Michael Hardman

Phylogenetic Relationships among Bullhead Catfishes of the Genus Ameiurus (Siluriformes: Ictaluridae)

Abstract Catfishes of the genus Ameiurus are a well-known component of the North American ichthyofauna. J. G. Lundberg estimated phylogenetic relationships among species of Ameiurus according to morphological variation. Two clades containing the extant species were recovered: the natalis clade (Ameiurus natalis, Ameiurus melas, and Ameiurus nebulosus) and the catus clade (Ameiurus serracanthus, Ameiurus catus, Ameiurus platycephalus, and Ameiurus brunneus). Original nucleotide sequence data were collected from mitochondrial (cytochrome b) and nuclear (recombination activation gene 2) genes and used to test the predictions of the hypothesis based on morphological data. The monophyly of both natalis and catus clades was rejected by the nucleotide dataset and an alternative phylogenetic hypothesis is provided.

Biodiversity and phylogeography of Arctic marine fauna: insights from molecular tools

The last decade has seen an increase in the frequency and breadth of application of molecular tools, many of which are beginning to shed light on long-standing questions in biogeography and evolutionary history of marine fauna. We explore new developments with respect to Arctic marine invertebrates, focusing on molecular taxonomy and phylogeography—two areas that have seen the most progress in the time-frame of the Census of Marine Life. International efforts to generate genetic ‘barcodes’ have yielded new taxonomic insights and applications ranging from diet analysis to identification of larval forms. Increasing availability of genetic data in public databases is also facilitating exploration of large-scale patterns in Arctic marine populations. We present new case-studies in meta-population analysis of barcode data from polychaetes and echinoderms that demonstrate such phylogeographic applications. Emerging patterns from ours and other published studies include influences of a complex climatic and glacial history on genetic diversity and evolution in the Arctic, and contrasting patterns of both high gene flow and persistent biogeographic boundaries in contemporary populations.

The phylogenetic relationships among Noturus catfishes (Siluriformes: Ictaluridae) as inferred from mitochondrial gene cytochrome b and nuclear recombination activating gene 2

Madtom catfishes of the genus Noturus are a well-known component of the North American ichthyofauna. Original nucleotide sequence data were collected from mitochondrial (cytochrome b) and nuclear (recombination activating gene 2) genes and used to estimate genetic variation and infer phylogenetic relationships among and within species of Noturus. Mitochondrial sequences were variable among species and several species were found to contain considerable genetic diversity. Relationships among members of the subgenus Rabida were resolved and in many cases well supported. Relationships among members of the subgenus Schilbeodes were poorly resolved. Previous phylogenetic hypotheses and the traditional classification (except the furiosus species group) were rejected in their explicit form according to the Kishino-Hasegawa and Shimodaira-Hasegawa tests of tree score difference.

The relative importance of body size and paleoclimatic change as explanatory variables influencing lineage diversification rate: an evolutionary analysis of bullhead catfishes (Siluriformes: Ictaluridae).

We applied Bayesian phylogenetics, divergence time estimation, diversification pattern analysis, and parsimony-based methods of ancestral state reconstruction to a combination of nucleotide sequences, maximum body sizes, fossils, and paleoclimate data to explore the influence of an extrinsic (climate change) and an intrinsic (maximum body size) factor on diversification rates in a North American clade of catfishes (Ictaluridae). We found diversification rate to have been significantly variable over time, with significant (or nearly significant) rate increases in the early history of Noturus. Though the latter coincided closely with a period of dramatic climate change at the Eocene-Oligocene boundary, we did not detect evidence for a general association between climate change and diversification rate during the entire history of Ictaluridae. Within Ictaluridae, small body size was found to be a near significant predictor of species richness. Morphological stasis of several species appears to be a consequence of a homoplastic increase in body size. We estimated the maximum standard length of the ictalurid ancestor to be approximately 50 cm, comparable to Eocene ictalurids (Astephus) and similar to modern sizes of Ameiurus and their Asian sister-taxon Cranoglanis. During the late Paleocene and early Eocene, the ictalurid ancestor diversified into the lineages represented by the modern epigean genera. The majority of modern species originated in the Oligocene and Miocene, most likely according to a peripheral isolates model of speciation. We discuss the difficulties of detecting macroevolutionary patterns within a lineage history and encourage the scrutiny of the terminal Eocene climatic event as a direct promoter of diversification.

Phylogenetic Relationships of Barcheek Darters (Percidae: Etheostoma, Subgenus Catonotus) with Descriptions of Two New Species

Abstract Etheostoma virgatum has been treated as a species occupying three widely separated regions of the Cumberland River drainage in Kentucky and Tennessee. To test the hypothesis that the three widely disjunct populations of E. virgatum are monophyletic, DNA sequence data from mitochondrial and nuclear loci were gathered on E. virgatum and other species of Catonotus including all species of barcheek darters. Morphological data were analyzed from populations throughout the range of E. virgatum. The three widely separated populations of E. virgatum, although morphologically similar, do not form a monophyletic group in phylogenetic analyses of molecular data. Consistent with this result, two of the populations are described as new species. These three species had been identified as E. virgatum because of the shared presence of bold dark stripes along the side of the body, a feature not found in the other four species of barcheeks. It is unclear whether the presence of bold stripes represents retention of a pleisiomorphic trait (lost in other barcheeks) or whether the condition arose independently in these three species.

Phylogenetics of the South American Catfish Family Pimelodidae (Teleostei: Siluriformes) using Nuclear and Mitochondrial Gene Sequences

ABSTRACT. Existing phylogenetic hypotheses on the intrarelationships of South American pimelodid catfishes are incompletely resolved and based almost entirely on morphological data. This study analyzed more than seven kilobases of aligned nucleotide sequences from the rag1 and rag2 nuclear genes, and the 12S, 16S and cytochrome b mitochondrial genes for 52 nominal and five undescribed pimelodid species representing 27 of 31 extant genera. Results of Bayesian likelihood and maximum parsimony analyses of the combined sequence data consistently recover 40 monophyletic pimelodid clades above the species level. The basal lineages of Pimelodidae are Steindachneridion and Phractocephalus that are serially, or together as small clade, sister to all other members of the family. Leiarius and the nominal Perrunichthys perruno are sister to the neopimelodines, a clade comprised of the remaining pimelodids divided into two major lineages: the sorubimines and the Pimelodus ornatus-Calophysus-Pimelodus (OCP) Clade. Sorubimines include seven well-supported units whose interrelationships are poorly resolved: Sorubim, Pseudoplatystoma-Sorubimichthys Clade, tribe Brachyplatystomatini, Platysilurus-Platystomatichthys Clade, Hypophthalmus, Zungaro and Hemisorubim. In conflict with morphological evidence, the molecular data do not support monophyly of the genus Brachyplatystoma. However, the subgenus Malacobagrus (B. rousseauxii, B. capapretum, B. filamentosum) and the sister species pair B. juruense and B. platynemum are each recovered as monophyletic. The OCP Clade comprises nominal Pimelodus ornatus that is sister to the Calophysus-Pimelodus Clade in turn split into the calophysines and pimelodines. Calophysines include a monophyletic Calophysus Group (Calophysus, Aguarunichthys, Luciopimelodus, Pinirampus, Pimelodina) and the Megalonema-Cheirocerus Group. Intrarelationships of the Calophysus Group recovered with molecular data are congruent with relationships based on morphology. Placement of Cheirocerus sister to Megalonema is unexpected but well supported by molecular data. Pimelodines include the Exallodontus-Pimelodus altissimus Group and Pimelodus Group. The former correspond to the “long-finned” pimelodids including Exallodontus sister to an undescribed miniature species from the Amazon, and those sister to undescribed species of Propimelodus. An undescribed species related to nominal Pimelodus altissimus is the sister to nominal Duopalatinus peruanus. Nominal Pimelodus pictus is sister to remaining members of the Pimelodus Group that in turn contains three subclades: Iheringichthys plus Parapimelodus, Pimelodus maculatus plus P. albicans, and P. blochii including P. argenteus. Pimelodus coprophagus is unresolved among the P. maculatus and P. blochii groups. A generic reclassification of the species now assigned to polyphyletic Pimelodus is needed based on more complete taxon sampling and character evidence. A modest sampling of multiple specimens from thirteen pimelodid species permitted a first examination of their genetic diversity within and across the major South American river basins. The rag and mitochondrial genes examined here show little divergence between distant allopatric populations of Pinirampus pirinampu, Brachyplatystoma vaillantii, B. rousseauxii, B. filamentosum and B. juruense. However, specimens representing allopatric populations of five nominal species are as divergent as distinct congeneric species: Pimelodus blochii, P. ornatus, P. pictus, Platysilurus mucosus and Megalonema platycephalum.

Molecular systematics and morphometrics of Anoplocephaloides dentata (Cestoda, Anoplocephalidae) and related species in voles and lemmings

This study presents extensive molecular phylogenetic and morphometric data for Anoplocephaloides dentata (Galli‐Valerio, 1905)‐like cestodes (Anoplocephalidae) and related species parasitizing arvicoline rodents (voles and lemmings) in the Holarctic region. The molecular phylogeny is based on nucleotide sequences of cytochrome oxidase I (mtDNA) and 28S ribosomal RNA. Anoplocephaloides dentata‐like cestodes included three main clades, two in western Eurasia and one in the Holarctic region (excluding western Eurasia). Three well‐supported sublineages were included in the southern European clade, one of which represents the true A. dentata from Chionomys nivalis and sympatric Microtus arvalis and Dinaromys bogdanovi. These clades generally had non‐overlapping distributions and showed a preference for certain host species. Multivariate analysis of morphometric data failed to discriminate unambiguously the various A. dentata‐like lineages recovered in the molecular phylogeny, although two to three of the (sub)lineages were morphologically divergent. The overall evidence suggests, however, that instead of a single host‐generalist species there are at least five more or less host‐specific species of A. dentata‐like cestodes. Colonization of new host lineages seems to have been the predominant mode of diversification, suggested by the considerable incongruence between host and parasite phylogenies at multiple taxonomic levels. Based on the results of the molecular survey, a redescription and neotype designation are provided for A. dentata.

Catfish Genus Corymbophanes (Loricariidae: Hypostominae) with Description of One New Species: Corymbophanes kaiei

Abstract The genus Corymbophanes and its type, Corymbophanes andersoni, are redescribed, and one new species, Corymbophanes kaiei is described. Among loricariids, Corymbophanes is diagnosed by a unique combination of characteristics: absence of dorsal flap of iris; absence of adipose fin; and presence of an elongate postdorsal ridge of 13–17 raised median unpaired plates. Corymbophanes kaiei differs from C. andersoni by the presence of vermiculations on the abdomen (vs abdomen lightly colored in C. andersoni), presence of distinct alternating light and dark bands on the caudal fin (vs light bands largely absent), anal fin I,5 (vs I,4), caudal peduncle moderately (vs strongly) compressed, and three to four (vs five) plates below the adpressed pectoral fin spine. Corymbophanes is known only from the Potaro River Drainage above Kaieteur Falls in west-central Guyana. Corymbophanes bahianus is transferred to Hemipsilichthys.

Molecular systematics of the Holarctic Anoplocephaloides variabilis (Douthitt, 1915) complex, with the proposal of Microcephaloides n. g. (Cestoda: Anoplocephalidae).

Phylograms based on mitochondrial cytochrome oxidase I gene sequences show that the Anoplocephaloides variabilis (Douthitt, 1915)-like cestodes (Cestoda: Anoplocephalidae) from voles (Microtus spp.) and Paranoplocephala krebsi Haukisalmi, Wickström, Hantula & Henttonen, 2001 from collared lemmings (Dicrostonyx spp.) comprise a monophyletic group within the anoplocephaline cestodes. The patterns of phylogenetic, biological and/or biogeographical distinction suggest six or seven species of A. variabilis-like cestodes, including P. krebsi. However, at this time we decline to describe them as a series of new species as no straightforward morphological differences were found between the A. variabilis-like cestodes. A new genus, Microcephaloides n. g., is proposed for the cestodes earlier assigned to A.variabilis, A. cf. variabilis, A. tenoramuraiae Genov & Georgiev, 1988 and P. krebsi. A redescription is provided for the type-species, M. variabilis n. comb., from pocket gophers (Geomys spp. and Thomomys spp.). In addition to Anoplocephaloides Baer, 1927 (sensu stricto) and Microcephaloides, Paranoplocephaloides Gulyaev, 1996, Flabelloskrjabinia Spasskii, 1951 and Leporidotaenia Genov, Murai, Georgiev & Harris, 1990 are considered valid genera among cestodes previously assigned to Anoplocephaloides (sensu Rausch, 1976). The host spectrum and present phylogenetic data suggest that Microcephaloides has been primarily associated with voles (Microtus spp.) and its basal lineage now occurs in M. guentheri (Danford & Alston) in Turkey. Although the distribution and current host of the basal lineage suggest a western Palaearctic origin, subsequent diversification has probably occurred in eastern Beringia, because most of the more derived lineages occur partly or exclusively in Alaska.

Comparison of the phylogenetic performance of neodermatan mitochondrial protein-coding genes

We examined the ability of all protein‐coding genes of 11 neodermatan mitochondrial genomes to recover the phylogeny of their combination. We subsampled randomly selected lengths (1–6000 bp) of contiguous sequence to consider the effect of length (100–6000 bp) on performance. All genes performed as well as randomly selected regions except ND2 (better) and ND5 (worse). All expected nodes were recovered (> 90% bootstrap) when 4.0 Kb had been sampled; 40 samples of 100 performed as well as four samples of 1000.