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.
95
datasets available to search
ShareScore release 0.9.0
Dataset results
95 results for “evolutionary lineages”
Data from: Unraveling the web of life: Incomplete lineage sorting and hybridization as primary mechanisms over polyploidization in the evolutionary dynamics of pear species
Open the record for dataset details and reuse information.
Data from: A 4-lineage statistical suite to evaluate the support of large-scale retrotransposon insertion data to reconstruct evolutionary trees
Open the record for dataset details and reuse information.
A new tree-based methodological framework to infer the evolutionary history of Mesopolyploid lineages: An application to the Brassiceae tribe (Brassicaceae)
Open the record for dataset details and reuse information.
Data From: Hyperspectral leaf reflectance of grasses varies with evolutionary lineage more than with site
Open the record for dataset details and reuse information.
Lineage identification affects estimates of evolutionary mode in marine snails
Open the record for dataset details and reuse information.
Evolutionary history, novel lineages, and symbiont coevolution in the ant tribe Camponotini (Hymenoptera: Formicidae)
Open the record for dataset details and reuse information.
Data from: Pleistocene diversification in an ancient lineage: a role for glacial cycles in the evolutionary history of Dioon Lindl. (Zamiaceae).
Premise of the study: Recent estimates of crown ages for cycad genera (Late Miocene) challenge us to consider what processes have produced the extant diversity of this ancient group in such relatively little time. Pleistocene climate change has driven major shifts in species distributions in Mexico and may have led to speciation in the genus Dioon by forcing populations to migrate up in elevation thereby becoming separated by topography. Methods: We inferred orthologs from transcriptomes of five species and sequenced these in 42 individuals representing all Dioon species. From these data and published plastid sequences we inferred dated species trees and lineage-specific diversification rates. Key results: 84 nuclear orthologs and plastid data confirm four major clades within Dioon, all of Pleistocene age. Gene tree analysis, divergence dates, and an increase in diversification rate support very recent and rapid divergence of extant taxa. Conclusions: This study confirms the Pleistocene age of Dioon species and implicates Pleistocene climate change and established topography in lineage spitting. These results add to our understanding of the cycads as evolutionarily dynamic lineages, not relicts or evolutionary dead ends. We also find that well-supported secondary calibration points can be reliable in the absence of fossils. Our hypothesis of lineage splitting mediated by habitat shifts may be applicable to other taxa that are restricted to elevation specific ecotones.
Data from: Cryptic divergent lineages of Pultenaea pauciflora M.B. Scott (Fabaceae, Mirbelieae) exhibit different evolutionary history
Genetic structure among disjunct population groups of Pultenaea pauciflora was assessed to determine the evolutionary history of this species as a basis for conservation management strategies. Analysis of individuals from all extant populations using 1737 amplified length polymorphism markers revealed two highly divergent genetic entities with strong geographical structuring. Populations located at Narrogin and Brookton clustered together in Bayesian assignment analysis with every individual optimally placed in a single cluster with complete membership. Genetic differentiation between populations in these two areas was very low. Populations at Boddington were highly divergent from those located at Narrogin and Brookton. All individuals from Boddington populations were optimally placed into a second cluster with complete membership. Populations located at Boddington maintain lower levels of allelic diversity, yet greater levels of mean heterozygosity than populations located at Narrogin and Brookton. The degree of genetic differentiation and different patterns of genetic diversity strongly suggest historical divergence and separate evolutionary influences on the two lineages that occur in different ecological habitat. These Evolutionary Significant Units are likely to represent two cryptic sister taxa in the extant populations currently recognized as P. pauciflora, and the reassessment of taxonomic and conservation status of both lineages is required.
Shift in reproductive strategies in the evolutionary trajectory of a plant lineage
<p>Target loci of The Angiosperms353 gene set (AGS) assembled on Easy353 pipeline for Saxifraga section Irregulares and related taxa.</p>
Fig. 1 in Evolutionary biogeography of the freshwater fish family Anablepidae (Teleostei: Cyprinodontiformes), a marine-derived Neotropical lineage
Fig. 1 Map showing the eight areas selected in the Neotropical region overlaid with the ecoregions defined by Abell et al. (2008). These areas were selected based on Amorim and Costa (2019) and Frota et al. (2019). For details, see the "Materials and methods" section
Fig. 3 in Evolutionary biogeography of the freshwater fish family Anablepidae (Teleostei: Cyprinodontiformes), a marine-derived Neotropical lineage
Fig. 3 Cladograms showing the results of Brooks Parsimony Analysis and the historical relationships among the selected areas using Anablepidae as a case study. The two most parsimonious general area cladograms are represented by a and b. Note that the positions of the Iguaçu River basin and Southeastern Brazil are decisive for biogeographic interpretations. The strict consensus cladogram is
Fig. 3 in A molecular phylogeny of nephilid spiders: Evolutionary history of a model lineage
Fig. 3. Tree shapes for seven genes obtained with ML (best tree out of 100 replicates) with ingroup in green and outgroups in red. Note that for the two nuclear ribosomal genes (18S and 28S) the ingroup branch lengths are disproportionately long. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Fig. 6 in A molecular phylogeny of nephilid spiders: Evolutionary history of a model lineage
Fig. 6. Typical web architectures of the six nephilid genera mirroring the phylogenetic results: (a) Nephila (N. pilipes); (b) Nephilingis (N. n. sp. from Seychelles); (c) ''Nephila'' (N. inaurata); (d) Herennia (H. multipuncta); (e) Nephilengys (N. papuana); (f) Clitaetra (C. episinoides).
Fig. 5. A in A molecular phylogeny of nephilid spiders: Evolutionary history of a model lineage
Fig. 5. A summary nephilid phylogeny based on the Bayesian tree in Fig. 2 with squares at terminals color coded according to biogeographical regions (see right map inset). Branches are also color coded for geography, with the ancestral values inferred using parsimony optimization. Although the tree is not ultrametric (all terminals are in fact contemporary) the roughly estimated main clade ages are labeled according to the scheme A in Fig. 4. The nephilid ancestral age is thus between 40 and 60 million years when the Gondwanan continents were already largely split (see left map inset).
Fig. 2 in A molecular phylogeny of nephilid spiders: Evolutionary history of a model lineage
Fig. 2. Summary results from the analyses of the molecular matrices. The topology is from the Bayesian analysis of the full matrix partitioned by gene, with posterior probability values above 95% labeled with green dots at nodes. The nine squares on branches summarize the results of the alternative analyses using maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) on different matrices and partition schemes (key in upper part of legend). Bar colors are indicative of clade support (key in lower part of legend) with solid squares indicating high support, gray squares indicating low support, and empty squares indicating a clade not recovered. Terminal legend as in Fig. 1, but with additional families (from top: MIC = Micropholcommatidae, NIC = Nicodamidae, MYS = Mysmenidae, MIM = Mimetidae, CYA = Cyatholipidae, MAL = Malkaridae, ANA = Anapidae, HOL = Holarchaeidae, SYM = Symphytognathidae, SYN = Synotaxidae). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
Fig. 4 in A molecular phylogeny of nephilid spiders: Evolutionary history of a model lineage
Fig. 4. Chronograms obtained under three different calibration schemes: (a) the fossil Nephila jurassica treated as stem orbicularian (red); (b) N. jurassica treated as stem nephilid (green); (c) N. jurassica treated as stem Nephila sensu stricto as implied by the original description (black). Inset plot shows posterior distribution of the ucld.mean parameter for each calibration scheme (color codes as in trees). The arrow and the dotted area in the plot indicate the mean and 95% interval of the ucld.mean estimated by Bidegaray-Batista and Arnedo (2011). Only the scheme shown in a falls roughly within the expected mitochondrial substitution rates. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Fig. 1. A in A molecular phylogeny of nephilid spiders: Evolutionary history of a model lineage
Fig. 1. A pictorial summary of nephilid phenotypic diversity (right, a–h), and a strict consensus of 36 trees resulting from parsimony analyses combining molecular markers (full matrix) with morphology (left). The three sets of squares on branches represent node supports from alternative analyses, as follows: the left set corresponds to the parsimony jackknife support for the full (above branch) and Gblocked (Gb, below) matrices, respectively. The middle bar shows maximum likelihood (ML) bootstrap support of the full matrix under the full codon partition scheme. The right set indicates the Bremer supports for the different partitions (PBS) on the reference tree: above branches, from left to right, values for morphology + behavior, followed by the Bremer support values for the nuclear genes and below branches for the mitochondrial genes. See legend for support thresholds.Terminals have the first three letters of current taxonomic familial placement (from bottom:NEP = Nephilidae, ARA = Araneidae, TET = Tetragnathidae, NES = Nesticidae, THE = Theridiidae, THS = Theridiosomatidae, PIM = Pimoidae, LIN = Linyphiidae, DEI = Deinopidae, ULO = Uloboridae). The ingroup, nephilid part of the tree is colored in green and the ingroup terminals are colored according to the accepted nomenclature prior to the classification changes in the current study. Terminals with original molecular data end with specimen codes (as in Table 1), those with data from GenBank end with GB, and those for which only morphological (and behavioral) data were used are labeled M.
Lineage-specific variation in the evolutionary stability of coral photosymbiosis.
<p><span class="pre-line-wrapping ng-binding">Over half of reef-building corals (Scleractinia) participate in a nutritional symbiosis, known as photosymbiosis, with photosynthetic dinoflagellates that ranges from obligate to facultative dependence. Fitting hidden-rates models allowing among-lineage variation in the rate of trait evolution to supertree and molecular phylogenies of Scleractinia, we reconstruct the history of photosymbiosis within Scleractinia and characterize its evolutionary stability. We find that most lineages of scleractinians are extraordinarily stable for the trait, evincing no instances of loss, but that in some clades photosymbiosis is more labile, thus providing a framework for comparative studies to further our mechanistic understanding of the factors that shape the evolutionary fates of scleractinian photosymbiosis.</span></p>
Non-adaptive evolutionary processes governed the diversification of a temperate conifer lineage after its migration into the tropics
<p class="western">Constructing phylogenetic relationships among closely related species is a recurrent challenge in evolutionary biology, particularly for long-lived taxa with large effective population sizes and uncomplete reproductive isolation, like conifers. Conifers further have slow evolutionary rates, which raises the question of whether adaptive or non/adaptive processes were predominantly involved when they rapidly diversified after migrating from temperate regions into the tropical mountains. Indeed, fine-scale phylogenetic relationships within several conifer genus remain under debate. Here, we studied the phylogenetic relationships of endemic firs (<i>Abies</i>, Pinaceae) discontinuously distributed in the montane forests from the Southwestern United States to Guatemala, and addressed several hypotheses related to adaptive and non-adaptive radiations. We derived over 80K SNPs from genotyping by sequencing (GBS) for 45 individuals of nine Mesoamerican species to perform phylogenetic analyses. Both Maximum Likelihood and quartets-inference phylogenies resulted in a well-resolved topology, showing a single fir lineage divided in four subgroups that coincided with the main mountain ranges of Mesoamerica; thus having important taxonomic implications. Such subdivision fitted a North-South isolation by distance framework, in which non-adaptive allopatric processes seemed the rule. Interestingly, several reticulations were observed within subgroups, especially in the central-south region, which may explain past difficulties for generating infrageneric phylogenies. Further evidence for non-adaptive processes was obtained from analyses of 21 candidate-gene regions, which exhibited diminishing values of <i>π</i><sub>a</sub>/<i>π</i><sub>s</sub> and <i>K</i><sub>a</sub>/<i>K</i><sub>s</sub> with latitude, thus indicating reduced efficiency of purifying selection towards the Equator. Our study indicates that non-adaptive allopatric processes may be key generators of species diversity and endemism in the tropics.</p>
Figure 4 in Phylogeography and evolutionary lineage diversity in the small-eared greater galago, Otolemur garnettii (Primates: Galagidae)
Figure 4. Summary of results from five different species-delimitation analyses for dataset 1, comprising 76 samples of partial cytochrome b (402 bp).
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.