scholarly journals A phylogenomic resolution of the sea urchin tree of life

2018 ◽  
Author(s):  
Nicolás Mongiardino Koch ◽  
Simon E. Coppard ◽  
Harilaos A. Lessios ◽  
Derek E. G. Briggs ◽  
Rich Mooi ◽  
...  
Keyword(s):  
De Novo ◽  
Sea Urchins ◽  
Phylogenetic Signal ◽  
Gene Tree ◽  
Tree Of Life ◽  
Morphological Data ◽  
Morphological Evidence ◽  
Phylogenomic Analysis ◽  
Marine Animals ◽  
Sand Dollars

AbstractBackgroundEchinoidea is a clade of marine animals including sea urchins, heart urchins, sand dollars and sea biscuits. Found in benthic habitats across all latitudes, echinoids are key components of marine communities such as coral reefs and kelp forests. A little over 1,000 species inhabit the oceans today, a diversity that traces its roots back at least to the Permian. Although much effort has been devoted to elucidating the echinoid tree of life using a variety of morphological data, molecular attempts have relied on only a handful of genes. Both of these approaches have had limited success at resolving the deepest nodes of the tree, and their disagreement over the positions of a number of clades remains unresolved.ResultsWe performed de novo sequencing and assembly of 17 transcriptomes to complement available genomic resources of sea urchins and produce the first phylogenomic analysis of the clade. Multiple methods of probabilistic inference recovered identical topologies, with virtually all nodes showing maximum support. In contrast, the coalescent-based method ASTRAL-II resolved one node differently, a result apparently driven by gene tree error induced by evolutionary rate heterogeneity. Regardless of the method employed, our phylogenetic structure deviates from the currently accepted classification of echinoids, with neither Acroechinoidea (all euechinoids except echinothurioids), nor Clypeasteroida (sand dollars and sea biscuits) being monophyletic as currently defined. We demonstrate the strength and distribution of phylogenetic signal throughout the genome for novel resolutions of these lineages and rule out systematic biases as possible explanations.ConclusionsOur investigation substantially augments the molecular resources available for sea urchins, providing the first transcriptomes for many of its main lineages. Using this expanded genomic dataset, we resolve the position of several clades in agreement with early molecular analyses but in disagreement with morphological data. Our efforts settle multiple phylogenetic uncertainties, including the position of the enigmatic deep-sea echinothurioids and the identity of the sister clade to sand dollars. We offer a detailed assessment of evolutionary scenarios that could reconcile our findings with morphological evidence, opening up new lines of research into the development and evolutionary history of this ancient clade.

Phylogenomic Analysis of Concatenated Ultraconserved Elements Reveals the Recent Evolutionary Radiation of the Fairy Wrasses (Teleostei: Labridae: Cirrhilabrus)

2021 ◽  
Author(s):  
Yi-Kai Tea ◽  
Xin Xu ◽  
Joseph D DiBattista ◽  
Nathan Lo ◽  
Peter F Cowman ◽  
...  
Keyword(s):  
Phylogenetic Signal ◽  
Estimation Error ◽  
Gene Tree ◽  
Molecular Dating ◽  
Morphological Data ◽  
Phylogenomic Analysis ◽  
Gene Trees ◽  
Data Set ◽  
Ultraconserved Elements ◽  
Species Complexes

Abstract The fairy wrasses (genus Cirrhilabrus) are among the most successful of the extant wrasse lineages (Teleostei: Labridae), with their 61 species accounting for nearly 10$\%$ of the family. Although species complexes within the genus have been diagnosed on the basis of coloration patterns and synapomorphies, attempts to resolve evolutionary relationships among these groups using molecular and morphological data have largely been unsuccessful. Here, we use a phylogenomic approach with a data set comprising 991 ultraconserved elements (UCEs) and mitochondrial COI to uncover the evolutionary history and patterns of temporal and spatial diversification of the fairy wrasses. Our analyses of phylogenetic signal suggest that most gene-tree incongruence is caused by estimation error, leading to poor resolution in a summary-coalescent analysis of the data. In contrast, analyses of concatenated sequences are able to resolve the major relationships of Cirrhilabrus. We determine the placements of species that were previously regarded as incertae sedis and find evidence for the nesting of Conniella, an unusual, monotypic genus, within Cirrhilabrus. Our relaxed-clock dating analysis indicates that the major divergences within the genus occurred around the Miocene–Pliocene boundary, followed by extensive cladogenesis of species complexes in the Pliocene–Pleistocene. Biogeographic reconstruction suggests that the fairy wrasses emerged within the Coral Triangle, with episodic fluctuations of sea levels during glacial cycles coinciding with shallow divergence events but providing few opportunities for more widespread dispersal. Our study demonstrates both the resolving power and limitations of UCEs across shallow timescales where there is substantial estimation error in individual gene trees.[Biogeography; concatenation; gene genealogy interrogation; gene trees; molecular dating; summary coalescent; UCEs.]

scholarly journals Phylogenomic analysis of echinoderm class relationships supports Asterozoa

2014 ◽  
Vol 281 (1786) ◽  
pp. 20140479 ◽  
Author(s):  
Maximilian J. Telford ◽  
Christopher J. Lowe ◽  
Christopher B. Cameron ◽  
Olga Ortega-Martinez ◽  
Jochanan Aronowicz ◽  
...  
Keyword(s):  
Convergent Evolution ◽  
Sea Urchins ◽  
Phylogenetic Signal ◽  
Strong Support ◽  
Phylogenomic Analysis ◽  
Phylogenetic Studies ◽  
Phylogenetic Methods ◽  
Complete Dataset ◽  
Type Larva ◽  
Molecular Phylogenetic

While some aspects of the phylogeny of the five living echinoderm classes are clear, the position of the ophiuroids (brittlestars) relative to asteroids (starfish), echinoids (sea urchins) and holothurians (sea cucumbers) is controversial. Ophiuroids have a pluteus-type larva in common with echinoids giving some support to an ophiuroid/echinoid/holothurian clade named Cryptosyringida. Most molecular phylogenetic studies, however, support an ophiuroid/asteroid clade (Asterozoa) implying either convergent evolution of the pluteus or reversals to an auricularia-type larva in asteroids and holothurians. A recent study of 10 genes from four of the five echinoderm classes used ‘phylogenetic signal dissection’ to separate alignment positions into subsets of (i) suboptimal, heterogeneously evolving sites (invariant plus rapidly changing) and (ii) the remaining optimal, homogeneously evolving sites. Along with most previous molecular phylogenetic studies, their set of heterogeneous sites, expected to be more prone to systematic error, support Asterozoa. The homogeneous sites, in contrast, support an ophiuroid/echinoid grouping, consistent with the cryptosyringid clade, leading them to posit homology of the ophiopluteus and echinopluteus. Our new dataset comprises 219 genes from all echinoderm classes; analyses using probabilistic Bayesian phylogenetic methods strongly support Asterozoa. The most reliable, slowly evolving quartile of genes also gives highest support for Asterozoa; this support diminishes in second and third quartiles and the fastest changing quartile places the ophiuroids close to the root. Using phylogenetic signal dissection, we find heterogenous sites support an unlikely grouping of Ophiuroidea + Holothuria while homogeneous sites again strongly support Asterozoa. Our large and taxonomically complete dataset finds no support for the cryptosyringid hypothesis; in showing strong support for the Asterozoa, our preferred topology leaves the question of homology of pluteus larvae open.

scholarly journals Phylogenetic Signal and Bias in Paleontology

2021 ◽  
Author(s):  
Robert J Asher ◽  
Martin R Smith
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Signal ◽  
Morphological Characters ◽  
Tree Of Life ◽  
Morphological Data ◽  
Phylogenetic Resolution ◽  
Phylogeny Estimation ◽  
Better Than

Abstract An unprecedented amount of evidence now illuminates the phylogeny of living mammals and birds on the Tree of Life. We use this tree to measure phylogenetic value of data typically used in paleontology (bones and teeth) from six datasets derived from five published studies. We ask three interrelated questions: 1) Can these data adequately reconstruct known parts of the Tree of Life? 2) Is accuracy generally similar for studies using morphology, or do some morphological datasets perform better than others? 3) Does the loss of non-fossilizable data cause taxa to occur in misleadingly basal positions? Adding morphology to DNA datasets usually increases congruence of resulting topologies to the well corroborated tree, but this varies among morphological datasets. Extant taxa with a high proportion of missing morphological characters can greatly reduce phylogenetic resolution when analyzed together with fossils. Attempts to ameliorate this by deleting extant taxa missing morphology are prone to decreased accuracy due to long-branch artefacts. We find no evidence that fossilization causes extinct taxa to incorrectly appear at or near topologically basal branches. Morphology comprises the evidence held in common by living taxa and fossils, and phylogenetic analysis of fossils greatly benefits from inclusion of molecular and morphological data sampled for living taxa, whatever methods are used for phylogeny estimation.

scholarly journals Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life

2020 ◽  
Vol 70 (1) ◽  
pp. 49-66 ◽  
Author(s):  
Paul M Hime ◽  
Alan R Lemmon ◽  
Emily C Moriarty Lemmon ◽  
Elizabeth Prendini ◽  
Jeremy M Brown ◽  
...  
Keyword(s):  
Tree Species ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Signal ◽  
Gene Tree ◽  
Strong Support ◽  
Species Tree ◽  
Tree Of Life ◽  
Lineage Sorting ◽  
Sister Relationship ◽  
Gene Tree Discordance

Abstract Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree–species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree–species tree discordance; genomics; information theory.]

scholarly journals ­Comparative spigot ontogeny across the spider tree of life

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4233 ◽  
Author(s):  
Rachael E. Alfaro ◽  
Charles E. Griswold ◽  
Kelly B. Miller
Keyword(s):  
Phylogenetic Signal ◽  
Correlation Coefficients ◽  
Generalized Least Squares ◽  
Tree Of Life ◽  
Morphological Data ◽  
Singular Fiber ◽  
Rigorous Testing ◽  
Ancestral Character Estimation ◽  
First Time ◽  
Hogna Carolinensis

Spiders are well known for their silk and its varying use across taxa. Very few studies have examined the silk spigot ontogeny of the entire spinning field of a spider. Historically the spider phylogeny was based on morphological data and behavioral data associated with silk. Recent phylogenomics studies have shifted major paradigms in our understanding of silk use evolution, reordering phylogenetic relationships that were once thought to be monophyletic. Considering this, we explored spigot ontogeny in 22 species, including Dolomedes tenebrosus and Hogna carolinensis, reported here for the first time. This is the first study of its kind and the first to incorporate the Araneae Tree of Life. After rigorous testing for phylogenetic signal and model fit, we performed 60 phylogenetic generalized least squares analyses on adult female and second instar spigot morphology. Six analyses had significant correlation coefficients, suggesting that instar, strategy, and spigot variety are good predictors of spigot number in spiders, after correcting for bias of shared evolutionary history. We performed ancestral character estimation of singular, fiber producing spigots on the posterior lateral spinneret whose potential homology has long been debated. We found that the ancestral root of our phylogram of 22 species, with the addition of five additional cribellate and ecribellate lineages, was more likely to have either none or a modified spigot rather than a pseudoflagelliform gland spigot or a flagelliform spigot. This spigot ontogeny approach is novel and we can build on our efforts from this study by growing the dataset to include deeper taxon sampling and working towards the capability to incorporate full ontogeny in the analysis.

scholarly journals Coalescent-based phylogenetic inference from genes with unequivocal historical signal suggests a polytomy at the root of the placental mammal tree of life

2018 ◽  
Author(s):  
Filipe R. R. Moreira ◽  
Carlos G. Schrago
Keyword(s):  
Unsolved Problem ◽  
Likelihood Function ◽  
Phylogenetic Signal ◽  
Gene Tree ◽  
Analytical Framework ◽  
Tree Of Life ◽  
Multispecies Coalescent ◽  
Phylogenetic Methods ◽  
Heterogeneous Models ◽  
Tree Estimation

AbstractFinding the correct place of the root of the Placentalia tree of life is an unsolved problem in mammalian systematics. Three major competing hypotheses were proposed, alternating the position of the supraordinal taxa Afrotheria, Xenarthra, or Atlantogenata as sister lineages to the remaining placentals. While all three phylogenetic associations were inferred by studies conducted so far, recent assessments applying heterogeneous models and coalescent-based phylogenetic methods found robust support for the Atlantogenata hypothesis. Current developments in theoretical phylogenetics, such as the demonstration that concatenating genes may bias the likelihood function, and that summary coalescent-based phylogenetic methods are sensitive to errors in gene tree estimation, calls for a reevaluation of the early placental split problem. We investigated the phylogenetic relationships between placental superorders by restricting the analysis to subsets of genes with unequivocal phylogenetic signal. In contrast to previous works, we show that the hypothesis of a polytomy at the placental root could not be rejected under the multispecies coalescent model. This result endorses conclusions from analyses of retroposon insertion patterns. We provide an analytical framework to access empirical polytomies employing summary coalescent methods and topological tests, helping the investigation of poorly resolved nodes in the tree of life.

scholarly journals A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data

2020 ◽  
Author(s):  
Nicolás Mongiardino Koch ◽  
Jeffrey R Thompson
Keyword(s):  
Large Scale ◽  
Sea Urchins ◽  
Phylogenetic Signal ◽  
Total Evidence ◽  
Morphological Data ◽  
Data Sets ◽  
Crown Group ◽  
Data Set ◽  
Paleontological Data ◽  
Time Calibration

Abstract Phylogenomic and paleontological data constitute complementary resources for unraveling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthesizing approaches, including a remarkable fossil record that can be incorporated into explicit phylogenetic hypotheses. We revisit the phylogeny of crown group Echinoidea using a total-evidence dating approach that combines the largest phylogenomic data set for the clade, a large-scale morphological matrix with a dense fossil sampling, and a novel compendium of tip and node age constraints. To this end, we develop a novel method for subsampling phylogenomic data sets that selects loci with high phylogenetic signal, low systematic biases, and enhanced clock-like behavior. Our results demonstrate that combining different data sources increases topological accuracy and helps resolve conflicts between molecular and morphological data. Notably, we present a new hypothesis for the origin of sand dollars, and restructure the relationships between stem and crown echinoids in a way that implies a long stretch of undiscovered evolutionary history of the crown group in the late Paleozoic. Our efforts help bridge the gap between phylogenomics and phylogenetic paleontology, providing a model example of the benefits of combining the two. [Echinoidea; fossils; paleontology; phylogenomics; time calibration; total evidence.]

scholarly journals New echinoderm remains in the buried offerings of the Templo Mayor of Tenochtitlan, Mexico City

2017 ◽  
Vol 65 (1-1) ◽  
pp. 168
Author(s):  
Carolina Martín-Cao-Romero ◽  
Francisco Alonso Solís-Marín ◽  
Andrea Alejandra Caballero-Ochoa ◽  
Yoalli Quetzalli Hernández-Díaz ◽  
Leonardo López Luján ◽  
...  
Keyword(s):  
Mexico City ◽  
Sea Urchins ◽  
World View ◽  
Sea Stars ◽  
Marine Animals ◽  
Sand Dollars ◽  
The Temple

Between 1978 and 1982 the ruins of the Templo Mayor of Tenochtitlan were exhumed a few meters northward from the central plaza (Zócalo) of Mexico City. The temple was the center of the Mexica’s ritual life and one of the most famous ceremonial buildings of its time (15th and 16th centuries). More than 200 offerings have been recovered in the temple and surrounding buildings. We identified vestiges of 14 species of echinoderms (mostly as disarticulated plates). These include six species of sea stars (Luidia superba, Astropecten regalis, Astropecten duplicatus, Phataria unifascialis, Nidorellia armata, Pentaceraster cumingi), one ophiuroid species (Ophiothrix rudis), two species of sea urchins (Eucidaris thouarsii, Echinometra vanbrunti), four species of sand dollars (Mellita quinquiesperforata, Mellita notabilis, Encope laevis, Clypeaster speciosus) and one species of sea biscuit (Meoma ventricosa grandis). They date back to the reigns of kings Axayacatl (AD 1469-1481), Tizoc (AD 1481-1486), Ahuitzotl (AD 1486-1502), and Motecuhzoma II (AD 1502-1520). Apparently the presence of echinoderms in the offerings is related to the realm of Tlaloc (god of rain and earth). It is believed this organisms, like other marine animals, were used by the priests, like other marine animals, to represent the aquatic underworld of Mesoamerican world-view. Rev. Biol. Trop. 65(Suppl. 1): S168-S179. Epub 2017 November 01. 

scholarly journals Sub-Chronic Effects of Slight PAH- and PCB-Contaminated Mesocosms in Paracentrotus lividus Lmk: A Multi-Endpoint Approach and De Novo Transcriptomic

2021 ◽  
Vol 22 (13) ◽  
pp. 6674
Author(s):  
Luisa Albarano ◽  
Valerio Zupo ◽  
Davide Caramiello ◽  
Maria Toscanesi ◽  
Marco Trifuoggi ◽  
...  
Keyword(s):  
De Novo ◽  
Sea Urchins ◽  
Transcriptome Assembly ◽  
Paracentrotus Lividus ◽  
Marine Biota ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Limit Values ◽  
The Impact ◽  
Endpoint Approach

Sediment pollution is a major issue in coastal areas, potentially endangering human health and the marine environments. We investigated the short-term sublethal effects of sediments contaminated with polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) on the sea urchin Paracentrotus lividus for two months. Spiking occurred at concentrations below threshold limit values permitted by the law (TLVPAHs = 900 µg/L, TLVPCBs = 8 µg/L, Legislative Italian Decree 173/2016). A multi-endpoint approach was adopted, considering both adults (mortality, bioaccumulation and gonadal index) and embryos (embryotoxicity, genotoxicity and de novo transcriptome assembly). The slight concentrations of PAHs and PCBs added to the mesocosms were observed to readily compartmentalize in adults, resulting below the detection limits just one week after their addition. Reconstructed sediment and seawater, as negative controls, did not affect sea urchins. PAH- and PCB-spiked mesocosms were observed to impair P. lividus at various endpoints, including bioaccumulation and embryo development (mainly PAHs) and genotoxicity (PAHs and PCBs). In particular, genotoxicity tests revealed that PAHs and PCBs affected the development of P. lividus embryos deriving from exposed adults. Negative effects were also detected by generating a de novo transcriptome assembly and its annotation, as well as by real-time qPCR performed to identify genes differentially expressed in adults exposed to the two contaminants. The effects on sea urchins (both adults and embryos) at background concentrations of PAHs and PCBs below TLV suggest a need for further investigations on the impact of slight concentrations of such contaminants on marine biota.

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