Phylogeny of the bee genus Halictus (Hymenoptera: halictidae) based on parsimony and likelihood analyses of nuclear EF-1alpha sequence data

We investigated higher-level phylogenetic relationships within the genus Halictus based on parsimony and maximum likelihood (ML) analysis of elongation factor-1alpha DNA sequence data. Our data set includes 41 OTUs representing 35 species of halictine bees from a diverse sample of outgroup genera and from the three widely recognized subgenera of Halictus (Halictus s.s., Seladonia, and Vestitohalictus). We analyzed 1513 total aligned nucleotide sites spanning three exons and two introns. Equal-weights parsimony analysis of the overall data set yielded 144 equally parsimonious trees. Major conclusions supported in this analysis (and in all subsequent analyses) included the following: (1) Thrincohalictus is the sister group to Halictus s.l., (2) Halictus s.l. is monophyletic, (3) Vestitohalictus renders Seladonia paraphyletic but together Seladonia + Vestitohalictus is monophyletic, (4) Michener's Groups 1 and 3 are monophyletic, and (5) Michener's Group 1 renders Group 2 paraphyletic. In order to resolve basal relationships within Halictus we applied various weighting schemes under parsimony (successive approximations character weighting and implied weights) and employed ML under 17 models of sequence evolution. Weighted parsimony yielded conflicting results but, in general, supported the hypothesis that Seladonia + Vestitohalictus is sister to Michener's Group 3 and renders Halictus s.s. paraphyletic. ML analyses using the GTR model with site-specific rates supported an alternative hypothesis: Seladonia + Vestitohalictus is sister to Halictus s.s. We mapped social behavior onto trees obtained under ML and parsimony in order to reconstruct the likely historical pattern of social evolution. Our results are unambiguous: the ancestral state for the genus Halictus is eusociality. Reversal to solitary behavior has occurred at least four times among the species included in our analysis.     

Phylogeny and classification of Marantaceae

Relationships of Marantaceae were estimated from nucleotide sequence variation in the rps16 intron (plastid DNA) and from morphological characters. Fifty-nine species (21 genera) formed the ingroup, and 12 species (12 genera) of other Zingiberales formed the outgroup. There is no support for the traditional subdivision of Marantaceae into a triovulate and a uniovulate tribe or the informal groups previously proposed. The so-called Donax group forms a paraphyletic grade that is basal within Marantaceae. Thalia appears as the distal branch of this grade, but its position is not supported in jackknife analysis. The so-called Calathea group is monophyletic in all shortest trees but not supported with greater than 50% jackknife. The genus Calathea appears to be paraphyletic. The Maranta and Phrynium groups are clearly polyphyletic. Maranta, Koernickanthe , and genera of the Mymsma group, all neotropical, form a strongly supported monophyletic group. The sister of this group is the palaeotropical genus Halopegia. Koernickanthe is nested within Maranta , as this genus is traditionally circumscribed. The African genera Ataenidia and Marantochloa form a strongly supported clade in which Ataenidia is the sister group to Marantochloa . Based on phylogeny it is concluded that Africa, in spite of being much poorer in species, is the most likely ancestral area of Marantaceae     

Phylogenetic relationships of sponges with placochelae or related spicules (Poecilosclerida, Guitarridae) with a systematic revision

All the currently known sponge species bearing placochelae or placochelae-like spicules (i.e. belonging to the genera Guitarra, Coelodischela, Tetrapocillon, Euchelipluma , and Hoplakithara ) have been reviewed and their relationships delineated by cladistic analysis. A matrix of 18 taxa and 14 characters is included. The species Isodictya palmata and Esperiopsis fucorum were used as an outgroup, because they shared either monactines or diactines and smooth palmate isochelae with different members of the ingroup. Cladistic analysis using PAUP produced two equally parsimonious trees of 33 steps (CI = 0.758). Strict, Semistrict and Majority Rule consensus trees displayed the same topology. The phylogeny of the trees was not totally resolved. The bootstrap 50% majority-rule consensus tree supported, to a greater or lesser extent, the previously detected monophyletic groups. A common linkage for the ingroup was found in 72% of instances. The genus Euchelipluma appeared as monophyletic in 75% of instances while the group which included the genus Guitarra did so in 66%. The monophyly of the species with sigmoid microscleres and without spiny isochelae (G. isabellae/sigmatifera/antarctica/dendyi and C. diatomorpha/massa ) received 56% support as did the group of species with spiny isochelae, whereas monophyly of the group laplani/ bipocillifera received 64% support and the genus Tetrapocillon 56%. According to our cladistic analysis, all the species bearing placochelae or derived forms should be allocated to Guitarridae. Within this family, the genus Euchelipluma appeared as monophyletic while Guitarra was paraphyletic. The single species of the genus Hoplakithara clearly belongs to the Guitarra ( sigmatifera ) group and thus becomes synonymous with Guitarra. G. solorzanoi is considered here a synonymy of G. laplani. A diagnosis for the 10 valid species of Guitarra known to date as well as for the two species of Coelodischela and the two of Euchelipluma is given.     

REEXAMINATION OF PHYLOGENETIC RELATIONSHIPS WITHIN THE COLONIAL VOLVOCALES (CHLOROPHYTA): AN ANALYSIS OF atpB AND rbcL GENE SEQUENCES

The chloroplast-encoded atp B gene was sequenced from 33 strains representing 28 species of the colonial Volvocales (the Volvocaceae and its relatives) to reexamine phylogenetic relationships as previously deduced by morphological data and rbc L gene sequence data.1128 base pairs in the coding regions of the atp B gene were analyzed by MP, NJ, and ML analyses. Although supported with relatively low bootstrap values (75% and 65% in the NJ and ML analyses, respectively), three anisogamous/oogamous volvocacean genera— Eudorina, Pleodorina, and Volvox, excluding the section Volvox (= Euvolvox, illegitimate name), constituted a large monophyletic group (Eudorina group). Outside the Eudorina group, a robust lineage composed of three species of Volvox sect. Volvox was resolved as in the rbc L gene trees, rejecting the hypothesis of the previous cladistic analysis based on morphological data that the genus Volvox is monophyletic. In addition, the NJ and ML trees suggested that Eudorina is a nonmonophyletic genus as inferred from the morphological data and rbc L gene sequences. Although phylogenetic status of the genus Gonium is ambiguous in the rbc L gene trees and the paraphyly of this genus is resolved in the cladistic analysis based on morphological data, the atp B gene sequence data suggest monophyly of Gonium with relatively low bootstrap values (56–61%) in the NJ and ML trees. On the basis of the combined sequence data (2256 base pairs) from atp B and rbc L genes, Gonium was resolved as a robust monophyletic genus in the NJ and ML trees (with 68–86% bootstrap values), and Eudorina elegans Ehrenberg represented a paraphyletic species positioned most basally within the Eudorina group. However, phylogenetic status and relationships of the families of the colonial Volvocales were still almost ambiguous even in the combined analysis.     

Molecular systematics and radiation of western North American nymphophiline gastropods

Three mitochondrial DNA (mtDNA) markers were used to infer the phylogenetic relationships of the morphologically diverse, species rich, and poorly understood western North American aquatic gastropod genus Pyrgulopsis (Hydrobiidae: Nymphophilinae). Sequences were obtained from 62 of 124 currently recognized species of Pyrgulopsis and representatives of four related genera of North American nymphophilines. Separate and combined analyses of the mtDNA datasets recovered a well supported clade composed of Pyrgulopsis and two other North American nymphophiline genera (Floridobia, Nymphophilus) consistent with the results of a prior study based on a single gene and with anatomical evidence suggesting that these taxa form a monophyletic group. Phylogenetic relationships among lineages of Pyrgulopsis were little resolved in our analyses and provided no obvious basis for splitting this large genus into multiple genera. The little differentiated Mexican genus Nymphophilus was consistently placed within Pyrgulopsis in our trees and is formally synonymized with it herein. Pyrgulopsis was also depicted as paraphyletic with respect to Floridobia in some of our trees while in others the latter was sister to a Nymphophilus + Pyrgulopsis clade. Based on these equivocal results and the morphological and geographical divergence of eastern North American Floridobia relative to Pyrgulopsis, we recommend that the former be maintained as a separate genus. The short, weakly supported branches within Pyrgulopsis and the noncongruence between our molecular phylogenetic hypotheses and geographical groupings of species are attributed to an early rapid diversification of the genus, perhaps triggered by the complex changes in western topography which occurred during the late Tertiary. Our results also indicate that penial morphologies used to define species groups of Pyrgulopsis have been subject to striking convergence throughout the West, suggesting another compelling facet of the radiation of these snails.     

基于核基因c-mos的鸫亚科部分鸟类系统发生关系

采用分子系统学方法对鸫亚科Turdinae 11属21种鸟类的核基因c-mos进行了系统发生分析.所测序列经对位排列后共572个位点,其中核苷酸变异位点111个,简约信息位点71个.以太平鸟Bombycilla garrulus作外群,采用邻接法、最大简约法和最大似然法分别构建其系统发生树.重建的系统发生树显示:所研究鸫亚科21种鸟类分成2个支系,第1个支系包括鸫属Turdus和地鸫属Zoothera.第2个支系包括红尾鸲属Phoenicurus、矶鸫属Monticola、水鸲属Rhyacornis、鸲属Tarsiger、溪鸲属Chainarrornis、石即鸟属Saxicola、燕尾属Enivurus、歌鸲属Luscinia和鹊鸲属Copsychus.红尾鸲属为并系类群,水鸲属和溪鸲属聚到这一支系;歌鸲属与燕尾属互为姐妹群,再与鸲属聚合构成另一支系;宝兴歌鸫Turdus mupinensis独立于鸫属及地鸫属之外,形成单独一个分支.     

Genets and 'genet-like' taxa (Carnivora, Viverrinae): phylogenetic analysis, systematics and biogeographic implications

The subfamily Viverrinae is a taxon of uncertain systematic status. This study consists of cladistic analyses based on morphological characters of specimens belonging to the genera Genetta , Osbornictis , Poiana and Prionodon . Two levels of analysis are carried out, one concerning generic relationships (intergeneric analysis) and one dealing with the interrelationships of species within the genus Genetta (intrageneric analysis). In the first analysis, different outgroups were used in order to test the ingroup topology.
With regard to the intergeneric analysis, Osbornictis , Poiana and Prionodon , together with Genetta johnstoni , constitute a monophyletic group (including Nandinia ), which is the sister-group of a clade formed by the other species of genets. Thus, the genus Genetta is regarded as paraphyletic. Prionodon appears to be a derived taxon. The Poiana – Prionodon clade is well supported, especially by ultrastructural hair characters. The cladogram topology in the intrageneric analysis indicates an ecological transition from the rain forest genets to the savanna genets. This supports a rain forest origin of the genus Genetta , a conclusion which may be generalized to the entire study group. © 2002 The Linnean Society of London, Zoological Journal of the Linnean Society , 2002, 134 , 317–334.     

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.     

Multilocus molecular systematics and evolution in time and space of Calligrapha (Coleoptera: Chrysomelidae,Chrysomelinae)

Calligrapha (Coleoptera: Chrysomelidae) is a genus with species present in most of the American continent, from the Arctic polar circle to the Pampas in Argentina. In its current concept, the genus comprises some 80 species, but the diagnosis of the genus is problematic, based on a combination of potentially symplesiomorphic character states. In this study, we investigate the largest taxonomic sample of Calligrapha diversity to date (43 species) using a phylogenetic perspective based on more than 6000 molecular characters from eight genes (four mitochondrial and four nuclear) for a systematic evaluation of the genus. The analyses also include thirteen species in the closely related Zygospila (currently a subgenus of Zygogramma) to assist the systematic delimitation of Calligrapha. Partitioned and total evidence phylogenetic trees were additionally used for molecular clock analyses and dating based on standard mtDNA evolutionary rates, and for likelihood‐based inference of ancestral areas. Calligrapha and Zygospila are reciprocally paraphyletic, and our interpretation of taxonomic stability merges both taxa into a larger genus Calligrapha which plausibly originated in the dry steppes of southern North America in the Late Miocene. The genus includes a minimum of five strongly supported lineages which initially diversified in the Pliocene, fully congruent with expectations from morphology, but of uncertain mutual relationships. Only two of these lineages dispersed to South America: the group of C. polyspila right at the time of the final closure of the Isthmus of Panama in the Early Pliocene and the group of C. argus only in recent times, well in the Pleistocene. The most species‐rich lineage of Calligrapha, associated to trees and shrubs typical of riverine and lacustrine environments (as opposed to herbaceous steppe plants, generally Malvaceae and Asteraceae, for most other groups) diversified and spread in North America in the Late Pliocene. The ecological shift to a stable habitat spreading in the continent due to climate change is hypothesized as one possible explanation for the evolutionary success of this group.     

PHYLOGENY OF THE NEMERTEAN SUBCLASS PALAEONEMERTEA (ANOPLA, NEMERTEA)

Abstract— A cladistic analysis based on 50 morphological characters was performed for 49 of the 98 species currently assigned to the subclass Palaeonemertea (phylum Nemertea), and six additional undescribed species. Thirty-five species were excluded from the parsimony analysis because of the high number of unknowns in the character matrix, and one species since it was considered a nomen nudum . An initial analysis suggested that the subclass Hoplonemertea is the sistergroup to the clade Palaeo- and Heteronemertea and the ingroup cladograms are rooted using a paraphyletic outgroup based on this information. Seventy-two equally most parsimonious cladograms were found; the consistency index was low but tree-length distribution for the character set is skewed to the left, and the cladograms are invariably shorter than trees based on random data. These cladograms suggested a character transformation series for the cerebral organ where this complex character reappeared several times after being absent. We considered this biologically implausible and the final discussion is based on three cladograms, one step longer than the most parsimonious, where the evolution of this character appears to be more realistic. The cladistic analysis indicates that many previously recognized genera (e.g. Cephalothrix, Procephalothrix and Cephalotrichella ), and higher taxa, are paraphyletic. It furthermore indicates that the previously suggested hypothesis of the Archinemertea as a monophyletic sistertaxon to Palaeonemertea is unsupported.     

Phylogeny of the Bee Genus Halictus (Hymenoptera: Halictidae) Based on Parsimony and Likelihood Analyses of Nuclear EF-1α Sequence Data

We investigated higher-level phylogenetic relationships within the genus Halictus based on parsimony and maximum likelihood (ML) analysis of elongation factor-1α DNA sequence data. Our data set includes 41 OTUs representing 35 species of halictine bees from a diverse sample of outgroup genera and from the three widely recognized subgenera of Halictus (Halictus s.s., Seladonia, and Vestitohalictus). We analyzed 1513 total aligned nucleotide sites spanning three exons and two introns. Equal-weights parsimony analysis of the overall data set yielded 144 equally parsimonious trees. Major conclusions supported in this analysis (and in all subsequent analyses) included the following: (1) Thrincohalictus is the sister group to Halictus s.l., (2) Halictus s.l. is monophyletic, (3) Vestitohalictus renders Seladonia paraphyletic but together Seladonia + Vestitohalictus is monophyletic, (4) Michener's Groups 1 and 3 are monophyletic, and (5) Michener's Group 1 renders Group 2 paraphyletic. In order to resolve basal relationships within Halictus we applied various weighting schemes under parsimony (successive approximations character weighting and implied weights) and employed ML under 17 models of sequence evolution. Weighted parsimony yielded conflicting results but, in general, supported the hypothesis that Seladonia + Vestitohalictus is sister to Michener's Group 3 and renders Halictus s.s. paraphyletic. ML analyses using the GTR model with site-specific rates supported an alternative hypothesis: Seladonia + Vestitohalictus is sister to Halictus s.s. We mapped social behavior onto trees obtained under ML and parsimony in order to reconstruct the likely historical pattern of social evolution. Our results are unambiguous: the ancestral state for the genus Halictus is eusociality. Reversal to solitary behavior has occurred at least four times among the species included in our analysis.     

Problems in using Robertsonian rearrangements in determining monophyly: examples from the genera Tatera and Gerbillurus

Chromosomal banding data on three species of Tatera from Kenya significantly alter the previous hypothesis of relationships between and within the genera Tatera and Gerbillurus based on cladistic analyses and the rule of parsimony (Qumsiyeh, 1986b). Of the many possible hypothetical relationships, the most parsimonious tree showed three homoplasies and allowed the genus Gerbillurus to be paraphyletic. The alternative trees, depicting larger number of homoplasies but with homoplasies restricted to fusion or fission events, were compatible with the morphological data in supporting the monophyly of Gerbillurus. To choose between the hypothesis based on the most parsimonious chromosomal tree and those supported by both morphology and slightly less parsimonious chromosomal trees, we performed an electrophoretic study on this group of gerbils. The conclusions are that the genus Gerbillurus is monophyletic and represents a branch that is closely related to the T. robusta group of Taterillini. The study documents that fissions and fusions must have occurred frequently and that in some cases the same fusions were acquired in two independent lineages in numbers exceeding those that are predicted by strict parsimony. The results raise questions about the validity of systematic conclusions based solely on fusion/fission data and utilizing the parsimony criterion.     

Phylogenetic relationships of phrynosomatid lizards based on nuclear and mitochondrial data,and a revised phylogeny for Sceloporus

Phrynosomatid lizards are among the most common and diverse groups of reptiles in western North America, Mexico, and Central America. Phrynosomatidae includes 136 species in 10 genera. Phrynosomatids are used as model systems in many research programs in evolution and ecology, and much of this research has been undertaken in a comparative phylogenetic framework. However, relationships among many phrynosomatid genera are poorly supported and in conflict between recent studies. Further, previous studies based on mitochondrial DNA sequences suggested that the most species-rich genus (Sceloporus) is possibly paraphyletic with respect to as many as four other genera (Petrosaurus, Sator, Urosaurus, and Uta). Here, we collect new sequence data from five nuclear genes and combine them with published data from one additional nuclear gene and five mitochondrial gene regions. We compare trees from nuclear and mitochondrial data from 37 phrynosomatid taxa, including a “species tree” (from BEST) for the nuclear data. We also present a phylogeny for 122 phrynosomatid species based on maximum likelihood analysis of the combined data, which provides a strongly-supported hypothesis for relationships among most phrynosomatid genera and includes most phrynosomatid species. Our results strongly support the monophyly of Sceloporus (including Sator) and many of the relationships within it. We present a new classification for phrynosomatid lizards and the genus Sceloporus, and offer a new tree with branch lengths for use in comparative studies.     

Phylogenetic relationships of freshwater sponges (Porifera, Spongillina) inferred from analyses of 18S rDNA, COI mtDNA, and ITS2 rDNA sequences

The phylogenetic relationships of nine species of freshwater sponges, representing the families Spongillidae, Lubomirskiidae, and Metaniidae, were inferred from analyses of 18S rDNA, cytochrome oxidase subunit I (COI) mtDNA, and internal transcribed spacer 2 (ITS2) rDNA sequences. These species form a strongly supported monophyletic group within the Demospongiae, with the lithistid Vetulina stalactites as the sister taxon. Within the freshwater sponge clade, the basal taxon is not resolved. Depending upon the method of analysis and sequence, the metaniid species, Corvomeyenia sp., or the spongillid species, Trochospongilla pennsylvanica , emerges as the basal species. Among the remaining freshwater sponge species, the spongillids, Spongilla lacustris and Eunapius fragilis , form a sister group to a clade comprised of the spongillid species, Clypeatula cooperensis , Ephydatia fluviatilis , and Ephydatia muelleri , and the lubomirskiid species, Baikalospongia bacillifera and Lubomisrkia baicalensis . C. cooperensis is the sister taxon of E. fluvialitis , and E. muelleri is the sister taxon of ( B. bacillifera + L. baicalensis ). The family Spongillidae and the genus Ephydatia are thus paraphyletic with respect to the lubomirskiid species; Ephydatia is also paraphyletic to C. cooperensis . We suggest that C. cooperensis be transferred to the genus Ephydatia and that the family Lubomirskiidae be subsumed into the Spongillidae.     

A phylogenetic analysis of the nursery-web spider family Pisauridae, with emphasis on the genera Architis and Staberius (Araneae: Lycosoidea)

This study presents a general cladistic analysis of pisaurid genera, with emphasis on the Neotropical genera Architis Simon and Staberius Simon. The analysis was based on a matrix with 21 terminal taxa: eight species of Architis , Staberius spinipes (Taczanowski), seven exemplars of other pisaurid genera and five outgroup taxa. These terminals were scored for 59 morphological and three behavioural characters. An analysis with all characters equally weighted resulted in two most parsimonious trees, differing only in the position of Architis colombo Santos. In both trees Pisauridae arouse as a monophyletic group, and the exemplars of Architis composed a clade with S. spinipes . Contrary to hypotheses from the literature, Thalassius Simon emerged as sister-group of all remaining pisaurids, not as a close relative of Dolomedes Latreille. The genera Tinus F.O.P. -Cambridge and Thaumasia Perty appeared in the trees as the closest relatives of Architis and Staberius Simon. The analysis strongly supported S. spinipes as the sister-group of A. helveola (Simon), indicating that Architis as currently delimited is paraphyletic. Based on these results, Staberius is considered a subjective junior synonym of Architis . Additionally, the genus Mimicosa Petrunkevitch, originally described in Tetragnathidae, is transferred to Pisauridae and considered a junior synonym of Architis . Two species are proposed as junior synonyms of A. spinipes comb.n. Mimicosa spinosa Petrunkevitch and Staberius lemoulti Caporiacco.     

A phylogenetic analysis of the Conchostraca and Cladocera (Crustacea, Branchiopoda, Diplostraca)

A computer-assisted cladistic analysis on morphological characters of the Diplostraca (Conchostraca and Cladocera) has been undertaken for the first time. The morphological information has been obtained from literature and transformed into 56 suitable characters. The analysis included 47 ingroup taxa, comprising five conchostracan taxa (four families of the Spinicaudata and the Laevicaudata) and 42 genera of the Cladocera. A detailed character discussion is presented which will be a useful working base for future phylogenetic studies on the group. A number of systematic groups were, with differing degrees of certainty, supported in all 218 equally short trees. These are the Diplostraca, Cladocera, Gymnomera (Onychopoda and Haplopoda), Onychopoda, Podonidae, Cercopagididae, Anomopoda, Daphniidae, Moininae, Scapholeberinae, Chydoridae, Chydorinae and Sididae. The Spinicaudata were only supported on some of the 218 equally short trees while no support was found for the Conchostraca. Two taxa—the Macrothricidae and Aloninae—were relatively strongly indicated to be paraphyletic. A suggested classificatory hierarchy, without indication of absolute rank, is presented.     

Molecular taxonomy of Camellia (Theaceae) inferred from nrITS sequences

Camellia, comprising more than 200 species, is the type genus of the family Theaceae. Currently, the interspecies relationship of the economically important genus is still a matter of great debate and controversy. In an attempt to help settle this dispute using molecular phylogeny, we analyzed ITS sequences of 112 species of Camellia. The maximum parsimony and Bayesian trees grouped these species into eight major clades and four isolates. The current study supported the monophyly of sections Thea and Furfuracea, a merged section of Theopsis and Eriandra and the formation of section Oleifera by H, -t. Chang (Flora of Reipulicae Popularis Sinicae. Tomus 49 (3), Science Press, China). The study suggested the polyphyletic nature of the sections Camellia, Paracamellia, Pseudocamellia, and Tuberculata and the paraphyletic nature of the section Chrysantha but did not support the sectional status of the three small sections, Archecamellia, Piquetia, and Sterocarpus. We also discuss the results in terms of morphology, geographic distribution and the results from an earlier molecular phylogeny analysis.     

Intra- and interspecific phylogenetic relationships among diploid Triticum-Aegilops species (Poaceae) based on base-pair substitutions, indels, and microsatellites in chloroplast noncoding sequences

This study analyzes intra- and interspecific variation in chloroplast DNA (cpDNA) in diploid Triticum-Aegilops species. This analysis focused on DNA sequence variation in noncoding regions of cpDNA, which included base-pair substitutions, insertion/deletions (indels, 50 loci pooled), microsatellites (7 loci pooled), and inversions. Nine of 13 Triticum-Aegilops species were successfully identified and genotyped using these data. Sixty-two haplotypes were detected in 115 accessions of 13 diploid species. Because of the large number of characters examined, novel deep relationships within and among Triticum-Aegilops species could be identified and evaluated. Phylogenetic trees for the genus Triticum-Aegilops were constructed with Hordeum vulgare and Dasypyrum villosum as outgroups, and the results were compared to previous studies. These data support the following inferences: (1) Aegilops species should be included in Triticum; (2) groups D, T, M, N, U, and section Sitopsis (except Ae. speltoides) underwent speciation concurrently, but most diploid species evolved independently; (3) Ae. mutica does not occupy a basal position in Triticum-Aegilops; (4) Ae. speltoides is in a basal position and differs significantly from other Sitopsis species; (5) Ae. caudata is polyphyletic in all trees; (6) the genus Aegilops is paraphyletic with Secale.     

AFLP markers as a tool to reconstruct complex relationships: A case study in Rosa (Rosaceae)

The genus Rosa has a complex evolutionary history caused by several factors, often in conjunction: extensive hybridization, recent radiation, incomplete lineage sorting, and multiple events of polyploidy. We examined the applicability of AFLP markers for reconstructing (species) relationships in Rosa, using UPGMA clustering, Wagner parsimony, and Bayesian inference. All trees were well resolved, but many of the deeper branches were weakly supported. The cluster analysis showed that the rose cultivars can be separated into a European and an Oriental cluster, each being related to different wild species. The phylogenetic analyses showed that (1) two of the four subgenera (Hulthemia and Platyrhodon) do not deserve subgeneric status; (2) section Carolinae should be merged with sect. Cinnamomeae; (3) subsection Rubigineae is a monophyletic group within sect. Caninae, making sect. Caninae paraphyletic; and (4) there is little support for the distinction of the five other subsections within sect. Caninae. Comparison of the trees with morphological classifications and with previous molecular studies showed that all methods yielded reliable trees. Bayesian inference proved to be a useful alternative to parsimony analysis of AFLP data. Because of their genome-wide sampling, AFLPs are the markers of choice to reconstruct (species) relationships in evolutionary complex groups.     

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.