CHLOROPLAST DNA RESTRICTION SITE VARIATION IN THE FERN GENUS PELLAEA: PHYLOGENETIC RELATIONSHIPS OF THE PELLAEA GLABELLA COMPLEX

The cheilanthoid ferns have long resisted efforts to circumscribe well-defined, phylogenetically natural generic and infrageneric groups, presumably because of homoplastic morphologies associated with their xeric habitats. This cladistic analysis of phylogenetically informative chloroplast DNA restriction site data from 14 enzymes and seven taxa in the cheilanthoid genus Pellaea provides new insights into the phylogenetic relationships of the P. glabella complex. It also assesses the congruence of results based on restriction site data at inter- and intraspecific levels in these sexually and apogamously reproducing ferns with those of earlier morphological and isozyme analyses of the same group. Wagner parsimony yielded a single most parsimonious tree of 187 steps and 11% homoplasy, based on a data matrix of 166 restriction sites of which 66 were phylogenetically informative. Phylogenetic analysis based on user-defined stepmatrix character-state weighting of site gains over losses produced an identical single most parsimonious tree. Dollo parsimony yielded two most parsimonious trees, one of which was topologically identical to the Wagner tree. Specific and infraspecific relationships in the P. glabella complex determined by the completely independent restriction site and isozyme data sets are identical. This lends confidence to the ongoing use of restriction site data in a broader study of Pellaea and other cheilanthoid taxa and to the present conclusions that P. atropurpurea is sister to the P. glabella complex, whereas P. breweri, previously considered the closest relative of this complex, is actually more distantly related to it than are the other taxa in this study.     

Chloroplast DNA restriction site variation and phylogeny of the Berberidaceae

Comparative restriction site mapping of the chloroplast genome was performed to examine phylogenetic relationships among 27 species representing 16 genera of the Berberidaceae and two outgroups. Chloroplast genomes of the species included in this study showed no major structural rearrangements (i.e., they are collinear to tobacco cpDNA) except for the extension of the inverted repeat in species of Berberis and Mahonia. Excluding several regions that exhibited severe length variation, a total of 501 phylogenetically informative sites was mapped for ten restriction enzymes. The strict consensus tree of 14 equally parsimonious trees indicated that some berberidaceous genera (Berberis, Mahonia, Diphylleia) are not monophyletic. To explore phylogenetic utility of different parsimony methods phylogenetic trees were generated using Wagner, Dollo, and weighted parsimony for a reduced data set that included 18 species. One of the most significant results was the recognition of the four chromosomal groups, which were strongly supported regardless of the parsimony method used. The most notable difference among the trees produced by the three parsimony methods was the relationships among the four chromosomal groups. The cpDNA trees also strongly supported a close relationship of several generic pairs (e.g., Berberis-Mahonia, Epimedium-Vancouveria, etc.). Maximum likelihood values were computed for the four different tree topologies of the chromosomal groups, two Wagner, one Dollo, and one weighted topology. The results indicate that the weighted tree has the highest likelihood value. The lowest likelihood value was obtained for the Dollo tree, which had the highest bootstrap and decay values. Separate analyses using only the Inverted Repeat (IR) region resulted in a tree that is identical to the weighted tree. Poor resolution and/or support for the relationships among the four chromosomal lineages of the Berberidaceae indicate that they may have radiated from an ancestral stock in a relatively short evolutionary time.     

Phylogenetic analysis of the Amphitritinae (Polycnaeta: Terebellidae)

The phylogenetic relationships of the Amphitritinae (Polychaeta: Terebellidae) were studied using parsimony analysis of 22 external morphological characters. To choose outgroups to polarize the characters, I carried out a preliminary analysis of the relationships of the four terebellid subfamilies and the Trichobranchidae. The single most parsimonious tree from the analysis supports monophyly of the Terebellidae by the presence of ventral glandular shields. However, this character is homoplasious within the Terebellomorpha, and further evaluation of the Terebellidae is recommended. Artacama and Thelepus were chosen as outgroups for the analysis of amphitritine genera. The generic level analysis yielded seven equally parsimonious trees, which are consistent in their topologies except for the relationships among seven genera in one large clade. In all trees, Artacama is the sister taxon to a large clade within the Amphitritinae; the Artacaminae is therefore synonymized with the Amphitritinae, which is diagnosed by the presence of double rows of uncini. Within the Amphitritinae, the status of several monotypic genera is questioned; plesiomorphic character states indicated by the analysis are discussed. The results presented are offered as working hypotheses of the relationships among amphitritine genera. The large number of homoplasies indicated by the analysis emphasizes the need to further evaluate these hypotheses using additional characters. With a robust phylogenetic hypothesis of amphitritine relationships, a re-classification of the group based on apomorphic character states can be undertaken, and questions regarding the evolution of morphological characters, reproductive modes, or biogeographical patterns can be properly addressed.     

Evolutionary systematics in African gerbilline rodents of the genus Gerbilliscus: inference from mitochondrial genes

Gerbilliscus has recently been proposed as an endemic African rodent genus distinct from the Asian Tatera. A molecular phylogeny of the genus, including nine species from southern, western and eastern Africa, is presented here based on the analysis of the cytochrome b and 16S mitochondrial genes. With an adequate taxonomic sampling over a wide geographic range, we here provide a clear picture of the phylogenetic relationships between species and species groups in this genus. Three distinct clades were resolved, corresponding to major geographical subdivisions: an eastern clade that possibly diverged first, then a southern and a western clades which appeared later. We suggest two possible hypotheses concerning the dispersal of the genus across Africa, considering also the patterns of karyotypic variation. Finally, we discuss the taxonomic status of G. gambianus and the relationships between Gerbillurus and Gerbilliscus, as previous studies have suggested that the former should be included in the latter. Our data seem to support the synonymy of the two taxa and suggest that Gerbillurus and Gerbilliscus lineages diverged from a common ancestor appeared in eastern Africa.     

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

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

Fission or fusion? Mitochondrial DNA phylogenetics of the chromosome races of Hemideina crassidens (Orthoptera: Anostostomatidae)

The weta Hemideina crassidens has two chromosomal races that differ by two centric fusions or fissions. The mitochondrial DNA of weta from both chromosomal races and a sister species were sequenced for a 750-bp region of the gene coding for cytochrome oxidase I. The average pairwise genetic distance among the 15 (XO)-chromosome race weta was almost four times greater than the average distance among the 19 (XO)-chromosome race weta. The weta from the 19-chromosome race formed a well-supported monophyletic clade in all shortest maximum parsimony trees. Maximum likelihood and neighbor-joining trees suggested that the 15-chromosome karyotype was paraphyletic with respect to the 19-chromosome karyotype, but this was not supported by maximum parsimony analyses. Although phylogenetic analysis could not exclude chromosome fusion as the rearrangement responsible for the karyotype differentiation, the level of sequence variation and pattern of distribution appear to implicate fission as the more likely event.     

Plethodontid salamander mitochondrial genomics: A parsimony evaluation of character conflict and implications for historical biogeography

A new parsimony analysis of 27 complete mitochondrial genomic sequences is conducted to investigate the phylogenetic relationships of plethodontid salamanders. This analysis focuses on the amount of character conflict between phylogenetic trees recovered from newly conducted parsimony searches and the Bayesian and maximum likelihood topology reported by Mueller et al. (2004 ; PNAS, 101, 13820–13825). Strong support for Hemidactylium as the sister taxon to all other plethodontids is recovered from parsimony analyses. Plotting area relationships on the most parsimonious phylogenetic tree suggests that eastern North America is the origin of the family Plethodontidae supporting the “Out of Appalachia” hypothesis. A new taxonomy that recognizes clades recovered from phylogenetic analyses is proposed. © The Willi Hennig Society 2005.     

THE PHYLOGENY OFLECANACTIS(OPEGRAPHACEAE)

The genusLecanactis, with 24 species, has been phylogenetically analysed using cladistic parsimony methods and support tests. Morphological, anatomical and chemical data were used, comprising 38 characters. Twelve equally most parsimonious trees were obtained. The successive approximations character weighting method gave one most parsimonious tree. The ingroup,Lecanactis, is supported as monophyletic. Although parsimony jackknifing and Bremer support indicate that the trees are poorly supported, some groups are wholly or partly distinguished in both the strict consensus tree, the successive weighting tree and the Jac tree.     

Generic interrelationships within the Spionidae (Annelida: Polychaeta)

The phylogenetic relationships of spionid genera are estimated from parsimony analyses of morphological characters, with Trochochaetidae, Poecilochaetidae and Uncispionidae as outgroups. A first analysis of currendy recognised genera proved inconclusive and even exclusion of six of the most polymorphic genera resulted in 13 305 equally parsimonious trees and a fully collapsed consensus tree. A second analysis using only the type species of each genus, yielded four equally parsimonious trees; reduced to two after successive weighting. The topologies of these two trees indicated division of the family into four main groups: (1) Aonidella and Xandaros; (2) Prionospio (sensu fato)-complex, Laonice, Spiophanes and Aonides; (3) a large assemblage of genera, including Polydora-{senm late), Scolelepis, Malacoceros and Spio; (4) Atherospio, Pseudatherospio and Pygospiopsis. Earlier literature classifications of the group are evaluated and compared with die new results.     

Gene tree parsimony of multilocus snake venom protein families reveals species tree conflict as a result of multiple parallel gene loss

The proliferation of gene data from multiple loci of large multigene families has been greatly facilitated by considerable recent advances in sequence generation. The evolution of such gene families, which often undergo complex histories and different rates of change, combined with increases in sequence data, pose complex problems for traditional phylogenetic analyses, and in particular, those that aim to successfully recover species relationships from gene trees. Here, we implement gene tree parsimony analyses on multicopy gene family data sets of snake venom proteins for two separate groups of taxa, incorporating Bayesian posterior distributions as a rigorous strategy to account for the uncertainty present in gene trees. Gene tree parsimony largely failed to infer species trees congruent with each other or with species phylogenies derived from mitochondrial and single-copy nuclear sequences. Analysis of four toxin gene families from a large expressed sequence tag data set from the viper genus Echis failed to produce a consistent topology, and reanalysis of a previously published gene tree parsimony data set, from the family Elapidae, suggested that species tree topologies were predominantly unsupported. We suggest that gene tree parsimony failure in the family Elapidae is likely the result of unequal and/or incomplete sampling of paralogous genes and demonstrate that multiple parallel gene losses are likely responsible for the significant species tree conflict observed in the genus Echis. These results highlight the potential for gene tree parsimony analyses to be undermined by rapidly evolving multilocus gene families under strong natural selection.     

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

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

BIOGEOGRAPHY OF NEW WORLD TAIGA-DWELLING MICROTUS (MAMMALIA: ARVICOLIDAE): A HYPOTHESIS TEST THAT ACCOUNTS FOR PHYLOGENETIC UNCERTAINTY

If we adopt a statistical approach to systematics and recognize that phylogenies are estimated with error, then we can begin to explore statistically justified methods for testing a variety of comparative hypotheses, including those concerning the evolution of life-history characters and biogeography. In this paper I examine two biogeographic hypotheses concerning the rodent genus Microtus. Like many comparative hypotheses, these can be phrased so that each predicts the existence of a particular monophyletic group. Neither of the predicted groups appear on the single best phylogeny as determined by both Dollo parsimony and maximum likelihood analysis of restriction site maps of mitochondrial DNA. Simulation studies, however, suggest that often the best phylogeny from a single data set has only a low probability of being exactly correct. We must also examine those trees that, while not the single best-supported tree, are not rejected by the data. If we find the best phylogeny for which a hypothesis is satisfied, then likelihood methods can be used to test whether that phylogeny is significantly worse then the best tree overall. If that tree can be rejected, then so can the hypothesis. Computational constraints limit the use of likelihood methods for searching among topologies, so parsimony is used as a data exploratory tool. One of the predicted groups cannot be rejected, even though the most parsimonious tree which includes that group requires 11 more steps than does the most parsimonious tree.     

Using Allele Frequencies and Geographic Subdivision to Reconstruct Gene Trees within a Species: Molecular Variance Parsimony

We formalize the use of allele frequency and geographic information for the construction of gene trees at the intraspecific level and extend the concept of evolutionary parsimony to molecular variance parsimony. The central principle is to consider a particular gene tree as a variable to be optimized in the estimation of a given population statistic. We propose three population statistics that are related to variance components and that are explicit functions of phylogenetic information. The methodology is applied in the context of minimum spanning trees (MSTs) and human mitochondrial DNA restriction data, but could be extended to accommodate other tree-making procedures, as well as other data types. We pursue optimal trees by heuristic optimization over a search space of more than 1.29 billion MSTs. This very large number of equally parsimonious trees underlines the lack of resolution of conventional parsimony procedures. This lack of resolution is highlighted by the observation that equally parsimonious trees yield very different estimates of population genetic diversity and genetic structure, as shown by null distributions of the population statistics, obtained by evaluation of 10,000 random MSTs. We propose a non-parametric test for the similarity between any two trees, based on the distribution of a weighted coevolutionary correlation. The ability to test for tree relatedness leads to the definition of a class of solutions instead of a single solution. Members of the class share virtually all of the critical internal structure of the tree but differ in the placement of singleton branch tips.     

Searching for Most Parsimonious Trees with Simulated Evolutionary Optimization

This study describes novel algorithms for searching for most parsimonious trees. These algorithms are implemented as a parsimony computer program, PARSIGAL, which performs well even with difficult data sets. For high level search, PARSIGAL uses an evolutionary optimization algorithm, which feeds good tree candidates to a branch-swapping local search procedure. This study also describes an extremely fast method of recomputing state sets for binary characters (additive or nonadditive characters with two states), based on packing 32 characters into a single memory word and recomputing the tree simultaneously for all 32 characters using fast bitwise logical operations. The operational principles of PARSIGAL are quite different from those previously published for other parsimony computer programs. Hence it is conceivable that PARSIGAL may be able to locate islands of trees that are different from those that are easily located with existing parsimony computer programs.     

Chromosomal phylogeny of Robertsonian races of the house mouse on the island of Madeira: testing between alternative mutational processes

The ancestral karyotype of the house mouse (Mus musculus) consists of 40 acrocentric chromosomes, but numerous races exist within the domesticus subspecies characterized by different metacentric chromosomes formed by the joining at the centromere of two acrocentrics. An exemplary case is present on the island of Madeira where six highly divergent chromosomal races have accumulated different combinations of 20 metacentrics in 500-1000 years. Chromosomal cladistic phylogenies were performed to test the relative performance of Robertsonian (Rb) fusions, Rb fissions and whole-arm reciprocal translocations (WARTs) in resolving relationships between the chromosomal races. The different trees yielded roughly similar topologies, but varied in the number of steps and branch support. The analyses using Rb fusions/fissions as characters resulted in poorly supported trees requiring six to eight homoplasious events. Allowance for WARTs considerably increased nodal support and yielded the most parsimonious trees since homoplasy was reduced to a single event. The WART-based trees required five to nine WARTs and 12 to 16 Rb fusions. These analyses provide support for the role of WARTs in generating the extensive chromosomal diversification observed in house mice. The repeated occurrence of Rb fusions and WARTs highlights the contribution of centromere-related rearrangements to accelerated rates of chromosomal change in the house mouse.     

Influence of Fruit Availability on the Fission–Fusion Dynamics of Spider Monkeys (<Emphasis Type="Italic">Ateles geoffroyi</Emphasis>)

Socioecological theory proposes that the flexibility in grouping patterns afforded by fission–fusion dynamics allows animals to cope with spatiotemporal variability in food abundance. We investigate the influence of fruit tree abundance and foraging environment heterogeneity on fission–fusion dynamics in a group of spider monkeys (Ateles geoffroyi) in the Yucatan peninsula, Mexico. We collected 1300 h of behavioral data and 23 samples of biweekly ecological data from August 2009 to July 2010. We measured fission–fusion dynamics through the temporal variation in the size and composition of subgroups, the spatial dispersion within and between subgroups, and the frequency of fissions and fusions. We measured habitat-wide food abundance of preferred species, including two that differ greatly in their relative abundance: Brosimum alicastrum (a hyperabundant resource) and Ficus spp. (a not so abundant resource but often represented by large trees). We evaluated the foraging environment heterogeneity through the variance in the number of trees with fruit between species. Our results show that, although habitat-wide food abundance is important, the availability of key resources strongly influences the spider monkeys’ fission–fusion dynamics. When there was a high abundance of fruit of Brosimum, subgroups tended to be more stable, smaller, and mixed sex, and their members remained close. In contrast, when Brosimum trees with fruit were scarce, females often formed large, more fluid and dispersed subgroups. Foraging environment heterogeneity had a positive effect on within-subgroup spatial dispersion and rates of fission and fusion. The complex relationships we have uncovered suggest that the flexibility afforded by fission–fusion dynamics is an adaptation to highly variable foraging environments.     

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.     

红豆杉科及相关类群rbcL基因PCR—RFLP分析

运用RFLP方法对红豆杉科及相关类群14种植物叶绿体rbcL基因PCR产物进行限制酶酶切分析,共获29个酶切变异位点。采用PHYLIP软件包对限制位点变异数据进行极大简约法分析得到18个步长为6的最简约树并求得一致树,结果显示：⑴红豆杉科和三尖杉科属单系群;⑵穗花杉属Amentotaxus以置于红豆杉科内为宜,不支持将穗花杉属独立成科的处理方式;⑶白豆杉应为红豆杉科内一个属Pseudotaxus;⑷三尖杉属内篦子三尖杉地位特殊,可设篦子三尖杉组;⑸不赞同将竹柏类从罗汉松属中分离出去成立新科;⑹红豆杉科、三尖杉科和罗汉松科三者间,前两者的关系更为接近。