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21 results for “Lineage fusion”
Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus)
Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (<em>Anaxyrus canorus</em>) <p>Species endemic to alpine environments can evolve via steep ecological selection gradients between lowland and upland environments. Additionally, many alpine environments have faced repeated glacial episodes over the past two million years, fracturing these endemics into isolated populations. In this "glacial pulse" model of alpine diversification, cycles of allopatry and ecologically divergent glacial refugia play a role in generating biodiversity, including novel admixed ("fused") lineages. We tested for patterns of glacial pulse lineage diversification in the Yosemite toad (<em>Anaxyrus</em> [<em>Bufo</em>] <em>canorus</em>), an alpine endemic tied to glacially influenced meadow environments. Using double-digest RADseq on populations densely sampled from a portion of the species range, we identified nine distinct lineages with divergence times ranging from 18–724 ka, coinciding with multiple Sierra Nevada glacial events. Three lineages have admixed origins, and demographic models suggest these fused lineages have persisted throughout past glacial cycles. Directionality indices supported the hypothesis that some lineages recolonized Yosemite from east of the ice sheet, whereas other lineages remained in western refugia. Finally, refugial niche reconstructions suggest that low- and high-elevation lineages have convergently adapted to similar climatic niches. Our results suggest glacial cycles and refugia may be important crucibles of adaptive diversity across deep evolutionary time.</p> <p> </p> Gene pool boundaries for the Yosemite toad (<em>Anaxyrus canorus</em>) reveal asymmetrical migration within meadow neighborhoods <p>The Yosemite toad (<em>Anaxyrus</em> [<em>Bufo</em>] <em>canorus</em>) is a federally threatened species of meadow-specializing amphibian endemic to the high-elevation Sierra Nevada Mountains of California. The species is one of the first amphibians to undergo a large demographic collapse that was well documented, and is reputed to remain in low abundance throughout its range. Recent phylogeographic work has demonstrated that Pleistocene toad lineages diverged and then admixed to differing extents across an elevational gradient. Although lineage divisions may have significant effects on evolutionary trajectories over large spatial and temporal scales, present-day population dynamics must be delineated in order to manage and conserve the species effectively. In this study, we used a double-digest RADseq dataset to address three primary questions: (1) Are single meadows or neighborhoods of nearby meadows most correlated with population boundaries? (2) Does asymmetrical migration occur among neighborhoods of nearby meadows? (3) What topographic or hydrological variables predict such asymmetrical migration in these meadow neighborhoods? Hierarchical STRUCTURE and AMOVA analyses suggested that populations are typically circumscribed by a single meadow, although 84% of meadows exist in neighborhoods of at least two meadows connected by low levels of migration, and over half (53%) of neighborhoods examined display strong asymmetrical migration. Meadow neighborhoods often contain one or more large and flat "hub" meadows that experience net immigration, surrounded by smaller and topographically rugged "satellite" meadows with net emigration. Hubs tend to contain more genetic diversity and could be prioritized for conservation and habitat management and as potential sources for reestablishment efforts.</p> <p> </p> Landscape genetics of a sub-alpine toad: Climate change predicted to induce upward range shifts via asymmetrical migration corridors <p>Climate change is expected to have a major hydrological impact on the core breeding habitat and migration corridors of many amphibians in the 21st century. The Yosemite toad (<em>Anaxyrus canorus</em>) is a species of meadow-specializing amphibian endemic to the high-elevation Sierra Nevada Mountains of California. Despite living entirely on federal lands, it has recently faced severe extirpations, yet our understanding of climatic influences on population connectivity is limited. In this study, we used a previously published double-digest RADseq dataset along with numerous remotely sensed habitat features in a landscape genetics framework to answer two primary questions in Yosemite National Park: (1) Which fine-scale climate, topographic, soil, and vegetation features most facilitate meadow connectivity? (2) How is climate change predicted to influence both the magnitude and net asymmetry of genetic migration? We developed an approach for simultaneously modeling multiple toad migration paths, akin to circuit theory, except raw environmental features can be separately considered. Our workflow identified the most likely migration corridors between meadows and used the unique cubist machine learning approach to fit and forecast environmental models of connectivity. We identified the permuted modeling importance of numerous snowpack-related features, such as runoff and groundwater recharge. Our results highlight the importance of considering phylogeographic structure, and asymmetrical migration in landscape genetics. We predict an upward elevational shift for this already high elevation species, as measured by the net vector of anticipated genetic movement, and a north-eastward shift in species distribution via the network of genetic migration corridors across the park.</p> <p> </p> <p>** Note: Multiple articles are associated with this dataset</p>
Data from: Genetic signatures of lineage fusion closely resemble population decline
<p>Accurate interpretation of the genetic signatures of past demographic events is crucial for reconstructing evolutionary history. Lineage fusion (complete merging, resulting in a single panmictic population) is a special case of secondary contact that is seldom considered. Here, the circumstances under which lineage fusion can be distinguished from population size constancy, growth, bottleneck, and decline were investigated. Multi-locus haplotype data were simulated under models of lineage fusion with different divergence versus sampling lag times (D:L ratios). These pseudo-observed datasets also differed in their allocation of a fixed amount of sequencing resources (number of sampled alleles, haplotype length, number of loci). Distinguishability of lineage fusion versus each of 10 untrue non-fusion scenarios was quantified based on six summary statistics (neutrality tests). Some datasets were also analyzed using extended Bayesian skyline plots. Results showed that signatures of lineage fusion very closely resemble those of decline—high distinguishability was generally limited to the most favorable scenario (D:L = 9), using the most sensitive summary statistics (<em>F</em><sub>S</sub> and <em>Z</em><sub>nS</sub>), coupled with the optimal sequencing resource allocation (maximizing number of loci). Also, extended Bayesian skyline plots often erroneously inferred population decline. Awareness of the potential for lineage fusion to carry the hallmarks of population decline is critical.</p>
Data from: Efficient summary statistics for detecting lineage fusion from phylogeographic datasets
<p>Aim: Lineage fusion (merging of two or more populations of a species resulting in a single panmictic group) is a special case of secondary contact. It has the potential to counteract diversification and speciation, or to facilitate it through creation of novel genotypes. Understanding the prevalence of lineage fusion in nature requires reliable detection of it, such that efficient summary statistics are needed. Here we report on simulations that characterized the initial intensity and subsequent decay of signatures of past fusion for 17 summary statistics applicable to DNA sequence haplotype data.</p> <p>Location: Global.</p> <p>Taxon: Diploid out-crossing species.</p> <p>Methods: We considered a range of scenarios that could reveal the impacts of different combinations of read length versus number of loci (arrangement of DNA sequence data), and whether or not pre-fusion populations experienced bottlenecks coinciding with their divergence (historical context of fusion). Post-fusion gene pools were sampled along 10 successive time points representing increasing lag times following merging of sister populations, and summary statistic values were recalculated at each.</p> <p>Results: Many summary statistics were able to detect signatures of complete merging of populations after a sampling lag time of 1.5 Ne generations, but the most informative ones included two neutrality tests and four diversity metrics, with ZnS being particularly powerful. Correlation was relatively low among the two neutrality tests and two of the diversity metrics. There were clear benefits of many short (200-bp × 200) loci over a handful of long (4-kb × 10) loci. Also, only the latter genetic dataset type was showed impacts of bottlenecks during divergence upon the number of informative summary statistics.<br> Main conclusions: This work contributes to identifying cases of lineage fusion, and advances phylogeography by enabling more nuanced reconstructions of how individual species, or multiple members of an ecological community, responded to past environmental change.</p>
Data from: Genetic signatures of lineage fusion closely resemble population decline
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Data from: Efficient summary statistics for detecting lineage fusion from phylogeographic datasets
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Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus)
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Data from: Lineage fusion in Galápagos giant tortoises
Although many classic radiations on islands are thought to be the result of repeated lineage splitting, the role of past fusion is rarely known because during these events, purebreds are rapidly replaced by a swarm of admixed individuals. Here we capture lineage fusion in action in a Galápagos giant tortoise species, Chelonoidis becki, from Wolf Volcano (Isabela Island). The long generation time of Galápagos tortoises and dense sampling (841 individuals) of genetic and demographic data were integral in detecting and characterizing this phenomenon. In C. becki we identified two genetically distinct, morphologically cryptic lineages. Historical reconstructions show that they colonized Wolf Volcano from Santiago Island in two temporally separated events, the first estimated to have occurred ~199 thousand years ago (KYA). Following arrival of the second wave of colonists, both lineages co-existed for approximately ~53 KY. Within that time they began fusing back together, as microsatellite data reveal widespread introgressive hybridization. Interestingly, greater mate selectivity seems to be exhibited by purebred females of one of the lineages. Forward-in-time simulations predict rapid extinction of the early arriving lineage. This study provides a rare example of reticulate evolution in action, and underscores the power of population genetics for understanding the past, present, and future consequences of evolutionary phenomena associated with lineage fusion.
Data from: Lineage fusion in Galápagos giant tortoises
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Data from: Extending phylogeography to account for lineage fusion
Secondary contact between long isolated populations has several possible outcomes. These include the strengthening of preexisting reproductive isolating mechanisms via reinforcement, the emergence of a hybrid lineage that is distinct from its extant parental lineages and which occupies a spatially restricted zone between them, or complete merging of two populations such that parental lineages are no longer extant ("lineage fusion" herein). The latter scenario has rarely been explicitly considered in single-species and comparative phylogeographic studies, yet it has the potential to impact inferences about population history and levels of congruence. In this paper, we explore the idea that insights into past lineage fusion may now be possible, owing to the advent of next-generation sequencing. Using simulated DNA sequence haplotype datasets (i.e., loci with alleles comprised of a set of linked nucleotide polymorphisms), we examined basic requirements (number of loci and individuals sampled) for identifying cases when a present-day panmictic population is the product of lineage fusion, using an exemplar statistical framework—approximate Bayesian computation. We found that with approximately 100 phased haplotype loci (400 bp) and modest sample sizes of individuals (10 per population), lineage fusion can be detected under rather challenging scenarios. This included some scenarios where reticulation was fully contained within a Last Glacial Maximum timeframe, provided that mixing was symmetrical, ancestral gene pools were moderately to deeply diverged, and the lag time between the fusion event and gene pool sampling was relatively short. However, the more realistic case of asymmetrical mixing is not prohibitive if additional genetic data (e.g., 400 loci) are available. Notwithstanding some simplifying assumptions of our simulations and the knowledge gaps that remain about the circumstances under which lineage fusion is potentially detectable, we suggest that the recent release from data limitation allows phylogeographers to expand the scope of inferences about long-term population history.
Data from: Extending phylogeography to account for lineage fusion
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Oncogenic fusions converge on shared mechanisms in initiating astroblastoma [RNA-seq of Pdgfra lineage cells]
GEO Series GSE289337. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Fusion of reprogramming factors alters trajectory of somatic lineage conversion
GEO Series GSE125740. Mus musculus. 7 samples. Type: Expression profiling by high throughput sequencing.
ZNF384 fusion oncoproteins drive lineage aberrancy in acute leukemia [RNA-seq 2]
GEO Series GSE191028. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing; Other.
SFPQ-TFE3 gene fusion reciprocally regulates mTORC1 activity and induces lineage plasticity in a novel mouse model of renal tumorigenesis
GEO Series GSE284169. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing.
ZNF384 fusion oncoproteins drive lineage aberrancy in acute leukemia [RNA-Seq]
GEO Series GSE181532. Homo sapiens; Mus musculus. 38 samples. Type: Expression profiling by high throughput sequencing.
ZNF384 fusion oncoproteins drive lineage aberrancy in acute leukemia [scRNA-Seq]
GEO Series GSE181495. Mus musculus. 3 samples. Type: Expression profiling by high throughput sequencing.
ZNF384 fusion oncoproteins drive lineage aberrancy in acute leukemia
GEO Series GSE181499. Homo sapiens; Mus musculus. 81 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Enhanced MyoD-Induced Transdifferentiation to a Myogenic Lineage by Fusion to a Potent Transactivation Domain
GEO Series GSE62448. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
ZNF384 fusion oncoproteins drive lineage aberrancy in acute leukemia [HiChIP]
GEO Series GSE181498. Mus musculus. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
ZNF384 fusion oncoproteins drive lineage aberrancy in acute leukemia [ChIP-seq]
GEO Series GSE181617. Mus musculus. 26 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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