Filtration of Gene Trees From 9,000 Exons, Introns, and UCEs Disentangles Conflicting Phylogenomic Relationships in Tree Frogs (Hylidae)

An emerging challenge in interpreting phylogenomic data sets is that concatenation and multi-species coalescent summary species tree approaches may produce conflicting results. Concatenation is problematic because it can strongly support an incorrect topology when incomplete lineage sorting (ILS) results in elevated gene-tree discordance. Conversely, summary species tree methods account for ILS to recover the correct topology, but these methods do not account for erroneous gene trees (“EGTs”) resulting from gene tree estimation error (GTEE). Third, site-based and full-likelihood methods promise to alleviate GTEE as these methods use the sequence data from alignments. To understand the impact of GTEE on species tree estimation in Hylidae tree frogs, we use an expansive data set of ∼9,000 exons, introns, and ultra-conserved elements and initially found conflict between all three types of analytical methods. We filtered EGTs using alignment metrics that could lead to GTEE (length, parsimony-informative sites, and missing data) and found that removing shorter, less informative alignments reconciled the conflict between concatenation and summary species tree methods with increased gene concordance, with the filtered topologies matching expected results from past studies. Contrarily, site-based and full-likelihood methods were mixed where one method was consistent with past studies and the other varied markedly. Critical to other studies, these results suggest a widespread conflation of ILS and GTEE, where EGTs rather than ILS are driving discordance. Finally, we apply these recommendations to an R package named PhyloConfigR, which facilitates phylogenetic software setup, summarizes alignments, and provides tools for filtering alignments and gene trees

Phylogenomic systematics, bioacoustics, and morphology of frogs from Madagascar reveals that background noise drives the evolution of high frequency acoustic signaling

Madagascar is considered a globally important biodiversity hotspot, having some of the highest rates of species endemism in the world and has been the focus of substantial effort from researchers to understand the evolution of its distinctive biota. This is especially true for frogs, where the microcontinent hosts an impressively diverse amphibian fauna totaling over 500 species, where a large amount of this diversity has only been described relatively recently. Much of this accelerated taxonomic progress can be attributed to the combination of DNA barcoding and the widespread application of bioacoustics enabling more efficient species identification and characterization of new lineages. The availability of bioacoustic data for the majority of species has revealed the incredible diversity of acoustic signals in Malagasy frogs; despite the incredible acoustic diversity in Madagascar, explanations for the evolution of distinct advertisement calls have been little explored. Acoustic signaling is important to frogs because it is the primary mechanism of communication and mate selection and therefore it is expected that acoustic communication and factors that drive variation in acoustic signals should be under strong selection. Frogs from the most species-rich genus Boophis from the family Mantellidae in Madagascar communicate acoustically during a rainy and short breeding season and aggregate around water bodies in high abundance making Boophis an ideal model system to address the evolution of advertisement calls. A potential explanation for signal diversity is the acoustic adaptation hypothesis, which predicts that natural and sexual selection drive optimization of signal transmission and perception across different habitats. In many organisms, the efficiency of acoustic signal transmission can be affected by habitat structure or background noise. One prediction of the acoustic adaptation hypothesis is that environmental ambient noise, which is the background level of sound in the environment, will drive signal evolution if the noise is sufficiently similar and lessens the receiver’s perception of the signal. Because Boophis reproduce near water bodies and most often in stream habitats that might be noisy from the sound of rushing water, they present an excellent system to address acoustic interference. In Chapter 1, I describe a new species of Boophis that is morphologically cryptic with its sister species but differs remarkably in advertisement call, which underlines the importance of call variation in the genus. To contribute to the taxonomic progress and integration of bioacoustic data, I describe a new species of Boophis by using these multiple lines of evidence and also suggesting future research to understand the evolution of advertisement calls in the genus. I also develop the acoustic analysis pipeline used for acquiring frequency traits from thousands of calls rapidly, where these methods will be used in Chapter 5. In this study, I also suggest that reproductive character displacement could be driving divergence in advertisement calls and that other important factors from the environment could lead to broad patterns in the evolution of advertisement calls. In Chapter 2, to understand signal evolution across a broad range of taxa, a strongly supported phylogenetic hypothesis is needed and I estimate a new multi-locus phylogeny using Sanger sequencing. The systematics of frogs from the family Mantellidae have had a long and turbulent history where Mantellidae was considered a family relatively recently. In Boophis tree frogs, early researchers considered them as belonging to the Asian genus Rhacophorus because of their strong similarities and breeding habitat in water bodies. Furthermore, despite the numerous works that contributed to understanding the molecular phylogeny of Boophis many aspects of their evolutionary relationships remain insufficiently supported and a complete Sanger multi-locus phylogeny had not been estimated. For understanding the relationships among Boophis frogs, I estimated a multi-locus phylogeny from eight Sanger markers that includes as much diversity as possible. Despite these efforts, I could not adequately support the phylogenetic relationships among Boophis taxa and adding additional Sanger markers would not be likely to resolve these relationships. In Chapter 3 I aim to expand upon this dataset and develop a new sequencing technology to obtain thousands of markers affordably. The widespread use of high-throughput sequencing technologies to sequence large portions of organisms’ genome has led to new and exciting challenges and questions that can be addressed with the massive increase in sequence data these new methods provide. The objective of sequence capture is to sequence genomic regions typically through hybridization-based capture from a previously designed set of known markers and benefits from the potential to acquire markers that are useful at all evolutionary time-scales. Therefore, I developed a sequence capture probe set called FrogCap to sequence ~15,000 genomic markers that can be used across the entire frog radiation. I compare the efficacy of the probe set on six phylogenetic scales and quantify the number of markers sequenced, depth of coverage, missing data, and parsimony informative sites, and I also compared differences between these measures across different types of data. The results from this chapter show that FrogCap is a very promising new sequence capture probe set that can be used across all frogs. In Chapter 4 I test the effectiveness of FrogCap by addressing the systematics of frogs from the family Mantellidae, by comparing the FrogCap sequence capture results to those from transcriptomes. The phylogeny of Mantellidae remains unresolved and contentious, where the phylogenetic relationships among subfamilies and genera are not well delimited. Prior to this it was thought the different groups in Madagascar were non-monophyletic and were thought to be from several different families. I address the weak phylogenetic support and also test the FrogCap probe set on Mantellidae frogs, comparing the probe set to transcriptomic sequencing of samples from the same groups. I find that both FrogCap and transcriptomes work similarly well for resolving these difficult and contentious relationships. FrogCap sequence capture also provided several advantages over the transcriptomic data; FrogCap sequences non-protein coding markers from across the genome, such that these other types of markers could be useful by providing sequence data from potentially neutrally evolving genomic regions and also can serve as another line of phylogenetic evidence when compared to other data types. Transcriptomes also provide advantages through a larger amount of sequence data and lesser gene discordance because the transcriptomes are much longer and thus providing more resolution than shorter markers. I find that the FrogCap probe set is an effective tool at disentangling difficult phylogenetic problems, and that transcriptomic sequencing is less effective for phylogenetics. In Chapter 5, I estimate a new phylogeny for Boophis tree frogs using the FrogCap probe set and address whether acoustic interference leads to the evolution of higher frequency advertisement calls in Boophis frogs. I integrate an unprecedented dataset incorporating data collected from all previous chapters which includes a massive dataset of 300+ acoustic recordings from nearly every species in the genus, a new Boophis time-calibrated phylogeny using a backbone of ~15,000 genomic markers acquired from the sequence capture data combined with the data from Chapter 2 for full species sampling and used soft tissue computed tomography on 28 species to acquire detailed morphological information from the larynges of males. After finding that the sequence capture dataset provides strong statistical support for nearly every node in the tree, I time-calibrate the phylogeny and test the acoustic adaptation hypothesis. I find that Boophis tree frogs are evolving higher frequency acoustic signals in loud stream habitats, which is supported after correcting for body size. These results are further evidenced by laryngeal measurements from the CT Scans, where I find that loud stream frog laryngeal morphology is decoupled from the predicted relationship to body size that is found in quiet stream frogs

Self-Correcting Bayesian Optimization through Bayesian Active Learning

Gaussian processes are cemented as the model of choice in Bayesian optimization and active learning. Yet, they are severely dependent on cleverly chosen hyperparameters to reach their full potential, and little effort is devoted to finding the right hyperparameters in the literature. We demonstrate the impact of selecting good hyperparameters for GPs and present two acquisition functions that explicitly prioritize this goal. Statistical distance-based Active Learning (SAL) considers the average disagreement among samples from the posterior, as measured by a statistical distance. It is shown to outperform the state-of-the-art in Bayesian active learning on a number of test functions. We then introduce Self-Correcting Bayesian Optimization (SCoreBO), which extends SAL to perform Bayesian optimization and active hyperparameter learning simultaneously. SCoreBO learns the model hyperparameters at improved rates compared to vanilla BO, while outperforming the latest Bayesian optimization methods on traditional benchmarks. Moreover, the importance of self-correction is demonstrated on an array of exotic Bayesian optimization task

PriorBand: Practical Hyperparameter Optimization in the Age of Deep Learning

Hyperparameters of Deep Learning (DL) pipelines are crucial for their downstream performance. While a large number of methods for Hyperparameter Optimization (HPO) have been developed, their incurred costs are often untenable for modern DL. Consequently, manual experimentation is still the most prevalent approach to optimize hyperparameters, relying on the researcher's intuition, domain knowledge, and cheap preliminary explorations. To resolve this misalignment between HPO algorithms and DL researchers, we propose PriorBand, an HPO algorithm tailored to DL, able to utilize both expert beliefs and cheap proxy tasks. Empirically, we demonstrate PriorBand's efficiency across a range of DL benchmarks and show its gains under informative expert input and robustness against poor expert belief

Species complexes and the importance of Data Deficient classification in Red List assessments: The case of Hylobatrachus frogs

This work is licensed under a Creative Commons Attribution 4.0 International License.Taxonomy is the cornerstone of extinction risk assessments. Currently, the IUCN Red List treats species complexes either under a single overarching species name—resulting in an unhelpfully broad circumscription and underestimated threat assessment that does not apply to any one species lineage—or omits them altogether—resulting in the omission of species that should be assessed. We argue that taxonomic uncertainty alone, as in species complexes, should be grounds for assessment as Data Deficient (DD). Yet, use of the DD category is currently discouraged, resulting in assessments based on poor data quality and dismissal of the importance of taxonomic confidence in conservation. This policy may be leading to volatile and unwarranted assessments of hundreds of species across the world, and needs to be revised. To illustrate this point, we here present a partial taxonomic revision of torrent frogs from eastern Madagascar in the Mantidactylus subgenus Hylobatrachus. Two named species, Mantidactylus (Hylobatrachus) lugubris and M. (H.) cowanii, and several undescribed candidate species are recognised, but the application of the available names has been somewhat ambiguous. In a recent re-assessment of its conservation status, M. (H.) lugubris was assessed including all complex members except M. (H.) cowanii within its distribution, giving it a status of Least Concern and distribution over most of eastern Madagascar. After describing two of the unnamed lineages as Mantidactylus (Hylobatrachus) atsimo sp. nov. (from southeastern Madagascar) and Mantidactylus (Hylobatrachus) petakorona sp. nov. (from the Marojejy Massif in northeastern Madagascar), we show that Mantidactylus (Hylobatrachus) lugubris is restricted to the central east of Madagascar, highlighting the inaccuracy of its current Red List assessment. We propose to re-assess its status under a more restrictive definition that omits well-defined candidate species, thus representing the actual species to which its assessment refers, to the best of current knowledge. We recommend that for species complexes in general, (1) nominal lineages that can be confidently restricted should be assessed under the strict definition, (2) non-nominal species-level lineages and ambiguous names should be prioritised for taxonomic research, and (3) ambiguous names should be assessed as DD to highlight the deficiency in data on their taxonomic status, which is an impediment to their conservation. This would reduce ambiguity and underestimation of threats involved in assessing species complexes, and place the appropriate emphasis on the importance of taxonomy in anchoring conservation.Deutscher Akademischer Austauschdienst fellowshipDeutsche Forschungsgemeinschaft (VE247/13-1 and 15-1

Morphological and ecological convergence at the lower size limit for vertebrates highlighted by five new miniaturised microhylid frog species from three different Madagascan genera

Miniaturised frogs form a fascinating but poorly understood amphibian ecomorph and have been exceptionally prone to taxonomic underestimation. The subfamily Cophylinae (family Microhylidae), endemic to Madagascar, has a particularly large diversity of miniaturised species which have historically been attributed to the single genus Stumpffia largely based on their small size. Recent phylogenetic work has revealed that several independent lineages of cophyline microhylids evolved towards highly miniaturised body sizes, achieving adult snout- vent lengths under 16 mm. Here, we describe five new species belonging to three clades that independently miniaturised and that are all genetically highly divergent from their relatives: (i) a new genus (Mini gen.nov.) with three new species from southern Madagascar, (ii) one species of Rhombophryne, and (iii) one species of Anodonthyla. Mini mum sp. nov. from Manombo in eastern Madagascar is one of the smallest frogs in the world, reaching an adult body size of 9.7 mm in males and 11.3 mm in females. Mini scule sp.nov. from Sainte Luce in southeastern Madagascar is slightly larger and has maxillary teeth. Mini ature sp.nov. from Andohahela in southeast Madagascar is larger than its congeners but is similar in build. Rhombophryne proportionalis sp.nov. from Tsaratanana in northern Madagascar is unique among Madagascar's miniaturised frogs in being a proportional dwarf, exhibiting far less advanced signs of paedomorphism than other species of similar size. Anodonthyla eximia sp.nov. from Ranomafana in eastern Madagascar is distinctly smaller than any of its congeners and is secondarily terrestrial, providing evidence that miniaturisation and terrestriality may be evolutionarily linked. The evolution of body size in Madagascar's microhylids has been more dynamic than previously understood, and future studies will hopefully shed light on the interplay between ecology and evolution of these remarkably diverse frogs

An integrative taxonomic revision and redefinition of Gephyromantis (Laurentomantis) malagasius based on archival DNA analysis reveals four new mantellid frog species from Madagascar

The subgenus Laurentomantis in the genus Gephyromantis contains some of the least known amphibian species of Madagascar. The six currently valid nominal species are rainforest frogs known from few individuals, hampering a full understanding of the species diversity of the clade. We assembled data on specimens collected during field surveys over the past 30 years and integrated analysis of mitochondrial and nuclear-encoded genes of 88 individuals, a comprehensive bioacoustic analysis, and morphological comparisons to delimit a minimum of nine species-level lineages in the subgenus. To clarify the identity of the species Gephyromantis malagasius, we applied a target-enrichment approach to a sample of the 110 year-old holotype of Microphryne malagasia Methuen and Hewitt, 1913 to assign this specimen to a lineage based on a mitochondrial DNA barcode. The holotype clustered unambiguously with specimens previously named G. ventrimaculatus. Consequently we propose to consider Trachymantis malagasia ventrimaculatus Angel, 1935 as a junior synonym of Gephyromantis malagasius. Due to this redefinition of G. malagasius, no scientific name is available for any of the four deep lineages of frogs previously subsumed under this name, all characterized by red color ventrally on the hindlimbs. These are here formally named as Gephyromantis fiharimpe sp. nov., G. matsilo sp. nov., G. oelkrugi sp. nov., and G. portonae sp. nov. The new species are distinguishable from each other by genetic divergences of >4% uncorrected pairwise distance in a fragment of the 16S rRNA marker and a combination of morphological and bioacoustic characters. Gephyromantis fiharimpe and G. matsilo occur, respectively, at mid-elevations and lower elevations along a wide stretch of Madagascar’s eastern rainforest band, while G. oelkrugi and G. portonae appear to be more range-restricted in parts of Madagascar’s North East and Northern Central East regions. Open taxonomic questions surround G. horridus, to which we here assign specimens from Montagne d’Ambre and the type locality Nosy Be; and G. ranjomavo, which contains genetically divergent populations from Marojejy, Tsaratanana, and Ampotsidy.info:eu-repo/semantics/publishedVersio

An initial molecular resolution of the mantellid frogs of the Guibemantis liber complex reveals three new species from northern Madagascar

The small arboreal frog Guibemantis liber (Anura: Mantellidae) has served as an example for the existence of deep conspecific lineages that differ by a substantial amount in mitochondrial DNA but are similar in morphology and bioacoustics and thus are assigned to the same nominal species. During fieldwork in northern Madagascar, we identified additional such lineages and surprisingly, observed close syntopy of two of these at various sites. In-depth study based on DNA sequences of the mitochondrial cytochrome b gene from 338 specimens of G. liber sensu lato from across its range, sequences of four nuclear-encoded markers for 154‒257 of these specimens, a phylogenomic dataset obtained by the FrogCap target capture approach, and additional mitochondrial genes for representatives of most mitochondrial lineages, as well as bioacoustic and morphological comparisons, revealed concordant differentiation among several lineages of the G. liber complex. We identify nine lineages differing by 5.3‒15.5% in cytochrome b and 2.4‒10.1% in the 16S rRNA gene, and find that several of these lack or have only limited allele sharing in the nuclear-encoded genes. Based on sympatric or parapatric occurrence without genetic admixture, combined with differences in bioacoustic and morphological characters, we scientifically name three lineages from northern Madagascar as new species: G. razoky sp. nov., G. razandry sp. nov., and G. fotsitenda sp. nov. Of these new species, G. razoky sp. nov. and G. razandry sp. nov. show widespread syntopy across northern Madagascar and differ in body size and advertisement calls. Guibemantis fotsitenda sp. nov. is sister to G. razandry sp. nov., but appears to occur at lower elevations, including in close geographic proximity on the Marojejy Massif. We also detected subtle differences in advertisement calls among various other mitochondrial lineages distributed in the Northern Central East and Southern Central East of Madagascar, but the status and nomenclatural identity of these lineages require further morphological and bioacoustic study of reliably genotyped individuals, and assignment of the three available names in the complex: Rhacophorus liber Peracca, 1893, Gephyromantis albogularis Guibé, 1947, and Gephyromantis variabilis Millot and Guibé, 1951. We discuss the identity and type material of these three nomina, designate a lectotype for Gephyromantis variabilis from Itremo, and flag the collection of new material from their type localities, Andrangoloaka and Itremo, as paramount for a comprehensive revision of the G. liber complex

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts