Phylogeny Estimation Research Articles

LMAP_S: Lightweight Multigene Alignment and Phylogeny eStimation

BackgroundRecent advances in genome sequencing technologies and the cost drop in high-throughput sequencing continue to give rise to a deluge of data available for downstream analyses. Among others, evolutionary biologists often make use of genomic data to uncover phenotypic diversity and adaptive evolution in protein-coding genes. Therefore, multiple sequence alignments (MSA) and phylogenetic trees (PT) need to be estimated with optimal results. However, the preparation of an initial dataset of multiple sequence file(s) (MSF) and the steps involved can be challenging when considering extensive amount of data. Thus, it becomes necessary the development of a tool that removes the potential source of error and automates the time-consuming steps of a typical workflow with high-throughput and optimal MSA and PT estimations.ResultsWe introduce LMAP_S (Lightweight Multigene Alignment and Phylogeny eStimation), a user-friendly command-line and interactive package, designed to handle an improved alignment and phylogeny estimation workflow: MSF preparation, MSA estimation, outlier detection, refinement, consensus, phylogeny estimation, comparison and editing, among which file and directory organization, execution, manipulation of information are automated, with minimal manual user intervention. LMAP_S was developed for the workstation multi-core environment and provides a unique advantage for processing multiple datasets. Our software, proved to be efficient throughout the workflow, including, the (unlimited) handling of more than 20 datasets.ConclusionsWe have developed a simple and versatile LMAP_S package enabling researchers to effectively estimate multiple datasets MSAs and PTs in a high-throughput fashion. LMAP_S integrates more than 25 software providing overall more than 65 algorithm choices distributed in five stages. At minimum, one FASTA file is required within a single input directory. To our knowledge, no other software combines MSA and phylogeny estimation with as many alternatives and provides means to find optimal MSAs and phylogenies. Moreover, we used a case study comparing methodologies that highlighted the usefulness of our software. LMAP_S has been developed as an open-source package, allowing its integration into more complex open-source bioinformatics pipelines. LMAP_S package is released under GPLv3 license and is freely available at https://lmap-s.sourceforge.io/.

Index to Titles and Authors/Editors of Books Reviewed

Index to Titles and Authors/Editors of Books Reviewed

New hypotheses concerning the earliest brachyurans (Crustacea, Decapoda, Brachyura)

All Jurassic brachyuran taxa known to date are based solely upon dorsal carapaces, and only a limited number of Early and mid-Cretaceous crabs retain ventral parts. Therefore, all Jurassic taxa and many forms from the first half of the Cretaceous are carapace-based entities. All of them are considered to be “dromiaceans”, podotremes to be precise. The recent discovery of an exceptionally well-preserved male crab from the Upper Cretaceous (lower Cenomanian) of Chiapas (Mexico), Archaeochiapasa mardoqueoiGuinot, Carbot-Chanona & Vega, 2019, at first sight of a podotreme nature, has allowed a detailed description of its thoracic sternum and pleon, which revealed that it was actually a typical eubrachyuran, in need of a new family, Archaeochiapasidae Guinot, Carbot-Chanona & Vega, 2019. This has brought back to life one of my earlier ideas about the possible non-podotreme nature of certain enigmatic Late Jurassic and Cretaceous Brachyura previously placed in various “dromiacean” (i.e., podotreme) families and superfamilies. My investigations have led the me to formulate the present hypothesis that the extinct families Bucculentidae Schweitzer & Feldmann, 2009 (currently assigned to the Homolodromioidea Alcock, 1900), Lecythocaridae Schweitzer & Feldmann, 2009, Glaessneropsidae Schweitzer & Feldmann, 2009, Nodoprosopidae Schweitzer & Feldmann, 2009, and Viaiidae Artal, Van Bakel, Fraaije, Jagt & Klompmaker, 2012 (all four in Glaessneropsoidea Schweitzer & Feldmann, 2009) might, in fact (at least for some of them), be true eubrachyurans (Eubrachyura Saint Laurent, 1980). If correct, these assumptions would date the first “true crabs” as Jurassic, contrary to the currently held view that the earliest Eubrachyura (heterotremes) did not appear until the Cretaceous, and suggest that the evolutionary history of brachyurans started much earlier. This was unpredictable, at least for palaeontologists, but not so in view of a molecular estimate of decapod phylogeny that recovered the Majoidea Samouelle, 1819 as the oldest brachyuran lineage, with a divergence from other brachyurans from, at least, the Middle Triassic. The basal majoid family Oregoniidae Garth, 1958, which comprises only three extant genera, has several characters in common with Archaeochiapasidae; these leave little doubt about their close relationships. Proposals made here are inevitably based on provisional assumptions, until the characteristics of the ventral parts and pereiopods prove or refute them, either entirely or in part. Our science, which is based on the observation of specimens and then on descriptive, explanatory and, above all, predictive concepts, especially where incomplete fossil animals are concerned, should be conceived as a step forward, rather than an achievement, each of these steps being, sooner or later, replaced by a better one, or considered to be such. That is why all species and the composition of the Jurassic and Early Cretaceous genera and families will need to be checked in light of new perspectives. In contrast to the presumed eubrachyurans (see above), the Tanidromitidae Schweitzer & Feldmann, 2008 and the apparently paraphyletic family Longodromitidae Schweitzer & Feldmann, 2009 are podotremes, within the Dynomeniformia Guinot, Tavares & Castro, 2013. The status and composition of the Goniodromitinae Beurlen, 1932 (in the Dromiidae De Haan, 1833), clearly paraphyletic, are briefly revised, while some genera, such as DistefaniaChecchia-Rispoli, 1917, are tentatively assigned to the Sphaerodromiinae Guinot & Tavares, 2003. A table summarises the changes in classification implied by these new proposals and research directions. Some remarks on the new section Callichimaeroida Luque, Feldmann, Vernygora, Schweitzer, Cameron, Kerr, Vega, Duque, Strange, Palmer & Jaramillo, 2019 are provided, as well as on the the putatively callichimaeroid-like... This abstract has been truncated. To view the complete abstract please download the PDF.

Plastid phylogenomic insights into the evolution of the Caprifoliaceae s.l. (Dipsacales)

The family Caprifoliaceae s.l. is an asterid angiosperm clade of ca. 960 species, most of which are distributed in temperate regions of the northern hemisphere. Recent studies show that the family comprises seven major clades: Linnaeoideae, Zabelia, Morinoideae, Dipsacoideae, Valerianoideae, Caprifolioideae, and Diervilloideae. However, its phylogeny at the subfamily or genus level remains controversial, and the backbone relationships among subfamilies are incompletely resolved. In this study, we utilized complete plastome sequencing to resolve the relationships among the subfamilies of the Caprifoliaceae s.l. and clarify several long-standing controversies. We generated and analyzed plastomes of 48 accessions of Caprifoliaceae s.l., representing 44 species, six subfamilies and one genus. Combined with available Caprifoliaceae s.l. plastomes on GenBank and 12 outgroups, we analyzed a final dataset of 68 accessions. Genome structure was strongly conserved in general, although the boundaries between the Inverted Repeat were found to have contracted across Caprifoliaceae s.l. to exclude rpl2, rps19, and ycf1, all or parts of which are typically present in the IR of most angiosperms. The ndhF gene was found to have been inverted in all plastomes of Adoxaceae. Phylogenomic analyses of 68 complete plastomes yielded a highly supported topology that strongly supported the monophyly of Zabelia and its sister relationship to Morinoideae. Moreover, a clade of Valerianoideae + Dipsacoideae was recovered as sister to a clade of Linnaeoideae + Zabelia + Morinoideae clade, and Heptacodium was sister to remaining Caprifolioideae. The Diervilloideae and Caprifolioideae were successively sister to all other Caprifoliaceae s.l. Major lineages of Caprifoliaceae s.l. were estimated to have diverged from the Upper Cretaceous to the Eocene (50–100 Ma), whereas within-genus diversification was dated to the Oligocene and later, concomitant with global cooling and drying. Our results demonstrate the power of plastid phylogenomics in improving estimates of phylogeny among genera and subfamilies, and provide new insights into plastome evolution across Caprifoliaceae s.l.

Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge

BackgroundDivide-and-conquer methods, which divide the species set into overlapping subsets, construct a tree on each subset, and then combine the subset trees using a supertree method, provide a key algorithmic framework for boosting the scalability of phylogeny estimation methods to large datasets. Yet the use of supertree methods, which typically attempt to solve NP-hard optimization problems, limits the scalability of such approaches.ResultsIn this paper, we introduce a divide-and-conquer approach that does not require supertree estimation: we divide the species set into pairwise disjoint subsets, construct a tree on each subset using a base method, and then combine the subset trees using a distance matrix. For this merger step, we present a new method, called NJMerge, which is a polynomial-time extension of Neighbor Joining (NJ); thus, NJMerge can be viewed either as a method for improving traditional NJ or as a method for scaling the base method to larger datasets. We prove that NJMerge can be used to create divide-and-conquer pipelines that are statistically consistent under some models of evolution. We also report the results of an extensive simulation study evaluating NJMerge on multi-locus datasets with up to 1000 species. We found that NJMerge sometimes improved the accuracy of traditional NJ and substantially reduced the running time of three popular species tree methods (ASTRAL-III, SVDquartets, and “concatenation” using RAxML) without sacrificing accuracy. Finally, although NJMerge can fail to return a tree, in our experiments, NJMerge failed on only 11 out of 2560 test cases.ConclusionsTheoretical and empirical results suggest that NJMerge is a valuable technique for large-scale phylogeny estimation, especially when computational resources are limited. NJMerge is freely available on Github (http://github.com/ekmolloy/njmerge).

<p class="HeadingRunIn"><strong>Phylogenetics of a small caddisfly genus (Thremmatidae: <em>Oligophlebodes</em>): comparison among multiple hypotheses from DNA barcode data</strong></p>

Barcoding datasets can serve as a resource for species associations and delineations, but single-gene trees estimated by distance methods do not provide strong estimates of phylogeny. Using DNA data from the Barcode of Life Database (BOLD), we calculate a phylogenetic tree for Oligophlebodes (Trichoptera: Thremmatidae), a small genus of caddisfly endemic to the Western United States. Here we estimate a preliminary phylogeny for Oligophlebodes using Bayesian likelihood, and compare it to trees produced by distance and standard likelihood methods. Using the barcode region of the cytochrome oxidase 1 (COI) gene, we analyzed 44 individuals representing five species (and 2 unknowns) and a sister-genus outgroup (Neophylax) from locations ranging from Southern New Mexico northwest into British Columbia. Partitioned Bayesian likelihood analysis under the F81 (1st codon positions) and HKY80 + I + Γ (for both the 2nd and 3rd codon positions) model gave the consensus topology (Neophylax toshi, (O. sierra, (O. ruthae inc. spc. 1 & 2, O. sigma, (spc. 3 & 4, (O. ardis, O. minutus)))). Species identifications were supported by monophyly of most species-level taxa. However, confirmation of species identifications of unknowns was complicated by incomplete taxon sampling for spc. 1 & 2. Placement of spc. 3 & 4 may serve as support for taxonomic review of O. minutus. Compared with an existing published phylogeny of Oligophlebodes BOLD sequences constructed under RAxML, the Bayesian hypothesis had higher resolution at the basal node of Oligophlebodes. Because of their support values, both likelihood trees are recommended over the BOLD TaxonID tree (an unrooted neighbor joining tree using the Kimura 2-parameter model). The novel topology produced in the Bayesian tree supports further explorations by likelihood-based methods, including partitioned analyses, of our preliminary Oligophlebodes dataset that can be used as additional lines of evidence to support morphological work.

Two new species of freshwater crabs of the genus Potamonautes MacLeay, 1838 (Decapoda: Brachyura: Potamonautidae) from the forests of KwaZulu-Natal, South Africa

ABSTRACTRecent taxonomic studies of forest habitats in South Africa have revealed the presence of three new species of freshwater crabs, suggesting that decapod diversity within the indigenous forest biome remain poorly documented. Surveys of the freshwater crabs of north eastern KwaZulu-Natal province produced a number of specimens from Ntendeka Wilderness Area (Ngome forest) and Nkandla and Ngoye forests that proved to belong to two new species following morphological and molecular analysis (mtDNA sequencing of three loci, 12S rRNA, 16S rRNA and COI). Two undescribed species, P. ntendekaensis sp. nov. and P. ngoyensis sp. nov. are described. The divergence time estimation of the new phylogeny for eastern and southern African freshwater crabs is discussed to illuminate biogeographic patterning and to understand factors responsible for cladogenesis.

Recent diversification in an ancient lineage of Notothenioid fishes (Bovichtus: Notothenioidei)

Notothenioids are among the most intensively studied lineages of marine fishes. However, notothenioid research is predominately focused on the approximately 100 species of Antarctic cryonotothenioids. Far less attention is devoted to the non-Antarctic lineages Bovichtidae, Pseudaphritis urvillii, and Eleginops maclovinus, all of which originated prior to the diversification of cryonotothenioid species. Here we utilize DNA sequence data from mitochondrial and nuclear genes, as well as meristic trait morphology to investigate the evolutionary history of Bovichtidae. Bovichtus is the only polytypic lineage of early diverging non-Antarctic notothenioids providing a unique opportunity to contextualize the diversification dynamics of cryonotothenioids with their non-Antarctic relatives. We find strong evidence that species of Bovichtus represent a recent evolutionary radiation with divergence times similar to those estimated among the most closely related species of cryonotothenioids. The divergence in traditional meristic trait morphology among species of Bovichtus is consistent with their phylogenetic relationships. The phylogeny of Bovichtus implies the wide geographic distribution of species in the clade is likely the result of West Wind drift-driven dispersal. The phylogeny and divergence time estimates results reject a hypothesis that species persistence in Bovichtus reflects long periods of evolutionary stasis. Instead, we hypothesize that patterns of extinction and diversification in Bovichtus closely mirror those observed in their Antarctic relatives.

Constrained incremental tree building: new absolute fast converging phylogeny estimation methods with improved scalability and accuracy

BackgroundAbsolute fast converging (AFC) phylogeny estimation methods are ones that have been proven to recover the true tree with high probability given sequences whose lengths are polynomial in the number of number of leaves in the tree (once the shortest and longest branch weights are fixed). While there has been a large literature on AFC methods, the best in terms of empirical performance was DCM_{NJ}, published in SODA 2001. The main empirical advantage of {DCM}_{NJ} over other AFC methods is its use of neighbor joining (NJ) to construct trees on smaller taxon subsets, which are then combined into a tree on the full set of species using a supertree method; in contrast, the other AFC methods in essence depend on quartet trees that are computed independently of each other, which reduces accuracy compared to neighbor joining. However, {DCM}_{NJ} is unlikely to scale to large datasets due to its reliance on supertree methods, as no current supertree methods are able to scale to large datasets with high accuracy.ResultsIn this study we present a new approach to large-scale phylogeny estimation that shares some of the features of {DCM}_{NJ} but bypasses the use of supertree methods. We prove that this new approach is AFC and uses polynomial time and space. Furthermore, we describe variations on this basic approach that can be used with leaf-disjoint constraint trees (computed using methods such as maximum likelihood) to produce other methods that are likely to provide even better accuracy. Thus, we present a new generalizable technique for large-scale tree estimation that is designed to improve scalability for phylogeny estimation methods to ultra-large datasets, and that can be used in a variety of settings (including tree estimation from unaligned sequences, and species tree estimation from gene trees).

The Systematics of theTrematoda.

The platyhelminth class Trematoda comprises two subclasses with largely disparate species diversity, 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 15 years. 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 the 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.

Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny.

Phylogenies of mammals based on morphological data continue to show several major areas of conflict with the current consensus view of their relationships, which is based largely on molecular data. This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships. We tested this under a hypothetical 'best case scenario' by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive DNA sequence-based phylogeny of mammals, and then seeing what effect the subsequent inclusion of these predicted ancestors had on unconstrained phylogenetic analyses of morphological data. We found that this resulted in topologies that are highly congruent with the current consensus phylogeny, at least when the predicted ancestors are assumed to be well preserved and densely sampled. Most strikingly, several analyses recovered the monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria. Our results suggest that, at least in principle, improvements in the fossil record-specifically the discovery of fossil taxa that preserve the ancestral or near-ancestral morphologies of the nodes in the current consensus-may be sufficient to largely reconcile morphological and molecular estimates of mammal phylogeny, even using current morphological character sets.

Cophenetic Median Trees.

Median tree inference under path-difference metrics has shown great promise for large-scale phylogeny estimation. Similar to these metrics is the family of cophenetic metrics that originates from a classic dendrogram comparison method introduced more than 50 years ago. Despite the appeal of this family of metrics, the problem of computing median trees under cophenetic metrics has not been analyzed. Like other standard median tree problems relevant in practice, as we show here, this problem is also NP-hard. NP-hard median tree problems have been successfully addressed by local search heuristics that are solving thousands of instances of a corresponding (local neighborhood) search problem. For the local neighborhood search problem under a cophenetic metric, the best known (naïve) algorithm has a time complexity that is typically prohibitive for effective heuristic searches. Building on the pioneering work on path-difference median trees, we develop efficient algorithms for Manhattan and Euclidean cophenetic search problems that improve on the naïve solution by a linear and a quadratic factor, respectively. We demonstrate the performance and effectiveness of the resulting heuristic methods in a comparative study using benchmark empirical datasets.

Species Tree Estimation using ddRADseq Data from Historical Specimens Confirms the Monophyly of Highly Disjunct Species of Chloropyron (Orobanchaceae)

Sequence data exist for only about 1/5 of plant species; therefore we are at risk of losing many branches of the tree of life even before they are placed into a molecular evolutionary context. This necessitates methods for phylogeny estimation of understudied, rare, and threatened taxa, which often forces researchers to utilize historical collections. The restriction site-associated DNA sequencing (RADseq) family of reduced representation sequence generation has provided a flexible and efficient method for the rapid generation of hundreds to tens of thousands of loci, and has recently seen adoption for phylogeny estimation. However, these methods have been primarily utilized with freshly collected or well preserved tissue. Here we sample all taxa of a genus of rare flowering plants, Chloropyron (Orobanchaceae), from herbarium sheets dating up to 25 yr and use double digest restriction site-associated DNA sequencing (ddRADseq) to resolve intraspecific relationships. We find all species in Chloropyron to be monophyletic, with the inland taxon C. maritimum ssp. canescens sister to the rest of the coastal C. maritimum (ssp. maritimum + ssp. palustre), and the two distinct subspecies of C. molle to be each other's closest relative with strong support. In addition, we demonstrate the utility of reduced representation libraries to address phylogenomic problems in a group of rare species and address pitfalls of accurately inferring relationships when the amount of missing data is large, as is often the case when using historical specimens and rare taxa.

SPhyR: tumor phylogeny estimation from single-cell sequencing data under loss and error.

MotivationCancer is characterized by intra-tumor heterogeneity, the presence of distinct cell populations with distinct complements of somatic mutations, which include single-nucleotide variants (SNVs) and copy-number aberrations (CNAs). Single-cell sequencing technology enables one to study these cell populations at single-cell resolution. Phylogeny estimation algorithms that employ appropriate evolutionary models are key to understanding the evolutionary mechanisms behind intra-tumor heterogeneity.ResultsWe introduce Single-cell Phylogeny Reconstruction (SPhyR), a method for tumor phylogeny estimation from single-cell sequencing data. In light of frequent loss of SNVs due to CNAs in cancer, SPhyR employs the k-Dollo evolutionary model, where a mutation can only be gained once but lost k times. Underlying SPhyR is a novel combinatorial characterization of solutions as constrained integer matrix completions, based on a connection to the cladistic multi-state perfect phylogeny problem. SPhyR outperforms existing methods on simulated data and on a metastatic colorectal cancer.Availability and implementationSPhyR is available on https://github.com/elkebir-group/SPhyR.Supplementary information Supplementary data are available at Bioinformatics online.

Anchored phylogenomics unravels the evolution of spider flies (Diptera, Acroceridae) and reveals discordance between nucleotides and amino acids

The onset of phylogenomics has contributed to the resolution of numerous challenging evolutionary questions while offering new perspectives regarding biodiversity. However, in some instances, analyses of large genomic datasets can also result in conflicting estimates of phylogeny. Here, we present the first phylogenomic scale study of a dipteran parasitoid family, built upon anchored hybrid enrichment and transcriptomic data of 240 loci of 43 ingroup acrocerid taxa. A new hypothesis for the timing of spider fly evolution is proposed, wielding recent advances in divergence time dating, including the fossilized birth-death process to show that the origin of Acroceridae is younger than previously proposed. To test the robustness of our phylogenetic inferences, we analyzed our datasets using different phylogenetic estimation criteria, including supermatrix and coalescent-based approaches, maximum-likelihood and Bayesian methods, combined with other approaches such as permutations of the data, homogeneous versus heterogeneous models, and alternative data and taxon sets. Resulting topologies based on amino acids and nucleotides are both strongly supported but critically discordant, primarily in terms of the monophyly of Panopinae. Conflict was not resolved by controlling for compositional heterogeneity and saturation in third codon positions, which highlights the need for a better understanding of how different biases affect different data sources. In our study, results based on nucleotides were both more robust to alterations of the data and different analytical methods and more compatible with our current understanding of acrocerid morphology and patterns of host usage.

PULLPRU: a practical approach to estimate phylogenies from single nucleotide polymorphism haplotypes under the maximum parsimony criterion

Phylogeny estimation has been the subject of several researches due to its significant importance and numerous applications. The aim of this research is to study the phylogeny estimation from Single Nucleotide Polymorphism (SNP) haplotypes under the maximum parsimony criterion (MPPEP-SNP). Previous exact methods have modeled the mentioned problem as a Mixed Integer Programming (MIP) problem. Since the problem, in general, proved to be NP-hard which causes MIP models to take long runtime for solving large-scale instances, the need for non-exact methods is obvious. In this paper, the authors propose a heuristic algorithm that attempts to find the MPPEP-SNP solution in several stages by solving a specific MIP model in each stage. Created based on network flows formulation, MIP models appearing in each stage are very small; therefore, their exact solutions could be found practically very fast. In order to evaluate the performance of the proposed algorithm, it has been tested on both simulated and real instances and compared with Pars and Flow-RM as two of the best known methods. Our numerical experiments show that the proposed method can compete with the previous methods in terms of accuracy, runtime, and specially the largeness of the solved instances.

Evolution at the tips: Asclepias phylogenomics and new perspectives on leaf surfaces.

Leaf surface traits, such as trichome density and wax production, mediate important ecological processes such as anti-herbivory defense and water-use efficiency. We present a phylogenetic analysis of Asclepias plastomes as a framework for analyzing the evolution of trichome density and presence of epicuticular waxes. We produced a maximum-likelihood phylogeny using plastomes of 103 species of Asclepias. We reconstructed ancestral states and used model comparisons in a likelihood framework to analyze character evolution across Asclepias. We resolved the backbone of Asclepias, placing the Sonoran Desert clade and Incarnatae clade as successive sisters to the remaining species. We present novel findings about leaf surface evolution of Asclepias-the ancestor is reconstructed as waxless and sparsely hairy, a macroevolutionary optimal trichome density is supported, and the rate of evolution of trichome density has accelerated. Increased sampling and selection of best-fitting models of evolution provide more resolved and robust estimates of phylogeny and character evolution than obtained in previous studies. Evolutionary inferences are more sensitive to character coding than model selection.

Evolution on the backbone: Apocynaceae phylogenomics and new perspectives on growth forms, flowers, and fruits.

We provide the largest phylogenetic analyses to date of Apocynaceae in terms of taxa and molecular data as a framework for analyzing the evolution of vegetative and reproductive traits. We produced maximum-likelihood phylogenies of Apocynaceae using 21 plastid loci sampled from 1045 species (nearly 25% of the family) and complete plastomes from 73 species. We reconstructed ancestral states and used model comparisons in a likelihood framework to analyze character evolution across Apocynaceae. We obtained a well-supported phylogeny of Apocynaceae, resolving poorly understood tribal and subtribal relationships (e.g., among Amsonieae and Hunterieae, within Asclepiadeae), rejecting monophyly of Melodineae and Odontadenieae, and placing previously unsampled and enigmatic taxa (e.g., Pycnobotrya). We provide new insights into the evolution of Apocynaceae, including frequent shifts between herbaceousness and woodiness, reversibility of twining, integrated evolution of the corolla and gynostegium, and ancestral baccate fruits. Increased sampling and selection of best-fitting models of evolution provide more resolved and robust estimates of phylogeny and character evolution than obtained in previous studies. Evolutionary inferences are sensitive to choice of phylogenetic frameworks and models.

Delimiting Coalescence Genes (C-Genes) in Phylogenomic Data Sets.

Summary coalescence methods have emerged as a popular alternative for inferring species trees with large genomic datasets, because these methods explicitly account for incomplete lineage sorting. However, statistical consistency of summary coalescence methods is not guaranteed unless several model assumptions are true, including the critical assumption that recombination occurs freely among but not within coalescence genes (c-genes), which are the fundamental units of analysis for these methods. Each c-gene has a single branching history, and large sets of these independent gene histories should be the input for genome-scale coalescence estimates of phylogeny. By contrast, numerous studies have reported the results of coalescence analyses in which complete protein-coding sequences are treated as c-genes even though exons for these loci can span more than a megabase of DNA. Empirical estimates of recombination breakpoints suggest that c-genes may be much shorter, especially when large clades with many species are the focus of analysis. Although this idea has been challenged recently in the literature, the inverse relationship between c-gene size and increased taxon sampling in a dataset—the ‘recombination ratchet’—is a fundamental property of c-genes. For taxonomic groups characterized by genes with long intron sequences, complete protein-coding sequences are likely not valid c-genes and are inappropriate units of analysis for summary coalescence methods unless they occur in recombination deserts that are devoid of incomplete lineage sorting (ILS). Finally, it has been argued that coalescence methods are robust when the no-recombination within loci assumption is violated, but recombination must matter at some scale because ILS, a by-product of recombination, is the raison d’etre for coalescence methods. That is, extensive recombination is required to yield the large number of independently segregating c-genes used to infer a species tree. If coalescent methods are powerful enough to infer the correct species tree for difficult phylogenetic problems in the anomaly zone, where concatenation is expected to fail because of ILS, then there should be a decreasing probability of inferring the correct species tree using longer loci with many intralocus recombination breakpoints (i.e., increased levels of concatenation).

Evidence that Myotis lucifugus "Subspecies" are Five Nonsister Species, Despite Gene Flow.

While genetic exchange between nonsister species was traditionally considered to be rare in mammals, analyses of molecular data in multiple systems suggest that it may be common. Interspecific gene flow, if present, is problematic for phylogenetic inference, particularly for analyses near the species level. Here, we explore how to detect and account for gene flow during phylogeny estimation using data from a clade of North American Myotis bats where previous results have led researchers to suspect that gene flow among lineages is present. Initial estimates of phylogenetic networks and species trees indicate that subspecies described within Myotis lucifugus are paraphyletic. In order to explore the extent to which gene flow is likely to interfere with phylogeny estimation, we use posterior predictive simulation and a novel Approximate Bayesian Computation approach based on gene tree distances. The former indicates that the species tree model is a poor fit to the data, and the latter provides evidence that a species tree with gene flow is a better fit. Taken together, we present evidence that the currently recognized M. lucifugus subspecies are paraphyletic, exchange alleles with other Myotis species in regions of secondary contact, and should be considered independent evolutionary lineages despite their morphological similarity.