Phylogenetic relationships within the aplocheiloid fish genus Rivulus (Cyprinodontiformes, Rivulidae): implications for Caribbean and Central American biogeography

We examined the phylogenetic relationships of 16 northern species of the aplocheiloid genus Rivulus inhabiting the Caribbean, Central America, and South America. A total of 714 base pairs per taxon were sequenced from two segments of the mitochondrial genome, 12S rRNA and cytochrome b. Both parsimony and neighbor-joining analyses suggest an ancient vicariant origin of the Greater Antillean taxa, in addition to a quite recent dispersal of species into the Lesser Antilles from the South American mainland. Combined analyses support the monophyly of the northern South American assemblage as the sister group of a Central American/Columbian biota. However, the monophyly of the Central American biota remains uncertain. Divergence estimates for the Central American taxa are calibrated from the Last Cretaceous separation of the proto-Antilles from the Americas. These data suggest that the extant Central American taxa represent the descendants of at least two separate invasions during the Cenozoic, prior to the closing of the Panamanian isthmus. Times are consistent with the extensive evidence for reptilian and mammalian exchange throughout the Cenozoic.      

First data on the molecular phylogeography of scincid lizards of the genus Mabuya

A 487-bp fragment of the mitochondrial 16S rRNA gene was sequenced in 26 species of the circumtropical lizard genus Mabuya and used to analyze phylogenetic relationships within the genus. The species from Africa and Madagascar formed a monophyletic group relative to the included Asian and South American taxa. The Malagasy species included (M. elegans, M. cf. dumasi, and M. comorensis) did not appear as a monophylum. Combined and separate analysis of the 16S data and additional sequences of the mitochondrial 12S rRNA, ND4, and cytochrome b genes (a total of 2255 bp) in one Asian, two Malagasy, and two African species also did not result consistently in a monophyletic grouping of the Malagasy taxa. However, a monophylum containing African and Malagasy taxa was strongly supported by the combined analysis. These preliminary results indicate that Mabuya probably colonized Madagascar from Africa through the Mozambique Channel.     

Reconstructing the evolutionary history of the Lorisidae using morphological, molecular, and geological data

Major aspects of lorisid phylogeny and systematics remain unresolved, despite several studies (involving morphology, histology, karyology, immunology, and DNA sequencing) aimed at elucidating them. Our study is the first to investigate the evolution of this enigmatic group using molecular and morphological data for all four well-established genera: Arctocebus, Loris, Nycticebus, and Perodicticus. Data sets consisting of 386 bp of 12S rRNA, 535 bp of 16S rRNA, and 36 craniodental characters were analyzed separately and in combination, using maximum parsimony and maximum likelihood. Outgroups, consisting of two galagid taxa (Otolemur and Galagoides) and a lemuroid (Microcebus), were also varied. The morphological data set yielded a paraphyletic lorisid clade with the robust Nycticebus and Perodicticus grouped as sister taxa, and the galagids allied with Arctocebus. All molecular analyses maximum parsimony (MP) or maximum likelihood (ML) which included Microcebus as an outgroup rendered a paraphyletic lorisid clade, with one exception: the 12S + 16S data set analyzed with ML. The position of the galagids in these paraphyletic topologies was inconsistent, however, and bootstrap values were low. Exclusion of Microcebus generated a monophyletic Lorisidae with Asian and African subclades; bootstrap values for all three clades in the total evidence tree were over 90%. We estimated mean genetic distances for lemuroids vs. lorisoids, lorisids vs. galagids, and Asian vs. African lorisids as a guide to relative divergence times. We present information regarding a temporary land bridge that linked the two now widely separated regions inhabited by lorisids that may explain their distribution. Finally, we make taxonomic recommendations based on our results.     

Phylogenetic relationships of African killifishes in the genera Aphyosemion and Fundulopanchax inferred from mitochondrial DNA sequences

We have analyzed the phylogenetic relationships of 52 species representing all defined species groups (J. J. Scheel, 1990, Atlas of Killifishes of the Old World, 448 pp.) of the African aplocheiloid fish genera Aphyosemion and Fundulopanchax in order to examine their interrelationships and to reveal trends of karyotypic evolution. The data set comprised 785 total nucleotides from the mitochondrial 12S rRNA and cytochrome b genes. The molecular-based topologies analyzed by both maximum parsimony and neighbor-joining support the monophyly of most previously defined species groups within these two killifish genera. The genus Aphyosemion is monophyletic except for the nested position of Fundulopanchax kunzi (batesi group; subgenus Raddaella) within this clade, suggesting that this taxon was improperly assigned to Fundulopanchax. The remaining Fundulopanchax species sampled were supported as being monophyletic in most analyses. Relationships among the species groups in both genera were not as strongly supported, suggesting that further data will be required to resolve these relationships. Additional sampling from the 16S rRNA gene allowed further resolution of relationships within Fundulopanchax, more specifically identifying the nonannual scheeli group as the basal lineage of this otherwise annual genus. Chromosomal evolution within Aphyosemion has been episodic, with the evolution of a reduced n = 9-10 metacentric complement having occurred in multiple, independent lineages. Polarity of chromosomal reductions within the elegans species group appears to support previous hypotheses concerning mechanisms of karyotypic change within the genus Aphyosemion.     

Total evidence: molecules, morphology, and the phylogenetics of cichlid fishes

We present a most comprehensive phylogenetic analysis of the family Cichlidae. New data analyzed include mitochondrial 16S rRNA sequences and two nuclear loci (Tmo-M27 and Tmo-4C4) for a large taxonomic sampling with emphasis on South American species. We also incorporate a published morphological data set for a total evidence analysis. Character congruence among mitochondrial (74 taxa) and nuclear data (50 taxa) was high. However, partition-homogeneity tests suggest significant heterogeneity among molecular and morphological data. In agreement with results obtained from molecular data alone, total evidence analysis (1,460 characters for 34 taxa) supports a robust phylogenetic hypothesis for the family Cichlidae that is congruent with drift-vicariance events associated with the fragmentation of Gondwana. Our analyses confirm the placement of Malagasy/Indian cichlids as the most basal lineages, with a sister-group relationship to the monophyletic African and Neotropical clades. Total evidence suggests that the controversial African genus Heterochromis is at the base of the African radiation. Among more than 50 Neotropical genera analyzed, Retroculus is identified as the basal taxon, with successive branching of Cichla, Astronotus, geophagines (including crenicichlines) + chaetobranchines, and cichlasomines + heroines. Relative rate tests applied to mitochondrial DNA suggest significantly higher rates of genetic variation in Neotropical than in African taxa, and both mitochondrial and nuclear sequences show that rate heterogeneity among Neotropical lineages is confined to the geophagine cichlids.     

Phylogenetic relationships among the Lorisoidea as indicated by craniodental morphology and mitochondrial sequence data

The phylogeny of the Afro-Asian Lorisoidea is controversial. While postcranial data attest strongly to the monophyly of the Lorisidae, most molecular analyses portray them as paraphyletic and group the Galagidae alternately with the Asian or African lorisids. One of the problems that has bedevilled phylogenetic analysis of the group in the past is the limited number of taxa sampled for both ingroup families. We present the results of a series of phylogenetic analyses based on 635 base pairs (bp) from two mitochondrial genes (12S and 16S rRNA) with and without 36 craniodental characters, for 11 galagid and five lorisid taxa. The outgroup was the gray mouse lemur (Microcebus murinus). Analyses of the molecular data included maximum parsimony (MP), neighbor joining (NJ), maximum likelihood (ML), and Bayesian methods. The model-based analyses and the combined "molecules+morphology" analyses supported monophyly of the Lorisidae and Galagidae. The lorisids form two geographically defined clades. We find no support for the taxonomy of Galagidae as proposed recently by Groves [Primate Taxonomy, Washington, DC: Smithsonian Institution Press. 350 p, 2001]. The taxonomy of Nash et al. [International Journal of Primatology 10:57-80, 1989] is supported by the combined "molecules+morphology" analysis; however, the model-based analyses suggest that Galagoides may be an assemblage of species united by plesiomorphic craniodental characters.     

A taxometric analysis of seed proteins in the genusBriza s. l. (Poaceae)

The species ofBriza L. s. l. are disjunctly distributed between Eurasia and South America. A taxometric analysis has been carried out, using data from electrophoresis of seed polypeptides and published morphological characters. Evidence from a cluster analysis of seed polypeptide data strongly supports the recognition of two different natural groups, a S. American group and a Eurasian group, and is consistent with karyotype data, but does not support the generic groupings of South American taxa derived from the morphological data.     

A molecular phylogeny for the South African limbless lizard taxa of the subfamily Acontinae (Sauria: Scincidae) with special emphasis on relationships within Acontias

In the present study, relationships among three genera Acontias, Acontophiops, and Typhlosaurus, that comprise the South African limbless lizard subfamily Acontinae, were assessed with partial sequences of the 16S rRNA mitochondrial DNA gene. In addition, relationships within Acontias were further investigated using sequence data from the cytochrome oxidase I gene (COI). Maximum likelihood and maximum parsimony analyses of the 16S rRNA mtDNA data revealed that within this subfamily, Typhlosaurus is basal while Acontophiops and Acontias are sister taxa. Based on the 16S rRNA mtDNA data, the relationships within Acontias placed A. meleagris orientalis as the sister taxon of A. percivali tasmani, with A. m. orientalis lineacauda morph and A. m. meleagrus being the sister taxa to this group. The small-bodied skinks A. lineatus lineatus and A. l. tristis formed a monophyletic group, with the medium-bodied species A. gracilicauda gracilicauda being their sister taxon. Analyses of the COI gene for Acontias place A. m. orientalis as the sister taxon of A. p. tasmani with both A. meleagris meleagris and A. m. orientalis lineacauda being distinct. In contrast to the 16S rRNA mtDNA data, the COI data placed A. g. gracilicauda as the sister taxon to these medium-bodied species; while the subspecies status of the small-bodied taxa A. l. lineatus and A. l. tristis is reaffirmed. Combined analysis of both gene fragments for Acontias taxa recovered the same clades as found using only COI data. Systematic affinities in Acontias are discussed. These results indicate that Acontias is more species rich than previously thought.     

Phylogenetic Relationships of African Killifishes in the GeneraAphyosemionandFundulopanchaxInferred from Mitochondrial DNA Sequences

We have analyzed the phylogenetic relationships of 52 species representing all defined species groups (J. J. Scheel, 1990, Atlas of Killifishes of the Old World, 448 pp.) of the African aplocheiloid fish generaAphyosemionandFundulopanchaxin order to examine their interrelationships and to reveal trends of karyotypic evolution. The data set comprised 785 total nucleotides from the mitochondrial 12S rRNA and cytochromebgenes. The molecular-based topologies analyzed by both maximum parsimony and neighbor-joining support the monophyly of most previously defined species groups within these two killifish genera. The genusAphyosemionis monophyletic except for the nested position ofFundulopanchax kunzi(batesigroup; subgenusRaddaella) within this clade, suggesting that this taxon was improperly assigned toFundulopanchax.The remainingFundulopanchaxspecies sampled were supported as being monophyletic in most analyses. Relationships among the species groups in both genera were not as strongly supported, suggesting that further data will be required to resolve these relationships. Additional sampling from the 16S rRNA gene allowed further resolution of relationships withinFundulopanchax,more specifically identifying the nonannualscheeligroup as the basal lineage of this otherwise annual genus. Chromosomal evolution withinAphyosemionhas been episodic, with the evolution of a reducedn= 9–10 metacentric complement having occurred in multiple, independent lineages. Polarity of chromosomal reductions within theelegansspecies group appears to support previous hypotheses concerning mechanisms of karyotypic change within the genusAphyosemion.     

Convergent evolution of gigantism in damselflies of Africa and South America? Evidence from nuclear and mitochondrial sequence data

Extreme large body size is rare in modern Zygoptera (damselflies). Only the South and Central American damselfly family Pseudostigmatidae and one African species, Coryphagrion grandis, share the morphological trait of gigantism. By means of phylogenetic analyses using two mitochondrial markers (16S rDNA and ND1) and one nuclear marker (EF1) in combination with an existing morphological data set, we trace the evolution of gigantism in damselflies. Individual and combined data sets were analyzed using the maximum parsimony, minimum evolution and maximum likelihood algorithms. Regardless of the algorithm used and the data set analyzed all principal tree topologies support a monophyly of the damselfly taxa displaying giant body size. This supports the view that the evolution of gigantism in damselflies from Africa and South America is not the result of convergent evolution due to strikingly similar habitat preferences, but rather the result of close genealogical relationship. Because modern odonates evolved before the split of Africa from Gondwanaland, the proposed phylogeny suggests that C. grandis represents a Gondwana relict.     

A molecular phylogeny of the Littorininae (Gastropoda: Littorinidae): unequal evolutionary rates,morphological parallelism,and biogeography of the Southern Ocean

A molecular phylogeny is presented for the subfamily Littorininae (including representatives of all subgeneric taxa and all members of a group of southern-temperate species formerly classified as 'Nodilittorina'), based on sequence data from two nuclear (18S rRNA, 28S rRNA) and two mitochondrial (12S rRNA, CO1) genes. The phylogeny shows considerable disagreement with earlier hypotheses derived from morphological data. In particular, 'Nodilittorina' is polyphyletic and is here divided into four genera (Echinolittorina, Austrolittorina, Afrolittorina new genus, and the monotypic Nodilittorina s.s.). The phylogenetic relationships of 'Littorina' striata have been controversial and it is here transferred to the genus Tectarius, a surprising relationship for which there is little morphological support. The relationships of the enigmatic Mainwaringia remain poorly resolved, but it is not a basal member of the subfamily. The two living species of Mainwaringia are remarkable for a greatly elevated rate of evolution in all four genes examined; it is suggested that this may be connected with their protandrous hermaphroditism, which is unique in the family. The molecular phylogeny provides a new framework for the adaptive radiation of the Littorininae, showing more frequent shifts between habitats and climatic regimes than previously suspected, and striking parallelism of morphological characters. The fossil record of littorinids is poor, but ages of clades are estimated using a calibration based on a Lower Eocene age of the genus Littoraria. Using these estimates, the antitropical distribution of Littorina and Afrolittorina is an ancient pattern of possibly Cretaceous age. The five members of Austrolittorina show a Gondwanan distribution in Australia, New Zealand, and South America. Based on the morphological uniformity within this clade, relatively recent (Plio-Pleistocene) trans-Pacific dispersal events seemed a likely explanation, as proposed for numerous other congeneric marine taxa. However, molecular estimation of ages of divergence suggest an initial vicariance between Australian and South American lineages at 40-73Ma, contemporary with the later stages of fragmentation of the Gondwanan supercontinent, followed by more recent (but still mid-Cenozoic) dispersal events across the Tasman Sea and the Pacific Ocean. Afrolittorina is another Cretaceous clade, now restricted to southern Africa and southern Australia, but divergence between these lineages (29-55Ma) post-dates Gondwanan fragmentation. Within both Austrolittorina and Afrolittorina all sister-species divergences are estimated to fall in the range 10-47Ma, so that there is no evidence for speciation events in the Plio-Pleistocene.     

The evolution of the diatoms (Bacillariophyta). I. Origin of the group and assessment of the monophyly of its major divisions

The diatoms are one of the best characterised algal groups. Despite this, little is known of the evolution of the group from the earliest cell to the myriad of taxa known today. Relationships among taxa at the family or generic level have been recognised in some diatoms. However, relationships at higher taxonomic levels are poorly understood and have often been strongly influenced by the first appearances of key taxa in the fossil record. An independent assessment of relationships among the diatoms at these higher taxonomic levels has been made using rRNA sequence data to infer phylogenetic relationships. In this paper we present an analysis of 18S rRNA data from several chosen centric, araphid and raphid pennate taxa. The phylogenetic inferences from these 18S rRNA sequences are supported by evidence from the fossil record and evidence from ontogenetic data. Ribosomal RNA data indicate that both the centric and araphid pennate lineages may not be monophyletic.     

Molecular phylogenetics and ecological diversification of the transisthmian fish genus Centropomus (Perciformes: Centropomidae).

Phylogenetic relationships among the 12 recognized fish species in the New World genus Centropomus (Pisces, Centropomidae) were analyzed using allozyme electrophoresis and 618 bp of the mitochondrial DNA 16S ribosomal RNA (rRNA) gene. Molecular phylogenetic trees were generally consistent with previously published partial hypotheses based on morphological evidence. However, previously undefined sister group relationships between major species groups were resolved using molecular data, and phylogenetic hypotheses for Centropomus based on 16S rRNA sequences were better supported than were allozyme-based hypotheses. The high level of congruence among the trees inferred from the nuclear and mitochondrial characters provided a firm phylogenetic basis for analysis of ecological diversification and molecular evolution in the genus. Compared to basal Centropomus species, members of the most nested species group were significantly larger in body size and occupied a marine niche only peripherally utilized by their congeners. We also observed substitution rate heterogeneity among 16S rRNA lineages; in contrast to expectations based on "metabolic rate" and "generation interval" models, relative substitution rates were faster than expected for the group of large-bodied snooks. Using the Pliocene rise of the Central American isthmian marine barrier to calibrate rates of 16S ribosomal gene evolution in Centropomus, we found that the rates for the genus were similar to those reported for higher vertebrates. Analysis of the three sets of transisthmian geminate taxa in Centropomus indicated that two of the pairs were probably formed during the Pliocene rise of the isthmus while the third pair diverged several million years earlier.     

Ribosomal DNA evidence and disjunctions of western American Portulacaceae

Phylogenetic analysis of ribosomal DNA internal transcribed spacer sequences from 35 members of western American Portulacaceae plus seven Portulacaceae outgroups generally supports morphologically based interpretations of multiple intercontinental disjunctions. The data neither support nor refute monophyly of the western American group but strongly support a group comprising the western American taxa plus Phemeranthus, the only strictly American genus of the morphology-based eastern American/African group of Portulacaceae, along with the Australian genus Parakeelya. Support is strong for the monophyly of Calandrinia, Montiopsis, Lewisia, Claytonia, and Montia, along with a sister relationship of the last two. The data neither strongly support nor refute the morphologically based diagnosis of Cistanthe, but they strongly support a clade including the North American Cistanthe section Calyptridium and the South American Cistanthe sections Amarantoideae and Philippiamra. The internal transcribed spacer data fail to resolve the phylogenetic relationships among most of the western American lineages, suggesting either rapid radiation or, alternatively, erratic evolution of the internal transcribed spacer. The internal transcribed spacer and morphological evidence together suggest that in this group there have been 8-13 dispersal and colonization events across >2000 km (1 for every 15-26 extant species in this group). The internal transcribed spacer data document complex molecular evolutionary patterns, including strong substitution biases, among-site rate heterogeneity, positional bias for deamination-type substitutions, nonstationarity, and variable rates of insertion/deletion. Our phylogenetic conclusions, however, do not appear to be sensitive to these patterns.     

Taxonomic subdivisions within the fossorial skink subfamily Acontinae (Squamata: Scincidae) reconsidered: a multilocus perspective

Despite recent molecular systematic studies on the fossorial southern African skink subfamily Acontinae, evolutionary relationships among the three genera remain unresolved and disputed. Among these, the most recent study suggests that both Typhlosaurus and Acontias are paraphyletic, contrasting earlier results that suggest the presence of two divergent clades within Acontias. Here we further investigate the evolutionary relationships in the limbless fossorial southern African subfamily Acontinae with partial sequenced data derived from four mitochondrial loci (16S rRNA, 12S rRNA, cytochrome oxidase I and cytochrome b), as well as two nuclear protein coding loci (c‐mos and RAG‐1), in an attempt to clarify evolutionary relationships. Phylogenetic results derived from combined data analyses (comprising all six loci and totalling ～3.1 kb) using maximum parsimony, maximum likelihood and Bayesian inferences converged on the same topology. The resulting phylogeny showed Typhlosaurus as monophyletic, while the monotypic genus Acontophiops was nested intermediate to two reciprocally monophyletic Acontias clades. These two Acontias clades can be distinguished on the basis of a number of morphological, morphometric and biogeographical characters, underscoring the presence of two distinct groups. In the present study, we propose the following taxonomic changes based on the multilocus phylogeny. We retain the genus name Acontias for the medium‐ and large‐bodied skinks in clade 2 comprising all taxa in the Acontias meleagris complex as well as Acontias plumbeus, Acontias gracilicauda gracilicauda, Acontias breviceps, Acontias percivali percivali and Acontias percivali occidentalis. We designate a new genus Microacontias gen. nov. for the reciprocally monophyletic taxa in clade 1 comprised of all the small‐bodied taxa that include Microacontias litoralis, Microacontias lineatus lineatus, Microacontias lineatus grayi and Microacontias lineatus tristis. We examine the evolution of characters used in the taxonomy of the Acontinae and suggest that symplesiomorphic morphological characters among fossorial taxa have been an impediment to understanding the evolution of this subfamily. This study underscores the importance of the application of multiple molecular markers (both nuclear and mitochondrial) in determining the taxonomic diversity among fossorial skinks and emphasizes the application of phylogenetics in defining synapomorphic (shared derived) features.     

A molecular phylogenetic study of the Palmae (Arecaceae) based on atpB, rbcL, and 18S nrDNA sequences

Notoriously slow rates of molecular evolution and convergent evolution among some morphological characters have limited phylogenetic resolution for the palm family (Arecaceae). This study adds nuclear DNA (18S SSU rRNA) and chloroplast DNA (cpDNA; atpB and rbcL) sequence data for 65 genera of palms and characterizes molecular variation for each molecule. Phylogenetic relationships were estimated with maximum likelihood and maximum parsimony techniques for the new data and for previously published molecular data for 45 palm genera. Maximum parsimony analysis was also used to compare molecular and morphological data for 33 palm genera. Incongruence among datasets was detected between cpDNA and 18S data and between molecular and morphological data. Most conflict between nuclear and cpDNA data was associated with the genus Nypa. Several taxa showed relatively long branches with 18S data, but phylogenetic resolution of these taxa was essentially the same for 18S and cpDNA data. Base composition bias for 18S that contributed to erroneous phylogenetic resolution in other taxa did not seem to be present in Palmae. Morphological data were incongruent with all molecular data due to apparent morphological homoplasy for Caryoteae, Ceroxyloideae, Iriarteae, and Thrinacinae. Both cpDNA and nuclear 18S data firmly resolved Caryoteae with Borasseae of Coryphoideae, suggesting that at least some morphological characters used to place Caryoteae in Arecoideae are homoplastic. In this study, increased character sampling seems to be more important than increased taxon sampling; a comparison of the full (65-taxon) and reduced (45- and 33-taxon) datasets suggests little difference in core topology but considerably more nodal support with the increased character sample sizes. These results indicate a general trend toward a stable estimate of phylogenetic relationships for the Palmae. Although the 33-taxon topologies are even better resolved, they lack several critical taxa and are affected by incongruence between molecular and morphological data. As such, a comparison of results from the 45- and 33-taxon trees offers the best available reference for phylogenetic inference on palms.     

A molecular phylogeny of apple snails (Gastropoda, Caenogastropoda, Ampullariidae) with an emphasis on African species

Ampullariids are widespread in Africa, Asia, South- and Central America, and the Caribbean Islands. Basal phylogenetic relationships of the African genera Afropomus and Saulea have been inferred based on anatomical evidence. Until recently the Viviparidae was regarded as the sister-group of Ampullariidae, but recent molecular data infer a sister-group relationship with Campanilidae. We have used members of both families as outgroups in the present investigation on ampullariid phylogeny. We have used data from portions of five molecular loci, that is, the nuclear genes 18S rRNA, 28S rRNA and H3, and the mitochondrial genes 16S rRNA and COI. Our data most often infer a basal position of Afropomus . The West African species Saulea is inferred as the basal member of a clade including the South American Marisa and Pomacea . We hypothesize that evolutionary lineages leading to Saulea and the American genera were isolated from each other by vicariance events (Gondwanaland break-up 130–110 Mya). Our individual gene analyses inferred two major clades of the African Lanistes . However, in some analyses they were not inferred as sister-groups making Lanistes paraphyletic. The African and Asian genus Pila is most often inferred to be monophyletic (except for the generally unresolved 28S). Our analyses most often inferred a sister-group relationship between Lanistes and Pila . The very low genetic diversity of the endemic radiation of Lanistes in Lake Malawi suggests that the morphological divergence has happened much faster than the molecular divergence as is also evidenced from the cichlid radiations.     

Molecular phylogeny of the endemic East African flightless grasshoppers Altiusambilla Jago, Usambilla (Sjöstedt) and Rhainopomma Jago (Orthoptera: Acridoidea: Lentulidae)

Abstract.  A molecular phylogeny of endemic flightless grasshoppers is presented for the three Lentulidae genera Altiusambilla Jago, 1981 , Usambilla Sjöstedt, 1909 and Rhainopomma Jago, 1981 based on DNA sequences (16S rRNA locus). Parsimony, distance and likelihood reconstructions were performed using different assumptions on sequence evolution. The generated phylogenies agree in almost all parts of the calculated trees and support the monophyly of the observed genera. It was shown that Usambilla and Rhainopomma are more closely related to each other, Altiusambilla being a separate clade. However, the investigated East African lentulid genera are clearly separated from South African taxa, underlining the monophyly of East African genera. Usambilla olivacea is re-established. Populations of Rhainopomma montanum from the Taita Hills of Kenya and from the West Usambara mountains of Tanzania are two separate species not closely related to each other. Rhainopomma samples from the North Pare mountains of Tanzania belong to a hitherto undescribed species.     

Searching for the closest living relative(s) of tetrapods through evolutionary analyses of mitochondrial and nuclear data

The phylogenetic relationships of the African lungfish (Protopterus dolloi) and the coelacanth (Latimeria chalumnae) with respect to tetrapods were analyzed using complete mitochondrial genome DNA sequences. A lungfish + coelancanth clade was favored by maximum parsimony (although this result is dependent on which transition:transversion weights are applied), and a lungfish + tetrapod clade was supported by neighbor-joining and maximum-likelihood analyses. These two hypotheses received the strongest statistical and bootstrap support to the exclusion of the third alternative, the coelacanth + tetrapod sister group relationship. All mitochondrial protein coding genes combined favor a lungfish + tetrapod grouping. We can confidently reject the hypothesis that the coelacanth is the closest living relative of tetrapods. When the complete mitochondrial sequence data were combined with nuclear 28S rRNA gene data, a lungfish + coelacanth clade was supported by maximum parsimony and maximum likelihood, but a lungfish + tetrapod clade was favored by neighbor-joining. The seeming conflicting results based on different data sets and phylogenetic methods were typically not statistically strongly supported based on Kishino-Hasegawa and Templeton tests, although they were often supported by strong bootstrap values. Differences in rate of evolution of the different mitochondrial genes (slowly evolving genes such as the cytochrome oxidase and tRNA genes favored a lungfish + coelacanth clade, whereas genes of relatively faster substitution rate, such as several NADH dehydrogenase genes, supported a lungfish + tetrapod grouping), as well as the rapid radiation of the lineages back in the Devonian, rather than base compositional biases among taxa seem to be directly responsible for the remaining uncertainty in accepting one of the two alternate hypotheses.     

Phylogenetic relationships and evolution of Orbiniidae (Annelida, Polychaeta) based on molecular data

The phylogenetic relationships of orbiniid taxa were reconstructed based on sequence data of the mitochondrial 16S rRNA and nuclear 18S rRNA genes. Both genes were analysed separately and in combination using maximum likelihood, Bayesian inference and maximum parsimony. Regardless of the method used, a clade consisting of the investigated Orbiniidae, Methanoaricia dendrobranchiata and Questa was strongly supported by the 18S dataset. The analysis of the combined dataset suggests inclusion of M. dendrobranchiata within the Orbiniidae with close relationships to species of Orbinia and Phylo, rather than as a sister taxon to all other orbiniids. Evidence is given for the paraphyletic status of Leitoscoloplos , Naineris , Orbinia , Phylo and Scoloplos , which represent the most species-rich genera of the Orbiniidae. It is thus reasoned that the morphological characters presently used for genus diagnosis are not informative for cladistic analysis. No support is found for the hypothesis that taxa of the Protoariciinae represent juveniles of Orbiniinae. Instead, in the case of Protoaricia oerstedi , strong support for a progenetic origin is found.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 144 , 59−73.