Phylogeny of bumble bees in the New World subgenus Fervidobombus (Hymenoptera: Apidae): congruence of molecular and morphological data

We present new DNA sequence data (12S, 16S, and opsin gene fragments) and morphological characters of the male genitalia for a phylogenetic analysis of the bumble bee subgenus Fervidobombus. There is no significant incongruence between the three molecular data sets, and little incongruence between the DNA and morphology. Simultaneous analysis of all the data partitions resulted in a tree that was entirely congruent with the All-DNA tree. Optimization of the geographic locations of the taxa onto the tree topology using dispersal/vicariance analysis suggests a complex picture of spread and diversification of Fervidobombus from the Old World into the southern New World. There is a phylogenetic component to their spread into tropical rain forest, as the two primary rain forest species (Bombus transversalis and Bombus pullatus) comprise a monophyletic clade, along with a third species, Bombus atratus, which is widely distributed in South America, including lowland subtropical habitats.     

Arbuscular mycorrhizal fungi in roots of non-photosynthetic plants, <Emphasis Type="Italic">Sciaphila japonica</Emphasis> and <Emphasis Type="Italic">Sciaphila tosaensis</Emphasis> (Triuridaceae)

The mycorrhizal fungi in the roots of achlorophyllous Sciaphila japonica and S. tosaensis (Triuridaceae) were identified by molecular methods. The habitats of S. japonica were in a tree plantation of Japanese cypress, Chamaecyparis obtusa, and bamboo forests, and those of S. tosaensis were in a camellia forest and a bamboo forest. In the root cortical cells of both plants, aseptate hyphal coils were observed, which suggested the Paris-type arbuscular mycorrhiza (AM). A phylogenetic analysis based on a partial sequence of an AM fungal nuclear small subunit ribosomal RNA gene showed that the fungal DNA sequences of S. japonica were separated into three closely related clades. Those of S. tosaensis were separated into two clades, which were also closely related to each other. The AM fungi of S. japonica and S. tosaensis were completely separated in the phylogenetic tree even among those found in the same habitat, which suggests the high specificities in the plant-fungal partnerships. All the detected AM fungi in these plants belonged to Glomus-group A. Even though the habitats are in quite common environments, both plant species are known as endangered species in Japan. Such a definite specificity in AM symbioses seems to restrict the distribution of the myco-heterotrophic plants.     

Gene and species trees reveal mitochondrial and nuclear discordance in the Drosophila cardini group (Diptera: Drosophilidae)

Abstract. The Drosophila cardini group includes 15 species, which are subdivided into the D. cardini and D. dunni subgroups. Although many phylogenetic hypotheses have been proposed for this group during the last five decades (based on patterns of reproductive isolation, morphology of male genitalia, chromosomal inversions, isozyme variation, or molecular sequence data), these are mostly discordant with each other. We aimed to clarify some of the evolutionary patterns related to the origin of this incongruence, while also attempting to provide a better-supported phylogenetic hypothesis for the D. cardini subgroup. For this purpose, sequences from three mitochondrial and three nuclear loci were gathered for at least eight species, and both individual gene trees and joint species tree estimates were evaluated. Although there was concordance among gene trees within each of the nuclear and mitochondrial sets, considerable incongruence was revealed in the comparisons between these two data sets. The branching position of D. neocardini was the main source of incongruence, and species trees reconstructed using different approaches with and without this species were particularly incongruent. In addition to providing a better approximation of the evolutionary history of the D. cardini group, this study suggests that incomplete lineage sorting or introgression may be biasing previous species tree estimates. More generally, the results also suggest that the use of supermatrix methods can lead to an overestimation of support for the inferred relationships, and highlight the potential effects of different taxon sampling strategies in phylogenetic reconstruction.     

Comparisons of phylogenetic hypotheses among different data sets in dwarf dandelions (Krigia,Asteraceae): Additional information from internal transcribed spacer sequences of nuclear ribosomal DNA

The internal transcribed spacer (ITS) region of the 18 S–25 S nuclear ribosomal DNA repeat was sequenced from 19 populations of the tribeLactuceae, including all species of dwarf dandelion (Krigia) and five outgroup genera. The incidence of length changes and base substitutions was at least two times higher for ITS 1 than ITS 2. Interspecific sequence divergence withinKrigia averaged 9.62% (1.61%–15.19%) and 4.26% (0%–6.64%) in ITS 1 and ITS 2, respectively. Intergeneric sequence divergence ranged from 15.6% to 44.5% in ITS 1 and from 8.0% to 28.6% in ITS 2. High sequence divergence and homoplasy among genera of tribeLactuceae suggest that the phylogenetic utility of ITS sequence data is limited to interspecific studies or comparisons among closely related genera. Trees generated from ITS sequences are essentially identical to those from restriction site comparisons of the entire nuclear ribosomal (nr) DNA region. The degree of tree resolution differed depending on how gaps were treated in phylogenetic analyses. The ITS trees were congruent with the chloroplast DNA and morphological phylogenies in three major ways: 1) the sister group relationship betweenKrigia andPyrrhopappus; 2) the recognition of two monophyletic sections,Krigia andCymbia, in genusKrigia; and 3) the monophyly of theK. occidentalis-K. cespitosa clade in sect.Cymbia. However, the two nrDNA-based trees are not congruent with morphology/chloroplast DNA-based trees for the interspecific relationships in sect.Krigia. An average of 22.5% incongruence was observed among fourKrigia data sets. The relatively high degree of incongruence among data sets is due primarily to conflict between trees based on nrDNA and morphological/cpDNA data. The incongruence is probably due to the concerted evolution of nrDNA repeating units. The results fromKrigia and theLactuceae suggest that nrDNA data may have limited utility in phylogenetic studies of plants, especially in groups which exhibit high levels of sequence divergence. Our combined phylogenetic analysis as a total evidence shows the least conflict to each of the individual data sets.     

A molecular phylogeny of the Old World cypresses (<Emphasis Type="Italic">Cupressus</Emphasis>: Cupressaceae): evidence from nuclear and chloroplast DNA sequences

Studies of phylogenetic relationships among cypresses of the Old World (Cupressus; Cupressaceae) have been plagued by unresolved relationships, poor branch support, and conflict between data sets and methods of analysis. In this study, we combined 5.4 kb of aligned DNA sequence and 157 binary characters with previously published data in examining phylogenetic relationships among Cupressus species. Bayesian and parsimony analysis of the combined data or of the nuclear data alone always recovered three principal clades of Cupressus; however, tests of phylogenetic incongruence could not distinguish between competing relationships among the three principal Cupressus lineages. In contrast, incongruence tests often found statistically significant conflict between the nuclear and plastid data, particularly with respect to the placement of C. chengiana. Consistent with previous studies and prevailing taxonomic opinion, we find C. darjeelingensis more closely related to cypresses of the New World (Hesperocyparis). In contrast, we placed accessions of C. assamica and C. tonkinensis, two putatively Old World species suggested to be misidentified New World taxa by some authors, within well-supported Old World clades. Statistical analysis of genetic distances suggests instances in which taxa recognized as distinct species by some authors are identical or nearly so and may best be considered a single taxon. Conversely, we identify instances in which infraspecific taxa are more distantly related to one another than those traditionally recognized as distinct species. Factors confounding cypress taxonomies, including poor morphological differentiation, misidentification, and the use of accessions of questionable provenance, are discussed.     

啄木鸟科内谱系生物地理学新探

啄木鸟群体共包含254种,但早期对啄木鸟的分类学研究局限于形态学、行为学和鸣唱法等方向,分子研究结果又彼此存在差异,因此啄木鸟分类系统目前还有争议。分子数据的大量累积为啄木鸟系统发育的研究提供了条件。利用从GenBank获取的ND2基因序列,对啄木鸟科179种啄木鸟采用NJ法、MP法以及ML法分别进行了分子进化树构建,同时用NJ法重建了Picumnus属分子进化树。此外又利用cytb基因序列采用NJ法对Dryobates属和Picoides属进行分子进化树重建。我们的结果显示,姬啄木亚科Picumnus属新大陆物种彼此的进化关系仍需进一步研究,而该属唯一一种旧大陆种P.innominatus,种内遗传差异在种间水平依然显著,这说明其种内遗传差异一直被低估了。在啄木鸟亚科内,Hemicircus属和Nesoctites属为姐妹关系,而Geocolaptes olivaceus插入了Campethera属支系中,并非与其构成姐妹群体。此外,一些姐妹群在新旧大陆上的分布,推测这种分布可能与第四纪冰川有关。啄木鸟从旧大陆向新大陆迁移,在第四纪冰川作用下不断发生分布范围的扩张与收缩,最终形成现存的分布格局。     

A biogeographic–ecological approach to disentangle reticulate evolution in the Triatoma phyllosoma species group (Heteroptera: Triatominae), vectors of Chagas disease

Introgression and incomplete lineage sorting (ILS) are two of the main sources of gene‐tree incongruence; both can confound the assessment of phylogenetic relationships among closely related species. The Triatoma phyllosoma species group is a clade of partially co‐distributed and cross‐fertile Chagas disease vectors. Despite previous efforts, the phylogeny of this group remains unresolved, largely because of substantial gene‐tree incongruence. Here, we sequentially address introgression and ILS to provide a robust phylogenetic hypothesis for the T. phyllosoma species group. To identify likely instances of introgression prior to molecular scrutiny, we assessed biogeographic data and information on fertility of inter‐specific crosses. We first derived a few explicit hybridization hypotheses by considering the degree of spatial overlap within each species pair. Then, we assessed the plausibility of these hypotheses in the light of each species pair's cross‐fertility. Using this contextual information, we evaluated mito‐nuclear (cyt b, ITS‐2) gene‐tree incongruence and found evidence suggesting introgression within two species pairs. Finally, we modeled ILS using a Bayesian multispecies coalescent approach and either (a) a “complete” dataset with all the specimens in our sample, or (b) a “filtered” dataset without putatively introgressed specimens. The “filtered tree” had higher posterior‐probability support, as well as more plausible topology and divergence times, than the “complete tree.” Detecting and filtering out introgression and modeling ILS allowed us to derive an improved phylogenetic hypothesis for the T. phyllosoma species group. Our results illustrate how biogeographic and ecological‐reproductive contextual information can help clarify the systematics and evolution of recently diverged taxa prone to introgression and ILS.     

Dynamics and Phylogenetic Implications of MtDNA Control Region Sequences in New World Jays (Aves: Corvidae)

To study the evolution of mtDNA and the intergeneric relationships of New World Jays (Aves: Corvidae), we sequenced the entire mitochondrial DNA control region (CR) from 21 species representing all genera of New World jays, an Old World jay, crows, and a magpie. Using maximum likelihood methods, we found that both the transition/transversion ratio (κ) and among site rate variation (α) were higher in flanking domains I and II than in the conserved central domain and that the frequency of indels was highest in domain II. Estimates of κ and α were much more influenced by the density of taxon sampling than by alternative optimal tree topologies. We implemented a successive approximation method incorporating these parameters into phylogenetic analysis. In addition we compared our study in detail to a previous study using cytochrome b and morphology to examine the effect of taxon sampling, evolutionary rates of genes, and combined data on tree resolution. We found that the particular weighting scheme used had no effect on tree topology and little effect on tree robustness. Taxon sampling had a significant effect on tree robustness but little effect on the topology of the best tree. The CR data set differed nonsignificantly from the tree derived from the cytochrome b/morphological data set primarily in the placement of the genus Gymnorhinus, which is near the base of the CR tree. However, contrary to conventional taxonomy, the CR data set suggested that blue and black jays (Cyanocorax sensu lato) might be paraphyletic and that the brown jay Psilorhinus (=Cyanocorax) morio is the sister group to magpie jays (Calocitta), a phylogenetic hypothesis that is likely as parsimonious with regard to nonmolecular characters as monophyly of Cyanocorax. The CR tree also suggests that the common ancestor of NWJs was likely a cooperative breeder. Consistent with recent systematic theory, our data suggest that DNA sequences with high substitution rates such as the CR may nonetheless be useful in reconstructing relatively deep phylogenetic nodes in avian groups. Received: 10 November 1999 / Accepted: 16 March 2000     

Mitochondrial DNA,morphology, and the phylogenetic relationships of Antarctic icefishes (Notothenioidei: Channichthyidae)

The Channichthyidae is a lineage of 16 species in the Notothenioidei, a clade of fishes that dominate Antarctic near-shore marine ecosystems with respect to both diversity and biomass. Among four published studies investigating channichthyid phylogeny, no two have produced the same tree topology, and no published study has investigated the degree of phylogenetic incongruence between existing molecular and morphological datasets. In this investigation we present an analysis of channichthyid phylogeny using complete gene sequences from two mitochondrial genes (ND2 and 16S) sampled from all recognized species in the clade. In addition, we have scored all 58 unique morphological characters used in three previous analyses of channichthyid phylogenetic relationships. Data partitions were analyzed separately to assess the amount of phylogenetic resolution provided by each dataset, and phylogenetic incongruence among data partitions was investigated using incongruence length difference (ILD) tests. We utilized a parsimony-based version of the Shimodaira-Hasegawa test to determine if alternative tree topologies are significantly different from trees resulting from maximum parsimony analysis of the combined partition dataset. Our results demonstrate that the greatest phylogenetic resolution is achieved when all molecular and morphological data partitions are combined into a single maximum parsimony analysis. Also, marginal to insignificant incongruence was detected among data partitions using the ILD. Maximum parsimony analysis of all data partitions combined results in a single tree, and is a unique hypothesis of phylogenetic relationships in the Channichthyidae. In particular, this hypothesis resolves the phylogenetic relationships of at least two species (Channichthys rhinoceratus and Chaenocephalus aceratus), for which there was no consensus among the previous phylogenetic hypotheses. The combined data partition dataset provides substantial statistical power to discriminate among alternative hypotheses of channichthyid relationships. These findings suggest the optimal strategy for investigating the phylogenetic relationships of channichthyids is one that uses all available phylogenetic data in analyses of combined data partitions.     

Chloroplast DNA inheritance and variation in <Emphasis Type="Italic">Leucadendron</Emphasis> species (Proteaceae) as revealed by PCR-RFLP

The inheritance of chloroplast DNA (cpDNA) in Leucadendron species was studied by polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analysis. A total of 100 progeny from five interspecific crosses involving seven parental species were tested, and all progeny exhibited the cpDNA restriction fragment pattern of the female parent, indicating that cpDNA in Leucadendron is maternally inherited. PCR-RFLP was also employed to study cpDNA variation among 21 Leucadendron species. Parsimony analysis using a heuristic search resulted in a phylogenetic tree that showed limited agreement to the taxonomic classification of Leucadendron species, based on morphological characteristics. The incongruence between cpDNA phylogenetic and taxonomic groupings in Leucadendron may be due to reticulate evolution involving a combination of hybridization and introgression, convergent evolution and/or lineage sorting at the interspecific, intersubsectional and intersectional levels.     

Phylogeny Reconstruction and Hybrid Analysis of Populus (Salicaceae) Based on Nucleotide Sequences of Multiple Single-Copy Nuclear Genes and Plastid Fragments

Populus (Salicaceae) is one of the most economically and ecologically important genera of forest trees. The complex reticulate evolution and lack of highly variable orthologous single-copy DNA markers have posed difficulties in resolving the phylogeny of this genus. Based on a large data set of nuclear and plastid DNA sequences, we reconstructed robust phylogeny of Populus using parsimony, maximum likelihood and Bayesian inference methods. The resulting phylogenetic trees showed better resolution at both inter- and intra-sectional level than previous studies. The results revealed that (1) the plastid-based phylogenetic tree resulted in two main clades, suggesting an early divergence of the maternal progenitors of Populus; (2) three advanced sections (Populus, Aigeiros and Tacamahaca) are of hybrid origin; (3) species of the section Tacamahaca could be divided into two major groups based on plastid and nuclear DNA data, suggesting a polyphyletic nature of the section; and (4) many species proved to be of hybrid origin based on the incongruence between plastid and nuclear DNA trees. Reticulate evolution may have played a significant role in the evolution history of Populus by facilitating rapid adaptive radiations into different environments.     

The <Emphasis Type="Italic">cadA</Emphasis> Gene in Cadmium-Resistant Bacteria from Cadmium-Polluted Soil in the Zhangshi Area of Northeast China

Cadmium-resistant bacteria were isolated from the farmland soil in Zhangshi Irrigation Area in Shenyang of Northeast China, an area has been polluted by heavy metals, especially cadmium, for more than 40 years. The cadA gene was detected in 4 Bacillus strains and for the first time in one Flavobacterium strain. The high sequence identity (93%–99%) of cadA gene, shared indels in different bacterial species and genera, and the phylogenetic incongruence between 16S rDNA gene tree and cadA gene tree suggested that lateral gene transfer (LGT) occurred among Bacillus and Flavobacterium spp. The LGT of cadA gene might play a vital role in promoting the spread of cadmium-resistant phenotypes throughout soil microbial communities. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Exploring data interaction and nucleotide alignment in a multiple gene analysis of Ips (Coleoptera: Scolytinae)

The possibility of gene tree incongruence in a species-level phylogenetic analysis of the genus Ips (Coleoptera: Scolytidae) was investigated based on mitochondrial 16S rRNA (16S) and nuclear elongation factor-1 alpha (EF-1 alpha) sequences, and existing cytochrome oxidase I (COI) and nonmolecular data sets. Separate cladistic analyses of the data partitions resulted in partially discordant most-parsimonious trees but revealed only low conflict of the phylogenetic signal. Interactions among data partitions, which differed in the extent of sequence divergence (COI > 16S > EF-1 alpha), base composition, and homoplasy, revealed that much of the branch support emerges only in the simultaneous analysis, particularly for deeper nodes in the tree, which are almost entirely supported through "hidden support" (sensu Gatesy et al., Cladistics 15:271-313, 1999). Apparent incongruence between data partitions is in part due to suboptimal alignments and bias of character transformations, but little evidence supports invoking incongruent phylogenetic histories of genetic loci. There is also no justification for eliminating or downweighting gene partitions on the basis of their apparent homoplasy or incongruence with other partitions, because the signal emerges only in the interaction of all data. In comparison with traditional taxonomy, the pini, plastographus, and perturbatus groups are polyphyletic, whereas the grandicollis group is monophyletic except for inclusion of the (monophyletic) calligraphus group. The latidens group and some European species are distantly related and closer to other genera within Ipini. Our robust cladogram was used to revise the classification of Ips. We provide new diagnoses for Ips and four subgeneric taxa.     

An altitudinal transect in rain forest in the Barrington Tops area,New South Wales

On the southern slopes of Barrington Tops, N.S.W., an exploratory study was made of altitudinal gradation between subantarctic or temperate rain forest (at higher elevations) and subtropical rain forest. The former is dominated by Nothofagus moorei while the latter has no clear dominants and is floristically and structurally more complex. To sample the ecotone, a single 800 m line containing thirty-seven 200 m² circular plots was placed on a S.S.W.-facing slope between altitudes of 800 and 1040 m. The inclinations of the surfaces of individual plots ranged from 5° to 35°. Measurement and analysis were restricted to trees (including coppices), vines and tree ferns, with emphasis on density, basal area and importance values. Vertical extent of the ecotone is determined rather arbitrarily as being about 90 m. Floristically, the ecotone has elements both of a mosaic and of a gradual mix of species of the upper and lower rain forests. Its areal complexity is increased by the presence of small-scale topographic features; the typical step-and-terrace sequence resulting from dissection of multiple basalt flows. There is a gradual dropping out of species of the subtropical rain forest upwards along the whole transect. The rate of drop-out is greatest at the bases of any steep steps on the slope. Certain species, notably Doryphora sassafras, are shared by the two kinds of rain forest. In physiognomy too, there is further evidence for continuity: the size and density of vines as well as leaf sizes of trees and vines decrease gradually upwards. In terms of Webb's system of structural types of Australian rain forest there is sustained gradation from notophyll-microphyll vinefern forest (at the bottom) to microphyll fern forest. There is strong evidence that Nothofagus moorei is not regenerating within most of the ecotone. Speculation is offered about ecotonal dynamics in terms of climatic change, fire frequency and the mode of reproduction of N. moorei.     

Phylogenetic analysis of Asian<Emphasis Type="Italic"> Symplocos</Emphasis> (Symplocaceae) based on nuclear and chloroplast DNA sequences

Thirty species and one variety of Symplocos (Symplocaceae), including all taxa distributed in Japan, were phylogenetically analyzed with DNA sequence data. The evolution of morphological characters is discussed on the basis of the phylogenetic relationships obtained. All species were Asian, except one, S. austromexicana, from Mexico. The nuclear ribosomal internal transcribed spacer (ITS) region and two intergenic spacer regions, between trnL and trnF, and between trnH and psbA of chloroplast DNA were used. The topologies of trees obtained from ITS and the chloroplast intergenic spacers are largely congruent. S. sonoharae, the representative of the subgenus Symplocos in Asia, was sister to all other species. The position of the American species, S. austromexicana, which also belongs to the subgenus Symplocos, was not well resolved. The phylogenetic tree based on combined sequence data largely supports the monophyletic origin of the infrageneric sections proposed earlier. However, the phylogenetic relationship between them is not well resolved, probably due to rapid diversification. The section Palura, a deciduous group, is well defined in the DNA analysis, suggesting its independent status in the genus Symplocos. In spite of their morphological divergence, the three endemic species of the Bonin Islands are monophyletic. The occurrence of curved seeds seems to be homoplastic, scattered over the phylogenetic tree without showing a particular infrageneric relationship.     

The phylogenetic systematics of blue‐tailed skinks (Plestiodon) and the family Scincidae

Blue‐tailed skinks (genus Plestiodon) are a common component of the terrestrial herpetofauna throughout their range in eastern Eurasia and North and Middle America. Plestiodon species are also frequent subjects of ecological and evolutionary research, yet a comprehensive, well‐supported phylogenetic framework does not yet exist for this genus. We construct a comprehensive molecular phylogeny of Plestiodon using Bayesian phylogenetic analyses of a nine‐locus data set comprising 8308 base pairs of DNA, sampled from 38 of the 43 species in the genus. We evaluate potential gene tree/species tree discordance by conducting phylogenetic analyses of the concatenated and individual locus data sets, as well as employing coalescent‐based methods. Specifically, we address the placement of Plestiodon within the evolutionary tree of Scincidae, as well as the phylogenetic relationships between Plestiodon species, and their taxonomy. Given our sampling of major Scincidae lineages, we also re‐evaluate ‘deep’ relationships within the family, with the goal of resolving relationships that have been ambiguous in recent molecular phylogenetic analyses. We infer strong support for several scincid relationships, including a major clade of ‘scincines’ and the inter‐relationships of major Mediterranean and southern African genera. Although we could not estimate the precise phylogenetic affinities of Plestiodon with statistically significant support, we nonetheless infer significant support for its inclusion in a large ‘scincine’ clade exclusive of Acontinae, Lygosominae, Brachymeles, and Ophiomorus. Plestiodon comprises three major geographically cohesive clades. One of these clades is composed of mostly large‐bodied species inhabiting northern Indochina, south‐eastern China (including Taiwan), and the southern Ryukyu Islands of Japan. The second clade comprises species inhabiting central China (including Taiwan) and the entire Japanese archipelago. The third clade exclusively inhabits North and Middle America and the island of Bermuda. A vast majority of interspecific relationships are strongly supported in the concatenated data analysis, but there is nonetheless significant conflict amongst the individual gene trees. Coalescent‐based gene tree/species tree analyses indicate that incongruence amongst the nuclear loci may severely obscure the phylogenetic inter‐relationships of the primarily small‐bodied Plestiodon species that inhabit the central Mexican highlands. These same analyses do support the sister relationship between Plestiodon marginatus Hallowell, 1861 and Plestiodon stimpsonii (Thompson, 1912), and differ with the mitochondrial DNA analysis that supports Plestiodon elegans (Boulenger, 1887) + P. stimpsonii. Finally, because the existing Plestiodon taxonomy is a poor representation of evolutionary relationships, we replace the existing supraspecific taxonomy with one congruent with our phylogenetic results. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 163–189.     

Phylogeny,biogeography and the stepwise evolutionary colonization of intertidal habitat in the Liparocephalini based on morphological and molecular characters (Coleoptera: Staphylinidae: Aleocharinae)

A phylogenetic analysis of the tribe Liparocephalini Fenyes is presented based on morphological and molecular characters. The data set comprised 50 adult morphological characters, partial COI (907 bp), COII (366 bp) and 12S rDNA (325–355 bp), and nearly complete sequences of 18S rDNA (1768–1902 bp) for 21 species. Eighteen species of liparocephaline beetles from all eight genera and three outgroups, are included. The sequences were analysed separately and simultaneously with morphological characters by direct optimization in the program POY4 and by partitioned Bayesian analysis for the combined data. The direct optimization (DO) tree for the combined data under equal weighting, which also shows a minimum incongruence length difference value, resulted in a monophyletic Liparocephalini with the following patterns of phylogenetic relationships (outgroup ((Baeostethus, Ianmoorea) (Paramblopusa ((Amblopusa, Halorhadinus) (Liparocephalus, Diaulota))))). A sensitivity analysis using 16 different parameter sets for the combined data shows the monophyly of the liparocephalines and all its genera under all parameter sets. Bayesian analysis resulted in topological differences in comparison with the DO tree under equal weighting only in the position of the genus Paramblopusa and clade (Amblopusa + Halorhadinus), which were reversed. Historical biogeography and the stepwise evolutionary colonization of intertidal habitat in the Liparocephalini are discussed. Based on the biogeographical analyses, we hypothesize that the ancestor of the Liparocephalini occurred along the Panthallassan Ocean, the direct antecedent of the Pacific Ocean, followed by repeated dispersals to the Nearctic from the Palearctic. We also hypothesize that ancestors of the Liparocephalini appear to have arisen in the littoral zone of beaches and then colonized rocky reef areas in the low tidal zone later through high‐ to mid‐tide zones. © The Willi Hennig Society 2009.     

Sources of character conflict in a clade of water striders (Heteroptera: Gerridae)

Incongruence among trees reconstructed with different data may stem from historical (gene tree‐species tree conflict) or process (character change biases) phenomena. Regardless of the source, incongruent data, as determined with “global” measures of homoplasy, have often been excluded from parsimony analysis of the combined data. Recent studies suggest that these homoplasy measures do not predict the contribution of each character to overall tree structure. Branch support measures identify, on a character to node basis, sources of support and conflict resulting from a simultaneous analysis of the data. We implement these branch support measures to identify sources of character conflict in a clade of water striders consisting of Gerris Fabricius, Aquarius Schellenberg, and Limnoporus Stål species. Separate analyses of morphology, mitochondrial cytochrome oxidase I (COI), large mitochondrial ribosomal subunit (16SrRNA), and elongation factor‐1α (EF‐1α) data resulted in cladograms that varied in resolution and topological concordance. Simultaneous analysis of the data resulted in two trees that were unresolved for one node in a strict consensus. The topology agreed with current classification except for the placements of Aquarius chilensis and the Aquarius remigis species group closer to Gerris than to congeneric species. Branch support measures indicated that support derived from each data set varied among nodes, but COI had an overall negative effect on branch support. However, Spearman rank correlation of partitioned branch support values indicated no negative associations of branch support between any data sets and a positive association between EF‐1α and 16SrRNA. Thus incongruence among data sets was not drastic and the gene‐tree versus species tree phenomenon was not implicated. Biases in character change were a more likely reason for incongruence, although saturation curves and incongruence length difference for COI indicated little potential for homoplasy. However, a posteriori inspection of COI nucleotide change with reference to the simultaneous analysis tree revealed AT and codon biases. These biases were not associated with branch support measures. Therefore, it is difficult to predict incongruence or identify its cause. Exclusion of data is ill advised because every character is potentially parsimony informative.     

Phylogeny, Biogeography, and Processes of Molecular Differentiation in Quercus Subgenus Quercus (Fagaceae)

Quercus is one of the most abundant and economically important genera of woody plants in the Northern Hemisphere. To infer phylogenetic relationships within Quercus subgenus Quercus, chloroplast DNA (cpDNA) restriction sites and nucleotide sequences of the internal transcribed spacers (ITS) and the 5.8S coding region of the nuclear ribosomal DNA repeat were obtained for 44 individuals, including 25 species, intraspecific samples, and three outgroups. Separate parsimony analyses of each data set showed that individual gene trees were congruent and often complementary in supporting clades that generally corresponded to previously recognized taxonomic groups. Only one instance of strongly supported gene tree incongruence was detected and this anomalous pattern was explained best by ancient introgression of cpDNA across sectional boundaries. Simultaneous parsimony analysis of the pruned data sets supported the recognition of the strictly Eurasian section Cerris and resolved a novel hypothesis for the major infrageneric groups (Cerris- (Lobatae- (Protobalanus + Quercus sensu stricto))). The biogeographic hypothesis that all major oak lineages evolved locally at middle latitudes within the general distribution of their fossil ancestors was fully supported. This set of relationships also suggested a New World origin for the widespread white oaks of the Northern Hemisphere (section Quercus s. s.). For both data sets, inter- and intraspecific sampling within section Protobalanus showed little correspondence to morphological species. Greater cladistic structure among the samples was obtained by cpDNA restriction sites and two well-delimited plastomes types comprising a total of 15 distinct haplotypes were resolved. Haplotypes of 2 of the peripheral species in this species complex occupy terminal portions of one of the plastome clades, suggesting a more recent origin relative to those of more widespread species. The phylogeography of the two divergent plastome types suggested a north–south pattern, consistent with a Late Tertiary disjunction in the ancestral distribution of section Protobalanus.     

Phylogenetic analysis of Themira (Sepsidae: Diptera): sensitivity analysis, alignment, and indel treatment in a multigene study

In this study we use sensitivity analysis sensu Wheeler (1995 ) for a matrix entirely composed of DNA sequences. We propose that not only congruence but also phylogenetic structure, as measured by character resampling, should be used to choose among competing weighting regimes. An extensive analysis of a five‐gene data set for Themira (Sepsidae: Diptera) reveals that even with different ways of partitioning the data, measures of topological congruence, character incongruence, and phylogenetic structure favor similar weighting regimes involving the down‐weighting of transitions. We furthermore use sensitivity analysis for obtaining empirical evidence that allows us to select weights for third positions, deciding between treating indels as fifth character states or missing values, and choosing between manual and computational alignments. For our data, sensitivity analysis favors manual alignment over a Clustal‐generated numerical alignment, the treatment of indels as fifth character states over considering them missing values, and equal weights for all positions in protein‐encoding genes over the down‐weighting of third positions. Among the topological congruence measures compared, symmetric tree distance performed best. Partitioned Bremer Support analysis reveals that COI contributes the largest amount of support for our phylogenetic tree for Themira. © The Willi Hennig Society 2005.