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.
18
datasets available to search
ShareScore release 0.9.0
Dataset results
18 results for “lineage introgression”
Genomic landscape of introgression from the ghost lineage in a gobiid fish uncovers the generality of forces shaping hybrid genomes
<p>Extinct lineages can leave legacies in the genomes of extant lineages through ancient introgressive hybridization. The patterns of genomic survival of these extinct lineages provide insight into the role of extinct lineages in current biodiversity. However, our understanding of the genomic landscape of introgression from extinct lineages remains limited due to challenges associated with locating the traces of unsampled "ghost" extinct lineages without ancient genomes. Herein, we conducted population genomic analyses on the East China Sea (ECS) lineage of <em>Chaenogobius annularis</em>, which was suspected to have originated from ghost introgression, with the aim of elucidating its genomic origins and characterizing its landscape of introgression. By combining phylogeographic analysis and demographic modeling, we demonstrated that the ECS lineage originated from ancient hybridization with an extinct ghost lineage. Forward simulations based on the estimated demography indicated that the statistic <em>γ</em> of the HyDe analysis can be used to distinguish the differences in local introgression rates in our data. Consistent with introgression between extant organisms, we found reduced introgression from extinct lineage in regions with low-recombination rates and with functional importance, thereby suggesting a role of linked selection that has eliminated the extinct lineage in shaping the hybrid genome. Moreover, we identified enrichment of repetitive elements in regions associated with ghost introgression, which was hitherto little-known but was also observed in the reanalysis of published data on introgression between extant organisms. Overall, our findings underscore the unexpected similarities in the characteristics of introgression landscapes across different taxa, even in cases of ghost introgression.</p>
Genomic landscape of introgression from the ghost lineage in a gobiid fish uncovers the generality of forces shaping hybrid genomes
Open the record for dataset details and reuse information.
Data from: Genome-specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two ancestral sexual species
Quantifying introgression between sexual species and polyploid lineages traditionally thought to be asexual is an important step in understanding what drives the longevity of putatively asexual groups. Here, we capitalize on three recent innovations—ultraconserved element (UCE) sequencing, bioinformatic techniques for identifying genome-specific variation in polyploids, and model-based methods for evaluating historical gene flow—to measure the extent and tempo of introgression over the evolutionary history of an allopolyploid lineage of all-female salamanders and two ancestral sexual species. Our analyses support a scenario in which the genomes sampled in unisexual salamanders last shared a common ancestor with genomes in their parental species ~3.4 million years ago, followed by a period of divergence between homologous genomes. Recently, secondary introgression has occurred at different times with each sexual species during the last 500,000 years. Sustained introgression of sexual genomes into the unisexual lineage is the defining characteristic of their reproductive mode, but this study provides the first evidence that unisexual genomes have undergone long periods of divergence without introgression. Unlike other sperm-dependent taxa in which introgression is rare, the alternating periods of divergence and introgression between unisexual salamanders and their sexual relatives could explain why these salamanders are among the oldest described unisexual animals.
Phylogenomic discordance is driven by wide-spread introgression and incomplete lineage sorting during rapid species diversification within rattlesnakes (Viperidae: Crotalus and Sistrurus)
<p>Phylogenomics allows us to uncover the historical signal of evolutionary processes through time and estimate phylogenetic networks accounting for these signals. Insight from genome-wide data further allows us to pinpoint the contributions to phylogenetic signal from hybridization, introgression, and ancestral polymorphism across the genome. Here, we focus on how these processes have contributed to phylogenetic discordance among rattlesnakes (genera <em>Crotalus</em> and <em>Sistrurus</em>), a group for which there are numerous conflicting phylogenetic hypotheses based on a diverse array of molecular datasets and analytical methods. We address the instability of the rattlesnake phylogeny using genomic data generated from transcriptomes sampled from nearly all known species. These genomic data, analyzed with coalescent and network-based approaches, reveal numerous instances of rapid speciation where individual gene trees conflict with the species tree. Moreover, the evolutionary history of rattlesnakes is dominated by incomplete speciation and frequent hybridization, both of which have likely influenced past interpretations of phylogeny. We present a new framework in which the evolutionary relationships of this group can only be understood in light of genome-wide data and network-based analytical methods. Our data suggest that network radiations, like those seen within the rattlesnakes, can only be understood in a phylogenomic context, necessitating similar approaches in our attempts to understand evolutionary history in other rapidly radiating species.</p> <p>La filogenómica nos permite descubrir la señal histórica de los procesos evolutivos a través del tiempo y estimar redes filogenéticas tomando en cuenta estas señales. El conocimiento de datos genómicos incluso permiten distinguir la contribución de la señal filogenética de la hibridación, introgresión, y de polimorfismos ancestrales a lo largo del genoma. En este trabajo nos enfocamos en como estos procesos han contribuido a la discordancia filogenética entre las serpientes de cascabel, un grupo en el que hay numerosos conflictos en las hipótesis filogenéticas obtenidas de un grupo variado de datos moleculares y métodos analíticos. Nosotros abordamos la inestabilidad de la filogenia de las serpientes de cascabel (generos <em>Crotalus</em> y <em>Sistrurus</em>) usando datos genómicos generados de transcriptomas muestreados en la mayoría de las especies conocidas. Estos datos genómicos, analizados con métodos basados en coalescencia y redes filogenéticas, revelaron numerosos casos de especiación rápida donde los arboles de genes individuales conflictúan con el árbol de especies. Además, la historia evolutiva de las serpientes de cascabel esta dominada por una especiación incompleta y una frecuente hibridación, las cuales probablemente han influenciado interpretaciones pasadas de las filogenias. Nosotros presentamos un nuevo marco en el que las relaciones evolutivas de este grupo solo pueden ser entendidas en base a datos de genomicos y métodos analíticos basados en redes filogenéticas. Nuestros datos sugieren que la radiación en redes filogenéticas, como se ha visto dentro de las serpientes de cascabel, solo puede ser entendida en un contexto filogenómico, necesitando aproximaciones similares en nuestro intento de entender la historia evolutiva en otras especies con radiaciones rápidas.</p>
Data from: Summary tests of introgression are highly sensitive to rate variation across lineages
<p>The evolutionary implications and frequency of hybridization and introgression are increasingly being recognized across the tree of life. To detect hybridization from multi-locus and genome-wide sequence data, a popular class of methods is based on summary statistics from subsets of 3 or 4 taxa. However, these methods often carry the assumption of a constant substitution rate across lineages and genes, which is commonly violated in many groups. In this work, we quantify the effects of rate variation on the <em>D </em>test (also known as ABBA-BABA test), the <em>D</em><sub>3</sub> test, and HyDe. All three tests are used widely across a range of taxonomic groups, in part because they are very fast to compute. We consider rate variation across species lineages, across genes, their lineage-by-gene interaction, and residual variation across gene-tree edges. We do so by simulating gene trees within species networks according to a birth-death-hybridization process so as to capture a range of realistic species phylogenies. For all three methods tested, we found a marked increase in the false discovery of reticulation (type-1 error rate) when there is rate variation across species lineages. The <em>D</em><sub>3</sub> test was the most sensitive, with around 80% type-1 error, such that <em>D</em><sub>3</sub> appears to be more sensitive to a departure from the clock than to the presence of reticulation. For all three tests, the power to detect hybridization events decreased as the number of hybridization events increased, indicating that multiple hybridization events can obscure one another if they occur within a small subset of taxa. Our study highlights the need to consider rate variation when using site-based summary statistics and points to the advantages of methods that do not require assumptions on evolutionary rates across lineages or across genes.</p>
Data for: Echoes of ancient introgression punctuate stable genomic lineages in the evolution of figs
<p class="MsoNormal"><span>Studies investigating the evolution of flowering plants have long focused on isolating mechanisms such as pollinator specificity. Some recent studies have proposed a role for introgressive hybridization between species, recognizing that isolating processes such as pollinator specialization may not be complete barriers to hybridization. Occasional hybridization may therefore lead to distinct yet reproductively connected lineages.</span></p> <p class="MsoNormal"><span>We investigate the balance between introgression and reproductive isolation in a diverse clade using a densely sampled phylogenomic study of fig trees (<em>Ficus</em>, Moraceae). Co-diversification with specialized pollinating wasps (Agaonidae) is recognized as a major engine of fig diversity, leading to about 850 species. Nevertheless, some studies have focused on the importance of hybridization in <em>Ficus</em>, highlighting the consequences of pollinator sharing. Here we employ dense taxon sampling (520 species) throughout Moraceae and 1,858 loci to investigate phylogenetic relationships and the prevalence of introgression among species throughout the history of <em>Ficus</em>.</span></p> <p class="MsoNormal"><span>We present a well-resolved phylogenomic backbone for <em>Ficus</em>, providing a solid foundation for an updated classification. Our results paint a picture of phylogenetically stable evolution within lineages punctuated by occasional local introgression events likely mediated by local pollinator sharing, illustrated by clear cases of cytoplasmic introgression that have been nearly drowned out of the nuclear genome through subsequent lineage fidelity. The phylogenetic history of figs thus highlights that while hybridization is an important process in plant evolution, the mere ability of species to hybridize locally does not necessarily translate into ongoing introgression between distant lineages, particularly in the presence of obligate plant-pollinator relationships.</span></p>
Phylogenomic discordance is driven by wide-spread introgression and incomplete lineage sorting during rapid species diversification within rattlesnakes (Viperidae: Crotalus and Sistrurus)
Open the record for dataset details and reuse information.
Data from: Genome-specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two ancestral sexual species
Open the record for dataset details and reuse information.
Data from: Summary tests of introgression are highly sensitive to rate variation across lineages
Open the record for dataset details and reuse information.
Data for: Echoes of ancient introgression punctuate stable genomic lineages in the evolution of figs
Open the record for dataset details and reuse information.
Data from: Phylogenomic signatures of ancient introgression in a rogue lineage of darters (Teleostei: Percidae)
Evolutionary history is typically portrayed as a branching phylogenetic tree, yet not all evolution proceeds in a purely bifurcating manner. Introgressive hybridization is one process that results in reticulate evolution. Most known examples of genome-wide introgression occur among closely related species with relatively recent common ancestry; however, we present evidence for ancient hybridization and genome-wide introgression between major stem lineages of darters, a species-rich clade of North American freshwater fishes. Previous attempts to resolve the relationships of darters have been confounded by the uncertain phylogenetic resolution of the lineage Allohistium. In this study we investigate the phylogenomics of darters, specifically the relationships of Allohistium, through analyses of ~30,000 RADseq loci sampled from 112 species. Our phylogenetic inferences are based on traditional approaches in combination with strategies that accommodate reticulate evolution. These analyses result in a novel phylogenetic hypothesis for darters that includes ancient introgression involving Allohistium and other two major darter lineages, minimally occurring 20 million years ago. Darters offer a compelling case for the necessity of incorporating phylogenetic networks in reconstructing the evolutionary history of diversification in species-rich lineages. We anticipate that the growing wealth of genomic data for clades of non-model organisms will reveal more examples of ancient hybridization, eventually requiring a re-evaluation of how evolutionary history is visualized and utilized in macroevolutonary investigations.
Seeing through the hedge: Phylogenomics of Thuja (Cupressaceae) reveals prominent incomplete lineage sorting and ancient introgression for Tertiary relict flora
<p>The eastern Asia (EA) – eastern North America (ENA) disjunction is a typical and well known biogeographic. Although its origin has been the topic of many studies, some new insights will arise when more complex evolutionary histories are revealed using phylogenomic methods. Here, we used targeted exon capture and sequenced >1,000 single copy nuclear, plus 73 chloroplast genes, to resolve interspecific relationships and the biogeographic history of an intercontinental disjunct genus <i>Thuja</i>. Two separate clades were detected: the "EA clade" comprised two species (<a name="_Hlk63130225"><i>T. standishii</i></a><i> </i>and <a name="_Hlk63130201"><i>T. sutchuenensis</i></a>) from EA, and the "disjunct clade" comprising <i>T. koraiensis</i>, <i>T. occidentalis</i>, and <i>T. plicata</i>, with the first two comprising an EA–ENA disjunct pattern and <i>T. plicata</i> in western North America. The disjunct clade experienced a rapid radiation in the Mid–Miocene, and furthermore multispecies coalescent analysis revealed that ancient lineages of <i>Thuja</i> had large population sizes. These two factors might have contributed to the significant levels of incomplete lineage sorting (ILS) we detected within <i>Thuja</i>, and especially the disjunct clade. Because of this, EA–ENA disjunct pattern of <i>T. koraiensis</i> and <i>T. occidentalis</i> is exhibited by only 13.98% of genes examined. In addition, we found that ~20% of the <i>T. sutchuenensis </i>nuclear genome is derived from an as–yet–unrecognized ancestral lineage<i> </i>of <i>Thuja</i>, which might explain the close resemblance of cone morphology between <i>T. sutchuenensis</i> and the Paleocene fossil species <i>T. ehrenswaerdii</i>. Overall, our study demonstrates that single genes may produce incomplete or inaccurate phylogenies for disjunct taxa, and that more accurate results will come from using genomic data, revealing a more complex evolutionary history. This will steadily improve our understanding of their origin and evolution.</p>
Data from: Phylogenomic signatures of ancient introgression in a rogue lineage of darters (Teleostei: Percidae)
Open the record for dataset details and reuse information.
Data from: Genomic data reveals potential for hybridization, introgression, and incomplete lineage sorting to confound phylogenetic relationships in an adaptive radiation of narrow-mouth frogs
Open the record for dataset details and reuse information.
Seeing through the hedge: Phylogenomics of Thuja (Cupressaceae) reveals prominent incomplete lineage sorting and ancient introgression for Tertiary relict flora
Open the record for dataset details and reuse information.
Data from: Disentangling incomplete lineage sorting and introgression to refine species-tree estimates for Lake Tanganyika cichlid fishes
Open the record for dataset details and reuse information.
Data from: Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus)
• Botanists have long recognized interspecific gene flow as a common occurrence within white oaks (Quercus section Quercus). Historical allele exchange, however, has not been fully characterized, and the complex genomic signals resulting from the combination of vertical and horizontal gene transmission may confound phylogenetic inference and obscure our ability to accurately infer the deep evolutionary history of oaks. • Using anchored enrichment, we obtained a phylogenomic dataset consisting of hundreds of single-copy nuclear loci. Concatenation, species tree, and network analyses were carried out in an attempt to uncover the genomic signal of ancient introgression and infer the divergent phylogenetic topology for the white oak clade. Locus and site-level likelihood comparisons were then conducted to further explore the introgressed signal within our dataset. • Historical, intersectional gene flow is suggested to have occurred between (1) an ancestor of the Eurasian Roburoid lineage and Quercus pontica and (2) North American Dumosae and Prinoideae lineages. • Despite extensive time past, our approach proved successful in detecting the genomic signature of ancient introgression. Our results, however, highlight the importance of sampling and the use of a plurality of analytical tools and methods to sufficiently explore genomic datasets, uncover this signal, and accurately infer evolutionary history.
Data from: Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus)
Open the record for dataset details and reuse information.
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.