Tube-dwelling in early animals exemplified by Cambrian scalidophoran worms

Abstract Background The radiation of ecdysozoans (moulting animals) during the Cambrian gave rise to panarthropods and various groups of worms including scalidophorans, which played an important role in the elaboration of early marine ecosystems. Although most scalidophorans were infaunal burrowers travelling through soft sediment at the bottom of the sea, Selkirkia lived inside a tube. Results We explore the palaeobiology of these tubicolous worms, and more generally the origin and evolutionary significance of tube-dwelling in early animals, based on exceptionally preserved fossils from the early Cambrian Chengjiang Lagerstätte (Stage 3, China) including a new species, Selkirkia transita sp. nov. We find that the best phylogenetic model resolves Selkirkia as a stem-group priapulid. Selkirkia secreted a protective cuticular thickening, the tube, inside which it was able to move during at least part of its life. Partly based on measured growth patterns, we construe that this tube was separated from the trunk during a moulting process that has no direct equivalent in other scalidophorans. Although the ontogeny of Selkirkia is currently unknown, we hypothesize that its conical tube might have had the same ecological function and possibly even deep development origin as the lorica, a protective cuticular thickening found in larval priapulids and adult loriciferans. Selkirkia is seen as a semi-sedentary animal capable of very shallow incursions below the water/sediment interface, possibly for feeding or during the tube-secreting phase. Brachiopod epibionts previously reported from the Xiaoshiba Lagerstätte (ca. 514 Ma) also presumably occur in Selkirkia sinica from Chengjiang (ca. 518 Ma). Conclusions Our critical and model-based approach provides a new phylogenetic framework for Scalidophora, upon which to improve in order to study the evolution of morphological characters in this group. Tube-dwelling is likely to have offered Selkirkia better protection and anchoring to sediment and has developed simultaneously in other Cambrian animals such as hemichordates, annelids or panarthropods. Often lost in modern representatives in favour of active infaunal lifestyles, tube-dwelling can be regarded as an early evolutionary response of various metazoans to increasing environmental and biological pressure in Cambrian marine ecosystems.

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Character evolution of modern fly-speck fungi and implications for interpreting thyriothecial fossils

10.1101/2020.03.13.989582 ◽

2020 ◽

Author(s):

Ludovic Le Renard ◽

André L. Firmino ◽

Olinto L. Pereira ◽

Ruth A. Stockey ◽

Mary. L. Berbee

Keyword(s):

Morphological Evolution ◽

Morphological Characters ◽

Small Subunit ◽

Leaf Surfaces ◽

The Matrix ◽

Character Matrix ◽

Phylogenetic Framework ◽

Single Hypha ◽

Objective Basis ◽

Ancestral Character States

AbstractPREMISE OF THE STUDYFossils show that fly-speck fungi have been reproducing with small, black thyriothecia on leaf surfaces for ∼250 million years. We analyze morphological characters of extant thyriothecial fungi to develop a phylogenetic framework for interpreting fossil taxa.METHODSWe placed 59 extant fly-speck fungi in a phylogeny of 320 Ascomycota using nuclear ribosomal large and small subunit sequences, including newly determined sequences from nine taxa. We reconstructed ancestral character states using BayesTraits and maximum likelihood after coding 11 morphological characters based on original observations and literature. We analyzed the relationships of three previously published Mesozoic fossils using parsimony and our morphological character matrix, constrained by the molecular phylogeny.KEY RESULTSThyriothecia evolved convergently in multiple lineages of superficial, leaf- inhabiting ascomycetes. The radiate and ostiolate scutellum organization is restricted to Dothideomycetes. Scutellum initiation by intercalary septation of a single hypha characterizes Asterinales and Asterotexiales, and initiation by coordinated growth of two or more adjacent hyphae characterizes Aulographaceae (order incertae sedis). Scutella in Microthyriales are initiated apically on a lateral hyphal branch. Patterns of hyphal branching in scutella contribute to distinguishing among orders. Parsimony resolves three fossil taxa as Dothideomycetes; one is further resolved as a member of a Microthyriales-Zeloasperisporiales clade within Dothideomycetes.CONCLUSIONSThis is the most comprehensive systematic study of thyriothecial fungi and their relatives to date. Parsimony analysis of the matrix of character states of modern taxa provides an objective basis for interpreting fossils, leading to insights into morphological evolution and geological ages of Dothideomycetes clades.

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Homoplasy: from detecting pattern to determining process in evolution, but with a secondary role for morphology?

Zootaxa ◽

10.11646/zootaxa.2984.1.3 ◽

2011 ◽

Vol 2984 (1) ◽

pp. 67 ◽

Cited By ~ 4

Author(s):

LEANDRO C. S. ASSIS ◽

MARCELO R. DE CARVALHO ◽

QUENTIN D. WHEELER

Keyword(s):

Sequence Data ◽

Morphological Characters ◽

Flow Chart ◽

Molecular Topology ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Secondary Role ◽

Molecular Phylogenetic ◽

Phylogenetic Framework

David Wake and colleagues provided a thought-provoking review of the concept of homoplasy through the integration, within a phylogenetic framework, of genetic and developmental data (Wake et al. 2011). According to them (p. 1032) “Molecular sequence data have greatly increased our ability to identify homoplastic traits.” This is made clear, for example, in their flow chart for homoplasy detection (Figure 2, p. 1034), wherein homoplasy is discovered through the mapping of “traits of interest” onto a phylogram, a practice common in the molecular phylogenetic paradigm. The “mapping” is usually of morphological characters that are employed to support the chosen (molecular) topology, but which, as a consequence, do not themselves contribute to the formation of those topologies (Assis & Carvalho 2010).

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Phylogeny of the genus Tethya (Tethyidae: Hadromerida: Porifera): molecular and morphological aspects

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315407058419 ◽

2007 ◽

Vol 87 (6) ◽

pp. 1615-1627 ◽

Cited By ~ 10

Author(s):

Isabel Heim ◽

Michael Nickel ◽

Franz Brümmer

Keyword(s):

Distinct Species ◽

Morphological Characters ◽

Phylogenetic Study ◽

Western Atlantic ◽

Morphological Aspects ◽

Northern European ◽

Phylogenetic Resolution ◽

Phylogenetic Framework ◽

Biogeographic Regions ◽

Character Set

The genus Tethya represents a large cosmopolitan group of 81 recognized and a significant number of additional, still undescribed sponge species. The phylogenetic relationships within this old taxon are almost unknown. This is represented by the fact that several species are regarded as cosmopolitan. However, some of them might represent groups of closely related but distinct species. Using molecular and morphological characters, we aimed at a fundamental phylogenetic study for the genus Tethya, evaluating an existing morphological matrix and the cytochrome oxidase subunit I (COI) as a molecular marker. Intending to create a basic phylogenetic framework for the genus we selected a number of species from main biogeographic regions covered by Tethya species: from the Mediterranean Sea (T. citrina and T. aurantium), the northern European seas (T. citrina, T. norvegica and T. hibernica), the western Atlantic (T. actinia), the eastern Pacific (T. californiana), the Indo-Pacific (T. seychellensis) as well as three species of unknown biogeographical origin, originally described from aquarium habitats (T. wilhelma, T. gracilis and T. minuta). Both the morphological matrix, consisting of 29 characters and 131 character states, as well as the molecular matrices (COI nucleotide sequences of 658 bp as well as deduced amino acid sequence of 219 aa), resolved major biogeographical subgroups within the genus. However, the nucleotide based matrices revealed a higher resolution. Two major branches seem to have diverged early: an Indo-Pacific (T. seychellensis, T. wilhelma, T. minuta) and a Pan-European clade (T. citrina, T. norvegica, T. hibernica). For T. aurantium as well as a North-American group (T. californiana, T. actinia and T. minuta) our results are not conclusive. The morphological character set will have to be re-evaluated to gain a higher phylogenetic resolution. The addition of more species to our basal phylogenetic framework will allow analysing the evolution of the various biogeographical subgroups in the genus Tethya.

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Phylogeny and circumscription of Dasyphyllum (Asteraceae: Barnadesioideae) based on molecular data with the recognition of a new genus, Archidasyphyllum

PeerJ ◽

10.7717/peerj.6475 ◽

2019 ◽

Vol 7 ◽

pp. e6475 ◽

Cited By ~ 6

Author(s):

Paola de Lima Ferreira ◽

Mariana Machado Saavedra ◽

Milton Groppo

Keyword(s):

Morphological Characters ◽

Molecular Data ◽

South American ◽

Tropical Andes ◽

Venation Pattern ◽

Infrageneric Classification ◽

Leaf Venation ◽

Coding Regions ◽

Phylogenetic Framework ◽

Ancestral States

Dasyphyllum Kunth is the most diverse genus of the South American subfamily Barnadesioideae (Asteraceae), comprising 33 species that occur in tropical Andes, Atlantic Forest, Caatinga, Cerrado, and Chaco. Based on distribution, variation in anther apical appendages, and leaf venation pattern, it has traditionally been divided into two subgenera, namely, Archidasyphyllum and Dasyphyllum. Further, based on involucre size and capitula arrangement, two sections have been recognized within subgenus Dasyphyllum: Macrocephala and Microcephala (=Dasyphyllum). Here, we report a phylogenetic analysis performed to test the monophyly of Dasyphyllum and its infrageneric classification based on molecular data from three non-coding regions (trnL-trnF, psbA-trnH, and ITS), using a broad taxonomic sampling of Dasyphyllum and representatives of all nine genera of Barnadesioideae. Moreover, we used a phylogenetic framework to investigate the evolution of the morphological characters traditionally used to recognize its infrageneric groups. Our results show that neither Dasyphyllum nor its infrageneric classification are currently monophyletic. Based on phylogenetic, morphological, and biogeographical evidence, we propose a new circumscription for Dasyphyllum, elevating subgenus Archidasyphyllum to generic rank and doing away with the infrageneric classification. Ancestral states reconstruction shows that the ancestor of Dasyphyllum probably had acrodromous leaf venation, bifid anther apical appendages, involucres up to 18 mm in length, and capitula arranged in synflorescence.

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Single-spore isolate variation: the effect on varietal designation in Phytophthora megasperma

Canadian Journal of Botany ◽

10.1139/b82-354 ◽

1982 ◽

Vol 60 (12) ◽

pp. 2931-2938 ◽

Cited By ~ 6

Author(s):

P. B. Hamm ◽

E. M. Hansen

Keyword(s):

Growth Rate ◽

Hyphal Growth ◽

Morphological Characters ◽

Single Parent ◽

Growth Patterns ◽

Wild Type ◽

Single Spore ◽

Phytophthora Megasperma ◽

Single Spore Isolate ◽

Isolate Variation

Eight single zoospore isolates (SSI) were collected from each of 35 parent isolates of Phytophthora megasperma from 14 hosts. Morphological characters, hyphal growth patterns, and growth rate at several temperatures were measured and compared to assess variation of characters among the SSI of each parent. Oogonia, usually with paragynous antheridia, were formed by 94% of the SSI. The number of oogonia formed and the proportion of paragynous to amphigynous antheridia varied among SSI. Some SSI differed significantly from their parent in all characters measured. Oogonium (and oospore) diameter and sporangium shape were relatively consistent, but sporangium size varied widely. Parent isolates could not easily be classified as P. megasperma var. megasperma or P. megasperma var. sojae by oogonium diameter. Of the 35 parent isolates, 43% produced some SSI with oogonia averaging < 45 μm and some with oogonia averaging > 45 μm, the spore diameter used for varietal separation. Basing varieties on oogonium diameter is not justified because of such differences among SSI of a single parent and between wild-type isolates. The results supported a revised description of P. megasperma.

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A novel phylogenetic group withinThozetella(Chaetosphaeriaceae): a new taxon based on morphology and DNA sequence analyses

Canadian Journal of Microbiology ◽

10.1139/w08-148 ◽

2009 ◽

Vol 55 (6) ◽

pp. 680-687 ◽

Cited By ~ 3

Author(s):

R. Jeewon ◽

S. Y.Q. Yeung ◽

K. D. Hyde

Keyword(s):

Rna Polymerase Ii ◽

Close Association ◽

Pinus Elliottii ◽

Morphological Characters ◽

Molecular Data ◽

New Taxon ◽

Protein Coding ◽

Phylogenetic Framework ◽

The Relationship ◽

Insight Into

A new species, Thozetella pinicola , was isolated from leaf litter of Pinus elliottii Engelm. in Hong Kong. This taxon is described and compared with existing species in the genus. It occurs on the substrate as creamy white sporodochia and has short black conidiophores. Morphological characters are typical of Thozetella and it most closely resembles Thozetella falcata , Thozetella gigantea and Thozetella nivea , but may be distinguished by its distinct microawns and different conidial size. To gain further taxonomic insight into the phylogenetic relationships of our new taxon and its allies, we sequenced and analysed 6 different regions of 3 genes (ribosomal DNA and protein coding genes: RNA polymerase II largest subunit (RBP2) and β-tubulin). Resulting phylogenies are compared with existing morphological information. Molecular data support the relationship between Thozetella species and the Chaetosphaeriaceae (Chaetosphaeriales, Sordariomycetes). In addition, we recovered a new phylogenetic lineage (or group) within the existing phylogenetic framework of Thozetella as previously proposed. In particular, there is a close association between T. pinicola and T. nivea, which is strongly supported. The affinities of these 2 newly sequenced taxa are discussed in light of morphological and molecular characters.

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Out of place and out of time – towards a more integrated approach to heterochrony

Animal Biology ◽

10.1163/157075606778967810 ◽

2006 ◽

Vol 56 (4) ◽

pp. 487-502 ◽

Cited By ~ 8

Author(s):

Simon Rundle ◽

John Spicer

Keyword(s):

Morphological Traits ◽

Evolutionary Ecology ◽

Integrated Approach ◽

Morphological Characters ◽

Relative Timing ◽

Developmental Sequence ◽

Future Studies ◽

Developmental Sequences ◽

Phylogenetic Framework ◽

Ecological Mechanisms

AbstractHeterochrony (changes in the relative timing of development between species) has been studied almost exclusively using morphological characters, with a focus on changes in size and shape (as a surrogate for time) between ancestral species and their descendents. Such an approach is restrictive in that it precludes the investigation of heterochronies in other, non-morphological traits and, therefore, hampers a more integrated approach to heterochrony. Such an integrated approach, where cellular, molecular and genetic approaches are used within a comparative phylogenetic framework to investigate developmental sequences, has been advocated by workers such as Smith and Raff. Here we suggest that equal emphasis should be given to the importance of physiological and ecological mechanisms that relate to changes in developmental sequence. Reviews of the history and status of physiological and ecological heterochrony reveal several examples for each, although progress has been hampered to some degree by a lack of recognition of physiological heterochrony and a lack of mechanistic understanding (heterochronies in evolutionary ecology). What emerges is that each discipline potentially brings something quite different, and complementary, to the study of heterochrony. The emergence of physiological heterochrony has arguably put the emphasis back on the object of selection and how the developing organism works: studies relating ecology and heterochrony have sought to establish whether or not there is an adaptive basis to altered sequences. We propose that any future studies of heterochrony should seek to exploit these different strengths rather than see them as merely complementary approaches.

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Phylogenomics of Selaginellaceae with special reference to the enigmatic sanguinolenta group

10.1101/615633 ◽

2019 ◽

Author(s):

Hong-Rui Zhang ◽

Ran Wei ◽

Qiao-Ping Xiang ◽

Xian-Chun Zhang

Keyword(s):

Substitution Rate ◽

Gc Content ◽

Synonymous Substitution ◽

Morphological Characters ◽

Phylogenetic Position ◽

Basal Clade ◽

Phylogenetic Framework ◽

Phylogenomic Analyses ◽

The Stability

AbstractSelaginellaceae has been repeatedly proved as monophyly by previous studies with only one genus being recognized. However, the subgeneric classification has been debated during the recent decades. Furthermore, phylogenetic position of the newly identified sanguinolenta group has not been resolved, varying depending on the datasets and analysis methods. We carried out the phylogenomic analyses of twenty-six species from Selaginellaceae with ten species being newly sequenced and three species representing the sanguinolenta group. Four of the ten newly sequenced plastomes are assembled into the complete molecules, whereas the other six species are only assembled into five to sixteen contigs owing to high numbers of repeats. The phylogenetic framework from our study is basically congruent with the subgeneric classification of Weststrand and Korall (2016b). The position of sanguinolenta group was resolved as the basal clade in subg. Stachygynandrum, which support the position β proposed by Weststrand and Korall (2016a), also supported by the morphological characters of dimorphic vegetative leaves, monomorphic sporophylls and intermixed sporangial arrangements. Both values of dS, dN and GC content in Selaginellaceae plastomes were significantly higher than those of other lycophytes (Isoetaceae and Lycopodiaceae). The correlation analysis showed that the elevated synonymous substitution rate was significantly correlated with the high GC content in Selaginellaceae. Besides, the values of dS and dN differs significantly between branches in the phylogenetic tree of Selaginellaceae. We propose that both high GC content and the extensive RNA editing sites contributed to the elevated substitution rate in Selaginellaceae, and all of these three factors could influence the stability of phylogenetic topology of Selaginellaceae.

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