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351 results for “gene tree”
Data from: Gene trees, species trees and Earth history combine to shed light on the evolution of migration in a model avian system
The evolution of migration in birds has fascinated biologists for centuries. In this study, we performed phylogenetic-based analyses of Catharus thrushes, a model genus in the study of avian migration, and their close relatives. For these analyses, we used both mitochondrial and nuclear genes, and the resulting phylogenies were used to trace migratory traits and biogeographic patterns. Our results provide the first robust assessment of relationships within Catharus and relatives and indicate that both mitochondrial and autosomal genes contribute to overall support of the phylogeny. Measures of phylogenetic informativeness indicated that mitochondrial genes provided more signal within Catharus than did nuclear genes, whereas nuclear loci provided more signal for relationships between Catharus and close relatives than did mitochondrial genes. Insertion and deletion events also contributed important support across the phylogeny. Across all taxa included in the study, and for Catharus, possession of long-distance migration is reconstructed as the ancestral condition, and a North American (north of Mexico) ancestral area is inferred. Within Catharus, sedentary behaviour evolved after the first speciation event in the genus and is geographically and temporally correlated with Central American distributions and the final closure of the Central American Seaway. Migratory behaviour subsequently evolved twice in Catharus and is geographically and temporally correlated with a recolonization of North America in the late Pleistocene. By temporally linking speciation events with changes in migratory condition and events in Earth history, we are able to show support for several competing hypotheses relating to the geographic origin of migration.
Data from: Adaptive evolution and segregating load contribute to the genomic landscape of divergence in two tree species connected by episodic gene flow
Speciation often involves repeated episodes of genetic contact between divergent populations before reproductive isolation (RI) is complete. Whole-genome sequencing (WGS) holds great promise for unravelling the genomic bases of speciation. We have studied two ecologically divergent, hybridizing species of the 'model tree' genus Populus (poplars, aspens, cottonwoods), Populus alba and P. tremula, using >8.6 million single nucleotide polymorphisms (SNPs) from WGS of population pools. We used the genomic data to (i) scan these species' genomes for regions of elevated and reduced divergence, (ii) assess key aspects of their joint demographic history based on genomewide site frequency spectra (SFS) and (iii) infer the potential roles of adaptive and deleterious coding mutations in shaping the genomic landscape of divergence. We identified numerous small, unevenly distributed genome regions without fixed polymorphisms despite high overall genomic differentiation. The joint SFS was best explained by ancient and repeated gene flow and allowed pinpointing candidate interspecific migrant tracts. The direction of selection (DoS) differed between genes in putative migrant tracts and the remainder of the genome, thus indicating the potential roles of adaptive divergence and segregating deleterious mutations on the evolution and breakdown of RI. Genes affected by positive selection during divergence were enriched for several functionally interesting groups, including well-known candidate 'speciation genes' involved in plant innate immunity. Our results suggest that adaptive divergence affects RI in these hybridizing species mainly through intrinsic and demographic processes. Integrating genomic with molecular data holds great promise for revealing the effects of particular genetic pathways on speciation.
Data from: Genetic differentiation in spite of high gene flow in the dominant rainforest tree of southeastern Australia, Nothofagus cunninghamii
Nothofagus cunninghamii is a long-lived, wind-pollinated tree species that dominates the cool temperate rainforests of southeastern Australia. The species' distribution is more or less continuous in western Tasmania but is fragmented elsewhere. However, it is unknown whether this fragmentation has affected the species' genetic architecture. Thus, we examined N. cunninghamii using 12 nuclear microsatellites and 633 individuals from 18 populations spanning the species' natural range. Typical of wind-pollinated trees, there was low range-wide genetic structure (FST=0.04) consistent with significant gene flow across most of the species' range. However, gene flow was not high enough to overcome the effects of drift across some disjunctions. Victorian populations (separated from Tasmania by the 240 km wide Bass Strait) formed a genetic group distinct from Tasmanian populations, had lower diversity (mean allelic richness (Ar)=5.4 in Victoria versus 6.9 in Tasmania) and were significantly more differentiated from one another than those in Tasmania (FST=0.045 in Victoria versus 0.012 in Tasmania). Evidence for bottlenecking was found in small populations that were at least 20 km from other populations. Interestingly, we found little divergence in microsatellite markers between the extremes of genetically based morphological and physiological altitudinal clines suggesting adaptive differentiation is strongly driven by selection because it is likely to be occurring in the presence of gene flow. Even though the cool temperate rainforests of Australia are highly relictual, the species is relatively robust to population fragmentation due to high levels of genetic diversity and gene flow, especially in Tasmania.
Data from: Long term impacts of selective logging on two Amazonian tree species with contrasting ecological and reproductive characteristics: inferences from Eco-gene model simulations
The impact of logging and subsequent recovery after logging is predicted to vary depending on specific life history traits of the logged species. The Eco-gene simulation model was used to evaluate the long-term impacts of selective logging over 300 years on two contrasting Brazilian Amazon tree species, Dipteryx odorata and Jacaranda copaia. D. odorata (Leguminosae), a slow growing climax tree, occurs at very low densities, whereas J. copaia (Bignoniaceae) is a fast growing pioneer tree that occurs at high densities. Microsatellite multilocus genotypes of the pre-logging populations were used as data inputs for the Eco-gene model and post-logging genetic data was used to verify the output from the simulations. Overall, under current Brazilian forest management regulations, there were neither short nor long-term impacts on J. copaia. By contrast, D. odorata cannot be sustainably logged under current regulations, a sustainable scenario was achieved by increasing the minimum cutting diameter at breast height from 50 to 100 cm over 30-year logging cycles. Genetic parameters were only slightly affected by selective logging, with reductions in the numbers of alleles and single genotypes. In the short term, the loss of alleles seen in J. copaia simulations was the same as in real data, whereas fewer alleles were lost in D. odorata simulations than in the field. The different impacts and periods of recovery for each species support the idea that ecological and genetic information are essential at species, ecological guild or reproductive group levels to help derive sustainable management scenarios for tropical forests.
Phylogenetic tree of S-protein genes of selected betacoronaviruses
<p>The emergence of SARS-CoV-2 has resulted in more than 200,000 infections and nearly 9,000 deaths globally so far. This novel virus is thought to have originated from an animal reservoir, and acquired the ability to infect human cells using the SARS-CoV cell receptor hACE2. In the wake of a global pandemic it is essential to improve our understanding of the evolutionary dynamics surrounding the origin and spread of a novel infectious disease. One way theory predicts selection pressures should shape viral evolution is to enhance binding with host cells. We first assessed evolutionary dynamics in select betacoronavirus spike protein genes to predict where these genomic regions are under directional or purifying selection between divergent viral lineages at various scales of relatedness. With this analysis, we determine a region inside the receptor-binding domain with putative sites under positive selection interspersed among highly conserved sites, which are implicated in structural stability of the viral spike protein and its union with human receptor hACE2. Next, to gain further insights into factors associated with coronaviruses recognition of the human host receptor, we performed modeling studies of five different coronaviruses and their potential binding to hACE2. Modeling results indicate that interfering with the salt bridges at hot spot 353 could be an effective strategy for inhibiting binding, and hence for the prevention of coronavirus infections. We also propose that a glycine residue at the receptor binding domain of the spike glycoprotein can have a critical role in permitting bat variants of the coronaviruses to infect human cells.</p>
Data from: Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales
PREMISE OF STUDY: The carnivorous members of the large, hyperdiverse Caryophyllales (e.g., Venus flytrap, sundews, and Nepenthes pitcher plants) represent perhaps the oldest and most diverse lineage of carnivorous plants. However, despite numerous studies seeking to elucidate their evolutionary relationships, the early-diverging relationships remain unresolved. METHODS: To explore the utility of phylogenomic data sets for resolving relationships among the carnivorous Caryophyllales, we sequenced 10 transcriptomes, including all the carnivorous genera except those in the rare West African liana family Dioncophyllaceae. We used a variety of methods to infer the species tree, examine gene tree conflict, and infer paleopolyploidy events. KEY RESULTS: Phylogenomic analyses supported the monophyly of the carnivorous Caryophyllales, with a crown age of 68–83 million years. In contrast to previous analyses, we recovered the remaining noncore Caryophyllales as nonmonophyletic, although the node supporting this relationship contained a significant amount of gene tree discordance. We present evidence that the clade contains at least seven independent paleopolyploidy events, previously unresolved nodes from the literature have high levels of gene tree conflict, and taxon sampling influences topology even in a phylogenomic data set, regardless of the use of coalescent or supermatrix methods. CONCLUSIONS: Our data demonstrate the importance of carefully considering gene tree conflict and taxon sampling in phylogenomic analyses. Moreover, they provide a remarkable example of the propensity for paleopolyploidy in angiosperms, with at least seven such events in a clade of less than 2500 species.
Data from: Accounting for uncertainty in gene tree estimation: summary-coalescent species tree inference in a challenging radiation of Australian lizards
Accurate gene tree inference is an important aspect of species tree estimation in a summary-coalescent framework. Yet, in empirical studies, inferred gene trees differ in accuracy due to stochastic variation in phylogenetic signal between targeted loci. Empiricists should, therefore, examine the consistency of species tree inference, while accounting for the observed heterogeneity in gene tree resolution of phylogenomic data sets. Here, we assess the impact of gene tree estimation error on summary-coalescent species tree inference by screening ${\sim}2000$ exonic loci based on gene tree resolution prior to phylogenetic inference. We focus on a phylogenetically challenging radiation of Australian lizards (genus Cryptoblepharus, Scincidae) and explore effects on topology and support. We identify a well-supported topology based on all loci and find that a relatively small number of high-resolution gene trees can be sufficient to converge on the same topology. Adding gene trees with decreasing resolution produced a generally consistent topology, and increased confidence for specific bipartitions that were poorly supported when using a small number of informative loci. This corroborates coalescent-based simulation studies that have highlighted the need for a large number of loci to confidently resolve challenging relationships and refutes the notion that low-resolution gene trees introduce phylogenetic noise. Further, our study also highlights the value of quantifying changes in nodal support across locus subsets of increasing size (but decreasing gene tree resolution). Such detailed analyses can reveal anomalous fluctuations in support at some nodes, suggesting the possibility of model violation. By characterizing the heterogeneity in phylogenetic signal among loci, we can account for uncertainty in gene tree estimation and assess its effect on the consistency of the species tree estimate. We suggest that the evaluation of gene tree resolution should be incorporated in the analysis of empirical phylogenomic data sets. This will ultimately increase our confidence in species tree estimation using summary-coalescent methods and enable us to exploit genomic data for phylogenetic inference.
Data from: Testing hypotheses of mitochondrial gene-tree paraphyly: unraveling mitochondrial capture of the Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis) by the Taiwan Scimitar Babbler (P. musicus)
Species-level paraphyly inferred from mitochondrial gene trees is a prevalent phenomenon in taxonomy and systematics, but there are several potential causes that are not easily explained by currently used methods. The present study aims to test the underlying causes behind the observed paraphyly of Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis) via statistical analyses of four mitochondrial (mtDNA) and nine nuclear (nuDNA) genes. Mitochondrial gene trees show paraphyly of P. ruficollis with respect to the Taiwan Scimitar Babbler (P. musicus), but nuclear genealogies support a sister-group relationship. Predictive coalescent simulations imply several hypothetical explanations, the most likely being mitochondrial capture of P. ruficollis by P. musicus for the observed cyto-nuclear incongruence. Further Approximate Bayesian Computation suggests a unidirectional introgression model with substantial level of gene flow from P. ruficollis to P. musicus during their initial divergence during the Late Pleistocene. This specific observation frames several potential causes for incongruent outcomes of mitochondrial and nuclear introgression in general, and on the whole, our results underscore the strength of multiple independent loci for species delimitation and importance of testing hypotheses that explain disparate causes of mitochondrial gene-tree paraphyly.
Data from: Inferring species networks from gene trees in high-polyploid North American and Hawaiian violets (Viola, Violaceae)
The phylogenies of allopolyploids take the shape of networks and cannot be adequately represented as bifurcating trees. Especially for high-polyploids (i.e., organisms with more than six sets of nuclear chromosomes), the signatures of gene homoeolog loss, deep coalescence and polyploidy may become confounded, with the result that gene trees may be congruent with more than one species network. Herein, we obtained the most parsimonious species network by objective comparison of competing scenarios involving polyploidization and homoeolog loss in a high-polyploid lineage of violets (Viola, Violaceae) mostly or entirely restricted to North America, Central America, or Hawaii. We amplified homoeologs of the low-copy nuclear gene GPI by single-molecule PCR and the chloroplast trnL-F region by conventional PCR for 51 species and subspecies. Topological incongruence among GPI homoeolog subclades, owing to deep coalescence and two instances of putative loss (or lack of detection) of homoeologs, were reconciled by applying the maximum tree topology for each subclade. The most parsimonious species network and the fossil-based calibration of the homoeolog tree favored monophyly of the high-polyploids, which has resulted from allodecaploidization 9–14 Ma ago, involving sympatric ancestors from the extant Viola sections Chamaemelanium (diploid), Plagiostigma (paleotetraploid), and Viola (paleotetraploid). While two of the high-polyploid lineages (Boreali-Americanae, Pedatae) remained decaploid, recurrent polyploidization with tetraploids of section Plagiostigma within the last 5 Ma has resulted in two 14-ploid lineages (Mexicanae, Nosphinium) and one 18-ploid lineage (Langsdorffianae). This implies a more complex phylogenetic and biogeographic origin of the Hawaiian violets (Nosphinium) than that previously inferred from rDNA data and illustrates the necessity of considering polyploidy in phylogenetic and biogeographic reconstruction.
Data from: Neighborhood defense gene similarity effects on tree performance: a community transcriptomic approach
The structure and dynamics of ecological communities are ultimately the outcome of the differential demographic rates of individuals. Individual growth and mortality rates largely result from the interaction between an organism's phenotype and the abiotic and biotic environment. Functional traits have been used extensively over the past decade to elucidate links among phenotypes, demography and community dynamics. A fundamental weakness of most functional trait approaches is the use of 'soft' traits associated with resource acquisition to examine how neighbourhood similarity affects tree survival and growth. However, these 'soft' traits are unlikely to be good predictors of similarities among co-occurring species. Less easily measured aspects of organismal function – such as those related to defence – have frequently gone unmeasured. This is particularly problematic for testing important hypotheses in forest ecology, such as the Janzen–Connell hypothesis where focal trees are expected to be at a disadvantage if their neighbours share the same natural enemies. A potential alternative to functional trait approaches is to quantify the transcriptomic or functional genomic similarity of species. Such analyses are now possible in natural systems where de novo transciptome assemblies can be used to conduct functional phylogenomic analyses where homologous gene trees are produced. Using demographic plot data for 21 species from a North American forest dynamic plot, we conduct a community functional phylogenomic analysis of a plant community to elucidate the similarity in defence response genes across species. This similarity was then used to ask whether the similarity in defence genes of heterospecific species in the local neighbourhood of a focal individual tree influences its growth and mortality rates. The results show that individual growth rates are higher when surrounded by dissimilar heterospecific species for 16 of 27 defence genes analysed. Additionally, survival rates are increased when an individual is in a neighbourhood with dissimilar species for 4 of the 27 defence genes studied. Lastly, strong conspecific effects were found in all analyses, underscoring that future analyses investigating the genetic variation and differential expression of defence-related genes in neighbourhoods may prove important. Synthesis. In summary, this research leverages recent advances in RNA sequencing and bioinformatics to conduct community-wide transcriptomic analyses and analyses of defence-related gene similarity across a tree community. The results demonstrate that defence gene similarity in neighbourhoods often does have negative effects on individual demographic performance as predicted by the Janzen–Connell hypothesis.
Data from: The effects of inference method, population sampling and gene sampling on species tree inferences: an empirical study in slender salamanders (Plethodontidae: Batrachoseps)
Species tree methods are now widely used to infer the relationships among species from multi-locus datasets. Many methods have been developed, which differ in whether gene and species trees are estimated simultaneously or sequentially, and in how gene trees are used to infer the species tree. While these methods perform well on simulated data, less is known about what impacts their performance on empirical data. We used a dataset including five nuclear genes and one mitochondrial gene for 22 species of Batrachoseps to compare the effects of method of analysis, within-species sampling and gene sampling on species tree inferences. For this dataset, the choice of inference method had the largest effect on the species tree topology. Exclusion of individual loci had large effects in *BEAST and STEM, but not in MP-EST. Different loci carried the greatest leverage in these different methods, showing that the causes of their disproportionate effects differ. Even though substantial information was present in the nuclear loci, the mitochondrial gene dominated the *BEAST species tree. This leverage is inherent to the mtDNA locus and results from its high variation and lower assumed ploidy. This mtDNA leverage may be problematic when mtDNA has undergone introgression, as is likely in this dataset. By contrast, the leverage of RAG1 in STEM analyses does not reflect properties inherent to the locus, but rather results from a gene tree that is strongly discordant with all others, and is best explained by introgression between distantly related species. Within-species sampling was also important, especially in *BEAST analyses, as shown by differences in tree topology across 100 subsampled datasets. Despite the sensitivity of the species tree methods to multiple factors, five species groups, the relationships among these, and some relationships within them, are generally consistently resolved for Batrachoseps.
Data from: Patterns of diversity and spatial variability of β-defensin innate immune genes in a declining wild population of tree swallows
Assessing the genetic variation and distribution of immune genes across heterogeneous environmental conditions in wild species is essential to further our understanding of the role of pathogen pressure and potential resistance or prevalence in hosts. Researchers have recently investigated β-defensin genes in the wild, because their variability suggests that they may play an important role in innate host defense. This study investigated the variation occurring at 6 innate immune genes of the β-defensin family in a declining population of tree swallows (Tachycineta bicolor) in southern Québec, Canada (N = 160). We found that all 6 genes showed synonymous and nonsynonymous single nucleotide polymorphisms (SNPs) within the exon coding for the mature peptide. These results indicated that this group of genes was diverse in tree swallows. Our results suggested a potential interaction of this group of genes with fluctuating pathogen diversity, however, we found no sign of positive or negative selection. We assessed whether or not the distribution of genetic diversity of β-defensin genes in our study population differed between 2 regions that strongly differ in their level of agricultural intensification. Adults are highly philopatric to their breeding sites and their immunological responses differ between these 2 regions. However, we found little evidence that the level and distribution of genetic variability differed between these heterogeneous environmental conditions. Further studies should aim to assess the link between genetic diversity of β-defensin genes and fitness-related traits in wild populations.
Data from: Asymmetric hybridization and gene flow between Joshua trees (Agavaceae: Yucca) reflects differences in pollinator host specificity.
The angiosperms are by far the largest group of terrestrial plants. Their spectacular diversity is often attributed to specialized pollination. Obligate pollination mutualisms where both a plant and its pollinator are dependent upon one another for reproduction are thought to be prone to rapid diversification through co-evolution and pollinator isolation. However, few studies have evaluated the degree to which pollinators actually mediate reproductive isolation in these systems. Here, we examine evidence for hybridization and gene flow between two subspecies of Joshua tree (Yucca brevifolia brevifolia and Yucca brevifolia jaegeriana) pollinated by two sister species of yucca moth. Previous work indicated that the pollinators differ in host specificity, and DNA sequence data suggested asymmetric introgression between the tree subspecies. Through intensive sampling in a zone of sympatry, a large number of morphologically intermediate trees were identified. These included trees with floral characters typical of Y. b. jaegeriana, but vegetative features typical of Y. b. brevifolia. The opposite combination—Y. b. brevifolia flowers with Y. b. jaegeriana vegetative morphology—never occurred. Microsatellite genotyping revealed a high frequency of genetically admixed, hybrid trees. Coalescent-based estimates of migration indicated significant gene flow between the subspecies and that the direction of gene flow matches differences in pollinator host fidelity. The data suggest that pollinator behaviour determines the magnitude and direction of gene flow between the two subspecies, but that specialized pollination alone is not sufficient to maintain species boundaries. Natural selection may be required to maintain phenotypic differences in the face of ongoing gene flow.
FIGURE 1. Bayesian tree inferred from SSU gene DNA sequences. Posterior probabilities exceeding 50 in A review of the genus Tripylina Brzeski, 1963 (Nematoda: Triplonchida), with descriptions of five new species from New Zealand
FIGURE 1. Bayesian tree inferred from SSU gene DNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species, GenBank numbers, locations are listed for each taxon if known.
FIGURE 2. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50 in A review of the genus Tripylina Brzeski, 1963 (Nematoda: Triplonchida), with descriptions of five new species from New Zealand
FIGURE 2. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species, GenBank numbers, locations are listed for each taxon if known.
FIGURE 5 Bayesian phylogenetic tree inferred from SSU gene DNA sequences. Posterior probabilities great than 50 in New Zealand species of the genus Tripyla Bastian, 1865 (Nematoda: Triplonchida: Tripylidae). I: A new species, a new record and key to long-tailed species
FIGURE 5 Bayesian phylogenetic tree inferred from SSU gene DNA sequences. Posterior probabilities great than 50% are given on appropriate clades. Nematode species, GenBank numbers, locations are listed for each taxon if known.
FIGURE 6 Bayesian phylogenetic tree inferred from LSU gene DNA sequences. Posterior probabilities greater than 50 in New Zealand species of the genus Tripyla Bastian, 1865 (Nematoda: Triplonchida: Tripylidae). I: A new species, a new record and key to long-tailed species
FIGURE 6 Bayesian phylogenetic tree inferred from LSU gene DNA sequences. Posterior probabilities greater than 50% are given on appropriate clades. Nematode species, GenBank numbers, locations are listed for each taxon if known.
FIGURE 3 Bayesian tree inferred from SSU gene rDNA sequences. Posterior probabilities exceeding 50 in A review of the genus Trischistoma Cobb, 1913 (Nematoda: Enoplida), with descriptions of four new species from New Zealand
FIGURE 3 Bayesian tree inferred from SSU gene rDNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species, GenBank numbers are listed for each taxon.
FIGURE 4 Bayesian tree inferred from LSU gene rDNA sequences. Posterior probabilities exceeding 50 in A review of the genus Trischistoma Cobb, 1913 (Nematoda: Enoplida), with descriptions of four new species from New Zealand
FIGURE 4 Bayesian tree inferred from LSU gene rDNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species and GenBank numbers are listed for each taxon if known.
FIGURE 6. Fast distance based analysis tree for 16s ribosomal RNA gene. Note total genetic uniformity among 28 in Billions and billions sold: Pet-feeder crickets (Orthoptera: Gryllidae), commercial cricket farms, an epizootic densovirus, and government regulations make for a potential disaster
FIGURE 6. Fast distance based analysis tree for 16s ribosomal RNA gene. Note total genetic uniformity among 28 individuals of G. locorojo from eight "localities" on three continents. See Appendix A for specimen source data.
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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)
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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.