Molecular Systematics and Evolution of the Growth Hormone Introns in the Salmoninae

DNA sequence data was collected for the C and D introns in the duplicate growth hormone loci (GH1 and GH2) from Brachmystax lenok, two subspecies of Hucho hucho, Hucho (Parahucho) perryi, Salmo salar, Salmo trutta, Acantholingua ohridana (Salmothymus), six species of Salvelinus, eight species of Oncorhynchus including O. masou, and three outgroups including Thymallus thymallus, Coregonus artedi, and Coregonus clupeaformis. Phylogenetic analyses were performed using maximum parsimony and maximum likelihood (PAUP, version 4.08beta) with gaps as missing data and as a fifth base. B. lenok was basal in all of the trees and all of the other genera were monophyletic with the exception that A. ohridana always placed within Salmo, and H. hucho sp. often placed with B. lenok. The GH1 introns supported a sister relationship between Oncorhynchus and Salvelinus, while the combined GH2 introns were ambiguous at this node. This result contrasts with trees based on morphology and the ribosomal ITS1 sequences that support a sister relationship between Salmo and Oncorhynchus. The only estrogen response element (ERE) in the gene is found in the C intron and has mutated in GH2 in all of the species except B. lenok. The ERE element in GH1 has undergone another mutation in all of the species except for B. lenok, and members of the two genera Salvelinus and Oncorhynchus. Thus these latter two genera are the only ones with a difference in expression of GH1 and GH2 in the presence of estrogen. Differences in selective pressure on the introns in the duplicate genes in different taxa could account for the conflicting results obtained in the phylogenetic analysis.     

Molecular Systematics of Selene (Perciformes: Carangidae) Based on Cytochrome b Sequences

The marine fishes of the genus Selene are morphologically unique, although little is known about how these species are related to other members of the family Carangidae (Perciformes). In addition, questions remain about the potential validity of two putative species and how species groups with unique body forms within Selene are related. We used DNA sequences of the mitochondrial cytochrome b gene to reconstruct the phylogeny of the seven species of Selene along with five additional species of carangids. Maximum-likelihood and maximum-parsimony analyses were used to examine the sequence data and both phylogenetic methods were compared. Maximum-likelihood produced a monophyletic Selene, whereas parsimony analyses did not. Both maximum-likelihood and maximum-parsimony produced similar support for species groups within Selene. Maximum-likelihood produced two monophyletic subgroups within the genus Selene, the "long-finned" and "short-finned" Selene. Maximum-parsimony produced the same monophyletic "long-finned" group but a paraphyletic "short-finned" group. Both analyses confirm that S. brownii and S. setapinnis are distinct species, expunging the question of conspecificity. The phylogenetic placement of the most basal taxon within Selene, S. orstedii, was problematic and differed among analyses. More data are needed to resolve with confidence its correct phylogenetic placement and, thus, the monophyly of the genus Selene.     

Molecular Systematics of Middle American Cichlid Fishes and the Evolution of Trophic-Types in ‘Cichlasoma(Amphilophus)’ and ‘C.(Thorichthys)’

The majority of Middle American cichlids are placed in the informal assemblage ‘Cichlasoma.’ The group is divided into eight sections which appear to be based primarily on trophic morphology. Although several members of ‘Cichlasoma’ have been used in ecomorphological, behavioral, and biogeographic studies, no phylogenetic hypotheses for the group exist. In an attempt to develop a better understanding of the phylogenetic relationships of ‘cichlasomine’ cichlids, we examined the evolution of the trophic specialization, substratum-sifting, in two sections, ‘Cichlasoma(Thorichthys)’ and ‘C.(Amphilophus),’ to determine whether the trait reflects common ancestry. We sequenced the complete mitochondrial cytochromebgene for 19 cichlids representing six sections of ‘Cichlasoma,’ and representatives of other Neotropical Cichlidae. Additional cichlid, and noncichlid outgroup sequences were included for a total of 22 taxa. The molecular phylogeny supports the recognition of the section ‘C.(Thoricthys)’ as a natural group, and we place those cichlids in the genusThorichthys.The phylogeny also depicts ‘C.(Amphilophus)’ as paraphyletic, with substratum-sifters and generalized predators forming separate nonsister clades. We recommend that the substratum-sifting clade of the section ‘C.(Amphilophus)’ be placed in the resurrected genusAstatheros.The generalized predator clade of ‘C.(Amphilophus)’ contains only two species, ‘C. (A.) citrinellum’ and ‘C. (A.) labiatum,’ which we place in the genusAmphilophus.The phylogenetic hypotheses generated indicate that the substratum-sifting generaThorichthysandAmphilophusdo not share a common ancestor. Reconstruction of the evolution of substratum-sifting is equivocal, requiring either the independent evolution of the trait on two separate occasions or its presence in a more inclusive clade and subsequent loss in nonsubstratum sifting species.     

分子方法在我国有尾类系统与进化研究中的应用

从系统发育、物种分类与界定和遗传多样性等方面,介绍了分子方法在我国有尾类系统与进化研究中的应用现状和最新进展.分析讨论了我国有尾类系统与进化研究中存在的问题,展望了该领域今后的研究趋势和发展前景.     

Molecular Systematics of Bats of the Genus Myotis (Vespertilionidae) Suggests Deterministic Ecomorphological Convergences

Based on extensive phenetic analyses, bats of the genus Myotis have been classically subdivided into four major subgenera each of which comprise many species with similar morphological and ecological adaptations. Each subgenus thus corresponds to a distinct “ecomorph” encompassing bat species exploiting their environment in a similar fashion. As three of these subgenera are cosmopolitan, regional species assemblages of Myotis usually include sympatric representatives of each ecomorph. If species within these ecomorphs are monophyletic, such assemblages would suggest extensive secondary dispersal across geographic areas. Conversely, these ecomorphological adaptations may have evolved independently through deterministic processes, such as adaptive radiation. In this case, phylogenetic reconstructions are not expected to sort species of the same ecomorph into monophyletic clades. To test these predictions, we reconstructed the phylogenetic history of 13 American, 11 Palaearctic, and 6 other Myotis species, using sequence data obtained from nearly 2 kb of mitochondrial genes (cytochrome b and nd1). Separate or combined analyses of these sequences clearly demonstrate the existence of several pairs of morphologically very similar species (i.e., sibling species) which are phylogenetically not closely related. None of the three tested subgenera constitute monophyletic units. For instance, Nearctic and Neotropical species currently classified into the three subgenera were clustered in a single, well-supported monophyletic clade. These species thus evolved independently of their ecological equivalents from the Palaearctic region. Independent adaptive radiations among species of the genus Myotis therefore produced strikingly similar evolutionary solutions in different parts of the world. Furthermore, all phylogenetic reconstructions based on mtDNA strongly supported the existence of an unsuspected monophyletic clade which included all assayed New World species plus M. brandtii (from the Palaearctic Region). This “American” clade thus radiated into a morphologically diverse species assemblage which evolved after the first Myotis species colonized the Americas. Molecular reconstructions support paleontological evidence that species of the genus Myotis had a burst of diversification during the late Miocene–early Pliocene epoch.     

Evolution of Annual Species of the GenusMedicago: A Molecular Phylogenetic Approach

We performed a molecular phylogenetic study based on the nuclear ribosomal internal and external transcribed spacer (ITS and ETS). Thirty-one annualMedicagospecies were included in the study, representing more than half of the genus and 85% of the annuals of the genus. Major incongruences were found between phylogenetic relationships and morphological classification of the genus. Morphological and cytological traits were mapped onto the phylogeny. The most parsimonious reconstruction suggested an ancestral spiny state and a recurrent transition from spiny to spineless state. From the ancestral state of 2n=16, three loss events of chromosomes must have occurred leading to the same specific number of 14 chromosomes whereas species having 30 chromosomes form a monophyletic clade.     

Molecular Systematics of the Order Crocodilia

Analyses of proteins, lipids and nucleic acids have been extremelyuseful for assessing the level of molecular divergence in theCrocodilia and for inferring the relationships of crocodiliansto each other and to other vertebrates. A large body of traditional(morphological and paleontological), as well as recent non-traditional(cytogenetic and molecular) evidence concurs that birds arethe closest living sister group to the Crocodilia. Relationshipswithin the order have been much more difficult to resolve usingtraditional analyses due to the problems of convergence/parallelismand general morphological conservatism. Studies of protein divergence,while in agreement with traditional interpretations of affinitiesbetween the alligators and caimans, suggest that the true andfalse gharials are more closely related to each other than toother crocodilians and that the true crocodiles are all veryclose relatives that may have diverged recently. Preliminaryanalyses from an ongoing study of restriction endonuclease analysisof crocodilian mitochondrial and ribosomal DNAs corroborateboth of these observations, suggesting that the molecular approachwill be very valuable for resolving crocodilian phylogeny.     

Complete Mitochondrial DNA Sequences of Six Snakes: Phylogenetic Relationships and Molecular Evolution of Genomic Features

Complete mitochondrial DNA (mtDNA) sequences were determined for representative species from six snake families: the acrochordid little file snake, the bold boa constrictor, the cylindrophiid red pipe snake, the viperid himehabu, the pythonid ball python, and the xenopeltid sunbeam snake. Thirteen protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 control regions were identified in these mtDNAs. Duplication of the control region and translocation of the tRNA^Leu gene were two notable features of the snake mtDNAs. The duplicate control regions had nearly identical nucleotide sequences within species but they were divergent among species, suggesting concerted sequence evolution of the two control regions. In addition, the duplicate control regions appear to have facilitated an interchange of some flanking tRNA genes in the viperid lineage. Phylogenetic analyses were conducted using a large number of sites (9570 sites in total) derived from the complete mtDNA sequences. Our data strongly suggested a new phylogenetic relationship among the major families of snakes: ((((Viperidae, Colubridae), Acrochordidae), (((Pythonidae, Xenopeltidae), Cylindrophiidae), Boidae)), Leptotyphlopidae). This conclusion was distinct from a widely accepted view based on morphological characters in denying the sister-group relationship of boids and pythonids, as well as the basal divergence of nonmacrostomatan cylindrophiids. These results imply the significance to reconstruct the snake phylogeny with ample molecular data, such as those from complete mtDNA sequences.[Reviewing Editor: Dr. Bill Ballard]     

Molecular Systematics of the Family Mormoopidae (Chiroptera) Based on Cytochrome b and Recombination Activating Gene 2 Sequences

We examined 1140 bp of the mitochondrial cytochrome b gene and 1398 bp of the nuclear RAG2 gene to investigate the systematics of the eight species of bats within the family Mormoopidae. It was concluded that within the genus Pteronotus there were four valid subgenera: Phyllodia, Chilonycteris, Pteronotus, and an undescribed subgenus. Within Pteronotus, P. parnellii either was part of an unresolved tetratomy with the other three subgenera (cytochrome b data) or was basal (RAG2 and combined data). For three species, P. gymnonotus, P. macleayii, and P. quadridens, our sample revealed little geographic variation. In P. davyi and P. parnellii, the magnitude of genetic distance suggests the possibility of two biological species existing within the currently recognized taxa. Within P. personatus, there was substantial geographic variation partitioned in a step-like fashion among our specimens. Neither of the species within the genus Mormoops showed the deep distance nodes present in P. davyi, P. parnellii, and P. personatus. Cytochrome b and RAG2 data indicated that M. megalophylla evolved recently from its common ancestor. Although there was considerable agreement among the branching patterns for the nuclear and mitochondrial genes, both genes failed to provide robust data concerning the evolutionary relationships among the subgenera.     

Journal of Systematics and Evolution VOLUME CONTENTS

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Systematics and biogeography of the Andean genusEriocnemis (Aves: Trochilidae)

Summary With 11 currently recognised species, the genusEriocnemis (Reichenbach, 1849) is one of the most diversified Andean trochilid groups occupying mainly open montane habitats such as the edges of cloud forest or páramos. On the basis of distributional and morphological patterns, this study highlights the geographical variation and biogeography of the taxon. Characteristics common to all these species are the greenish dorsal plumage, the conspicuous and mostly whitish tibial tufts, and a fairly pronounced tail bifurcation. With the help of plumage synapomorphies for a cladistic analysis (PAUP*), several species groups or superspecies can be distinguished: theE. vestitus group (incl.E. vestitus, E. godini, E. nigrivestis), theE. luciani group (incl.E. luciani, E. cupreoventris, E. sapphiropygia), and theE. alinae group (incl.E. alinae, E. mirabilis).E. glaucopoides, E. mosquera, andE. derbyi differ quite widely in morphology and ecological requirements from the other species. Three new subspecies are described,E. vestitus arcosi from southern Ecuador and northern Peru, andE. luciani baptistae from central and southern Ecuador. A previously overlooked specimen ofE. luciani from the Andes of Mérida represents the first species record for Venezuela, about 1100 km northeast of the main population range, and should be recognised taxonomically asE. luciani meridae, subsp. nov., on the basis of its unique plumage morphology and geographical separation. Additionally, the unique type ofE. ventralis (Salvin, 1891) is probably of hybrid origin (E. vestitus × cupreoventris). The genus may have evolved in the northern Andes, subsequently spreading southward and invading the central Andes. Its recent range and phylogenetic patterns indicate vicariance events as the major speciation factor inEriocnemis.In memoriam Dr. Luis F. Baptista (1941–2000)     

Journal of Systematics and Evolution: Looking forward

Systematics and evolution are the most comprehensive fields in biological sciences,and unify all areas of biology by providing a conceptual framework for interpreting biological diversity.Journal of Systematics and Evolution (JSE),established in 1951 as Acta Phytotaxonomica,has a long history of publishing papers on plant taxonomy.In 1954 (Vol.3),the journal name was changed to Acta Phytotaxonomica Sinica.Half a century later,in 2008,the current name was approved and used and the journal became all-English in 2009,with the expanded scope to include molecular evolution,evolutionary genomics,evolutionary developmental biology,evolutionary ecology,biogeography,and other related fields,beyond the core area of plant taxonomy.     

蚂蚁分子系统学研究进展

蚂蚁是分布广泛、种类和数量丰富的社会性昆虫.蚂蚁的传统分类学研究存在一定局限性,而分子生物学为蚂蚁的系统学研究提供了新途径.概述了蚂蚁分子系统学在研究内容和技术方法上的研究进展,并对今后的研究做了展望.