Evolutionary relationships among eight species of South American phyllotine rodents (Rodentia: Muridae) based on allozymic data

Rodents of the tribe Phyllotini represents one of the main radiations of South American Sigmodontini. Phylogenetic relationships among species of this highly diversified group are poorly known. In this paper we analyse evolutionary relationships among eight phyllotine species belonging to the genera Calomys , Graomys , Phyllotis and Eligmodontia , on the basis of allozymic polymorphisms. Most of the differences among species were in allele frequencies and not of allele class. Neighbour-joining and maximum likelihood methods place P. xanthopygus in the same group as E. typus and G. griseoflavus , in agreement with results obtained by several authors on the basis of morphological characters. Parsimony analysis of 0–9 coded data suggest that the genus Calomys is paraphyletic, but with a low bootstrap support. In the tree based on genetic distance data, the genus also appears as paraphyletic. The maximum likelihood method yields a tree where Calomys is monophyletic, but this phylogeny is supported by only two out of 78 alleles analysed. Calomys hummelincki and C. venustus occupy a basal position among Calomys species. Calomys musculinus and C. lepidus are the most closely related species of the genus, with C. laucha as sister to them. These relationships are strongly supported by bootstrap percentages.     

Molecular systematics and evolution in New Zealand: Applications to cryptic skink species

Abstract

The polymerase chain reaction (PCR) and DNA sequencing are being used for the study of the origin and evolution of New Zealand plants and animals. Here we describe methods for rapidly obtaining DNA sequences from small amounts of fresh and preserved tissue, and apply them to the problem ofresolving relationships among skinks of the Austrnlasian genus Leiolopisma. DNA extracted from frozen tail muscle was used for the main part of the study. Part ofthe mitochondrial12S ribosomal RNA gene was isolated using PCR. Direct sequencing of this 400 nucleotide region supports the separation of “L. nigriplantare” into several genetically distinct but morphologically similar species. The sequence data have also identified a potential case of hybridisation between two sympatric species in Otago, L. nigriplantare polychroma and L. maccanni. The data set supports the view that skinks have been in New Zealand very much longer than five million years.

From these results we expect that application of the PCR and other techniques in molecular biology will help solve many questions about the origins and evolution of New Zealand's biota, as well as help identify unique populations for conservation.     

Higher-level systematics of rodents (Mammalia,Rodentia): Evidence from the mitochondrial 12S rRNA gene

Phylogenetic relationships among major rodent superfamilies traditionally have been difficult to establish because of the apparent high level of convergence and parallelism seen among morphological characters and/or rapid differentiation of rodent groups in the Paleocene/Eocene. Nucleotide sequence data from the mitochondrial 12S rRNA gene were used to clarify phylogenetic relationships among the major groups of rodents as defined by Brandt (1855) and Tullberg (1899). Based on the approximately 800 bp analyzed for the 12S rRNA gene in 59 mammalian species, including 25 of the 32 extant rodent families, the major rodent groups that could be defined as monophyletic clades were the Hystricognathi, the Muroidea, and the Geomyoidea. In addition, support for superfamilial sister-group relationships was found for Aplodontoidea with Sciuroidea and Dipodoidea with Muroidea.     

Molecular phylogeny of the family Tephritidae (Insecta: Diptera): New insight from combined analysis of the mitochondrial 12S, 16S,and COII genes

The phylogeny of the family Tephritidae (Diptera: Tephritidae) was reconstructed from mitochondrial 12S, 16S, and COII gene fragments using 87 species, including 79 tephritid and 8 outgroup species. Minimum evolution and Bayesian trees suggested the following phylogenetic relationships: (1) A sister group relationship between Ortalotrypeta and Tachinisca, and their basal phylogenetic position within Tephritidae; (2) a sister group relationship between the tribe Acanthonevrini and Phytalmiini; (3) monophyly of Plioreocepta, Taomyia and an undescribed new genus, and their sister group relationship with the subfamily Tephritinae; (4) a possible sister group relationship of Cephalophysa and Adramini; and (5) reconfirmation of monophyly for Trypetini, Carpomyini, Tephritinae, and Dacinae. The combination of 12S, 16S, and COII data enabled resolution of phylogenetic relationships among the higher taxa of Tephritidae.     

基于16S rDNA部分序列探讨中国近海30种石斑鱼类的分子系统进化关系

石斑鱼因其种类繁多、分布广泛及缺乏显著的形体特征,使其系统分类的研究颇为困难。为探讨中国近海石斑鱼类的系统进化关系,通过PCR扩增获得了石斑鱼亚科(Epinephelinae)6属30个种类的线粒体16SrDNA基因片段序列。采用多个生物软件对序列变异和碱基组成进行分析,计算了Kimura2parameter遗传距离、转换/颠换比等遗传信息指数,并结合GenBank石斑鱼属的同源序列,以多纹长尾(Pronotogrammusmultifasciatus)和皮氏叫姑鱼(Johniusbelengerii)为外群构建NJ、MP和ML系统树。根据所得分子依据并结合形态学特征,推论如下:1)在本研究的30种石斑鱼中,鳃棘鲈属(Plectropomus)最先分化,并呈明显单系性;九棘鲈属(Cephalopholis)是一个单系群,并且较石斑鱼属(Epinephelus)原始;侧牙鲈属(Variola)的进化地位介于鳃棘鲈属与九棘鲈属之间;2)宽额鲈(Promicropslanceolatus)可以归入石斑鱼属,而驼背鲈(Cromileptesaltivelis)也与石斑鱼属有很近的亲缘关系,甚至可能是石斑鱼属内的特化类群;3)石斑鱼属内部存在两个平行进化的姐妹分支,分支内部的种类组成与地理分布无关,暗示了石斑鱼属早期的分化模式。     

Early evolutionary differentiation of morphological variation in the mandible of South American caviomorph rodents (Rodentia, Caviomorpha)

Caviomorphs are a clade of South American rodents recorded at least since the early Oligocene (> 31.5 Ma) that exhibit ample eco-morphological variation. It has been proposed that phylogenetic structure is more important than ecological factors for understanding mandibular shape variation in this clade. This was interpreted as a result of the long-standing evolutionary history of caviomorphs and the early divergence of major lineages. In this work, we test this hypothesis through the analysis of morphological variation in the mandible of living and extinct species and compare this information with that obtained through comparative phylogenetic analyses. Our results support the hypothesis of early origin of mandibular variation; moreover, they suggest the conservation of early differentiated morphologies, which could indicate the existence of constrained evolutionary diversification.     

从12S rRNA基因部分序列探讨络新妇亚科升格为科级阶元的有效性

络新妇亚科曾归入园蛛科,后改为属于肖蛸科,目前又升格为科级阶元。为对络新妇亚科的分类地位作进一步研究,测定了9种蜘蛛线粒体12SrRNA基因的部分序列;另外还从GenBank检索到17种蜘蛛的12SrRNA基因的的相应序列。基于12SrRNA基因序列进行的分子系统发生分析结果表明络新妇亚科即不属于园蛛科、也不属于肖蛸科,而是与肖蛸科或园蛛科均无直接关联的独立支系,这个结果证实了将络新妇亚科升格为科级阶元的有效性。     

Phylogenetic relationships within the class mammalia: A study using mitochondrial 12S RNA sequences

The interrelationships of the three mammalian groups, Monotremata, Marsupialia, and Eutheria, have been studied using DNA sequences from the mitochondrial 12S ribosomal RNA gene. The results suggest that the monotremes diverged from the living therians only shortly before eutherians and marsupials separated from each other, although there is some evidence for a slowdown in rate of base change in the monotreme lineage. Whtin the Monotremata, the two extant species of tachyglossids show a very close genetic relationship and the data suggest a very recent divergence. We have also confirmed that the Patagonian Monito del Monte,Dromiciops australis, is more closely related to the australidephian marsupials than it is to other South American species.     

Widespread polyphyly among Alopiinae snail genera: when phylogeny mirrors biogeography more closely than morphology

Consider a group of species that is evenly divided by an easily identifiable complex morphological character. Most biologists would assume that this character should provide better phylogenetic information than, say, the spatial distribution of these species over a fairly continuous 500-km radius area. Paradoxically, this is not the case among terrestrial snail genera in the clausiliid subfamily Alopiinae. Phylogenetic analysis using the nuclear markers ITS1/ITS2 and mitochondrial markers COI/12S reveals widespread homoplasy in the clausilial apparatus (a complex aperture-closing mechanism), and concomitant extensive polyphyly among Carinigera, Isabellaria, and Sericata. In contrast, phylogenetic relationships as revealed by molecular data are closely congruent with biogeography at a relatively small scale. A combination of extremely low vagility and extremely high morphological convergence has conspired to produce this unexpected result. Implications as to the function of the clausilial apparatus are discussed.     

Molecular relationships between closely related strains and species of nematodes

Summary Electrophoretic comparisons have been made for 24 enzymes in theBergerac andBristol strains ofCaenorhabditis elegans and the related species,Caenorhabditis briggsae. No variation was detected between the two strains ofC. elegans. In contrast, the two species,C. elegans andC. briggsae exhibited electrophoretic differences in 22 of 24 enzymes. A consensus 5S rRNA sequence was determined forC. elegans and found to be identical to that fromC. briggsae. By analogy with other species with relatively well established fossil records it can be inferred that the time of divergence between the two nematode species is probably in the tens of millions of years.The limited anatomical evolution during a time period in which proteins undergo extensive changes supports the hypothesis that anatomical evolution is not dependent on overall protein changes.     

Evolutionary relationships within the protostome phylum Sipuncula: a molecular analysis of ribosomal genes and histone H3 sequence data

The phylogenetic relationships of the members of the phylum Sipuncula are investigated by means of DNA sequence data from three nuclear markers, two ribosomal genes (18S rRNA and the D3 expansion fragment of 28S rRNA), and one protein-coding gene, histone H3. Phylogenetic analysis via direct optimization of DNA sequence data using parsimony as optimality criterion is executed for 12 combinations of parameter sets accounting for different indel costs and transversion/transition cost ratios in a sensitivity analysis framework. Alternative outgroup analyses are also performed to test whether they affected rooting of the sipunculan topology. Nodal support is measured by parsimony jackknifing and Bremer support values. Results from the different partitions are highly congruent, and the combined analysis for the parameter set that minimizes overall incongruence supports monophyly of Sipuncula, but nonmonophyly of several higher taxa recognized for the phylum. Mostly responsible for this is the split of the family Sipunculidae in three main lineages, with the genus Sipunculus being the sister group to the remaining sipunculans, the genus Phascolopsis nesting within the Golfingiiformes, and the genus Siphonosoma being associated to the Phascolosomatidea. Other interesting results are the position of Phascolion within Golfingiidae and the position of Antillesoma within Aspidosiphonidae. These results are not affected by the loci selected or by the outgroup chosen. The position of Apionsoma is discussed, although more data would be needed to better ascertain its phylogenetic affinities. Monophyly of the genera with multiple representatives (Themiste, Aspidosiphon, and Phascolosoma) is well supported, but not the monophyly of the genera Nephasoma or Golfingia. Interesting phylogeographic questions arise from analysis of multiple representatives of a few species.     

Phylogenetic relationships among four species and a sub-species of Mullidae (Actinopterygii; Perciformes) based on mitochondrial cytochrome B, 12S rRNA and cytochrome oxidase II genes

DNA sequence comparisons of three mitochondrial DNA genes were used to reveal phylogenetic relationships among four species and a sub-species of Mullidae family. This is the first report using mitochondrial DNA sequence data to infer intraspecific relationship among different populations of Mullus barbatus and Mullus surmuletus; phylogenetic relationships between M. barbatus and its sub-species; M. barbatus ponticus. Cytochrome b, 12S ribosomal RNA, and cytochrome oxidase II regions of 242 individuals belonging to species M. barbatus, M. surmuletus, Upeneus moluccensis, Upeneus pori and sub-species M. barbatus ponticus were sequenced and phylogenetic trees were constructed using four different algorithms. The phylogenetic trees constructed support the existing taxonomical data of two mullid genera (Mullus, Upeneus). Molecular data shows no significant difference between same species of different geographical populations. The results suggest that the molecular difference is not large enough between M. barbatus and M. barbatus ponticus to consider them as sub-species.     

Higher-level relationships of snakes inferred from four nuclear and mitochondrial genes

Higher-level snake relationships are inferred from sequence analyses of one nuclear gene (C-mos) and three mitochondrial genes (12S rRNA, 16S rRNA and cytochrome b). Extant snakes belong to two lineages: the fossorial Scolecophidia, which feed on small prey on a frequent basis, and the ecologically diverse Alethinophidia ('typical' snakes), which feed on large prey on an infrequent basis. The vast majority of Alethinophidia, if not all of them, belong to two clades, corresponding to two distinct prey neutralization modes: unimodal constriction for the Henophidia (locomotor and feeding systems coupled) and injection of toxic saliva, in addition (or not) to diverse alternate modes of constriction, for the Caenophidia (locomotor and feeding systems uncoupled). Within Alethinophidia, non-macrostomatan (small gape) Aniliidae (genus Anilius) and macrostomatan (large gape) Tropidophiidae (genera Trachyboa and Tropidophis), both from the Neotropics, are closest relatives. Although our data are insufficient to robustly infer the ancestral mode of life of snakes, we find evidence of plasticity in the basic ecological and trophic modes of snakes. Consequently, the macrostomatan condition should not be treated a priori as a derived character state devoid of homoplasy.     

Reconstruction of phylogenetic relationships within Grapsidae (Crustacea: Brachyura) and comparison of trans-isthmian versus amphi-atlantic gene flow based on mtDNA

Following taxonomic revisions in recent years, the originally large family Grapsidae MacLeay, 1838 has become a relatively small and morphologically homogeneous family in terms of adult and larval morphology. Most available molecular studies including more than one genus of the family have also suggested monophyly of the corresponding taxa. However, no single phylogenetic study has ever included all constituent genera of the Grapsidae. In the current study, a molecular phylogeny based on sequences of the mitochondrial 16S rRNA gene from all eight grapsid genera and 34 species is presented and suggests that up to four genera are not monophyletic. This is mainly due to the polyphyletic nature of the genus Pachygrapsus which can be found in six different lineages of the phylogeny, suggesting that the genus currently does not represent a single evolutionary lineage and is in need of taxonomic revision. Amphi-atlantic and trans-isthmian species pairs or populations in four genera are compared and reveal relatively constant and pronounced divergences across the Panama Isthmus as opposed to moderate divergences across the Atlantic Ocean, thereby suggesting occurrence of gene flow across the Atlantic Ocean during the past three million years.     

Molecular phylogeny of gobioid fishes (Perciformes: Gobioidei) based on mitochondrial 12S rRNA sequences

The molecular phylogeny of the gobioid fishes, comprising 33 genera and 43 valid species, was examined by use of complete mitochondrial 12S rRNA and tRNA(VAL)genes. Both parsimony and neighbor-joining analyses revealed comparable results and are generally congruent with those of morphological studies. The Odontobutis, which was always placed at the base of the phylogenetic trees, can be treated as a sister group of all other nonrhyacichthyid gobioids. Within eleotrid fishes, the monophyly of the Eleotrinae is strongly supported by molecular data. The Butinae is closer to fishes with five branchiostegal rays and should be treated as a sister group of the latter. The group with five branchiostegal rays, except for sicydiines, can be divided into two groups according to their epural counts. Fish with one epural, the Gobiinae of Pezold plus Microdesmidae, form a monophyletic group which is sister to those with two epurals, the Oxudercinae and Gobionellinae of Pezold. However, Sicydiinae, which have one epural, are closer to the Oxudercinae and Gobionellinae rather than to the Gobiinae. Since progressive reduction in epural number has been observed along this lineage, the sicydiines should be treated as a derived group within the groups with two epurals.     

Shifting ditypic site analysis: Heuristics for expanding the phylogenetic range of nucleotide sequences in Sankoff analyses

Summary We describe and illustrate a simple heuristic approach to the Sankoff methods for construction of parsimonious evolutionary trees from nucleotide sequence data. The procedure is intended to permit more valid inferences, particularly from relatively short sequences, concerning relationships among taxa separated for long time intervals. The procedure is based on the freat variability of evolutionary plasticity among sites in the molecules and removes from consideration the more highly variable sites. Editing is accomplished after classifying sites in carefully aligned arrays of sequences. Only “ditypic sites,” i.e., sites observed in only two evolutionary states within the array, are used in making phylogenetic inferences. This strategy makes possible the construction of good approximations to the most parsimonious Steiner strees, by means of efficient programs that require “dense species arrays,” i.e., species sets that differ from each other by relatively small numbers of differences in conservative sites. The technique is illustrated with 5S and 5.8S rRNA sequence data from published catalogs.