A novel supermatrix approach improves resolution of phylogenetic relationships in a comprehensive sample of danthonioid grasses

Phylogeny reconstruction is challenging when branch lengths vary and when different genetic loci show conflicting signals. The number of DNA sequence characters required to obtain robust support for all the nodes in a phylogeny becomes greater with denser taxon sampling. We test the usefulness of an approach mixing densely sampled, variable non-coding sequences (trnL-F; rpl16; atpB-rbcL; ITS) with sparsely sampled, more conservative protein coding and ribosomal sequences (matK; ndhF; rbcL; 26S), for the grass subfamily Danthonioideae. Previous phylogenetic studies of Danthonioideae revealed extensive generic paraphyly, but were often impeded by insufficient character and taxon sampling and apparent inter-gene conflict. Our variably-sampled supermatrix approach allowed us to represent 79% of the species with up to c. 9900 base pairs for taxa representing the major clades. A 'taxon duplication' approach for taxa with conflicting phylogenetic signals allowed us to combine the data whilst representing the differences between chloroplast and nuclear encoded gene trees. This approach efficiently improves resolution and support whilst maximising representation of taxa and their sometimes composite evolutionary histories, resulting in a phylogeny of the Danthonioideae that will be useful both for a wide range of evolutionary studies and to inform forthcoming realignment of generic delimitations in the subfamily.     

Phylogenetic relationships of the Lake Tanganyika cichlid tribe Lamprologini: the story from mitochondrial DNA

The Lamprologini are the most species-rich and diverse tribe of Lake Tanganyika cichlids, comprising around 90 described species. We reconstruct the most complete ( approximately 70 species) mtDNA phylogeny to date for this tribe, based on NADH dehydrogenase subunit 2 (ND2 approximately 1047 bp) and the non-coding control region ( approximately 874 bp) and examine the degree to which mtDNA trees are good proxies for species trees. Phylogenetic relationships are assessed using Bayesian inference, maximum likelihood and maximum parsimony to determine the robustness of relationships. The resulting topologies are largely congruent and only the tree produced by an unpartitioned BI analysis is rejected using the non-parametric likelihood-based AU test. The trees are remarkably balanced, with two major clades consistently recovered in all analyses and with reasonable support. A smaller clade of deep-water species is also recovered. Overall support is good, when compared to some groups that have undergone adaptive radiation and rapid lineage formation. The much-expanded phylogeny of the group helps resolve the placement of some previously problematic taxa, such as Neolamprologus moori, highlighting the importance of greater taxonomic sampling. The results include a number of divergent placements of closely related species, and the following genera Neolamprologus, Lamprologus, Julidiochromis, Telmatochromis are not monophyletic, with alternative hypotheses consistent with traditional taxonomy providing a significantly worse fit to the data. We find several examples of divergent mtDNA taxa sequences of presumed closely related species. This could be due to incorrect taxonomy or to the failure of the mtDNA to reflect species relationships and may support the hypothesis that speciation within this group has been facilitated by introgressive hybridisation.     

A molecular phylogeny of the New World orioles (Icterus): the importance of dense taxon sampling.

We sequenced 2005 bp of the mitochondrial ND2 and cytochrome b genes from the 25 recognized species of New World orioles (Icterus). Our data confirmed the monophyly of Icterus and produced a well-resolved phylogeny showing three main clades of orioles. We also sequenced multiple subspecies for most polytypic taxa. Our findings demonstrated the importance of dense taxon sampling below the species level in two ways. First, we found evidence that two species are polyphyletic, I. galbula (Northern oriole) and I. dominicensis (Black-cowled oriole). Choosing different subspecies from either of these taxa would lead to different species-level phylogenies. Second, adding subspecies even to monophyletic groups produced a bootstrap tree with significantly more support. Of the two genes that we used, ND2 provided more resolution than did cytochrome b. ND2 evolved up to 40% faster than cytochrome b, yet shows a higher saturation threshold. Our findings suggest that ND2 may be superior to cytochrome b for resolving species-level phylogenies in passerine birds.     

Hylid frog phylogeny and sampling strategies for speciose clades

How should characters and taxa be sampled to resolve efficiently the phylogeny of ancient and highly speciose groups? We addressed this question empirically in the treefrog family Hylidae, which contains > 800 species and may be nonmonophyletic with respect to other anuran families. We sampled 81 species (54 hylids and 27 outgroups) for two mitochondrial genes (12S, ND1), two nuclear genes (POMC, c-myc), and morphology (144 characters) in an attempt to resolve higher-level relationships. We then added 117 taxa to the combined data set, many of which were sampled for only one gene (12S). Despite the relative incompleteness of the majority of taxa, the resulting trees placed all taxa in the expected higher-level clades with strong support, despite some taxa being > 90% incomplete. Furthermore, we found no relationship between the completeness of a taxon and the support (parsimony bootstrap or Bayesian posterior probabilities) for its localized placement on the tree. Separate analysis of the data set with the most taxa (12S) gives a somewhat problematic estimate of higher-level relationships, suggesting that data sets scored only for some taxa (ND1, nuclear genes, morphology) are important in determining the outcome of the combined analysis. The results show that hemiphractine hylids are not closely related to other hylids and should be recognized as a distinct family. They also show that the speciose genus Hyla is polyphyletic, but that its species can be arranged into three monophyletic genera. A new classification of hylid frogs is proposed. Several potentially misleading signals in the morphological data are discussed.     

Phylogenetic relationships of horned lizards (Phrynosoma) based on nuclear and mitochondrial data: evidence for a misleading mitochondrial gene tree

It has proven remarkably difficult to obtain a well-resolved and strongly supported phylogeny for horned lizards (Phrynosoma) because of incongruence between morphological and mitochondrial DNA sequence data. We infer the phylogenetic relationships among all 17 extant Phrynosoma species using >5.1 kb of mtDNA (12S rRNA, 16S rRNA, ND1, ND2, ND4, Cyt b, and associated tRNA genes), and >2.2kb from three nuclear genes (RAG-1, BDNF, and GAPD) for most taxa. We conduct separate and combined phylogenetic analyses of these data using maximum parsimony, maximum likelihood, and Bayesian methods. The phylogenetic relationships inferred from the mtDNA data are congruent with previous mtDNA analyses based on fewer characters and provide strong support for most branches. However, we detected strong incongruence between the mtDNA and nuclear data using comparisons of branch support and Shimodaira-Hasegawa tests, with the (P. platyrhinos+P. goodei) clade identified as the primary source of this conflict. Our analysis of a P. mcalliixP. goodei hybrid suggests that this incongruence is caused by reticulation via introgressive hybridization. Our preferred phylogeny based on an analysis of the combined data (excluding the introgressed mtDNA data) provides a new framework for interpreting character evolution and biogeography within Phrynosoma. In the context of this improved phylogeny we propose a phylogenetic taxonomy highlighting four clades: (1) Tapaja, containing the viviparous short-horned lizards P. ditmarsi, P. hernandesi, P. douglasii, and P. orbiculare; (2) Anota, containing species with prominent cranial horns (P. solare, P. mcallii, and the P. coronatum group); (3) Doliosaurus, containing three species lacking antipredator blood-squirting (P. modestum, P. platyrhinos, and P. goodei); and (4) Brevicauda, containing two viviparous species with extremely short tails that lack blood-squirting (P. braconnieri and P. taurus).     

Phylogeny of the tree swallow genus, Tachycineta (Aves: Hirundinidae), by Bayesian analysis of mitochondrial DNA sequences

To set the stage for historical analyses of the ecology and behavior of tree swallows and their allies (genus Tachycineta), we reconstructed the phylogeny of the nine Tachycineta species by comparing DNA sequences of six mitochondrial genes: Cytochrome b (990 base pairs), the second subunit of nicotinamide adenine dinucleotide dehydrogenase (839 base pairs), cytochrome oxidase II (85 base pairs), ATPase 8 (158 base pairs), tRNA-lysine (73 base pairs), and tRNA-methionine (25 base pairs). The phylogeny consisted of two main clades: South and Central American species ((T. stolzmanni, T. albilinea, T. albiventris), (T. leucorrhoa, T. meyeni)), and North American and Caribbean species (T. bicolor, (T. thalassina, T. euchrysea, T. cyaneoviridis)). The genetic distances among the species suggested that Tachycineta is a relatively old group compared to other New World swallow genera. One interesting biogeographic discovery was the close relationship between Caribbean and western North American taxa. This historical connection occurs in other groups of swallows and swifts as well. To reconstruct the phylogeny, we employed Bayesian as well as traditional maximum-likelihood methods. The Bayesian approach provided probability values for trees produced from the different genes and gene combinations, as well as probabilities of branches within those trees. We compared Bayesian and maximum-likelihood bootstrap branch support and found that all branches with Bayesian probabilities > or = 95% received bootstrap support >70%.     

Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support

Four New World genera of dwarf boas (Exiliboa, Trachyboa, Tropidophis, and Ungaliophis) have been placed by many systematists in a single group (traditionally called Tropidophiidae). However, the monophyly of this group has been questioned in several studies. Moreover, the overall relationships among basal snake lineages, including the placement of the dwarf boas, are poorly understood. We obtained mtDNA sequence data for 12S, 16S, and intervening tRNA-val genes from 23 species of snakes representing most major snake lineages, including all four genera of New World dwarf boas. We then examined the phylogenetic position of these species by estimating the phylogeny of the basal snakes. Our phylogenetic analysis suggests that New World dwarf boas are not monophyletic. Instead, we find Exiliboa and Ungaliophis to be most closely related to sand boas (Erycinae), boas (Boinae), and advanced snakes (Caenophidea), whereas Tropidophis and Trachyboa form an independent clade that separated relatively early in snake radiation. Our estimate of snake phylogeny differs significantly in other ways from some previous estimates of snake phylogeny. For instance, pythons do not cluster with boas and sand boas, but instead show a strong relationship with Loxocemus and Xenopeltis. Additionally, uropeltids cluster strongly with Cylindrophis, and together are embedded in what has previously been considered the macrostomatan radiation. These relationships are supported by both bootstrapping (parametric and nonparametric approaches) and Bayesian analysis, although Bayesian support values are consistently higher than those obtained from nonparametric bootstrapping. Simulations show that Bayesian support values represent much better estimates of phylogenetic accuracy than do nonparametric bootstrap support values, at least under the conditions of our study.     

Phylogenetics of advanced snakes (Caenophidia) based on four mitochondrial genes

Phylogenetic relationships among advanced snakes (Acrochordus + Colubroidea = Caenophidia) and the position of the genus Acrochordus relative to colubroid taxa are contentious. These concerns were investigated by phylogenetic analysis of fragments from four mitochondrial genes representing 62 caenophidian genera and 5 noncaenophidian taxa. Four methods of phylogeny reconstruction were applied: matrix representation with parsimony (MRP) supertree consensus, maximum parsimony, maximum likelihood, and Bayesian analysis. Because of incomplete sampling, extensive missing data were inherent in this study. Analyses of individual genes retrieved roughly the same clades, but branching order varied greatly between gene trees, and nodal support was poor. Trees generated from combined data sets using maximum parsimony, maximum likelihood, and Bayesian analysis had medium to low nodal support but were largely congruent with each other and with MRP supertrees. Conclusions about caenophidian relationships were based on these combined analyses. The Xenoderminae, Viperidae, Pareatinae, Psammophiinae, Pseudoxyrophiinae, Homalopsinae, Natricinae, Xenodontinae, and Colubrinae (redefined) emerged as monophyletic, whereas Lamprophiinae, Atractaspididae, and Elapidae were not in one or more topologies. A clade comprising Acrochordus and Xenoderminae branched closest to the root, and when Acrochordus was assessed in relation to a colubroid subsample and all five noncaenophidians, it remained associated with the Colubroidea. Thus, Acrochordus + Xenoderminae appears to be the sister group to the Colubroidea, and Xenoderminae should be excluded from Colubroidea. Within Colubroidea, Viperidae was the most basal clade. Other relationships appearing in all final topologies were (1) a clade comprising Psammophiinae, Lamprophiinae, Atractaspididae, Pseudoxyrophiinae, and Elapidae, within which the latter four taxa formed a subclade, and (2) a clade comprising Colubrinae, Natricinae, and Xenodontinae, within which the latter two taxa formed a subclade. Pareatinae and Homalopsinae were the most unstable clades.     

The relative contribution of band number to phylogenetic accuracy in AFLP data sets

We examined the effect of increasing the number of sampled amplified fragment length polymorphism (AFLP) bands to reconstruct an accurate and well-supported AFLP-based phylogeny. In silico AFLP was performed using simulated DNA sequences evolving along balanced and unbalanced model trees with recent, uniform and ancient radiations and average branch lengths (from the most internal node to the tip) ranging from 0.02 to 0.05 substitutions per site. Trees were estimated by minimum evolution (ME) and maximum parsimony (MP) methods from both DNA sequences and virtual AFLP fingerprints. The comparison of the true tree with the estimated AFLP trees suggests that moderate numbers of AFLP bands are necessary to recover the correct topology with high bootstrap support values (i.e. >70%). Fewer numbers of bands are necessary for shorter tree lengths and for balanced than for unbalanced tree topologies. However, branch length estimation was rather unreliable and did not improve substantially after a certain number of bands were sampled. These results hold for different levels of genome coverage and number of taxa analysed. In silico AFLP using bacterial genomic DNA sequences recovered a well-supported tree topology that mirrored an empirical phylogeny based on a set of 31 orthologous gene sequences when as few as 263 AFLP bands were scored. These results suggest that AFLPs may be an efficient alternative to traditional DNA sequencing for accurate topology reconstruction of shallow trees when not very short ancestral branches exist.     

Phylogenetic Relationships among Higher Nemertean (Nemertea) Taxa Inferred from 18S rDNA Sequences

We estimated the phylogenetic relationships of 15 nemertean (phylum Nemertea) species from the four subclasses Hoplo-, Hetero-, Palaeo-, and Bdellonemertea with 18S rDNA sequence data. Three outgroup taxa were used for rooting: Annelida, Platyhelminthes, and Mollusca. Parsimony and maximum-likelihood analyses supported the monophyletic status of the Heteronemertea and a taxon consisting of hoplonemerteans and Bdellonemertea, while indicating that Palaeonemertea is paraphyletic. The monophyletic status of the two nemertean classes Anopla and Enopla is not supported by the data. The unambiguous clades are well supported, as assessed by a randomization test (bootstrapping) and branch support values.     

Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion

We explored the phylogenetic utility and limits of the individual and concatenated mitochondrial genes for reconstructing the higher-level relationships of teleosts, using the complete (or nearly complete) mitochondrial DNA sequences of eight teleosts (including three newly determined sequences), whose relative phylogenetic positions were noncontroversial. Maximum-parsimony analyses of the nucleotide and amino acid sequences of 13 protein-coding genes from the above eight teleosts, plus two outgroups (bichir and shark), indicated that all of the individual protein-coding genes, with the exception of ND5, failed to recover the expected phylogeny, although unambiguously aligned sequences from 22 concatenated transfer RNA (tRNA) genes (stem regions only) recovered the expected phylogeny successfully with moderate statistical support. The phylogenetic performance of the 13 protein-coding genes in recovering the expected phylogeny was roughly classified into five groups, viz. very good (ND5, ND4, COIII, COI), good (COII, cyt b), medium (ND3, ND2), poor (ND1, ATPase 6), and very poor (ND4L, ND6, ATPase 8). Although the universality of this observation was unclear, analysis of successive concatenation of the 13 protein-coding genes in the same ranking order revealed that the combined data sets comprising nucleotide sequences from the several top-ranked protein-coding genes (no 3rd codon positions) plus the 22 concatenated tRNA genes (stem regions only) best recovered the expected phylogeny, with all internal branches being supported by bootstrap values >90%. We conclude that judicious choice of mitochondrial genes and appropriate data weighting, in conjunction with purposeful taxonomic sampling, are prerequisites for resolving higher-level relationships in teleosts under the maximum-parsimony optimality criterion.     

Phylogenetic relationships of catostomid fishes (Actinopterygii: Cypriniformes) based on mitochondrial ND4/ND5 gene sequences

Family Catostomidae is a diverse group of benthic freshwater fishes that are distributed across North America and in parts of East Asia. In this study, the phylogenetic relationships of Catostomidae is examined using 3436 nucleotides of mitochondrial ND4 and ND5 protein coding genes and intervening tRNAs. All 13 genera and 60 species of catostomids were sampled to represent diversity of the family. Catostomidae and its four subfamilies were found to be monophyletic; however, relationships of the subfamilies are not strongly supported with bootstrapping. The analysis provides strong support for recognizing four tribes in subfamily Catostominae.     

Understanding the formation of ancient intertropical disjunct distributions using Asian and Neotropical hinged-teeth snakes (Sibynophis and Scaphiodontophis: Serpentes: Colubridae)

Numerous taxa show ancient intertropical disjunct distributions. Many can be explained by well-known processes of historical vicariance, such as the breakup of Gondwanaland. Others, such as Asian–Neotropical divergences are not as well understood. To clarify the phylogenetic position and understand biogeographic and temporal origins of the geographically disjunct and morphologically unique genera of hinged-teeth snakes, Scaphiodontophis (n = 1) and Sibynophis (n = 9; Colubridae), we inferred a time-calibrated phylogeny with additional 107 taxa representing the superfamily Colubroidea using four genes (c-mos, cyt-b, ND2, RAG-1; 3085 bp). We used this tree to estimate ancestral areas for the group. The results show that Scaphiodontophis is sister to Sibynophis, both originated in the late Eocene/Oligocene in Asia and likely dispersed through Beringia to the New World, but unlike other snake groups left no extant species in temperate North America. Current recognition of Scaphiodontophiinae renders Colubrinae paraphyletic, and we resurrect the previously named subfamily Sibynophiinae to encompass both genera and use the tribes Sibynophiini (Sibynophis) and Scaphiodontophiini (Scaphiodontophis) to highlight the geographically distinct areas occupied by these taxa. These results suggest that intercontinental dispersal with extinction in intermediate areas can explain puzzling patterns of ancient intertropical disjunct distributions.     

Mitochondrial phylogeny of the Chrysisignita (Hymenoptera: Chrysididae) species group based on simultaneous Bayesian alignment and phylogeny reconstruction

The ignita species group within the genus Chrysis includes over 100 cuckoo wasp species, which all lead a parasitic lifestyle and exhibit very similar morphology. The lack of robust, diagnostic morphological characters has hindered phylogenetic reconstructions and contributed to frequent misidentification and inconsistent interpretations of species in this group. Therefore, molecular phylogenetic analysis is the most suitable approach for resolving the phylogeny and taxonomy of this group. We present a well-resolved phylogeny of the Chrysis ignita species group based on mitochondrial sequence data from 41 ingroup and six outgroup taxa. Although our emphasis was on European taxa, we included samples from most of the distribution range of the C. ignita species group to test for monophyly. We used a continuous mitochondrial DNA sequence consisting of 16S rRNA, tRNA(Val), 12S rRNA and ND4. The location of the ND4 gene at the 3' end of this continuous sequence, following 12S rRNA, represents a novel mitochondrial gene arrangement for insects. Due to difficulties in aligning rRNA genes, two different Bayesian approaches were employed to reconstruct phylogeny: (1) using a reduced data matrix including only those positions that could be aligned with confidence; or (2) using the full sequence dataset while estimating alignment and phylogeny simultaneously. In addition maximum-parsimony and maximum-likelihood analyses were performed to test the robustness of the Bayesian approaches. Although all approaches yielded trees with similar topology, considerably more nodes were resolved with analyses using the full data matrix. Phylogenetic analysis supported the monophyly of the C. ignita species group and divided its species into well-supported clades. The resultant phylogeny was only partly in accordance with published subgroupings based on morphology. Our results suggest that several taxa currently treated as subspecies or names treated as synonyms may in fact constitute separate species. Our study provides a solid basis for further systematic investigations of this enigmatic insect group.     

木蓝根瘤菌的16S rDNA全序列分析及DNA-DNA杂交

通过数值分类、ＳＤＳ－全细胞蛋白电泳分析,对分离自西北黄土高原地区的木蓝根瘤菌进行了研究,获得了１个新类群。在此基础上,进行了中心菌株ＳＨＬ０４２的１６Ｓ ｒＤＮＡ全序列分析,得到系统发育树状图。 ＳＨＬ０４２与 Ｒ.ｔｒｏｐｉｃｉ Ａ、 Ｒ.ｔｒｏｐｉｃｉ Ｂ、 Ｒ.ｌｅｇｕｍｉｎｏｓａｒｕｍ、 Ｒ ｅｔｌｉ、 Ｒｈａｎａｎｅｓｉｓ、Ｒ. ｍｏｎｇｏｌｅｎｓｅ和Ｒ.ｇａｌｌｉｃｕｍ构成一个发育分支,其与这些种模式菌株 １６Ｓ　ｒＤＮＡ全序列的相似性分别为９５．４％、９５．５％、９６．３％、９５．８％、９６．３％、９７．９％和９７．７％,均大于９５％,应属于同一个属。新类群群内ＤＮＡ同源性大于８０％,而中心菌株ＳＨＬ０４２与分支内各已知种的ＤＮＡ同源性小于５０％,表明ＳＨＬ０４２代表１个新的根瘤菌菌种。     

First molecular evidence for the phylogenetic placement of the enigmatic snake genus Brachyorrhos (Serpentes: Caenophidia)

BrachyorrhosSchlegel, 1826a is a terrestrial-fossorial snake genus endemic to eastern Indonesia that has been assigned to six different families and subfamilies within Colubroidea (advanced snakes) over the past ~200 years. Here we report the first molecular sequences for Brachyorrhos and use them to test the position of the genus within snake phylogeny. Our Bayesian and Maximum Likelihood analyses of three mitochondrial and one nuclear gene strongly resolve Brachyorrhos within the rear-fanged semiaquatic Homalopsidae (Colubroidea), as the sister taxon to all other genera and sampled species.     

Conservation of biotrophy in Hygrophoraceae inferred from combined stable isotope and phylogenetic analyses

The nutritional modes of genera in Hygrophoraceae (Basidiomycota: Agaricales), apart from the ectomycorrhizal Hygrophorus and lichen-forming taxa, are uncertain. New δ(15)N and δ(13)C values were obtained from 15 taxa under Hygrophoraceae collected in central Massachusetts and combined with isotopic datasets from five prior studies including a further 12 species using a data standardization method to allow cross-site comparison. Based on these data, we inferred the probable nutritional modes for species of Hygrophorus, Hygrocybe, Humidicutis, Cuphophyllus and Gliophorus. A phylogeny of Hygrophoraceae was constructed by maximum likelihood analysis of nuclear ribosomal 28S and 5.8S sequences and standardized δ(15)N and δ(13)C values were used for parsimony optimization on this phylogeny. Our results supported a mode of biotrophy in Hygrocybe, Humidicutis, Cuphophyllus and Gliophorus quantitatively unlike that in more than 450 other fungal taxa sampled in the present and prior studies. Parsimony optimization of stable isotope data suggests moderate conservation of nutritional strategies in Hygrophoraceae and a single switch to a predominantly ectomycorrhizal life strategy in the lineage leading to Hygrophorus. We conclude that Hygrophoraceae of previously unknown nutritional status are unlikely to be saprotrophs and are probably in symbiosis with bryophytes or other understory plants.     

Molecular phylogeny and insular biogeography of the lowland tailorbirds of Southeast Asia (Cisticolidae: Orthotomus)

The lowland tailorbirds of Southeast Asia (Orthotomus) offer an excellent opportunity for comparative biogeography because of their diversity in the Greater Sunda and Philippine islands. We reconstructed the phylogeny of all species in the genus using maximum likelihood, Bayesian, and coalescent methods on DNA sequences of three gene segments: an autosomal intron (TGF), a Z-linked intron (MUSK), and a mitochondrial coding gene (ND2). Although resolution is low in parts of the phylogeny, several well defined clades emerge. When considered in light of distribution, these clades indicate that the Greater Sunda and Philippine islands were occupied early in Orthotomus history by the ancestors of O. sericeus in the Greater Sundas and O. frontalis in the Philippines. Subsequently, tailorbirds diversified further in each island group: O. atrogularis, O. ruficeps, and O. sepium arose in the Greater Sundas, and O. castaneiceps castaneiceps, O. c. chloronotus, O. derbianus, O. samarensis, O. nigriceps, and O. cinereiceps in the Philippines. Among the continental taxa (including Sundaic birds), the older lineages (O. sutorius and O. sericeus) are habitat generalists and the recently evolved taxa are more specialized. In the Philippines, several taxa once considered conspecific with O. atrogularis turn out to be highly divergent species (>9% in ND2). Indeed, all Philippine allospecies are well diverged from one another. This finding supports the recent assertion of higher-than-appreciated bird endemicity in the Philippines.     

木蓝根瘤菌的16S rDNA全序列分析及DNA朌NA杂交

通过数值分类、SDS-全细胞蛋白电泳分析,对分离自西北黄土高原地区的木蓝根瘤菌进行了研究,获得了1个新类群。在此基础上,进行了中心菌株SHL042的16S rDNA全序列分析,得到系统发育树状图。SHL042与R.tropici A、R.tropici B、R. leguminosarum、R. etli、R. hananesis、R. mongolense和R. gallicum构成一个发育分支,其与这些种模式菌株16S rDNA全序列的相似性分别为95.4%、95.5%、96.3%、95.8%、96.3%、97.9%和97.7%,均大于95%,应属于同一个属。新类群群内DNA同源性大于80%,而中心菌株SHL042与分支内各已知种的DNA同源性小于50%,表明SHL042代表1个新的根瘤菌菌种。     

A mitochondrial-DNA-based phylogeny for some evolutionary-genetic model species of Colias butterflies (Lepidoptera, Pieridae)

We study the phylogenetic relationships among some North American Colias ("sulfur") butterflies, using mitochondrial gene sequences (ribosomal RNA, cytochrome oxidase I+II) totaling about 20% of the mitochondrial genome. We find that (1) the lowland species complex shows a branching order different from earlier views; (2) several montane and northern taxa may be more distinct than in earlier views; (3) one morphologically conservative Holarctic assemblage, C. hecla, is differentiated at the molecular-genetic level into at least three taxa which occupy distinct positions in the phylogeny and are sisters to diverse other taxa. These conclusions, constituting phylogenetic hypotheses, are supported by parsimony, maximum-likelihood, and Bayesian reconstruction algorithms. They are tested formally, by interior branch tests and paired-site tests, against alternative hypotheses derived from conventional species and subspecies naming combinations. In all cases our hypotheses are supported by these tests and the conventional alternatives are rejected. The "barcoding" subset of cytochrome oxidase I sequence identifies only some of the taxa supported by our full data set. Comparison of genetic divergence values among Colias taxa with those among related Pierid butterflies suggests that species radiations within Colias are comparatively younger. This emerging Colias phylogeny facilitates comparisons of genetic polymorphism and other adaptive mechanisms among taxa, thereby connecting micro- and macro-evolutionary processes.