Phylogeny Estimation Research Articles

An independent base composition of each rate class for improved likelihood-based phylogeny estimation; the 5rf model.

The combination of a time reversible Markov process with a "hidden" mixture of gamma distributed relative site rates plus invariant sites have become the most favoured options for likelihood and other probabilistic models of nucleotide evolution (e.g., tr4gi which approximates a gamma with four rate classes). However, these models assume a homogeneous and stationary distribution of nucleotide (character or base) frequencies. Here, we explore the potential benefits and pitfalls of allowing each rate category (rate class) of a 4gi mixture model to have its own base frequencies. This is achieved by starting each of the five rate classes, at the tree's root, with its own free choice of nucleotide frequencies to create a 4gi5rf model or a 5rf model in shorthand. We assess the practical identifiability of this approach with a BEAST 2 implementation, aiming to determine if it can accurately estimate credibility intervals and expected values for a wide range of plausible parameter values. Practical identifiability, as distinguished from mathematical identifiability, gauges the model's ability to identify parameters in real-world scenarios, as opposed to theoretically with infinite data. One of the most common types of phylogenetic data is mitochondrial DNA (mtDNA) protein coding sequence. It is often assumed current models analyse robustly such data and that higher likelihood/posterior probability models do better. However, this abstract shows that vertebrate mtDNA remains a very difficult type of data to fully model, and that dramatically higher likelihoods do not mean a model is measurably more accurate with respect to recovering key parameters of biological interest (e.g., monophyletic groups, their support and their ages). The 4gi5rf model considerably improves marginal likelihoods and seems to reverse some apparent errors exacerbated by the 4gi model, while introducing others. Problems appear to be linked to non-stationary DNA repair processes that alter the mutation/substitution spectra across lineages and time. We also show such problems are not unique to mtDNA and are encountered in analysing nuclear sequences. Non-stationarity of DNA repair processes mutation/substitution spectra thus pose an active challenge to obtaining reliable inferences of relationships and divergence times near the root of placental mammals, for example. An open source implementation is available under the LGPL 3.0 license in the beastbooster package for BEAST 2, available from https://github.com/rbouckaert/beastbooster.

Polyphest: fast polyploid phylogeny estimation.

Despite the widespread occurrence of polyploids across the Tree of Life, especially in the plant kingdom, very few computational methods have been developed to handle the specific complexities introduced by polyploids in phylogeny estimation. Furthermore, methods that are designed to account for polyploidy often disregard incomplete lineage sorting (ILS), a major source of heterogeneous gene histories, or are computationally very demanding. Therefore, there is a great need for efficient and robust methods to accurately reconstruct polyploid phylogenies. We introduce Polyphest (POLYploid PHylogeny ESTimation), a new method for efficiently and accurately inferring species phylogenies in the presence of both polyploidy and ILS. Polyphest bypasses the need for extensive network space searches by first generating a multilabeled tree based on gene trees, which is then converted into a (uniquely labeled) species phylogeny. We compare the performance of Polyphest to that of two polyploid phylogeny estimation methods, one of which does not account for ILS, namely PADRE, and another that accounts for ILS, namely MPAllopp. Polyphest is more accurate than PADRE and achieves comparable accuracy to MPAllopp, while being significantly faster. We also demonstrate the application of Polyphest to empirical data from the hexaploid bread wheat and confirm the allopolyploid origin of bread wheat along with the closest relatives for each of its subgenomes. Polyphest is available at https://github.com/NakhlehLab/Polyphest.

UCE-based phylogenomics of the lepidopteran endoparasitoid wasp subfamily Rogadinae (Hymenoptera: Braconidae) unveils a new Neotropical tribe.

During the past two decades, the phylogenetic relationships and higher-level classification of the subfamily Rogadinae have received relevant contributions based on Sanger, mitogenome and genome-wide nuclear DNA sequence data. These studies have helped to update the circumscription and tribal classification of this subfamily, with six tribes currently recognised (Aleiodini, Betylobraconini, Clinocentrini, Rogadini, Stiropiini and Yeliconini). The tribal relationships within Rogadinae, however, are yet to be fully resolved, including the status of tribe Facitorini, previously regarded as betylobraconine, with respect to the members of Yeliconini. We conducted a phylogenomic analysis among the tribes of Rogadinae based on genomic ultraconserved element (UCE) data and extensive taxon sampling including three undescribed genera of uncertain tribal placement. Our almost fully supported estimate of phylogeny confirmed the basal position of Rogadini within the subfamily and a Facitorini clade (Yeliconini+Aleiodini) that led us to propose the former group as a valid rogadine tribe (Facitorini stat. res.). Stiropiini, however, was recovered for the first time as sister to the remaining rogadine tribes except Rogadini, and Clinocentrini as sister to a clade with Betylobraconini+the three undescribed genera. The relationships recovered and morphological examination of the material included led us to place the latter three new genera and recently described genus Gondwanocentrus within a new rogadine tribe, Gondwanocentrini Shimbori & Zaldívar-Riverón trib. nov. We described these genera (Ghibli Shimbori & Zaldívar-Riverón gen. nov., Racionais Shimbori & Zaldívar-Riverón gen. nov. and Soraya Shimbori gen. nov.) with two or three new species each (G. miyazakii Shimbori & Zaldívar-Riverón sp. nov., G. totoro Shimbori & Zaldívar-Riverón sp. nov., R. brunus Shimbori & Zaldívar-Riverón sp. nov., R. kaelejay Shimbori & Zaldívar-Riverón sp. nov., R. superstes Shimbori & Zaldívar-Riverón sp. nov., S. alencarae Shimbori sp. nov. and S. venus Shimbori & Zaldívar-Riverón sp. nov.). A new species of Facitorini, Jannya pasargadae Gadelha & Shimbori sp. nov., is also described. Our newly proposed classification expands the number of tribes and genera within Rogadinae to 8 and 66 respectively. ZooBank: urn:lsid:zoobank.org:pub:51951C78-069A-4D8B-B5F0-7EBD4D9D21CE.

Phylogenetic insights into the Salicaceae: The evolution of willows and beyond

The Salicaceae includes approximately 54 genera and over 1,400 species with a cosmopolitan distribution. Members of the family are well-known for their diverse secondary plant metabolites, and they play crucial roles in tropical and temperate forest ecosystems. Phylogenetic reconstruction of the Salicaceae has been historically challenging due to the limitations of molecular markers and the extensive history of hybridization and polyploidy within the family. Our study employs whole-genome sequencing of 74 species to generate an extensive phylogeny of the Salicaceae. We generated two RAD-Seq enriched whole-genome sequence datasets and extracted two additional gene sets corresponding to the universal Angiosperms353 and Salicaceae-specific targeted-capture arrays. We reconstructed maximum likelihood-based molecular phylogenies using supermatrix and coalescent-based supertree approaches. Our fossil-calibrated phylogeny estimates that the Salicaceae originated around 128 million years ago and unravels the complex taxonomic relationships within the family. Our findings confirm the non-monophyly of the subgenus Salix s.l. and further support the merging of subgenera Chamaetia and Vetrix, both of which exhibit intricate patterns within and among different sections. Overall, our study not only enhances our understanding of the evolution of the Salicaceae, but also provides valuable insights into the complex relationships within the family.

An alignment-free method for detection of missing regions for phylogenetic analysis

Phylogenetic tree estimation using conventional approaches usually requires pairwise or multiple sequence alignment. However, sequence alignment has difficulties related to scalability and accuracy in case of long sequences such as whole genomes, low sequence identity, and in presence of genomic rearrangements. To address these issues, alignment-free approaches have been proposed. While these methods have demonstrated promising results, many of these lead to errors when regions are missing from the sequences of one or more species that are trivially detected in alignment-based methods. Here, we present an alignment-free method for detecting missing regions in sequences of species for which phylogeny is to be estimated. It is based on counts of k-mers and can be used to filter out k-mers belonging to regions in one species that are missing in one or more of the other species. We perform experiments with real and simulated datasets containing missing regions and find that it can successfully detect a large fraction of such k-mers and can lead to improvements in the estimated phylogenies. Our method can be used in k-mer based alignment-free phylogeny estimation methods to filter out k-mers corresponding to missing regions.

A new abelisaurid dinosaur from the end Cretaceous of Patagonia and evolutionary rates among the Ceratosauria.

Gondwanan dinosaur faunae during the 20 Myr preceding the Cretaceous-Palaeogene (K/Pg) extinction included several lineages that were absent or poorly represented in Laurasian landmasses. Among these, the South American fossil record contains diverse abelisaurids, arguably the most successful groups of carnivorous dinosaurs from Gondwana in the Cretaceous, reaching their highest diversity towards the end of this period. Here we describe Koleken inakayali gen. et sp. n., a new abelisaurid from the La Colonia Formation (Maastrichtian, Upper Cretaceous) of Patagonia. Koleken inakayali is known from several skull bones, an almost complete dorsal series, complete sacrum, several caudal vertebrae, pelvic girdle and almost complete hind limbs. The new abelisaurid shows a unique set of features in the skull and several anatomical differences from Carnotaurus sastrei (the only other abelisaurid known from the La Colonia Formation). Koleken inakayali is retrieved as a brachyrostran abelisaurid, clustered with other South American abelisaurids from the latest Cretaceous (Campanian-Maastrichtian), such as Aucasaurus, Niebla and Carnotaurus. Leveraging our phylogeny estimates, we explore rates of morphological evolution across ceratosaurian lineages, finding them to be particularly high for elaphrosaurine noasaurids and around the base of Abelisauridae, before the Early Cretaceous radiation of the latter clade. The Noasauridae and their sister clade show contrasting patterns of morphological evolution, with noasaurids undergoing an early phase of accelerated evolution of the axial and hind limb skeleton in the Jurassic, and the abelisaurids exhibiting sustained high rates of cranial evolution during the Early Cretaceous. These results provide much needed context for the evolutionary dynamics of ceratosaurian theropods, contributing to broader understanding of macroevolutionary patterns across dinosaurs.

Sequential Bayesian Phylogenetic Inference.

The ideal approach to Bayesian phylogenetic inference is to estimate all parameters of interest jointly in a single hierarchical model. However, this is often not feasible in practice due to the high computational cost. Instead, phylogenetic pipelines generally consist of sequential analyses, whereby a single point estimate from a given analysis is used as input for the next analysis (e.g., a single multiple sequence alignment is used to estimate a gene tree). In this framework, uncertainty is not propagated from step to step, which can lead to inaccurate or spuriously confident results. Here, we formally develop and test a sequential inference approach for Bayesian phylogenetic inference, which uses importance sampling to generate observations for the next step of an analysis pipeline from the posterior distribution produced in the previous step. Our sequential inference approach presented here not only accounts for uncertainty between analysis steps, but also allows for greater flexibility in software choice (and hence model availability) and can be computationally more efficient than the traditional joint inference approach when multiple models are being tested. We show that our sequential inference approach is identical in practice to the joint inference approach only if sufficient information in the data is present (a narrow posterior distribution) and/or sufficiently many importance samples are used. Conversely, we show that the common practice of using a single point estimate can be biased, e.g., a single phylogeny estimate to transform an unrooted phylogeny into a time-calibrated phylogeny. We demonstrate the theory of sequential Bayesian inference using both a toy example and an empirical case study of divergence-time estimation in insects using a relaxed clock model from transcriptome data. In the empirical example, we estimate three posterior distributions of branch lengths from the same data (DNA character matrix with a GTR+Γ+I substitution model, an amino acid data matrix with empirical substitution models, and an amino acid data matrix with the PhyloBayes CAT-GTR model). Finally, we apply three different node-calibration strategies and show that divergence-time estimates are affected by both the data source and underlying substitution process to estimate branch lengths as well as the node-calibration strategies. Thus, our new sequential Bayesian phylogenetic inference provides the opportunity to efficiently test different approaches for divergence time estimation, including branch-length estimation from other software.

SNP‐based analysis of European Thymallus spp. (Salmonidae) reveals extensive mito‐nuclear discordance relevant for biogeographic inferences, taxonomy and conservation

AbstractAimPaleohydrological dynamics are well‐documented for European river systems, promoting shifting phases of isolation and connectivity of their aquatic fauna. These conditions coupled with high rates of hybridisation found in freshwater fishes may introduce considerable complexity and potential mito‐nuclear discordance of phylogenetic patterns. We evaluate this hypothesis using the first large‐scale analysis of nuclear SNPs in European species of grayling (Thymallus) compared to mtDNA data with the aim of reassessing the evolutionary history of this group of rheophilic fishes.LocationFreshwater systems in Europe.MethodsBased on mitochondrial (mitogenomes, control region) and nuclear (ddRADseq) data, we applied population‐genetic, phylogenetic, and biogeographic tools to evaluate lineage diversity in the context of paleohydrological alterations.ResultsThe results corroborated previously recognised high levels of lineage diversity, but revealed several cases of mito‐nuclear discordance and signals of both historical (natural) and human‐mediated introgression among major inter‐ and intraspecific lineages of Thymallus in Europe. A time‐calibrated phylogeny and ancestral area estimation, based on nuclear SNP data, supported a late Pliocene diversification of the genus in Europe and suggested an early colonisation of the Black Sea basin with subsequent dispersal into Central and Western Europe.Main ConclusionsThe genetic structure of Thymallus in Europe recovered by nuclear SNPs contrasts considerably with that supported by mtDNA. Several instances of mito‐nuclear discordance underscore frequent contact of allopatric lineages in a dynamic paleohydrological landscape and reveal the weakness of basing both taxonomic and conservation decisions on inferences based on mtDNA alone. The Danube and Rhine drainages were inferred as important zones of contact between divergent phylogeographic lineages. Additionally, our data cast doubt on the genetic integrity of the endangered T. aeliani. Its divergence from T. thymallus, using nuclear SNPs, appears minimal as samples of T. aeliani group within Danubian lineages, despite carrying highly divergent reciprocally monophyletic mtDNA.

Efficient phylogenetic tree inference for massive taxonomic datasets: harnessing the power of a server to analyze 1 million taxa.

Phylogenies play a crucial role in biological research. Unfortunately, the search for the optimal phylogenetic tree incurs significant computational costs, and most of the existing state-of-the-art tools cannot deal with extremely large datasets in reasonable times. In this work, we introduce the new VeryFastTree code (version 4.0), which is able to construct a tree on 1 server using single-precision arithmetic from a massive 1 million alignment dataset in only 36hours, which is 3 times and 3.2 times faster than its previous version and FastTree-2, respectively. This new version further boosts performance by parallelizing all tree traversal operations during the tree construction process, including subtree pruning and regrafting moves. Additionally, it introduces significant new features such as support for new and compressed file formats, enhanced compatibility across a broader range of operating systems, and the integration of disk computing functionality. The latter feature is particularly advantageous for users without access to high-end servers, as it allows them to manage very large datasets, albeit with an increase in computing time. Experimental results establish VeryFastTree as the fastest tool in the state-of-the-art for maximum likelihood phylogeny estimation. It is publicly available at https://github.com/citiususc/veryfasttree. In addition, VeryFastTree is included as a package in Bioconda, MacPorts, and all Debian-based Linux distributions.

TheSystematics of the Trematoda.

The platyhelminth class Trematoda comprises two subclasses with largely disparate species diversity, with the small Aspidogastrea with c.80 species and the speciose Digenea with c.18,000 species, which has attracted much effort towards our understanding of evolutionary relationships among suprageneric taxa. This chapter focuses on insights into the classification of the Digenea, that have become apparent from our advanced understanding of both morphological and molecular data. The field of molecular systematics of the Digenea has experienced significant advances over the past 15years. Phylogenetic analyses of sequence data predominantly from the 18S and 28S rRNA genes have incorporated a considerable diversity of taxa, thus increasing the accuracy of phylogenetic inferences at higher taxonomic levels. As a result, the status of long-standing supraspecific taxa has been revised, new higher-level taxa have been defined, and inferences made in association with morphological and life-cycle evidence. A substantial effort has been made towards a classification reflecting a natural system of the Digenea by considering morphological evidence in conjunction with phylogenies inferred from molecular data; this has resulted in considerable congruence. However, limited taxon sampling in the phylogeny of the Digenea still remains relevant, especially in relation to some higher-level taxa, and an outline of these omissions is presented. A framework that has led to robust estimates of phylogeny is outlined, and the application of advanced morphological and molecular approaches in digenean taxonomy and systematics is illustrated using the most comprehensively studied digenean superfamilies.

Microbial Diversity in Children with Gastroenteritis in the Amazon Region of Brazil: Development and Validation of a Molecular Method for Complete Sequencing of Viral Genomes.

Metagenomic sequencing is a powerful tool that is widely used in laboratories worldwide for taxonomic characterization of microorganisms in clinical and environmental samples. In this study, we utilized metagenomics to investigate comprehensively the microbial diversity in fecal samples of children over a four-year period. Our methods were carefully designed to ensure accurate and reliable results. Validated and analyzed were metagenomic data obtained from sequencing 27 fecal samples from children under 10 years old with gastroenteritis over a four-year period (2012-2016). The fecal specimens were collected from patients who received care at public health facilities in the northern region of Brazil. Sequencing libraries were prepared from cDNA and sequenced on the Illumina HiSeq. Kraken-2 was utilized to classify bacterial taxonomy based on the 16S rRNA gene, using the Silva rRNA database. Additionally, the Diamond program was used for mapping to the non-redundant protein database (NR database). Phylogenomic analyses were conducted using Geneious R10 and MEGA X software, and Bayesian estimation of phylogeny was performed using the MrBayes program. The results indicate significant heterogeneity among norovirus strains, with evidence of recombination and point mutations. This study presents the first complete genome of parechovirus 8 in the region. Additionally, it describes the bacterial populations and bacteriophages present in feces, with a high abundance of Firmicutes and Proteobacteria, including an increased proportion of the Enterobacteriaceae family. The presented data demonstrate the genetic diversity of microbial populations and provide a comprehensive report on viral molecular characterization. These findings are relevant for genomic studies in gastrointestinal infections. The metagenomic approach is a powerful tool for investigating microbial diversity in children with gastroenteritis. However, further studies are imperative to conduct genomic analysis of identified bacterial strains and thoroughly analyze antimicrobial resistance genes.

Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines

BackgroundDespite recent advances, reliable tools to simultaneously handle different types of sequencing data (e.g., target capture, genome skimming) for phylogenomics are still scarce. Here, we evaluate the performance of the recently developed pipeline Captus in comparison with the well-known target capture pipelines HybPiper and SECAPR. As test data, we analyzed newly generated sequences for the genus Thladiantha (Cucurbitaceae) for which no well-resolved phylogeny estimate has been available so far, as well as simulated reads derived from the genome of Arabidopsis thaliana.ResultsOur pipeline comparisons are based on (1) the time needed for data assembly and locus extraction, (2) locus recovery per sample, (3) the number of informative sites in nucleotide alignments, and (4) the topology of the nuclear and plastid phylogenies. Additionally, the simulated reads derived from the genome of Arabidopsis thaliana were used to evaluate the accuracy and completeness of the recovered loci. In terms of computation time, locus recovery per sample, and informative sites, Captus outperforms HybPiper and SECAPR. The resulting topologies of Captus and SECAPR are identical for coalescent trees but differ when trees are inferred from concatenated alignments. The HybPiper phylogeny is similar to Captus in both methods. The nuclear genes recover a deep split of Thladiantha in two clades, but this is not supported by the plastid data.ConclusionsCaptus is the best choice among the three pipelines in terms of computation time and locus recovery. Even though there is no significant topological difference between the Thladiantha species trees produced by the three pipelines, Captus yields a higher number of gene trees in agreement with the topology of the species tree (i.e., fewer genes in conflict with the species tree topology).

Museomics unveil systematics, diversity and evolution of Australian cycad-pollinating weevils.

Weevils have been shown to play significant roles in the obligate pollination of Australian cycads. In this study, we apply museomics to produce a first molecular phylogeny estimate of the Australian cycad weevils, allowing an assessment of their monophyly, placement and relationships. Divergence dating suggests that the Australian cycad weevils originated from the Late Oligocene to the Middle Miocene and that the main radiation of the cycad-pollinating groups occurred from the Middle to the Late Miocene, which is congruent with the diversification of the Australian cycads, thus refuting any notion of an ancient ciophilous system in Australia. Taxonomic studies reveal the existence of 19 Australian cycad weevil species and that their associations with their hosts are mostly non-species-specific. Co-speciation analysis shows no extensive co-speciation events having occurred in the ciophilous system of Australian cycads. The distribution pattern suggests that geographical factors, rather than diversifying coevolution, constitute the overriding process shaping the Australian cycad weevil diversity. The synchronous radiation of cycads and weevil pollinators is suggested to be a result of the post-Oligocene diversification common in Australian organisms.

Frog phylogeny: A time-calibrated, species-level tree based on hundreds of loci and 5,242 species

Large-scale, time-calibrated phylogenies from supermatrix studies have become crucial for evolutionary and ecological studies in many groups of organisms. However, in frogs (anuran amphibians), there is a serious problem with existing supermatrix estimates. Specifically, these trees are based on a limited number of loci (15 or fewer), and the higher-level relationships estimated are discordant with recent phylogenomic estimates based on much larger numbers of loci. Here, we attempted to rectify this problem by generating an expanded supermatrix and combining this with data from phylogenomic studies. To assist in aligning ribosomal sequences for this supermatrix, we developed a new program (TaxonomyAlign) to help perform taxonomy-guided alignments. The new combined matrix contained 5,242 anuran species with data from 307 markers, but with 95% missing data overall. This dataset represented a 71% increase in species sampled relative to the previous largest supermatrix analysis of anurans (adding 2,175 species). Maximum-likelihood analyses generated a tree in which higher-level relationships (and estimated clade ages) were generally concordant with those from phylogenomic analyses but were more discordant with the previous largest supermatrix analysis. We found few obvious problems arising from the extensive missing data in most species. We also generated a set of 100 time-calibrated trees for use in comparative analyses. Overall, we provide an improved estimate of anuran phylogeny based on the largest number of combined taxa and markers to date. More broadly, we demonstrate the potential to combine phylogenomic and supermatrix analyses in other groups of organisms.

Rampant chloroplast capture in Sarracenia revealed by plastome phylogeny.

Introgression can produce novel genetic variation in organisms that hybridize. Sympatric species pairs in the carnivorous plant genus Sarracenia L. frequently hybridize, and all known hybrids are fertile. Despite being a desirable system for studying the evolutionary consequences of hybridization, the extent to which introgression occurs in the genus is limited to a few species in only two field sites. Previous phylogenomic analysis of Sarracenia estimated a highly resolved species tree from 199 nuclear genes, but revealed a plastid genome that is highly discordant with the species tree. Such cytonuclear discordance could be caused by chloroplast introgression (i.e. chloroplast capture) or incomplete lineage sorting (ILS). To better understand the extent to which introgression is occurring in Sarracenia, the chloroplast capture and ILS hypotheses were formally evaluated. Plastomes were assembled de-novo from sequencing reads generated from 17 individuals in addition to reads obtained from the previous study. Assemblies of 14 whole plastomes were generated and annotated, and the remaining fragmented assemblies were scaffolded to these whole-plastome assemblies. Coding sequence from 79 homologous genes were aligned and concatenated for maximum-likelihood phylogeny estimation. The plastome tree is extremely discordant with the published species tree. Plastome trees were simulated under the coalescent and tree distance from the species tree was calculated to generate a null distribution of discordance that is expected under ILS alone. A t-test rejected the null hypothesis that ILS could cause the level of discordance seen in the plastome tree, suggesting that chloroplast capture must be invoked to explain the discordance. Due to the extreme level of discordance in the plastome tree, it is likely that chloroplast capture has been common in the evolutionary history of Sarracenia.

Quartet Fiduccia-Mattheyses Revisited for Larger Phylogenetic Studies.

With the recent breakthroughs in sequencing technology, phylogeny estimation at a larger scale has become a huge opportunity. For accurate estimation of large-scale phylogeny, substantial endeavour is being devoted in introducing new algorithms or upgrading current approaches. In this work, we endeavour to improve the QFM (Quartet Fiduccia and Mattheyses) algorithm to resolve phylogenetic trees of better quality with better running time. QFM was already being appreciated by researchers for its good tree quality, but fell short in larger phylogenomic studies due to its excessively slow running time. We have re-designed QFM so that it can amalgamate millions of quartets over thousands of taxa into a species tree with a great level of accuracy within a short amount of time. Named QFM Fast and Improved (QFM-FI), our version is 20,000x faster than the previous version and 400x faster than the widely used variant of QFM implemented in PAUP* on larger datasets. We have also provided a theoretical analysis of the running time and memory requirements of QFM-FI. We have conducted a comparative study of QFM-FI with other state-of-the-art phylogeny reconstruction methods, such as QFM, QMC, wQMC, wQFM and ASTRAL, on simulated as well as real biological datasets. Our results show that QFM-FI improves on the running time and tree quality of QFM and produces trees that are comparable with state-of-the-art methods. QFM-FI is open source and available at https://github.com/sharmin-mim/qfm_java. Supplementary Information is available at Bioinformatics online.

One step closer but still far from solving the puzzle – The phylogeny of marine associated mites (Acari, Oribatida, Ameronothroidea) inferred from morphological and molecular genetic data

Abstract Marine associated oribatid mites belong mainly to the Ameronothroidea which represent a very small percentage of all Oribatida. Over the last decades the systematics and evolutionary history of this group has been discussed controversially and still there is no consensus concerning several issues. The extreme marine environment may have resulted in parallel morphologies complicating the classification and estimation of phylogeny based on discrete morphological traits. In the present study, we performed a molecular genetic study using a mitochondrial and two nuclear markers to infer the phylogeny of this group. Additionally, we reconstructed the phylogeny of Ameronothroidea based on morphological data using different algorithms. Both methods resulted in largely congruent topologies and highlight the following important points: the Ameronothroidea represent a paraphyletic assemblage; the Podacaridae are a distinct family and should be excluded from Ameronothridae; the Fortuyniidae, Selenoribatidae and Tegeocranellidae constitute a monophyletic lineage; and certain genera of Selenoribatidae need a revision. These results demonstrate that the classification of Ameronothroidea and certain positions within this group need to be thoroughly reconsidered and revised. The present study also shows that phylogenetic estimates based on coded morphological data can be a very helpful tool for verifying and supporting molecular phylogenies.

Mitochondrial genome phylogeny reveals the deep‐time origin of Gomphomastacinae (Orthoptera: Eumastacidae) and its alpine genera in China

AbstractGomphomastacinae is a grasshopper subfamily in Eumastacidae, with a morphology and distribution distinct from other subfamilies. The alpine genera of Gomphomastacinae that inhabit the Qinghai–Tibet Plateau in China show unique characteristics adapted to high‐altitude life. However, their phylogenetic position and biogeographic history remain controversial. Thus, to determine the diversification history of these alpine genera and the origin of the subfamily, we obtained mitochondrial genome sequences from all seven Gomphomastacinae genera distributed in China. The reconstructed phylogeny was well supported and confirmed the phylogenetic position of Gomphomastacinae within Eumastacidae. Time calibration revealed a deep‐time origin of the subfamily dating back to the Cretaceous period, and the diversification among alpine genera was also an ancient pre‐Miocene event (30–50 Ma). Based on phylogeny and time estimates, the most likely biogeographic scenario is that Gomphomastacinae originated from an ancestral lineage that lived in East Gondwana and dispersed to Central and Western Asia through India. Subsequently, the alpine genera likely diverged along with the uplift of the Qinghai–Tibet Plateau and survived drastic climate change by in situ adaptation to high‐altitude dwellings.

Evaluating Compression-Based Phylogeny Estimation in the Presence of Incomplete Lineage Sorting.

This study assesses characteristics of the normalized compression distance (NCD) technique for building phylogenetic trees from molecular data. We examined results from a mammalian biological data set as well as a collection of simulated data with varying levels of incomplete lineage sorting. The implementation of NCD we analyze is a concatenation-based, distance-based, alignment-free, and model-free phylogeny estimation method, which takes concatenated unaligned sequence data as input and outputs a matrix of distances. We compare the NCD phylogeny estimation method with various other methods, including coalescent- and concatenation-based methods.

Mitochondrial genome characterization and mitogenome phylogenetics in the central Mexican Stenopelmatus talpa complex (Orthoptera: Stenopelmatidae: Stenopelmatini)

The Stenopelmatus talpa species-group (Stenopelmatidae) comprises cricket-like orthopterans distributed across the Trans-Mexican Volcanic Belt (TMVB) morphotectonic province and adjacent areas in central Mexico. Despite recent efforts, the taxonomy and evolutionary relationships for members of this complex still are far from completely known. Here we generated and characterized the mitochondrial (mt) genome of 14 specimens of the S. talpa species-group and evaluated its species limits with the cox1 barcoding locus. Moreover, based on the mt genome DNA sequence data, we also reconstructed its phylogenetic relationships and made inferences about its biogeographic history based on a relaxed molecular clock analysis. A total of 9 species were delimited using a 2% pairwise distance criterion, which were consistent with our best estimate of phylogeny. The relationships recovered for the S. talpa species-group were similar although with more recent divergence time estimates than those obtained in a previous phylogenetic study, suggesting that its origin and subsequent diversification in the TMVB followed an east-central pattern, with its earliest divergence occurring during the late Pliocene to early Pleistocene.