Evaluating phylogenetic informativeness as a predictor of phylogenetic signal for metazoan, fungal, and mammalian phylogenomic data sets

Phylogenomic analysis of brachyuran crabs using transcriptome data reveals possible sources of conflicting phylogenetic relationships within the group

Despite extensive morphological and molecular studies, the phylogenetic interrelationships within the infraorder Brachyura and the phylogenetic positions of many taxa remain uncertain. Studies that used a limited number of molecular markers have often failed to provide sufficient resolution, and may be susceptible to stochastic errors and incomplete lineage sorting (ILS). Here we reconstructed the phylogenetic relationships within the Brachyura using transcriptome data of 56 brachyuran species, including 14 newly sequenced taxa. Five supermatrices were constructed in order to exclude different sources of systematic error. The results of the phylogenetic analyses indicate that Heterotremata is non-monophyletic, and that the two Old World primary freshwater crabs (Potamidae and Gecarcinucidae) and the Hymenosomatoidea form a clade that is sister to the Thoracotremata, and outside the Heterotremata. We also found that ILS is the main cause of the gene-tree discordance of these freshwater crabs. Divergence time estimations indicate that the Brachyura has an ancient origin, probably either in the Triassic or Jurassic, and that the majority of extant families and superfamilies first appeared during the Cretaceous, with a constant increase of diversity in Post-Cretaceous-Palaeogene times. The results support the hypothesis that the two Old World freshwater crab families included in this study (Potamidae and Gecarcinucidae) diverged from their marine ancestors around 120 Ma, in the Cretaceous. In addition, this work provides new insights that may aid in the reclassification of some of the more problematic brachyuran groups.

Historical biogeography and the evolution of habitat preference in the North American camel spider family, Eremobatidae (Arachnida:Solifugae)

Abiotic variables can influence species distributions, often restricting taxa to an acquired climatic signature or conversely, related species are conserved in the same ecological space over millions of years. An investigation into how abiotic change has shaped geographic distributions of taxa may be key to understanding diversification of lineages, and in the absence of reliable morphological characteristics, such information may support taxonomic units at multiple scales. Here, we examine the historical biogeography and patterns of habitat preference within the North American solifuge family, Eremobatidae. A previous study demonstrated that a major taxonomic revision of Eremobatidae is warranted, however recent studies demonstrate high levels of morphological convergence within the group, thus a re-classification of generic boundaries using additional information must be prioritized before we can formally begin solid revisionary efforts. In this study, we aimed to reconstruct a well-resolved phylogenetic hypothesis of Eremobatidae by filtering UCE loci based on informativeness, by mitigating the effect of cogenic UCE on phylogenetic estimation, and by supplementing our curated UCE loci with mitochondrial information. Using our preferred topology, in conjunction with published estimated divergence dates for Eremobatidae, we inferred a time-calibrated phylogenetic hypothesis to inform the historical biogeography and patterns of habitat preference. The two major habitat types that were observed for Eremobatidae were warm deserts for early diverging taxa and a subsequent evolution to cold deserts and Mediterranean California ecoregions for later diverging taxa. Eremobatid niche space, determined by temperature and precipitation, has been conserved for at least 25 million years in North America, supporting a warm desert origin, and thus supporting high species richness in the Sonoran and Mexican Plateau. Overall, our study provides support for new generic level designations within Eremobatidae.

Exon-capture data and locus screening provide new insights into the phylogeny of flatfishes (Pleuronectoidei)

There is an extensive collection of literature on the taxonomy and phylogenetics of flatfishes (Pleuronectiformes) that extends over two centuries, but consensus on many of their evolutionary relationships remains elusive. Phylogenetic uncertainty stems from highly divergent results derived from morphological and genetic characters, and between various molecular datasets. Deciphering relationships is complicated by rapid diversification early in the Pleuronectiformes tree and an abundance of studies that incompletely and inconsistently sample taxa and genetic markers. We present phylogenies based on a genome-wide dataset (4,434 nuclear markers via exon-capture) and wide taxon sampling (86 species spanning 12 of 16 families) of the largest flatfish suborder (Pleuronectoidei). Nine different subsets of the data and two tree construction approaches (eighteen phylogenies in total) are remarkably consistent with other recent molecular phylogenies, and show strong support for the monophyly of all families included except Pleuronectidae. Analyses resolved a novel phylogenetic hypothesis for the family Rhombosoleidae as being within the Pleuronectoidea rather than the Soleoidea, and failed to support the subfamily Hippoglossinae as a monophyletic group. Our results were corroborated with evidence from previous phylogenetic studies to outline regions of persistent phylogenetic uncertainty and identify groups in need of further phylogenetic inference.

Resolving the Early Divergence Pattern of Teleost Fish Using Genome-Scale Data

Regarding the phylogenetic relationship of the three primary groups of teleost fishes, Osteoglossomorpha (bonytongues and others), Elopomorpha (eels and relatives), Clupeocephala (the remaining teleost fish), early morphological studies hypothesized the first divergence of Osteoglossomorpha, whereas the recent prevailing view is the first divergence of Elopomorpha. Molecular studies supported all the possible relationships of the three primary groups. This study analyzed genome-scale data from four previous studies: 1) 412 genes from 12 species, 2) 772 genes from 15 species, 3) 1,062 genes from 30 species, and 4) 491 UCE loci from 27 species. The effects of the species, loci, and models used on the constructed tree topologies were investigated. In the analyses of the data sets (1)–(3), although the first divergence of Clupeocephala that left the other two groups in a sister relationship was supported by concatenated sequences and gene trees of all the species and genes, the first divergence of Elopomorpha among the three groups was supported using species and/or genes with low divergence of sequence and amino-acid frequencies. This result corresponded to that of the UCE data set (4), whose sequence divergence was low, which supported the first divergence of Elopomorpha with high statistical significance. The increase in accuracy of the phylogenetic construction by using species and genes with low sequence divergence was predicted by a phylogenetic informativeness approach and confirmed by computer simulation. These results supported that Elopomorpha was the first basal group of teleost fish to have diverged, consistent with the prevailing view of recent morphological studies.

Integrative systematics untangles the evolutionary history of Stenochrus (Schizomida: Hubbardiidae), a neglected junkyard genus of North American short-tailed whipscorpions

Until recently, the Nearctic short-tailed whipscorpion genus, StenochrusChamberlin, 1922, included 27 species distributed primarily in Mexico, the USA and Central America. Morphological disparity among its species, associated with their adaptation to diverse habitats, raised the question as to whether Stenochrus was monophyletic. The phylogenetic relationships among short-tailed whipscorpions have only recently begun to be explored, and the monophyly of Stenochrus had never been tested. The present contribution provides the first phylogeny of Stenochrus and related genera, based on 61 morphological characters and 2991 aligned DNA nucleotides from two nuclear and two mitochondrial gene markers, for 73 terminal taxa. Separate and simultaneous analyses of the morphological and molecular data sets were conducted with Bayesian Inference, Maximum Likelihood, and parsimony with equal and implied weighting. Terminals represented only by morphological data (‘orphans’) were included in some analyses for evaluation of their phylogenetic positions. As previously defined, Stenochrus sensuReddell & Cokendolpher (1991, 1995) was consistently polyphyletic and comprised eight monophyletic clades, justifying its reclassification into eight genera including Heteroschizomus Rowland, 1973, revalidated from synonymy with Stenochrus by Monjaraz-Ruedas et al. (2019). Rowland & Reddell’s (1980)mexicanus and pecki species groups were consistently paraphyletic. Orphans grouped with the most morphologically similar taxa.

The efficiency of universal mitochondrial DNA barcodes for species discrimination of Pomacea canaliculata and Pomacea maculata

Invasive apple snails, Pomacea canaliculata and P. maculata, have a widespread distribution globally and are regarded as devastating pests of agricultural wetlands. The two species are morphologically similar, which hinders species identification via morphological approaches and species-specific management efforts. Advances in molecular genetics may contribute effective diagnostic tools to potentially resolve morphological ambiguity. DNA barcoding has revolutionized the field of taxonomy by providing an alternative, simple approach for species discrimination, where short sections of DNA, the cytochrome c oxidase subunit I (COI) gene in particular, are used as ‘barcodes’ to delineate species boundaries. In our study, we aimed to assess the effectiveness of two mitochondrial markers, the COI and 16S ribosomal deoxyribonucleic acid (16S rDNA) markers for DNA barcoding of P. canaliculata and P. maculata. The COI and 16S rDNA sequences of 40 Pomacea specimens collected from six localities in Peninsular Malaysia were analyzed to assess their barcoding performance using phylogenetic methods and distance-based assessments. The results confirmed both markers were suitable for barcoding P. canaliculata and P. maculata. The phylogenies of the COI and 16S rDNA markers demonstrated species-specific monophyly and were largely congruent with the exception of one individual. The COI marker exhibited a larger barcoding gap (6.06–6.58%) than the 16S rDNA marker (1.54%); however, the magnitude of barcoding gap generated within the barcoding region of the 16S rDNA marker (12-fold) was bigger than the COI counterpart (approximately 9-fold). Both markers were generally successful in identifying P. canaliculata and P. maculata in the similarity-based DNA identifications. The COI + 16S rDNA concatenated dataset successfully recovered monophylies of P. canaliculata and P. maculata but concatenation did not improve individual datasets in distance-based analyses. Overall, although both markers were successful for the identification of apple snails, the COI molecular marker is a better barcoding marker and could be utilized in various population genetic studies of P. canaliculata and P. maculata.

Interrogating Genomic-Scale Data for Squamata (Lizards, Snakes, and Amphisbaenians) Shows no Support for Key Traditional Morphological Relationships

Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards, snakes, and amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a consensus on the relationships among them has been highly problematic. In this study, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome-scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites (PIS), phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously well-supported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a few undesirable gene properties, such as an insufficient number of PIS), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata. We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; among the three toxicoferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families).

Phylogenomic analysis on the exceptionally diverse fish clade Gobioidei (Actinopterygii: Gobiiformes) and data-filtering based on molecular clocklikeness

The use of genome-scale data to infer phylogenetic relationships has gained in popularity in recent years due to the progress made in target-gene capture and sequencing techniques. Data filtering, the approach of excluding data inconsistent with the model from analyses, presumably could alleviate problems caused by systematic errors in phylogenetic inference. Different data filtering criteria, such as those based on evolutionary rate and molecular clocklikeness as well as others have been proposed for selecting useful phylogenetic markers, yet few studies have tested these criteria using phylogenomic data. We developed a novel set of single-copy nuclear coding markers to capture thousands of target genes in gobioid fishes, a species-rich lineages of vertebrates, and tested the effects of data-filtering methods based on substitution rate and molecular clocklikeness while attempting to control for the compounding effects of missing data and variation in locus length. We found that molecular clocklikeness was a better predictor than overall substitution rate for phylogenetic usefulness of molecular markers in our study. In addition, when the 100 best ranked loci for our predictors were concatenated and analyzed using maximum likelihood, or combined in a coalescent-based species-tree analysis, the resulting trees showed a well-resolved topology of Gobioidei that mostly agrees with previous studies. However, trees generated from the 100 least clocklike frequently recovered conflicting, and in some cases clearly erroneous topologies with strong support, thus indicating strong systematic biases in those datasets. Collectively these results suggest that data filtering has the potential improve the performance of phylogenetic inference when using both a concatenation approach as well as methods that rely on input from individual gene trees (i.e. coalescent species-tree approaches), which may be preferred in scenarios where incomplete lineage sorting is likely to be an issue.

Genomic Mining of Phylogenetically Informative Nuclear Markers in Bark and Ambrosia Beetles

Deep level insect relationships are generally difficult to resolve, especially within taxa of the most diverse and species rich holometabolous orders. In beetles, the major diversity occurs in the Phytophaga, including charismatic groups such as leaf beetles, longhorn beetles and weevils. Bark and ambrosia beetles are wood boring weevils that contribute 12 percent of the diversity encountered in Curculionidae, one of the largest families of beetles with more than 50000 described species. Phylogenetic resolution in groups of Cretaceous age has proven particularly difficult and requires large quantity of data. In this study, we investigated 100 nuclear genes in order to select a number of markers with low evolutionary rates and high phylogenetic signal. A PCR screening using degenerate primers was applied to 26 different weevil species. We obtained sequences from 57 of the 100 targeted genes. Sequences from each nuclear marker were aligned and examined for detecting multiple copies, pseudogenes and introns. Phylogenetic informativeness (PI) and the capacity for reconstruction of previously established phylogenetic relationships were used as proxies for selecting a subset of the 57 amplified genes. Finally, we selected 16 markers suitable for large-scale phylogenetics of Scolytinae and related weevil taxa.

A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference

Molecular phylogenetic inference is inherently dependent on choices in both methodology and data. Many insightful studies have shown how choices in methodology, such as the model of sequence evolution or optimality criterion used, can strongly influence inference. In contrast, much less is known about the impact of choices in the properties of the data, typically genes, on phylogenetic inference. We investigated the relationships between 52 gene properties (24 sequence-based, 19 function-based, and 9 tree-based) with each other and with three measures of phylogenetic signal in two assembled data sets of 2,832 yeast and 2,002 mammalian genes. We found that most gene properties, such as evolutionary rate (measured through the percent average of pairwise identity across taxa) and total tree length, were highly correlated with each other. Similarly, several gene properties, such as gene alignment length, Guanine-Cytosine content, and the proportion of tree distance on internal branches divided by relative composition variability (treeness/RCV), were strongly correlated with phylogenetic signal. Analysis of partial correlations between gene properties and phylogenetic signal in which gene evolutionary rate and alignment length were simultaneously controlled, showed similar patterns of correlations, albeit weaker in strength. Examination of the relative importance of each gene property on phylogenetic signal identified gene alignment length, alongside with number of parsimony-informative sites and variable sites, as the most important predictors. Interestingly, the subsets of gene properties that optimally predicted phylogenetic signal differed considerably across our three phylogenetic measures and two data sets; however, gene alignment length and RCV were consistently included as predictors of all three phylogenetic measures in both yeasts and mammals. These results suggest that a handful of sequence-based gene properties are reliable predictors of phylogenetic signal and could be useful in guiding the choice of phylogenetic markers.

Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction

Myriapods, including the diverse and familiar centipedes and millipedes, are one of the dominant terrestrial arthropod groups. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes from many species) or on maximizing matrix size (e.g., by including hundreds or thousands of genes in just a few species), but a phylogeny maximizing sampling at both levels remains elusive. In this study, we analyzed 40 Illumina transcriptomes representing 3 of the 4 myriapod classes (Diplopoda, Chilopoda, and Symphyla); 25 transcriptomes were newly sequenced to maximize representation at the ordinal level in Diplopoda and at the family level in Chilopoda. Ten supermatrices were constructed to explore the effect of several potential phylogenetic biases (e.g., rate of evolution, heterotachy) at 3 levels of gene occupancy per taxon (50%, 75%, and 90%). Analyses based on maximum likelihood and Bayesian mixture models retrieved monophyly of each myriapod class, and resulted in 2 alternative phylogenetic positions for Symphyla, as sister group to Diplopoda + Chilopoda, or closer to Diplopoda, the latter hypothesis having been traditionally supported by morphology. Within centipedes, all orders were well supported, but 2 deep nodes remained in conflict in the different analyses despite dense taxon sampling at the family level. Relationships among centipede orders in all analyses conducted with the most complete matrix (90% occupancy) are at odds not only with the sparser but more gene-rich supermatrices (75% and 50% supermatrices) and with the matrices optimizing phylogenetic informativeness or most conserved genes, but also with previous hypotheses based on morphology, development, or other molecular data sets. Our results indicate that a high percentage of ribosomal proteins in the most complete matrices, in conjunction with distance from the root, can act in concert to compromise the estimated relationships within the ingroup. We discuss the implications of these findings in the context of the ever more prevalent quest for completeness in phylogenomic studies.

Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes

Ultraconserved elements (UCEs) have become popular markers in phylogenomic studies because of their cost effectiveness and their potential to resolve problematic phylogenetic relationships. Although UCE datasets typically contain a much larger number of loci and sites than more traditional datasets of PCR-amplified, single-copy, protein coding genes, a fraction of UCE sites are expected to be part of a nearly invariant core, and the relative performance of UCE datasets versus protein coding gene datasets is poorly understood. Here we use phylogenetic informativeness (PI) to compare the resolving power of multi-locus and UCE datasets in a sample of percomorph fishes with sequenced genomes (genome-enabled). We compare three data sets: UCE core regions, flanking sequence adjacent to the UCE core and a set of ten protein coding genes commonly used in fish systematics. We found the net informativeness of UCE core and flank regions to be roughly ten-fold and 100-fold more informative than that of the protein coding genes. On a per locus basis UCEs and protein coding genes exhibited similar levels of phylogenetic informativeness. Our results suggest that UCEs offer enormous potential for resolving relationships across the percomorph tree of life.