Phylogenetic Problems Research Articles

Targeted NGS for species level phylogenomics: "made to measure" or "one size fits all"?

Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations. The targets in question can either be adopted directly from more or less universal tools, or custom made for particular clades at considerably greater effort. We applied custom made scripts to select sets of homologous sequence markers from transcriptome and WGS data for use in the flowering plant genus Erica (Ericaceae). We compared the resulting targets to those that would be selected both using different available tools (Hyb-Seq; MarkerMiner), and when optimising for broader clades of more distantly related taxa (Ericales; eudicots). Approaches comparing more divergent genomes (including MarkerMiner, irrespective of input data) delivered fewer and shorter potential markers than those targeted for Erica. The latter may nevertheless be effective for sequence capture across the wider family Ericaceae. We tested the targets delivered by our scripts by obtaining an empirical dataset. The resulting sequence variation was lower than that of standard nuclear ribosomal markers (that in Erica fail to deliver a well resolved gene tree), confirming the importance of maximising the lengths of individual markers. We conclude that rather than searching for “one size fits all” universal markers, we should improve and make more accessible the tools necessary for developing “made to measure” ones.

Cartography of Tree Space

How can vibrant, contemporary art be produced that deals with vibrant, contemporary mathematics? To address this question, a collaboration began between an artist (Schuh) and a mathematician (Devadoss), revolving around recent problems in phylogenetics and the space of evolutionary trees. The result was twofold: First, a triptych of paintings was created, using acrylic, graphite, watercolor and metal leaf, that focused on different navigations within this tree space. Second, a novel set of open mathematics problems was discovered solely as a result of this investigation.

Anthopleura and the phylogeny of Actinioidea (Cnidaria: Anthozoa: Actiniaria)

Members of the sea anemone genus Anthopleura are familiar constituents of rocky intertidal communities. Despite its familiarity and the number of studies that use its members to understand ecological or biological phenomena, the diversity and phylogeny of this group are poorly understood. Many of the taxonomic and phylogenetic problems stem from problems with the documentation and interpretation of acrorhagi and verrucae, the two features that are used to recognize members of Anthopleura. These anatomical features have a broad distribution within the superfamily Actinioidea, and their occurrence and exclusivity are not clear. We use DNA sequences from the nucleus and mitochondrion and cladistic analysis of verrucae and acrorhagi to test the monophyly of Anthopleura and to evaluate the pattern of distribution of acrorhagi and verrucae. We find that Anthopleura is paraphyletic: although species of the genus cluster together, some groups also include members of genera like Bunodosoma, Aulactinia, Oulactis, and Actinia. This paraphyly is explained in part by the discovery that acrorhagi and verrucae are pleisiomorphic for the subset of Actinioidea studied.

The genus Syllis Savigny in Lamarck, 1818 (Annelida: Syllidae: Syllinae) from Australia (second part): four new species and re-description of twelve previously described species.

Syllis Savigny in Lamarck, 1818, the type genus of Syllidae, is the largest and most diverse within the family. This genus presents many taxonomic and phylogenetic problems due mainly to the lack of molecular data and morphological synapomorphies for many of the species, but also to poor or inadequate descriptions. In order to improve the knowledge of the genus, we have undertaken a morphological revision of Australian species, based on type material and material from the Australian Museum. Sixteen species are herein described, of which four are new and twelve are redescriptions of alreadyknown species, with six new combinations: Syllis boggemanni, n. sp.; S. joaoi, n. sp.; S. karlae, n. sp.; S. marceloi, n. sp.; S. albanyensis (Hartmann-Schröder, 1984) n. comb.; S. erikae (Hartmann-Schröder, 1981) n. comb.; S. krohnii Ehlers 1864; S. lunaris (Imajima, 1966) n. comb.; S. lutea (Hartmann-Schröder, 1960); S. macrodentata (Hartmann-Schröder, 1982) n. comb.; S. monilaris Savigny in Lamarck, 1818; S. nigropunctata Haswell, 1886; S. pectinans Haswell, 1920; S. rosea (Langerhans, 1879); S. warrnamboolensis (Hartmann-Schröder, 1987) n. comb.; and S. yallingupensis (Hartmann-Schröder, 1982), n. comb.

A practical exact maximum compatibility algorithm for reconstruction of recent evolutionary history

BackgroundMaximum compatibility is a method of phylogenetic reconstruction that is seldom applied to molecular sequences. It may be ideal for certain applications, such as reconstructing phylogenies of closely-related bacteria on the basis of whole-genome sequencing.ResultsHere I present an algorithm that rapidly computes phylogenies according to a compatibility criterion. Although based on solutions to the maximum clique problem, this algorithm deals properly with ambiguities in the data. The algorithm is applied to bacterial data sets containing up to nearly 2000 genomes with several thousand variable nucleotide sites. Run times are several seconds or less. Computational experiments show that maximum compatibility is less sensitive than maximum parsimony to the inclusion of nucleotide data that, though derived from actual sequence reads, has been identified as likely to be misleading.ConclusionsMaximum compatibility is a useful tool for certain phylogenetic problems, such as inferring the relationships among closely-related bacteria from whole-genome sequence data. The algorithm presented here rapidly solves fairly large problems of this type, and provides robustness against misleading characters than can pollute large-scale sequencing data.

The ups and downs of amphioxus biology: a history.

Humans (at least a select few) have long known about the cephalochordate amphioxus, first as something to eat and later as a subject for scientific study. The rate of publication on these animals has waxed and waned several times. The first big surge, in the late nineteenth century, was stimulated by Darwin's evolutionary ideas and by Kowalevsky's embryologic findings suggesting that an amphioxus-like creature might have bridged the gap between the invertebrates and the vertebrates. Interest declined sharply in the early twentieth century and remained low for the next 50 years. An important contributing factor (in addition to inhibition by two world wars and the Great Depression) was the indifference of the new evolutionary synthesis toward broad phylogenetic problems like the origin of the vertebrates. Then, during the 1960s and 1970s, interest in amphioxus resurged, driven especially by increased government support for basic science as well as opportunities presented by electron microscopy. After faltering briefly in the 1980s (electron microscopists were running out of amphioxus tissues to study), a third and still-continuing period of intensive amphioxus research began in the early 1990s, stimulated by the advent of evolutionary developmental biology (evo-devo) and genomics. The volume of studies peaked in 2008 with the publication of the genome of the Florida amphioxus. Since then, although the number of papers per year has dropped somewhat, sequencing of additional genomes and transcriptomes of several species of amphioxus (both in the genus Branchiostoma and in a second genus, Asymmetron) is providing the raw material for addressing the major unanswered question of the relationship between genotype and phenotype.

Leaf and stem anatomy and essential oil composition of four Brazilian Aldama species (Asteraceae) and their taxonomic significance

Aldama La Llave is one of several Asteraceae genera that pose phylogenetic problems. The close similarity between species, as well as the inconsistencies found in the most recent phylogenetic analysis, shows that new data are needed to help delimit group species. Aldama anchusifolia (DC) E.E.Schill. & Panero, Aldama megapotamica (Malme) Magenta & Pirani, Aldama nudibasilaris (S.F.Blake) E.E.Schill. & Panero and Aldama pilosa (Baker) E.E.Schill. & Panero are difficult to identify because they are very closely related. Therefore, the aim of this study was to detect anatomical and phytochemical characteristics to help elucidate phylogenetic issues raised by Aldama. Aerial vegetative organs were prepared using the standard histological techniques. Essential oils were obtained by hydrodistillation, and their components identified using a gas chromatograph coupled to a mass spectrometer and flame ionization detector. Each species presented a set of unique leaf and stem anatomical features. The front view of the epidermal cell walls in the leaves, the presence of secretory ducts in the phloem and medulla sclerification in the stems proved useful in delimiting these species. The essential oils were characterized by the predominance of sesquiterpenes such as t-caryophyllene, germacrene D and bicyclogermacrene. Some unique constituents in each species were also identified as potential chemical markers.

Molecules, morphology, and phylogeny

A complicated, almost conflicting situation exists in contemporary biology, i.e., there are two scientific concepts in existence that solve some phylogenetic problems in a different way. These concepts are evolutionary morphology and molecular biology. Modern biology urgently needs these contradictions to be examined and removed.

Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction.

BackgroundInferring species trees from gene trees using the coalescent-based summary methods has been the subject of much attention, yet new scalable and accurate methods are needed.ResultsWe introduce DISTIQUE, a new statistically consistent summary method for inferring species trees from gene trees under the coalescent model. We generalize our results to arbitrary phylogenetic inference problems; we show that two arbitrarily chosen leaves, called anchors, can be used to estimate relative distances between all other pairs of leaves by inferring relevant quartet trees. This results in a family of distance-based tree inference methods, with running times ranging between quadratic to quartic in the number of leaves.ConclusionsWe show in simulated studies that DISTIQUE has comparable accuracy to leading coalescent-based summary methods and reduced running times.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3098-z) contains supplementary material, which is available to authorized users.

Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye.

BackgroundFlatfish cranial asymmetry represents one of the most remarkable morphological innovations among vertebrates, and has fueled vigorous debate on the manner and rate at which strikingly divergent phenotypes evolve. A surprising result of many recent molecular phylogenetic studies is the lack of support for flatfish monophyly, where increasingly larger DNA datasets of up to 23 loci have either yielded a weakly supported flatfish clade or indicated the group is polyphyletic. Lack of resolution for flatfish relationships has been attributed to analytical limitations for dealing with processes such as nucleotide non-stationarity and incomplete lineage sorting (ILS). We tackle this phylogenetic problem using a sequence dataset comprising more than 1,000 ultraconserved DNA element (UCE) loci covering 45 carangimorphs, the broader clade containing flatfishes and several other specialized lineages such as remoras, billfishes, and archerfishes.ResultsWe present a phylogeny based on UCE loci that unequivocally supports flatfish monophyly and a single origin of asymmetry. We document similar levels of discordance among UCE loci as in previous, smaller molecular datasets. However, relationships among flatfishes and carangimorphs recovered from multilocus concatenated and species tree analyses of our data are robust to the analytical framework applied and size of data matrix used. By integrating the UCE data with a rich fossil record, we find that the most distinctive carangimorph bodyplans arose rapidly during the Paleogene (66.0–23.03 Ma). Flatfish asymmetry, for example, likely evolved over an interval of no more than 2.97 million years.ConclusionsThe longstanding uncertainty in phylogenetic hypotheses for flatfishes and their carangimorph relatives highlights the limitations of smaller molecular datasets when applied to successive, rapid divergences. Here, we recovered significant support for flatfish monophyly and relationships among carangimorphs through analysis of over 1,000 UCE loci. The resulting time-calibrated phylogeny points to phenotypic divergence early within carangimorph history that broadly matches with the predictions of adaptive models of lineage diversification.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0786-x) contains supplementary material, which is available to authorized users.

Tanglegrams: A Reduction Tool for Mathematical Phylogenetics.

Many discrete mathematics problems in phylogenetics are defined in terms of the relative labeling of pairs of leaf-labeled trees. These relative labelings are naturally formalized as tanglegrams, which have previously been an object of study in coevolutionary analysis. Although there has been considerable work on planar drawings of tanglegrams, they have not been fully explored as combinatorial objects until recently. In this paper, we describe how many discrete mathematical questions on trees "factor" through a problem on tanglegrams, and how understanding that factoring can simplify analysis. Depending on the problem, it may be useful to consider a unordered version of tanglegrams, and/or their unrooted counterparts. For all of these definitions, we show how the isomorphism types of tanglegrams can be understood in terms of double cosets of the symmetric group, and we investigate their automorphisms. Understanding tanglegrams better will isolate the distinct problems on leaf-labeled pairs of trees and reveal natural symmetries of spaces associated with such problems.

Stock Selection as a Problem in Phylogenetics—Evidence from the ASX

We report the results of fifteen sets of portfolio selection simulations using stocks in the ASX200 index for the period May 2000 to December 2013. We investigated five portfolio selection methods, random selection, selection within industrial groups, and three based on neighbor-Net phylogenetic networks. We report that using random, industrial groups, or neighbor-Net phylogenetic networks alone rarely produced statistically significant reduction in risk, though in four out of the five cases in which it did so, the portfolios selected using the phylogenetic networks had the lowest risk. However, we report that when using the neighbor-Net phylogenetic networks in combination with industry group selection that substantial reductions in portfolio return spread were achieved.

Progress, pitfalls and parallel universes: a history of insect phylogenetics.

The phylogeny of insects has been both extensively studied and vigorously debated for over a century. A relatively accurate deep phylogeny had been produced by 1904. It was not substantially improved in topology until recently when phylogenomics settled many long-standing controversies. Intervening advances came instead through methodological improvement. Early molecular phylogenetic studies (1985-2005), dominated by a few genes, provided datasets that were too small to resolve controversial phylogenetic problems. Adding to the lack of consensus, this period was characterized by a polarization of philosophies, with individuals belonging to either parsimony or maximum-likelihood camps; each largely ignoring the insights of the other. The result was an unfortunate detour in which the few perceived phylogenetic revolutions published by both sides of the philosophical divide were probably erroneous. The size of datasets has been growing exponentially since the mid-1980s accompanied by a wave of confidence that all relationships will soon be known. However, large datasets create new challenges, and a large number of genes does not guarantee reliable results. If history is a guide, then the quality of conclusions will be determined by an improved understanding of both molecular and morphological evolution, and not simply the number of genes analysed.

EmpPrior: using outside empirical data to inform branch-length priors for Bayesian phylogenetics.

BackgroundBranch-length parameters are a central component of phylogenetic models and of intrinsic biological interest. Default branch-length priors in some Bayesian phylogenetic software can be unintentionally informative and lead to branch- and tree-length estimates that are unreasonable. Alternatively, priors may be uninformative, but lead to diffuse posterior estimates. Despite the widespread availability of relevant datasets from other groups, biologists rarely leverage outside information to specify branch-length priors that are specific to the analysis they are conducting.ResultsWe developed the software package EmpPrior to facilitate the collection and incorporation of relevant, outside information when setting branch-length priors for phylogenetics. EmpPrior efficiently queries TreeBASE to find data that are similar to focal data, in terms of taxonomic and genetic sampling, and uses them to inform branch-length priors for the focal analysis. EmpPrior consists of two components: EmpPrior-search, written in Java to query TreeBASE, and EmpPrior-fit, written in R to parameterize branch-length distributions. In an example analysis, we show how the use of relevant, outside data is made possible by EmpPrior and improves tree-length estimates from a focal dataset.ConclusionEmpPrior is easy to use, fast, and improves both the accuracy and precision of branch-length estimates in many circumstances. While EmpPrior’s focus is on branch lengths, the strategy it employs could easily be extended to address other prior parameterization problems in phylogenetics.

Application of multigene phylogenetics and site-stripping to resolve intraordinal relationships in the Rhodymeniales (Rhodophyta).

Previous molecular assessments of the red algalorder Rhodymeniales have confirmed its monophyly and distinguished the six currently recognized families (viz. Champiaceae, Faucheaceae, Fryeellaceae, Hymenocladiaceae, Lomentariaceae, and Rhodymeniaceae); however, relationships among most of these families have remained unresolved possibly as a result of substitution saturation at deeper phylogenetic nodes. The objective of the current study was to improve rhodymenialean systematics by increasing taxonomic representation and using a more robust multigene dataset of mitochondrial (COB, COI/COI-5P), nuclear (LSU, EF2) and plastid markers (psbA, rbcL). Additionally, we aimed to prevent phylogenetic inference problems associated with substitution saturation (particularly at the interfamilial nodes) by removing fast-evolving sites and analyzing a series of progressively more conservative alignments. The Rhodymeniales was resolved as two major lineages: (i) the Fryeellaceae as sister to the Faucheaceae and Lomentariaceae; and (ii) the Rhodymeniaceae allied to the Champiaceae and Hymenocladiaceae. Support at the interfamilial nodes was highest when 20% ofvariable sites were removed. Inclusion of Binghamiopsis, Chamaebotrys, and Minium, which wereabsent in previous phylogenetic investigations, established their phylogenetic affinities while assessment of two genera consistently polyphyletic in phylogenetic analyses, Erythrymenia and Lomentaria, resulted in the proposition of the novel genera Perbella and Fushitsunagia. The taxonomic position of Drouetia was reinvestigated with re-examination ofholotype material of D.coalescens to clarify tetrasporangial development in this genus. In addition, we added three novel Australian species to Drouetia as a result of ongoing DNA barcoding assessments-D.aggregata sp. nov., D.scutellata sp. nov., and D.viridescens sp. nov.

Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods

Rapid evolutionary radiations are expected to require large amounts of sequence data to resolve. To resolve these types of relationships many systematists believe that it will be necessary to collect data by next-generation sequencing (NGS) and use multispecies coalescent ("species tree") methods. Ultraconserved element (UCE) sequence capture is becoming a popular method to leverage the high throughput of NGS to address problems in vertebrate phylogenetics. Here we examine the performance of UCE data for gallopheasants (true pheasants and allies), a clade that underwent a rapid radiation 10-15 Ma. Relationships among gallopheasant genera have been difficult to establish. We used this rapid radiation to assess the performance of species tree methods, using ∼600 kilobases of DNA sequence data from ∼1500 UCEs. We also integrated information from traditional markers (nuclear intron data from 15 loci and three mitochondrial gene regions). Species tree methods exhibited troubling behavior. Two methods [Maximum Pseudolikelihood for Estimating Species Trees (MP-EST) and Accurate Species TRee ALgorithm (ASTRAL)] appeared to perform optimally when the set of input gene trees was limited to the most variable UCEs, though ASTRAL appeared to be more robust than MP-EST to input trees generated using less variable UCEs. In contrast, the rooted triplet consensus method implemented in Triplec performed better when the largest set of input gene trees was used. We also found that all three species tree methods exhibited a surprising degree of dependence on the program used to estimate input gene trees, suggesting that the details of likelihood calculations (e.g., numerical optimization) are important for loci with limited phylogenetic information. As an alternative to summary species tree methods we explored the performance of SuperMatrix Rooted Triple - Maximum Likelihood (SMRT-ML), a concatenation method that is consistent even when gene trees exhibit topological differences due to the multispecies coalescent. We found that SMRT-ML performed well for UCE data. Our results suggest that UCE data have excellent prospects for the resolution of difficult evolutionary radiations, though specific attention may need to be given to the details of the methods used to estimate species trees.

A navigation system for tree space

The reconstruction of evolutionary trees from data sets on overlapping sets of species is a central problem in phylogenetics. Provided that the tree reconstructed for each subset of species is rooted and that these trees fit together consistently, the space of all parent trees that 'display' these trees was recently shown to satisfy the following strong property: there exists a path from any one parent tree to any other parent tree by a sequence of local rearrangements (nearest neighbour interchanges) so that each intermediate tree also lies in this same tree space. However, the proof of this result uses a non-constructive argument. In this paper we describe a specific, polynomial-time procedure for navigating from any given parent tree to another while remaining in this tree space. The results are of particular relevance to the recent study of 'phylogenetic terraces'.

Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae).

The anomaly zone, defined by the presence of gene tree topologies that are more probable than the true species tree, presents a major challenge to the accurate resolution of many parts of the Tree of Life. This discrepancy can result from consecutive rapid speciation events in the species tree. Similar to the problem of long-branch attraction, including more data via loci concatenation will only reinforce the support for the incorrect species tree. Empirical phylogenetic studies often employ coalescent-based species tree methods to avoid the anomaly zone, but to this point these studies have not had a method for providing any direct evidence that the species tree is actually in the anomaly zone. In this study, we use 16 species of lizards in the family Scincidae to investigate whether nodes that are difficult to resolve place the species tree within the anomaly zone. We analyze new phylogenomic data (429 loci), using both concatenation and coalescent-based species tree estimation, to locate conflicting topological signal. We then use the unifying principle of the anomaly zone, together with estimates of ancestral population sizes and species persistence times, to determine whether the observed phylogenetic conflict is a result of the anomaly zone. We identify at least three regions of the Scincidae phylogeny that provide demographic signatures consistent with the anomaly zone, and this new information helps reconcile the phylogenetic conflict in previously published studies on these lizards. The anomaly zone presents a real problem in phylogenetics, and our new framework for identifying anomalous relationships will help empiricists leverage their resources appropriately for investigating and overcoming this challenge.

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference.

Placental mammals comprise three principal clades: Afrotheria (e.g., elephants and tenrecs), Xenarthra (e.g., armadillos and sloths), and Boreoeutheria (all other placental mammals), the relationships among which are the subject of controversy and a touchstone for debate on the limits of phylogenetic inference. Previous analyses have found support for all three hypotheses, leading some to conclude that this phylogenetic problem might be impossible to resolve due to the compounded effects of incomplete lineage sorting (ILS) and a rapid radiation. Here we show, using a genome scale nucleotide data set, microRNAs, and the reanalysis of the three largest previously published amino acid data sets, that the root of Placentalia lies between Atlantogenata and Boreoeutheria. Although we found evidence for ILS in early placental evolution, we are able to reject previous conclusions that the placental root is a hard polytomy that cannot be resolved. Reanalyses of previous data sets recover Atlantogenata + Boreoeutheria and show that contradictory results are a consequence of poorly fitting evolutionary models; instead, when the evolutionary process is better-modeled, all data sets converge on Atlantogenata. Our Bayesian molecular clock analysis estimates that marsupials diverged from placentals 157–170 Ma, crown Placentalia diverged 86–100 Ma, and crown Atlantogenata diverged 84–97 Ma. Our results are compatible with placental diversification being driven by dispersal rather than vicariance mechanisms, postdating early phases in the protracted opening of the Atlantic Ocean.

The mitochondrial genome of Murina huttoni rubella (Chiroptera: Vespertilionidae) from China

Murina huttoni rubella is a common Murina species in China, with a medium forearm length and reddish brown hairs. In this study, based on a male M. h. rubella individual from Jiangxi, China, its complete mitochondrial genome was sequenced and analyzed. The genome is 16,707 bp in length, including 22 tRNA genes, two rRNA genes, 13 protein-coding genes and a control region. The composition and arrangement of genes are similar to other bats. Phylogenetic trees that covered all released complete mitochondrial genome of bats were constructed using Bayesian Inference and maximum likelihood methods. Both phylogenetic results showed that M. h. rubella and M. ussuriensis have closer phylogenetic relationship. The complete mtDNA genome sequence of M. h. rubella would provide valuable information for solving taxonomic and phylogenetic problem in future.