Parsimony analysis of phylogenomic datasets (I): scripts and guidelines for using TNT (Tree Analysis using New Technology)

Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China

Resolving evolutionary relationships among closely related species with interspecific gene flow is challenging. Genome-scale data provide opportunities to clarify complex evolutionary relationships in closely related species and to observe variations in species relationships across the genomes of such species. The Himalayan-Hengduan subalpine oaks have a nearly completely sympatric distribution in southwest China and probably constitute a syngameon. In this study, we mapped resequencing data from different species in this group to the Quercus aquifolioides reference genome to obtain a high-quality filtered single nucleotide polymorphism (SNP) dataset. We also assembled their plastomes. We reconstructed their phylogenetic relationships, explored the level and pattern of introgression among these species and investigated gene tree variation in the genomes of these species using sliding windows. The same or closely related plastomes were found to be shared extensively among different species within a specific geographical area. Phylogenomic analyses of genome-wide SNP data found that most oaks in the Himalayan-Hengduan subalpine clade showed genetic coherence, but several species were found to be connected by introgression. The gene trees obtained using sliding windows showed that the phylogenetic relationships in the genomes of oaks are highly heterogeneous and therefore highly obscured. Our study found that all the oaks of the Himalayan-Hengduan subalpine clade from southwest China form a syngameon. The obscured phylogenetic relationships observed empirically across the genome are best explained by interspecific gene flow in conjunction with incomplete lineage sorting.

Wincladtree: Publication-quality tree-diagrams with TNT scripts

This note describes the implementation and use of wincladtree, a TNT script to plot publication-quality tree-diagrams. This is intended to assist analysis of morphological datasets, where displaying the synapomorphies for the different groups in a compact "Hennigian" style is the norm.

Phylogenomics of the geometrid tribe Palyadini (Lepidoptera: Geometridae) reveals contrasting patterns of phylogenetic signal in wing colour characters

Next generation sequencing techniques currently represent a practical and efficient way to infer robust evolutionary hypotheses. Palyadini is a small Neotropical tribe of geometrid moths composed of six genera that feature strikingly colourful wings. Here, we investigated patterns of evolution and amount of phylogenetic signal contained in various colour characters featured in the wings of members of this tribe by (i) inferring a robust phylogenetic hypothesis using ultraconserved elements (UCEs), and afterwards, (ii) mapping the morphological characters onto the molecular topology under a parsimonious ancestral character optimization. Our matrix, obtained with 60% completeness, includes 754 UCE loci and 73 taxa (64 ingroup, nine outgroup). Maximum likelihood and parsimony generated largely identical topologies with strongly supported nodes, except for one node inside the genus Opisthoxia. According to our topology, most wing colour characters are reconstructed as homoplastic, particularly at the tribe level, but five of the seven provide evidence supporting common ancestry at the genus level. Our results emphasize, once again, that no character system is infallible, and that more research is necessary to take our understanding of the evolution of wing colour in moths to a level comparable with the knowledge we have for butterflies.

Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment Including Long Indels

Despite having important biological implications, insertion, and deletion (indel) events are often disregarded or mishandled during phylogenetic inference. In multiple sequence alignment, indels are represented as gaps and are estimated without considering the distinct evolutionary history of insertions and deletions. Consequently, indels are usually excluded from subsequent inference steps, such as ancestral sequence reconstruction and phylogenetic tree search. Here, we introduce indel-aware parsimony (indelMaP), a novel way to treat gaps under the parsimony criterion by considering insertions and deletions as separate evolutionary events and accounting for long indels. By identifying the precise location of an evolutionary event on the tree, we can separate overlapping indel events and use affine gap penalties for long indel modeling. Our indel-aware approach harnesses the phylogenetic signal from indels, including them into all inference stages. Validation and comparison to state-of-the-art inference tools on simulated data show that indelMaP is most suitable for densely sampled datasets with closely to moderately related sequences, where it can reach alignment quality comparable to probabilistic methods and accurately infer ancestral sequences, including indel patterns. Due to its remarkable speed, our method is well suited for epidemiological datasets, eliminating the need for downsampling and enabling the exploitation of the additional information provided by dense taxonomic sampling. Moreover, indelMaP offers new insights into the indel patterns of biologically significant sequences and advances our understanding of genetic variability by considering gaps as crucial evolutionary signals rather than mere artefacts.

Ultraconserved elements from transcriptome and genome data provide insight into the phylogenomics of Sternorrhyncha (Insecta: Hemiptera)

Sternorrhyncha, one of the four major suborders of Hemiptera, is a phytophagous taxon inclusive of nearly 18 000 described species. The phylogenetic relationships within the taxon and the earliest-branching lineage of its infraorders remain incompletely understood. This study attempted to illuminate the phylogenetic relationships within Sternorrhyncha through the use of maximum likelihood, Bayesian inference and maximum parsimony analyses, employing ultraconserved element (UCE) data from 39 genomic and 62 transcriptomic datasets and thereby representing most families within the taxon. The probe set Hemiptera 2.7Kv1 was used to recover a total of 2731 UCE loci: from 547 to 1699 (with an average of 1084) across all genomic datasets and from 108 to 849 (with an average of 329) across all transcriptomic datasets. All three types of phylogenetic analyses employed in this study produced robust statistical support for Sternorrhyncha being a monophyletic group. The different methods of phylogenetic analysis produced inconsistent descriptions of topological structure at the infraorder level: while maximum likelihood and Bayesian inference analyses produced strong statistical evidence (100%) indicating the clade Psylloidea + Aleyrodoidea to be a sister of the clade Aphidoidea (Aphidomorpha) + Coccoidea (Coccomorpha), the maximum parsimony analysis failed to recover a similar result. Our results also provide detail on the phylogenetic relationships within each infraorder. This study presents the first use of UCE data to investigate the phylogeny of Sternorrhyncha. It also shows the viability of amalgamating genomic and transcriptomic data in studies of phylogenetic relationships, potentially highlighting a resource-efficient approach for future inquiries into diverse taxa through the integration of varied data sources.

A new mayfly subfamily sheds light on the early evolution and Pangean origin of Baetiscidae (Insecta: Ephemeroptera)

The family Baetiscidae Edmunds & Traver, 1954 is recognisable among mayflies due to its bizarre larvae, equipped with a robust and spiked thoracic notal shield covering part of the abdomen up to sixth segment. Originally being described as extant species from the USA and Canada, Baetiscidae were later found in the fossil record as well, specifically in Cretaceous of Brazil and Eocene Baltic amber. An enigmatic piece of fossil evidence are two larvae from the Early Cretaceous Koonwarra Fossil Bed in Australia, which have been presumed as attributable to Baetiscidae and briefly discussed in previous studies. In the present contribution, we reinvestigate these fossils and confirm their attribution to the family Baetiscidae. These larvae are depicted and described as Koonwarrabaetisca jelli gen. et sp. nov. and Koonwarrabaetisca duncani sp. nov. For both Cretaceous genera Protobaetisca Staniczek, 2007 and Koonwarrabaetisca gen. nov. we establish a new subfamily Protobaetiscinae subfam. nov. within the family Baetiscidae, based on the presence of markedly shortened thoracic sterna. The phylogenetic position of newly described subfamily is clarified using a cladistic analysis; Protobaetiscinae subfam. nov. forms a monophyletic clade, sister to Baetiscinae. The confirmation of the distribution of Baetiscidae in the Cretaceous of Australia suggests almost worldwide distribution of this family in the deep time. Given their limited dispersal abilities, this distributional pattern can be best explained by the Pangean origin for this family, moving the time of their origin at least to the Early Jurassic. The larvae of Koonwarrabaetisca gen. nov. exhibit the same ecomorphological specialization as the rest of Baetiscidae, that supporting with a high probability their lifestyle similar to extant Baetisca Walsh, 1862. The larvae probably lived in the flowing water with stony substrate densely covered by filamentous algae, and in the places of accumulation of dead plant and algae matter during the last instars. Thus, Koonwarrabaetisca gen. nov. could be the allochthonous component in mayfly fauna of the Koonwarra paleolake.

What else is dentition telling us? A new specimen-level phylogeny of Mesotheriidae (Mammalia, Notoungulata)

Mesotheriidae (Panperissodactyla, Notoungulata) are an extinct clade (early Oligocene-Pleistocene) of small to medium-sized herbivorous mammals that were widely distributed in South America. Although two subfamilies traditionally have been recognized (Trachytheriinae and Mesotheriinae), recent cladistic analyses based on discrete characters have indicated that "Trachytheriinae" is a paraphyletic assemblage. Given the availability of a large number of specimens and the fact that dental characters are the most common characters used in mesotheriid phylogenies, we performed specimen-level cladistic analyses combining discrete, continuous and geometric morphometrics-based dental characters. The aim was to: (1) include new scored morphological characters to solve the phylogenetic relationships of Mesotheriidae; (2) compare the results of the upper and lower dentition analyses as different character partitions and in combination, to establish phylogenetic hypotheses; and (3) trace the evolution of dental traits. Phylogenetic analyses employing characters of associated upper and lower dentitions recovered one most parsimonious tree with Archaeohyracidae (outgroup) as the sister group of Pan-Mesotheriidae (= Mesotheriidae; converted clade name), this latter composed of trachytheriines (stem-mesotheriine) + Mesotheriinae (converted clade name). Within Mesotheriinae, we recovered two main lineages phylogenetically defined here as Bolivarini and Pampaini (new clade names). Analyses of isolated upper and lower dentition sub-datasets each resulted in one most parsimonious tree congruent with the associated dentition. Our study emphasizes the use of geometric morphometrics characters to resolve additional clades in phylogenetic analyses, provides information on the evolution of size and morphology of teeth, and exposes specimen assignment issues at a taxonomic level. The integration of osteological characters might be crucial to further understanding the evolution of Mesotheriidae.

Middle ear innovation in Early Cretaceous eutherian mammals

The middle ear ossicles in modern mammals are repurposed from postdentary bones in non-mammalian cynodonts. Recent discoveries by palaeontological and embryonic studies have developed different models for the middle ear evolution in mammaliaforms. However, little is known about the evolutionary scenario of the middle ear in early therians. Here we report a detached middle ear preserved in a new eutherian mammal from the Early Cretaceous Jehol Biota. The well-preserved articulation of the malleus and incus suggest that the saddle-shaped incudomallear joint is a major apomorphy of Early Cretaceous eutherians. By contrast to the distinct saddle-like incudomallear articulation in therians, differences between the overlapping versus the half-overlapping incudomallear joints in monotremes and stem mammals would be relatively minor. The middle ear belongs to the microtype by definition, indicating its adaptation to high-frequency hearing. Current evidence indicates that significant evolutionary innovations of the middle ear in modern therians evolved in Early Cretaceous.

Quantification of congruence among gene trees with polytomies using overall success of resolution for phylogenomic coalescent analyses

Gene-tree-inference error can cause species-tree-inference artefacts in summary phylogenomic coalescent analyses. Here we integrate two ways of accommodating these inference errors: collapsing arbitrarily or dubiously resolved gene-tree branches, and subsampling gene trees based on their pairwise congruence. We tested the effect of collapsing gene-tree branches with 0% approximate-likelihood-ratio-test (SH-like aLRT) support in likelihood analyses and strict consensus trees for parsimony, and then subsampled those partially resolved trees based on congruence measures that do not penalize polytomies. For this purpose we developed a new TNT script for congruence sorting (congsort), and used it to calculate topological incongruence for eight phylogenomic datasets using three distance measures: standard Robinson-Foulds (RF) distances; overall success of resolution (OSR), which is based on counting both matching and contradicting clades; and RF contradictions, which only counts contradictory clades. As expected, we found that gene-tree incongruence was often concentrated in clades that are arbitrarily or dubiously resolved and that there was greater congruence between the partially collapsed gene trees and the coalescent and concatenation topologies inferred from those genes. Coalescent branch lengths typically increased as the most incongruent gene trees were excluded, although branch supports typically did not. We investigated two successful and complementary approaches to prioritizing genes for investigation of alignment or homology errors. Coalescent-tree clades that contradicted concatenation-tree clades were generally less robust to gene-tree subsampling than congruent clades. Our preferred approach to collapsing likelihood gene-tree clades (0% SH-like aLRT support) and subsampling those trees (OSR) generally outperformed competing approaches for a large fungal dataset with respect to branch lengths, support and congruence. We recommend widespread application of this approach (and strict consensus trees for parsimony-based analyses) for improving quantification of gene-tree congruence/conflict, estimating coalescent branch lengths, testing robustness of coalescent analyses to gene-tree-estimation error, and improving topological robustness of summary coalescent analyses. This approach is quick and easy to implement, even for huge datasets.

A novel probe set for the phylogenomics and evolution of RTA spiders

Spiders are important models for evolutionary studies of web building, sexual selection and adaptive radiation. The recent development of probes for UCE (ultra-conserved element)-based phylogenomic studies has shed light on the phylogeny and evolution of spiders. However, the two available UCE probe sets for spider phylogenomics (Spider and Arachnida probe sets) have relatively low capture efficiency within spiders, and are not optimized for the retrolateral tibial apophysis (RTA) clade, a hyperdiverse lineage that is key to understanding the evolution and diversification of spiders. In this study, we sequenced 15 genomes of species in the RTA clade, and using eight reference genomes, we developed a new UCE probe set (41 845 probes targeting 3802 loci, labelled as the RTA probe set). The performance of the RTA probes in resolving the phylogeny of the RTA clade was compared with the Spider and Arachnida probes through an in-silico test on 19 genomes. We also tested the new probe set empirically on 28 spider species of major spider lineages. The results showed that the RTA probes recovered twice and four times as many loci as the other two probe sets, and the phylogeny from the RTA UCEs provided higher support for certain relationships. This newly developed UCE probe set shows higher capture efficiency empirically and is particularly advantageous for phylogenomic and evolutionary studies of RTA clade and jumping spiders.

Total-evidence phylogeny and evolutionary morphology of New World pitvipers (Serpentes: Viperidae: Crotalinae)

Crotalines (pitvipers) in the Americas are distributed from southern Canada to southern Argentina, and are represented by 13 genera and 163 species that constitute a monophyletic group. Their phylogenetic relationships have been assessed mostly based on DNA sequences, while morphological data have scarcely been used for phylogenetic inquiry. We present a total-evidence phylogeny of New World pitvipers, the most taxon/character comprehensive phylogeny to date. Our analysis includes all genera, morphological data from external morphology, cranial osteology and hemipenial morphology, and DNA sequences from mitochondrial and nuclear genes. We performed analyses with parsimony as an optimality criterion, using different schemes for character weighting. We evaluated the contribution of the different sources of characters to the phylogeny through analyses of reduced datasets and calculation of weighted homoplasy and retention indexes. We performed a morphological character analysis to identify synapomorphies for the main clades. In terms of biogeography, our results support a single colonization event of the Americas by pitvipers, and a cladogenetic event into a Neotropical clade and a North American/Neotropical clade. The results also shed light on the previously unstable position of some taxa, although they could not sufficiently resolve the position of Bothrops lojanus, which may lead to the paraphyly of either Bothrops or Bothrocophias. The morphological character analyses demonstrated that an important phylogenetic signal is contained in characters related to head scalation, the jaws and the dorsum of the skull, and allowed us to detect morphological convergences in external morphology associated with arboreality.

TNT version 1.6, with a graphical interface for MacOS and Linux, including new routines in parallel

A new graphical user interface (GUI) for the parsimony program TNT is presented that works under the Linux and Mac operating systems, as well as the Cygwin environment (which runs under Windows). The new interface is based on the GIMP Tool Kit, GTK (version 3). Formerly, only Windows versions of TNT had a GUI. The new interface improves upon the existing Windows GUI in several respects. These changes, together with several additions to the program since the publication of version 1.5, warrant a change in minor version, thus moving from version 1.5 to 1.6. Among the most notable improvements are the possibility to access graphical user dialogs by means of simple commands, to easily save trees in SVG format ("Scalable Vector Graphics") directly from any tree-diagram being displayed, and to manage analyses in parallel (using multiple processors, by means of the PVM system or "Parallel Virtual Machine"), as well as a generally more stable and consistent behaviour. As the binaries for the new version are compiled as native 64-bit applications, this removes the limitations for accessing large amounts of memory in the previous GUI Windows interface (which is a 32-bit application).

New TNT routines for parallel computing with MPI

Phylogenetic inference, which involves time-consuming calculations, is a field where parallelization can speed up the resolution of many problems. TNT (a widely used program for phylogenetic analysis under parsimony) allows parallelization under the PVM system (Parallel Virtual Machine). However, as the basic aspects of the implementation remain unpublished, few studies have taken advantage of the parallelization routines of TNT. In addition, the PVM system is deprecated by many system administrators. One of the most common standards for high performance computing is now MPI (Message Passing Interface). To facilitate the use of the parallel analyses offered by TNT, this paper describes the basic aspects of the implementation, as well as a port of the parallelization interface of TNT into MPI. The use of the new routines is illustrated by reanalysis of seven significant datasets, either recent phylogenomic datasets with many characters (up to 2,509,064 characters) or datasets with large numbers of taxa (up to 13,921 taxa). Versions of TNT including the MPI functionality are available at: http://www.lillo.org.ar/phylogeny/tnt/.

Benefits of alignment quality-control processing steps and an Angiosperms353 phylogenomics pipeline applied to the Celastrales

We examined the impact of successive alignment quality-control steps on downstream phylogenomic analyses. We applied a recently published phylogenomics pipeline that was developed for the Angiosperms353 target-sequence-capture probe set to the flowering plant order Celastrales. Our final dataset consists of 158 species, including at least one exemplar from all 109 currently recognized Celastrales genera. We performed nine quality-control steps and compared the inferred resolution, branch support, and topological congruence of the inferred gene and species trees with those generated after each of the first six steps. We describe and justify each of our quality-control steps, including manual masking, in detail so that they may be readily applied to other lineages. We found that highly supported clades could generally be relied upon even if stringent orthology and alignment quality-control measures had not been applied. But separate instances were identified, for both concatenation and coalescence, wherein a clade was highly supported before manual masking but then subsequently contradicted. These results are generally reassuring for broad-scale analyses that use phylogenomics pipelines, but also indicate that we cannot rely exclusively on these analyses to conclude how challenging phylogenetic problems are best resolved.