What's old and new in molecular phylogenetics

While it is fairly easy to devise a phylogenetic tree based on molecular data, it has proven difficult to tell how reliable any such tree is. Thus while the genetic inference that humans, chimpanzees, and gorillas cluster together is widely accepted, the genetic inference that the primary division among Old World human populations is between Asia and EurAfrica is not. A molecular phylogenetic inference linking humans and chimpanzees was proposed in the 1980s based on the technique of DNA hybridization. Despite several recent publications in primary and secondary source material, much confusion still exists surrounding the work. This paper tries to clarify issues that may still be confusing to physical anthropologists, and proposes criteria upon which to judge the robusticity of a phylogenetic inference based on DNA hybridization, in light of a recent published claim of replication. The claim of replication is considered critically. Interestingly, the original DNA hybridization data may actually show a chimp-gorilla link, in harmony with other phylogenetic results.     

Molecular phylogenetics of the gomphoid-phalloid fungi with an establishment of the new subclass Phallomycetidae and two new orders

Molecular phylogenetic analyses for the gomphoid-phalloid fungi were conducted based on the five gene dataset with extensive taxon sampling. The monophyly of the gomphoid-phalloid clade was strongly supported, and four well supported major subclades were recognized. Three of the four subclades were represented entirely by gastroid taxa, and only Gomphales contained both gastroid and non-gastroid taxa. While the gastroid morphology is derived from epigeous, nongastroid taxa in Gomphales, the topology of Phallales indicated that truffle-like form is an ancestral morphology of the stinkhorn fruiting bodies. Although basidiospore maturation occurs within the enclosed fruiting bodies of the stinkhorn, the elevation of the mature spore-producing tissue represents an independent origin of the stipe among Basidiomycota. Comparisons are made between previous and new classification schemes, which are based on the results of phylogenetic analyses. Based on the results of these analyses, a new subclass Phallomycetidae, and two new orders, Hysterangiales and Geastrales, are proposed.     

Molecular phylogenetics of Thysanoptera

Analyses of morphological data on the higher-level phylogenetics of Thysanoptera have suggested two alternative hypotheses: (1) sister-taxon status of the monophyletic suborders Terebrantia and Tubulifera. and (2) paraphyly of Terebrantia with respect to Tubulifera. Analyses of nucleotide sequence data from the mitochondrial gene cytochrome oxidase I and the nuclear gene I8S rONA using maximum parsimony. neighbour joining. and maximum likelihood provide strong support for the hypothesis of a sister-taxon relationship between the Terebrantia and Tubulifera. These data resolve this long-standing controversy in thysanopteran phylogenetics and provide a framework for further studies of higher-level relationships in this order.     

Spatial phylogenetics of the North American flora

North America is a large continent with extensive climatic, geological, soil, and biological diversity. As biota faces threat from habitat destruction and climate change, making a quantitative assessment of biodiversity becomes critically important. Rapid digitization of plant specimen records and accumulation of DNA sequence data enable a much‐needed broad synthesis of species occurrences with phylogenetic data. In this study, the first such synthesis of a flora from such a large and diverse part of the world is attempted, all seed plants from the North American continent (here defined to include Canada, United States, and Mexico), with a focus on examining phylogenetic diversity and endemism. We collected digitized plant specimen records and chose a coarse grain for analysis, recognizing that this grain is currently necessary for reasonable completeness per sampling unit. We found that raw richness and endemism patterns largely support previous hypotheses of biodiversity hotspots. The application of phylogenetic metrics and a randomization test revealed novel results, including a significant phylogenetic clustering across the continent, a striking east–west geographical difference in the distribution of branch lengths, and the discovery of centers of neo‐ and paleoendemism in Mexico, the southwestern USA, and the southeastern USA. Finally, our examination of phylogenetic beta diversity provides a new approach to compare centers of endemism. We discuss the empirical challenges of working at the continental scale and the need for more sampling across large parts of the continent, for both DNA data for terminal taxa and spatial data for poorly understood regions, to confirm and extend these results.     

莲科系统位置评述

莲科含1属1种2亚种,以具有最古老的有活力的种子而著称。形态学研究显示,莲不仅具有双子叶植物特征,而且又具有单子叶植物的某些性状。因此,对研究被子植物(有花植物)的起源与演化以及单子叶植物的起源具有重要价值。被子植物(有花植物)的起源与辐射一直是植物学家关注的热点,有关莲科的系统位置存在争议。该文对该科系统位置的研究历史与现状进行评述。     

Molecular phylogenetics of gnathostomous (jawed) fishes: old bones, new cartilage

Cartilaginous fishes (chondrichthyans) have traditionally been taken as an early offshoot among jawed vertebrates. To examine some crucial chondrichthyan relationships, we have sequenced the mitochondrial genomes of the holocephalan Chimaera monstrosa (ratfish) and the basal galeomorph species Heterodontus francisci (horn shark) and analysed them together with the corresponding data set of several other chondrichthyans, teleosts, the coelacanth, the African lungfish and the bichir. The rooting point of the tree was established using unequivocal outgroups, the sea lamprey , the sea lancelet or echinoderms. The phylogenetic analyses identified monophyletic Chondrichthyes in a terminal position in the piscine tree, lending no support to the traditionally accepted basal position of cartilaginous fishes among extant gnathostomes. The findings suggest that the cartilage characterizing extant chondrichthyans is a retention of an embryonic condition, thus representing a derived rather than a primitive phylogenetic and developmental stage. Similarly, the analyses suggest that the open gill slits of neoselachians (sharks and rays) constitute a derived state compared to the operculum (gill cover) characterizing bony fishes and holocephalans. The analyses did not support the so-called Squalea/Galea hypothesis which posits that batomorphs (sharks, rays) have arisen from recent selachians (sharks). Inconsistent with the common understanding of piscine and gnathostome evolution, the two taxa having lungs, the African lungfish and the bichir, had a basal position in the piscine tree. The findings put into question the phylogenetic validity of the taxonomic nomenclature attributed to various vertebrate, notably piscine, clades.     

Comparative phylogenetics offer new insights into the biogeographic history of Macaca fascicularis and the origin of the Mauritian macaques

We employ a comparative phylogenetic analysis to gain insight into the recent evolutionary history of Macaca fascicularis, the long-tailed macaque. Mitochondrial and Y-chromosomal topologies both show that, in general, the deepest intraspecific bifurcations separate Indochinese and Sundaic forms of this species. Sumatran populations, however, are an exception: they carry one Y-chromosomal lineage that clusters with continental populations, and another that clusters with insular stocks. This discovery provides insight into two events in the history of M. fascicularis. First, the presence of the 'continental' Y-lineage on Sumatra is one of the strongest lines of evidence to date for recent (Late Pleistocene) gene flow between Indochinese and Sundaic populations. Second, since Sumatra is the only region known to carry 'continental' YDNA and 'insular' mtDNA, it is considered the most likely source of the Mauritian macaques-an important biomedical research stock that appears to carry this mtDNA/YDNA combination exclusively.     

Molecular phylogenetics of Candida albicans

We analyzed data on multilocus sequence typing (MLST), ABC typing, mating type-like locus (MAT) status, and antifungal susceptibility for a panel of 1,391 Candida albicans isolates. Almost all (96.7%) of the isolates could be assigned by MLST to one of 17 clades. eBURST analysis revealed 53 clonal clusters. Diploid sequence type 69 was the most common MLST strain type and the founder of the largest clonal cluster, and examples were found among isolates from all parts of the world. ABC types and geographical origins showed statistically significant variations among clades by univariate analysis of variance, but anatomical source and antifungal susceptibility data were not significantly associated. A separate analysis limited to European isolates, thereby minimizing geographical effects, showed significant differences in the proportions of isolates from blood, commensal carriage, and superficial infections among the five most populous clades. The proportion of isolates with low antifungal susceptibility was highest for MAT homozygous a/a types and then alpha/alpha types and was lowest for heterozygous a/alpha types. The tree of clades defined by MLST was not congruent with trees generated from the individual gene fragments sequenced, implying a separate evolutionary history for each fragment. Analysis of nucleic acid variation among loci and within loci supported recombination. Computational haplotype analysis showed a high frequency of recombination events, suggesting that isolates had mixed evolutionary histories resembling those of a sexually reproducing species.     

Species concepts and phylogenetics

Concepts of species proposed within the phylogenetic paradigm arecritically reviewed. Most so called phylogenetic species concepts relyheavily on factors immaterial to phylogenetic hypotheses. Thus, theyhave limited empirical content and offer weak bases on which to makedecisions about real problems related to species. Any workable notion ofspecies relies on an explicit character analysis, rather than onabstract properties of lineages, narrative predications and speculationson tokogenetic relationships. Species only exist conjecturally, as thesmallest meaningful units for phylogenetic analysis, as based oncharacter evidence. Such an idea considers species to be conjecturesbased on similarity, that are subsequently subject to testing by theresults of analysis. Species, thus, are units of phylogenetic analysisin the same way as hypotheses of homology are units of comparablesimilarities, i.e. conjectures to be tested by congruence. Althoughmonophyly need not be demonstrated for species-level taxa, hypotheses ofrelationships are the only basis to refute species limits and guidenecessary rearrangements. The factor that leads to recognition ofspecies is similarity in observed traits. The concept of life cycle isintroduced as an important element in the discussion of species, as anefficient way to convey subsidiary notions of sexual dimorphism,polymorphism, polytypy and clusters of diagnosable semaphoronts. Thenotion of exemplars is used to expand the concept ofspecies-as-individual-organisms into a more generally usable concept.Species are therefore proposed for a diagnosable sample of(observed or inferred) life cycles represented by exemplars all of whichare hypothesized to attach to the same node in a cladogram, and whichare not structured into other similarly diagnosable clusters. Thisdefinition is character-based, potentially testable by reference to abranching diagram, and dispenses with reference to ancestor-descendantrelationships or regression into population concepts. It provides aworkable basis on which to proceed with phylogenetic analysis and abasis for that analysis to refute or refine species limits. A protocolis offered for testing hypotheses of species boundaries in cladograms.     

RAPD problems in phylogenetics

This paper is intended to clarify some of the questions related with the application of RAPD for phylogenetic reconstruction purposes. Using different specimens of mammals selected across various taxonomic levels, we assessed the validity of RAPD to recover a known phylogeny, using four distance coefficients (simple matching, Russell & Rao, Jaccard, and Dice). We assessed the minimum number of primers required in the computations to obtain stable results in terms of distance estimates and/or topologies of the derived trees. These results based on distance methods were compared with those obtained with parsimony analyses of RAPD markers. Both approaches have shown to be equally problematic for comparing taxa above the family level. On the basis of these comparisons among various indices and methods, we recommend the use of Jaccard or Dice coefficients, with no less than twelve primers. We also suggest validation of any phylogeny based on RAPD data with a resampling procedure (i.e. the bootstrap or the jackknife) before any sound conclusion can be drawn.     

Closure operations in phylogenetics

Closure operations are a useful device in both the theory and practice of tree reconstruction in biology and other areas of classification. These operations take a collection of trees (rooted or unrooted) that classify overlapping sets of objects at their leaves, and infer further tree-like relationships. In this paper we investigate closure operations on phylogenetic trees; both rooted and unrooted; as well as on X-splits, and in a general abstract setting. We derive a number of new results, particularly concerning the completeness (and incompleteness) and complexity of various types of closure rules.     

Ribosomal RNA phylogenetics: the third dimension

With integration of secondary structures, ribosomal genes have once again become very popular for phylogenetic analyses. This additional source of information to the nucleotide sequence provides a massive boost for taxonomic inferences. Herein, we propose that in the near future a further benefit for phylogenetics with such genes will be very likely by inclusion of the third dimension. For the first time, we determined the tertiary structure of the ribosomal internal transcribed spacer 2 for Chlamydomonas rheinhardtii by application of two different in silico prediction algorithms. We compared these methods with focus on phylogenetic usability. Further, we determined the tertiary structures for closely related green algae to provide a small phylogenetic example. The results suggest that the tertiary structure inherits evolutionary information observable neither within the sequence nor in the secondary structure.     

缺失数据和贝叶斯系统发育分析精确度之探索

The effect of missing data on phylogenetic methods is a potentially important issue in our attempts to reconstruct the Tree of Life. If missing data are truly problematic, then it may be unwise to include species in an analysis that lack data for some characters (incomplete taxa) or to include characters that lack data for some species. Given the difficulty of obtaining data from all characters for all taxa (e.g., fossils), missing data might seriously impede efforts to reconstruct a comprehensive phylogeny that includes all species. Fortunately, recent simulations and empirical analyses suggest that missing data cells are not themselves problematic, and that incomplete taxa can be accurately placed as long as the overall number of characters in the analysis is large. However, these studies have so far only been conducted on parsimony, likelihood, and neighbor-joining methods. Although Bayesian phylogenetic methods have become widely used in recent years, the effects of missing data on Bayesian analysis have not been adequately studied. Here, we conduct simulations to test whether Bayesian analyses can accurately place incomplete taxa despite extensive missing data. In agreement with previous studies of other methods, we find that Bayesian analyses can accurately reconstruct the position of highly incomplete taxa (i.e., 95% missing data), as long as the overall number of characters in the analysis is large. These results suggest that highly incomplete taxa can be safely included in many Bayesian phylogenetic analyses.     

Evolutionary relationships in Trypanosoma cruzi: molecular phylogenetics supports the existence of a new major lineage of strains

For the purpose of investigating the evolutionary relationships among strains of the human parasite Trypanosoma cruzi, we have determined the nucleotide sequence, in 16 T. cruzi stocks, of a DNA fragment having approximately 1030 nucleotides in length. Phylogenetic analyses show the presence of at least three major groups of T. cruzi strains, a result that contradicts previous phylogenetic inferences based on polymorphism data. We also performed an analysis of the relative extent of nucleotide divergence among T. cruzi strains compared to the divergence between Leishmania species, using the gene encoding pteridine reductase. The results presented in this work show that the divergence among the most distant T. cruzi strains is at least as high as the divergence between two different species complexes of Leishmania, those containing L. major and L. mexicana.     

Molecular phylogenetics of mouse opossums: new findings on the phylogeny of Thylamys (Didelphimorphia,Didelphidae)

The mouse opossums of the genus Thylamys constitute a group of species mainly adapted to open xeric‐like habitats and restricted to the southern portion of South America. We used molecular data (mitochondrial and nuclear sequences) to evaluate the phylogenetic and biogeographical relationships of all currently known living species of the genus, recognizing a new taxon from the middle and high elevations of the Peruvian Andes and evaluating the phylogenetic structuring within T. pallidior and T. elegans, as well as the validity of T. sponsorius, T. cinderella and T. tatei, and the haplogroups recognized within T. pusillus. Our results confirm the monophyly of the genus and that the Caatinga and the Cerrado inhabitants Thylamys karimii and T. velutinus are the most basal species in the radiation of Thylamys. We also calibrated a molecular clock which hypothesized a time of origin of the genus of about 24 My, with most species differentiating in middle and late Miocene and Plio‐Pleistocene times of South America.