睡莲科的系统发育:核糖体DNA ITS区序列证据

以金鱼藻Ceratophyllum demersum为外类群,使用PAUP4.0b4A软件对睡莲科Nymphaeaceae植物7属11个代表种的ITS区序列进行了系统发育分析。采用最大简约法分析获得了3个最简约树,步长为1125,一致性指数(CI)和维持性指数(RI)值分别为0.7618和0.7214。利用3个最简约树获取严格一致树。结果表明:(1)莲属Nelumbo位于系统树的基部,自展支持率为100%,可从睡莲科中独立出来成立莲科Nelumbonaceae和莲目Nelumbonales;(2)萍蓬草属Nuphar是一单系类群,位于分支Ⅱ的基部,并和睡莲科其他属(不包括莲属)植物聚在一起构成姐妹群,故萍蓬草属仍应置于睡莲科中;(3)水盾草属Cabomba和莼菜属Brasenia聚成一小支并构成姐妹群,自展支持率为99%,说明这两属之间亲缘关系较近;(4)睡莲属和芡实属Euryale、王莲属Victoria聚成一小支并构成姐妹群,自展支持率为94%,说明三者亲缘关系较近,仍应置于睡莲科中。     

Rapid evolutionary divergences in reef fishes of the family Acanthuridae (Perciformes: Teleostei)

A phylogenetic analysis of the sugeonfish family Acanthuridae was conducted to investigate: (a) the pattern of divergences among outgroup and basal ingroup taxa, (b) the pattern of species divergences within acanthurid genera, (c) monophyly in the genus Acanthurus, and (d) the evolution of thick-walled stomach morphology in the genera Acanthurus and Ctenochaetus. Fragments of the 12S, 16S, t-Pro, and control region mitochondrial genes were sequenced for 21 acanthurid taxa (representing all extant genera) and four outgroup taxa. Unweighted parsimony analysis produced two optimal trees. Both of these were highly incongruent with a previous morphological phylogeny, especially with regard to the placement of the monotypic outgroups Zanclus and Luvarus. The maximum likelihood tree and the morphological phylogeny were not significantly different and the conflicting branches were very short. Split decomposition analysis identified conflict in the placement of long basal branches separated by short internodes, providing further evidence that long branch attraction is an important cause of disagreement between molecular and morphological trees. Parametric bootstrapping rejected hypotheses of monophyly of: (a) the genus Acanthurus and (b) a group containing representatives of Acanthurus/Ctenochaetus with thick-walled stomachs. The branching pattern of the likelihood and split decomposition trees indicates that evolution in the acanthurid clade has involved at least three periods of intense speciation.     

Cymbonotus (Compositae: Arctotideae, Arctotidinae): an endemic Australian genus embedded in a southern African clade

The Compositae (Asteraceae) is the largest flowering plant family if described, accepted taxa are considered. Recent revisions in the taxonomy of the family have resulted in the recognition of ten subfamilies and 35 tribes. The tribe Arctotideae is one of the smallest, with around 200 species; it contains two subtribes and several hard-to-place taxa. Previous work has shown that the subtribe Arctotidinae is well defined and is restricted to southern Africa, except for the Australian genus Cymbonotus . Molecular data from internal transcribed spacer (ITS), ndh F, and trn L-F sequences were used (24 previously published sequences; 47 new sequences) to determine the patterns of relationships within the subtribe. Twenty-three samples from the ingroup, including members of all genera and all three species of Cymbonotus , were included in the analysis, together with two outgroup taxa. Cymbonotus is monophyletic and deeply embedded in the subtribe; Haplocarpha is paraphyletic and basal in position; all other genera are monophyletic; however, Arctotis has over 60 species and only eight were sampled for this study, so additional work may prove otherwise. Arctotis is nested high in the tree and has short branch lengths; this may reflect recent radiation. By contrast, the species of the paraphyletic and basal Haplocarpha have long branches, which may indicate an older radiation and a shared ancestry with the remainder of the subtribe. The presence of Cymbonotus in Australia is most probably the result of long-distance dispersal.  Journal compilation © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 153 , 1–8. No claim to original US government works     

中鲤亚属的分支系统学分析

基于外部形态特征和内部骨骼特征对鲤科鲤属中鲤亚属进行了分支系统学分析,内群包括中鲤亚属的全部5种和鲤亚属的2种鱼类,外群采用乌原鲤。在鲤属鱼类和外群间共有48个性状存在变化。系统发育分析采用PAUP^*软件的Parsimony和Bootstrap两种方式的Branch-and-Bound算法,排除不能极化的特征和特有离征之后,还有28个特征可用,由这28个特征可得到唯一的系统树,树长69,一致性系数0.7246,排除无用特征的一致性系数0.6122,保留系数0.6346。由5种中鲤组成的中鲤亚属明显不构成一个单系群。结果表明：中鲤亚属是一个复系群,该类元应该被撤销。     

Polemoniaceae phylogeny and classification: implications of sequence data from the chloroplast gene ndhF

The chloroplast gene ndhF was used to study phylogenetic relationships of the Polemoniaceae at two levels: among members of the Ericales and among genera of the family. Sequence data for interfamilial analyses consisted of 2266 bp for 14 members of the Ericales, including four species of the Polemoniaceae, plus three outgroup taxa. The Polemoniaceae were found to be related to Diospyros, Fouquieria, the Primulales, Rhododendron, and Impatiens, but relationships among taxa were generally not well supported. The precise position of the Polemoniaceae within the Ericales remains obscure. Data for intrafamilial analyses consisted of 1031 bp for 27 species of the Polemoniaceae, including at least one species from most genera of the family, plus five outgroup taxa. A single most parsimonious tree was identified. The analyses suggested that subfamily Cobaeoideae, excluding Loeselia, is monophyletic and that Huthia is sister to Cantua. Acanthogilia was sister to the remainder of subfamily Cobaeoideae. Subfamily Polemonioideae plus Loeselia formed four subclades that were strongly supported as monophyletic and represent the major lineages of the subfamily.     

ITS sequence data resolve higher level relationships among the eucalypts.

Sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA were obtained for 35 species of Eucalyptus s.s. and seven taxa representing five outgroup genera (Allosyncarpia, Angophora, Arillastrum, Corymbia, and Stockwellia). The sequences were analyzed cladistically. The data distinguished clearly between the two major subgenera of Eucalyptus s.s. (Symphyomyrtus and Monocalyptus) but indicated that subgenus Eudesmia may be paraphyletic. ITS sequence data demonstrated the potential to resolve relationships between sections within subgenus Symphyomyrtus. Within sections, however, taxa were poorly differentiated. At the generic level, Corymbia appeared to be paraphyletic due to the exclusion of Angophora. The positions of Allosyncarpia and Arillastrum relative to the ingroup remain unresolved. ITS sequence data may prove valuable for resolving other phylogenetic relationships at higher taxonomic levels within Eucalyptus.     

Phylogeny of the Nymphaeaceae inferred from

The Nymphaeaceae are one of the most important taxa for understanding the origin and evolution of primitive angiosperms due to its basal position in the cladograms of the angiosperms recently given based both on several gene sequences and on morphological characters, but phylogenetic relationships within the family have not as yet been resolved. The sequences of nrDNA ITS region of 11 species representing seven genera of the Nymphaeaceae and one outgroup, Ceratophyllum demersum, were used to reconstruct the phylogeny of the family using PAUP4.0b4A. Three most parsimonious trees (Length=1125, CI=0.7618 and RI=0.7214) were obtained. In the consensus tree: (1) Nelumbo was basal to the other genera with a bootstrap value of 100% and occupied an isolated position, so it could be separated from the Nymphaeaceae and placed in its own family, Nelumbonaceae, and its own order, Nelumbonales; (2) Nuphar was monophyletic, nested in the basal position of clade II and was strongly supported to be the sister group of the other genera (excluding Nelumbo) of the Nymphaeaceae, suggesting that its traditional inclusion in the Nymphaeaceae should be maintained; (3) Cabomba and Brasenia were sister group and formed a subclade with a bootstrap value of 99%, indicating their close affinity; (4) Nymphaea was strongly supported to be the sister group of a subclade comprising Euryale and Victoria with a bootstrap value of 94%, indicating that they should be placed in the Nymphaeaceae.     

Molecular phylogeny of the sawfly subfamily Nematinae (Hymenoptera: Tenthredinidae)

Abstract.  Nematinae is one of the largest subfamilies in the sawfly family Tenthredinidae, but internal relationships are unknown in the absence of any formal phylogenetic analysis. To understand the internal phylogeny of Nematinae, we sequenced a portion of the mitochondrial cytochrome oxidase I gene and the nuclear elongation factor-1α gene from thirteen outgroup taxa and sixty-eight nematine species, the ingroup taxa of which represent all major genera and subgenera within the subfamily. Maximum parsimony and Bayesian phylogenetic analyses of the DNA sequence data show that: (1) Nematinae are monophyletic in a broad sense which includes Hoplocampa , Susana and the tribe Cladiini, which have been classified often into separate subfamilies; together with Craterocercus , these taxa form a paraphyletic basal grade with respect to the remaining Nematinae, but among-group relationships within the grade remain weakly resolved; (2) the remainder of the ingroup, Nematinae s. str, is monophyletic in all combined-data analyses; (3) within Nematinae s. str, the 'Higher' Nematinae is divided into three groups, Mesoneura and the large tribes Nematini and Pristiphorini; (4) although the traditional classifications at the tribal level are largely upheld, some of the largest tribes and genera are obviously para- or polyphyletic; (5) according to rate-smoothed phylogenies dated with two fossil calibration points, Nematinae originated 50–120 million years ago. In addition, the results from all Bayesian analyses provide strong and consistent support for the monophyly of Tenthredinidae, which has been difficult to demonstrate in previous parsimony analyses of morphological and molecular data.     

A global phylogeny of apple snails: Gondwanan origin, generic relationships, and the influence of outgroup choice (Caenogastropoda: Ampullariidae)

Apple snails (Ampullariidae) are a diverse family of pantropical freshwater snails and an important evolutionary link to the common ancestor of the largest group of living gastropods, the Caenogastropoda. A clear understanding of relationships within the Ampullariidae, and identification of their sister taxon, is therefore important for interpreting gastropod evolution in general. Unfortunately, the overall pattern has been clouded by confused systematics within the family and equivocal results regarding the family's sister group relationships. To clarify the relationships among ampullariid genera and to evaluate the influence of including or excluding possible sister taxa, we used data from five genes, three nuclear and two mitochondrial, from representatives of all nine extant ampullariid genera, and species of Viviparidae, Cyclophoridae, and Campanilidae, to reconstruct the phylogeny of apple snails, and determine their affinities to these possible sister groups. The results obtained indicate that the Old and New World ampullariids are reciprocally monophyletic with probable Gondwanan origins. All four Old World genera, Afropomus, Saulea, Pila, and Lanistes, were recovered as monophyletic, but only Asolene, Felipponea, and Pomella were monophyletic among the five New World genera, with Marisa paraphyletic and Pomacea polyphyletic. Estimates of divergence times among New World taxa suggest that diversification began shortly after the separation of Africa and South America and has probably been influenced by hydrogeological events over the last 90 Myr. The sister group of the Ampullariidae remains unresolved, but analyses omitting certain outgroup taxa suggest the need for dense taxonomic sampling to increase phylogenetic accuracy within the ingroup. The results obtained also indicate that defining the sister group of the Ampullariidae and clarifying relationships among basal caenogastropods will require increased taxon sampling within these four families, and synthesis of both morphological and molecular data. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98 , 61–76.     

A phylogenetic analysis of the extant Aeshnidae (Odonata: Anisoptera)

Abstract A cladistic analysis of the world Aeshnidae is presented, based on fifty-eight characters of adult and larval anatomy. The ingroup taxa include all the extant genera of Aeshnidae, and the austropetaliid genera Phyllopetalia and Hypopetalia were chosen as the outgroup. The strict consensus tree obtained after successive weighting shows that the subgroups defined traditionally for Aeshnidae are paraphyletic or polyphyletic. The previous reclassification derived from analyses based on wing venation is supported in terms of the monophyly of Aeshnidae, Gomphaeschninae and its sister group comprising the remaining Aeshnidae. Gomphaeschninae is confirmed as sister group of the remaining Aeshnidae (= Aeshnodea Bechly). The sister-group relationships between Gomphaeschna + Sarasaeschna and Linaeschna + Oligoaeschna are corroborated. Within Aeshnodea, three monophyletic groups emerged: Boyeria + ( Petaliaeschna + ( Limnetron + Gynacanthaeschna + Periaeschna )) + (( Cephalaeschna + Caliaeschna ) + ( Allopetalia ( Notoaeschna + Spinaeschna ))); Dendroaeschna + ( Epiaeschna + ( Aeschnophlebia + ( Nasiaeschna + ( Tetracanthagyna + Brachytron )))); and Polycanthagyna + ( Basiaeschna + ( Amphiaeschna + ( Indaeschna + ( Oplonaeschna + ( Racenaeschna + Plattycantha + Agyrtacantha + Triacanthagyna + ( Subaeschna + Austrogynacantha + Gynacantha ) + ( Heliaeschna + ( Neuraeschna + Staurophlebia ))) + (( Castoraeschna + Coryphaeschna + Remartinia ) + ( Oreaeschna + ( Aeshna + ( Anaciaeschna + ((' A .' isosceles + Andaeshna ) + ( Anax + Hemianax )))))). Additional informative characters are required to test the relationships suggested here between the main groups of Aeshnodea and some enigmatic basal taxa ( Antipodophlebia , Austroaeschna , Acanthaeschna , Telephlebia , Austrophlebia and Planaeschna ).     

Molecular phylogeny of basal gobioid fishes: Rhyacichthyidae, Odontobutidae, Xenisthmidae, Eleotridae (Teleostei: Perciformes: Gobioidei)

Morphological character analyses indicate that Rhyacichthyidae, Odontobutidae, Eleotridae, and Xenisthmidae are the basal families within the perciform suborder Gobioidei. This study uses DNA sequence data to infer the relationships of genera within these families, as well as determine the placement of more derived gobioids (family Gobiidae) and the identity of the outgroup to Gobioidei. Complete sequences of the mitochondrial ND1, ND2, COI, and cyt b genes (4397 base pairs) are analyzed for representatives of 27 gobioid genera and a variety of perciform and scorpaeniform outgroup candidates; the phylogeny is rooted with a beryciform as a distal outgroup. The single most parsimonious tree that results indicates that, of the outgroups sampled, the perciform family Apogonidae is most closely related to Gobioidei. Gobioidei is monophyletic, and Rhyacichthys aspro is the most basal taxon. The remainder of Gobioidei is resolved into clades corresponding to the families Odontobutidae (plus Milyeringa) and Eleotridae+Xenisthmidae+Gobiidae. Within Eleotridae, the subfamily Butinae (minus Milyeringa) is paraphyletic with respect to Gobiidae, and Eleotrinae is paraphyletic with respect to Xenisthmidae. Other than these groupings, the primary disagreement with the current morphology-based classification is that the molecular data indicate that the troglodytic Milyeringa should be placed in Odontobutidae, not Butinae, although support for this placement is weak. The most basal lineage of Gobioidei is known from the freshwaters of the Indo-Pacific, with marine-dwelling lineages arising several times independently in the group. The phylogeny also indicates that different gobioid lineages are distributed in Asia, Africa, Madagascar and the Neotropics. Five sister pairs of basal gobioid species inhabit Atlantic and Pacific drainages of Panama, with widely varying divergences.     

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.     

18S rDNA phylogeny of Clitellata (Annelida)

The phylogeny of Clitellata was analysed using 18S rDNA sequences of a selection of species representing Hirudinida, Acanthobdellida, Branchiobdellida and 10 oligochaetous families. Eleven new 18S sequences of Capilloventridae (one), Haplotaxidae (one), Propappidae (one), Enchytraeidae (two), Lumbricidae (one), Almidae (one), Megascolecidae (two), Lumbriculidae (one), and Phreodrilidae (one) are reported and aligned together with corresponding sequences of 28 previously studied clitellate taxa. Twelve polychaete species were used as an outgroup. The analysis supports an earlier hypothesis based on morphological features that Capilloventridae represents a basal clade of Clitellata; in the 18S tree it shows a sister-group relationship to all other clitellates. The remaining clitellate taxa form a basal dichotomy, one clade containing Tubificidae (including the former 'Naididae'), Phreodrilidae, Haplotaxidae, and Propappidae, the other clade with two subgroups: (1) Lumbriculidae together with all leech-like taxa (Acanthobdellida, Branchiobdellida and Hirudinida), and (2) Enchytraeidae together with a monophyletic group of all earthworms included in the study (Lumbricidae, Almidae and Megascolecidae). These earthworms are members of the taxon Crassiclitellata, the monophyly of which is thus supported by the data. The tree also shows support for the hypothesis that the first clitellates were aquatic. The position of the single species representing Haplotaxidae is not as basal as could have been expected from earlier morphology-based conclusions about the ancestral status of this family. However, if Haplotaxidae is indeed a paraphyletic assemblage of relict taxa, a higher number of representatives will be needed to resolve its exact relationships with the other clitellates.     

Molecular phylogenetics and evolutionary history of the neotropical Satyrine Subtribe Euptychiina (Nymphalidae: Satyrinae)

The Euptychiina is one of the more diverse lineages of satyrine butterflies, represented by over 300 species. The first phylogenetic analyses of the subtribe is presented based on 2506 aligned nucleotide sequences obtained from 69 individuals spanning 28 ingroup genera and nine outgroup genera. Two genes were used, the mitochondrial gene cytochrome oxidase 1 (1268 bp) and the nuclear gene elongation factor-1alpha (1238 bp). The subtribe is never recovered as monophyletic in analyses using parsimony, maximum likelihood, or Bayesian inference. Several euptychiine genera are placed basal to the ingroup, but support is found only for Euptychia and Oressinoma. Three main lineages within the ingroup were clearly defined and many taxonomic groupings within the clades strongly supported. The majority of genera tested were paraphyletic or polyphyletic. Based on results presented here and novel host use, a close relationship of Euptychia to the Indo-Australian tribe Ragadiini is hypothesized. Origins of the group remain unclear, but the basal position of most of the Nearctic genera is discussed.     

Phylogeny of Tubificidae (Annelida, Clitellata) based on mitochondrial and nuclear sequence data

The tubificid clitellates are a common component in the freshwater bottom fauna and are also the most abundant oligochaete group in marine habitats. There are over 800 described species classified in six subfamilies; Tubificinae, Limnodriloidinae, Rhyacodrilinae, Telmatodrilinae, Phallodrilinae, and Naidinae. In this study we examine the phylogenetic relationships in Tubificidae using a combination of mitochondrial 16S rDNA and nuclear 18S rDNA sequence data. Sequences were obtained from five outgroup and 56 ingroup taxa, including five of the six subfamilies of Tubificidae. The data were analysed by maximum parsimony and Bayesian inference. The resulting tree topologies are virtually without conflict. Several associations traditionally recognized within the family Tubificidae are supported, in the Bayesian analysis including a sister group relationship between Tubificinae and Limnodriloidinae. The results also indicate that Rhyacodrilinae is polyphyletic--some of its members (Heterodrilus spp.) fall into a clade with Phallodrilinae, all other groups with Naidinae. Naidinae is also polyphyletic with two rhyacodriline genera, Monopylephorus and Ainudrilus, nested within. Most of the tubificid genera included in the study are supported as monophyletic; however, Tubifex and Limnodriloides are refuted, and Tubificoides is unresolved from other tubificine taxa.     

Phylogenetics of Chondrichthyes and the problem of rooting phylogenies with distant outgroups

Erroneous estimates of ingroup relationships can be caused by attributes in the outgroup chosen to root the tree. Phylogenetic analyses of DNA sequences frequently yield incorrect estimates of ingroup relationships when the outgroup used to "root" the tree is highly divergent from the ingroup. This is especially the case when the outgroup has a different base composition than the ingroup. Unfortunately, in many instances, alternative less divergent outgroups are not available. In such cases, investigators must either target genes with attributes that minimize the problem (slowly evolving genes with stationary base compositions--which are often not ideal for estimating relationships among the more closely related ingroup taxa) or use inference models that are explicitly tailored to deal with an attenuated historical signal with a superimposed non-stationary base composition. In this paper we explore the problem both empirically and through simulation. For the empirical component we looked at the phylogenetic relationships among elasmobranch fishes (sharks and rays), a group whose closest living outgroup, the holocephalan Ghost fishes, are separated from the elasmobranchs by more than 100 million years of evolution. We compiled a data set for analysis comprising 10 single-copy nuclear protein-coding genes (12,096 bp) for representatives of the major lineages within elasmobranchs and holocephalans. For the simulation, we used an evolutionary model on a fixed tree topology to generate DNA sequence data sets which varied both in their distance to the outgroup, and in their base compositional difference between ingroup and outgroup. Results from both the empirical data set and the simulation, support the idea that deviation from base compositional stationarity, in conjunction with distance from the root can act in concert to compromise accuracy of estimated relationships within the ingroup. We tested several approaches to mitigate such problems. We found, that excluding genes with overall faster rates and heterogeneous base compositions, while the least sophisticated of the methods evaluated, seemed to be the most effective.     

外群选择对隧蜂科（膜翅目：蜜蜂总科）系统重建的影响

外群用于给树附根和推断祖先性状状态。通常,来自内群的姐妹群中的多个分类单元被共同选择作为外群。为了在经验上验证这一方法, 我们采用了3种外群选择策略： 姐妹群中的单一分类单元, 姐妹群中的多个分类单元和连续姐妹群中的多个分类单元。以隧蜂科（膜翅目： 蜜蜂总科）的系统发育重建为例, 我们评估了这3种策略对树拓扑结构的影响, 包括最大似然树、 最大简约树和贝叶斯树。初步结果表明： 相比其他两种策略, 采用姐妹群中的多个分类单元作为外群更有利于系统发育重建得到现已被广泛认可的隧蜂科系统发育关系; 相比最大似然法和贝叶斯法, 虽然隧蜂科系统发育关系没有被很好地解决, 但最大简约法在不同外群选择策略下得到了较为一致的拓扑结构     

Phylogenetic relationships among loliginid squids (Cephalopoda: Myopsida) based on analyses of multiple data sets

The phylogenetic relationships among the loliginid squids, a species-rich group of shallowwater muscular squids, have been investigated recently using several approaches, including allozyme electrophoresis and analyses of morphological and DNA sequence data, yet no consensus has been reached. This study examines the effects of combining multiple data sets (morphology, allozymes and DNA sequence data from two mitochondrial genes) on estimates of loliginid phylogeny. Various data combinations were analysed under three maximum parsimony weighting schemes: equal weights for all characters, successive approximations and implicit weights parsimony. When feasible, support for branches within trees was assessed with nonparametric bootstrapping and decay analysis. Some ingroup relationships were consistent across all analyses, but relationships among outgroup taxa and basal ingroup taxa varied. Combining data increased bootstrap support for several nodes. Methods that downweight highly variable characters (i.e. successive approximations and implicit weights parsimony) produced very similar trees which included two major clades: a clade consisting of all species sampled from American waters (except Sepioteuthis ), and a clade of several east Atlantic species ( Loligo forbesi Steenstrup, Loligo vulgaris Lamarck and Loligo reynaudi d'Orbigny) plus several Indo-West Pacific species in the genera Uroteuthis and Loliolus. The Sepioteuthis species occupied a basal position within Loliginidae, but Sepioteuthis itself was not always monophyletic. The position of a clade of a few Lolliguncula species and Loligo (Alloteuthis) also varied across analyses. A new loliginid classification is proposed based on these findings.     

Molecular phylogenetic relationships among Lemnaceae and Araceae using the chloroplast trnL-trnF intergenic spacer

We test competing hypotheses of relationships among Aroids (Araceae) and duckweeds (Lemnaceae) using sequences of the trnL-trnF spacer region of the chloroplast genome. Included in the analysis were 22 aroid genera including Pistia and five genera of Lemnaceae including the recently segregated genus Landoltia. Aponogeton was used as an outgroup to root the tree. A data set of 522 aligned nucleotides yielded maximum parsimony and maximum likelihood trees similar to those previously derived from restriction site data. Pistia and the Lemnaceae are placed in two separate and well-supported clades, suggesting at least two independent origins of the floating aquatic growth form within the aroid clade. Within the Lemnaceae there is only partial support for the paradigm of sequential morphological reduction, given that Wolffia is sister to Wolffiella+Lemna. As in the results of the restriction site analysis, pantropical Pistia is placed with Colocasia and Typhonium of southeastern Asia, indicative of Old World affinities. Branch lengths leading to duckweed terminal taxa are much longer relative to other ingroup taxa (including Pistia), evidently as a result of higher rates of nucleotide substitutions and insertion/deletion events. Morphological reduction within the duckweeds roughly correlates with accelerated chloroplast genome evolution.     

Finding Optimal Ingroup Topologies and Convexities When the Choice of Outgroups Is Not Obvious

Considerable confusion remains among theoreticians and practicioners of phylogenetic science on the use of outgroup taxa. Here, we show that, despite claims to the contrary, details of the optimal ingroup topology can be changed by switching outgroup taxa. This has serious implications for phylogenetic accuracy. We delineate between the process of outgroup selection and the various possible processes involved in using an outgroup taxon after one has been selected. Criteria are needed for the determination that particular outgroup taxa do not reduce the accuracy of evolutionary tree topologies and inferred character state transformations. We compare previous results from a sensitivity bootstrap analysis of the mitochondrial cytochromebphylogenetic relationships among whales to the results of a Bremer support sensitivity analysis and of a recently developed application of RASA theory to the question of putative outgroup taxon plesiomorphy content.