Fredrik Pleijel

Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies

Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies

A molecular phylogeny of annelids

We present parsimony analyses of annelids based on the largest taxon sample and most extensive molecular data set yet assembled, with two nuclear ribosomal genes (18S rDNA and the D1 region of 28S rDNA), one nuclear protein coding‐gene (Histone H3) and one mitochondrial ribosomal gene (16S rDNA) from 217 terminal taxa. Of these, 267 sequences are newly sequenced, and the remaining were obtained from GenBank. The included taxa are based on the criteria that the taxon must have 18S rDNA or at least two other loci. Our analyses show that 68% of annelid family ranked taxa represented by more than one taxon in our study are supported by a jackknife value > 50%. In spite of the size of our data set, the phylogenetic signal in the deepest part of the tree remains weak and the majority of the currently recognized major polychaete clades (except Amphinomida and Aphroditiformia) could not be recovered. Terbelliformia is monophyletic (with the exclusion of Pectinariidae, for which only 18S data were available), whereas members of taxa such as Phyllodocida, Cirratuliformia, Sabellida and Scolecida are scattered over the trees. Clitellata is monophyletic, although Dinophilidae should possibly be included, and Clitellata has a sister group within the polychaetes. One major problem is the current lack of knowledge on the closest relatives to annelids and the position of the annelid root. We suggest that the poor resolution in the basal parts of the trees presented here may be due to lack of signal connected to incomplete data sets both in terms of terminal and gene sampling, rapid radiation events and/or uneven evolutionary rates and long‐branch attraction.

Taxonomic surrogacy in biodiversity assessments, and the meaning of Linnaean ranks

Abstract The majority of biodiversity assessments use species as the base unit. Recently, a series of studies have suggested replacing numbers of species with higher ranked taxa (genera, families, etc.); a method known as taxonomic surrogacy that has an important potential to save time and resources in assesments of biological diversity. We examine the relationships between taxa and ranks, and suggest that species/higher taxon exchanges are founded on misconceptions about the properties of Linnaean classification. Rank allocations in current classifications constitute a heterogeneous mixture of various historical and contemporary views. Even if all taxa were monophyletic, those referred to the same rank would simply denote separate clades without further equivalence. We conclude that they are no more comparable than any other, non‐nested taxa, such as, for example, the genus Rattus and the phylum Arthropoda, and that taxonomic surrogacy lacks justification. These problems are also illustrated with data of polychaetous annelid worms from a broad‐scale study of benthic biodiversity and species distributions in the Irish Sea. A recent consensus phylogeny for polychaetes is used to provide three different family‐level classifications of polychaetes. We use families as a surrogate for species, and present Shannon‐Wiener diversity indices for the different sites and the three different classifications, showing how the diversity measures rely on subjective rank allocations.

Least-inclusive taxonomic unit: a new taxonomic concept for biology.

Phylogenetic taxonomy has been introduced as a replacement for the Linnaean system. It differs from traditional nomenclature in defining taxon names with reference to phylogenetic trees and in not employing ranks for supraspecific taxa. However, ‘species’ are currently kept distinct. Within a system of phylogenetic taxonomy we believe that taxon names should refer to monophyletic groups only and that species should not be recognized as taxa. To distinguish the smallest identified taxa, we here introduce the least–inclusive taxonomic unit (LITU), which are differentiated from more inclusive taxa by initial lower–case letters. LITUs imply nothing absolute about inclusiveness, only that subdivisions are not presently recognized.

The phylogenetic position of Siboglinidae (Annelida) inferred from 18S rRNA, 28S rRNA and morphological data

We assess the phylogenetic position of Siboglinidae (previously known as the phyla Pogonophora and Vestimentifera, but now referred to Annelida) in parsimony analyses of 1100 bp from 18S rRNA, 320 bp from the D1 region of 28S rRNA, and 107 morphological characters, totaling 667 parsimony informative characters. The 34 terminal taxa, apart from six siboglinids, include polychaete members of Sabellida, Terbelliformia, Cirratuliformia and Spionida, plus two Aciculata polychaetes as outgroups. Our results contradict most recent hypotheses in showing a sistergroup relationship between Siboglinidae and Oweniidae, and in that the latter taxon is not a member of Sabellida. Furthermore, our results indicate that Sabellariidae is not closely related to Sabellida, that Serpulidae may be nested within Sabellidae, and that Alvinellidae is nested within Ampharetidae.

The fauna of hydrothermal vents on the Mohn Ridge (North Atlantic)

Abstract The macrofauna of the newly discovered hydrothermal vent field on the Mohn Ridge at 71°N was investigated. Samples were collected during the cruise BIODEEP 2006 using the ROV ‘Bathysaurus’. A total of 180 species-level taxa were identified. The region contains very few vent-endemic species, but some species of Porifera, Crustacea and Mollusca may be vent-associated. Dense aggregations of motile non-vent species such as Heliometra glacialis and Gorgonocephalus eucnemis surrounded the vent area, but the area in general only held small numbers of sedentary animals. Calcareous sponges comprised an unusually high portion of the sponge species found and they constitute one of the first pioneers among the sessile invertebrates settling on these vents. Possible explanations for the structure of the fauna in the region are discussed.

The phylogenetic relationships between Amphinomidae, Archinomidae and Euphrosinidae (Amphinomida: Aciculata: Polychaeta), inferred from molecular data

Amphinomida is an ‘isolated’ clade within the polychaete group Aciculata and traditionally includes the families Amphinomidae, Archinomidae and Euphrosinidae. Archinomidae were erected for a single species, the hydrothermal vent polychaete Archinome rosacea. Originally, A. rosacea was assigned to Euphrosinidae although it shares more morphological similarities with Amphinomidae. In this study we assess the position of Archinome, Euphrosinidae and Amphinomidae by using molecular data from nuclear 18S rDNA and 28S rDNA. Parsimony, maximum likelihood and Bayesian analyses are performed on the nucleotide datasets covering in total 19 terminals from Amphinomidae, Euphrosinidae, Archinomidae and outgroups. Our results conclusively show that Euphrosinidae and Amphinomidae are sister taxa and that Archinome is sister to Chloeia within Amphinomidae. Based on these results the family name Archinomidae is treated as a junior synonym of Amphinomidae.

Phyllodoce (Polychaeta, Phyllodocidae) from Northern Europe

Descriptions of species of Phyllodoce Savigny, 1818 from Northern Europe [P. laminosa Savigny, 1818, P. citrna Malmgren, 1865, P. groenlandicaÖrsted, 1843, P. lineata (Claparède, 1870), P. longipes Kinberg, 1866, P. maculata (Linnaeus, 1767), P. mucosaÖrsted, 1843 and P. rosea (Melntosh, 1877) comb.n.] are given. A key to the species is included. The examined material consists of newly collected material as well as collections in museums. Available type material has been checked. A number of junior synonyms are proposed. Anaitides Czerniavsky, 1882 and Aponaitides MeCammon & Montagne, 1979 are considered not valid.

Phylogenetic relationships within Nereididae (Annelida : Phyllodocida)

Nereididae Johnston, 1865, part of the large clade Phyllodocida, is one of the best-known annelid groups. Presently, there are some 500 nominal species grouped into 42 genera, although there is little consensus among different authors as to how they should be classified. The relationships of nereidids were assessed in a morphology-based parsimony analysis of 41 terminal taxa, with members of Chrysopetalidae and Hesionidae used as outgroups. Type species for the majority of currently recognised nereidid genera were used as terminal taxa, and character information was based on examination of type and non-type specimens, together with literature descriptions. High degrees of homoplasy were found for several features that are traditionally applied to delineate subgroups of Nereididae, including the presence of paragnaths and the distribution of different kinds of chaetae. Six major groups were recovered: Namanereidinae, including Namalycastis and Namanereis, characterised by spherical shape of palpostyles and ventrally displaced notoaciculae; one clade corresponding in part to previous authors concepts of Nereidinae, including Nereis, Eunereis, Hediste and Platynereis (the relationships of several well known nereidids, such as Neanthes and Perinereis, commonly referred to Nereidinae, could not be unambiguously resolved); one unnamed and not previously recognised clade (A), including Australonereis, Laeonereis, Dendronereides and Olganereis, characterised by the presence of papillae on the maxillary ring; a second unnamed clade (B), including Leptonereis, Sinonereis, Tylonereis and Tylorrhynchus, characterised by enlarged notopodial ligulae; a well supported Gymnonereidinae, restricted to Ceratocephale, Gymnonereis, Tambalagamia and Micronereides; and a third unnamed clade (C), including Ceratonereis, Solomononereis, Unanereis, Cheilonereis and Websterinereis, characterised by unilobated neuropodial postchaetal lobes. Among these groups we found good support for the Namanereidinae, the Gymnonereidinae and for the whole of Nereididae. The subfamilies Dendronereidinae and Notophycinae (based on Micronereis, senior synonym of Notophycus) are regarded here as monotypic.

A revision of Micropodarke (Psamathini, Hesionidae, Polychaeta)

Micropodarke Okuda, 1938 (Psamathini, Hesionidae, Polychaeta) is revised based on examination of all available types, other museum specimens, and a large number of newly collected specimens from Japan, Hong Kong, Papua New Guinea, Australia, New Caledonia, California, the west coast of Canada, and the Red Sea. The previous synonymy of Micropodarke amemiyai Okuda, 1938 with M. dubia (Hessle, 1925) is substantiated, and M. trilobata Hartmann‐Schröder, 1983 is newly synonymized with M. dubia, leaving Micropodarke monotypic. A lectotype is selected for M. dubia. Micropodarke dubia is identified by the apomorphies of a proboscis diaphragm, segmental ventral adhesive papillae, distally nobbed and slightly curved neuroaciculae, and median neurochaetae with few, basally situated prolonged teeth (“spurs”), with abrupt transition to the following, much shorter teeth. Micropodarke dubia has a main distribution in the tropical and warm temperate Indo‐Pacific region, and appears to be absent from the Atlantic Ocean.