A novel supermatrix approach improves resolution of phylogenetic relationships in a comprehensive sample of danthonioid grasses

Phylogeny reconstruction is challenging when branch lengths vary and when different genetic loci show conflicting signals. The number of DNA sequence characters required to obtain robust support for all the nodes in a phylogeny becomes greater with denser taxon sampling. We test the usefulness of an approach mixing densely sampled, variable non-coding sequences (trnL-F; rpl16; atpB-rbcL; ITS) with sparsely sampled, more conservative protein coding and ribosomal sequences (matK; ndhF; rbcL; 26S), for the grass subfamily Danthonioideae. Previous phylogenetic studies of Danthonioideae revealed extensive generic paraphyly, but were often impeded by insufficient character and taxon sampling and apparent inter-gene conflict. Our variably-sampled supermatrix approach allowed us to represent 79% of the species with up to c. 9900 base pairs for taxa representing the major clades. A 'taxon duplication' approach for taxa with conflicting phylogenetic signals allowed us to combine the data whilst representing the differences between chloroplast and nuclear encoded gene trees. This approach efficiently improves resolution and support whilst maximising representation of taxa and their sometimes composite evolutionary histories, resulting in a phylogeny of the Danthonioideae that will be useful both for a wide range of evolutionary studies and to inform forthcoming realignment of generic delimitations in the subfamily.     

A methodological investigation of hominoid craniodental morphology and phylogenetics

The evolutionary relationships of extant great apes and humans have been largely resolved by molecular studies, yet morphology-based phylogenetic analyses continue to provide conflicting results. In order to further investigate this discrepancy we present bootstrap clade support of morphological data based on two quantitative datasets, one dataset consisting of linear measurements of the whole skull from 5 hominoid genera and the second dataset consisting of 3D landmark data from the temporal bone of 5 hominoid genera, including 11 sub-species. Using similar protocols for both datasets, we were able to 1) compare distance-based phylogenetic methods to cladistic parsimony of quantitative data converted into discrete character states, 2) vary outgroup choice to observe its effect on phylogenetic inference, and 3) analyse male and female data separately to observe the effect of sexual dimorphism on phylogenies. Phylogenetic analysis was sensitive to methodological decisions, particularly outgroup selection, where designation of Pongo as an outgroup and removal of Hylobates resulted in greater congruence with the proposed molecular phylogeny. The performance of distance-based methods also justifies their use in phylogenetic analysis of morphological data. It is clear from our analyses that hominoid phylogenetics ought not to be used as an example of conflict between the morphological and molecular, but as an example of how outgroup and methodological choices can affect the outcome of phylogenetic analysis.     

A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data,with Zabelioideae recognized as a new subfamily

The use of diverse data sets in phylogenetic studies aiming for understanding evolutionary histories of species can yield conflicting inference. Phylogenetic conflicts observed in animal and plant systems have often been explained by hybridization, incomplete lineage sorting (ILS), or horizontal gene transfer. Here, we used target enrichment data, species tree, and species network approaches to infer the backbone phylogeny of the family Caprifoliaceae, while distinguishing among sources of incongruence. We used 713 nuclear loci and 46 complete plastome sequence data from 43 samples representing 38 species from all major clades to reconstruct the phylogeny of the family using concatenation and coalescence approaches. We found significant nuclear gene tree conflict as well as cytonuclear discordance. Additionally, coalescent simulations and phylogenetic species network analyses suggested putative ancient hybridization among subfamilies of Caprifoliaceae, which seems to be the main source of phylogenetic discordance. Ancestral state reconstruction of six morphological characters revealed some homoplasy for each character examined. By dating the branching events, we inferred the origin of Caprifoliaceae at approximately 66.65 Ma in the late Cretaceous. By integrating evidence from molecular phylogeny, divergence times, and morphology, we here recognize Zabelioideae as a new subfamily in Caprifoliaceae. This work shows the necessity of using a combination of multiple approaches to identify the sources of gene tree discordance. Our study also highlights the importance of using data from both nuclear and plastid genomes to reconstruct deep and shallow phylogenies of plants.     

Phytoserological contribution to the systematic placement of the Typhales

Serological methods were used to compare the major storage seed proteins, the legumin-like proteins, from the Typhales with other monocot taxa to obtain a more complete understanding of the phylogenetic relationships of the Typhales. Both reference taxa, Typha latifolia and Sparganium erectum were found to be serologically very similar and reveal the close relationship of the Typhaceae and Sparganiaceae and should best be placed in a common order Typhales. Furthermore, the data indicate a close phylogenetic relationship between the Typhales and the wind pollinated Pandaniflorae and also the animal pollinated Zingiberiflorae. Additionally, relationships to the Commeliniflorae (Juncales, Cyperales, Poales) as well as towards the Asparagales (especially the xeromorphic Agavaceae) are indicated. In phylogeny, a branch from pro-Asparagales is postulated leading to the Zingiberiflorae and at least diphyletically to the wind pollinated Pandanaceae plus Typhales and to the Commeliniflorae.     

Recent developments in the analysis of comparative data

Comparative methods can be used to test ideas about adaptation by identifying cases of either parallel or convergent evolutionary change across taxa. Phylogenetic relationships must be known or inferred if comparative methods are to separate the cross-taxonomic covariation among traits associated with evolutionary change from that attributable to common ancestry. Only the former can be used to test ideas linking convergent or parallel evolutionary change to some aspect of the environment. The comparative methods that are currently available differ in how they manage the effects brought about by phylogenetic relationships. One method is applicable only to discrete data, and uses cladistic techniques to identify evolutionary events that depart from phylogenetic trends. Techniques for continuous variables attempt to control for phylogenetic effects in a variety of ways. One method examines the taxonomic distribution of variance to identify the taxa within which character variation is small. The method assumes that taxa with small amounts of variation are those in which little evolutionary change has occurred, and thus variation is unlikely to be independent of ancestral trends. Analyses are then concentrated among taxa that show more variation, on the assumption that greater evolutionary change in the character has taken place. Several methods estimate directly the extent to which ancestry can predict the observed variation of a character, and subtract the ancestral effect to reveal variation of phylogeny. Yet another can remove phylogenetic effects if the true phylogeny is known. One class of comparative methods controls for phylogenetic effects by searching for comparative trends within rather than across taxa. With current knowledge of phylogenies, there is a trade-off in the choice of a comparative method: those that control phylogenetic effects with greater certainty are either less applicable to real data, or they make restrictive or untestable assumptions. Those that rely on statistical patterns to infer phylogenetic effects may not control phylogeny as efficiently but are more readily applied to existing data sets.     

Quality and quantity of data recovered from massively parallel sequencing: Examples in Asparagales and Poaceae

? Premise of the study: Genome survey sequences (GSS) from massively parallel sequencing have potential to provide large, cost-effective data sets for phylogenetic inference, replace single gene or spacer regions as DNA barcodes, and provide a plethora of data for other comparative molecular evolution studies. Here we report on the application of this method to estimating the molecular phylogeny of core Asparagales, investigating plastid gene losses, assembling complete plastid genomes, and determining the type and quality of assembled genomic data attainable from Illumina 80-120-bp reads. ? Methods: We sequenced total genomic DNA from samples in two lineages of monocotyledonous plants, Poaceae and Asparagales, on the Illumina platform in a multiplex arrangement. We compared reference-based assemblies to de novo contigs, evaluated consistency of assemblies resulting from use of various references sequences, and assessed our methods to obtain sequence assemblies in nonmodel taxa. ? Key results: Our method returned reliable, robust organellar and nrDNA sequences in a variety of plant lineages. High quality assemblies are not dependent on genome size, amount of plastid present in the total genomic DNA template, or relatedness of available reference sequences for assembly. Phylogenetic results revealed familial and subfamilial relationships within Asparagales with high bootstrap support, although placement of the monotypic genus Aphyllanthes was placed with moderate confidence. ? Conclusions: The well-supported molecular phylogeny provides evidence for delineation of subfamilies within core Asparagales. With advances in technology and bioinformatics tools, the use of massively parallel sequencing will continue to become easier and more affordable for phylogenomic and molecular evolutionary biology investigations.     

Advances in the use of DNA barcodes to build a community phylogeny for tropical trees in a Puerto Rican forest dynamics plot

Background

Species number, functional traits, and phylogenetic history all contribute to characterizing the biological diversity in plant communities. The phylogenetic component of diversity has been particularly difficult to quantify in species-rich tropical tree assemblages. The compilation of previously published (and often incomplete) data on evolutionary relationships of species into a composite phylogeny of the taxa in a forest, through such programs as Phylomatic, has proven useful in building community phylogenies although often of limited resolution. Recently, DNA barcodes have been used to construct a robust community phylogeny for nearly 300 tree species in a forest dynamics plot in Panama using a supermatrix method. In that study sequence data from three barcode loci were used to generate a well-resolved species-level phylogeny.

Methodology/Principal Findings

Here we expand upon this earlier investigation and present results on the use of a phylogenetic constraint tree to generate a community phylogeny for a diverse, tropical forest dynamics plot in Puerto Rico. This enhanced method of phylogenetic reconstruction insures the congruence of the barcode phylogeny with broadly accepted hypotheses on the phylogeny of flowering plants (i.e., APG III) regardless of the number and taxonomic breadth of the taxa sampled. We also compare maximum parsimony versus maximum likelihood estimates of community phylogenetic relationships as well as evaluate the effectiveness of one- versus two- versus three-gene barcodes in resolving community evolutionary history.

Conclusions/Significance

As first demonstrated in the Panamanian forest dynamics plot, the results for the Puerto Rican plot illustrate that highly resolved phylogenies derived from DNA barcode sequence data combined with a constraint tree based on APG III are particularly useful in comparative analysis of phylogenetic diversity and will enhance research on the interface between community ecology and evolution.     

Combined support for wholesale taxic atavism in gavialine crocodylians

Morphological and molecular data sets favor robustly supported, contradictory interpretations of crocodylian phylogeny. A longstanding perception in the field of systematics is that such significantly conflicting data sets should be analyzed separately. Here we utilize a combined approach, simultaneous analyses of all relevant character data, to summarize common support and to reconcile discrepancies among data sets. By conjoining rather than separating incongruent classes of data, secondary phylogenetic signals emerge from both molecular and morphological character sets and provide solid evidence for a unified hypothesis of crocodylian phylogeny. Simultaneous analyses of four gene sequences and paleontological data suggest that putative adaptive convergences in the jaws of gavialines (gavials) and tomistomines (false gavials) offer character support for a grouping of these taxa, making Gavialinae an atavistic taxon. Simple new methods for measuring the influence of extinct taxa on topological support indicate that in this vertebrate order fossils generally stabilize relationships and accentuate hidden phylogenetic signals. Remaining inconsistencies in minimum length trees, including concentrated hierarchical patterns of homoplasy and extensive gaps in the fossil record, indicate where future work in crocodylian systematics should be directed.     

Rapid radiation events in the family Ursidae indicated by likelihood phylogenetic estimation from multiple fragments of mtDNA.

The bear family (Ursidae) presents a number of phylogenetic ambiguities as the evolutionary relationships of the six youngest members (ursine bears) are largely unresolved. Recent mitochondrial DNA analyses have produced conflicting results with respect to the phylogeny of ursine bears. In an attempt to resolve these issues, we obtained 1916 nucleotides of mitochondrial DNA sequence data from six gene segments for all eight bear species and conducted maximum likelihood and maximum parsimony analyses on all fragments separately and combined. All six single-region gene trees gave different phylogenetic estimates; however, only for control region data was this significantly incongruent with the results from the combined data. The optimal phylogeny for the combined data set suggests that the giant panda is most basal followed by the spectacled bear. The sloth bear is the basal ursine bear, and there is weak support for a sister taxon relationship of the American and Asiatic black bears. The sun bear is sister taxon to the youngest clade containing brown bears and polar bears. Statistical analyses of alternate hypotheses revealed a lack of strong support for many of the relationships. We suggest that the difficulties surrounding the resolution of the evolutionary relationships of the Ursidae are linked to the existence of sequential rapid radiation events in bear evolution. Thus, unresolved branching orders during these time periods may represent an accurate representation of the evolutionary history of bear species.     

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.     

A comparative analysis of Y chromosome and mtDNA phylogenies of the Hylobates gibbons

ABSTRACT: BACKGROUND: The evolutionary relationships of closely related species have long been of interest to biologists since these species experienced different evolutionary processes in a relatively short period of time. Comparison of phylogenies inferred from DNA sequences with differing inheritance patterns, such as mitochondrial, autosomal, and X and Y chromosomal loci, can provide more comprehensive inferences of the evolutionary histories of species. Gibbons, especially the genus Hylobates, are particularly intriguing as they consist of multiple closely related species which emerged rapidly and live in close geographic proximity. Our current understanding of relationships among Hylobates species is largely based on data from the maternally-inherited mitochondrial DNAs (mtDNAs). RESULTS: To infer the paternal histories of gibbon taxa, we sequenced multiple Y chromosomal loci from 26 gibbons representing 10 species. As expected, we find levels of sequence variation some five times lower than observed for the mitochondrial genome (mtgenome). Although our Y chromosome phylogenetic tree shows relatively low resolution compared to the mtgenome tree, our results are consistent with the monophyly of gibbon genera suggested by the mtgenome tree. In a comparison of the molecular dating of divergences and on the branching patterns of phylogeny trees between mtgenome and Y chromosome data, we found: 1) the inferred divergence estimates were more recent for the Y chromosome than for the mtgenome, 2) the species H. lar and H. pileatus are reciprocally monophyletic in the mtgenome phylogeny but a H. pileatus individual falls into the H. lar Y chromosome clade. CONCLUSIONS: Based on the ~6.4 kb of Y chromosomal DNA sequence data generated for each of the 26 individuals in this study, we provide molecular inferences on gibbon and particularly on Hylobates evolution complementary to those from mtDNA data. Overall, our results illustrate the utility of comparative studies of loci with different inheritance patterns for investigating potential sex specific processes on the evolutionary histories of closely related taxa, and emphasize the need for further sampling of gibbons of known provenance.     

Phylogeny estimation of the radiation of western North American chipmunks (Tamias) in the face of introgression using reproductive protein genes

The causes and consequences of rapid radiations are major unresolved issues in evolutionary biology. This is in part because phylogeny estimation is confounded by processes such as stochastic lineage sorting and hybridization. Because these processes are expected to be heterogeneous across the genome, comparison among marker classes may provide a means of disentangling these elements. Here we use introns from nuclear-encoded reproductive protein genes expected to be resistant to introgression to estimate the phylogeny of the western chipmunks (Tamias: subgenus: Neotamias), a rapid radiation that has experienced introgressive hybridization of mitochondrial DNA (mtDNA). We analyze the nuclear loci using coalescent-based species-tree estimation methods and concatenation to estimate a species tree and we use parametric bootstraps and coalescent simulations to differentiate between phylogenetic error, coalescent stochasticity and introgressive hybridization. Results indicate that the mtDNA gene tree reflects several introgression events that have occurred between taxa of varying levels of divergence and at different time points in the tree. T. panamintinus and T. speciosus appear to be fixed for ancient mitochondrial introgressions from T. minimus. A southern Rocky Mountains clade appears well sorted (i.e., species are largely monophyletic) at multiple nuclear loci, while five of six taxa are nonmonophyletic based on cytochrome b. Our simulations reject phylogenetic error and coalescent stochasticity as causes. The results represent an advance in our understanding of the processes at work during the radiation of Tamias and suggest that sampling reproductive-protein genes may be a viable strategy for phylogeny estimation of rapid radiations in which reproductive isolation is incomplete. However, a genome-scale survey that can statistically compare heterogeneity of genealogical process at many more loci will be necessary to test this conclusion.     

SuperTRI: A new approach based on branch support analyses of multiple independent data sets for assessing reliability of phylogenetic inferences

Supermatrix and supertree are two methods for constructing a phylogenetic tree by using multiple data sets. However, these methods are not a panacea, as conflicting signals between data sets can lead to misinterpret the evolutionary history of taxa. In particular, the supermatrix approach is expected to be misleading if the species-tree signal is not dominant after the combination of the data sets. Moreover, most current supertree methods suffer from two limitations: (i) they ignore or misinterpret secondary (non-dominant) phylogenetic signals of the different data sets; and (ii) the logical basis of node robustness measures is unclear.To overcome these limitations, we propose a new approach, called SuperTRI, which is based on the branch support analyses of the independent data sets, and where the reliability of the nodes is assessed using three measures: the supertree Bootstrap percentage and two other values calculated from the separate analyses: the mean branch support (mean Bootstrap percentage or mean posterior probability) and the reproducibility index.The SuperTRI approach is tested on a data matrix including seven genes for 82 taxa of the family Bovidae (Mammalia, Ruminantia), and the results are compared to those found with the supermatrix approach. The phylogenetic analyses of the supermatrix and independent data sets were done using four methods of tree reconstruction: Bayesian inference, maximum likelihood, and unweighted and weighted maximum parsimony. The results indicate, firstly, that the SuperTRI approach shows less sensitivity to the four phylogenetic methods, secondly, that it is more accurate to interpret the relationships among taxa, and thirdly, that interesting conclusions on introgression and radiation can be drawn from the comparisons between SuperTRI and supermatrix analyses. To cite this article: A. Ropiquet et al., C. R. Biologies 332 (2009).     

Old trees, new trees--is there any progress?

The amount of comparative data for phylogenetic analyses is constantly increasing. Data come from different directions such as morphology, molecular genetics, developmental biology and paleontology. With the increasing diversity of data and of analytical tools, the number of competing hypotheses on phylogenetic relationships rises, too. The choice of the phylogenetic tree as a basis for the interpretation of new data is important, because different trees will support different evolutionary interpretations of the data investigated. I argue here that, although many problematic aspects exist, there are several phylogenetic relationships that are supported by the majority of analyses and may be regarded as something like a robust backbone. This accounts, for example, for the monophyly of Metazoa, Bilateria, Deuterostomia, Protostomia (= Gastroneuralia), Gnathifera, Spiralia, Trochozoa and Arthropoda and probably also for the branching order of diploblastic taxa (“Porifera”, Trichoplax adhaerens, Cnidaria and Ctenophora). Along this “backbone”, there are several problematic regions, where either monophyly is questionable and/or where taxa “rotate” in narrow regions of the tree. This is illustrated exemplified by the probable paraphyly of Porifera and the phylogenetic relationships of basal spiralian taxa. Two problems span wider regions of the tree: the position of Arthropoda either as the sister taxon of Annelida (= Articulata) or of Cycloneuralia (= Ecdysozoa) and the position of tentaculate taxa either as sister taxa of Deuterostomia (= Radialia) or within the taxon Spiralia. The backbone makes it possible to develop a basic understanding of the evolution of genes, molecules and structures in metazoan animals.     

The phylogeny of land plants inferred from 18S rDNA sequences: pushing the limits of rDNA signal?

Previous studies of the phylogeny of land plants based on analysis of 18S ribosomal DNA (rDNA) sequences have generally found weak support for the relationships recovered and at least some obviously spurious relationships, resulting in equivocal inferences of land plant phylogeny. We hypothesized that greater sampling of both characters and taxa would improve inferences of land plant phylogeny based on 18S rDNA sequences. We therefore conducted a phylogenetic analysis of complete (or nearly complete) 18S rDNA sequences for 93 species of land plants and 7 green algal relatives. Parsimony analyses with equal weighting of characters and characters state changes and parsimony analyses weighting (1) stem bases half as much as loop bases and (2) transitions half as much as transversions did not produce substantially different topologies. Although the general structure of the shortest trees is consistent with most hypotheses of land plant phylogeny, several relationships, particularly among major groups of land plants, appear spurious. Increased character and taxon sampling did not substantially improve the performance of 18S rDNA in phylogenetic analyses of land plants, nor did analyses designed to accommodate variation in evolutionary rates among sites. The rate and pattern of 18S rDNA evolution across land plants may limit the usefulness of this gene for phylogeny reconstruction at deep levels of plant phylogeny. We conclude that the mosaic structure of 18S rDNA, consisting of highly conserved and highly variable regions, may contain historical signal at two levels. Rapidly evolving regions are informative for relatively recent divergences (e.g., within angiosperms, seed plants, and ferns), but homoplasy at these sites makes it difficult to resolve relationships among these groups. At deeper levels, changes in the highly conserved regions of small-subunit rDNAs provide signal across all of life. Because constraints imposed by the secondary structure of the rRNA may affect the phylogenetic information content of 18S rDNA, we suggest that 18S rDNA sequences be combined with other data and that methods of analysis be employed to accommodate these differences in evolutionary patterns, particularly across deep divergences in the tree of life.     

Chloroplast phylogenomics of unicellular and colonial Volvocales provides perspectives on the evolution of morphological characters

Volvocales forms a species-rich clade with wide morphological variety and is regarded as an ideal model for tracing the evolutionary transitions in multicellularity. The phylogenetic relationships among the colonial volvocine algae and its relatives are important for investigating the origin of multicellularity in the clade Reinhardtinia. Therefore, a robust phylogenetic framework of the unicellular and colonial volvocine algae with broad taxon and gene sampling is essential for illuminating the evolution of multicellularity. Recent chloroplast phylogenomic studies have uncovered five major orders in the Chlorophyceae, but the family-level relationships within Sphaeropleales and Volvocales remain elusive due to the uncertain positions of some incertae sedis taxa. In this study, we contributed six newly sequenced chloroplast genomes in the Volvocales and analyzed a dataset with 91 chlorophycean taxa and 58 protein-coding genes. Conflicting phylogenetic signals were detected among chloroplast genes that resulted in discordant tree topologies among different analyses. We compared the phylogenetic trees inferred from original nucleotide, RY-coding, codon-degenerate, and amino acid datasets, and improved the robustness of phylogenetic inference in the Chlorophyceae by reducing base compositional bias. Our analyses indicate that the unicellular Chlamydomonas and Vitreochlamys are close to or nested within the colonial taxa, and all the incertae sedis taxa are nested within the monophyletic Sphaeropleales s.l. We propose that the colonial taxa in the Reinhardtinia are paraphyletic and multicellularity evolved once in the volvocine green algae and might be lost in Chlamydomonas and Vitreochlamys.     

Palynological data on Illiciaceae and Schisandraceae confirm phylogenetic relationships within these two basally-branching angiosperm families

Illiciaceae and Schisandraceae, together with other members of Austrobaileyales have been identified as one of the earliest diverging lineages of angiosperms, within the ANITA grade. The specialized Illiciaceae and Schisandraceae comprise a clade defined by apomorphic characters including pollen grains with three or six colpate apertures. In both these families, pollen apertures and exine sculpture were found to be very informative when considered in the context of recent understanding of evolutionary patterns. In the current study, pollen grains of 21 taxa from Illiciaceae and Schisandraceae were investigated. These data, together with palynological data for taxa previously studied, were mapped into recent molecular phylogenetic trees to re-evaluate the existing classification and phylogenetic relationships in the two families. Palynological data were found to be relatively congruent with recent molecular phylogenies, while traditional delimitations of infra-generic taxa were somewhat conflicting and did not reflect phylogeny and evolution. The evolution of pollen morphology in the two families, together with other members of Austrobaileyales, is discussed in comparison with the molecular phylogenies.     

Cyprinid phylogeny based on Bayesian and maximum likelihood analyses of partitioned data: implications for Cyprinidae systematics

Cyprinidae is the biggest family of freshwater fish, but the phylogenetic relationships among its higher-level taxa are not yet fully resolved. In this study, we used the nuclear recombination activating gene 2 and the mitochondrial 16S ribosomal RNA and cytochrome b genes to reconstruct cyprinid phylogeny. Our aims were to (i) demonstrate the effects of partitioned phylogenetic analyses on phylogeny reconstruction of cyprinid fishes; (ii) provide new insights into the phylogeny of cyprinids. Our study indicated that unpartitioned strategy was optimal for our analyses; partitioned analyses did not provide better-resolved or -supported estimates of cyprinid phylogeny. Bayesian analyses support the following relationships among the major monophyletic groups within Cyprinidae: (Cyprininae, Labeoninae), ((Acheilognathinae, ((Leuciscinae, Tincinae), Gobioninae)), Xenocyprininae). The placement of Danioninae was poorly resolved. Estimates of divergence dates within the family showed that radiation of the major cyprinid groups occurred during the Late Oligocene through the Late Miocene. Our phylogenetic analyses improved our understanding of the evolutionary history of this important fish family.