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Gesneriaceae (ca. 3400 species) is a pantropical plant family with a wide range of growth form and floral morphology that are associated with repeated adaptations to different environments and pollinators. Although Gesneriaceae systematics has been largely improved by the use of Sanger sequencing data, our understanding of the evolutionary history of the group is still far from complete due to the limited number of informative characters provided by this type of data. To overcome this limitation, we developed here a Gesneriaceae-specific gene capture kit targeting 830 single-copy loci (776,754 bp in total), including 279 genes from the Universal Angiosperms-353 kit. With an average of 557,600 reads and 87.8% gene recovery, our target capture was successful across the family Gesneriaceae and also in other families of Lamiales. From our bait set, we selected the most informative 418 loci to resolve phylogenetic relationships across the entire Gesneriaceae family using maximum likelihood and coalescent-based methods. Upon testing the phylogenetic performance of our baits on 78 taxa representing 20 out of 24 subtribes within the family, we showed that our data provided high support for the phylogenetic relationships among the major lineages, and were able to provide high resolution within more recent radiations. Overall, the molecular resources we developed here open new perspectives for the study of Gesneriaceae phylogeny at different taxonomical levels and the identification of the factors underlying the diversification of this plant group., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Lack of knowledge of taxonomic biodiversity and reliable genetic markers in Trypanosomatidae limit our understanding of their phylogenetic relationships. Ultraconserved elements (UCEs) have improved phylogenetic analyses and inferences in many vertebrate and invertebrate taxa. However, it is unknown whether protozoans have these markers, their abundance, and if these could be reliably used for phylogenetics. In this study I design a target enrichment bait set for UCE loci for this group. In silico testing showed good loci recovery rates across 63 taxa and produced consistent, highly supported phylogenetic trees. This bait set adds a new resource of useful genetic markers for Trypanosomatidae phylogenetics., (Copyright © 2020 Elsevier Inc. All rights reserved.)

The origin of the mammalian order Eulipotyphla has been debated intensively with arguments around whether they began diversifying before or after the Cretaceous-Palaeogene (K-Pg) boundary at 66 Ma. Here, we used an in-solution nucleotide capture method and next generation DNA sequencing to determine the sequence of hundreds of ultra-conserved elements (UCEs), and conducted phylogenomic and molecular dating analyses for the four extant eulipotyphlan lineages-Erinaceidae, Solenodontidae, Soricidae, and Talpidae. Concatenated maximum-likelihood analyses with single or partitioned models and a coalescent species-tree analysis showed that divergences among the four major eulipotyphlan lineages occurred within a short period of evolutionary time, but did not resolve the interrelationships among them. Alternative suboptimal phylogenetic hypotheses received consistently the same amount of support from different UCE loci, and were not significantly different from the maximum likelihood tree topology, suggesting the prevalence of stochastic lineage sorting. Molecular dating analyses that incorporated among-lineage evolutionary rate differences supported a scenario where the four eulipotyphlan families diversified between 57.8 and 63.2 Ma. Given short branch lengths with low support values, traces of rampant genome-wide stochastic lineage sorting, and post K-Pg diversification, we concluded that the crown eulipotyphlan lineages arose through a rapid diversification after the K-Pg boundary when novel niches were created by the mass extinction of species., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Newts of the genus Triturus (marbled and crested newts) exhibit substantial variation in the number of trunk vertebrae (NTV) and a higher NTV corresponds to a longer annual aquatic period. Because the Triturus phylogeny has thwarted resolution to date, the evolutionary history of NTV, annual aquatic period, and their potential coevolution has remained unclear. To resolve the phylogeny of Triturus, we generated a c. 6000 transcriptome-derived marker data set using a custom target enrichment probe set, and conducted phylogenetic analyses using: (1) data concatenation with RAxML, (2) gene-tree summary with ASTRAL, and (3) species-tree estimation with SNAPP. All analyses produce the same, highly supported topology, despite cladogenesis having occurred over a short timeframe, resulting in short internal branch lengths. Our new phylogenetic hypothesis is consistent with the minimal number of inferred changes in NTV count necessary to explain the diversity in NTV observed today. Although a causal relationship between NTV, body form, and aquatic ecology has yet to be experimentally established, our phylogeny indicates that these features have evolved together, and suggest that they may underlie the adaptive radiation that characterizes Triturus., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Target enrichment of conserved genomic regions facilitates collecting sequences of many orthologous loci from non-model organisms to address phylogenetic, phylogeographic, population genetic, and molecular evolution questions. Bait sets for sequence capture can simultaneously target thousands of loci, which opens new avenues of research on speciose groups. Current phylogenetic hypotheses on the >103,000 species of Hemiptera have failed to unambiguously resolve major nodes, suggesting that alternative datasets and more thorough taxon sampling may be required to resolve relationships. We use a recently designed ultraconserved element (UCE) bait set for Hemiptera, with a focus on the suborder Heteroptera, or the true bugs, to test previously proposed relationships. We present newly generated UCE data for 36 samples representing three suborders, all seven heteropteran infraorders, 23 families, and 34 genera of Hemiptera and one thysanopteran outgroup. To improve taxon sampling, we also mined additional UCE loci in silico from published hemipteran genomic and transcriptomic data. We obtained 2271 UCE loci for newly sequenced hemipteran taxa, ranging from 265 to 1696 (average 904) per sample. These were similar in number to the data mined from transcriptomes and genomes, but with fewer loci overall. The amount of missing data correlates with greater phylogenetic divergence from taxa used to design the baits. This bait set hybridizes to a wide range of hemipteran taxa and specimens of varying quality, including dried specimens as old as 1973. Our estimated phylogeny yielded topologies consistent with other studies for most nodes and was strongly-supported. We also demonstrate that UCE loci are almost exclusively from the transcribed portion of the genome, thus data can be successfully integrated with existing genomic and transcriptomic resources for more comprehensive phylogenetic sampling, an important feature in the era of phylogenomics. UCE approaches can be used by other researchers for additional studies on hemipteran evolution and other research that requires well resolved phylogenies., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Rapid evolutionary radiations are difficult to resolve because divergence events are nearly synchronous and gene flow among nascent species can be high, resulting in a phylogenetic "bush". Large datasets composed of sequence loci from across the genome can potentially help resolve some of these difficult phylogenetic problems. A suitable test case is the Liolaemus fitzingerii species group of lizards, which includes twelve species that are broadly distributed in Argentinean Patagonia. The species in the group have had a complex evolutionary history that has led to high morphological variation and unstable taxonomy. We generated a sequence capture dataset for 28 ingroup individuals of 580 nuclear loci, alongside a mitogenomic dataset, to infer phylogenetic relationships among species in this group. Relationships among species were generally weakly supported with the nuclear data, and along with an inferred age of ∼2.6 million years old, indicate either rapid evolution, hybridization, incomplete lineage sorting, non-informative data, or a combination thereof. We inferred a signal of mito-nuclear discordance, indicating potential hybridization between L. melanops and L. martorii, and phylogenetic network analyses provided support for 5 reticulation events among species. Phasing the nuclear loci did not provide additional insight into relationships or suspected patterns of hybridization. Only one clade, composed of L. camarones, L. fitzingerii, and L. xanthoviridis was recovered across all analyses. Genomic datasets provide molecular systematists with new opportunities to resolve difficult phylogenetic problems, yet the lack of phylogenetic resolution in Patagonian Liolaemus is biologically meaningful and indicative of a recent and rapid evolutionary radiation. The phylogenetic relationships of the Liolaemus fitzingerii group may be best modeled as a reticulated network instead of a bifurcating phylogeny., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Mountain formation in Mexico has played an important role in the diversification of many Mexican taxa. The Trans-Mexican Volcanic Belt in particular has served as both a cradle of diversification and conduit for dispersal. We investigated the evolutionary history of the Isthmura bellii group of salamanders, a widespread amphibian across the Mexican highlands, using sequence capture of ultraconserved elements. Results suggest that the I. bellii group probably originated in southeastern Mexico in the late Miocene and later dispersed across the Trans-Mexican Volcanic Belt and into the Sierra Madre Occidental. Pre-Pleistocene uplift of the Trans-Volcanic Belt likely promoted early diversification by serving as a mesic land-bridge across central Mexico. These findings highlight the importance of the Trans-Volcanic Belt in generating Mexico's rich biodiversity., (Copyright © 2018 Elsevier Inc. All rights reserved.)

The advent of next-generation sequencing technology has allowed for thecollection of large portions of the genome for phylogenetic analysis. Hybrid enrichment and transcriptomics are two techniques that leverage next-generation sequencing and have shown much promise. However, methods for processing hybrid enrichment data are still limited. We developed a pipeline for anchored hybrid enrichment (AHE) read assembly, orthology determination, contamination screening, and data processing for sequences flanking the target "probe" region. We apply this approach to study the phylogeny of butterflies and moths (Lepidoptera), a megadiverse group of more than 157,000 described species with poorly understood deep-level phylogenetic relationships. We introduce a new, 855 locus AHE kit for Lepidoptera phylogenetics and compare resulting trees to those from transcriptomes. The enrichment kit was designed from existing genomes, transcriptomes, and expressed sequence tags and was used to capture sequence data from 54 species from 23 lepidopteran families. Phylogenies estimated from AHE data were largely congruent with trees generated from transcriptomes, with strong support for relationships at all but the deepest taxonomic levels. We combine AHE and transcriptomic data to generate a new Lepidoptera phylogeny, representing 76 exemplar species in 42 families. The tree provides robust support for many relationships, including those among the seven butterfly families. The addition of AHE data to an existing transcriptomic dataset lowers node support along the Lepidoptera backbone, but firmly places taxa with AHE data on the phylogeny. Combining taxa sequenced for AHE with existing transcriptomes and genomes resulted in a tree with strong support for (Calliduloidea $+$ Gelechioidea $+$ Thyridoidea) $+$ (Papilionoidea $+$ Pyraloidea $+$ Macroheterocera). To examine the efficacy of AHE at a shallow taxonomic level, phylogenetic analyses were also conducted on a sister group representing a more recent divergence, the Saturniidae and Sphingidae. These analyses utilized sequences from the probe region and data flanking it, nearly doubled the size of the dataset; resulting trees supported new phylogenetics relationships, especially within the Saturniidae and Sphingidae (e.g., Hemarina derived in the latter). We hope that our data processing pipeline, hybrid enrichment gene set, and approach of combining AHE data with transcriptomes will be useful for the broader systematics community., (© The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Phylogenomic approaches have proven able to resolve difficult branches in the tree of life. New World direct-developing frogs (Terraranae) represent a large evolutionary radiation in which interrelationships at key points in the phylogeny have not been adequately determined, affecting evolutionary, biogeographic, and taxonomic interpretations. We employed anchored hybrid enrichment to generate a data set containing 389 loci and >600,000 nucleotide positions for 30 terraranan and several outgroup frog species encompassing all major lineages in the clade. Concatenated maximum likelihood and coalescent species-tree approaches recover nearly identical topologies with strong support for nearly all relationships in the tree. These results are similar to previous phylogenetic results but provide additional resolution at short internodes. Among taxa whose placement varied in previous analyses, Ceuthomantis is shown to be the sister taxon to all other terraranans, rather than deeply embedded within the radiation, and Strabomantidae is monophyletic rather than paraphyletic with respect to Craugastoridae. We present an updated taxonomy to reflect these results, and describe a new subfamily for the genus Hypodactylus., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Museum specimens provide a wealth of information to biologists, but obtaining genetic data from formalin-fixed and fluid-preserved specimens remains challenging. While DNA sequences have been recovered from such specimens, most approaches are time-consuming and produce low data quality and quantity. Here, we use a modified DNA extraction protocol combined with high-throughput sequencing to recover DNA from formalin-fixed and fluid-preserved snakes that were collected over a century ago and for which little or no modern genetic materials exist in public collections. We successfully extracted DNA and sequenced ultraconserved elements (x¯ = 2318 loci) from 10 fluid-preserved snakes and included them in a phylogeny with modern samples. This phylogeny demonstrates the general use of such specimens in phylogenomic studies and provides evidence for the placement of enigmatic snakes, such as the rare and never-before sequenced Indian Xylophis stenorhynchus. Our study emphasizes the relevance of museum collections in modern research and simultaneously provides a protocol that may prove useful for specimens that have been previously intractable for DNA sequencing., (© 2017 John Wiley & Sons Ltd.)

The anomaly zone, defined by the presence of gene tree topologies that are more probable than the true species tree, presents a major challenge to the accurate resolution of many parts of the Tree of Life. This discrepancy can result from consecutive rapid speciation events in the species tree. Similar to the problem of long-branch attraction, including more data via loci concatenation will only reinforce the support for the incorrect species tree. Empirical phylogenetic studies often employ coalescent-based species tree methods to avoid the anomaly zone, but to this point these studies have not had a method for providing any direct evidence that the species tree is actually in the anomaly zone. In this study, we use 16 species of lizards in the family Scincidae to investigate whether nodes that are difficult to resolve place the species tree within the anomaly zone. We analyze new phylogenomic data (429 loci), using both concatenation and coalescent-based species tree estimation, to locate conflicting topological signal. We then use the unifying principle of the anomaly zone, together with estimates of ancestral population sizes and species persistence times, to determine whether the observed phylogenetic conflict is a result of the anomaly zone. We identify at least three regions of the Scincidae phylogeny that provide demographic signatures consistent with the anomaly zone, and this new information helps reconcile the phylogenetic conflict in previously published studies on these lizards. The anomaly zone presents a real problem in phylogenetics, and our new framework for identifying anomalous relationships will help empiricists leverage their resources appropriately for investigating and overcoming this challenge., (© The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

The formation of allopolyploid cotton precipitated a rapid diversification and colonization of dry coastal American tropical and subtropical regions. Previous phylogenetic analyses, combined with molecular divergence analyses, have offered a temporal framework for this radiation, but provide only weak support for some of the resolved branches. Moreover, these earlier analyses did not include the recently recognized sixth polyploid species, G. ekmanianum Wittmack. Here we use targeted sequence capture of multiple loci in conjunction with both concatenated and Bayesian concordance analyses to reevaluate the phylogeny of allopolyploid cotton species. Although phylogenetic resolution afforded by individual genes is often low, sufficient signal was attained both through the concatenated and concordance analyses to provide robust support for the Gossypium polyploid clade, which is reported here., (Copyright © 2015 Elsevier Inc. All rights reserved.)

Africa is renowned for its biodiversity and endemicity, yet little is known about the factors shaping them across the continent. African Agama lizards (45 species) have a pan-continental distribution, making them an ideal model for investigating biogeography. Many species have evolved conspicuous sexually dimorphic traits, including extravagant breeding coloration in adult males, large adult male body sizes, and variability in social systems among colorful versus drab species. We present a comprehensive time-calibrated species tree for Agama, and their close relatives, using a hybrid phylogenetic-phylogenomic approach that combines traditional Sanger sequence data from five loci for 57 species (146 samples) with anchored phylogenomic data from 215 nuclear genes for 23 species. The Sanger data are analyzed using coalescent-based species tree inference using (*)BEAST, and the resulting posterior distribution of species trees is attenuated using the phylogenomic tree as a backbone constraint. The result is a time-calibrated species tree for Agama that includes 95% of all species, multiple samples for most species, strong support for the major clades, and strong support for most of the initial divergence events. Diversification within Agama began approximately 23 million years ago (Ma), and separate radiations in Southern, East, West, and Northern Africa have been diversifying for >10Myr. A suite of traits (morphological, coloration, and sociality) are tightly correlated and show a strong signal of high morphological disparity within clades, whereby the subsequent evolution of convergent phenotypes has accompanied diversification into new biogeographic areas., (Copyright © 2014 Elsevier Inc. All rights reserved.)

The alpine butterfly genus Parnassius is a popular model group for studying biogeography, evolution, conservation biology, and ecology. Despite its scientific importance, a comprehensive and robust phylogeny of this group is still lacking. In this study, we used an amplicon capture strategy to sequence 144 nuclear protein‐coding genes and complete mitochondrial genomes for 60 Parnassius specimens covering 42 species and all eight subgenera of Parnassius. Our results strongly support the monophyly of the genus and eight subgenera. The relationships among subgenera are robustly resolved as (Sachaia, (Kreizbergia, (Driopa, (Parnassius, (Tadumia, Lingamius), (Kailasius, Koramius))))), which is different from all previous results. Biogeographic and divergence time analyses indicate that the ancestor of Parnassius originated in an area including the Himalayas and Tibetan Plateau (HTP) and Mongolian steppes in the middle Miocene approximately 13.19 Mya. The middle Miocene global cooling event (starting from ~13.9 Mya) probably provided climatic opportunities for the diversification of cold‐adapted Parnassius. The ancestral state reconstruction analyses suggest that the ancestor of Parnassius butterflies most likely lived in a medium elevational area (2000–4000 m) and fed on Papaveraceae plants. The host shift from Papaveraceae to Crassulaceae in the subgenus Parnassius increases the species diversity of this subgenus, concurring with the "escape and radiate" hypothesis. Overall, our work provides valuable nuclear gene and mitochondrial genome data and a robust phylogenetic framework of Parnassius for future studies of the taxonomy, evolution, and ecology of this group. [ABSTRACT FROM AUTHOR]

Intra- and interspecific communication is crucial to fitness via its role in facilitating mating, territoriality and defence. Yet, the evolution of animal communication systems is puzzling—how do they originate and change over time? Studying stridulatory morphology provides a tractable opportunity to deduce the origin and diversification of a communication mechanism. Stridulation occurs when two sclerotized structures rub together to produce vibratory and acoustic (vibroacoustic) signals, such as a cricket ‘chirp’. We investigated the evolution of stridulatory mechanisms in the superfamily Coreoidea (Hemiptera: Heteroptera), a group of insects known for elaborate male fighting behaviours and enlarged hindlegs. We surveyed a large sampling of taxa and used a phylogenomic dataset to investigate the evolution of stridulatory mechanisms. We identified four mechanisms, with at least five evolutionary gains. One mechanism, occurring only in male Harmostini (Rhopalidae), is described for the first time. Some stridulatory mechanisms appear to be non-homoplastic apomorphies within Rhopalidae, while others are homoplastic or potentially homoplastic within Coreidae and Alydidae, respectively. We detected no losses of these mechanisms once evolved, suggesting they are adaptive. Our work sets the stage for further behavioural, evolutionary and ecological studies to better understand the context in which these traits evolve and change.

Recent phylogenomic analyses within the insect superfamily Coreoidea (Hemiptera: Heteroptera) have begun to challenge previous phylogenetic hypotheses of the Coreidae and Alydidae based on more traditional cladistic and non-cladistic studies. Phylogenomic studies have found the coreid subfamilies Hydarinae and Pseudophloeinae to be more closely related to a potentially paraphyletic Alydidae (an "AHP" clade) in contrast with traditional cladistic studies. However, taxon sampling within these higher-level groups has remained sparse in current phylogenetic analyses, and the taxonomic positions and monophyly of some of these taxa continue to be unclear. Here, we expand upon previous phylogenomic studies using ultraconserved element loci by increasing taxon sampling within the AHP clade. Using concatenation and summary coalescent approaches, we specifically tested previous support for an AHP clade, the paraphyly of Alydidae, the phylogenetic position of Hydarinae, and the monophyly of the two tribes of Pseudophloeinae. Our results robustly support an AHP clade and resolved the position of Hydarinae as the sister group to a clade consisting of a paraphyletic Alydidae and Pseudophloeinae, regardless of analytical method and locus/gene tree filtering strategies we employed. We also found support for the monophyly of the pseudophloeine tribes Clavigrallini and Pseudophloeini, but generic relationships within each of these tribes varied across analyses. We discuss past non-cladistic morphological studies that have suggested the potential for an AHP clade in light of our results, and we highlight further systematic work needed to discern the AHP clade as a morphologically diagnosable group for future re-classification of the Alydidae and Coreidae. [ABSTRACT FROM AUTHOR]

Schistosomatidae Stiles and Hassall 1898 is a medically significant family of digenetic trematodes (Trematoda: Digenea), members of which infect mammals or birds as definitive hosts and aquatic or amphibious gastropods as intermediate hosts. Currently, there are 17 named genera, for many of which evolutionary interrelationships remain unresolved. The lack of a resolved phylogeny has encumbered our understanding of schistosomatid evolution, specifically patterns of host-use and the role of host-switching in diversification. Here, we used targeted sequence capture of ultra-conserved elements (UCEs) from representatives of 13 of the 17 named genera and 11 undescribed lineages that are presumed to represent either novel genera or species to generate a phylogenomic dataset for the estimation of schistosomatid interrelationships. This study represents the largest phylogenetic effort within the Schistosomatidae in both the number of loci and breadth of taxon sampling. We present a near-comprehensive family-level phylogeny providing resolution to several clades of long-standing uncertainty within Schistosomatidae, including resolution for the placement of the North American mammalian schistosomes, implying a second separate capture of mammalian hosts. Additionally, we present evidence for the placement of Macrobilharzia at the base of the Schistosoma + Bivitellobilharzia radiation. Patterns of definitive and intermediate host use and a strong role for intermediate host-switching are discussed relative to schistosomatid diversification. [ABSTRACT FROM AUTHOR]

Resolving intractable phylogenetic relationships often requires simultaneously analyzing a large number of coding and non-coding orthologous loci. To gather both coding and non-coding data, traditional sequence capture methods require custom-designed commercial probes. Here, we present a cost-effective sequence capture method based on homemade probes, to capture thousands of coding and non-coding orthologous loci simultaneously, suitable for all organisms. This approach, called “FLc-Capture,” synthesizes biotinylated full-length cDNAs from mRNA as capture probes, eliminates the need for costly commercial probe design and synthesis. To demonstrate the utility of FLc-Capture, we prepared full-length cDNA probes from mRNA extracted from a common colubrid snake. We performed capture experiments with these homemade cDNA probes and successfully obtained thousands of coding and non-coding genomic loci from 24 Colubridae species and 12 distantly related snake species of other families. The average capture specificity of FLc-Capture across all tested snake species is 35%, similar to the previously published EecSeq method. We constructed two phylogenomic data sets, one including 1,075 coding loci (∼817,000 bp) and the other including 1,948 non-coding loci (∼1,114,000 bp), to study the phylogeny of Colubridae. Both data sets yielded highly similar and well-resolved trees, with 85% of nodes having >95% bootstrap support. Our experimental tests show that FLc-Capture is a flexible, fast, and cost-effective sequence capture approach for simultaneously gathering coding and non-coding phylogenomic data sets to study intractable phylogenetic questions. We hope that this method will serve as a new data collection tool for evolutionary biologists working in the era of phylogenomics.

Sequence capture studies result in rich data sets comprising hundreds to thousands of targeted genomic regions that are superseding Sanger‐based data sets comprised of a few well‐known loci with historical uses in phylogenetics ('legacy loci'). However, integrating sequence capture and Sanger‐based data sets is of interest as legacy loci can include different types of loci (e.g. mitochondrial and nuclear) across a potentially larger sample of species from past studies. Sequence capture data sets include nontargeted sequences, and there has been recent interest in extracting legacy loci from invertebrate data sets. Here, we use published legacy data from leaf‐footed bugs (Hemiptera: Coreoidea) to recover 15 mitochondrial and seven nuclear legacy loci from off‐target sequences in a sequence capture data set, explore approaches to improve legacy locus recovery, and combine these loci with sequence capture data for phylogenetic analysis. Two nuclear loci were determined to already be targeted by sequence capture baits. Most of the remaining loci were successfully recovered from off‐target sequences, but this recovery varied greatly. Additionally, complementing complete mitogenomes with additional reference mitochondrial sequences from a genetic depository did not offer improvement for most of our taxa; however, supplementing these reference sequences with extracted legacy loci offered ≥6% improvement across taxa for a given mitochondrial locus (negligible improvement for nuclear loci). Phylogenetic analysis of legacy and sequence capture data produced a topology generally congruent with recent studies, but support was lower. Thus, future studies may employ the approaches used in this study to integrate legacy data with newly generated sequence capture data sets without added expenses. [ABSTRACT FROM AUTHOR]

Sequence capture across large phylogenetic scales is not easy because hybridization capture is only effective when the genetic distance between the bait and target is small. Here, we propose a simple but effective strategy to tackle this issue: pooling DNA from a number of selected representative species of different clades to prepare PCR‐generated baits to minimize the genetic distance between the bait and target. To demonstrate the utility of this strategy, we newly developed a set of universal nuclear markers (including 94 nuclear protein‐coding genes) for Lepidoptera, a superdiverse insect group. We used a DNA pool from six lepidopteran species (representing six superfamilies) to prepare PCR baits for the 94 markers. These homemade PCR baits were used to capture sequence data from 43 species of 17 lepidopteran families, and 94% of the target loci were recovered. We constructed two data sets from the obtained data (one containing ~90 kb target coding sequences and the other containing ~120 kb target + flanking coding sequences). Both data sets yielded highly similar and well‐resolved trees with 90% of nodes having >95% bootstrap support. Our capture experiment indicated that using DNA mixtures pooled from different clade‐representative species of Lepidoptera to prepare PCR baits can reliably capture a large number of targeted nuclear markers across different Lepidoptera lineages. We hope that this newly developed nuclear marker set will serve as a new phylogenetic tool for Lepidoptera phylogenetics, and the PCR bait preparation strategy can facilitate the application of sequence capture techniques by researchers to accelerate data collection. [ABSTRACT FROM AUTHOR]

Comprising more than 25 000 species, the Sunflower Family (Compositae or Asteraceae) is the largest family of flowering plants. Many of its lineages have experienced recent and rapid radiations, and the family has a deep and widespread history of large-scale gene duplications and polyploidy. Many of the most important evolutionary questions about the family's diversity remain unanswered due to poor resolution and lack of support for major nodes of the phylogeny. Our group has employed a phylogenomics approach using Hyb-Seq that includes sequencing ∼1000 low-copy number nuclear markers, plus partial plastomes for large numbers of species. Here we discuss our progress to date and present two phylogenies comprising nine subfamilies and 25 tribes using concatenated and coalescence-based analyses. We discuss future plans for incorporating high-quality reference genomes and transcriptomes to advance systematic and evolutionary studies in the Compositae. While we have made great strides toward developing tools for employing phylogenomics and resolving relationships within Compositae, much work remains. Recently formed global partnerships will work to solve the unanswered evolutionary questions for this megafamily. [ABSTRACT FROM AUTHOR]

Custom sequence capture experiments are becoming an efficient approach for gathering large sets of orthologous markers in nonmodel organisms. Transcriptome-based exon capture utilizes transcript sequences to design capture probes, typically using a reference genome to identify intron-exon boundaries to exclude shorter exons (<200 bp). Here, we test directly using transcript sequences for probe design, which are often composed of multiple exons of varying lengths. Using 1260 orthologous transcripts, we conducted sequence captures across multiple phylogenetic scales for frogs, including outgroups ~100 Myr divergent from the ingroup. We recovered a large phylogenomic data set consisting of sequence alignments for 1047 of the 1260 transcriptome-based loci (~561 000 bp) and a large quantity of highly variable regions flanking the exons in transcripts (~70 000 bp), the latter improving substantially by only including ingroup species (~797 000 bp). We recovered both shorter (<100 bp) and longer exons (>200 bp), with no major reduction in coverage towards the ends of exons. We observed significant differences in the performance of blocking oligos for target enrichment and nontarget depletion during captures, and differences in PCR duplication rates resulting from the number of individuals pooled for capture reactions. We explicitly tested the effects of phylogenetic distance on capture sensitivity, specificity, and missing data, and provide a baseline estimate of expectations for these metrics based on a priori knowledge of nuclear pairwise differences among samples. We provide recommendations for transcriptome-based exon capture design based on our results, cost estimates and offer multiple pipelines for data assembly and analysis. [ABSTRACT FROM AUTHOR]

[Display omitted] • First subspecies-level phylogeny for Lepidothrix manakins clarifies relationships. • Results suggest Blue-crowned Manakins comprise two biological species. • An F1 hybrid between two manakin species suggests postmating reproductive barriers. Although recent molecular phylogenetic analyses of Lepidothrix manakins (family Pipridae) have helped clarify their evolutionary relationships, the placement of several lineages remains in question because of low or conflicting branch support. In particular, the relationship of L. coronata to other members of the genus and relationships within the L. nattereri + L. vilasboasi + L. iris clade have been difficult to resolve. We used RADcap to collect restriction site-associated DNA sequence data and estimate the first subspecies-level phylogeny of the genus Lepidothrix (17 of 18 currently recognized subspecies), and we included extensive geographic representation of the widespread and phenotypically variable L. coronata. We found strong support for the phylogenetic position and monophyly of L. coronata , and we resolved two clades separated by the Andes that, along with previous divergence time estimates and our assessment of morphological and vocal evidence, suggest the presence of two biological species: Velvety Manakin (L. velutina) west of the Andes and Blue-capped Manakin (L. coronata) east of the Andes. Species-level relationships within the L. nattereri + L. vilasboasi + L. iris clade remained poorly resolved in concatenated and coalescent-based analyses, with SNAPP analyses suggesting that the lack of reciprocal monophyly is due to extensive allele sharing among these taxa. Finally, we confirmed a previously documented hybrid between L. coronata and L. suavissima as an F1 individual, consistent with the view that hybridization between these two species is a rare event and that postmating reproductive barriers prevent successful backcrossing. [ABSTRACT FROM AUTHOR]

Recent advances in high-throughput sequencing library preparation and subgenomic enrichment methods have opened new avenues for population genetics and phylogenetics of nonmodel organisms. To multiplex large numbers of indexed samples while sequencing predominantly orthologous, targeted regions of the genome, we propose modifications to an existing, in-solution capture that utilizes PCR products as target probes to enrich library pools for the genomic subset of interest. The sequence capture using PCR-generated probes ( SCPP) protocol requires no specialized equipment, is highly flexible and significantly reduces experimental costs for projects where a modest scale of genetic data is optimal (25-100 genomic loci). Our alterations enable application of this method across a wider phylogenetic range of taxa and result in higher capture efficiencies and coverage at each locus. Efficient and consistent capture over multiple SCPP experiments and at various phylogenetic distances is demonstrated, extending the utility of this method to both phylogeographic and phylogenomic studies. [ABSTRACT FROM AUTHOR]

The field of phylogenetics is on the cusp of a major revolution, enabled by new methods of data collection that leverage both genomic resources and recent advances in DNA sequencing. Previous phylogenetic work has required laborintensive marker development coupled with single-locus polymerase chain reaction and DNA sequencing on clade-by-clade and locus-by-locus basis. Here, we present a new, cost-efficient, and rapid approach to obtaining data from hundreds of loci for potentially hundreds of individuals for deep and shallow phylogenefic studies. Specifically, we designed probes for target enrichment of >500 loci in highly conserved anchor regions of vertebrate genomes (flanked by less conserved regions) from five model species and tested enrichment efficiency in nonmodel species up to 508 million years divergent from the nearest model. We found that hybrid enrichment using conserved probes (anchored enrichment) can recover a large number of unlinked loci that are useful at a diversity of phylogenetic timescales. This new approach has the potential not only to expedite resolution of deep-scale portions of the Tree of Life but also to greatly accelerate resolution of the large number of shallow clades that remain unresolved. The combination of low cost (~1% of the cost of traditional Sanger sequencing and ~3.5% of the cost of high-throughput amplicon sequencing for projects on the scale of 500 loci x 100 individuals) and rapid data collection (~2 weeks of laboratory time) are expected to make this approach tractable even for researchers working on systems with limited or nonexistent genomic resources. [ABSTRACT FROM AUTHOR]

Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota because UCEs and phylogenetic relationships are well-known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2386 UCE-anchored loci from nine, nonmodel avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels. [ABSTRACT FROM AUTHOR]

• We sequenced 94 nuclear protein-coding genes for all ten genera of Epicopeiidae. • The higher-level phylogeny of Epicopeiidae is resolved for the first time. • We presented the first molecular divergence timescale for the Epicopeiidae. • We found that the last common ancestor of epicopeiids is non-mimetic. The family Epicopeiidae is a small group of day-flying moths, known for mimicking many different groups of butterflies and moths. So far, there still lacks a reliable phylogenetic framework of Epicopeiidae that is necessary to our understanding of the evolutionary process of their mimicry. In this study, we sequenced 94 nuclear protein-coding markers for 56 epicopeiid samples and 11 outgroups, covering all ten genera of Epicopeiidae. We used homemade PCR-generated baits to capture target sequences, which allowed us to utilize old and dried specimens that were difficult to handle by conventional PCR + Sanger sequencing. Maximum likelihood and Bayesian analyses of the newly obtained dataset (86,388 bp) at both DNA and protein levels produced identical phylogenies with strong support. The non-mimicry genus Deuveia is the sister group of other epicopeiid genera. Epicopeia and Nossa are not monophyletic, and these two genera nest together to form a clade. We also estimated divergence times of Epicopeiidae and found that their initial diversification happened in Eocene about 41 million years ago. The ancestral state reconstruction of mimicry type for this family suggested that the last common ancestor of epicopeiid moths is non-mimetic, and the Riodinidae-mimicry type evolved first. In summary, our work provides a comprehensive and robust time-calibrated phylogeny of Epicopeiidae that provides a sound framework for revising their classification and interpreting character evolution. [ABSTRACT FROM AUTHOR]

• Two deep genetic lineages detected in the Malagasy frog, Mantidactylus ambreensis. • Co-occurrence without admixture confirms separate species status of these lineages. • The lineages are segregated by elevation. • Phylogeography suggests this co-occurrence originated by secondary contact. • No evidence for sympatric or parapatric speciation. Madagascar's biota is characterized by a high degree of microendemism at different taxonomic levels, but how colonization and in-situ speciation contribute to the assembly of local species communities has rarely been studied on this island. Here we analyze the phylogenetic relationships of riparian frogs of the Mantidactylus ambreensis species complex, which is distributed in the north of Madagascar and was originally described from Montagne d'Ambre, an isolated mountain of volcanic origin, currently protected within Montagne d'Ambre National Park (MANP). Data from mitochondrial DNA, and phylogenomic data from FrogCap, a sequence capture method, independently confirm that this species complex is monophyletic within the subgenus Ochthomantis , and identify two main clades within it. These two clades are separated by 5.6–6.8% pairwise distance in the mitochondrial 16S rRNA gene and co-occur in MANP, with one distributed at high elevations (940–1375 m a.s.l.) and the other at lower elevations (535–1010 m a.s.l.), but show almost no haplotype sharing in the nuclear RAG1 gene. This occurrence in syntopy without admixture confirms them as independent evolutionary lineages that merit recognition as separate species, and we here refer to them as high-elevation (HE) and low-elevation (LE) lineage; they will warrant taxonomic assessment to confidently assign the name ambreensis to one or the other. Populations of the M. ambreensis complex from elsewhere in northern Madagascar all belong to the LE lineage, although they do occur over a larger elevational range than in Montagne d'Ambre (285–1040 m a.s.l.). Within LE there are several phylogroups (LE1–LE4) of moderately deep divergence (1.5–2.8% in 16S), but phylogroup LE4 that occurs in MANP has a deeply nested phylogenetic position, as recovered separately by mitochondrial and sequence capture datasets. This suggests that HE and LE did not diverge by a local fission of lower and upper populations, but instead arose through a more complex biogeographic scenario. The branching pattern of phylogroups LE1–LE4 shows a clear south-to-north phylogeographic pattern. We derive from these results a testable hypothesis of vicariant speciation that restricted the HE lineage to MANP and the LE candidate species to a climatic refugium further south, with subsequent northwards range expansion and secondary colonization of MANP by LE. These results provide an example for complex assembly of local microendemic amphibian faunas on Madagascar. [ABSTRACT FROM AUTHOR]