Pragmatic Assignment of Species Groups Based on Primary Species Hypotheses: The Case of a Dominant Component of the Southern Ocean Benthic Fauna

Ecological studies that enhance our understanding of the structure and function of the natural world rely heavily on accurate species identification. With rapid sample accumulation and declining taxonomic expertise, cladistics, phylogenetics and coalescent-based analyses have become key tools for identification or discrimination of species. These tools differ in effectiveness and interpretation depending on researcher perspective and the unique evolutionary histories of the taxa. Given the cost and time required for taxonomic assessment of ambiguous species groups, we advocate a pragmatic approach to clarify species assignment. We carried out a case-study on species from the diverse ophiuroid genus Ophiacantha common in shelf habitats around the Southern Ocean. Although several of the species are formally described with clear and distinctive morphological characters and reproductive strategies (O. vivipara, O. pentactis, O. densispina, O. antarctica, and O. wolfarntzi), recent molecular data has highlighted issues with these morphospecies, the characters that formally define them and their evolutionary histories. Here we provide evidence that key morphological features of species can be deceptive and show that six-armed O. vivipara, for example, is not a widely distributed Southern Ocean species as currently accepted, rather, three disparate clades. Ophiacantha pentactis, described as having five arms, frequently has six arms and the six-armed form is mistakenly classified as O. vivipara. All six-armed specimens collected from the Antarctic continental shelf fall into the O. pentactis species clade. Molecular tools designed for species delimitation appear to fail to reflect the “true” species composition. Rather than rely on a single tool for species recognition, we advocate an integrated approach using traditional detailed taxonomic morphology, summary statistics of molecular sequence data from populations, robust phylogenies, sufficient geographical sampling and local biological knowledge to ensure that species hypotheses can be built on mutually supporting lines of evidence.

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Living and fossil placentals

The Origin and Evolution of Mammals ◽

10.1093/oso/9780198507604.003.0010 ◽

2004 ◽

Author(s):

T.S. Kemp

Keyword(s):

Sequence Data ◽

Sister Group ◽

Morphological Characters ◽

Molecular Data ◽

Molecular Sequence Data ◽

Minor Characters ◽

Molecular Sequence ◽

Large Sets ◽

Anterior Teeth ◽

Basal Group

The vast majority of living and fossil mammals are placentals. Today there are about 4,400 species, which are traditionally organised into 18 Orders, with an extra one if the Pinnipedia are separated from the Carnivora, and a twentieth if the recently extinct Malagasy order Bibymalagasia is recognised as such. There have been many attempts to discover supraordinal groupings from amongst these Orders based on morphological characters, though few proposals have been universally accepted. It is only with the advent of increasingly large sets of molecular sequence data in the last few years that a reasonably robust resolution looks imminent, although these contemporary analyses are remarkably and controversially at odds with the traditional ones. Novacek et al. (1988) summarised the then current situation regarding supraordinal classification of placentals, a time at which morphology was still dominant but molecular data was at the threshold of significance. They accepted a basal group Edentata that combined the Xenarthra of the New World with the Pholidota of the Old, based on a few cranial characters, loss of the anterior teeth, and reduction of the enamel of the remaining ones. This left the rest of the living placentals as a monophyletic group Epitheria, sharing such apparently minor characters as the shape of the stapes bone in the ear. They found very little resolution within the Epitheria, and concluded that there was a polychotomy of no less than nine lineages arranged as a ‘star’ phylogeny. No remnant of the previously recognised taxon Ferungulata, created by Simpson (1945) for the Carnivora plus the ungulate orders Artiodactyla, Perissodactyla, Proboscidea, Hyracoidea, Sirenia, and Tubulidentata remained. On the other hand, three supra ordinal taxa of earlier authors did survive. One was Gregory’s (1910) Archonta, consisting of generally conservative forms and by now composed of the Primates, Dermoptera, Scandentia, and Chiroptera, but excluding the Lipotyphla. The second was Glires, originating with Linnaeus (1758) and widely accepted ever since, for the Rodentia and Lagomorpha; Novacek et al. (1988) tentatively placed the Macroscelidea as the sister-group of the Glires. The third supraordinal taxon recognised was, like Glires, well-established if not universally accepted.

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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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Combined molecular and morphological phylogeny of Ephemerellinae (Ephemerellidae: Ephemeroptera), with remarks about classification

Zootaxa ◽

10.11646/zootaxa.1991.1.2 ◽

2009 ◽

Vol 1991 (1) ◽

pp. 28-42 ◽

Cited By ~ 6

Author(s):

T. HEATH OGDEN ◽

JONATHAN T. OSBORNE ◽

LUKE M. JACOBUS ◽

MICHAEL F. WHITING

Keyword(s):

Morphological Analysis ◽

Sequence Data ◽

Histone H3 ◽

Morphological Characters ◽

Morphological Data ◽

Rdna Genes ◽

Dna Sequence Data ◽

Extant Genus ◽

Species Groups ◽

Combined Data

This study represents the first combined molecular and morphological analysis for the mayfly family Ephemerellidae (Ephemeroptera), with a focus on the relationships of genera and species groups of the subfamily Ephemerellinae. The phylogeny was constructed based on DNA sequence data from 3 nuclear (18S rDNA, 28S rDNA, histone H3) and 2 mitochondrial (12S rDNA, 16S rDNA) genes, and 23 morphological characters. Taxon sampling for Ephemerellidae included exemplars from all 25 extant genus groups and additional representatives from those genera with the highest diversity. Ephemerellidae appears to consist of three major clades. Ephemerella, the largest genus of Ephemerellidae, and Serratella were not supported as monophyletic, and each had representatives in two of the three major clades. However, the genera Drunella and Cincticostella were supported as monophyletic. Lineages strongly supported as monophyletic include a grouping of the Timpanoginae genera Timpanoga, Dannella, Dentatella and Eurylophella, and groupings of the Ephemerellinae genera Torleya, Hyrtanella and Crinitella and the genera Kangella, Uracanthella and Teloganopsis. The placement of the Timpanoginae genus Attenella fell within Ephemerellinae, based on molecular and combined data, but it grouped with other Timpanoginae based on morphological data alone. Further study and analysis of Ephemerellidae morphology is needed, and classification should be revised, if it is to reflect phylogenetic relationships.

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Evaluating methodologies for species delimitation: the mismatch between phenotypes and genotypes in lichenized fungi (Bryoria sect. Implexae, Parmeliaceae)

Persoonia - Molecular Phylogeny and Evolution of Fungi ◽

10.3767/persoonia.2019.42.04 ◽

2019 ◽

Vol 42 (1) ◽

pp. 75-100 ◽

Cited By ~ 11

Author(s):

C.G. Boluda ◽

V.J. Rico ◽

P.K. Divakar ◽

O. Nadyeina ◽

L. Myllys ◽

...

Keyword(s):

Dna Sequences ◽

Species Delimitation ◽

Sequence Data ◽

Species Recognition ◽

Phylogenetic Analyses ◽

Phylogenetic Reconstruction ◽

Haplotype Network ◽

Molecular Data ◽

Integrative Taxonomy ◽

Molecular Sequence Data

In many lichen-forming fungi, molecular phylogenetic analyses lead to the discovery of cryptic species within traditional morphospecies. However, in some cases, molecular sequence data also questions the separation of phenotypically characterised species. Here we apply an integrative taxonomy approach – including morphological, chemical, molecular, and distributional characters – to re-assess species boundaries in a traditionally speciose group of hair lichens, Bryoria sect. Implexae. We sampled multilocus sequence and microsatellite data from 142 specimens from a broad intercontinental distribution. Molecular data included DNA sequences of the standard fungal markers ITS, IGS, GAPDH, two newly tested loci (FRBi15 and FRBi16), and SSR frequencies from 18 microsatellite markers. Datasets were analysed with Bayesian and maximum likelihood phylogenetic reconstruction, phenogram reconstruction, STRUCTURE Bayesian clustering, principal coordinate analysis, haplotype network, and several different species delimitation analyses (ABGD, PTP, GMYC, and DISSECT). Additionally, past population demography and divergence times are estimated. The different approaches to species recognition do not support the monophyly of the 11 currently accepted morphospecies, and rather suggest the reduction of these to four phylogenetic species. Moreover, three of these are relatively recent in origin and cryptic, including phenotypically and chemically variable specimens. Issues regarding the integration of an evolutionary perspective into taxonomic conclusions in species complexes, which have undergone recent diversification, are discussed. The four accepted species, all epitypified by sequenced material, are Bryoria fuscescens, B. glabra, B. kockiana, and B. pseudofuscescens. Ten species rank names are reduced to synonymy. In the absence of molecular data, they can be recorded as the B. fuscescens complex. Intraspecific phenotype plasticity and factors affecting the speciation of different morphospecies in this group of Bryoria are outlined.

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Molecular phylogenetics of snailfishes (Cottoidei: Liparidae) based on MtDNA and RADseq genomic analyses, with comments on selected morphological characters

Zootaxa ◽

10.11646/zootaxa.4642.1.1 ◽

2019 ◽

Vol 4642 (1) ◽

pp. 1-79 ◽

Cited By ~ 9

Author(s):

JAMES WILDER ORR ◽

INGRID SPIES ◽

DUANE E. STEVENSON ◽

GARY C. LONGO ◽

YOSHIAKI KAI ◽

...

Keyword(s):

Molecular Phylogenetics ◽

Sequence Data ◽

Morphological Characters ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Genome Wide ◽

The Pacific ◽

The Family ◽

Genomic Analyses ◽

Gene Coi

Phylogenetic relationships of snailfishes of the family Liparidae were analyzed on the basis of two sets of molecular sequence data: one from the mitochondrial DNA cytochrome c oxidase subunit one gene (COI) and another from restriction-site associated genome-wide sequences (RADseq). The analysis of COI sequence data from at least 122 species of 18 genera from the Pacific, Atlantic, and Southern oceans resulted in a moderately well-resolved phylogeny among the major clades, albeit with significant polytomy among central clades. Nectoliparis was the sister of all other members of the family, followed by Liparis. Liparis, Careproctus, and Paraliparis were paraphyletic. Liparis was recovered in two closely related clades, with L. fucensis sister of all other liparids except Nectoliparis, and both Careproctus and Paraliparis were each recovered among at least three widely separated clades. The RADseq analysis of 26 species of 11 genera from the eastern North Pacific strongly confirmed the overall results of the COI analysis, with the exception of the paraphyly of Liparis due to the absence of L. fucensis. Our results show that the pelvic disc has been independently lost multiple times and the pectoral-fin girdle has been independently reduced in multiple lineages.

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Investigating the Bivalve Tree of Life – an exemplar-based approach combining molecular and novel morphological characters

Invertebrate Systematics ◽

10.1071/is13010 ◽

2014 ◽

Vol 28 (1) ◽

pp. 32 ◽

Cited By ~ 130

Author(s):

Rüdiger Bieler ◽

Paula M. Mikkelsen ◽

Timothy M. Collins ◽

Emily A. Glover ◽

Vanessa L. González ◽

...

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Analytical Framework ◽

Morphological Characters ◽

Molecular Data ◽

Probabilistic Methods ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Protein Encoding ◽

Encoding Genes

To re-evaluate the relationships of the major bivalve lineages, we amassed detailed morpho-anatomical, ultrastructural and molecular sequence data for a targeted selection of exemplar bivalves spanning the phylogenetic diversity of the class. We included molecular data for 103 bivalve species (up to five markers) and also analysed a subset of taxa with four additional nuclear protein-encoding genes. Novel as well as historically employed morphological characters were explored, and we systematically disassembled widely used descriptors such as gill and stomach ‘types’. Phylogenetic analyses, conducted using parsimony direct optimisation and probabilistic methods on static alignments (maximum likelihood and Bayesian inference) of the molecular data, both alone and in combination with morphological characters, offer a robust test of bivalve relationships. A calibrated phylogeny also provided insights into the tempo of bivalve evolution. Finally, an analysis of the informativeness of morphological characters showed that sperm ultrastructure characters are among the best morphological features to diagnose bivalve clades, followed by characters of the shell, including its microstructure. Our study found support for monophyly of most broadly recognised higher bivalve taxa, although support was not uniform for Protobranchia. However, monophyly of the bivalves with protobranchiate gills was the best-supported hypothesis with incremental morphological and/or molecular sequence data. Autobranchia, Pteriomorphia, Heteroconchia, Palaeoheterodonta, Archiheterodonta, Euheterodonta, Anomalodesmata and Imparidentia new clade ( = Euheterodonta excluding Anomalodesmata) were recovered across analyses, irrespective of data treatment or analytical framework. Another clade supported by our analyses but not formally recognised in the literature includes Palaeoheterodonta and Archiheterodonta, which emerged under multiple analytical conditions. The origin and diversification of each of these major clades is Cambrian or Ordovician, except for Archiheterodonta, which diverged from Palaeoheterodonta during the Cambrian, but diversified during the Mesozoic. Although the radiation of some lineages was shifted towards the Palaeozoic (Pteriomorphia, Anomalodesmata), or presented a gap between origin and diversification (Archiheterodonta, Unionida), Imparidentia showed steady diversification through the Palaeozoic and Mesozoic. Finally, a classification system with six major monophyletic lineages is proposed to comprise modern Bivalvia: Protobranchia, Pteriomorphia, Palaeoheterodonta, Archiheterodonta, Anomalodesmata and Imparidentia.

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Systematics of Bulbostyla, a new subgenus of Sarcophaga Meigen, and change of status for Robackina Lopes (Diptera: Sarcophagidae)

Zootaxa ◽

10.11646/zootaxa.2553.1.2 ◽

2010 ◽

Vol 2553 (1) ◽

pp. 35 ◽

Cited By ~ 10

Author(s):

MARJOLAINE GIROUX ◽

TERRY A. WHEELER

Keyword(s):

Phylogenetic Relationships ◽

Type Species ◽

New World ◽

Sequence Data ◽

Morphological Characters ◽

Molecular Sequence Data ◽

World Species ◽

Molecular Sequence ◽

New Subgenus

Sarcophaga (Bulbostyla) subgen. nov. is described as a new subgenus of Sarcophaga Meigen to accommodate some species previously assigned to the subgenus S. (Neobellieria) Blanchard. Sarcophaga (Bulbostyla) contains nine species: S. airosalis sp. nov., S. cadyi sp. nov. (type species), S. cuautla sp. nov., S. fattigina sp. nov., S. ironalis sp. nov., S. semimarginalis Hall, S. sternalis (Reinhard), S. subdiscalis Aldrich and S. yorkii Parker. All species are described and illustrated and a key to the species is provided. The species within the subgenus are morphologically uniform externally and are distinguished mostly on male genitalic characters. Phylogenetic relationships within Bulbostyla are unresolved based on morphological characters and will require consideration of additional characters, such as molecular sequence data. The genus-group taxon Robackina Lopes is removed from synonymy with the subgenus Sarcophaga (Neobellieria) and reinstated as a valid subgenus of Sarcophaga (stat. nov.) to accommodate the single New World species Sarcophaga triplasia Wulp. A lectotype is designated for S. triplasia. The subgenus and species are redescribed and illustrated.

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Inferring Species Trees Using Integrative Models of Species Evolution

10.1101/242875 ◽

2018 ◽

Cited By ~ 9

Author(s):

Huw A. Ogilvie ◽

Timothy G. Vaughan ◽

Nicholas J. Matzke ◽

Graham J. Slater ◽

Tanja Stadler ◽

...

Keyword(s):

Gene Evolution ◽

Sequence Data ◽

A Priori ◽

Morphological Characters ◽

Mirror Image ◽

Integrative Model ◽

Species Trees ◽

Data Set ◽

Molecular Sequence Data ◽

Molecular Sequence

AbstractBayesian methods can be used to accurately estimate species tree topologies, times and other parameters, but only when the models of evolution which are available and utilized sufficiently account for the underlying evolutionary processes. Multispecies coalescent (MSC) models have been shown to accurately account for the evolution of genes within species in the absence of strong gene flow between lineages, and fossilized birth-death (FBD) models have been shown to estimate divergence times from fossil data in good agreement with expert opinion. Until now dating analyses using the MSC have been based on a fixed clock or informally derived node priors instead of the FBD. On the other hand, dating analyses using an FBD process have concatenated all gene sequences and ignored coalescence processes. To address these mirror-image deficiencies in evolutionary models, we have developed an integrative model of evolution which combines both the FBD and MSC models. By applying concatenation and the MSC (without employing the FBD process) to an exemplar data set consisting of molecular sequence data and morphological characters from the dog and fox subfamily Caninae, we show that concatenation causes predictable biases in estimated branch lengths. We then applied concatenation using the FBD process and the combined FBD-MSC model to show that the same biases are still observed when the FBD process is employed. These biases can be avoided by using the FBD-MSC model, which coherently models fossilization and gene evolution, and does not require an a priori substitution rate estimate to calibrate the molecular clock. We have implemented the FBD-MSC in a new version of StarBEAST2, a package developed for the BEAST2 phylogenetic software.

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A review of species recognition in the Phenacoccus aceris species-group (Hemiptera: Coccomorpha: Pseudococcidae) using molecular and morphological data

Zootaxa ◽

10.11646/zootaxa.4319.3.4 ◽

2017 ◽

Vol 4319 (3) ◽

pp. 483

Author(s):

XU-BO WANG ◽

SAN-AN WU

Keyword(s):

Sequence Data ◽

Species Recognition ◽

Morphological Characters ◽

Species Group ◽

Morphological Data ◽

Character State ◽

Relative Width ◽

Nucleotide Sequence Data ◽

Putative Species ◽

Species Separation

The maple mealybug, Phenacoccus aceris (Signoret) (Hemiptera: Pseudococcidae), is a widespread polyphagous pest. The taxonomy of P. aceris and some congeners is controversial. This study utilized molecular analysis of one mitochondrial (cytochrome oxidase I) and two nuclear (EF-1α and 28S D2D3) genes, and morphological data, to investigate the P. aceris species-group based on 120 individuals collected from 16 localities in China. Analyses of the nucleotide sequence data recovered four well-supported clades that enabled us to reassess the taxonomic utility of some morphological characters used for species recognition in the P. aceris species-group, such as the number, location and width of circuli, and the distribution pattern of oral-collar tubular ducts on the dorsum. Polymorphism in the number of circuli indicated that this character-state alone is unreliable for species separation, but a combination of the number, location and relative width of the circuli provides a significant taxonomic character. The distribution of oral-collar tubular ducts on dorsal segments of the cephalothorax can be used also for species separation. In addition, specimens that keyed morphologically to P. aceris contained three putative species that are not separated by host-plant preferences. These putative species are genetically and morphologically different from P. aceris in France (the type locality of P. aceris) and are thus probably new to science. A network analysis of the COI haplotypes showed that the hosts Fraxinus spp. (Oleaceae) and Zanthoxylum bungeanum (Rutaceae) in North China are attacked by both P. aceris and P. azaleae, so previous identifications of this group based on the identity of these host plants is misleading. The taxonomic confusion in the P. aceris species-group may be due to the co-occurrence of multiple putative species.

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The Phylogeny of Rhizocephalan Parasites of the Genus Heterosaccus using Molecular and Larval Data (Cirripedia: Rhizocephala; Sacculinidae)

Israel Journal of Ecology and Evolution ◽

10.1080/15659801.2008.10639616 ◽

2008 ◽

Vol 54 (2) ◽

pp. 223-238 ◽

Cited By ~ 6

Author(s):

Henrik Glenner ◽

Philip Francis Thomsen ◽

Alexey V. Rybakov ◽

Bella S. Galil ◽

Jens T. Hoeg

Keyword(s):

Sequence Data ◽

Morphological Characters ◽

Molecular Data ◽

Sem Analysis ◽

Accurate Identification ◽

Generic Level ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

The Third ◽

The Family

Within parasitic barnacles of the family Sacculinidae, the genus Heterosaccus is the third largest, with 12 species infesting various brachyuran hosts throughout the world. As part of an effort to reconstruct rhizocephalan phylogeny we performed an analysis of four species of Heterosaccus and of selected sacculinid and non-sacculinid rhizocephalans. We used both molecular sequence data (16s rDNA and 18s rDNA) and morphological characters from an SEM analysis of the cypris larvae. Using Bayesian methods we obtained a highly supported tree in which the four species of Heterosaccus form a monophylum, whereas both the genus Sacculina and the family Sacculinidae are polyphyletic. The sistergroup to Heterosaccus is a clade consisting of the sacculinids Loxothylacus panopaei and the "classical" rhizocephalan Sacculina carcini. The molecular results found support in cypris morphology, where we identified two distinct synapomorphies for Heterosaccus, both present in male cyprids only: A large flap extending posteriorly from the third antennular segment, and the male-specific aesthetasc on the third segment being reduced to a rudiment or lacking completely. Female cyprids didn't show generic level apomorphies but resembled those of other sacculinid species. No morphological synapomorphies were identified between Heterosaccus, L. panopaei and S. carcini. While larval characters proved to be informative, we conclude that future studies on rhizocephalan taxonomy must rely primarily on molecular data, both to provide an overall phylogenetic framework and to assure an accurate identification of species for biogeographical and other biological purposes.

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