Ultraconserved Elements Research Articles

Phylogenomic analyses reveal non-monophyly of the antbird generaHerpsilochmusandSakesphorus(Thamnophilidae), with description of a new genus forHerpsilochmus sellowi

AbstractThe 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 Herpsilochmus, Sakesphorus, Thamnophilus, Biatas, and Dysithamnus using DNA sequences from the mitochondrion, nuclear exons, and ultraconserved elements, with further attention to interspecific relationships within Herpsilochmus. We show that Herpsilochmus and Sakesphorus are not monophyletic. We resolve Herpsilochmus sellowi as a deep-branch sister to the monotypic genus Biatas and Sakesphorus cristatus as sister to a clade comprising Herpsilochmus sensu stricto and Dysithamnus. 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 H. sellowi and Biatas argues against merging them into a single genus. Because no generic name is available for H. sellowi, we describe a monotypic genus. The polyphyly of Sakesphorus warrants recognition of the available generic name Sakesphoroides for the distinctive and monotypic S. cristatus. Furthermore, we recover 6 well-supported species groups within Herpsilochmus 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.

Testing the Utility of Alternative Metrics of Branch Support to Address the Ancient Evolutionary Radiation of Tunas, Stromateoids, and Allies (Teleostei: Pelagiaria)

The use of high-throughput sequencing technologies to produce genome-scale data sets was expected to settle some long-standing controversies across the Tree of Life, particularly in areas where short branches occur at deep timescales. Instead, these data sets have often yielded many well-supported but conflicting topologies, and highly variable gene-tree distributions. A variety of branch-support metrics beyond the nonparametric bootstrap are now available to assess how robust a phylogenetic hypothesis may be, as well as new methods to quantify gene-tree discordance. We applied multiple branch-support metrics to a study of an ancient group of marine fishes (Teleostei: Pelagiaria) whose interfamilial relationships have proven difficult to resolve due to a rapid accumulation of lineages very early in its history. We analyzed hundreds of loci including published ultraconserved elements and newly generated exonic data along with their flanking regions to represent all 16 extant families for more than 150 out of 284 valid species in the group. Branch support was typically lower at inter- than intra-familial relationships regardless of the type of marker used. Several nodes that were highly supported with bootstrap had a very low site and gene-tree concordance, revealing underlying conflict. Despite this conflict, we were able to identify four consistent interfamilial clades, each comprised of two or three families. Combining exons with their flanking regions also produced increased branch lengths at the deep branches of the pelagiarian tree. Our results demonstrate the limitations of employing current metrics of branch support and species-tree estimation when assessing the confidence of ancient evolutionary radiations and emphasize the necessity to embrace alternative measurements to explore phylogenetic uncertainty and discordance in phylogenomic data sets.[Concatenation; exons; introns; phylogenomics; species-tree methods; target capture.].

Evolution of host use in fungivorous ciid beetles (Coleoptera: Ciidae): Molecular phylogeny focusing on Japanese taxa

Consumer–resource interactions between trophic levels are ubiquitous and important factors in shaping the diversity of insects. However, dietary patterns such as host specificity and conservatism have been insufficiently examined in fungivorous insects. Here we reconstructed the evolutionary history of host use in fungivorous ciid beetles (Coleoptera: Ciidae) and tested for host conservatism. Phylogenetic relationships among 49 species from Japan were inferred by using a large sequence data set from ultraconserved elements (UCEs). In addition, sequences of three genes (COI, 28S rRNA, 18S rRNA) were analyzed to reconstruct the phylogeny for 130 OTUs from a broader range of taxa and geographic regions using the UCE tree as a backbone topology. We found that Ciini and Orophiini are not recovered as reciprocally monophyletic groups. As previously suggested, the largest genus Cis Latreille was also not monophyletic. Ancestral-state reconstruction of host use in both datasets showed that Ciidae species were clustered by host-use group across the tree. This pattern was confirmed by the significantly lower transition rate compared with expectations under the random shift hypothesis. The observed conservatism in host use implied these beetles possess unique adaptations to specific fungal taxa, just as herbivorous insects are adapted to specific plant taxa.

Evolutionary history of Heptapteridae catfishes using ultraconserved elements (Teleostei, Siluriformes)

AbstractHeptapteridae is composed of 228 valid species allocated in 24 genera, making it the most diverse family within superfamily Pimelodoidea, a clade endemic to the Neotropical freshwaters. Heptapterids are widely distributed from southern Mexico to the Pampas of Argentina and occupy a variety of habitats generally in small‐ to medium‐sized rivers. To evaluate the phylogenetic relationships of Heptapteridae, we used a matrix with 1,319 ultraconserved elements (UCEs) from the genome from 56 specimens spanning 42 species and 24 genera of Heptapteridae and 19 related siluriform taxa. Maximum likelihood, Bayesian and coalescent‐based analyses strongly supported the monophyly of Heptapteridae and confirmed previous hypotheses of a sister relationship between Heptapteridae and Conorhynchos conirostris. We provide the evidence to recognize two subfamilies: (1) Rhamdiinae (Goeldiella, Rhamdella, Rhamdia, Brachyrhamdia, Pimelodella) and (2) Heptapterinae; with two tribes: Brachyglaniini new tribe (Gladioglanis, Myoglanis, Brachyglanis and Leptorhamdia) and Heptapterini (Mastiglanis, Chasmocranus, Cetopsorhamdia, Pariolius, Phenacorhamdia, Nemuroglanis, Imparfinis, Taunayia, Rhamdioglanis, Acentronichthys, Rhamdiopsis and Heptapterus). Inside Heptapterini, we recognize five subclades and provide putative morphological synapomorphies. This paper represents the first molecular hypothesis of intergeneric and interspecific relationships helping to better delineate heptapterid taxa.

Museomics and phylogenomics with protein-encoding ultraconserved elements illuminate the evolution of life history and phallic morphology of flesh flies (Diptera: Sarcophagidae)

BackgroundThe common name of the Flesh flies (Sarcophagidae) usually relates them with organisms feeding on decomposing organic matter, although the biology of one of the largest radiations among insects also includes predation, coprophagy, and even kleptoparasitism. The question of whether the ancestor of all sarcophagids was a predator or a decomposer, or in association to which host have sarcophagids evolved, has thus always piqued the curiosity of flesh fly specialists. Such curiosity has often been hindered by both the impossibility of having a well-supported phylogeny of Sarcophagidae and its sister group to trace live habits and the scarcity of information on the biology of the group. Using a phylogenomic dataset of protein-encoding ultraconserved elements from representatives of all three subfamilies of Sarcophagidae as ingroup and a large Calyptratae outgroup, a robust phylogenetic framework and timescale are generated to understand flesh fly systematics and the evolution of their life histories.ResultsThe evolutionary history for Sarcophagidae reconstructed here differs considerably from previous hypotheses. Within subfamily Sarcophaginae, a group of predatory flies, including genera Lepidodexia and Boettcheria, emerged as sister-group to the rest of Sarcophaginae. The genera Oxysarcodexia, Ravinia, and Tricharaea, long considered archaic and early-branching coprophagous and sarcosaprophagous lineages, were found nested well within the Sarcophaginae as sister-group to the sarcosaprophagous Microcerella. Predation on invertebrates is suggested as the ancestral and dominant strategy throughout the early evolution of flesh flies. Several transitions from predation to sarcosaprophagy and coprophagy occur across the sarcophagid phylogenetic tree, in contrast with almost no transitions from sarcosaprophagy or coprophagy to predatory habits. Regarding the morphological evolution of flesh flies, there might be a concerted evolution of male genitalia traits, such as the phallotrema position and the juxta, or the vesica and the folding of the phallotrema. One diversification rate shift was inferred in the evolution of sarcophagids, which is related to the origin of genus Sarcophaga.ConclusionsThis study has a significant impact on understanding sarcophagid evolution and highlights the importance of having a robust phylogenetic framework to reconstruct the ancestral character state of biological and morphological characters. I discuss the evolution of life histories of the family in relation to their hosts or substrates and outline how sarcosaprophagy, coprophagy, and kleptoparasitism behavior on various hosts may have evolved from predation on invertebrates. This study provides a phylogenetic framework for further physiological and comparative genomic work between predatory, sarcosaprophagous, coprophagous, and kleptoparasitic lineages, which could also have significant implications for the evolution of diverse life histories in other Diptera.

Morphology and genetics concur that Anoura carishina is a synonym of Anoura latidens (Chiroptera, Glossophaginae)

Abstract Anoura carishina was described based on cranial and dental morphology, but the original analyses did not include Anoura latidens, a similar species of Anoura. We used morphological, morphometric, and genetic analyses to evaluate the taxonomic identity of A. carishina. We performed a principal components analysis to evaluate the correspondence between morphological and taxonomic groups for 260 specimens of large-bodied Anoura (A. carishina, Anoura geoffroyi, A. latidens, and Anoura peruana), and statistically analyzed traits diagnostic for A. latidens, including (1) morphology of the third upper premolar (P4), (2) size of the second (P3) and third (P4) upper premolars, and (3) angle formed by the maxillary toothrows. We find that A. latidens and A. carishina are indistinguishable, and share several characters lacking in A. geoffroyi, including a P4 with triangular shape, an under-developed anterobasal cusp in the P3, a smaller braincase, and a shorter rostrum. Phylogenetic analyses using ultra-conserved elements infer that the holotype and two paratype specimens of A. carishina are paraphyletic and nested within A. latidens, while one paratype diagnosable by morphology as A. geoffroyi nests within A. geoffroyi samples. We demonstrate that A. carishina should be considered a junior synonym of A. latidens, updating the distribution of the latter.

Phylogenomics of Ichneumoninae (Hymenoptera, Ichneumonidae) reveals pervasive morphological convergence and the shortcomings of previous classifications

AbstractThe evolutionary history of Ichneumoninae, the largest subfamily of ichneumonid wasps, is investigated using genomic ultraconserved elements (UCEs). The dataset includes 147 species in 130 genera of Ichneumoninae and 155 outgroup taxa from 19 subfamilies. Matrices with varying degrees of completeness were analysed with different partition schemes and the resulting topologies were found to be mostly congruent. All analyses recovered Ichneumoninae as a monophyletic group, sister to all other Ichneumoniformes except Agriotypinae. Almost no support was found for previous tribal classification schemes, except that the tribes Phaeogenini and Platylabini are largely monophyletic. A new tribal classification is proposed based on the relationships recovered, consisting of seven tribes: Alomyini Förster, Phaeogenini Förster, Notosemini Townes, Eurylabini Heinrich, Platylabini Berthoumieu, Ichneumonini Latreille and a new monogeneric tribe, Abzariini Santos & Wahl. As documented in other lineages of Ichneumonidae, pervasive morphological convergence poses a challenge to the establishment of higher‐level groups that are both monophyletic and diagnosable. Extremely short branches at the base of the Ichneumoninae clade suggest that the group may have undergone a rapid radiation when it first diverged, potentially associated with its specialization on lepidopteran hosts. Multiple changes in the morphology of the female abdomen suggest that morphological convergence is associated with multiple transitions in the use of pupal versus larval hosts across the subfamily. The results demonstrate the power of phylogenomic approaches to resolve evolutionary relationships in hyper‐diverse and poorly studied insect groups and to provide a framework for testing evolutionary hypotheses.

Phylogenomics and Historical Biogeography of Seahorses, Dragonets, Goatfishes, and Allies (Teleostei: Syngnatharia): Assessing Factors Driving Uncertainty in Biogeographic Inferences.

The charismatic trumpetfishes, goatfishes, dragonets, flying gurnards, seahorses, and pipefishes encompass a recently defined yet extraordinarily diverse clade of percomorph fishes-the series Syngnatharia. This group is widely distributed in tropical and warm-temperate regions, with a great proportion of its extant diversity occurring in the Indo-Pacific. Because most syngnatharians feature long-range dispersal capabilities, tracing their biogeographic origins is challenging. Here, we applied an integrative phylogenomic approach to elucidate the evolutionary biogeography of syngnatharians. We built upon a recently published phylogenomic study that examined ultraconserved elements by adding 62 species (total 169 species) and one family (Draconettidae), to cover ca. 25% of the species diversity and all 10 families in the group. We inferred a set of time-calibrated trees and conducted ancestral range estimations. We also examined the sensitivity of these analyses to phylogenetic uncertainty (estimated from multiple genomic subsets), area delimitation, and biogeographic models that include or exclude the jump-dispersal parameter ($j)$. Of the three factors examined, we found that the $j$ parameter has the strongest effect in ancestral range estimates, followed by number of areas defined, and tree topology and divergence times. After accounting for these uncertainties, our results reveal that syngnatharians originated in the ancient Tethys Sea ca. 87 Ma (84-94 Ma; Late Cretaceous) and subsequently occupied the Indo-Pacific. Throughout syngnatharian history, multiple independent lineages colonized the eastern Pacific (6-8 times) and the Atlantic (6-14 times) from their center of origin, with most events taking place following an east-to-west route prior to the closure of the Tethys Seaway ca. 12-18 Ma. Ultimately, our study highlights the importance of accounting for different factors generating uncertainty in macroevolutionary and biogeographic inferences.[Historical biogeography; jump-dispersal parameter; macroevolutionary uncertainty; marine fishes; syngnathiformes; ultraconserved elements].

Cryptic diversity across the Trans-Mexican Volcanic Belt of Mexico in the montane bunchgrass lizard Sceloporus subniger/ (Squamata: Phrynosomatidae).

Sceloporus subniger Poglaygen Smith is a montane bunchgrass lizard distributed across pine-oak forests of central Mexico. Prompted by the discovery of a new population of this lizard in far western Mexico, and by recent studies suggesting S. subniger may be a composite of several distinct species, we examined in more detail the genetic structure of S. subniger. We generated a mitochondrial DNA (mtDNA) dataset from 81 specimens and an ultraconserved elements (UCE) dataset representing thousands of genomic regions from 12 specimens to specifically evaluate the genetic distinctiveness of populations from western Michoacán and adjacent Jalisco along with the newly discovered population in the Sierra de Mascota in western Jalisco. We also recorded morphological data from 47 museum specimens to compare to our genetic data. Results from our analyses of the genetic data, augmented by specimen measurements and scale counts, support the notion that S. subniger is indeed a composite of distinct species. Montane bunchgrass lizards from western Michoacán and adjacent Jalisco, and from the Sierra de Mascota in western Jalisco, each represent distinct new species, which we describe and name here.

Ultraconserved elements reconstruct the evolution of Chagas disease‐vectoring kissing bugs (Reduviidae: Triatominae)

AbstractTriatominae are the largest radiation of haematophagous species within the true bugs (Hemiptera) and the sole vectors of Trypanosoma cruzi Chagas, the causative agent of Chagas disease, a neglected human disease that affects millions. We used a combined ultraconserved element (UCE) and ribosomal dataset from ethanol‐preserved and pinned specimens in a museomics approach to elucidate the phylogenetic relationships among triatomines, including taxa of four of the five tribes with substantial representation of the Old World fauna. We conclude that: (i) Triatominae are monophyletic and Opisthacidius Berg is their predatory sister taxon; (ii) the three large genera (Rhodnius Stål, Triatoma Laporte and Panstrongylus Berg) are not monophyletic; (iii) Triatomini fall into nine well‐supported clades, only two of which are identical in composition to previously recognized groups; and (iv) the Old World clade is deeply nested within Triatomini. Ancestral character state reconstructions of specific character traits provide insights into the evolutionary history of Triatominae.

Phylogenomic resolution of the monotypic and enigmatic Amarsipus, the Bagless Glassfish (Teleostei, Amarsipidae)

AbstractAmarsipus carlsbergi is a rare mesopelagic fish distributed in the Indian and Pacific Oceans and is the only species classified in the family Amarsipidae. Since its description in 1969, phylogenetic hypotheses have varied regarding its relationship with other percomorph lineages, but most have indicated a close relationship with the traditional suborder Stromateoidei. Molecular phylogenies place families previously classified in Stromateoidei within a diverse clade—Pelagiaria—that includes fishes such as tunas, cutlassfishes and pomfrets. A recent analysis of a small number of loci resolved a clade containing Amarsipus and the stromateoid lineage Tetragonurus. A subsequent high‐throughput sequence phylogeny based on ultraconserved elements (UCEs) of Pelagiaria lacked Amarsipus, but revealed both strong support for stromateoid paraphyly and high levels of gene tree incongruence. We gathered UCE sequence data for 610 UCE loci from Amarsipus and integrate these with samples from all remaining pelagiarian families. This provides a taxonomically comprehensive phylogenomic framework to test the evolutionary relationships of Amarsipus, and evaluate the support for stromateoid monophyly. As in previous studies, our analyses find high levels of gene tree topological discordance with regard to some deeper pelagiarian inter‐relationships. However, we resolve Amarsipus as the sister lineage of a clade containing Tetragonurus and a family not considered a stromateoid lineage, Chiasmodontidae. This relationship is supported by both high gene tree concordance and node support. Our analyses also provide strong support for the paraphyly of Stromateoidei, casting uncertainty on previous hypotheses of the evolution of morphological traits across members of Pelagiaria.

HReg-CNCC reconstructs a regulatory network in human cranial neural crest cells and annotates variants in a developmental context

Cranial Neural Crest Cells (CNCC) originate at the cephalic region from forebrain, midbrain and hindbrain, migrate into the developing craniofacial region, and subsequently differentiate into multiple cell types. The entire specification, delamination, migration, and differentiation process is highly regulated and abnormalities during this craniofacial development cause birth defects. To better understand the molecular networks underlying CNCC, we integrate paired gene expression & chromatin accessibility data and reconstruct the genome-wide human Regulatory network of CNCC (hReg-CNCC). Consensus optimization predicts high-quality regulations and reveals the architecture of upstream, core, and downstream transcription factors that are associated with functions of neural plate border, specification, and migration. hReg-CNCC allows us to annotate genetic variants of human facial GWAS and disease traits with associated cis-regulatory modules, transcription factors, and target genes. For example, we reveal the distal and combinatorial regulation of multiple SNPs to core TF ALX1 and associations to facial distances and cranial rare disease. In addition, hReg-CNCC connects the DNA sequence differences in evolution, such as ultra-conserved elements and human accelerated regions, with gene expression and phenotype. hReg-CNCC provides a valuable resource to interpret genetic variants as early as gastrulation during embryonic development. The network resources are available at https://github.com/AMSSwanglab/hReg-CNCC.

Ultraconserved Elements Improve the Resolution of Difficult Nodes within the Rapid Radiation of Neotropical Sigmodontine Rodents (Cricetidae: Sigmodontinae).

Sigmodontine rodents (Cricetidae, Sigmodontinae) represent the second largest muroid subfamily and the most species-rich group of New World mammals, encompassing above 410 living species and ca. 87 genera. Even with advances on the clarification of sigmodontine phylogenetic relationships that have been made recently, the phylogenetic relationships among the 12 main groups of genera (i.e., tribes) remain poorly resolved, in particular among those forming the large clade Oryzomyalia. This pattern has been interpreted as consequence of a rapid radiation upon the group entrance into South America. Here, we attempted to resolve phylogenetic relationships within Sigmodontinae using target capture and high-throughput sequencing of ultraconserved elements (UCEs). We enriched and sequenced UCEs for 56 individuals and collected data from four already available genomes. Analyses of distinct data sets, based on the capture of 4634 loci, resulted in a highly resolved phylogeny consistent across different methods. Coalescent species-tree-based approaches, concatenated matrices, and Bayesian analyses recovered similar topologies that were congruent at the resolution of difficult nodes. We recovered good support for the intertribal relationships within Oryzomyalia; for instance, the tribe Oryzomyini appears as the sister taxa of the remaining oryzomyalid tribes. The estimates of divergence times agree with the results of previous studies. We inferred the crown age of the sigmodontine rodents at the end of the Middle Miocene, while the main lineages of Oryzomyalia appear to have radiated in a short interval during the Late Miocene. Thus, the collection of a genomic-scale data set with a wide taxonomic sampling provided resolution for the first time of the relationships among the main lineages of Sigmodontinae. We expect the phylogeny presented here will become the backbone for future systematic and evolutionary studies of the group.[Coalescent; Muroidea; Oryzomyalia; phylogenomics; polytomy; Rodentia; Sigmodontalia; species tree; UCEs.].

Complex histories of gene flow and a mitochondrial capture event in a nonsister pair of birds.

Hybridization, introgression, and reciprocal gene flow during speciation, specifically the generation of mitonuclear discordance, are increasingly observed as parts of the speciation process. Genomic approaches provide insight into where, when, and how adaptation operates during and after speciation and can measure historical and modern introgression. Whether adaptive or neutral in origin, hybridization can cause mitonuclear discordance by placing the mitochondrial genome of one species (or population) in the nuclear background of another species. The latter, introgressed species may eventually have its own mtDNA replaced or “captured” by other species across its entire geographical range. Intermediate stages in the capture process should be observable. Two nonsister species of Australasian monarch‐flycatchers, Spectacled Monarch (Symposiachrus trivirgatus) mostly of Australia and Indonesia and Spot‐winged Monarch (S. guttula) of New Guinea, present an opportunity to observe this process. We analysed thousands of single nucleotide polymorphisms (SNPs) derived from ultraconserved elements of all subspecies of both species. Mitochondrial DNA sequences of Australian populations of S. trivirgatus form two paraphyletic clades, one being sister to and presumably introgressed by S. guttula despite little nuclear signal of introgression. Population genetic analyses (e.g., tests for modern and historical gene flow and selection) support at least one historical gene flow event between S. guttula and Australian S. trivirgatus. We also uncovered introgression from the Maluku Islands subspecies of S. trivirgatus into an island population of S. guttula, resulting in apparent nuclear paraphyly. We find that neutral demographic processes, not adaptive introgression, are the most likely cause of these complex population histories. We suggest that a Pleistocene extinction of S. guttula from mainland Australia resulted from range expansion by S. trivirgatus.

Evolutionary impacts of introgressive hybridization in a rapidly evolving group of jumping spiders (F. Salticidae, Habronattus americanus group)

Introgressive hybridization can be a powerful force impacting patterns of evolution at multiple taxonomic levels. We aimed to understand how introgression has affected speciation and diversification within a species complex of jumping spiders. The Habronattus americanus subgroup is a recently radiating group of jumping spiders, with species now in contact after hypothesized periods of isolation during glaciation cycles of the Pleistocene. Effects of introgression on genomes and morphology were investigated using phylogenomic and clustering methods using RADseq, ultraconserved elements (UCEs), and morphological data. We characterized 14 unique species/morphs using non-metric multidimensional scaling of morphological data, a majority of which were not recovered as monophyletic in our phylogenomic analyses. Morphological clusters and genetic lineages are highly incongruent, such that geographic region was a greater predictor of phylogenetic relatedness and genomic similarity than species or morph identity. STRUCTURE analyses support this pattern, revealing clusters corresponding to larger geographic regions. A history of rapid radiation in combination with frequent introgression seems to have mostly homogenized the genomes of species in this system, while selective forces maintain distinct male morphologies. GEMMA analyses support this idea by identifying SNPs correlated with distinct male morphologies. Overall, we have uncovered a system at odds with a typical bifurcating evolutionary model, instead supporting one where closely related species evolve together connected through multiple introgression events, creating a reticulate evolutionary history.

Ultra-conserved sequences in the genomes of highly diverse Anopheles mosquitoes, with implications for malaria vector control.

DNA sequences that are exactly conserved over long evolutionary time scales have been observed in a variety of taxa. Such sequences are likely under strong functional constraint and they have been useful in the field of comparative genomics for identifying genome regions with regulatory function. A potential new application for these ultra-conserved elements (UCEs) has emerged in the development of gene drives to control mosquito populations. Many gene drives work by recognizing and inserting at a specific target sequence in the genome, often imposing a reproductive load as a consequence. They can therefore select for target sequence variants that provide resistance to the drive. Focusing on highly conserved, highly constrained sequences lowers the probability that variant, gene drive-resistant alleles can be tolerated. Here, we search for conserved sequences of 18 bp and over in an alignment of 21 Anopheles genomes, spanning an evolutionary timescale of 100 million years, and characterize the resulting sequences according to their location and function. Over 8000 UCEs were found across the alignment, with a maximum length of 164 bp. Length-corrected gene ontology analysis revealed that genes containing Anopheles UCEs were over-represented in categories with structural or nucleotide-binding functions. Known insect transcription factor binding sites were found in 48% of intergenic Anopheles UCEs. When we looked at the genome sequences of 1142 wild-caught mosquitoes, we found that 15% of the Anopheles UCEs contained no polymorphisms. Our list of Anopheles UCEs should provide a valuable starting point for the selection and testing of new targets for gene-drive modification in the mosquitoes that transmit malaria.

Molecular phylogeny, historical biogeography and revised classification of andrenine bees (Hymenoptera: Andrenidae)

The mining bee subfamily Andreninae (Hymenoptera: Andrenidae) is a widely distributed and diverse group of ground-nesting solitary bees, including numerous species known to be important pollinators. Most of the species diversity of Andreninae is concentrated in the mainly Holarctic genus Andrena, comprising ca. 1550 described species. The subfamily and especially the genus have remained relatively neglected by recent molecular phylogenetic studies, with current classifications relying largely on morphological characters. We sampled ultraconserved element (UCE) sequences from 235 taxa, including all andrenine genera and 98 out of 104 currently recognized Andrena subgenera. Using 419,858 aligned nucleotide sites from 1009 UCE loci, we present a comprehensive molecular phylogenetic analysis of the subfamily. Our analysis supports the recognition of seven distinct genera in the Andreninae: Alocandrena, Ancylandrena, Andrena, Cubiandrena, Euherbstia, Megandrena, and Orphana. Within the genus Andrena, present-day subgeneric concepts revealed high degrees of paraphyly and polyphyly, due to strong homoplasy of morphological characters, necessitating a thorough, extensive revision of the higher classification of the genus. Based on our findings, we place the subgenus Calcarandrena in synonymy with Andrena (Lepidandrena); Hyperandrena, Nemandrena, Scoliandrena, Tylandrena and Zonandrena with A. (Melandrena); Distandrena, Fumandrena and Proxiandrena with A. (Micrandrena); Carandrena with A. (Notandrena); Agandrena with A. (Plastandrena); Geandrena and Xanthandrena with A. (Ptilandrena); Xiphandrena with A. (Scrapteropsis); and Platygalandrena and Poliandrena with A. (Ulandrena) (new synonymies). We additionally reestablish the groups known as Opandrena and Truncandrena as valid subgenera of Andrena. Our results also show that the MRCA of Andrena + Cubiandrena dispersed from the New World to the Palaearctic probably during the Eocene–early Oligocene, followed by 10–14 Neogene dispersal events from the Palaearctic to the Nearctic and 1–6 Neogene dispersals back into the Palaearctic, all within the genus Andrena.

Prioritizing non-coding regions based on human genomic constraint and sequence context with deep learning

Elucidating functionality in non-coding regions is a key challenge in human genomics. It has been shown that intolerance to variation of coding and proximal non-coding sequence is a strong predictor of human disease relevance. Here, we integrate intolerance to variation, functional genomic annotations and primary genomic sequence to build JARVIS: a comprehensive deep learning model to prioritize non-coding regions, outperforming other human lineage-specific scores. Despite being agnostic to evolutionary conservation, JARVIS performs comparably or outperforms conservation-based scores in classifying pathogenic single-nucleotide and structural variants. In constructing JARVIS, we introduce the genome-wide residual variation intolerance score (gwRVIS), applying a sliding-window approach to whole genome sequencing data from 62,784 individuals. gwRVIS distinguishes Mendelian disease genes from more tolerant CCDS regions and highlights ultra-conserved non-coding elements as the most intolerant regions in the human genome. Both JARVIS and gwRVIS capture previously inaccessible human-lineage constraint information and will enhance our understanding of the non-coding genome.

Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New WorldSysciaSpecies (Formicidae: Dorylinae)

AbstractThe ant genus Syscia Roger, 1861 is part of the cryptic ant fauna inhabiting leaf litter and rotten wood in the Asian and American tropics. It is a distinct clade within the Dorylinae, the subfamily from which army ants arose. Prior to this work, the genus comprised seven species, each known from a single or very few collections. Extensive collecting in Middle America revealed an unexpected and challenging diversity of morphological forms. Locally distinct forms could be identified at many sites, but assignment of specimens to species spanning multiple sites was problematic. To improve species delimitation, Ultra-Conserved Element (UCE) phylogenomic data were sequenced for all forms, both within and among sites, and a phylogeny was inferred. Informed by phylogeny, species delimitation was based on monophyly, absence of within-clade sympatry, and a subjective degree of morphological uniformity. UCE phylogenomic results for 130 specimens were complemented by analysis of mitochondrial COI (DNA barcode) data for an expanded taxon set. The resulting taxonomy augments the number of known species in the New World from 3 to 57. We describe and name 31 new species, and 23 species are assigned morphospecies codes pending improved specimen coverage. Queens may be fully alate or brachypterous, and there is a wide variety of intercaste female forms. Identification based on morphology alone is very difficult due to continuous character variation and high similarity of phylogenetically distant species. An identification aid is provided in the form of a set of distribution maps and standard views, with species ordered by size.

Phylogenomic Analysis of Concatenated Ultraconserved Elements Reveals the Recent Evolutionary Radiation of the Fairy Wrasses (Teleostei: Labridae: Cirrhilabrus).

The fairy wrasses (genus Cirrhilabrus) are among the most successful of the extant wrasse lineages (Teleostei: Labridae), with their 61 species accounting for nearly 10$\%$ of the family. Although species complexes within the genus have been diagnosed on the basis of coloration patterns and synapomorphies, attempts to resolve evolutionary relationships among these groups using molecular and morphological data have largely been unsuccessful. Here, we use a phylogenomic approach with a data set comprising 991 ultraconserved elements (UCEs) and mitochondrial COI to uncover the evolutionary history and patterns of temporal and spatial diversification of the fairy wrasses. Our analyses of phylogenetic signal suggest that most gene-tree incongruence is caused by estimation error, leading to poor resolution in a summary-coalescent analysis of the data. In contrast, analyses of concatenated sequences are able to resolve the major relationships of Cirrhilabrus. We determine the placements of species that were previously regarded as incertae sedis and find evidence for the nesting of Conniella, an unusual, monotypic genus, within Cirrhilabrus. Our relaxed-clock dating analysis indicates that the major divergences within the genus occurred around the Miocene-Pliocene boundary, followed by extensive cladogenesis of species complexes in the Pliocene-Pleistocene. Biogeographic reconstruction suggests that the fairy wrasses emerged within the Coral Triangle, with episodic fluctuations of sea levels during glacial cycles coinciding with shallow divergence events but providing few opportunities for more widespread dispersal. Our study demonstrates both the resolving power and limitations of UCEs across shallow timescales where there is substantial estimation error in individual gene trees.[Biogeography; concatenation; gene genealogy interrogation; gene trees; molecular dating; summary coalescent; UCEs.].