scholarly journals Mind the Outgroup: Influence of Taxon Sampling on Total-Evidence Dating of Pimpliform Parasitoid Wasps (Hymenoptera, Ichneumonidae)

2019 ◽  
Author(s):  
Tamara Spasojevic ◽  
Gavin R. Broad ◽  
Ilari E. Sääksjärvi ◽  
Martin Schwarz ◽  
Masato Ito ◽  
...  
Keyword(s):  
Molecular Dating ◽  
Total Evidence ◽  
Morphological Data ◽  
Phylogenetic Study ◽  
Taxon Sampling ◽  
Parasitoid Wasps ◽  
Crown Group ◽  
The Family ◽  
The Impact ◽  
Age Estimates

ABSTRACTTaxon sampling is a central aspect of phylogenetic study design, but it has received limited attention in the context of molecular dating and especially in the framework of total-evidence dating, a widely used dating approach that directly integrates molecular and morphological information from extant and fossil taxa. We here assess the impact of different outgroup sampling schemes on age estimates in a total-evidence dating analysis under the uniform tree prior. Our study group are Pimpliformes, a highly diverse, rapidly radiating group of parasitoid wasps of the family Ichneumonidae. We cover 201 extant and 79 fossil taxa, including the oldest fossils of the family from the Early Cretaceous and the first unequivocal representatives of extant subfamilies from the mid Paleogene. Based on newly compiled molecular data from ten nuclear genes and a morphological matrix that includes 222 characters, we show that age estimates become both older and less precise with the inclusion of more distant and more poorly sampled outgroups. In addition, we discover an artefact that might be detrimental for total-evidence dating: “bare-branch attraction”, namely high attachment probabilities of, especially, older fossils to terminal branches for which morphological data are missing. After restricting outgroup sampling and adding morphological data for the previously attracting, bare branches, we recover a Middle and Early Jurassic origin for Pimpliformes and Ichneumonidae, respectively. This first age estimate for the group not only suggests an older origin than previously thought, but also that diversification of the crown group happened before the Cretaceous-Paleogene boundary. Our case study demonstrates that in order to obtain robust age estimates, total-evidence dating studies need to be based on a thorough and balanced sampling of both extant and fossil taxa, with the aim of minimizing evolutionary rate heterogeneity and missing morphological information.

scholarly journals Mind the Outgroup and Bare Branches in Total-Evidence Dating: a Case Study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae)

2020 ◽  
Author(s):  
Tamara Spasojevic ◽  
Gavin R Broad ◽  
Ilari E Sääksjärvi ◽  
Martin Schwarz ◽  
Masato Ito ◽  
...  
Keyword(s):  
Evolutionary Rate ◽  
Total Evidence ◽  
Morphological Data ◽  
Phylogenetic Study ◽  
Phylogenetic Distance ◽  
Rate Heterogeneity ◽  
The Family ◽  
The Impact ◽  
Age Estimates

Abstract Taxon sampling is a central aspect of phylogenetic study design, but it has received limited attention in the context of total-evidence dating, a widely used dating approach that directly integrates molecular and morphological information from extant and fossil taxa. We here assess the impact of commonly employed outgroup sampling schemes and missing morphological data in extant taxa on age estimates in a total-evidence dating analysis under the uniform tree prior. Our study group is Pimpliformes, a highly diverse, rapidly radiating group of parasitoid wasps of the family Ichneumonidae. We analyze a data set comprising 201 extant and 79 fossil taxa, including the oldest fossils of the family from the Early Cretaceous and the first unequivocal representatives of extant subfamilies from the mid Paleogene. Based on newly compiled molecular data from ten nuclear genes and a morphological matrix that includes 222 characters, we show that age estimates become both older and less precise with the inclusion of more distant and more poorly sampled outgroups. These outgroups not only lack morphological and temporal information, but also sit on long terminal branches and considerably increase the evolutionary rate heterogeneity. In addition, we discover an artefact that might be detrimental for total-evidence dating: “bare-branch attraction”, namely high attachment probabilities of certain fossils to terminal branches for which morphological data are missing. Using computer simulations, we confirm the generality of this phenomenon and show that a large phylogenetic distance to any of the extant taxa, rather than just older age, increases the risk of a fossil being misplaced due to bare-branch attraction. After restricting outgroup sampling and adding morphological data for the previously attracting, bare branches, we recover a Jurassic origin for Pimpliformes and Ichneumonidae. This first age estimate for the group not only suggests an older origin than previously thought, but also that diversification of the crown group happened well before the Cretaceous-Paleogene boundary. Our case study demonstrates that in order to obtain robust age estimates, total-evidence dating studies need to be based on a thorough and balanced sampling of both extant and fossil taxa, with the aim of minimizing evolutionary rate heterogeneity and missing morphological information.

scholarly journals The Influence of Taxon Sampling and Tree Shape on Molecular Dating: An Empirical Example from Mammalian Mitochondrial Genomes

2012 ◽  
Vol 6 ◽  
pp. BBI.S9677 ◽  
Author(s):  
André E.R. Soares ◽  
Carlos G. Schrago
Keyword(s):  
Divergence Time ◽  
Molecular Dating ◽  
Taxon Sampling ◽  
Mitochondrial Genomes ◽  
Tree Shape ◽  
Topological Parameters ◽  
Divergence Time Estimates ◽  
Taxonomic Sampling ◽  
The Impact ◽  
Age Estimates

Over the last decade, molecular dating methods have been among the most studied subjects in statistical phylogenetics. Although the evolutionary modelling of substitution rates and the handling of calibration information are the primary focus of species divergence time research, parameters that influence topological estimation, such as taxon sampling and tree shape, also have the potential to influence evolutionary age estimates. However, the impact of topological parameters on chronological estimates is rarely considered. In this study, we use mitochondrial genomes to evaluate the influence of tree shape and taxon sampling on the divergence times of selected nodes of the mammalian tree. Our results show that taxon sampling affects divergence time estimates; the credibility intervals for age estimates decrease as taxonomic sampling increases (i.e., estimates become more precise). The influence of taxonomic sampling was not observed on nodes that lay deep in the mammalian phylogeny, although the means of the posterior distributions tend to converge with increased taxon sampling, an effect that is independent of the location of the node. In the majority of cases, the effect of tree shape was negligible.

A molecular phylogeny of Callianassidae and related families (Crustacea : Decapoda : Axiidea) with morphological support

2020 ◽  
Vol 34 (2) ◽  
pp. 113 ◽  
Author(s):  
Rafael Robles ◽  
Peter C. Dworschak ◽  
Darryl L. Felder ◽  
Gary C. B. Poore ◽  
Fernando L. Mantelatto
Keyword(s):  
Bayesian Analysis ◽  
Molecular Analysis ◽  
Single Species ◽  
Molecular Data ◽  
Total Evidence ◽  
Morphological Data ◽  
12S Rrna ◽  
New Genera ◽  
Key Species ◽  
The Family

The axiidean families Callianassidae and Ctenochelidae, sometimes treated together as Callianassoidea, are shown to represent a monophyletic taxon. It comprises 265 accepted species in 74 genera, twice this number of species if fossil taxa are included. The higher taxonomy of the group has proved difficult and fluid. In a molecular phylogenetic approach, we inferred evolutionary relationships from a maximum-likelihood (ML) and Bayesian analysis of four genes, mitochondrial 16S rRNA and 12S rRNA along with nuclear histone H3 and 18S rRNA. Our sample consisted of 298 specimens representing 123 species plus two species each of Axiidae and Callianideidae serving as outgroups. This number represented about half of all known species, but included 26 species undescribed or not confidently identified, 9% of all known. In a parallel morphological approach, the published descriptions of all species were examined and detailed observations made on about two-thirds of the known fauna in museum collections. A DELTA (Description Language for Taxonomy), database of 135 characters was made for 195 putative species, 18 of which were undescribed. A PAUP analysis found small clades coincident with the terminal clades found in the molecular treatment. Bayesian analysis of a total-evidence dataset combined elements of both molecular and morphological analyses. Clades were interpreted as seven families and 53 genera. Seventeen new genera are required to reflect the molecular and morphological phylograms. Relationships between the families and genera inferred from the two analyses differed between the two strategies in spite of retrospective searches for morphological features supporting intermediate clades. The family Ctenochelidae was recovered in both analyses but the monophyly of Paragourretia was not supported by molecular data. The hitherto well recognised family Eucalliacidae was found to be polyphyletic in the molecular analysis, but the family and its genera were well defined by morphological synapomorphies. The phylogram for Callianassidae suggested the isolation of several species from the genera to which they had traditionally been assigned and necessitated 12 new generic names. The same was true for Callichiridae, with stronger ML than Bayesian support, and five new genera are proposed. Morphological data did not reliably reflect generic relationships inferred from the molecular analysis though they did diagnose terminal taxa treated as genera. We conclude that discrepancies between molecular and morphological analyses are due at least in part to missing sequences for key species, but no less to our inability to recognise unambiguously informative morphological synapomorphies. The ML analysis revealed the presence of at least 10 complexes wherein 2–4 cryptic species masquerade under single species names.

scholarly journals Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses

2016 ◽  
Vol 12 (5) ◽  
pp. 20151003 ◽  
Author(s):  
Thomas Guillerme ◽  
Natalie Cooper
Keyword(s):  
Data Collection ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Total Evidence ◽  
Morphological Data ◽  
Living Species ◽  
Anatomical Characters ◽  
The Impact

Analyses of living and fossil taxa are crucial for understanding biodiversity through time. The total evidence method allows living and fossil taxa to be combined in phylogenies, using molecular data for living taxa and morphological data for living and fossil taxa. With this method, substantial overlap of coded anatomical characters among living and fossil taxa is vital for accurately inferring topology. However, although molecular data for living species are widely available, scientists generating morphological data mainly focus on fossils. Therefore, there are fewer coded anatomical characters in living taxa, even in well-studied groups such as mammals. We investigated the number of coded anatomical characters available in phylogenetic matrices for living mammals and how these were phylogenetically distributed across orders. Eleven of 28 mammalian orders have less than 25% species with available characters; this has implications for the accurate placement of fossils, although the issue is less pronounced at higher taxonomic levels. In most orders, species with available characters are randomly distributed across the phylogeny, which may reduce the impact of the problem. We suggest that increased morphological data collection efforts for living taxa are needed to produce accurate total evidence phylogenies.

scholarly journals Undersampling Taxa Will Underestimate Molecular Divergence Dates: An Example from the South American Lizard Clade Liolaemini

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
James A. Schulte
Keyword(s):  
Divergence Time ◽  
Penalized Likelihood ◽  
Molecular Data ◽  
Molecular Dating ◽  
Taxon Sampling ◽  
South American ◽  
The South ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Age Estimates

Methods for estimating divergence times from molecular data have improved dramatically over the past decade, yet there are few studies examining alternative taxon sampling effects on node age estimates. Here, I investigate the effect of undersampling species diversity on node ages of the South American lizard clade Liolaemini using several alternative subsampling strategies for both time calibrations and taxa numbers. Penalized likelihood (PL) and Bayesian molecular dating analyses were conducted on a densely sampled (202 taxa) mtDNA-based phylogenetic hypothesis of Iguanidae, including 92 Liolaemini species. Using all calibrations and penalized likelihood, clades with very low taxon sampling had node age estimates younger than clades with more complete taxon sampling. The effect of Bayesian and PL methods differed when either one or two calibrations only were used with dense taxon sampling. Bayesian node ages were always older when fewer calibrations were used, whereas PL node ages were always younger. This work reinforces two important points: (1) whenever possible, authors should strongly consider adding as many taxa as possible, including numerous outgroups, prior to node age estimation to avoid considerable node age underestimation and (2) using more, critically assessed, and accurate fossil calibrations should yield improved divergence time estimates.

scholarly journals Resurrecting the genus Geomorium: Systematic study of fungi in the genera Underwoodia and Gymnohydnotrya (Pezizales) with the description of three new South American species

2020 ◽  
Vol 44 (1) ◽  
pp. 98-112
Author(s):  
N. Kraisitudomsook ◽  
R.A. Healy ◽  
D.H. Pfister ◽  
C. Truong ◽  
E. Nouhra ◽  
...  
Keyword(s):  
South America ◽  
Southern Hemisphere ◽  
Phylogenetic Analyses ◽  
Systematic Position ◽  
Fungal Species ◽  
Molecular Dating ◽  
Phylogenetic Study ◽  
South American Species ◽  
New Family ◽  
The Family

Molecular phylogenetic analyses have addressed the systematic position of several major Northern Hemisphere lineages of Pezizales but the taxa of the Southern Hemisphere remain understudied. This study focuses on the molecular systematics and taxonomy of Southern Hemisphere species currently treated in the genera Underwoodia and Gymnohydnotrya. Species in these genera have been identified as the monophyletic/gymnohydnotrya lineage, but no further research has been conducted to determine the evolutionary origin of this lineage or its relationship with other Pezizales lineages. Here, we present a phylogenetic study of fungal species previously described in Underwoodia and Gymnohydnotrya, with sampling of all but one described species. We revise the taxonomy of this lineage and describe three new species from the Patagonian region of South America. Our results show that none of these Southern Hemisphere species are closely related to Underwoodia columnaris, the type species of the genus Underwoodia. Accordingly, we recognize the genus Geomorium described by Spegazzini in 1922 for G. fuegianum. We propose the new family, Geomoriaceae fam. nov., to accommodate this phylogenetically and morphologically unique Southern Hemisphere lineage. Molecular dating estimated that Geomoriaceae started to diverge from its sister clade Tuberaceae c. 112 MYA, with a crown age for the family in the late Cretaceous (c. 67 MYA). This scenario fits well with a Gondwanan origin of the family before the split of Australia and South America from Antarctica during the Paleocene-Eocene boundary (c. 50 MYA).

scholarly journals An integrated phylogenetic analysis of turtles

2015 ◽  
Author(s):  
Anieli Pereira ◽  
Carlos Schrago
Keyword(s):  
Divergence Time ◽  
Nuclear Data ◽  
Phylogenetic Inference ◽  
Sister Group ◽  
Total Evidence ◽  
Morphological Data ◽  
Nonparametric Bootstrap ◽  
Data Set ◽  
Divergence Time Estimates ◽  
The Family

Background. Testudines is a reptilian order with unique morphological features among vertebrates. This order is currently divided into two suborders: Pleurodira and Cryptodira; which comprises approimately 14 extant families with 95 genera, about 320 species. Phylogenetic affinities below the family level remain largely unresolved. The main discrepancies among previous studies concern the position of the superfamily Trionychoidea and the families Chelydridae and Platystenidae. The recent improvement in combined phylogenetic inference and divergence time estimates, as well as the increased taxon sampling available in databases, prompted us to investigate their evolutionary relationships. Methods. In order to clarify the phylogenetic relatioships of Testudines, we inferred phylogenies from two datasets: (1) molecular dataset based on 12 genes, including 294 species; and (2) total evidence based on 12 genes plus 235 morphologic caracteres from the matrix of Sterli et al. (2013), including 28 extant and 69 extinct taxa. Maximum likelihood phylogenetic inference was performed with the data set partitioned into: (1) molecular nuclear data under GTR model of substitution, and (2) morphological data under Mk model. Statistical support for clades was assessed with 2000 nonparametric bootstrap replicates (BT). Results. Our results supported a split between Pleurodira and Cryptodira (BT > 97). In Cryptodira, we inferred an early split between Trionychoidea and all other Cryptodira, known as Durocryptodira (BT = 100). The monophyly of all families and superfamilies were recovered with high support (BT=100), except for the family Podocnemididae (BT=59). In both analyses, Chelydridae was recovered as sister-group to the superfamily Kinosternoidae (BT=99). With regard to Platysternidae, this monotypic asian family would split from Emydidae in the molecular phylogeny (BT = 81), whereas in the total analysis this split was between Emydidae and all remaining Testudinoidea: Emydidae + Geomydidae + Testudinidae. Discussion. All 14 families were represented in both analyses, although the molecular analysis contains 294 species-level taxa and total-evidence one has only 29 genus-level taxa. Pleurodira and Cryptodira were recovered as monophyletic as in most previous works. Trionychoidea was recovered as a clade within Cryptodira, in contrast to previous hypotheses, which placed this superfamily either as sister to Pleurodira or Cryptodira, or as sister group of all Testudines altogether. Chelydridae was recovered as sister-group of Kinosternoidae, whereas Platysternidae, a monotypic Asian family, was recovered as a member of Testudinoidae; although his position within the group was conflicting. This position of Platysternidae was the only conflict between crown groups found between our datasets.

scholarly journals Ancient dates or accelerated rates? Morphological clocks and the antiquity of placental mammals

2014 ◽  
Vol 281 (1793) ◽  
pp. 20141278 ◽  
Author(s):  
Robin M. D. Beck ◽  
Michael S. Y. Lee
Keyword(s):  
Morphological Evolution ◽  
Fold Increase ◽  
Evolutionary Rates ◽  
Total Evidence ◽  
Morphological Data ◽  
Slight Reduction ◽  
Crown Group ◽  
Divergence Dates ◽  
Clock Models ◽  
Relaxed Clock

Analyses of a comprehensive morphological character matrix of mammals using ‘relaxed’ clock models (which simultaneously estimate topology, divergence dates and evolutionary rates), either alone or in combination with an 8.5 kb nuclear sequence dataset, retrieve implausibly ancient, Late Jurassic–Early Cretaceous estimates for the initial diversification of Placentalia (crown-group Eutheria). These dates are much older than all recent molecular and palaeontological estimates. They are recovered using two very different clock models, and regardless of whether the tree topology is freely estimated or constrained using scaffolds to match the current consensus placental phylogeny. This raises the possibility that divergence dates have been overestimated in previous analyses that have applied such clock models to morphological and total evidence datasets. Enforcing additional age constraints on selected internal divergences results in only a slight reduction of the age of Placentalia. Constraining Placentalia to less than 93.8 Ma, congruent with recent molecular estimates, does not require major changes in morphological or molecular evolutionary rates. Even constraining Placentalia to less than 66 Ma to match the ‘explosive’ palaeontological model results in only a 10- to 20-fold increase in maximum evolutionary rate for morphology, and fivefold for molecules. The large discrepancies between clock- and fossil-based estimates for divergence dates might therefore be attributable to relatively small changes in evolutionary rates through time, although other explanations (such as overly simplistic models of morphological evolution) need to be investigated. Conversely, dates inferred using relaxed clock models (especially with discrete morphological data and M r B ayes ) should be treated cautiously, as relatively minor deviations in rate patterns can generate large effects on estimated divergence dates.

scholarly journals Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets

2020 ◽  
Author(s):  
Johannes S Neumann ◽  
Rob Desalle ◽  
Apurva Narechania ◽  
Bernd Schierwater ◽  
Michael Tessler
Keyword(s):  
A Priori ◽  
Genomic Data ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Taxon Sampling ◽  
Data Sets ◽  
Analysis Tool ◽  
Character Weighting ◽  
The Impact

Abstract There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: the sister to all other Metazoa (SOM). Here, we use published phylogenomic data sets ($\sim $45,000–400,000 characters in size with $\sim $15–100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological data sets ($\sim $15–275 characters). We additionally use small exemplar data sets to quantify how increased taxon sampling can help stabilize phylogenetic inferences. We apply a plethora of common methods, that is, likelihood models and their “equivalent” under parsimony: character weighting schemes. Our results are at odds with the typical view of phylogenomics, that is, that genomic-scale data sets will swamp out inferences from morphological data. Instead, weighting morphological data 2–10$\times $ in both likelihood and parsimony can in some cases “flip” which phylum is inferred to be the SOM. This typically results in the molecular hypothesis of Ctenophora as the SOM flipping to Porifera (or occasionally Placozoa). However, greater taxon sampling improves phylogenetic stability, with some of the larger molecular data sets ($>$200,000 characters and up to $\sim $100 taxa) showing node stability even with $\geqq100\times $ upweighting of morphological data. Accordingly, our analyses have three strong messages. 1) The assumption that genomic data will automatically “swamp out” morphological data is not always true for the SOM question. Morphological data have a strong influence in our analyses of combined data sets, even when outnumbered thousands of times by molecular data. Morphology therefore should not be counted out a priori. 2) We here quantify for the first time how the stability of the SOM node improves for several genomic data sets when the taxon sampling is increased. 3) The patterns of “flipping points” (i.e., the weighting of morphological data it takes to change the inferred SOM) carry information about the phylogenetic stability of matrices. The weighting space is an innovative way to assess comparability of data sets that could be developed into a new sensitivity analysis tool. [Metazoa; Morphology; Phylogenomics; Weighting.]

scholarly journals Phylogeny of the stink bug tribe Chlorocorini (Heteroptera, Pentatomidae) based on DNA and morphological data: the evolution of key phenotypic traits

2020 ◽  
Author(s):  
Bruno C. Genevcius ◽  
Caroline Greve ◽  
Samantha Koehler ◽  
Rebecca B. Simmons ◽  
David A. Rider ◽  
...  
Keyword(s):  
Morphological Characters ◽  
Molecular Data ◽  
Predatory Behavior ◽  
Morphological Data ◽  
Phylogenetic Study ◽  
Phenotypic Traits ◽  
Stink Bug ◽  
Phylogenetic Studies ◽  
The Family

ABSTRACTPentatomidae is the third largest family of true bugs, comprising over 40 tribes. Few tribes have been studied in a phylogenetic context, and none of them have been examined using molecular data. Moreover, little is known about the evolution of key morphological characters widely used in taxonomic and phylogenetic studies at multiple levels. Here, we conduct a phylogenetic study of the tribe Chlorocorini (Pentatominae) combining 69 morphological characters and five DNA loci. We use the inferred phylogeny to reconstruct the evolution of key morphological characters such as the spined humeral angles of the pronotum, a dorsal projection on the apices of the femora and characters of male genitalia. We provide solid evidence that the tribe as currently recognized is not monophyletic based both on DNA and morphological data. The genera Arvelius Spinola and Eludocoris Thomas were consistently placed outside of the Chlorocorini, while the remaining genera were found to form a monophyletic group. We also show that nearly all morphological diagnostic characters for the tribe are homoplastic. The only exception is the development of the hypandrium, which, contrary to expectations for genital traits, showed the slowest evolutionary rates. In contrast, the most rapidly evolving trait is the length of the ostiolar ruga, which may be attributed to selection favoring anti-predatory behavior and other functions of its associated scent glands. Lastly, we also provide a preliminary glimpse of the main phylogenetic relationships within the Pentatomidae, which indicates that most of the included subfamilies and tribes are not monophyletic. Our results suggest that the current subfamily-level classification of Pentatomidae is not adequate to reflect its evolutionary history, and we urge for a more complete phylogeny of the family.

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