scholarly journals Use of Continuous Traits Can Improve Morphological Phylogenetics

2017 ◽  
Author(s):  
Caroline Parins-Fukuchi
Keyword(s):  
Morphological Evolution ◽  
Phylogenetic Reconstruction ◽  
Continuous Measurements ◽  
Extant Species ◽  
Discrete Character ◽  
Significant Step ◽  
Biological Interpretation ◽  
Feasible Alternative ◽  
Character Coding ◽  
Continuous Traits

ABSTRACTThe recent surge in enthusiasm for simultaneously inferring relationships from extinct and extant species has reinvigorated interest in statistical approaches for modelling morphological evolution. Current statistical methods use the Mk model to describe substitutions between discrete character states. Although representing a significant step forward, the Mk model presents challenges in biological interpretation, and its adequacy in modelling morphological evolution has not been well explored. Another major hurdle in morphological phylogenetics concerns the process of character coding of discrete characters. The often subjective nature of discrete character coding can generate discordant results that are rooted in individual researchers’ subjective interpretations. Employing continuous measurements to infer phylogenies may alleviate some of these issues. Although not widely used in the inference of topology, models describing the evolution of continuous characters have been well examined, and their statistical behaviour is well understood. Also, continuous measurements avoid the substantial ambiguity often associated with the assignment of discrete characters to states. I present a set of simulations to determine whether use of continuous characters is a feasible alternative or supplement to discrete characters for inferring phylogeny. I compare relative reconstruction accuracy by inferring phylogenies from simulated continuous and discrete characters. These tests demonstrate significant promise for continuous traits by demonstrating their higher overall accuracy as compared to reconstruction from discrete characters under Mk when simulated under unbounded Brownian motion, and equal performance when simulated under an Ornstein-Uhlenbeck model. Continuous characters also perform reasonably well in the presence of covariance between sites. I argue that inferring phylogenies directly from continuous traits may be benefit efforts to maximise phylogenetic information in morphological datasets by preserving larger variation in state space compared to many discretisation schemes. I also suggest that the use of continuous trait models in phylogenetic reconstruction may alleviate potential concerns of discrete character model adequacy, while identifying areas that require further study in this area. This study provides an initial controlled demonstration of the efficacy of continuous characters in phylogenetic inference.

Cleaning a taxonomic dustbin: placing the European Hypnum species in a phylogenetic context!

2018 ◽  
Vol 40 (2) ◽  
pp. 37 ◽  
Author(s):  
SASKIA SCHLESAK ◽  
LARS HEDENÄS ◽  
MARTIN NEBEL ◽  
DIETMAR QUANDT
Keyword(s):  
18Th Century ◽  
Morphological Evolution ◽  
Phylogenetic Reconstruction ◽  
Moss Species ◽  
New Family ◽  
Pleurocarpous Mosses ◽  
Tree Topologies ◽  
Molecular Information ◽  
Pleurocarpous Moss ◽  
Rps4 Gene

The pleurocarpous moss genus Hypnum s.l. is a species-rich (> 40 species) cosmopolitan genus, of which 21 taxa occur in Europe. Although several of these species show high morphological resemblance there are strong indications that the genus is highly paraphyletic, which may be masked by convergent morphological evolution. Using molecular information, we analyse whether the morphological similarity of gametophytes of the European Hypnum taxa is explained by common ancestry or convergence. We provide a phylogenetic reconstruction of the relationships of the currently recognized European Hypnum taxa in a broad pleurocarpous moss context (192 taxa) using the nuclear ITS1-5.8S-ITS2, the plastid rps4 gene and trnL-F, and the mitochondrial nad5 intron. Bayesian tree topologies show that the genus is polyphyletic, and we retain only the Hypnum cupressiforme complex within Hypnum. The genus originally represented half of the moss species diversity, as it accommodated basically all pleurocarpous mosses; here we retain only seven species and one variety. The remainder of the species where resolved either within the three families Amblystegiaceae, Entodontaceae, and Pylaisiaceae, or in an independent clade that we describe as the new family Stereodontaceae. The Stereodontaceae includes five European species, all in the genus Stereodon, where they were already placed in the 18th century. In addition, we describe the four new genera Aquilonium, Insomniella, Jochenia, and Lignocariosa, and make new combinations for several Hypnum species.

scholarly journals Evolution of seahorses' upright posture was linked to Oligocene expansion of seagrass habitats

2009 ◽  
Vol 5 (4) ◽  
pp. 521-523 ◽  
Author(s):  
Peter R. Teske ◽  
Luciano B. Beheregaray
Keyword(s):  
Fossil Record ◽  
Sequence Data ◽  
Morphological Evolution ◽  
Molecular Techniques ◽  
Molecular Dating ◽  
Upright Posture ◽  
Tectonic Events ◽  
Extant Species ◽  
The Family ◽  
Transitional Forms

Seahorses (Syngnathidae: Hippocampus ) are iconic marine teleosts that are readily identifiable by their upright posture. The fossil record is inadequate to shed light on the evolution of this trait because it lacks transitional forms. There are, however, extant syngnathid species (the pygmy pipehorses) that look like horizontally swimming seahorses and that might represent a surviving evolutionary link between the benthic seahorses and other, free-swimming members of the family Syngnathidae. Using sequence data from five nuclear loci, we confirm the sister taxon relationship between seahorses and pygmy pipehorses. Molecular dating indicates that the two taxa diverged during the Late Oligocene. During this time, tectonic events in the Indo-West Pacific resulted in the formation of vast amounts of new shallow-water areas and associated expansion of seagrass habitats that would have favoured the seahorses’ upright posture by improving their camouflage while not affecting their manoeuvrability negatively. The molecular techniques employed here provide new insights into the evolution of a taxon whose fossil record is incomplete, but whose evolutionary history is so recent that the major stages of morphological evolution are still represented in extant species.

scholarly journals Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity

2020 ◽  
Author(s):  
Michael R. May ◽  
Dori L. Contreras ◽  
Michael A. Sundue ◽  
Nathalie S. Nagalingum ◽  
Cindy V. Looy ◽  
...  
Keyword(s):  
Morphological Evolution ◽  
Divergence Time ◽  
Time Estimation ◽  
Bayes Factors ◽  
Total Evidence ◽  
Rate Variation ◽  
Divergence Time Estimation ◽  
Extinction Rates ◽  
Extant Species ◽  
Tree Models

AbstractPhylogenetic divergence-time estimation has been revolutionized by two recent developments: 1) total-evidence dating (or “tip-dating”) approaches that allow for the incorporation of fossils as tips in the analysis, with their phylogenetic and temporal relationships to the extant taxa inferred from the data, and 2) the fossilized birth-death (FBD) class of tree models that capture the processes that produce the tree (speciation, extinction, and fossilization), and thus provide a coherent and biologically interpretable tree prior. To explore the behaviour of these methods, we apply them to marattialean ferns, a group that was dominant in Carboniferous landscapes prior to declining to its modest extant diversity of slightly over 100 species. We show that tree models have a dramatic influence on estimates of both divergence times and topological relationships. This influence is driven by the strong, counter-intuitive informativeness of the uniform tree prior and the inherent nonidentifiability of divergence-time models. In contrast to the strong influence of the tree models, we find minor effects of differing the morphological transition model or the morphological clock model. We compare the performance of a large pool of candidate models using a combination of posterior-predictive simulation and Bayes factors. Notably, an FBD model with epoch-specific speciation and extinction rates was strongly favored by Bayes factors. Our best-fitting model infers stem and crown divergences for the Marattiales in the Middle Devonian and Upper Cretaceous, respectively, with elevated speciation rates in the Mississippian and elevated extinction rates in the Cisuralian leading to a peak diversity of ∼2800 species at the end of the Carboniferous, representing the heyday of the Psaroniaceae. This peak is followed by the rapid decline and ultimate extinction of the Psaroniaceae, with their descendants, the Marattiaceae, persisting at approximately stable levels of diversity until the present. This general diversification pattern appears to be insensitive to potential biases in the fossil record; despite the preponderance of available fossils being from Pennsylvanian coal balls, incorporating fossilization-rate variation does not improve model fit. In addition, by incorporating temporal data directly within the model and allowing for the inference of the phylogenetic position of the fossils, our study makes the surprising inference that the clade of extant Marattiales is relatively young, younger than any of the fossils historically thought to be congeneric with extant species. This result is a dramatic demonstration of the dangers of node-based approaches to divergence-time estimation, where the assignment of fossils to particular clades are made a priori (earlier node-based studies that constrained the minimum ages of extant genera based on these fossils resulted in much older age estimates than in our study) and of the utility of explicit models of morphological evolution and lineage diversification.

Fossil horses from “Eohippus” (Hyracotherium) to Equus: scaling, Cope's Law, and the evolution of body size

Paleobiology ◽  
1986 ◽  
Vol 12 (4) ◽  
pp. 355-369 ◽  
Author(s):  
Bruce J. MacFadden
Keyword(s):  
Body Size ◽  
Body Mass ◽  
Morphological Evolution ◽  
Natural Populations ◽  
Evolutionary Rates ◽  
Middle Pleistocene ◽  
Gradual Change ◽  
Regression Equations ◽  
Extant Species ◽  
Body Sizes

The evolution of body size in fossil horses is frequently depicted as a gradual, progressive trend toward increased body size (Cope's Law). Body size (actually body mass) was estimated for 40 species of fossil horses using dental and skeletal characters and regression equations derived from the same characters in extant species of Equus with known body mass. After body sizes were estimated, rates of morphological evolution, in darwins (d), were calculated between known ancestral and descendant fossil horse species. For the first half of horse evolution (from ca. 57 to 25 ma) body mass remained relatively static between about 25 and 50 kg with very slow evolutionary rates of 0.003–0.04 d. During the early–middle Miocene (from ca. 25 to 10 ma) there was a major diversification of body mass to about 75–400 kg and consistently higher evolutionary rates between 0.04 and 0.24 d. Since the late Miocene, body mass has generally increased with a maximum seen (in natural populations) in Equus scotti (ca. 500 kg) during the middle Pleistocene. Therefore, for horses, the traditional interpretation of gradual increase in body size through time is oversimplified because: (1) although the exception to the rule, 5 of 24 species lineages studied are characterized by dwarfism; and (2) the general trend seems to have been a long period (32 ma) of relative stasis followed by 25 ma of diversification and progressive (although not necessarily gradual) change in body size.

scholarly journals Bayesian phylogenetic estimation of fossil ages

2016 ◽  
Vol 371 (1699) ◽  
pp. 20150129 ◽  
Author(s):  
Alexei J. Drummond ◽  
Tanja Stadler
Keyword(s):  
Internal Consistency ◽  
Morphological Evolution ◽  
Divergence Time ◽  
Morphological Data ◽  
Bayesian Probability ◽  
Estimation Accuracy ◽  
Relative Standard Error ◽  
Good Precision ◽  
Extant Species ◽  
Relative Standard

Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth–death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the ‘morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.

Phenetic discrimination of biometric simpletons: paleobiological implications of morphospecies in the lingulide brachiopod Glottidia

Paleobiology ◽  
1997 ◽  
Vol 23 (4) ◽  
pp. 444-469 ◽  
Author(s):  
Michał Kowalewski ◽  
Eric Dyreson ◽  
Jonathan D. Marcot ◽  
José A. Vargas ◽  
Karl W. Flessa ◽  
...  
Keyword(s):  
Fossil Record ◽  
Quantitative Methods ◽  
Morphological Evolution ◽  
Taxonomic Diversity ◽  
Error Rates ◽  
Shell Morphology ◽  
Taxonomic Resolution ◽  
Turnover Rates ◽  
Morphological Complexity ◽  
Extant Species

The extreme morphological simplicity of lingulide brachiopod shells makes them particularly useful for investigating the species-level taxonomic resolution of the fossil record as well as the relationships between taxonomy, morphological complexity, and evolutionary rates. Lingulides have undergone little change in shell morphology and have had low taxonomic diversity since the Paleozoic. Is this pattern an evolutionary phenomenon or an artifact of the shell's simplicity? Multivariate methods were used to establish morphogroups among seven populations of four extant species of Glottidia. Six characters (three shell dimensions and three internal septa) were measured for 162 specimens from field and museum collections. All populations follow similar allometric trajectories: internal septa display positive allometry and shell dimensions display negative allometry. The allometric pattern may reflect D'Arcy Thompson's Principle of Similitude. Principal component analysis does not reveal any distinct clusters in Glottidia morphospace but suggests that some differences independent from ontogeny exist among the populations. Size-free canonical variate analysis indicates the presence of five size-invariant groups that are statistically distinct. Bootstrap-corrected error rates indicate that four specimens are enough to classify a sample correctly at α = 0.05 and eight specimens at α = 0.01. The groups are consistent with neontological classification with the exception of two populations of G. pyramidata identified by discriminant analysis as two distinct groups. The size-free morphogroups reflect geographic separation rather than ontogenetic or substrate differences among the populations.Despite the morphological simplicity of the shell, size-free multivariate analysis of Glottidia delineates groups that offer taxonomic resolution comparable with the neontological classification. The method offers a promising tool for identifying natural morphogroups on the basis of few morphological characters. Moreover, the agreement between neontological taxonomy and the morphogroups suggests that the size-free approach can be applicable for evaluating the reality of the low diversity and turnover rates observed in the fossil record of lingulide brachiopods (= Family Lingulidae). Assuming that the neontological species of Glottidia are biologically meaningful, this study shows that morphological simplicity of lingulides does not necessarily result in taxonomic underresolution. Our analysis, as well as several previous case studies, suggests that taxonomic diversity and turnover rates do not have to be dependent on the morphological complexity of preservable parts. In many cases, when rigorous quantitative methods are employed, the differences in the rates of morphological evolution may be a real evolutionary phenomenon and not artifacts of morphological complexity.

Comparing patterns of evolution: larval and adult life history stages and ribosomal RNA of post-Palaeozoic echinoids

1995 ◽  
Vol 349 (1327) ◽  
pp. 11-18 ◽  
Keyword(s):  
Ribosomal Rna ◽  
Gene Sequence ◽  
Morphological Evolution ◽  
Large Subunit ◽  
Adult Life ◽  
Molecular Data ◽  
Total Evidence ◽  
Adult Morphology ◽  
Extant Species ◽  
Combining Data

We have taken a total-evidence approach to the phylogeny of 29 extant echinoids, combining data from larval morphology, adult morphology, small subunit rRNA complete gene sequence and large subunit rRNA partial gene sequence: a total of 176 morphological and 121 molecular phylogenetically informative characters. Also included are 13 extinct taxa for which we know only adult morphology. Parsimony analysis of the combined data generated 28 equally parsimonious solutions, differing primarily in the positioning of a few fossil taxa. We reduced these to a single working hypothesis of echinoid relationships by pruning fossil taxa and one extant species. Patterns of morphological evolution of larval and adult stages were compared by optimizing character sets onto the total evidence tree and assigning each character transformation to a branch. Branch nodes were dated by reference to the first appearance of one or other sister taxon in the fossil record. From this we demonstrate that larval and adult morphological evolution has proceeded in a mosaic-like fashion over the last 250 Ma. A similar comparison between morphological and molecular data finds equally weak correlation between rates of ribosomal RNA evolution and rates of morphological evolution, implying that morphology and ribosomal genes have also evolved largely independently. Larval characters appear to be more prone to homoplasy than adult characters, even when comparison is restricted to adult organs of similar size and structural complexity as the larvae. As morphological and molecular apomorphies accrue over time, there is a general correspondence between the duration of a particular branch and the number of apomorphies assigned to that branch. However, we found no evidence that overall molecular rates of evolution were any more strictly clock-like than morphological character transformations, although mapping transversions only improved the fit to a clock-like model for molecular data.

A review of bristly ground squirrels Xerini and a generic revision in the African genus Xerus

Mammalia ◽  
2016 ◽  
Vol 80 (5) ◽  
Author(s):  
Boris Kryštufek ◽  
Ahmad Mahmoudi ◽  
Alexey S. Tesakov ◽  
Jan Matějů ◽  
Rainer Hutterer
Keyword(s):  
Fossil Record ◽  
Phylogenetic Reconstruction ◽  
Ground Squirrels ◽  
Small Rodent ◽  
Extant Species ◽  
African Genus

AbstractBristly ground squirrels Xerini are a small rodent tribe of six extant species. Despite a dense fossil record the group was never diverse. Our phylogenetic reconstruction, based on the analysis of cytochrome

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