from tokogenetic versus cladogenetic processes. We provide the first phylogeny inferred from the heterostyly supergene <span>that includes</span> all species of <em>Primula</em> sect. <em>Primula</em>.</p> <p>3. Our results identified recurrent admixture at deep nodes between lineages in the Caucasus as the cause of non-monophyly in <em>Primula</em>. Biogeographic analyses support the "out-of-the-Caucasus" hypothesis, emphasizing the importance of this hotspot as a cradle for biodiversity.</p> <p>4. Our findings provide novel insights into causal processes of phylogenetic discordance, demonstrating that genome-wide analyses from partitions with contrasting genetic characteristics and broad geographic sampling are crucial for disentangling the diversification of species-rich clades in biodiversity hotspots.</p>
Data from: Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae)
Hybridization is a frequent and important force in plant evolution. Next-generation sequencing (NGS) methods offer new possibilities for clade resolution and ambitious sampling of gene genealogies, yet difficulty remains in detecting deep reticulation events using currently available methods. We reconstructed the phylogeny of diploid representatives of Amaryllidaceae tribe Hippeastreae to test the hypothesis of ancient hybridizations preceding the radiation of its major subclade, Hippeastrinae. Through hybrid enrichment of DNA libraries and NGS, we obtained data for 18 nuclear loci through a curated assembly approach and nearly complete plastid genomes for 35 ingroup taxa plus 5 outgroups. Additionally, we obtained alignments for 39 loci through an automated assembly algorithm. These data were analyzed with diverse phylogenetic methods, including concatenation, coalescence-based species tree estimation, Bayesian concordance analysis, and network reconstructions, to provide insights into the evolutionary relationships of Hippeastreae. Causes for gene tree heterogeneity and cytonuclear discordance were examined through a Bayesian posterior predictive approach (JML) and coalescent simulations. Two major clades were found, Hippeastrinae and Traubiinae, as previously reported. Our results suggest the presence of two major nuclear lineages in Hippeastrinae characterized by different chromosome numbers: 1) Tocantinia and Hippeastrum with 2n = 22, and 2) Eithea, Habranthus, Rhodophiala, and Zephyranthes mostly with 2n = 12, 14, and 18. Strong cytonuclear discordance was confirmed in Hippeastrinae, and a network scenario with at least six hybridization events is proposed to reconcile nuclear and plastid signals, along a backbone that may also have been affected by incomplete lineage sorting at the base of each major subclade.
Data from: Structural and defensive roles of angiosperm leaf venation network reticulation across an Andes-Amazon elevation gradient
1.The network of minor veins of angiosperm leaves may include loops (reticulation). Variation in network architecture has been hypothesized to have hydraulic and also structural and defensive functions. 2.We measured venation network trait space in eight dimensions for 136 biomass-dominant angiosperm tree species along a 3,300 m elevation gradient in southeastern Peru. We then examined the relative importance of multiple ecological, and evolutionary predictors of reticulation. 3.Variation in minor venation network reticulation was constrained to three axes. These axes described branching vs. reconnecting veins, elongated vs. compact areoles, and high vs. low density veins. Variation in the first two axes was predicted by traits related to mechanical strength and secondary compounds, and in the third axis by site temperature. 4.Synthesis. Defensive and structural factors primarily explain variation in multiple axes of reticulation, with a smaller role for climate-linked hydraulic factors. These results suggest that venation network reticulation may be determined more by species interactions than by hydraulic functions.
Unveiling the Patterns of Reticulated Evolutionary Processes with Phylogenomics: Hybridization and Polyploidy in the genus Rosa
<p>Reticulation, caused by hybridization and allopolyploidization, is considered an important and frequent phenomenon in the evolution of numerous plant lineages. Although both processes represent important driving forces of evolution, they are mostly ignored in phylogenetic studies involving a large number of species. Indeed only a scattering of methods exists to recover a comprehensive reticulated evolutionary history for a broad taxon sampling. Plastid markers, sometimes combined with a few nuclear sequences, are therefore favored, even though they restrict in-depth studies of hybridization and polyploidization. The genus <i>Rosa</i> encompasses c. 150 species widely distributed throughout the northern hemisphere and represents a challenging taxonomic group in which hybridization and polyploidization are prominent. Our main objective was to develop a general framework that would take patterns of reticulation into account in the study of the phylogenetic relationships among <i>Rosa</i> species. Using amplicon sequencing we targeted allele variation in the nuclear genome as well as haploid sequences in the chloroplast genome. A stepwise diploids-first approach was developed to reconstruct the reticulate evolutionary history of the genus <i>Rosa</i>. We successfully recovered robust plastid and nuclear phylogenies and performed in-depth tests for several scenarios of hybridization. Using this strategy, we were able to resolve most of the evolutionary relationships among <i>Rosa</i> subgenera, sections, and selected species, and we provide new directions for a future revision of the infrageneric classification in <i>Rosa</i>. The stepwise strategy proposed here can be used to reconstruct the phylogenetic relationships of other challenging taxonomic groups with large numbers of hybrid and polyploid taxa.</p>
Figure 2 in A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change
Figure 2 (See legend on next page.)
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.