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1,344 results for “: phylogenomics”
Between a rock and a hard polytomy: phylogenomics of the rock-dwelling mbuna cichlids of Lake Malawi
<p>Whole genome sequences are beginning to revolutionise our understanding of phylogenetic relationships. Yet, even whole genome sequences can fail to resolve the evolutionary history of the most rapidly radiating lineages, where incomplete lineage sorting, standing genetic variation, introgression, and other factors obscure the phylogenetic history of the group. To overcome such challenges, one emerging strategy is to integrate results across different methods. Most such approaches have been implemented on reduced representation genomic datasets, but whole genomes should provide the maximum possible evidence approach. Here, we test the ability of SNPs extracted from whole genome resequencing data, implemented in an integrative genomic approach, to resolve key nodes in the phylogeny of the mbuna, rock-dwelling cichlid fishes of Lake Malaŵi, which epitomise the phylogenetic intractability that often accompanies explosive lineage diversification. This monophyletic radiation has diversified at an unparalleled rate into several hundred species in less than two million years. Using an array of phylogenomic methods, we consistently recovered four major clades of mbuna, but a large basal polytomy among them. Although introgression between clades apparently contributed to the challenge of phylogenetic reconstruction, reduction of the dataset to non-introgressed sites still did not help to resolve the basal polytomy. On the other hand, relationships among six congeneric species pairs were resolved without ambiguity, even in one case where existing data led us to predict that resolution would be difficult. We conclude that the bursts of diversification at the earliest stages of the mbuna radiation may be phylogenetically unresolvable, but other regions of the tree are phylogenetically clearly supported. Integration of multiple phylogenomic approaches will continue to increase confidence in relationships inferred from these and other whole-genome datasets.</p>
UCE Phylogenomics resolves major relationships among Ectaheteromorph ants (Hymenoptera: Formicidae: Ectatomminae, Heteroponerinae): A new classification for the subfamilies and the description of a new genus
<p>Uncovering the evolutionary history of the subfamilies Ectatomminae and Heteroponerinae, or ectaheteromorphs, is key to understanding a major branch of the ant tree of life. Despite their diversity and ecological importance, phylogenetic relationships in the group have not been well explored. One particularly suitable tool for resolving phylogeny is the use of ultraconserved elements (UCEs), which have been shown to be ideal markers at a variety of evolutionary time scales. In the present study, we enriched and sequenced 2,127 UCEs from 135 specimens of ectaheteromorph ants and investigated phylogeny using a variety of model-based phylogenomic methods. Trees recovered from partitioned maximum-likelihood and species-tree analyses were well resolved and largely congruent. The results are consistent with an expanded concept of Ectatomminae that now includes the subfamily Heteroponerinae new synonym and its single tribe Heteroponerini new combination. Eleven monophyletic groups are recognized as genera: Acanthoponera, Alfaria status revived, Boltonia Camacho and Feitosa new genus, Ectatomma, Gnamptogenys, Heteroponera, Holcoponera status revived, Poneracantha status revived, Rhytidoponera, Stictoponera status revived, and Typhlomyrmex. The new phylogenetic framework and classification proposed here will shed light on the study of Ectatomminae taxonomy and systematics, as well as on the morphological evolution of the groups that it comprises.</p>
Data from: Phylogenomics of paleoendemic lampshade spiders (Araneae, Hypochilidae, Hypochilus), with description of a new species from montane California
<p>The spider genus <em>Hypochilus</em> is a relictual lineage of Nearctic species distributed disjunctly across the United States in three montane regions (California, southern Rocky Mountains, southern Appalachia). Phylogenetic resolution of species relationships in <em>Hypochilus</em> has been challenging, with different data types recovering sometimes conflicting topologies. Furthermore, conserved morphology coupled with extreme genetic divergence and paraphyletic topologies at the species level has led to uncertain species limits in some complexes. Using a combination of ultraconserved elements (UCEs), mitochondrial CO1 by-catch, and studies of morphology, we have reconstructed <em>Hypochilus</em> interspecies relationships and have more critically evaluated the possibility of cryptic species in California and in southern Appalachia. Phylogenomic data from hundreds of nuclear loci strongly support the monophyly of regional clades, and furthermore support a ((California, Appalachia), southern Rocky Mountains)) topology. We hypothesize late Cenozoic age divergences in North America, but acknowledge that more research is needed to reliably date divergences in this genus. Within the southern Appalachian fauna, five species are resolved as four lineages (<em>H. thorelli</em> Marx, 1888 and <em>H. coylei</em> Platnick, 1987 are clearly sister taxa), but the interrelationships of these four lineages remain unresolved despite phylogenomic-scale data. The Appalachian species <em>H. pococki</em> Platnick, 1987 is recovered as monophyletic, which differs from prior mitochondrial evidence, but is clearly highly genetically structured at the nuclear level. Although algorithmic analyses of the nuclear data indicate many species (e.g., all populations as species), scanning electron microscopy (SEM) surveys of male morphology instead reveal striking morphological stasis, clearly illustrating the cryptic species problem. Within the California clade, nuclear and mitochondrial lineages of <em>H. petrunkevitchi</em> Gertsch, 1958 correspond directly to drainage basins of the southern Sierra Nevada, with <em>H. bernardino</em> Catley, 1994 nested within <em>H. petrunkevitchi</em> and sister to the southernmost basin populations. Again, algorithmic analyses of nuclear and mitochondrial data suggest many species, but we take a more conservative approach, allowing for population genetic structure within species. Combining nuclear, mitochondrial, geographic and morphological evidence we describe a new species from the Tule River and Cedar Creek drainages, <em>Hypochilus</em> <em>xomote</em> sp. nov. We also emphasize the conservation issues that face several microendemic, habitat-specialized species in this remarkable genus.</p>
Data for: Phylogenomic analyses reveal non-monophyly of the antbird genera Herpsilochmus and Sakesphorus (Thamnophilidae), with description of a new genus for Herpsilochmus sellowi
<p>The family Thamnophilidae is a species-rich Neotropical radiation of passerine birds. Current classification of its 235 species is mostly based on morphological similarities, but recent studies integrating comprehensive phenotypic and phylogenetic data have redefined taxonomic limits of several taxa. Here, we assess generic relationships of <i>Herpsilochmus</i>, <i>Sakesphorus</i>, <i>Thamnophilus</i>, <i>Biatas</i>, and <i>Dysithamnus</i> using DNA sequences from the mitochondrion, nuclear exons, and ultraconserved elements (UCEs), with further attention to interspecific relationships within <i>Herpsilochmus</i>. We show that <i>Herpsilochmus</i> and <i>Sakesphorus</i> are not monophyletic. We resolve <i>H. sellowi</i> as a deep-branch sister species to the monotypic genus <i>Biatas and S. cristatus </i>as sister to a clade comprising<i> Herpsilochmus </i>sensu stricto and<i> Dysithamnus</i>. These results are consistent across loci, obtained via concatenation and coalescent-based analyses, and supported by likelihood-ratio tests of the distribution of our sampled coalescent histories. The phenotypic distinctiveness of both <i>H.</i> <i>sellowi</i> and <i>Biatas</i> argues against merging them into a single genus. Because no generic name is available for <i>H.</i> <i>sellowi</i>, we describe a monotypic genus. The polyphyly of <i>Sakesphorus </i>warrants recognition of the available generic name <i>Sakesphoroides</i> for the distinctive and monotypic <i>S. cristatus</i>. Furthermore, we recover six well-supported species groups within <i>Herpsilochmus</i> sensu stricto. Within the context of the family as a whole, the ubiquity of long terminal branches representing monotypic genera points to extinction events among ancestors of these lineages. We suggest that retention of ancestral characters or random genetic drift coupled with extensive extinction could explain the high degree of morphological and ecological similarity across these taxa, but we highlight the potential role of the environment in driving adaptive phenotypic convergence. Finally, our results send a cautionary message against the blind use of phylogenies containing imputed data based on taxonomy due to the increasingly frequent mismatches between traditional taxonomic classification and molecular phylogenies.</p>
A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set
<p>The premise of this study is to further advance the understanding of the species-rich, economically and ecologically important Myrtales, an angiosperm order in the rosid clade comprising nine families, approximately 400 genera and almost 14000 species occurring on all continents (except Antarctica). The potential of High Throughput Sequencing (HTS) and target enrichment with the Angiosperms353 probe kit is evaluated on a sample of 485 species in 305 genera (76% of all genera in the order). Results provide technical considerations for processing HTS data and the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks such as the relationship of the early diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. HTS and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to enable selection of genes and gene trees that account for incomplete lineage sorting and hybridisation events. </p>
Rare and widespread: Integrating Bayesian MCMC approaches, Sanger sequencing and Hyb-Seq phylogenomics to reconstruct the origin of the enigmatic Rand Flora genus Camptoloma
<p class="MsoCommentText">Premise</p> <p class="MsoCommentText">Genera that are widespread but have a geographically discontinuous distribution and are represented by few species are intriguing. Did they achieve their disjunct distribution recently, or is it ancient in origin? Why are they species-poor? The Rand Flora is a continental-scale floristic pattern in which closely related species appear co-distributed in isolated regions over the edges of Africa and nearby archipelagos. Genus <i>Camptoloma</i> (Scrophulariaceae) is the most notable example, comprising three species isolated from each other at the ends of the African continent: <i>C. canariense </i>in the west, endemic to the Canary Islands; <i>C. lyperiiflorum </i>in the east, endemic to the Horn of Africa - Southern Arabia; and <i>C. rotundifolia</i>, restricted to Southern Africa.</p> <p class="MsoCommentText">Methods</p> <p class="MsoCommentText">Here, we employed Sanger sequencing of nuclear and plastid markers, together with genomic target sequencing of 2190 low-copy nuclear genes, to infer interspecies relationships and the position of <i>Camptoloma</i> within Scrophulariaceae, using supermatrix and multispecies-coalescent approaches. Lineage divergence times and ancestral ranges were inferred with Bayesian MCMC approaches. Population history was estimated with phylogeographic structured coalescent methods.</p> <p class="MsoCommentText">Key Results</p> <p class="MsoCommentText">Our results support <i>C. rotundifolia</i> as sister to the disjunct clade formed by <i>C. canariense</i> and <i>C. lyperiiflorum.</i> Stem divergence was dated in the Late Miocene, while the origin of extant diversification within the genus was inferred as Early Pliocene.</p> <p class="MsoCommentText">Conclusions</p> <p>We show that the current disjunct distribution of <i>Camptoloma </i>across Africa was likely the result of fragmentation and extinction/population bottlenecking events associated to historical aridification cycles, consistent with the "climatic refugia" hypothesis.</p>
Phylogenomic resolution of the root of Panpulmonata, a hyperdiverse radiation of gastropods: new insight into the evolution of air breathing
<p class="MsoBodyText">Transitions to terrestriality have been associated with major animal radiations including land snails and slugs in Stylommatophora (>20,000 described species), the most successful lineage of 'pulmonates' (a non-monophyletic assemblage of air-breathing gastropods). However, phylogenomic studies have failed to robustly resolve relationships among traditional pulmonates and affiliated marine lineages that comprise clade Panpulmonata (Mollusca, Gastropoda), especially two key taxa: Sacoglossa, a group including photosynthetic sea slugs; and Siphonarioidea, intertidal limpet-like snails with a non-contractile pneumostome (narrow opening to a vascularized pallial cavity). To clarify the evolutionary history of the panpulmonate radiation, we performed phylogenomic analyses on datasets of up to 1,160 nuclear protein-coding genes for 110 gastropods, including 40 new transcriptomes for Sacoglossa and Siphonarioidea. All 18 analyses recovered Sacoglossa as the sister group to a clade we named Pneumopulmonata, within which Siphonarioidea was sister to the remaining lineages in most analyses. Comparative modeling indicated shifts to marginal habitat (estuarine, mangrove and intertidal zones) preceded and accelerated the evolution of a pneumostome, present in the pneumopulmonate ancestor along with a one-sided plicate gill. These findings highlight key intermediate stages in the evolution of air-breathing snails, supporting the hypothesis that adaptation to marginal zones played an important role in major sea-to-land transitions.</p>
Phylogenomic analyses in Phrymaceae reveal extensive gene tree discordance in relationships among major clades
<p>• Premise of the study: Phylogenomic datasets using genomes and transcriptomes provide rich opportunities beyond resolving bifurcating phylogenetic relationships. Monkeyflower (Phrymaceae) is a model system for evolutionary ecology. However, it lacks a well-supported phylogeny for a stable taxonomy and for macroevolutionary comparisons.</p> <p>• Methods: We sampled 24 genomes and transcriptomes in Phrymaceae and closely related families, including eight newly sequenced transcriptomes. We reconstructed the phylogeny using IQ-TREE and ASTRAL, evaluated gene tree discordance using PhyParts, Quartet Sampling, and cloudogram, and carried out phylogenetic network analyses using PhyloNet and HyDe. We searched for whole genome duplication (WGD) events using chromosome numbers, synonymous distance, and gene duplication events.</p> <p>• Key results: Most gene trees support the monophyly of Phrymaceae and each of its tribes. Most gene trees also support the tribe Mimuleae being sister to Phrymeae + Diplaceae + Leucocarpeae, with extensive gene tree discordance among the latter three. Despite the discordance, polyphyly of Mimulus s.l. is strongly supported, and no particular reticulation event among the Phrymaceae tribes is well supported. Reticulation likely occurred among Erythranthe bicolor and close relatives. No ancient WGD event was detected in Phrymaceae. Instead, small-scale duplications are among potential drivers of macroevolutionary diversification of Phrymaceae.</p> <p>• Conclusions: We show that analysis of reticulate evolution is sensitive to taxon sampling and methods used. We also demonstrate that genome-scale data do not always fully "resolve" phylogenetic relationships. They present rich opportunities to investigate reticulate evolution, and gene and genome evolution involved in lineage diversification and adaptation.</p>
Out of the temperate zone: a phylogenomic test of the biogeographical conservatism hypothesis in a contrarian clade of ants (Hymenoptera: Formicidae: Stenammini)
<p><strong>Aim: </strong>The standard latitudinal diversity gradient (LDG), in which species richness decreases from equator to pole, is a pervasive pattern observed in most organisms. Some lineages, however, exhibit inverse LDGs. Seemingly problematic, documenting and studying contrarian groups can advance understanding of LDGs generally. Here, we identify the ant tribe Stenammini as a contrarian clade and use a historical approach to evaluate alternative hypotheses that might explain the group's atypical diversity pattern. We focus on the biogeographical conservatism hypothesis (BCH) and the diversification rate hypothesis (DRH).</p> <p><strong>Location:</strong> Global.</p> <p><strong>Taxon:</strong> Ants.</p> <p><strong>Methods: </strong>We examined the shape of the LDG in Stenammini by plotting latitudinal midpoints for all described, extant species. We then inferred a genome-scale phylogeny and used the tree to estimate divergence dates and ancestral areas. We also examined diversification rate heterogeneity across the tree and tested for a correlation between rate and latitude.</p> <p><strong>Results: </strong>Stenammini has a skewed inverse LDG with a richness peak in the northern temperate zone. Phylogenomic analyses revealed five major clades and several instances of non-monophyly among genera (<em>Goniomma, Aphaenogaster</em>). Stenammini and all its major lineages arose in the northern temperate zone. The tribe originated ~51 Ma during a climatic optimum and then diversified and dispersed southward as global climate cooled. Stenammini invaded the tropics at least seven times, but these events occurred more recently and were not linked with increased diversification. There is evidence for a diversification rate increase in Holarctic <em>Aphaenogaster</em> + <em>Messor</em>, but we found no significant correlation between latitude and diversification rate generally.</p> <p><strong>Main Conclusions:</strong> Our results largely support the BCH as an explanation for the inverse latitudinal gradient in Stenammini. The clade originated in the Holarctic and likely became more diverse there due to the combined effects of center-of-origin, time-for-speciation, and niche conservatism, rather than latitudinal differences in diversification rate.</p>
Data from: Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record
<p>Echinoids are key components of modern marine ecosystems. Despite a remarkable fossil record, the emergence of their crown group is documented by few specimens of unclear affinities, rendering their early history uncertain. The origin of sand dollars, one of its most distinctive clades, is also unclear due to an unstable phylogenetic context. We employ eighteen novel genomes and transcriptomes to build a phylogenomic dataset with a near-complete sampling of major lineages. With it, we revise the phylogeny and divergence times of echinoids, and place their history within the broader context of echinoderm evolution. We also introduce the concept of a chronospace—a multidimensional representation of node ages—and use it to explore methodological decisions involved in time calibrating phylogenies. We find the choice of clock model to have the strongest impact on divergence times, while the use of site-heterogeneous models and alternative node prior distributions showing minimal effects. The choice of loci has an intermediate impact, affecting mostly deep Paleozoic nodes, for which clock-like genes recover dates more congruent with fossil evidence. Our results reveal that crown group echinoids originated in the Permian and diversified rapidly in the Triassic, despite the relative lack of fossil evidence for this early diversification. We also clarify the relationships between sand dollars and their close relatives and confidently date their origins to the Cretaceous, implying ghost ranges spanning approximately 50 million years, a remarkable discrepancy with their rich fossil record.</p>
A comparative phylogenomic analysis of birds reveals heterogeneous differentiation processes among Neotropical Savannas
<p>The main objective of this study is to evaluate biogeographic hypotheses of diversification and connection between isolated savannas north (Amazonian savannas) and south (Cerrado core) of the Amazon River. To achieve our goal, we employed genomic markers (genotyping by sequencing) to evaluate the genetic structure, population phylogenetic relationships, and historical range shifts of four Neotropical passerines with peri-Atlantic distributions: the Narrow-billed Woodcreeper (<em>Lepidocolaptes angustirostris</em>), the Plain-crested Elaenia (<em>Elaenia cristata</em>), the Grassland Sparrow (<em>Ammodramus humeralis</em>), and the White-banded Tanager (<em>Neothraupis fasciata</em>). The population genetic analyses indicated that landscape (e.g., geographic distance, landscape resistance, and percentage of tree cover) and climate metrics explained divergence among populations in most species, but without indicating a differential role between current and historical factors. Our results did not fully support the hypothesis that isolated populations at Amazonian savannas have been recently derived from the Cerrado core domain. Intraspecific phylogenies and gene flow analyses supported multiple routes of connection between the Cerrado and Amazonian savannas, rejecting the hypothesis that the Atlantic corridor explains the peri-Atlantic distribution. Our results reveal that the biogeographic history of the region is complex and cannot be explained by simple vicariant models.</p>
Joining forces in Ochnaceae phylogenomics: A tale of two targeted sequencing probe kits
<p><strong>Premise:</strong> Both universal and family-specific targeted sequencing probe kits are becoming widely used for the reconstruction of phylogenetic relationships in angiosperms. Within the pantropical Ochnaceae, we show that with careful data filtering, universal kits are equally as capable in resolving intergeneric relationships as custom probe kits. Furthermore, we show the strength in combining data from both kits to mitigate bias and provide a more robust result to resolve evolutionary relationships.</p> <p><strong>Methods:</strong> We sampled 23 Ochnaceae genera and used targeted sequencing with two probe kits, the universal Angiosperms353 kit, and a family-specific kit. We used maximum likelihood inference with a concatenated matrix of loci and multispecies-coalescence approaches to infer relationships in the family. We explored phylogenetic informativeness and the impact of missing data on resolution and tree support.</p> <p><strong>Results:</strong> For the Angiosperms353 data set, the concatenation approach provided results more congruent with those of the Ochnaceae-specific data set. Filtering missing data was most impactful on the Angiosperms353 data set, with a relaxed threshold being the optimum scenario. The Ochnaceae-specific data set resolved consistent topologies using both inference methods, and no major improvements were obtained after data filtering. The merging of data obtained with the two kits resulted in a well-supported phylogenetic tree.</p> <p><strong>Conclusions:</strong> The Angiosperms353 data set improved upon data filtering, and missing data played an important role in phylogenetic reconstruction. The Angiosperms353 data set resolved the phylogenetic backbone of Ochnaceae as equally well as the family-specific data set. All analyses indicated that both Sauvagesia L. and Campylospermum Tiegh. as currently circumscribed are polyphyletic and require revised delimitation.</p>
Phylogenomics of the Scaly-toed geckos and allies (Gekkonidae: Lepidodactylus and Gekko) reveal a continental origin with unidirectional patterns of island arc diversification
<p>Absolute time tree based on 1696 loci (1,923,100bp) estimated in MCMCTree with three secondary calibrations and a conservative root height calibration (Table1). The light green density distributions at the nodes are based on the posterior age distributions estimated in MCMCTree and the numbers represent the mean age at the respective nodes.</p>
A phylogenomic backbone for gastropod molluscs
<p>Gastropods have survived several mass extinctions during their evolutionary history resulting in extraordinary diversity in morphology, ecology, and developmental modes, which complicate the reconstruction of a robust phylogeny. Currently, gastropods are divided into six subclasses: Caenogastropoda, Heterobranchia, Neomphaliones, Neritimorpha, Patellogastropoda, and Vetigastropoda. Phylogenetic relationships among these taxa historically lack consensus, despite numerous efforts using morphological and molecular information. We generated sequence data for transcriptomes derived from twelve taxa belonging to clades with little or no prior representation in previous studies in order to infer the deeper cladogenetic events within Gastropoda and, for the first time, infer the position of the deep-sea Neomphaliones using a phylogenomic approach. We explored the impact of missing data, homoplasy, and compositional heterogeneity on the inferred phylogenetic hypotheses. We recovered a highly supported backbone for gastropod relationships that is congruent with morphological and mitogenomic evidence, in which Patellogastropoda, true limpets, are the sister lineage to all other gastropods (Orthogastropoda) which are divided into two main clades (i) Vetigastropoda s.l. (including Pleurotomariida + Neomphaliones) and (ii) Neritimorpha + (Caenogastropoda + Heterobranchia). As such, our results support the recognition of five subclasses (or infraclasses) in Gastropoda: Patellogastropoda, Vetigastropoda, Neritimorpha, Caenogastropoda and Heterobranchia.</p>
Phylogenomic analysis of chitinase
<p><strong><span>Supplemental Information: Phylogenomic analysis of chitinase</span></strong></p> <p>Picocyanobacterial sequences for genes involved in chitin degradation and peptidoglycan recycling pathways were found nested within branches of cyanobacterial genes, indicating vertical inheritance of peptidoglycan recycling. Picocyanobacterial sequences for chitinase (ChiA and ChiA-like) and N-acetylglucosamine kinase (NagK) were nested within non-cyanobacterial taxa, indicating Horizontal Gene Transfer (HGT) to picocyanobacteria after their divergence from other cyanobacteria. To contextualize the HGT of chitinase genes into ancestors of marine SynPro, we examined their phylogenetic relationships to similar sequences found within other bacteria. Picocyanobacterial chitinases contained two major chitin-binding domains that were homologous to different chitinase sequence variants found within other bacterial genomes. Gene sequence alignments suggest that the marine SynPro variant is likely the product of a fusion of two genes that were both acquired from Planctomycetes via Horizontal Gene Transfer (HGT).</p>
Phylogenomic analyses of 2,786 genes in 158 lineages support a root of the eukaryotic tree of life between opisthokonts and all other lineages
<p>Advances in phylogenetic methods and high-throughput sequencing have allowed the reconstruction of deep phylogenetic relationships in the evolutionary history of eukaryotes. Yet, the root of the eukaryotic tree of life remains elusive. The most 'popular' (i.e. in textbooks and reviews) hypothesis for the root is between Unikonta (Opisthokonta + Amoebozoa) and Bikonta (all other eukaryotes), which emerged from analyses of a single gene fusion and a limited sampling of eukaryotic lineages. Subsequent highly-cited studies based on concatenation of genes supported this hypothesis with some variations or proposed a root within the Excavata. However, concatenation of genes neither considers phylogenetically-informative events (i.e. gene duplications and losses) nor provides an estimate of the root. A more recent study using gene tree-species tree reconciliation methods suggested the root lies between Opisthokonta and all other eukaryotes, but only including 59 taxa and 20 genes. Here we apply a gene tree – species tree reconciliation approach to a gene-rich and taxon-rich dataset (i.e. 2,786 gene families from two sets of ~158 diverse eukaryotic lineages) to assess the root, and we iterate each analysis 100 times to quantify tree space uncertainty. Our results estimate a root between Fungi and all other eukaryotes, or between Opisthokonta and all other eukaryotes, and reject alternative popular roots from the literature. Based on further analysis of genome size, we propose Opisthokonta + others as the most likely root. Finding the root of the eukaryotic tree of life is critical for the field of comparative biology as it allows us to understand the timing and mode of evolution of characters across the evolutionary history of eukaryotes.</p>
Phylogenomics shows unique traits in Noctilucales are derived rather than ancestral
<p><span>Dinoflagellates are a diverse group of protists that possess many unique traits. These include (but are not limited to) expansive genomes packaged into permanently condensed chromosomes, photosynthetic or cryptic plastids acquired vertically or horizontally in serial endosymbioses, and a ruffle-like transverse flagellum attached along its length to the cell. When reconstructing </span><span>character evolution, early branching lineages with unusual features that distinguish them from the rest of the group have proven useful for inferring ancestral states. The Noctilucales are one such lineage, possessing relaxed chromosomes in some life stages and a trailing, thread-like transverse flagellum. However, most of the cellular and molecular data for the entire group come from a single cultured species, </span><em><span>Noctiluca scintillans</span></em><span>, and because its phylogenetic position is unresolved, it remains unclear if these traits are ancestral or derived. Here, we use single cell transcriptomics to characterize three diverse</span><span> Noctilucales genera: </span><em><span>Spatulodinium</span></em><span>, <em>Kofoidinium</em>, and a new lineage, <em>Fabadinium</em> gen. nov. We also provide transcriptomes for undescribed species in <em>Amphidinium</em></span><span> and Abediniales</span><span>, critical taxa for clarifying the phylogenetic position of </span><span>Noctilucales</span><span>. Phylogenomic analyses suggest that the Noctilucales are sister to <em>Amphidinium</em> rather than an independent branch outside the core dinoflagellates. This topology is consistent with observations of shared characteristics between some members of Noctilucales and <em>Amphidinium</em> and provides the most compelling evidence to date that the unusual traits within this group are derived rather than ancestral. We also confirm that <em>Spatulodinium</em> </span><span>plastids are photosynthetic and of ancestral origin</span><span>, and show that all non-photosynthetic Noctilucales retain plastid </span><span>genes</span><span> indicating a cryptic organelle.</span></p>
Supplementary Materials for: Phylogenomics, lineage diversification rates, and the evolution of diadromy in Clupeiformes (anchovies, herrings, sardines, and relatives)
<p>Migration independently evolved numerous times in animals, with a myriad of ecological and evolutionary implications. In fishes, perhaps the most extreme form of migration is diadromy, the migration between marine and freshwater environments. A key and longstanding question is how does diadromy influence lineage diversification rates? Many diadromous species travel long distances during migration, have large geographic ranges, and use isolated freshwater habitats, which may increase the likelihood of speciation. Alternatively, diadromy may reduce lineage diversification rates if migration facilitates gene flow, homogenizing populations and stymieing speciation. Clupeiformes (herrings, sardines, shads and anchovies) is a model clade for testing hypotheses about the evolution of diadromy because it includes an exceptionally high proportion of diadromous species and several independent evolutionary origins of diadromy. However, relationships among major clupeiform lineages remain unresolved with sparse (<50%) sampling of diadromous species, limiting the resolution of phylogenetically-informed statistical analyses. We assembled a phylogenomic dataset and used multi-species coalescent and concatenation approaches to generate the most comprehensive, highly-resolved clupeiform phylogeny to date, clarifying relationships among major clades of Clupeiformes, revealing taxa requiring revision, and identifying recalcitrant relationships needing further examination. Using this phylogeny as the evolutionary framework for downstream comparative analyses, we tested the hypothesis that diadromous lineages diversified faster than lineages restricted to either marine or freshwater habitats. We found that transitions to diadromy were more common than transitions from diadromy to non-diadromy. The largest lineage diversification rate increase in clupeiforms is associated with a transition to diadromy, but we uncovered little statistical support for categorically faster lineage diversification rates in diadromous versus non-diadromous fishes. We propose that diadromy may increase the potential for accelerated lineage diversification, particularly in species that migrate long distances, but this potential may only be realized in certain biogeographic contexts.</p>
Data from: Phylogenomic structure and speciation in an emerging model: The Sphagnum magellanicum complex (Bryophyta)
<p>The moss genus <em>Sphagnum</em> has unparalleled ecological importance because some 30% of the total terrestrial carbon pool is bound up in <em>Sphagnum</em>-dominated peatlands. A major peat-former, <em>S. magellanicum</em>, is one of two species for which a reference-quality genome exists to facilitate research in ecological genomics, but recently published work indicated that <em>S. magellanicum</em> s. str. is restricted to South America and two other species, <em>S. divinum</em> and <em>S. medium</em> occur in North America and Europe. We report herein that there are four clades/species within the <em>S. magellanicum</em> complex in eastern North America, two in South America, and another in eastern Asia. The reference genome belongs to <em>S. divinum</em>. Phylogenetic analyses at the whole genome and chromosome levels, using genome resequencing and RADseq, resolve sister group relationships within the complex. Species are monophyletic in most analyses and exhibit tens of thousands (RADseq) to millions (resequencing) of fixed nucleotide differences, but two, referred to informally as <em>S. diabolicum</em> and <em>S. magni</em> because they have not been formally described, are differentiated by only hundreds (RADseq) to thousands (resequencing) of differences. Data from 14 of the 19 resequenced chromosomes (7 chromosomes for RADseq) resolve the reciprocal monophyly of <em>S. magni</em> and <em>S. diabolicum</em>. These two appear to be in the process of speciation and because they differ in geographic ranges and the climate zones they occupy – <em>S. diabolicum</em> in boreal peatlands and <em>S. magni</em> in warm temperate to subtropical communities of the southern U.S. – they provide an exciting opportunity for comparative genomic analyses of climate niche evolution. Introgression among species in the complex is demonstrated using <em>D</em>-statistics and <em>f</em><sub>4</sub>-ratios. One ecologically important functional trait that underlies peat (carbon) accumulation, tissue decomposability, does not differ between segregate North American species in the <em>S. magellanicum</em> complex although previous research showed that many related <em>Sphagnum</em> species have evolved differences in decomposability/carbon sequestration. Phylogenetic resolution and more accurate species delimitation in the <em>S. magellanicum</em> complex substantially increase the value of this group for studying the early evolutionary stages of climate adaptation, and ecological evolution more broadly.</p>
Dataset for: Smith et al., Phylogenomic analysis of the parrots of the world distinguishes artifactual from biological sources of gene tree discordance
<p>Gene tree discordance is expected in phylogenomic trees and biological processes are often invoked to explain it. However, heterogeneous levels of phylogenetic signal among individuals within datasets may cause artifactual sources of topological discordance. We examined how the information content in tips and subclades impacts topological discordance in the parrots (Order: Psittaciformes), a diverse and highly threatened clade of nearly 400 species. Using ultraconserved elements from 96% of the clade's species-level diversity, we estimated concatenated and species trees for 382 ingroup taxa. We found that discordance among tree topologies was most common at nodes dating between the late Miocene and Pliocene, and often at the taxonomic level of genus. Accordingly, we used two metrics to characterize information content in tips and assess the degree to which conflict between trees was being driven by lower quality samples. Most instances of topological conflict and non-monophyletic genera in the species tree could be objectively identified using these metrics. For subclades still discordant after tip-based filtering, we used a machine learning approach to determine whether phylogenetic signal or noise was the more important predictor of metrics supporting the alternative topologies. We found that when signal favored one of the topologies, noise was the most important variable in poorly performing models that favored the alternative topology. In sum, we show that artifactual sources of gene tree discordance, which are likely a common phenomenon in many datasets, can be distinguished from biological sources by quantifying the information content in each tip and modeling which factors support each topology.</p>
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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)
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.