Phylogenetic relationships,subdivision, and biogeography of the cyprinid tribe Labeonini (sensu ) (Teleostei: Cypriniformes), with comments on the implications of lips and associated structures in the labeonin classification

The Labeonini (sensu Rainboth, 1991) is a tribe of the subfamily Cyprininae, the largest subfamily of Cypriniformes. With around 400 species in 34 genera, this tribe is widely distributed in the freshwaters of tropical Africa and Asia. Most species are adapted to fast-flowing streams and rivers, and exhibit unique morphological modifications associated with their lips and other structures around the mouth. The monophyly of this tribe has been tested and generally accepted in previous morphological and molecular studies. The major objectives of this study were to reconstruct the phylogenetic relationships within the tribe Labeonini, test its monophyly and explore the taxonomic subdivisions, intrarelationships and biogeography of the group. The value of the morphological characters associated with the lips and other associated structures in the taxonomic classification of labeonins was also discussed. Nucleotide sequences (3867 bp) of four unlinked nuclear loci were obtained from 51 species in 18 Labeonini genera from throughout the range of the tribe. Maximum parsimony, partitioned maximum likelihood and partitioned Bayesian analyses were used for phylogenetic inference from combined and separate gene data sets. Based on our results, the monophyly of Labeonini was well supported. Two major clades could be recovered within the tribe. Three subclades could further be recognized from the first clade. These clades/subclades are not consistent with groupings of any of previous workers using either morphological or molecular characters for phylogenetic inference. Only five currently recognized genera in this analysis are monophyletic. The similarity between some lips and associated structures (e.g. suctorial discs) of labeonins may due to convergence or parallelism instead of common ancestry. Labeonins of Southeast Asia, India and China are closely related to each other; the multiple clades of African taxa do not form a single monophyletic group, indicating multiple, independent dispersal events of labeonins into Africa from Asia.     

Molecular phylogeny and divergence of major clades in the Puntius complex (Teleostei: Cypriniformes)

Puntius sensu lato (s.l.) was one of the most speciose genera in the family Cyprinidae. There are around 120 valid species widely distributed in South-East and South Asia, and South China. Puntius has long been known as an artificial assemblage and ‘catch-all’ genus in which a large number of small, unrelated cyprinids have been placed. With new species and genera being described each year, obtaining detailed knowledge of the phylogenetic relationships of this complex is critically important in the assessment of a natural classification. In the present study, two mitochondrial and four nuclear genes were used to examine the inter-specific and inter-generic relationships of the Puntius complex and to test the monophyly of the current genera. Divergence time analysis was performed to explore the origin, evolution, and divergence of major clades in Puntius s.l. Results revealed that the genera Puntius seusu stricto (s.s.), Systomus, Pethia, Haludaria, Desmopuntius and Puntigrus were monophyletic with high support. However, monophyly of Barbodes, Striuntius and Sahyadria was not supported. Dawkinsia and Sahyadria formed a highly supported clade. Puntius semifasciolatus and P. snyderi from South China and Taiwan represent a new lineage. Inferences from divergence time analysis indicated that Puntius s.l. likely dated to early Miocene. Major clades in Puntius s.l. diverged during Miocene as well.     

Molecular phylogeny of the fishes traditionally referred to Cyprinini sensu stricto (Teleostei: Cypriniformes)

Yang, L., Mayden, R. L., Sado, T., He, S., Saitoh, K. & Miya, M. (2010). Molecular phylogeny of the fishes traditionally referred to Cyprinini sensu stricto (Teleostei: Cypriniformes). —Zoologica Scripta, 39, 527–550. Carps (e.g. Koi) of the genus Cyprinus and Crucian carps (e.g. Goldfish) of the genus Carassius are among the most popular freshwater fishes around the world. However, their phylogenetic positions within the subfamily Cyprininae, relationships with their allies (e.g. Procypris, Carassioides), and the monophyly of the group formed by them and their allies, which is referred as the tribe Cyprinini sensu stricto, are far from clear. Historically, the Cyprinini was defined by different people according to whether a cyprinine fish possessed a spinous anal‐fin ray (or anal spine), the spine was serrated or not, and occasionally, the number of branched dorsal‐fin rays. Some definitions were established without providing any diagnostic characters. In this study, we investigated the monophyly of the tribe Cyprinini sensu stricto, based on four different historical definitions, and explored the phylogenetic relationships of these members in the subfamily Cyprininae. Using five mitochondrial genes as markers, both maximum‐likelihood and Bayesian trees were constructed using the optimal partitioning strategy. Both analyses successfully resolved a monophyletic Cyprininae and recovered seven major clades from this subfamily. The diagnosis limiting the tribe Cyprinini sensu stricto to four genera, Cyprinus, Carassius, Carassioides and Procypris, received most support. We propose that only those cyprinines that possess a serrated anal spine and have no <10 branched dorsal‐fin rays should be considered members of this tribe. Cyprinini is sister to the Sinocyclocheilus clade, a group traditionally considered a barbin, and together they form the ‘Cyprinini‐Sinocyclocheilus’ clade. Procypris forms the basal clade of the Cyprinini, whereas species of Carassius and Carassioides locate at the top.     

Molecular phylogeny of the subfamily Schizothoracinae (Teleostei: Cypriniformes: Cyprinidae) inferred from complete mitochondrial genomes

The schizothoracine fishes, members of the Teleost order Cypriniformes, are one of the most diverse group of cyprinids in the Qinghai–Tibetan Plateau and surrounding regions. However, taxonomy and phylogeny of these species remain unclear. In this study, we determined the complete mitochondrial genome of Schizopygopsis malacanthus. We also used the newly obtained sequence, together with 31 published schizothoracine mitochondrial genomes that represent eight schizothoracine genera and six outgroup taxa to reconstruct the phylogenetic relationships of the subfamily Schizothoracinae by different partitioned maximum likelihood and partitioned Bayesian inference at nucleotide and amino acid levels. The schizothoracine fishes sampled form a strongly supported monophyletic group that is the sister taxon to Barbus barbus. A sister group relationship between the primitive schizothoracine group and the specialized schizothoracine group + the highly specialized schizothoracine group was supported. Moreover, members of the specialized schizothoracine group and the genera Schizothorax, Schizopygopsis, and Gymnocypris were found to be paraphyletic.     

Molecular phylogeny and biogeography of the Neotropical cichlid fish tribe Cichlasomatini (Teleostei: Cichlidae: Cichlasomatinae)

We have conducted the first comprehensive molecular phylogeny of the tribe Cichlasomatini including all valid genera as well as important species of questionable generic status. To recover the relationships among cichlasomatine genera and to test their monophyly we analyzed sequences from two mitochondrial (16S rRNA, cytochrome b) and one nuclear marker (first intron of S7 ribosomal gene) totalling 2236 bp. Our data suggest that all genera except Aequidens are monophyletic, but we found important disagreements between the traditional morphological relationships and the phylogeny based on our molecular data. Our analyses support the following conclusions: (a) Aequidens sensu stricto is paraphyletic, including also Cichlasoma (CA clade); (b) Krobia is not closely related to Bujurquina and includes also the Guyanan Aequidens species A. potaroensis and probably A. paloemeuensis (KA clade). (c) Bujurquina and Tahuantinsuyoa are sister groups, closely related to an undescribed genus formed by the 'Aequidens'pulcher-'Aequidens'rivulatus groups (BTA clade). (d) Nannacara (plus Ivanacara) and Cleithracara are found as sister groups (NIC clade). Acaronia is most probably the sister group of the BTA clade, and Laetacara may be the sister group of this clade. Estimation of divergence times suggests that the divergence of Cichlasomatini started around 44Mya with the vicariance between coastal rivers of the Guyanas (KA and NIC clades) and remaining cis-andean South America, followed by evolution of the Acaronia-Laetacara-BTA clade in Western Amazon, and the CA clade in the Eastern Amazon. Vicariant divergence has played importantly in evolution of cichlasomatine genera, with dispersal limited to later range extension of species within genera.     

Molecular phylogeny of the Cobitoidea (Teleostei: Cypriniformes) revisited: position of enigmatic loach Ellopostoma resolved with six nuclear genes

Molecular variation in six nuclear genes provides substantive phylogenetic evidence for the recognition of a new cypriniform family, the Ellopostomatidae, to include the enigmatic Southern Asia loach genus Ellopostoma. The current six loach families form a monophyletic group, with the Nemacheilidae as the sister group to Ellopostomatidae; Vaillantellidae forms the sister group to all families exclusive of Botiidae. While the superfamily Cobitoidea includes eight families, the monophyly of this large clade within the Cypriniformes remains a vexing problem despite extensive molecular analyses and is in need of further investigation.     

Molecular phylogeny of the ant tribe Myrmicini (Hymenoptera: Formicidae)

The interrelationships within ant subfamilies remain elusive, despite the recent establishment of the phylogeny of the major ant lineages. The tribe Myrmicini belongs to the subfamily Myrmicinae, and groups morphologically unspecialized genera. Previous research has struggled with defining Myrmicini, leading to considerable taxonomic instability. Earlier molecular phylogenetic studies have suggested the nonmonophyly of Myrmicini, but were based on limited taxon sampling. We investigated the composition of Myrmicini with phylogenetic analyses of an enlarged set of taxa, using DNA sequences of eight gene fragments taken from 37 representatives of six of the seven genera (Eutetramorium, Huberia, Hylomyrma, Manica, Myrmica, and Pogonomyrmex), and eight outgroups. Our results demonstrate the invalidity of Myrmicini as currently defined. We recovered sister‐group relationships between the genera Myrmica and Manica, and between Pogonomyrmex and Hylomyrma. This study illustrates that to understand the phylogeny of over 6000 myrmicine species, comprehensive taxon sampling and DNA sequencing are an absolute requisite. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 160 , 482–495.     

Molecular phylogeny and systematics of the tribe Chorisporeae (Brassicaceae)

Sequence data from nuclear (ITS) and chloroplast (trnL-F) regions for 89 accessions representing 56 out of 64 species from all five genera of the tribe Chorisporeae (plus Dontostemon tibeticus) have been studied to test the monophyly of the tribe and its component genera, clarify its boundaries, and elucidate its phylogenetic position in the family. Both data sets showed strong support for the monophyly of the Chorisporeae as currently delimited, though the position of its tentative member D. tibeticus was not resolved by ITS. Parrya and Pseudoclausia are poly- and paraphyletic with regard to each other, and Chorispora is either polyphyletic or at least paraphyletic (comprising Diptychocarpus) within a weakly supported monophyletic clade. The incongruence in branching pattern among the markers was most likely caused by hybridization and possibly influenced by incomplete lineage sorting. The present results suggest uniting Pseudoclausia, Clausia podlechii, and Achoriphragma with Parrya and transferring P. beketovii and P. saposhnikovii to Leiospora (Euclidieae). We also obtained support for splitting Chorispora into two geographically defined groups, one of which is closer to Diptychocarpus. Both data sets revealed a close relationship of the Chorisporeae to Dontostemoneae, while ITS also indicated affinity to Hesperideae. Therefore, the position of Chorisporeae needs further verification.     

Molecular phylogeny of the gobioid fishes (Teleostei: Perciformes: Gobioidei)

The phylogeny of groups within Gobioidei is examined with molecular sequence data. Gobioidei is a speciose, morphologically diverse group of teleost fishes, most of which are small, benthic, and marine. Efforts to hypothesize relationships among the gobioid groups have been hampered by the prevalence of reductive evolution among goby species; such reduction can make identification of informative morphological characters particularly difficult. Gobies have been variously grouped into two to nine families, several with included subfamilies, but most existing taxonomies are not phylogenetic and few cladistic hypotheses of relationships among goby groups have been advanced. In this study, representatives of eight of the nine gobioid familes (Eleotridae, Odontobutidae, Xenisthmidae, Gobiidae, Kraemeriidae, Schindleriidae, Microdesmidae, and Ptereleotridae), selected to sample broadly from the range of goby diversity, were examined. Complete sequence from the mitochondrial ND1, ND2, and COI genes (3573 bp) was used in a cladistic parsimony analysis to hypothesize relationships among the gobioid groups. A single most parsimonious topology was obtained, with decay indices indicating strong support for most nodes. Major phylogenetic conclusions include that Xenisthmidae is part of Eleotridae, and Eleotridae is paraphyletic with respect to a clade composed of Gobiidae, Microdesmidae, Ptereleotridae, Kraemeriidae, and Schindleriidae. Within this five-family clade, two clades are recovered. One includes Gobionellinae, which is paraphyletic with respect to Kraemeriidae, Sicydiinae, Oxudercinae, and Amblyopinae. The other contains Gobiinae, also paraphyletic, and including Microdesmidae, Ptereleotridae, and Schindleriidae. Previous morphological evidence for goby groupings is discussed; the phylogenetic hypothesis indicates that the morphological reduction observed in many goby species has been derived several times independently.     

Molecular phylogeny of the beetle tribe Oxypodini (Coleoptera: Staphylinidae: Aleocharinae)

This is the first study to comprehensively address the phylogeny of the tribe Oxypodini Thomson and its phylogenetic relationships to other tribes within the staphylinid subfamily Aleocharinae. Using the hitherto largest molecular dataset of Aleocharinae comprising of 4599 bp for representatives of 22 tribes, the Oxypodini are recovered as non‐monophyletic. Members of the tribe belong to three distantly related lineages within the Aleocharinae: (i) the Amarochara group as sister clade to the tribe Aleocharini, (ii) the subtribe Tachyusina within a clade that also includes the tribes Athetini and Hygronomini, (iii) all other Oxypodini in a clade that also includes the tribes Placusini, Hoplandriini and Liparocephalini. Based on the inferred phylogeny, five subtribes of the Oxypodini are recognized: Dinardina Mulsant & Rey, Meoticina Seevers, Microglottina Fenyes, Oxypodina Thomson and Phloeoporina Thomson. The following changes in the classification of the Aleocharinae are proposed: (i) Amarochara Thomson is removed from the Oxypodini and placed in the tribe Aleocharini; (ii) the subtribe Taxicerina Lohse of the Athetini is reinstated as tribe Taxicerini to include Discerota Mulsant & Rey, Halobrecta Thomson (both removed from the Oxypodini) and Taxicera Mulsant & Rey; (iii) the subtribe Tachyusina Thomson is excluded from the Oxypodini and provisionally treated as tribe Tachyusini; (iv) the oxypodine subtribe name Blepharhymenina Klimaszewski & Peck is placed in synonymy with the subtribe name Dinardina Mulsant & Rey.     

Molecular phylogeny of the freshwater fish family Cobitidae (Cypriniformes: Teleostei): delimitation of genera, mitochondrial introgression and evolution of sexual dimorphism

The family Cobitidae represents a characteristic element of the Eurasian ichthyofauna. Despite diverse features of sexual dimorphism, comparably few morphological characters have been utilized for taxonomic studies resulting in many unresolved puzzles. Here we present the phylogenetic relationships of Cobitidae as inferred from the mitochondrial cytochrome b gene and the nuclear gene RAG-1. Analyses of both markers show a group of eight nominal genera, which all occur in Europe and eastern, northern and western Asia, forming a monophyletic lineage (northern clade) while all other clades inhabit South and Southeast Asia (southern lineages). While all eight southern lineages correspond to genera as defined by morphological studies, only four lineages were reliably recovered within the northern clade, and of these only one (Sabanejewia) corresponds to a formerly considered genus. The genera Cobitis, Iksookimia and Niwa?lla were polyphyletic. A comparison of the two markers shows several incongruities within the northern clade and mitochondrial introgression at least in the genus Misgurnus. Mapping the characters of sexual dimorphism on our cladogram, we identified five character states that are diagnostic for certain lineages. Estimations of the divergence times dated the separation of the northern clade from the southern lineages to the middle Eocene (46 MYA) and the origin of "Cobitis"misgurnoides, the basal taxon of the northern clade, during early Oligocene (30-35 MYA). The geographic distribution of the major clades supports recently developed hypotheses about the river history of East Asia and further suggests that a range expansion of the northern clade in late Miocene (15 MYA) led to the colonisation of Europe by three already distinct genera.     

Molecular phylogeny of Sinocyclocheilus (Cypriniformes: Cyprinidae) inferred from mitochondrial DNA sequences

More than 10 species within the freshwater fish genus Sinoncyclocheilus adapt to caves and show different degrees of degeneration of eyes and pigmentation. Therefore, this genus can be useful for studying evolutionary developmental mechanisms, role of natural selection and adaptation in cave animals. To better understand these processes, it is indispensable to have background knowledge about phylogenetic relationships of surface and cave species within this genus. To investigate phylogenetic relationships among species within this genus, we determined nucleotide sequences of complete mitochondrial cytochrome b gene (1140 bp) and partial ND4 gene (1032 bp) of 31 recognized ingroup species and one outgroup species Barbodes laticeps. Phylogenetic trees were reconstructed using maximum parsimony, Bayesian, and maximum likelihood analyses. Our phylogenetic results showed that all species except for two surface species S. jii and S. macrolepis clustered as five major monophyletic clades (I, II, III, IV, and V) with strong supports. S. jii was the most basal species in all analyses, but the position of S. macrolepis was not resolved. The cave species were polyphyletic and occurred in these five major clades. Our results indicate that adaptation to cave environments has occurred multiple times during the evolutionary history of Sinocyclocheilus. The branching orders among the clades I, II, III, and IV were not resolved, and this might be due to early rapid radiation in Sinocyclocheilus. All species distributed in Yunnan except for S. rhinocerous and S. hyalinus formed a strongly supported monophyletic group (clade V), probably reflecting their common origins. This result suggested that the diversification of Sinocyclocheilus in Yunnan may correlate with the uplifting of Yunnan Plateau.     

Molecular phylogeny of the fungus gnat tribe Exechiini (Mycetophilidae, Diptera)

The phylogenetic relationships within the fungus gnat tribe Exechiini have been left unattended for many years. Recent studies have not shed much light on the intergeneric relationship within the tribe. Here the first attempt to resolve the phylogeny of the tribe Exechiini using molecular markers is presented. The nuclear 18S and the mitochondrial 16S, and cytochrome oxidase subunit I (COI) genes were successfully sequenced for 20 species representing 15 Exechiini genera and five outgroup genera. Bayesian, maximum parsimony and maximum likelihood analyses revealed basically congruent tree topologies and the monophyly of Exechiini, including the genus Cordyla , is confirmed. The molecular data corroborate previous morphological studies in several aspects. Cordyla is found in a basal clade together with Brachypeza , Pseudorymosia and Stigmatomeria . The splitting of the genera Allodiopsis s.l. and Brevicornu s.l. as well as the sistergroup relationship of Exechia and Exechiopsis is also supported. The limited phylogenetic information provided by morphological characters is mirrored in the limited resolution of the molecular markers used in this study. Short internal and long-terminal branches obtained may indicate a rapid radiation of the Exechiini genera during a short evolutionary period.     

Molecular phylogeny of the tribe Bovini (Mammalia: Artiodactyla): alternative placement of the Anoa

Noncoding regions from the genes encoding aromatase cytochrome P450 and lactoferrin have been sequenced in ten bovine and one cervid species for an investigation of the evolutionary relationships within the tribe Bovini. The evolutionary rate of DNA-nucleotide alterations along the ancestral bovine lineage amounts to 0.38% per million years, as estimated from this combined 0.478-kb-single copy nuclear (scn) DNA sequence data set. Whereas rate homogenity is apparent within the Bovini, the relative rate test suggests that the boselaphine lineage (as represented by Boselaphus) has evolved at only about one third of the rate found within the Bovini. Consistent with other results, the scnDNA data provide evidence for (i) a monophyletic origin of the Bovini, (ii) a sister group position of the Boselaphini, and (iii) two different clades within the Bovini, the buffaloes (Bubalus and Syncerus) and the cattle (Bos/Bibos and Bison). Surprisingly, the results indicate very clearly that the enigmatic dwarf buffalo of Sulawesi Island (Anoa depressicornis) is most closely related to Boselaphus and that the divergence from the true Bovini occurred close to the base of bovine cladogenesis in the Middle Miocene (≈ 14—12 million years ago).     

The oral sucker of Gyrinocheilus aymonieri (Teleostei: Cypriniformes)

The sucker was studied in young and mature fish by light microscopy, histochemistry, transmission and scanning electron microscopy, X-ray probe microanalysis, dissection, staining preparations of whole skeletons, and watching the animals in aquaria. The fleshy lips are supported by highly flexible, chondroid tissues, the structure and histochemistry of which differ substantially from those of cartilage. They allow the sucker to evert when the fish attaches to a stone or aquarium wall and are connected to the maxillae, premaxillae and dentaries. Lining the inside of the lips are two horny rasps, each with several regular rows of small hooks. The scraping blades of these hooks are keratinized and point towards the mouth. They increase the coefficient of friction for adhesion and enable the fish to feed on encrusting algae. Between the posterior rasp and the -anterior margin of the mandible are two invaginations of the lower lip that extend the sucker chamber beneath large hollows in the dentaries. The anterior margin itself contacts the outer surface of the maxillary oral valve when the mouth is closed, and isolates the sucker chamber from the rest of the buccal and pharyngeal cavities. Contrary to previous views, it is thought that a true vacuum is produced, and that attached fish spend long periods without taking water in through the mouth. The attachments of the principal jaw muscles are described and their role in sucker action discussed. There are similarities with the jaw mechanism of catostomids.     

Molecular phylogeny of the genus Capoeta (Teleostei: Cyprinidae) in Anatolia,Turkey

Phylogeny of Capoeta genus distributed in Anatolia were carried out by analysing mitochondrial cytochrome b gene (1140 bp) sequences from 332 samples representing 59 populations of 15 species across their geographical distribution. Haplotype network and phylogenetic analysis (neighbor-joining, maximum-likelihood, maximum parsimony, and bayesian inference) of the 103 cytochrome b haplotypes detected in Capoeta species resulted in similar tree topologies including four distinct clades, in congruent with taxonomic classification of Capoeta based on morphological characteristics such as scale size, mouth shape, and body spotting. Based on cyt b nucleotide sequences, the present study suggests that four undescribed Capoeta species may exist in Anatolia freshwater; one species in the Kizilirmak River, the second species in the Dirgine River, the third species B. Menderes River, and the fourth species in the some Yesilirmak tributaries that run into the Black Sea Basin. Capoeta taxa distributed in the rivers of Anatolian freshwater basins are isolated from each other during middle Miocene (Serravallian)-late Pleistocene (Ionian) (about 13.75–0.41 million years). This suggests that distribution and presence of Capoeta species were shaped under paleogeographic conditions such as Pleistocene climate changes in Quarternary period as well as tectonic uplift and faulting, which probably has not changed up to now.     

Molecular phylogeny reveals the non-monophyly of tribe Yinshanieae(Brassicaceae) and description of a new tribe,Hillielleae

The taxonomic treatment within the unigeneric tribe Yinshanieae(Brassicaceae) is controversial, owing to differences in generic delimitation applied to its species. In this study, sequences from nuclear ITS and chloroplast trn L-F regions were used to test the monophyly of Yinshanieae, while two nuclear markers(ITS, ETS) and four chloroplast markers(trnL-F, trn H-psbA, rps16, rpL32-trnL) were used to elucidate the phylogenetic relationships within the tribe. Using maximum parsimony, maximum likelihood, and Bayesian inference methods, we reconstructed the phylogeny of Brassicaceae and Yinshanieae. The results show that Yinshanieae is not a monophyletic group, with the taxa splitting into two distantly related clades: one clade contains four taxa and falls in Lineage I, whereas the other includes all species previously placed in Hilliella and is embedded in the Expanded Lineage II. The tribe Yinshanieae is redefined, and a new tribe, Hillielleae, is proposed based on combined evidence from molecular phylogeny, morphology, and cytology.     

Molecular phylogeny and larval morphological diversity of the lanternfish genus Hygophum (Teleostei: Myctophidae)

Larvae of the deep-sea lanternfish genus Hygophum (Myctophidae) exhibit a remarkable morphological diversity that is quite unexpected, considering their homogeneous adult morphology. In an attempt to elucidate the evolutionary patterns of such larval morphological diversity, nucleotide sequences of a portion of the mitochondrially encoded 16S ribosomal RNA gene were determined for seven Hygophum species and three outgroup taxa. Secondary structure-based alignment resulted in a character matrix consisting of 1172 bp of unambiguously aligned sequences, which were subjected to phylogenetic analyses using maximum-parsimony, maximum-likelihood, and neighbor-joining methods. The resultant tree topologies from the three methods were congruent, with most nodes, including that of the genus Hygophum, being strongly supported by various tree statistics. The most parsimonious reconstruction of the three previously recognized, distinct larval morphs onto the molecular phylogeny revealed that one of the morphs had originated as the common ancestor of the genus, the other two having diversified separately in two subsequent major clades. The patterns of such diversification are discussed in terms of the unusual larval eye morphology and geographic distribution.     

Molecular phylogeny of the tribe Sphodrini (Coleoptera: Carabidae) based on mitochondrial and nuclear markers

A phylogenetic analysis of 6.4 kb of nucleotide sequence data from seven genes (mitochondrial cox1-cox2 and tRNA(leu), and nuclear Ef-1alpha C0, Ef-1alpha C1, 28S, and 18S) was done to reconstruct the phylogenetic relationships of the ground-beetle tribe Sphodrini. Gene regions of variable nucleotide length were aligned using both a secondary structure model, Clustal W, and a combination of the two. Sensitivity analysis was performed in order to explore the effect of alignment methods. The ribosomal and protein-coding genes were largely congruent based on the ILD test and partitioned Bremer support measures. MtDNA analysis provided high resolution and high support for most clades. The tribe Sphodrini and the related tribes Platynini, Pterostichini and Zabrini made up monophyletic clades, but the relationship between them was weakly resolved and sensitive to alignment strategy. Previously suggested relationships between subtribes of Sphodrini were not corroborated, and only the subtribe Atranopsina revealed high support as the sister clade to the other subtribes. The analyses clearly demonstrated the importance of exploring effects of alignment methods that may become particularly important in resolving polytomies and nodes with low support.