The evolution of anther morphology in orchids: incumbent anthers, superposed pollinia, and the vandoid complex

The anther is the source of several of the principal characters traditionally used for classification in Orchidaceae, especially in Epidendroideae. In particular, anther and pollinium orientation are important, but little-studied characters; it is not known whether various instances of these states are achieved in the same way. We examined variation in anther and pollinium orientation in Epidendroideae and Vanilloideae using anatomical sections of columns at successive ontogenetic stages and related the observed changes to the final anther morphology to reexamine our homology hypotheses for these characters. Anther bending in vanilloids is achieved primarily by massive expansion of the connective. In nonvandoid epidendroids it is the result of column elongation and tipping of the mature anther, while in vandoids it is due to a redirection of growth in very early ontogenetic stages. Superposed pollinia result from a reorientation of developing thecae; those is Sobralia result from incurving of the thecae, while vandoids have thecae that are directed outward (latrorse). Contrasting ontogenetic and phylogenetic patterns suggest heterochronic changes in these characters, especially in vandoids. These observations allow us to further refine character states that are crucial to our understanding of orchid relationships.     

Phylogeny of subfamily Epidendroideae (Orchidaceae) inferred from ndhF chloroplast gene sequences

This project undertakes the first molecular-based phylogenetic study of subfamily Epidendroideae (Orchidaceae). Approximately 1200 nucleotides (from the 3' half of the chloroplast gene ndhF for 34 orchid taxa and a lilioid monocot, Clivia miniata (Amaryllidaceae), were subjected to phylogenetic analysis using parsimony and maximum likelihood methods. Oryza sativa (Poaceae), a nonlilioid monocot, was designated as outgroup. Trees from both parsimony and maximum likelihood methods suggest that subfamily Epidendroideae is monophyletic, with Listera (Neottieae) as sister. Although subtribal relationships are typically well resolved and have strong branch support, intertribal relationships are generally poorly resolved. Perhaps this general lack of resolution among tribes reflects a rapid species radiation that coincided with anatomical, physiological, and anatomical adaptations that initiated large-scale epiphytism in the ancestral Epidendroideae. Six taxa in this study exhibit deletions that are not evenly divisible by three and result in extensive sequence frameshifts. For example, one deletion is 227 bp in length and is flanked by the short direct repeat sequence; TCAATAGGAATTTCTTTT. Multiple deletions and frameshifts suggest that ndhF may be a pseudogene, in at least some orchid taxa.     

Multilocus analyses of an Antarctic fish species flock (Teleostei, Notothenioidei, Trematominae): phylogenetic approach and test of the early-radiation event

Clades that have undergone episodes of rapid cladogenesis are challenging from a phylogenetic point of view. They are generally characterised by short or missing internal branches in phylogenetic trees and by conflicting topologies among individual gene trees. This may be the case of the subfamily Trematominae, a group of marine teleosts of coastal Antarctic waters, which is considered to have passed through a period of rapid diversification. Despite much phylogenetic attention, the relationships among Trematominae species remain unclear. In contrast to previous studies that were mostly based on concatenated datasets of mitochondrial and/or single nuclear loci, we applied various single-locus and multilocus phylogenetic approaches to sequences from 11 loci (eight nuclear) and we also used several methods to assess the hypothesis of a radiation event in Trematominae evolution. Diversification rate analyses support the hypothesis of a period of rapid diversification during Trematominae history and only a few nodes in the hypothetical species tree were consistently resolved with various phylogenetic methods. We detected significant discrepancies among trees from individual genes of these species, most probably resulting from incomplete lineage sorting, suggesting that concatenation of loci is not the most appropriate way to investigate Trematominae species interrelationships. These data also provide information about the possible effects of historic climate changes on the diversification rate of this group of fish.     

Pollinium development and number in the Orchidaceae

Development of anthers in three subfamilies of Orchidaceae was studied anatomically to examine homology hypotheses for pollinium number characters and to produce a model of pollinium development for the family. Serial sections of plastic-embedded embryonic inflorescences revealed that anther primordia were either flattened or ovoid; subsequent expansion of thecae and their inward (adaxial) reorientation (“rotation”), achieved by differential cell division and elongation in the connective, result in a mature anther with strongly introrse morphology and pollinia oriented side by side (juxtaposed). Strongly introrse anthers occur in at least some members of all subfamilies and are probably the basal state for the family. All anthers examined (from Orchidoideae, Spiranthoideae, and Epidendroideae) showed a single meristematic region, which would later give rise to pollen, per theca at earliest stages; septation of each of these regions resulted in four or eight pollinia per anther, while lack of septation in some members of the Epidendroideae gave two pollinia. In contrast, the two bipartite pollinia found in many Spiranthoideae and Orchidoideae were produced by adherence of the contents of two locules at a late ontogenetic stage, and should be recognized as a distinct character state. Eight pollinia result from partitioning by two longitudinal septa or a longitudinal and a transverse septum; these two morphologies may also represent separate character states.     

Effects of data incompleteness on the relative performance of parsimony and Bayesian approaches in a supermatrix phylogenetic reconstruction of Mustelidae and Procyonidae (Carnivora)

Missing data are commonly thought to impede a resolved or accurate reconstruction of phylogenetic relationships, and probabilistic analysis techniques are increasingly viewed as less vulnerable to the negative effects of data incompleteness than parsimony analyses. We test both assumptions empirically by conducting parsimony and Bayesian analyses on an approximately 1.5 × 10⁶‐cell (27 965 characters × 52 species) mustelid–procyonid molecular supermatrix with 62.7% missing entries. Contrary to the first assumption, phylogenetic relationships inferred from our analyses are fully (Bayesian) or almost fully (parsimony) resolved topologically with mostly strong support and also largely in accord with prior molecular estimations of mustelid and procyonid phylogeny derived with parsimony, Bayesian, and other probabilistic analysis techniques from smaller but complete or nearly complete data sets. Contrary to the second assumption, we found no compelling evidence in support of a relationship between the inferior performance of parsimony and taxon incompleteness (i.e. the proportion of missing character data for a taxon), although we found evidence for a connection between the inferior performance of parsimony and character incompleteness (i.e. no overlap in character data between some taxa). The relatively good performance of our analyses may be related to the large number of sampled characters, so that most taxa (even highly incomplete ones) are represented by a sufficient number of characters allowing both approaches to resolve their relationships. © The Willi Hennig Society 2009.     

Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling

In this paper we included a very broad representation of grass family diversity (84% of tribes and 42% of genera). Phylogenetic inference was based on three plastid DNA regions rbcL, matK and trnL-F, using maximum parsimony and Bayesian methods. Our results resolved most of the subfamily relationships within the major clades (BEP and PACCMAD), which had previously been unclear, such as, among others the: (i) BEP and PACCMAD sister relationship, (ii) composition of clades and the sister-relationship of Ehrhartoideae and Bambusoideae + Pooideae, (iii) paraphyly of tribe Bambuseae, (iv) position of Gynerium as sister to Panicoideae, (v) phylogenetic position of Micrairoideae. With the presence of a relatively large amount of missing data, we were able to increase taxon sampling substantially in our analyses from 107 to 295 taxa. However, bootstrap support and to a lesser extent Bayesian inference posterior probabilities were generally lower in analyses involving missing data than those not including them. We produced a fully resolved phylogenetic summary tree for the grass family at subfamily level and indicated the most likely relationships of all included tribes in our analysis.     

Phylogeny of haplo–diploid,fungus‐growing ambrosia beetles (Curculionidae: Scolytinae: Xyleborini) inferred from molecular and morphological data

Cognato, A. I., Hulcr, J., Dole, S. A. & Jordal, B. H. (2010). Phylogeny of haplo‐diploid, fungus‐growing ambrosia beetles (Curculionidae: Scolytinae: Xyleborini) inferred from molecular and morphological data. —Zoologica Scripta, 40, 174–186. The ambrosia beetle tribe Xyleborini currently contains 30 genera and approximately 1200 species which are distributed throughout worldwide forests with most diversity located in the tropics. They also represent the most invasive scolytines in North America. Despite economic concerns and biological curiosity with this group, a comprehensive understanding of generic boundaries and the evolutionary relationship among species is lacking. In this study, we include 155 xyleborine species representing 23 genera in parsimony and Bayesian analyses using 3925 nucleotides from mitochondrial (COI) and nuclear genomes (28S, ArgK, CAD, EF‐1α) and 39 morphological characters. The phylogenies resulting from the parsimony analyses, which treated gap positions either as missing or fifth character states, and the Bayesian analysis were generally similar. Clades with high support or posterior probabilities were found in all trees, while those with low support were not recovered by all analyses. Fourteen of the 23 genera were monophyletic although not all relationships among the genera were resolved. We show monophyly of several species groups associated with particular morphological and biological characters and suggest recognition of these groups as genera. Most interesting was the monophyly of South and Central American species representing several genera. This finding suggests recent and fast radiation of xyleborines in the New World accompanied by morphological and biological diversification.     

An expanded plastid DNA phylogeny of Orchidaceae and analysis of jackknife branch support strategy

An expanded plastid DNA phylogeny for Orchidaceae was generated from sequences of rbcL and matK for representatives of all five subfamilies. The data were analyzed using equally weighted parsimony, and branch support was assessed with jackknifing. The analysis supports recognition of five subfamilies with the following relationships: (Apostasioideae (Vanilloideae (Cypripedioideae (Orchidoideae (Epidendroideae))))). Support for many tribal-level groups within Epidendroideae is evident, but relationships among these groups remain uncertain, probably due to a rapid radiation in the subfamily that resulted in short branches along the spine of the tree. A series of experiments examined jackknife parameters and strategies to determine a reasonable balance between computational effort and results. We found that support values plateau rapidly with increased search effort. Tree bisection-reconnection swapping in a single search replicate per jackknife replicate and saving only two trees resulted in values that were close to those obtained in the most extensive searches. Although this approach uses considerably more computational effort than less extensive (or no) swapping, the results were also distinctly better. The effect of saving a maximal number of trees in each jackknife replicate can also be pronounced and is important for representing support accurately.     

Phylogeny of feather mite subfamily Avenzoariinae (Acari: Analgoidea: Avenzoariidae) inferred from combined analyses of molecular and morphological data.

Phylogenetic relationships among feather mites of the subfamily Avenzoariinae (Acari: Analgoidea: Avenzoariidae) were reconstructed by parsimony analysis of a combined data matrix. We analyzed 41 morphological characters and 246 molecular characters from a fragment of the 16S rDNA. Morphological trees were well supported at deep branches (genera and above), but showed much less support and resolution within genera. Molecular analyses produced trees with better resolution and support on terminal branches and worse support on basal branches. I(MF) index for the combined matrix pointed to the significant congruence of both data subsets with the whole of the data. The topology of the combined tree was close to the morphological tree in the deep branches and had well-resolved terminal branches as in the molecular tree. This suggests a considerable level of complimentarity between the two data sets. An analysis of association patterns of the mites and their hosts was conducted based on the results of the combined analyses for the Avenzoariinae and a phylogeny of their charadriiform hosts (compiled from various bird phylogeny hypotheses). The trees could be reconciled by the invoking of 12-13 cospeciation events, 6-7 duplications, 2 host shifts, and 26-29 sorting events. This suggests a high degree of cospeciation.     

A morphological supermatrix‐based phylogeny for the Neotropical fish superfamily Anostomoidea (Ostariophysi: Characiformes): phylogeny,missing data and homoplasy

Although 11 studies have addressed the systematics of the four families and 281 fish species of the ecomorphologically diverse Anostomoidea, none has proposed a global hypothesis of relationships. We synthesized these studies to yield a supermatrix with 463 morphological characters among 174 ingroup species, and inferred phylogeny with parsimony and Bayesian optimization. We evaluated the applicability of the supermatrix approach to morphological datasets, tested its sensitivity to missing data, determined the impact of homoplastic characters on phylogenetic resolution, and determined the distribution of homologies and homoplasies on the topology. Despite more than 60% missing data, analyses supported the monophyly of all families, and phylogenetic structure degraded only with inclusion of species with high percentages of missing data and in analyses limited to homoplasies. The latter differs modestly from the full matrix indicating phylogenetic signal in homoplastic characters. Character distributions differ across the phylogeny, with a greater prevalence of homologies at deeper nodes and homoplasies nearer the tips than expected by chance. This may suggest early diversification into distinct bauplans with subsequent diversification of faster evolving character systems. The morphological supermatrix approach is powerful and allows integration of classical data with modern methods to examine the evolution of multiple character systems.     

Systematic Position of the African Dormouse Graphiurus (Rodentia, Gliridae) Assessed from Cytochrome b and 12S rRNA Mitochondrial Genes

Gliridae is a small family of rodents including three subfamilies: the Eurasian Glirinae (with three genera) and Leithiinae (with four genera) and the African Graphiurinae (with a single genus). Phylogenetic relationships among these eight genera are not fully resolved based on morphological characters. Moreover, the genus Graphiurus is characterized by numerous peculiar features (morphological characters and geographical distribution), raising the question of its relationships to the family Gliridae. The phylogenetic position of Graphiurus and the intra-Gliridae relationships are here addressed by a molecular analysis of 12S RNA and cytochrome b mitochondrial gene sequences for six glirid genera. Phylogenetic analyses are performed with three construction methods (neighbor-joining, maximum parsimony and maximum likelihood) and tests of alternative topologies with respect to the most likely. Our analyses reveal that Graphiurus is clearly a member of the Gliridae, refuting the hypothesis that the family could be paraphyletic. Among Gliridae, phylogenetic relationships are poorly resolved: the Leithiinae could be monophyletic, there is no support for the subfamily Glirinae, and the closest relative of Graphiurus is not identified. The inclusion of Graphiurus among Gliridae allows us to postulate that its hystricomorphous condition has been achieved convergently with other hystricomorphous rodents.     

Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees

Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony (GTP) is a phylogenetic optimization criterion in which a species tree that minimizes the number of gene duplications induced among a set of gene trees is selected. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic advances to examine the performance of GTP on a plant data set consisting of 18,896 gene trees containing 510,922 protein sequences from 136 plant taxa (giving a combined alignment length of >2.9 million characters). The relationships inferred from the GTP analysis were largely consistent with previous large-scale studies of backbone plant phylogeny and resolved some controversial nodes. The placement of taxa that were present in few gene trees generally varied the most among GTP bootstrap replicates. Excluding these taxa either before or after the GTP analysis revealed high levels of phylogenetic support across plants. The analyses supported magnoliids sister to a eudicot + monocot clade and did not support the eurosid I and II clades. This study presents a nuclear genomic perspective on the broad-scale phylogenic relationships among plants, and it demonstrates that nuclear genes with a history of duplication and loss can be phylogenetically informative for resolving the plant tree of life.     

Evaluation of atpB nucleotide sequences for phylogenetic studies of ferns and other pteridophytes

Inferring basal relationships among vascular plants poses a major challenge to plant systematists. The divergence events that describe these relationships occurred long ago and considerable homoplasy has since accrued for both molecular and morphological characters. A potential solution is to examine phylogenetic analyses from multiple data sets. Here I present a new source of phylogenetic data for ferns and other pteridophytes. I sequenced the chloroplast gene atpB from 23 pteridophyte taxa and used maximum parsimony to infer relationships. A 588-bp region of the gene appeared to contain a statistically significant amount of phylogenetic signal and the resulting trees were largely congruent with similar analyses of nucleotide sequences from rbcL. However, a combined analysis of atpB plus rbcL produced a better resolved tree than did either data set alone. In the shortest trees, leptosporangiate ferns formed a monophyletic group. Also, I detected a well-supported clade of Psilotaceae (Psilotum and Tmesipteris) plus Ophioglossaceae (Ophioglossum and Botrychium). The demonstrated utility of atpB suggests that sequences from this gene should play a role in phylogenetic analyses that incorporate data from chloroplast genes, nuclear genes, morphology, and fossil data.     

Molecular phylogeny of the subfamily Exoristinae (Diptera,Tachinidae), with discussions on the evolutionary history of female oviposition strategy

Abstract. Phylogenetic relationships among tribes in the tachinid subfamily Exoristinae (Diptera, Tachinidae) are inferred from four genes, namely white, 18S, 28S and 16S rDNA. For phylogenetic inferences, maximum parsimony, maximum likelihood and Bayesian Markov chain Monte Carlo analyses were performed. The resultant, very similar, trees are nearly concordant with the traditional classification based on morphological characters. Our results suggest that the Tachinidae are monophyletic and sister to the Sarcophagidae. The tribal relationships within Exoristinae are supported in part with high reliabilities and are similar to those inferred by Stireman. Based on the resultant trees, the phylogenetic relationships and possible morphological synapomorphies were investigated. In addition, we evaluated the transformation of female reproductive habits in the Exoristinae, finding support for the hypothesis that ovolarviparity evolved independently from oviparity in several clades, and obtaining different results concerning the evolutionary history of micro‐ovolarviparity depending on character optimization.     

Phylogenetic relationships of Steinernema Travassos, 1927 (Nematoda: Cephalobina: Steinernematidae) based on nuclear, mitochondrial and morphological data

Entomopathogenic nematodes of the genus Steinernema are lethal parasites of insects that are used as biological control agents of several lepidopteran, dipteran and coleopteran pests. Phylogenetic relationships among 25 Steinernema species were estimated using nucleotide sequences from three genes and 22 morphological characters. Parsimony analysis of 28S (LSU) sequences yielded a well-resolved phylogenetic hypothesis with reliable bootstrap support for 13 clades. Parsimony analysis of mitochondrial DNA sequences (12S rDNA and cox 1 genes) yielded phylogenetic trees with a lower consistency index than for LSU sequences, and with fewer reliably supported clades. Combined phylogenetic analysis of the 3-gene dataset by parsimony and Bayesian methods yielded well-resolved and highly similar trees. Bayesian posterior probabilities were high for most clades; bootstrap (parsimony) support was reliable for approximately half of the internal nodes. Parsimony analysis of the morphological dataset yielded a poorly resolved tree, whereas total evidence analysis (molecular plus morphological data) yielded a phylogenetic hypothesis consistent with, but less resolved than trees inferred from combined molecular data. Parsimony mapping of morphological characters on the 3-gene trees showed that most structural features of steinernematids are highly homoplastic. The distribution of nematode foraging strategies on these trees predicts that S. hermaphroditum, S. diaprepesi and S. longicaudum (US isolate) have cruise forager behaviours.     

Phylogenetic relationships and taxonomic ranking of pipizine flower flies (Diptera: Syrphidae) with implications for the evolution of aphidophagy

The taxonomic rank and phylogenetic relationships of the pipizine flower flies (Diptera: Syrphidae: Pipizini) were estimated based on DNA sequence data from three gene regions (COI, 28S and 18S) and 111 adult morphological characters. Pipizini has been treated as a member of the subfamily Eristalinae based on diagnostic adult morphological characteristics, while the larval feeding mode and morphology is shared with members of the subfamily Syrphinae. We analysed each dataset, both separately and combined, in a total evidence approach under maximum parsimony and maximum likelihood. To evaluate the influence of different alignment strategies of rDNA 28S and 18S genes on the resulting topologies, we compared the topologies inferred from a multiple alignment using fast Fourier transform (MAFFT) program with those topologies resulting from aligning the secondary structure of these rDNA genes. Total evidence analyses resolved pipizines as a sister group of the subfamily Syrphinae. Although the structural alignment and the MAFFT alignment differed in the inferred relationships of some clades and taxa, there was congruence in the placement of pipizines. The homogeneous morphology of the Pipizini clade in combination with their unique combination of characters among the Syrphidae suggest a change of rank to subfamily. Thus, we propose to divide Syrphidae into four subfamilies, including the subfamily Pipizinae stat. rev.     

基于28S rDNA D2基因片段与形态特征的优茧蜂亚科系统发育研究

本研究选取优茧蜂亚科Euphorinae(膜翅目Hymenoptera:茧蜂科Braconidae)的8族19属23种作为内群,茧蜂其它6个亚科的8属8种作外群,首次结合同源核糖体28S rDNA D2基因序列片段和41个形态学特征对该亚科进行了系统发育学研究。利用"圆口类"的内茧蜂亚科Rogadinae、茧蜂亚科Braconinae、矛茧蜂亚科Doryctinae的3个亚科为根,以PAUP*4.0和MrBayes3.0B4软件分别应用最大简约法(MP)和贝叶斯法对优茧蜂亚科的分子数据和分子数据与非分子数据的结合体进行了分析;并以PAUP*4.0对优茧蜂亚科的28S rDNA D2基因序列的片段的碱基组成与碱基替代情况进行了分析。结果表明:优茧蜂亚科的28S rDNA D2基因序列片段的GC%含量在40.00%~49.25%之间变动,而对于碱基替代情况来讲,优茧蜂亚科各个成员间序列变异位点上颠换(transversion)大于转换(transition);不同的分析和算法所产生的系统发育树都表明目前根据形态定义出的优茧蜂亚科Euphorinae不是一个单系群,而是一个与蚁茧蜂亚科Neoneurinae和高腹茧蜂亚科Cenocoelinae混杂在一起的并系群;在优茧蜂亚科内部,悬茧蜂族Meterorini和食甲茧蜂族Microctonini(排除猎户茧蜂属Orionis)为单系群,而宽鞘茧蜂族Centistini、大颚茧蜂族Cosmophorini、优茧蜂族Euphorini、瓢虫茧蜂族Dinocampini为并系群;悬茧蜂族Meterorini在优茧蜂亚科Euphorinae内位于基部位置的观点得到部分的支持,同时食甲茧蜂族Microctonini被判定为相对进化的类群。此外对于优茧蜂亚科内各属之间的相互亲缘关系,不同算法所得到的系统发育属的结果不完全一致,这表明优茧蜂亚科内(属及族)的系统发育关系还有待于进一步研究。