Automatic selection of partitioning schemes for phylogenetic analyses using iterative k-means clustering of site rates

Eleven New Species of the Genus Tarzetta (Tarzettaceae, Pezizales) from Mexico

The genus Tarzetta is distributed mainly in temperate forests and establishes ectomycorrhizal associations with angiosperms and gymnosperms. Studies on this genus are scarce in México. A visual, morphological, and molecular (ITS-LSU) description of T. americupularis, T. cupressicola, T. davidii, T. durangensis, T. mesophila, T. mexicana, T. miquihuanensis, T. poblana, T. pseudobronca, T. texcocana, and T. victoriana was carried out in this work, associated with Abies, Quercus, and Pinus. The results of SEM showed an ornamented ascospores formation by Mexican Taxa; furthermore, the results showed that T. catinus and T. cupularis are only distributed in Europe and are not associated with any American host.

A comprehensive phylogenomic study unveils evolutionary patterns and challenges in the mitochondrial genomes of Carcharhiniformes: A focus on Triakidae

The complex evolutionary patterns in the mitochondrial genome (mitogenome) of the most species-rich shark order, the Carcharhiniformes (ground sharks) has led to challenges in the phylogenomic reconstruction of the families and genera belonging to the order, particularly the family Triakidae (houndsharks). The current state of Triakidae phylogeny remains controversial, with arguments for both monophyly and paraphyly within the family. We hypothesize that this variability is triggered by the selection of different a priori partitioning schemes to account for site and gene heterogeneity within the mitogenome. Here we used an extensive statistical framework to select the a priori partitioning scheme for inference of the mitochondrial phylogenomic relationships within Carcharhiniformes, tested site heterogeneous CAT + GTR + G4 models and incorporated the multi-species coalescent model (MSCM) into our analyses to account for the influence of gene tree discordance on species tree inference. We included five newly assembled houndshark mitogenomes to increase resolution of Triakidae. During the assembly procedure, we uncovered a 714 bp-duplication in the mitogenome of Galeorhinus galeus. Phylogenetic reconstruction confirmed monophyly within Triakidae and the existence of two distinct clades of the expanded Mustelus genus. The latter alludes to potential evolutionary reversal of reproductive mode from placental to aplacental, suggesting that reproductive mode has played a role in the trajectory of adaptive divergence. These new sequences have the potential to contribute to population genomic investigations, species phylogeography delineation, environmental DNA metabarcoding databases and, ultimately, improved conservation strategies for these ecologically and economically important species.

Nucleotide Substitution Model Selection Is Not Necessary for Bayesian Inference of Phylogeny With Well-Behaved Priors

Model selection aims to choose the most adequate model for the statistical analysis at hand. The model must be complex enough to capture the complexity of the data but should be simple enough not to overfit. In phylogenetics, the most common model selection scenario concerns selecting an adequate substitution and partition model for sequence evolution to infer a phylogenetic tree. Previously, several studies showed that substitution model under-parameterization can bias phylogenetic studies. Here, we explored the impact of substitution model over-parameterization in a Bayesian statistical framework. We performed simulations under the simplest substitution model, the Jukes-Cantor model, and compare posterior estimates of phylogenetic tree topologies and tree length under the true model to the most complex model, the $\text{GTR}+\Gamma+\text{I}$ substitution model, including over-splitting the data into additional subsets (i.e., applying partitioned models). We explored 4 choices of prior distributions: the default substitution model priors of MrBayes, BEAST2, and RevBayes and a newly devised prior choice (Tame). Our results show that Bayesian inference of phylogeny is robust to substitution model over-parameterization and over-partitioning but only under our new prior settings. All 3 current default priors introduced biases for the estimated tree length. We conclude that substitution and partition model selection are superfluous steps in Bayesian phylogenetic inference pipelines if well-behaved prior distributions are applied and more effort should focus on more complex and biologically realistic substitution models.

ModelRevelator: Fast phylogenetic model estimation via deep learning

Selecting the best model of sequence evolution for a multiple-sequence-alignment (MSA) constitutes the first step of phylogenetic tree reconstruction. Common approaches for inferring nucleotide models typically apply maximum likelihood (ML) methods, with discrimination between models determined by one of several information criteria. This requires tree reconstruction and optimisation which can be computationally expensive. We demonstrate that neural networks can be used to perform model selection, without the need to reconstruct trees, optimise parameters, or calculate likelihoods. We introduce ModelRevelator, a model selection tool underpinned by two deep neural networks. The first neural network, NNmodelfind, recommends one of six commonly used models of sequence evolution, ranging in complexity from Jukes and Cantor to General Time Reversible. The second, NNalphafind, recommends whether or not a Γ-distributed rate heterogeneous model should be incorporated, and if so, provides an estimate of the shape parameter, ɑ. Users can simply input an MSA into ModelRevelator, and swiftly receive output recommending the evolutionary model, inclusive of the presence or absence of rate heterogeneity, and an estimate of ɑ. We show that ModelRevelator performs comparably with likelihood-based methods and the recently published machine learning method ModelTeller over a wide range of parameter settings, with significant potential savings in computational effort. Further, we show that this performance is not restricted to the alignments on which the networks were trained, but is maintained even on unseen empirical data. We expect that ModelRevelator will provide a valuable alternative for phylogeneticists, especially where traditional methods of model selection are computationally prohibitive.

Five New Species of Aureoboletus and Chalciporus (Boletaceae, Boletales) and Their Ethnomycological Aspects

Among Boletales, the family Boletaceae has the highest diversity worldwide. Additionally, this fungal group has great ecological relevance because it not only includes mainly ectomycorrhizal but also saprotrophic species. Furthermore, some species are used as food and have sociocultural and economic importance worldwide. In Mexico, the Boletaceae family boasts a substantial number of species, yet our understanding of these species remains far from comprehensive. In this work, by using macro- and micromorphological and phylogenetic analyses of DNA sequences from multi-gene analyses based on ITS, nrLSU, rpb1, rpb2, and tef1, we report five new species belonging to the genera Aureoboletus and Chalciporus: A. ayuukii and A. elvirae from a Quercus scytophylla forest, A. readii from a mixed forest, C. perezsilvae from cloud forest, and C. piedracanteadensis from both a mixed coniferous forest and a Quercus-Pinus forest. In Mexico, four species of Aureoboletus are used as a food source, and in this work, we add another one, A. readii, which is traditionally consumed by members of the Tlahuica-Pjiekakjoo culture, who are located in the central part of the country. This work contributes to our knowledge of two genera of Boletaceae in a geographical area that is scarcely studied, and thus, our understanding of its biocultural relevance is enriched.

A new species of Trimma of the T. taylori species group (Teleostei: Gobiidae) from the Red Sea, Indian Ocean

A new species of Trimma is described from the Red Sea along the Saudi Arabian coast. Specimens and/or photographs of this species are available from the Egyptian Red Sea to Eritrea. These specimens, formerly identified as T. taylori, differ from all other samples from the Indo-Pacific currently identified as T. taylori in having 9 and 89 dorsal- and anal-fin rays respectively (vs. usually 10 and 10 rays), 13 pectoral-fin rays (vs. usually 14 rays), and cycloid scales covering the entire predorsal region from the upper base of the pectoral fin anterior to a convex line posterodorsally to just lateral to the base of the sixth first dorsal-fin spine (vs. predorsal region mostly or entirely covered with ctenoid scales). In addition, specimens from the Red Sea form a monophyletic lineage in a Maximum Likelihood analysis of the COI gene. In this tree, the new species is the sister group to a clade composed of three lineages. One is composed of specimens from the Maldives, which is the sister group of a single available specimen from the Seychelles. These two together are the sister group of specimens of a widespread western Pacific clade.

New Ascomycetes from the Mexican Tropical Montane Cloud Forest

The tropical montane cloud forest is the most diverse and threatened vegetation type in Mexico. In the last decade, the number of described Ascomycetes species has notably increased, reaching more than 1300 species. This study describes six new species based on their molecular and morphological characteristics. Our results suggest that Mexico has the highest number of described species in the Neotropics. However, many other Mexican lineages still need to be described.

Novelties in Macrofungi of the Tropical Montane Cloud Forest in Mexico

The tropical montane cloud forest in Mexico is the most diverse and threatened ecosystem. Mexican macrofungi numbers more than 1408 species. This study described four new species of Agaricomycetes (Bondarzewia, Gymnopilus, Serpula, Sparassis) based on molecular and morphological characteristics. Our results support that Mexico is among the most biodiverse countries in terms of macrofungi in the Neotropics.

Elaphomyces castilloi (Elaphomycetaceae, Ascomycota) and Entoloma secotioides (Entolomataceae, Basidiomycota), two new sequestrate fungi from tropical montane cloud forest from south Mexico

Two new species of sequestrate fungi are described from south Mexico based on morphological and molecular evidences. Here we describe Elaphomyces castilloi characterized by the yellowish mycelial mat, dull blue gleba and ascospores of 9.7–11.5 µm; Entoloma secotioides is characterized by the secotioid basidiomata, sulcate, pale cream pileus, and basidiospores of 7–13 × 5–9 µm. Both species grow in montane cloud forest under Quercus sp. in the state of Chiapas, Mexico. Descriptions, photographs, and multilocus phylogeny for both species are presented.

Evolutionary history and divergence times of Odonata (dragonflies and damselflies) revealed through transcriptomics

Dragonflies and damselflies are among the earliest flying insects with extant representatives. However, unraveling details of their long evolutionary history, such as egg laying (oviposition) strategies, is impeded by unresolved phylogenetic relationships, particularly in damselflies. Here we present a transcriptome-based phylogenetic reconstruction of Odonata, analyzing 2,980 protein-coding genes in 105 species representing nearly all the order's families. All damselfly and most dragonfly families are recovered as monophyletic. Our data suggest a sister relationship between dragonfly families of Gomphidae and Petaluridae. According to our divergence time estimates, both crown-Zygoptera and -Anisoptera arose during the late Triassic. Egg-laying with a reduced ovipositor apparently evolved in dragonflies during the late Jurassic/early Cretaceous. Lastly, we also test the impact of fossil choice and placement, particularly, of the extinct fossil species, †Triassolestodes asiaticus, and †Proterogomphus renateae on divergence time estimates. We find placement of †Proterogomphus renateae to be much more impactful than †Triassolestodes asiaticus.

Three new species of Rhytidhysteron (Dothideomycetes, Ascomycota) from Mexico

The genus Rhytidhysteron is characterised by forming navicular to apothecial hysterothecia, exposing the green, yellow, orange, red, vinaceous or black colours of the hymenium which generally releases pigments in the presence of KOH. The exciple is smooth or striated, the asci bitunicate and ascospores have 1–5 transverse septa. To date, twenty-six Rhytidhysteron species have been described from the Tropics. The present study aims to describe three new species in the Neotropics of Mexico based on molecular methods and morphological features. Illustrations and a taxonomic key are provided for all known species of this genus. Rhytidhysteroncozumelense from the Isla Cozumel Biosphere Reserve, R.esperanzae from the Sierra Juárez, Oaxaca and R.mesophilum from the Sierra Madre Oriental, Hidalgo are described as new species. With the present study, the number of species of Rhytidhysteron known from Mexico is now increased to eight.

Review of the cardinalfishes of the genus Cercamia (Percomorpha: Apogonidae) of the Red Sea and Indian Ocean with descriptions of three new species

The representatives of Cercamia from the Indian Ocean including Red Sea are reviewed and three new species are described: Cercamia spio n. sp., formerly known as C. eremia (Allen, 1987), is described from 14 specimens, 1733 mm SL, collected in 1015 meters from northern (Duba) to central (Jeddah) Saudi Arabia and from Jezirat Faraun, Egypt. It also has been photographed from the Gulf of Aqaba (Dahab, Egypt) and El Quseir (Mangrove Bay, Egypt). The new species is distinguished from other Indian Ocean Cercamia in having fewer developed gill rakers on lower limb (usually 11 versus usually 1213) and fewer anal-fin rays (11 versus usually 1213). Another new species, Cercamia laamu, n. sp., is described only from the Maldives and Chagos Archipelago based on five specimens 16.030.5 mm SL. It differs from all Indian Ocean Cercamia in having more greater number of the second dorsal-fin rays (10 versus usually 9), and a translucent body devoid of reddish marks versus small reddish dots and crisscross lines. The third new species, Cercamia mascarene, n. sp., is described from 40 specimens 1936 mm SL, from Rodrigues Island, Mauritius. It differs from Cercamia eremia in having a greater number of developed gill rakers on the lower limb of the first gill arch (usually 13 versus usually 12). Free neuromasts and cephalic pores are illustrated for Cercamia mascarene and free neuromasts on the body and caudal fin are illustrated for Japanese specimens of C. cf. eremia. New diagnoses are provided for Cercamia cladara, the type species of the genus, and C. eremia. A map of collection locations for species of Cercamia is presented to show the breath of known occurrences in the Red Sea and Indian Ocean. A new morphologic diagnosis is provided for Cercamia. A phylogenetic analysis of the barcoding portion of the mitochondrial COI gene, including all available sequences from members of the genus Cercamia, displays a much higher species diversity than expected, with high levels of divergence among recognized and undescribed species. A key to the described Indian Ocean species is provided.

Mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families

Motivation

Reconstruction of gene copy number evolution is an essential approach for understanding how complex biological systems have been organized. Although various models have been proposed for gene copy number evolution, existing evolutionary models have not appropriately addressed the fact that different gene families can have very different gene gain/loss rates.

Results

In this study, we developed Mirage (MIxtuRe model for Ancestral Genome Estimation), which allows different gene families to have flexible gene gain/loss rates. Mirage can use three models for formulating heterogeneous evolution among gene families: the discretized Γ model, probability distribution-free model and pattern mixture (PM) model. Simulation analysis showed that Mirage can accurately estimate heterogeneous gene gain/loss rates and reconstruct gene-content evolutionary history. Application to empirical datasets demonstrated that the PM model fits genome data from various taxonomic groups better than the other heterogeneous models. Using Mirage, we revealed that metabolic function-related gene families displayed frequent gene gains and losses in all taxa investigated.

Availability and implementation

The source code of Mirage is freely available at https://github.com/fukunagatsu/Mirage.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

Joint optimization of an autoencoder for clustering and embedding

Deep embedded clustering has become a dominating approach to unsupervised categorization of objects with deep neural networks. The optimization of the most popular methods alternates between the training of a deep autoencoder and a k-means clustering of the autoencoder’s embedding. The diachronic setting, however, prevents the former to benefit from valuable information acquired by the latter. In this paper, we present an alternative where the autoencoder and the clustering are learned simultaneously. This is achieved by providing novel theoretical insight, where we show that the objective function of a certain class of Gaussian mixture models (GMM’s) can naturally be rephrased as the loss function of a one-hidden layer autoencoder thus inheriting the built-in clustering capabilities of the GMM. That simple neural network, referred to as the clustering module, can be integrated into a deep autoencoder resulting in a deep clustering model able to jointly learn a clustering and an embedding. Experiments confirm the equivalence between the clustering module and Gaussian mixture models. Further evaluations affirm the empirical relevance of our deep architecture as it outperforms related baselines on several data sets.

Assessing the suitability of mitochondrial and nuclear DNA genetic markers for molecular systematics and species identification of helminths

BACKGROUND

Genetic markers are employed widely in molecular studies, and their utility depends on the degree of sequence variation, which dictates the type of application for which they are suited. Consequently, the suitability of a genetic marker for any specific application is complicated by its properties and usage across studies. To provide a yardstick for future users, in this study we assess the suitability of genetic markers for molecular systematics and species identification in helminths and provide an estimate of the cut-off genetic distances per taxonomic level.

METHODS

We assessed four classes of genetic markers, namely nuclear ribosomal internal transcribed spacers, nuclear rRNA, mitochondrial rRNA and mitochondrial protein-coding genes, based on certain properties that are important for species identification and molecular systematics. For molecular identification, these properties are inter-species sequence variation; length of reference sequences; easy alignment of sequences; and easy to design universal primers. For molecular systematics, the properties are: average genetic distance from order/suborder to species level; the number of monophyletic clades at the order/suborder level; length of reference sequences; easy alignment of sequences; easy to design universal primers; and absence of nucleotide substitution saturation. Estimation of the cut-off genetic distances was performed using the 'K-means' clustering algorithm.

RESULTS

The nuclear rRNA genes exhibited the lowest sequence variation, whereas the mitochondrial genes exhibited relatively higher variation across the three groups of helminths. Also, the nuclear and mitochondrial rRNA genes were the best possible genetic markers for helminth molecular systematics, whereas the mitochondrial protein-coding and rRNA genes were suitable for molecular identification. We also revealed that a general gauge of genetic distances might not be adequate, using evidence from the wide range of genetic distances among nematodes.

CONCLUSION

This study assessed the suitability of DNA genetic markers for application in molecular systematics and molecular identification of helminths. We provide a novel way of analyzing genetic distances to generate suitable cut-off values for each taxonomic level using the 'K-means' clustering algorithm. The estimated cut-off genetic distance values, together with the summary of the utility and limitations of each class of genetic markers, are useful information that can benefit researchers conducting molecular studies on helminths.

mPartition: A Model-Based Method for Partitioning Alignments

Maximum likelihood (ML) analysis of nucleotide or amino-acid alignments is widely used to infer evolutionary relationships among species. Computing the likelihood of a phylogenetic tree from such alignments is a complicated task because the evolutionary processes typically vary across sites. A number of studies have shown that partitioning alignments into sub-alignments of sites, where each sub-alignment is analyzed using a different model of evolution (e.g., GTR + I + G), is a sensible strategy. Current partitioning methods group sites into subsets based on the inferred rates of evolution at the sites. However, these do not provide sufficient information to adequately reflect the substitution processes of characters at the sites. Moreover, the site rate-based methods group all invariant sites into one subset, potentially resulting in wrong phylogenetic trees. In this study, we propose a partitioning method, called mPartition, that combines not only the evolutionary rates but also substitution models at sites to partition alignments. Analyses of different partitioning methods on both real and simulated datasets showed that mPartition was better than the other partitioning methods tested. Notably, mPartition overcame the pitfall of grouping all invariant sites into one subset. Using mPartition may lead to increased accuracy of ML-based phylogenetic inference, especially for multiple loci or whole genome datasets.

An integrative phylogenomic approach to elucidate the evolutionary history and divergence times of Neuropterida (Insecta: Holometabola)

BACKGROUND

The latest advancements in DNA sequencing technologies have facilitated the resolution of the phylogeny of insects, yet parts of the tree of Holometabola remain unresolved. The phylogeny of Neuropterida has been extensively studied, but no strong consensus exists concerning the phylogenetic relationships within the order Neuroptera. Here, we assembled a novel transcriptomic dataset to address previously unresolved issues in the phylogeny of Neuropterida and to infer divergence times within the group. We tested the robustness of our phylogenetic estimates by comparing summary coalescent and concatenation-based phylogenetic approaches and by employing different quartet-based measures of phylogenomic incongruence, combined with data permutations.

RESULTS

Our results suggest that the order Raphidioptera is sister to Neuroptera + Megaloptera. Coniopterygidae is inferred as sister to all remaining neuropteran families suggesting that larval cryptonephry could be a ground plan feature of Neuroptera. A clade that includes Nevrorthidae, Osmylidae, and Sisyridae (i.e. Osmyloidea) is inferred as sister to all other Neuroptera except Coniopterygidae, and Dilaridae is placed as sister to all remaining neuropteran families. Ithonidae is inferred as the sister group of monophyletic Myrmeleontiformia. The phylogenetic affinities of Chrysopidae and Hemerobiidae were dependent on the data type analyzed, and quartet-based analyses showed only weak support for the placement of Hemerobiidae as sister to Ithonidae + Myrmeleontiformia. Our molecular dating analyses suggest that most families of Neuropterida started to diversify in the Jurassic and our ancestral character state reconstructions suggest a primarily terrestrial environment of the larvae of Neuropterida and Neuroptera.

CONCLUSION

Our extensive phylogenomic analyses consolidate several key aspects in the backbone phylogeny of Neuropterida, such as the basal placement of Coniopterygidae within Neuroptera and the monophyly of Osmyloidea. Furthermore, they provide new insights into the timing of diversification of Neuropterida. Despite the vast amount of analyzed molecular data, we found that certain nodes in the tree of Neuroptera are not robustly resolved. Therefore, we emphasize the importance of integrating the results of morphological analyses with those of sequence-based phylogenomics. We also suggest that comparative analyses of genomic meta-characters should be incorporated into future phylogenomic studies of Neuropterida.

Current Affairs of Microbial Genome-Wide Association Studies: Approaches, Bottlenecks and Analytical Pitfalls

Microbial genome-wide association studies (mGWAS) are a new and exciting research field that is adapting human GWAS methods to understand how variations in microbial genomes affect host or pathogen phenotypes, such as drug resistance, virulence, host specificity and prognosis. Several computational tools and methods have been developed or adapted from human GWAS to facilitate the discovery of novel mutations and structural variations that are associated with the phenotypes of interest. However, no comprehensive, end-to-end, user-friendly tool is currently available. The development of a broadly applicable pipeline presents a real opportunity among computational biologists. Here, (i) we review the prominent and promising tools, (ii) discuss analytical pitfalls and bottlenecks in mGWAS, (iii) provide insights into the selection of appropriate tools, (iv) highlight the gaps that still need to be filled and how users and developers can work together to overcome these bottlenecks. Use of mGWAS research can inform drug repositioning decisions as well as accelerate the discovery and development of more effective vaccines and antimicrobials for pressing infectious diseases of global health significance, such as HIV, TB, influenza, and malaria.

Estimating Improved Partitioning Schemes for Ultraconserved Elements

Ultraconserved (UCEs) are popular markers for phylogenomic studies. They are relatively simple to collect from distantly-related organisms, and contain sufficient information to infer relationships at almost all taxonomic levels. Most studies of UCEs use partitioning to account for variation in rates and patterns of molecular evolution among sites, for example by estimating an independent model of molecular evolution for each UCE. However, rates and patterns of molecular evolution vary substantially within as well as between UCEs, suggesting that there may be opportunities to improve how UCEs are partitioned for phylogenetic inference. We propose and evaluate new partitioning methods for phylogenomic studies of UCEs: Sliding-Window Site Characteristics (SWSC), and UCE Site Position (UCESP). The first method uses site characteristics such as entropy, multinomial likelihood, and GC content to generate partitions that account for heterogeneity in rates and patterns of molecular evolution within each UCE. The second method groups together nucleotides that are found in similar physical locations within the UCEs. We examined the new methods with seven published data sets from a variety of taxa. We demonstrate the UCESP method generates partitions that are worse than other strategies used to partition UCE data sets (e.g., one partition per UCE). The SWSC method, particularly when based on site entropies, generates partitions that account for within-UCE heterogeneity and leads to large increases in the model fit. All of the methods, code, and data used in this study, are available from https://github.com/Tagliacollo/PartitionUCE. Simplified code for implementing the best method, the SWSC-EN, is available from https://github.com/Tagliacollo/PFinderUCE-SWSC-EN.

Machine learning technology in the application of genome analysis: A systematic review

Machine learning (ML) is a powerful technique to tackle many problems in data mining and predictive analytics. We believe that ML will be of considerable potentials in the field of bioinformatics since the high-throughput technology is producing ever increasing biological data. In this review, we summarized major ML algorithms and conditions that must be paid attention to when applying these algorithms to genomic problems in details and we provided a list of examples from different perspectives and data analysis challenges at present.

Evolutionary history of Polyneoptera and its implications for our understanding of early winged insects

Polyneoptera represents one of the major lineages of winged insects, comprising around 40,000 extant species in 10 traditional orders, including grasshoppers, roaches, and stoneflies. Many important aspects of polyneopteran evolution, such as their phylogenetic relationships, changes in their external appearance, their habitat preferences, and social behavior, are unresolved and are a major enigma in entomology. These ambiguities also have direct consequences for our understanding of the evolution of winged insects in general; for example, with respect to the ancestral habitats of adults and juveniles. We addressed these issues with a large-scale phylogenomic analysis and used the reconstructed phylogenetic relationships to trace the evolution of 112 characters associated with the external appearance and the lifestyle of winged insects. Our inferences suggest that the last common ancestors of Polyneoptera and of the winged insects were terrestrial throughout their lives, implying that wings did not evolve in an aquatic environment. The appearance of the first polyneopteran insect was mainly characterized by ancestral traits such as long segmented abdominal appendages and biting mouthparts held below the head capsule. This ancestor lived in association with the ground, which led to various specializations including hardened forewings and unique tarsal attachment structures. However, within Polyneoptera, several groups switched separately to a life on plants. In contrast to a previous hypothesis, we found that social behavior was not part of the polyneopteran ground plan. In other traits, such as the biting mouthparts, Polyneoptera shows a high degree of evolutionary conservatism unique among the major lineages of winged insects.

Phylogenomic Evidence Overturns Current Conceptions of Social Evolution in Wasps (Vespidae)

The hypothesis that eusociality originated once in Vespidae has shaped interpretation of social evolution for decades and has driven the supposition that preimaginal morphophysiological differences between castes were absent at the outset of eusociality. Many researchers also consider casteless nest-sharing an antecedent to eusociality. Together, these ideas endorse a stepwise progression of social evolution in wasps (solitary → casteless nest-sharing → eusociality with rudimentary behavioral castes → eusociality with preimaginal caste-biasing (PCB) → morphologically differentiated castes). Here, we infer the phylogeny of Vespidae using sequence data generated via anchored hybrid enrichment from 378 loci across 136 vespid species and perform ancestral state reconstructions to test whether rudimentary and monomorphic castes characterized the initial stages of eusocial evolution. Our results reject the single origin of eusociality hypothesis, contest the supposition that eusociality emerged from a casteless nest-sharing ancestor, and suggest that eusociality in Polistinae + Vespinae began with castes having morphological differences. An abrupt appearance of castes with ontogenetically established morphophysiological differences conflicts with the current conception of stepwise social evolution and suggests that the climb up the ladder of sociality does not occur through sequential mutation. Phenotypic plasticity and standing genetic variation could explain how cooperative brood care evolved in concert with nest-sharing and how morphologically dissimilar castes arose without a rudimentary intermediate. Furthermore, PCB at the outset of eusociality implicates a subsocial route to eusociality in Polistinae + Vespinae, emphasizing the role of mother-daughter interactions and subfertility (i.e. the cost component of kin selection) in the origin of workers.

A simple method for data partitioning based on relative evolutionary rates

BACKGROUND

Multiple studies have demonstrated that partitioning of molecular datasets is important in model-based phylogenetic analyses. Commonly, partitioning is done a priori based on some known properties of sequence evolution, e.g. differences in rate of evolution among codon positions of a protein-coding gene. Here we propose a new method for data partitioning based on relative evolutionary rates of the sites in the alignment of the dataset being analysed. The rates are inferred using the previously published Tree Independent Generation of Evolutionary Rates (TIGER), and the partitioning is conducted using our novel python script RatePartitions. We conducted simulations to assess the performance of our new method, and we applied it to eight published multi-locus phylogenetic datasets, representing different taxonomic ranks within the insect order Lepidoptera (butterflies and moths) and one phylogenomic dataset, which included ultra-conserved elements as well as introns.

METHODS

We used TIGER-rates to generate relative evolutionary rates for all sites in the alignments. Then, using RatePartitions, we partitioned the data into partitions based on their relative evolutionary rate. RatePartitions applies a simple formula that ensures a distribution of sites into partitions following the distribution of rates of the characters from the full dataset. This ensures that the invariable sites are placed in a partition with slowly evolving sites, avoiding the pitfalls of previously used methods, such as k-means. Different partitioning strategies were evaluated using BIC scores as calculated by PartitionFinder.

RESULTS

Simulations did not highlight any misbehaviour of our partitioning approach, even under difficult parameter conditions or missing data. In all eight phylogenetic datasets, partitioning using TIGER-rates and RatePartitions was significantly better as measured by the BIC scores than other partitioning strategies, such as the commonly used partitioning by gene and codon position. We compared the resulting topologies and node support for these eight datasets as well as for the phylogenomic dataset.

DISCUSSION

We developed a new method of partitioning phylogenetic datasets without using any prior knowledge (e.g. DNA sequence evolution). This method is entirely based on the properties of the data being analysed and can be applied to DNA sequences (protein-coding, introns, ultra-conserved elements), protein sequences, as well as morphological characters. A likely explanation for why our method performs better than other tested partitioning strategies is that it accounts for the heterogeneity in the data to a much greater extent than when data are simply subdivided based on prior knowledge.

Multiple origins of sexual dichromatism and aposematism within large carpenter bees

The evolution of reversed sexual dichromatism and aposematic coloration has long been of interest to both theoreticians and empiricists. Yet despite the potential connections between these phenomena, they have seldom been jointly studied. Large carpenter bees (genus Xylocopa) are a promising group for such comparative investigations as they are a diverse clade in which both aposematism and reversed sexual dichromatism can occur either together or separately. We investigated the evolutionary history of dichromatism and aposematism and a potential correlation of these traits with diversification rates within Xylocopa, using a newly generated phylogeny for 179 Xylocopa species based on ultraconserved elements (UCEs). A monochromatic, inconspicuous ancestor is indicated for the genus, with subsequent convergent evolution of sexual dichromatism and aposematism in multiple lineages. Aposematism is found to covary with reversed sexual dichromatism in many species; however, reversed dichromatism also evolved in non-aposematic species. Bayesian Analysis of Macroevolutionary Models (BAMM) did not show increased diversification in any specific clade in Xylocopa, whereas support from Hidden State Speciation and Extinction (HiSSE) models remained inconclusive regarding an association of increased diversification rates with dichromatism or aposematism. We discuss the evolution of color patterns and diversification in Xylocopa by considering potential drivers of dichromatism and aposematism.

A phylogenomic perspective on the robust capuchin monkey (Sapajus) radiation: First evidence for extensive population admixture across South America

Phylogenetic relationships amongst the robust capuchin monkeys (genus Sapajus) are poorly understood. Morphology-based taxonomies have recognized anywhere from one to twelve different species. The current IUCN (2017) classification lists eight robust capuchins: S. xanthosternos, S. nigritus, S. robustus, S. flavius, S. libidinosus, S. cay, S. apella and S. macrocephalus. Here, we assembled the first phylogenomic data set for Sapajus using ultra-conserved elements (UCEs) to reconstruct a capuchin phylogeny. All phylogenomic analyses strongly supported a deep divergence of Sapajus and Cebus clades within the capuchin monkeys, and provided support for Sapajus nigritus, S. robustus and S. xanthosternos as distinct species. However, the UCE phylogeny lumped the putative species S. cay, S. libidinosus, S. apella, S. macrocephalus, and S. flavius together as a single widespread lineage. A SNP phylogeny constructed from the UCE data was better resolved and recovered S. flavius and S. libidinosus as sister species; however, S. apella, S. macrocephalus, and S. cay individuals were recovered in two geographic clades, from northeastern and southwestern Amazon, rather than clustering by currently defined morphospecies. STRUCTURE analysis of population clustering revealed widespread admixture among Sapajus populations within the Amazon and even into the Cerrado and Atlantic Forest. Difficulty in assigning species by morphology may be a result of widespread population admixture facilitated through frequent movement across major rivers and even ecosystems by robust capuchin monkeys.

SWPhylo - A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees

Modern phylogenetic studies may benefit from the analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome-scale analysis are believed to be more accurate than the gene-based alternative. However, the computational complexity of current phylogenomic procedures, inappropriateness of standard phylogenetic tools to process genome-wide data, and lack of reliable substitution models which correlates with alignment-free phylogenomic approaches deter microbiologists from using these opportunities. For example, the super-matrix and super-tree approaches of phylogenomics use multiple integrated genomic loci or individual gene-based trees to infer an overall consensus tree. However, these approaches potentially multiply errors of gene annotation and sequence alignment not mentioning the computational complexity and laboriousness of the methods. In this article, we demonstrate that the annotation- and alignment-free comparison of genome-wide tetranucleotide frequencies, termed oligonucleotide usage patterns (OUPs), allowed a fast and reliable inference of phylogenetic trees. These were congruent to the corresponding whole genome super-matrix trees in terms of tree topology when compared with other known approaches including 16S ribosomal RNA and GyrA protein sequence comparison, complete genome-based MAUVE, and CVTree methods. A Web-based program to perform the alignment-free OUP-based phylogenomic inferences was implemented at http://swphylo.bi.up.ac.za/. Applicability of the tool was tested on different taxa from subspecies to intergeneric levels. Distinguishing between closely related taxonomic units may be enforced by providing the program with alignments of marker protein sequences, eg, GyrA.

A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination

Genome-Wide Association Studies (GWAS) in microbial organisms have the potential to vastly improve the way we understand, manage, and treat infectious diseases. Yet, microbial GWAS methods established thus far remain insufficiently able to capitalise on the growing wealth of bacterial and viral genetic sequence data. Facing clonal population structure and homologous recombination, existing GWAS methods struggle to achieve both the precision necessary to reject spurious findings and the power required to detect associations in microbes. In this paper, we introduce a novel phylogenetic approach that has been tailor-made for microbial GWAS, which is applicable to organisms ranging from purely clonal to frequently recombining, and to both binary and continuous phenotypes. Our approach is robust to the confounding effects of both population structure and recombination, while maintaining high statistical power to detect associations. Thorough testing via application to simulated data provides strong support for the power and specificity of our approach and demonstrates the advantages offered over alternative cluster-based and dimension-reduction methods. Two applications to Neisseria meningitidis illustrate the versatility and potential of our method, confirming previously-identified penicillin resistance loci and resulting in the identification of both well-characterised and novel drivers of invasive disease. Our method is implemented as an open-source R package called treeWAS which is freely available at https://github.com/caitiecollins/treeWAS.

Measurable differences often exist within a microbial population, with important ecological or epidemiological consequences. Examples include differences in growth rates, host range, transmissibility, antimicrobial resistance, virulence, etc. Understanding the genetic factors involved in these phenotypic properties is a crucial aim in microbial genomics. A fundamental approach for doing so is to perform a Genome-Wide Association Study (GWAS), where genomes are compared to search for genetic markers systematically correlated with the property of interest. If this strategy were implemented naively in microbes, it could lead to spurious results due to the confounding effects of population structure and recombination. Here we present treeWAS, a new phylogenetic method to perform microbial GWAS that avoids these pitfalls. We show, using simulated datasets, that treeWAS is able to distinguish between genetic markers that are truly associated with the property of interest and those that are not. Furthermore, we demonstrate that treeWAS offers advantages in both sensitivity and specificity over alternative cluster-based and dimension-reduction techniques. We also showcase treeWAS in two applications to real datasets from N. meningitidis. We have developed an easy-to-use implementation of treeWAS in the R environment, which should be useful to a wide range of researchers in microbial genomics.

Insights into the evolution, biogeography and natural history of the acorn ants, genus Temnothorax Mayr (hymenoptera: Formicidae)

BACKGROUND

Temnothorax (Formicidae: Myrmicinae) is a diverse genus of ants found in a broad spectrum of ecosystems across the northern hemisphere. These diminutive ants have long served as models for social insect behavior, leading to discoveries about social learning and inspiring hypotheses about the process of speciation and the evolution of social parasitism. This genus is highly morphologically and behaviorally diverse, and this has caused a great deal of taxonomic confusion in recent years. Past efforts to estimate the phylogeny of this genus have been limited in taxonomic scope, leaving the broader evolutionary patterns in Temnothorax unclear. To establish the monophyly of Temnothorax, resolve the evolutionary relationships, reconstruct the historical biogeography and investigate trends in the evolution of key traits, I generated, assembled, and analyzed two molecular datasets: a traditional multi-locus Sanger sequencing dataset, and an ultra-conserved element (UCE) dataset. Using maximum likelihood, Bayesian, and summary-coalescent based approaches, I analyzed 22 data subsets consisting of 103 ingroup taxa and a maximum of 1.8 million base pairs in 2485 loci.

RESULTS

The results of this study suggest an origin of Temnothorax at the Eocene-Oligocene transition, concerted transitions to arboreal nesting habits in several clades during the Oligocene, coinciding with ancient global cooling, and several convergent origins of social parasitism in the Miocene and Pliocene. As with other Holarctic taxa, Temnothorax has a history of migration across Beringia during the Miocene.

CONCLUSIONS

Temnothorax is corroborated as a natural group, and the notion that many of the historical subgeneric and species group concepts are artificial is reinforced. The strict form of Emery's Rule, in which a socially parasitic species is sister to its host species, is not well supported in Temnothorax.

Quantitative validation of anti-PTBP1 antibody for diagnostic neuropathology use: Image analysis approach

Traditional diagnostic neuropathology relies on subjective interpretation of visual data obtained from a brightfield microscopy. This approach causes high variability, unsatisfactory reproducibility, and inability for multiplexing even among experts. These problems may affect patient outcomes and confound clinical decision-making. Also, standard histological processing of pathological specimens leads to auto-fluorescence and other artifacts, a reason why fluorescent microscopy is not routinely implemented in diagnostic pathology. To overcome these problems, objective and quantitative methods are required to help neuropathologists in their clinical decision-making. Therefore, we propose a computerized image analysis method to validate anti-PTBP1 antibody for its potential use in diagnostic neuropathology. Images were obtained from standard neuropathological specimens stained with anti-PTBP1 antibody. First, the noise characteristics of the images were modeled and images are de-noised according to the noise model. Next, images are filtered with sigma-adaptive Gaussian filtering for normalization, and cell nuclei are detected and segmented with a k-means-based deterministic approach. Experiments on 29 data sets from 3 cases of brain tumor and reactive gliosis show statistically significant differences between the number of positively stained nuclei in images stained with and without anti-PTBP1 antibody. The experimental analysis of specimens from 3 different brain tumor groups and 1 reactive gliosis group indicates the feasibility of using anti-PTBP1 antibody in diagnostic neuropathology, and computerized image analysis provides a systematic and quantitative approach to explore feasibility.

Dry habitats were crucibles of domestication in the evolution of agriculture in ants

The evolution of ant agriculture, as practised by the fungus-farming 'attine' ants, is thought to have arisen in the wet rainforests of South America about 55-65 Ma. Most subsequent attine agricultural evolution, including the domestication event that produced the ancestor of higher attine cultivars, is likewise hypothesized to have occurred in South American rainforests. The 'out-of-the-rainforest' hypothesis, while generally accepted, has never been tested in a phylogenetic context. It also presents a problem for explaining how fungal domestication might have occurred, given that isolation from free-living populations is required. Here, we use phylogenomic data from ultra-conserved element (UCE) loci to reconstruct the evolutionary history of fungus-farming ants, reduce topological uncertainty, and identify the closest non-fungus-growing ant relative. Using the phylogeny we infer the history of attine agricultural systems, habitat preference and biogeography. Our results show that the out-of-the-rainforest hypothesis is correct with regard to the origin of attine ant agriculture; however, contrary to expectation, we find that the transition from lower to higher agriculture is very likely to have occurred in a seasonally dry habitat, inhospitable to the growth of free-living populations of attine fungal cultivars. We suggest that dry habitats favoured the isolation of attine cultivars over the evolutionary time spans necessary for domestication to occur.

A Dimensionality Reduction-Based Multi-Step Clustering Method for Robust Vessel Trajectory Analysis

The Shipboard Automatic Identification System (AIS) is crucial for navigation safety and maritime surveillance, data mining and pattern analysis of AIS information have attracted considerable attention in terms of both basic research and practical applications. Clustering of spatio-temporal AIS trajectories can be used to identify abnormal patterns and mine customary route data for transportation safety. Thus, the capacities of navigation safety and maritime traffic monitoring could be enhanced correspondingly. However, trajectory clustering is often sensitive to undesirable outliers and is essentially more complex compared with traditional point clustering. To overcome this limitation, a multi-step trajectory clustering method is proposed in this paper for robust AIS trajectory clustering. In particular, the Dynamic Time Warping (DTW), a similarity measurement method, is introduced in the first step to measure the distances between different trajectories. The calculated distances, inversely proportional to the similarities, constitute a distance matrix in the second step. Furthermore, as a widely-used dimensional reduction method, Principal Component Analysis (PCA) is exploited to decompose the obtained distance matrix. In particular, the top k principal components with above 95% accumulative contribution rate are extracted by PCA, and the number of the centers k is chosen. The k centers are found by the improved center automatically selection algorithm. In the last step, the improved center clustering algorithm with k clusters is implemented on the distance matrix to achieve the final AIS trajectory clustering results. In order to improve the accuracy of the proposed multi-step clustering algorithm, an automatic algorithm for choosing the k clusters is developed according to the similarity distance. Numerous experiments on realistic AIS trajectory datasets in the bridge area waterway and Mississippi River have been implemented to compare our proposed method with traditional spectral clustering and fast affinity propagation clustering. Experimental results have illustrated its superior performance in terms of quantitative and qualitative evaluations.

PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses

PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder. The source code is available at https://github.com/brettc/partitionfinder.

Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods

Egypt, located on the isthmus of Africa, is an ideal region to study historical population dynamics due to its geographic location and documented interactions with ancient civilizations in Africa, Asia and Europe. Particularly, in the first millennium BCE Egypt endured foreign domination leading to growing numbers of foreigners living within its borders possibly contributing genetically to the local population. Here we present 90 mitochondrial genomes as well as genome-wide data sets from three individuals obtained from Egyptian mummies. The samples recovered from Middle Egypt span around 1,300 years of ancient Egyptian history from the New Kingdom to the Roman Period. Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times. This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt's past at a genome-wide level.

Archaeological and historical records had shown ancient Egypt before and after Ptolemaic and Roman periods to be a hub of human migration and exchange. Here, Schuenemann and colleagues analyse ancient mitochondrial and nuclear DNA to investigate the genetic history of Egypt.

The Cyprinodon variegatus genome reveals gene expression changes underlying differences in skull morphology among closely related species

BACKGROUND

Understanding the genetic and developmental origins of phenotypic novelty is central to the study of biological diversity. In this study we identify modifications to the expression of genes at four developmental stages that may underlie jaw morphological differences among three closely related species of pupfish (genus Cyprinodon) from San Salvador Island, Bahamas. Pupfishes on San Salvador Island are trophically differentiated and include two endemic species that have evolved jaw morphologies unlike that of any other species in the genus Cyprinodon.

RESULTS

We find that gene expression differs significantly across recently diverged species of pupfish. Genes such as Bmp4 and calmodulin, previously implicated in jaw diversification in African cichlid fishes and Galapagos finches, were not found to be differentially expressed among species of pupfish. Instead we find multiple growth factors and cytokine/chemokine genes to be differentially expressed among these pupfish taxa. These include both genes and pathways known to affect craniofacial development, such as Wnt signaling, as well as novel genes and pathways not previously implicated in craniofacial development. These data highlight both shared and potentially unique sources of jaw diversity in pupfish and those identified in other evolutionary model systems such as Galapagos finches and African cichlids.

CONCLUSIONS

We identify modifications to the expression of genes involved in Wnt signaling, Igf signaling, and the inflammation response as promising avenues for future research. Our project provides insight into the magnitude of gene expression changes contributing to the evolution of morphological novelties, such as jaw structure, in recently diverged pupfish species.

Rediscovery of the enigmatic fungus-farming ant "Mycetosoritis" asper Mayr (Hymenoptera: Formicidae): Implications for taxonomy, phylogeny, and the evolution of agriculture in ants

We report the rediscovery of the exceedingly rarely collected and enigmatic fungus-farming ant species Mycetosoritis asper. Since the description of the type specimen in 1887, only four additional specimens are known to have been added to the world's insect collections. Its biology is entirely unknown and its phylogenetic position within the fungus-farming ants has remained puzzling due to its aberrant morphology. In 2014 we excavated and collected twenty-one colonies of M. asper in the Floresta Nacional de Chapecó in Santa Catarina, Brazil. We describe here for the first time the male and larva of the species and complement the previous descriptions of both the queen and the worker. We describe, also for the first time, M. asper biology, nest architecture, and colony demographics, and identify its fungal cultivar. Molecular phylogenetic analyses indicate that both M. asper and M. clorindae are members of the genus Cyphomyrmex, which we show to be paraphyletic as currently defined. More precisely, M. asper is a member of the Cyphomyrmex strigatus group, which we also show to be paraphyletic with respect to the genus Mycetophylax. Based on these results, and in the interest of taxonomic stability, we transfer the species M. asper, M. clorindae, and all members of the C. strigatus group to the genus Mycetophylax, the oldest available name for this clade. Based on ITS sequence data, Mycetophylax asper practices lower agriculture, cultivating a fungal species that belongs to lower-attine fungal Clade 2, subclade F.

The acacia ants revisited: convergent evolution and biogeographic context in an iconic ant/plant mutualism

Phylogenetic and biogeographic analyses can enhance our understanding of multispecies interactions by placing the origin and evolution of such interactions in a temporal and geographical context. We use a phylogenomic approach-ultraconserved element sequence capture-to investigate the evolutionary history of an iconic multispecies mutualism: Neotropical acacia ants (Pseudomyrmex ferrugineus group) and their associated Vachellia hostplants. In this system, the ants receive shelter and food from the host plant, and they aggressively defend the plant against herbivores and competing plants. We confirm the existence of two separate lineages of obligate acacia ants that convergently occupied Vachellia and evolved plant-protecting behaviour, from timid ancestors inhabiting dead twigs in rainforest. The more diverse of the two clades is inferred to have arisen in the Late Miocene in northern Mesoamerica, and subsequently expanded its range throughout much of Central America. The other lineage is estimated to have originated in southern Mesoamerica about 3 Myr later, apparently piggy-backing on the pre-existing mutualism. Initiation of the Pseudomyrmex/Vachellia interaction involved a shift in the ants from closed to open habitats, into an environment with more intense plant herbivory. Comparative studies of the two lineages of mutualists should provide insight into the essential features binding this mutualism.

Phylogeny and chromosomal diversification in the Dichroplus elongatus species group (Orthoptera, Melanoplinae)

In an attempt to track the chromosomal differentiation in the Dichroplus elongatus species group, we analyzed the karyotypes of four species with classical cytogenetic and mapping several multigene families through fluorescent in situ hybridization (FISH). We improved the taxon sampling of the D. elongatus species group adding new molecular data to infer the phylogeny of the genus and reconstruct the karyotype evolution. Our molecular analyses recovered a fully resolved tree with no evidence for the monophyly of Dichroplus. However, we recovered several stable clades within the genus, including the D. elongatus species group, under the different strategies of tree analyses (Maximum Parsimony and Maximum Likelihood). The chromosomal data revealed minor variation in the D. elongatus species group's karyotypes caused by chromosome rearrangements compared to the phylogenetically related D. maculipennis species group. The karyotypes of D. intermedius and D. exilis described herein showed the standard characteristics found in most Dichroplini, 2n = 23/24, X0♂ XX♀, Fundamental number (FN) = 23/24. However, we noticed two established pericentric inversions in D. intermedius karyotype, raising the FN to 27♂/28♀. A strong variation in the heterochromatic blocks distribution was evidenced at interespecific level. The multigene families' mapping revealed significant variation, mainly in rDNA clusters. These variations are probably caused by micro chromosomal changes, such as movement of transposable elements (TEs) and ectopic recombination. These observations suggest a high genomic dynamism for these repetitive DNA sequences in related species. The reconstruction of the chromosome character "variation in the FN" posits the FN = 23/24 as the ancestral state, and it is hypothesized that variations due to pericentric inversions has arisen independently three times in the evolutionary history of Dichroplus. One of these independent events occurred in the D. elongatus species group, where D. intermedius is the unique case with the highest FN described in the tribe Dichroplini.

Advances using molecular data in insect systematics

The size of molecular datasets has been growing exponentially since the mid 1980s, and new technologies have now dramatically increased the slope of this increase. New datasets include genomes, transcriptomes, and hybrid capture data, producing hundreds or thousands of loci. With these datasets, we are approaching a consensus on the higher level insect phylogeny. Huge datasets can produce new challenges in interpreting branch support, and new opportunities in developing better models and more sophisticated partitioning schemes. Dating analyses are improving as we recognize the importance of careful fossil calibration selection. With thousands of genes now available, coalescent methods have come of age. Barcode libraries continue to expand, and new methods are being developed for incorporating them into phylogenies with tens of thousands of individuals.

Sequence Capture and Phylogenetic Utility of Genomic Ultraconserved Elements Obtained from Pinned Insect Specimens

Obtaining sequence data from historical museum specimens has been a growing research interest, invigorated by next-generation sequencing methods that allow inputs of highly degraded DNA. We applied a target enrichment and next-generation sequencing protocol to generate ultraconserved elements (UCEs) from 51 large carpenter bee specimens (genus Xylocopa), representing 25 species with specimen ages ranging from 2-121 years. We measured the correlation between specimen age and DNA yield (pre- and post-library preparation DNA concentration) and several UCE sequence capture statistics (raw read count, UCE reads on target, UCE mean contig length and UCE locus count) with linear regression models. We performed piecewise regression to test for specific breakpoints in the relationship of specimen age and DNA yield and sequence capture variables. Additionally, we compared UCE data from newer and older specimens of the same species and reconstructed their phylogeny in order to confirm the validity of our data. We recovered 6-972 UCE loci from samples with pre-library DNA concentrations ranging from 0.06-9.8 ng/μL. All investigated DNA yield and sequence capture variables were significantly but only moderately negatively correlated with specimen age. Specimens of age 20 years or less had significantly higher pre- and post-library concentrations, UCE contig lengths, and locus counts compared to specimens older than 20 years. We found breakpoints in our data indicating a decrease of the initial detrimental effect of specimen age on pre- and post-library DNA concentration and UCE contig length starting around 21-39 years after preservation. Our phylogenetic results confirmed the integrity of our data, giving preliminary insights into relationships within Xylocopa. We consider the effect of additional factors not measured in this study on our age-related sequence capture results, such as DNA fragmentation and preservation method, and discuss the promise of the UCE approach for large-scale projects in insect phylogenomics using museum specimens.

Methodological congruence in phylogenomic analyses with morphological support for teiid lizards (Sauria: Teiidae)

A well-known issue in phylogenetics is discordance among gene trees, species trees, morphology, and other data types. Gene-tree discordance is often caused by incomplete lineage sorting, lateral gene transfer, and gene duplication. Multispecies-coalescent methods can account for incomplete lineage sorting and are believed by many to be more accurate than concatenation. However, simulation studies and empirical data have demonstrated that concatenation and species tree methods often recover similar topologies. We use three popular methods of phylogenetic reconstruction (one concatenation, two species tree) to evaluate relationships within Teiidae. These lizards are distributed across the United States to Argentina and the West Indies, and their classification has been controversial due to incomplete sampling and the discordance among various character types (chromosomes, DNA, musculature, osteology, etc.) used to reconstruct phylogenetic relationships. Recent morphological and molecular analyses of the group resurrected three genera and created five new genera to resolve non-monophyly in three historically ill-defined genera: Ameiva, Cnemidophorus, and Tupinambis. Here, we assess the phylogenetic relationships of the Teiidae using "next-generation" anchored-phylogenomics sequencing. Our final alignment includes 316 loci (488,656bp DNA) for 244 individuals (56 species of teiids, representing all currently recognized genera) and all three methods (ExaML, MP-EST, and ASTRAL-II) recovered essentially identical topologies. Our results are basically in agreement with recent results from morphology and smaller molecular datasets, showing support for monophyly of the eight new genera. Interestingly, even with hundreds of loci, the relationships among some genera in Tupinambinae remain ambiguous (i.e. low nodal support for the position of Salvator and Dracaena).