Bernard L. Cohen

Monophyly of brachiopods and phoronids: reconciliation of molecular evidence with Linnaean classification (the subphylum Phoroniformea nov.).

Molecular phylogenetic analyses of aligned 18S rDNA gene sequences from articulate and inarticulate brachiopods representing all major extant lineages, an enhanced set of phoronids and several unrelated protostome taxa, confirm previous indications that in such data, brachiopod and phoronids form a well–supported clade that (on previous evidence) is unambiguously affiliated with protostomes rather than deuterostomes. Within the brachiopod–phoronid clade, an association between phoronids and inarticulate brachiopods is moderately well supported, whilst a close relationship between phoronids and craniid inarticulates is weakly indicated. Brachiopod–phoronid monophyly is reconciled with the most recent Linnaean classification of brachiopods by abolition of the phylum Phoronida and rediagnosis of the phylum Brachiopoda to include tubiculous, shell–less forms. Recognition that brachiopods and phoronids are close genealogical allies of protostome phyla such as molluscs and annelids, but are much more distantly related to deuterostome phyla such as echinoderms and chordates, implies either (or both) that the morphology and ontogeny of blastopore, mesoderm and coelom formation have been widely misreported or misinterpreted, or that these characters have been subject to extensive homoplasy. This inference, if true, undermines virtually all morphology–based reconstructions of phylogeny made during the past century or more.

Phylogenetic relationships of Indian caecilians (Amphibia: Gymnophiona) inferred from mitochondrial rRNA gene sequences.

India has a diverse caecilian fauna, including representatives of three of the six currently recognized families, the Caeciliidae, Ichthyophiidae, the endemic Uraeotyphlidae, but previous molecular phylogenetic studies of caecilians have not included sequences for any Indian caecilians. Partial 12S and 16S mitochondrial gene sequences were obtained for a single representative of each of the caecilian families found in India and aligned against previously reported sequences for 13 caecilian species. The resulting alignment (16 taxa, 1200 sites, of which 288 cannot be aligned unambiguously) was analyzed using parsimony, maximum-likelihood, and distance methods. As judged by bootstrap proportions, decay indices, and leaf stabilities, well-supported relationships of the Indian caecilians are recovered from the alignment. The data (1) corroborate the hypothesis, based on morphology, that the Uraeotyphlidae and Ichthyophiidae are sister taxa, (2) recover a monophyletic Ichthyophiidae, including Indian and South East Asian representatives, and (3) place the Indian caeciliid Gegeneophis ramaswamii as the sister group of the caeciliid caecilians of the Seychelles. Rough estimates of divergence times suggest an origin of the Uraeotyphlidae and Ichthyophiidae while India was isolated from Laurasia and Africa and are most consistent with an Indian origin of these families and subsequent dispersal of ichthyophiids into South East Asia.

Phylogenetic relationships of African caecilians (Amphibia: Gymnophiona): Insights from mitochondrial rRNA gene sequences

Abstract Africa (excluding the Seychelles) has a diverse caecilian fauna, including the endemic family Scolecomorphidae and six endemic genera of the more cosmopolitan Caeciliidae. Previous molecular phylogenetic studies have not included any caecilians from the African mainland. Partial 12S and 16S mitochondrial gene sequences were obtained for two species of the endemic African Scolecomorphidae and five species and four genera of African caeciliids, aligned against previously reported sequences for 16 caecilian species, and analysed using parsimony, maximum likelihood, Bayesian and distance methods. Results are in agreement with traditional taxonomy in providing support for the monophyly of the African caeciliid genera Boulengerula and Schistometopum, and for the Scolecomorphidae. They disagree in indicating that the Caeciliidae is paraphyletic with respect to the Scolecomorphidae. Although more data from morphology and/or molecules will be required to resolve details of the interrelationships of the African caecilian genera, the data provide strong support for at least two origins of caecilians in which the eye is reduced and covered with bone, and do not support the hypotheses that the caecilian assemblages of Africa, and of East and of West Africa are monophyletic.

The Golden Tree Frog of Trinidad, Phyllodytes auratus (Anura: Hylidae): systematic and conservation status

Analyses of mitochondrial 12S and 16S rDNA sequences lead us to propose that the Neotropical hylid genus Phyllodytes is paraphyletic. The level of divergence between the Trinidadian endemic P. auratus and the two Brazilian Phyllodytes included in the analyses (Phyllodytes sp. and P. luteolus) is greater than that of inter‐generic distances within the Lophiohylini. The molecular evidence here reported, behavioural differences and restriction to a single host plant in a geographically limited area differentiates Phyllodytes auratus from other supposed Phyllodytes evidencing its unique taxonomic status. We therefore propose a new genus, Phytotriades gen. nov., for Phyllodytes auratus. P. auratus mitochondrial cytochrome b sequences obtained from one locality (seven individuals) contained two haplotypes, one individual differing by a single transition. The other locality (one individual) had the commoner haplotype. The low genetic divergence between the two populations suggests recent isolation at these two localities.

Provenance Of Atlantic Lingulid Brachiopods

Living lingulid brachiopods are ubiquitous in low-latitude, marine infaunas. Lingula occurs throughout the Pacific and Indian oceans with the only Atlantic species, L. parva, confined to West Africa. Glottidia is restricted to offshore America from Virginia to California and Peru, and is assumed to have descended from a Pacific Lingula during the early Tertiary. Lingulid organophosphatic shells differ structurally. That of Glottidia is characterizedby trellised rods (baculate); that of Indo-Pacific species of Lingula by spheroidal and rod-like microstructures (virgose); and that of L. parva by apatitic rods arranged as spherulites. A spherulitic fabric is unknown in fossil lingulids, but the distinction between GlottidiaLingula can be traced back to the Carboniferous, which accords with the deep molecular divergence between the two genera. The common occurrence of lingulids with baculate shells in European post-Palaeozoic sediments suggests that ancestral Glottidia entered the Atlantic by the Tethyan Current during the Late Cretaceous/early Cenozoic, and migrated into the Pacific before the formation of the Panama Isthmus. Penecontemporaneously, antecedents of L. parva possibly migrated from east Tethys along the trans-Saharan seaway.

MOLECULAR PHYLOGENY OF RHYNCHONELLIDE ARTICULATE BRACHIOPODS (BRACHIOPODA, RHYNCHONELLIDA)

We present here the first report based on phylogenetic analyses of small subunit (SSU/18S) and large subunit (LSU/28S) ribosomal DNA (rDNA) sequences from a wider-than-token sample of rhynchonellide articulate brachiopods, with data from 11 of ∼20 extant genera (12 species) belonging to all four extant superfamilies. Data exploration by network and saturation analyses shows that the molecular sequence data are free from major aberrations and are suitable for phylogenetic reconstruction despite the presence of large deletions in four SSU rDNA sequences. Although molecular sequence analyses cannot directly illuminate the systematics of fossils, the independent, genealogical evidence and phylogenetic inferences about extant forms that they make possible are highly relevant to paleontological systematics because they highlight the limitations of evolutionary inference from morphology. Parsimony, distance, maximum likelihood (no clock) and Bayesian (relaxed-clock) analyses all find a tree topology that disagrees strongly with the existing superfamily classification. All tested phylogenetic reconstructions agree that the taxa analyzed fall into three clades designated A1, A2, and B that reflect two major divergence events. The relaxed-clock analysis indicates that clades A and B diverged in the Paleozoic, while clades A1 and A2 reflect Permo-Triassic (and later) events. Morphological homoplasy and possible gene co-option are suggested as the main sources for the discord between the morpho-classification, the results of cladistic analyses of morphology, and the relationships reconstructed from molecular sequences. The origin, function and evolutionary implications of the deletion-bearing rhynchonellide SSU rDNA sequences are briefly discussed in relation to pseudogenes and concerted evolution in the rDNA genomic region.

Molecular and morphometric variation in European populations of the articulate brachiopod Terebratulina retusa

Molecular and morphometric variation within and between population samples of the articulate brachiopod Terebratulina spp., collected in 1985–1987 from a Norwegian fjord, sea-lochs and coastal sites in western Scotland, the southern English Channel (Brittany) and the western Mediterranean, were measured by the analysis of variation in the lengths of mitochondrial DNA (mtDNA) fragments produced by digestion with nine restriction endonucleases and by multivariate statistical analysis of six selected morphometric parameters. Nucleotide difference within each population sample was high. Nucleotide difference between population samples from the Scottish sites, both those that are tidally contiguous and those that appear to be geographically isolated, were not significantly different from zero. Nucleotide differences between the population samples from Norway, Brittany, Scotland and the western Mediterranean were also very low. Morphometric analysis confirmed the absence of substantial differentiation.

Functional anatomy inspires recognition of Ediacaran Dickinsonia and similar fossils as Mollusca (Coleoidea) and precursors of Cambrian Nectocaridids and extant cuttlefish and squid

A functional interpretation of the problematic Ediacaran fossils Podolimurus and similar organisms such as Dickinsonia indicates that they are hitherto unrecognized members of Mollusca: Coleoidea and precursors of Cambrian Nectocaridids and of extant cuttlefish and squid. This interpretation enables a new understanding of their taphonomy and reveals how this has deceived previous attempts to understand them.