Phylogenomic analysis of echinoderm class relationships supports Asterozoa

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.

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Transfer of four species of Cryptantha to the genus Johnstonella (Boraginaceae)

Phytotaxa ◽

10.11646/phytotaxa.425.5.3 ◽

2019 ◽

Vol 425 (5) ◽

pp. 279-289

Author(s):

MICHAEL G. SIMPSON ◽

MAKENZIE E. MABRY ◽

KRISTEN HASENSTAB-LEHMAN

Keyword(s):

Sequence Data ◽

Strong Support ◽

Herbaceous Plant ◽

New Combinations ◽

Morphological Similarity ◽

Additional Species ◽

Phylogenetic Studies ◽

The Family ◽

Molecular Phylogenetic ◽

Close Relatives

Based on a previous molecular phylogenetic analysis, Cryptantha, an herbaceous plant genus of the family Boraginaceae, subtribe Amsinckiinae, was split into five genera: Eremocarya, Greeneocharis, Johnstonella, Oreocarya, and a reduced Cryptantha, the last in two separate clades. As a result of this study, Johnstonella was expanded to 13 species and 15 minimum-rank taxa, these formerly classified in Cryptantha s.l. More recent analyses of this complex, with an increased sample size and high-throughput sequence data, indicate that four additional Cryptantha species not previously sampled—C. albida, C. mexicana, C. texana—plus what was originally identified as C. hispida nest within Johnstonella with strong support. However, the identity of C. hispida used in this analysis is now in doubt. The material used likely represents a new species, in the process of being investigated. Two additional species not sequenced to date—C. geohintonii and C. gypsites—are clearly close relatives of C. albida and C. mexicana, based on morphological similarity. In order to maintain monophyly of genera, we here make new combinations in transferring four of these species from Cryptantha to Johnstonella, with the new combinations Johnstonella albida, J. geohintonii, J. gypsites, and J. mexicana. We delay the transfer of Cryptantha texana to Johnstonella because of its morphological similarity to other species that clearly nest within Cryptantha s.s. These same molecular phylogenetic studies may also support the transfer of two previously recognized Johnstonella species—J. echinosepala and J. micromeres—to Cryptantha, one to each of two separate clades. Additional phylogenetic studies focusing on some of these taxa are needed to confirm the position of these latter three species and the possible recognition of a new genus in the complex.

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Museomics: Phylogenomics of the Moth Family Epicopeiidae (Lepidoptera) Using Target Enrichment

Insect Systematics and Diversity ◽

10.1093/isd/ixaa021 ◽

2021 ◽

Vol 5 (2) ◽

Author(s):

Elsa Call ◽

Christoph Mayer ◽

Victoria Twort ◽

Lars Dietz ◽

Niklas Wahlberg ◽

...

Keyword(s):

Strong Support ◽

Sister Group ◽

Molecular Data ◽

Museum Specimens ◽

Target Enrichment ◽

History Museum ◽

Phylogenetic Studies ◽

A Genome ◽

Molecular Phylogenetic ◽

Genomic Studies

Abstract Billions of specimens can be found in natural history museum collections around the world, holding potential molecular secrets to be unveiled. Among them are intriguing specimens of rare families of moths that, while represented in morphology-based works, are only beginning to be included in genomic studies: Pseudobistonidae, Sematuridae, and Epicopeiidae. These three families are part of the superfamily Geometroidea, which has recently been defined based on molecular data. Here we chose to focus on these three moth families to explore the suitability of a genome reduction method, target enrichment (TE), on museum specimens. Through this method, we investigated the phylogenetic relationships of these families of Lepidoptera, in particular the family Epicopeiidae. We successfully sequenced 25 samples, collected between 1892 and 2001. We use 378 nuclear genes to reconstruct a phylogenetic hypothesis from the maximum likelihood analysis of a total of 36 different species, including 19 available transcriptomes. The hypothesis that Sematuridae is the sister group of Epicopeiidae + Pseudobistonidae had strong support. This study thus adds to the growing body of work, demonstrating that museum specimens can successfully contribute to molecular phylogenetic studies.

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A phylogenomic resolution of the sea urchin tree of life

10.1101/430595 ◽

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.

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Convergent evolution of the army ant syndrome and congruence in big-data phylogenetics

10.1101/134064 ◽

2017 ◽

Cited By ~ 2

Author(s):

Marek L. Borowiec

Keyword(s):

Convergent Evolution ◽

Phylogenetic Signal ◽

Strong Support ◽

Taxon Sampling ◽

Data Sets ◽

Sequence Evolution ◽

Army Ants ◽

Data Set ◽

Army Ant ◽

Ant Behavior

AbstractThe evolution of the suite of morphological and behavioral adaptations underlying the ecological success of army ants has been the subject of considerable debate. This “army ant syn-drome” has been argued to have arisen once or multiple times within the ant subfamily Dorylinae. To address this question I generated data from 2,166 loci and a comprehensive taxon sampling for a phylogenetic investigation. Most analyses show strong support for convergent evolution of the army ant syndrome in the Old and New World but certain relationships are sensitive to analytics. I examine the signal present in this data set and find that conflict is diminished when only loci less likely to violate common phylogenetic model assumptions are considered. I also provide a temporal and spatial context for doryline evolution with timecalibrated, biogeographic, and diversification rate shift analyses. This study underscores the need for cautious analysis of phylogenomic data and calls for more efficient algorithms employing better-fitting models of molecular evolution.SignificanceRecent interpretation of army ant evolution holds that army ant behavior and morphology originated only once within the subfamily Dorylinae. An inspection of phylogenetic signal in a large new data set shows that support for this hypothesis may be driven by bias present in the data. Convergent evolution of the army ant syndrome is consistently supported when sequences violating assumptions of a commonly used model of sequence evolution are excluded from the analysis. This hypothesis also fits with a simple scenario of doryline biogeography. These results highlight the importance of careful evaluation of signal and conflict within phylogenomic data sets, even when taxon sampling is comprehensive.

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Transfer of the Kobresia taxa of the flora of Russia and adjacent countries to the genus Carex (Cyperaceae)

Novitates Systematicae Plantarum Vascularium ◽

10.31111/novitates/2020.51.125 ◽

2020 ◽

pp. 125-129

Author(s):

D. G. Melnikov ◽

L. I. Krupkina

Keyword(s):

International Collaboration ◽

Morphological Characters ◽

Published Data ◽

Phylogenetic Studies ◽

Molecular Phylogenetic ◽

New Nomenclatural Combinations

Based on the published data of molecular phylogenetic studies of the tribe Cariceae Dumort. genera (Cyperaceae), obtained by an international collaboration (The Global Carex Group, 2016; et al.), and morphological characters of the genera (Kukkonen, 1990; and others), new nomenclatural combinations and replacement names in the genus Carex L. are published for 11 species, one subspecies and two sections previously included in the genus Kobresia Willd.

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Systematics and evolution of Lentibulariaceae: III. Utricularia

10.1093/oso/9780198779841.003.0008 ◽

2018 ◽

Cited By ~ 3

Author(s):

Richard W. Jobson ◽

Paulo C. Baleeiro ◽

Cástor Guisande

Keyword(s):

Gene Flow ◽

Species Diversity ◽

Population Level ◽

Oceanic Islands ◽

Vulnerable Species ◽

Phylogenetic Studies ◽

Molecular Phylogenetic

Utricularia is a morphologically and ecologically diverse genus currently comprising more than 230 species divided into three subgenera—Polypompholyx, Utricularia, and Bivalvaria—and 35 sections. The genus is distributed worldwide except on the poles and most oceanic islands. The Neotropics has the highest species diversity, followed by Australia. Compared to its sister genera, Utricularia has undergone greater rates of speciation, which are linked to its extreme morphological flexibility that has resulted in the evolution of habitat-specific forms: terrestrial, rheophytic, aquatic, lithophytic, and epiphytic. Molecular phylogenetic studies have resolved relationships for 44% of the species across 80% of the sections. Scant data are available for phylogeography or population-level processes such as gene flow, hybridization, or pollination. Because nearly 90% of the species are endemics, data are urgently needed to determine how to protect vulnerable species and their habitats.

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Lack of support for Deuterostomia prompts reinterpretation of the first Bilateria

Science Advances ◽

10.1126/sciadv.abe2741 ◽

2021 ◽

Vol 7 (12) ◽

pp. eabe2741

Author(s):

Paschalia Kapli ◽

Paschalis Natsidis ◽

Daniel J. Leite ◽

Maximilian Fursman ◽

Nadia Jeffrie ◽

...

Keyword(s):

Systematic Error ◽

Tree Reconstruction ◽

Simulation Experiments ◽

Animal Evolution ◽

Phylogenetic Studies ◽

Branch Lengths ◽

Molecular Phylogenetic ◽

Common Ancestors

The bilaterally symmetric animals (Bilateria) are considered to comprise two monophyletic groups, Protostomia (Ecdysozoa and the Lophotrochozoa) and Deuterostomia (Chordata and the Xenambulacraria). Recent molecular phylogenetic studies have not consistently supported deuterostome monophyly. Here, we compare support for Protostomia and Deuterostomia using multiple, independent phylogenomic datasets. As expected, Protostomia is always strongly supported, especially by longer and higher-quality genes. Support for Deuterostomia, however, is always equivocal and barely higher than support for paraphyletic alternatives. Conditions that cause tree reconstruction errors—inadequate models, short internal branches, faster evolving genes, and unequal branch lengths—coincide with support for monophyletic deuterostomes. Simulation experiments show that support for Deuterostomia could be explained by systematic error. The branch between bilaterian and deuterostome common ancestors is, at best, very short, supporting the idea that the bilaterian ancestor may have been deuterostome-like. Our findings have important implications for the understanding of early animal evolution.

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Tracing the origins of hybrids through history: monstrous cultivars and Napoléon Bonaparte’s exiled paper daisies (Asteraceae; Gnaphalieae)

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boab020 ◽

2021 ◽

Author(s):

Timothy L Collins ◽

Jeremy J Bruhl ◽

Alexander N Schmidt-Lebuhn ◽

Ian R H Telford ◽

Rose L Andrew

Keyword(s):

Gene Flow ◽

Phylogenetic Analyses ◽

Strong Support ◽

Napoleon Bonaparte ◽

Snp Data ◽

Cast Doubt ◽

Molecular Phylogenetic ◽

St Helena ◽

New Evidence

Abstract Golden everlasting paper daisies (Xerochrysum, Gnaphalieae, Asteraceae) were some of the earliest Australian native plants to be cultivated in Europe. Reputedly a favourite of Napoléon Bonaparte and Empress Joséphine, X. bracteatum is thought to have been introduced to the island of St Helena in the South Atlantic during Napoléon’s exile there. Colourful cultivars were developed in the 1850s, and there is a widely held view that these were produced by crossing Xerochrysum with African or Asian Helichrysum spp. Recent molecular phylogenetic analyses and subtribal classification of Gnaphalieae cast doubt on this idea. Using single-nucleotide polymorphism (SNP) data, we looked for evidence of gene flow between modern cultivars, naturalized paper daisies from St Helena and four Xerochrysum spp. recorded in Europe in the 1800s. There was strong support for gene flow between cultivars and X. macranthum. Paper daisies from St Helena were genotypically congruent with X. bracteatum and showed no indications of ancestry from other species or from the cultivars, consistent with the continuous occurrence of naturalized paper daisies introduced by Joséphine and Napoléon. We also present new evidence for the origin of colourful Xerochrysum cultivars and hybridization of congeners in Europe from Australian collections.

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A fossil record of land plant origins from charophyte algae

Science ◽

10.1126/science.abj2927 ◽

2021 ◽

Vol 373 (6556) ◽

pp. 792-796 ◽

Cited By ~ 1

Author(s):

Paul K. Strother ◽

Clinton Foster

Keyword(s):

Fossil Record ◽

Evolutionary History ◽

Phylogenetic Signal ◽

Land Plant ◽

Fossil Plants ◽

Fossil Plant ◽

Molecular Phylogenetic ◽

History Of ◽

Time Gap ◽

Evolutionary Continuity

Molecular time trees indicating that embryophytes originated around 500 million years ago (Ma) during the Cambrian are at odds with the record of fossil plants, which first appear in the mid-Silurian almost 80 million years later. This time gap has been attributed to a missing fossil plant record, but that attribution belies the case for fossil spores. Here, we describe a Tremadocian (Early Ordovician, about 480 Ma) assemblage with elements of both Cambrian and younger embryophyte spores that provides a new level of evolutionary continuity between embryophytes and their algal ancestors. This finding suggests that the molecular phylogenetic signal retains a latent evolutionary history of the acquisition of the embryophytic developmental genome, a history that perhaps began during Ediacaran-Cambrian time but was not completed until the mid-Silurian (about 430 Ma).

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Paracarphalea, a new genus of the coffee family segregated from the Malagasy endemic genus Carphalea (Rubiaceae, Rubioideae, Knoxieae)

Phytotaxa ◽

10.11646/phytotaxa.263.2.2 ◽

2016 ◽

Vol 263 (2) ◽

pp. 98 ◽

Cited By ~ 1

Author(s):

JULIA FERM ◽

JESPER KÅREHED ◽

BIRGITTA BREMER ◽

SYLVAIN G. RAZAFIMANDIMBISON

Keyword(s):

Bayesian Methods ◽

Type Species ◽

New Genus ◽

Sequence Data ◽

Conservation Status ◽

Endemic Genus ◽

Phylogenetic Studies ◽

Molecular Phylogenetic ◽

Nuclear Its ◽

Iucn Criteria

The Malagasy genus Carphalea (Rubiaceae) consists of six species (C. angulata, C. cloiselii, C. kirondron, C. linearifolia, C. madagascariensis, C. pervilleana) of shrubs or small trees and is recognizable by a distinctly lobed calyx, 2(–4)-locular ovaries, each locule with several ovules on a rod-like stalk arising from the base of the locule, and indehiscent fruits. Carphalea linearifolia, rediscovered in 2010, has not previously been included in any Rubiaceae molecular phylogenetic studies. We re-investigated the monophyly of Carphalea using sequence data from chloroplast (rps16 and trnT-F) and nuclear (ITS and ETS) markers analysed with parsimony and Bayesian methods. Carphalea linearifolia forms a clade with C. cloiselii and the type species C. madagascariensis. This clade is sister to a clade consisting of the rest of the Carphalea species plus the genus Triainolepis. According to these results, the new genus Paracarphalea is here described to accommodate Carphalea angulata, C. kirondron, and C. pervilleana. The conservation status of Carphalea linearifolia is assessed as critically endangered according to IUCN criteria.

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