Phylogenetic relationships and heterogeneous evolutionary processes among phrynosomatine sand lizards (Squamata, Iguanidae) revisited

Phylogenetic analyses of DNA sequences were conducted to evaluate four alternative hypotheses of phrynosomatine sand lizard relationships. Sequences comprising 2871 aligned base pair positions representing the regions spanning ND1-COI and cyt b-tRNA(Thr) of the mitochondrial genome from all recognized sand lizard species were analyzed using unpartitioned parsimony and likelihood methods, likelihood methods with assumed partitions, Bayesian methods with assumed partitions, and Bayesian mixture models. The topology (Uma, (Callisaurus, (Cophosaurus, Holbrookia))) and thus monophyly of the "earless" taxa, Cophosaurus and Holbrookia, is supported by all analyses. Previously proposed topologies in which Uma and Callisaurus are sister taxa and those in which Holbrookia is the sister group to all other sand lizard taxa are rejected using both parsimony and likelihood-based significance tests with the combined, unparitioned data set. Bayesian hypothesis tests also reject those topologies using six assumed partitioning strategies, and the two partitioning strategies presumably associated with the most powerful tests also reject a third previously proposed topology, in which Callisaurus and Cophosaurus are sister taxa. For both maximum likelihood and Bayesian methods with assumed partitions, those partitions defined by codon position and tRNA stem and nonstems explained the data better than other strategies examined. Bayes factor estimates comparing results of assumed partitions versus mixture models suggest that mixture models perform better than assumed partitions when the latter were not based on functional characteristics of the data, such as codon position and tRNA stem and nonstems. However, assumed partitions performed better than mixture models when functional differences were incorporated. We reiterate the importance of accounting for heterogeneous evolutionary processes in the analysis of complex data sets and emphasize the importance of implementing mixed model likelihood methods.     

Phylogenetic systematics and biogeography of hummingbirds: Bayesian and maximum likelihood analyses of partitioned data and selection of an appropriate partitioning strategy

Hummingbirds are an important model system in avian biology, but to date the group has been the subject of remarkably few phylogenetic investigations. Here we present partitioned Bayesian and maximum likelihood phylogenetic analyses for 151 of approximately 330 species of hummingbirds and 12 outgroup taxa based on two protein-coding mitochondrial genes (ND2 and ND4), flanking tRNAs, and two nuclear introns (AK1 and BFib). We analyzed these data under several partitioning strategies ranging between unpartitioned and a maximum of nine partitions. In order to select a statistically justified partitioning strategy following partitioned Bayesian analysis, we considered four alternative criteria including Bayes factors, modified versions of the Akaike information criterion for small sample sizes (AIC(c)), Bayesian information criterion (BIC), and a decision-theoretic methodology (DT). Following partitioned maximum likelihood analyses, we selected a best-fitting strategy using hierarchical likelihood ratio tests (hLRTS), the conventional AICc, BIC, and DT, concluding that the most stringent criterion, the performance-based DT, was the most appropriate methodology for selecting amongst partitioning strategies. In the context of our well-resolved and well-supported phylogenetic estimate, we consider the historical biogeography of hummingbirds using ancestral state reconstructions of (1) primary geographic region of occurrence (i.e., South America, Central America, North America, Greater Antilles, Lesser Antilles), (2) Andean or non-Andean geographic distribution, and (3) minimum elevational occurrence. These analyses indicate that the basal hummingbird assemblages originated in the lowlands of South America, that most of the principle clades of hummingbirds (all but Mountain Gems and possibly Bees) originated on this continent, and that there have been many (at least 30) independent invasions of other primary landmasses, especially Central America.     

Mosaicism, modules, and the evolution of birds: results from a Bayesian approach to the study of morphological evolution using discrete character data

The study of morphological evolution after the inferred origin of active flight homologous with that in Aves has historically been characterized by an emphasis on anatomically disjunct, mosaic patterns of change. Relatively few prior studies have used discrete morphological character data in a phylogenetic context to quantitatively investigate morphological evolution or mosaic evolution in particular. One such previously employed method, which used summed unambiguously optimized synapomorphies, has been the basis for proposing disassociated and sequential "modernizing" or "fine-tuning" of pectoral and then pelvic locomotor systems after the origin of flight ("pectoral early-pelvic late" hypothesis). We use one of the most inclusive phylogenetic data sets of basal birds to investigate properties of this method and to consider the application of a Bayesian phylogenetic approach. Bayes factor and statistical comparisons of branch length estimates were used to evaluate support for a mosaic pattern of character change and the specific pectoral early-pelvic late hypothesis. Partitions were defined a priori based on anatomical subregion (e.g., pelvic, pectoral) and were based on those hypothesized using the summed synapomorphy approach. We compare 80 models all implementing the M(k) model for morphological data but varying in the number of anatomical subregion partitions, the models for among-partition rate variation and among-character rate variation, as well as the branch length prior. Statistical analysis reveals that partitioning data by anatomical subregion, independently estimating branch lengths for partitioned data, and use of shared or per partition gamma-shaped among-character rate distribution significantly increases estimated model likelihoods. Simulation studies reveal that partitioned models where characters are randomly assigned perform significantly worse than both the observed model and the single-partition equal-rate model, suggesting that only partitioning by anatomical subregion increases model performance. The preference for models with partitions defined a priori by anatomical subregion is consistent with a disjunctive pattern of character change for the data set investigated and may have implications for parameterization of Bayesian analyses of morphological data more generally. Statistical tests of differences in estimated branch lengths from the pectoral and pelvic partitions do not support the specific pectoral early-pelvic late hypothesis proposed from the summed synapomorphy approach; however, results suggest limited support for some pectoral branch lengths being significantly longer only early at/after the origin of flight.     

Optimal data partitioning and a test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci

Data partitioning, the combined phylogenetic analysis of homogeneous blocks of data, is a common strategy used to accommodate heterogeneities in complex multilocus data sets. Variation in evolutionary rates and substitution patterns among sites are typically addressed by partitioning data by gene, codon position, or both. Excessive partitioning of the data, however, could lead to overparameterization; therefore, it seems critical to define the minimum numbers of partitions necessary to improve the overall fit of the model. We propose a new method, based on cluster analysis, to find an optimal partitioning strategy for multilocus protein-coding data sets. A heuristic exploration of alternative partitioning schemes, based on Bayesian and maximum likelihood (ML) criteria, is shown here to produce an optimal number of partitions. We tested this method using sequence data of 10 nuclear genes collected from 52 ray-finned fish (Actinopterygii) and four tetrapods. The concatenated sequences included 7995 nucleotide sites maximally split into 30 partitions defined a priori based on gene and codon position. Our results show that a model based on only 10 partitions defined by cluster analysis performed better than partitioning by both gene and codon position. Alternative data partitioning schemes also are shown to affect the topologies resulting from phylogenetic analysis, especially when Bayesian methods are used, suggesting that overpartitioning may be of major concern. The phylogenetic relationships among the major clades of ray-finned fish were assessed using the best data-partitioning schemes under ML and Bayesian methods. Some significant results include the monophyly of "Holostei" (Amia and Lepisosteus), the sister-group relationships between (1) esociforms and salmoniforms and (2) osmeriforms and stomiiforms, the polyphyly of Perciformes, and a close relationship of cichlids and atherinomorphs.     

Attributes and congruence of three molecular data sets: inferring phylogenies among Septoria-related species from woody perennial plants

To improve our understanding of phylogenetic relationships within the anamorphic genus Septoria, three molecular data sets representing 2,417 bp of nuclear and mitochondrial genes were evaluated. Separate gene analyses and combined analyses were performed using first, the maximum parsimony criterion and second, a Bayesian framework. The homogeneity of data partitions was evaluated via a combination of homogeneity partition tests and tree topology incongruence tests before conducting combined analyses. A last incongruence re-evaluation using partitioned Bremer support was performed on the combined tree, which corroborated the previous estimates. After each separate data set attributes were examined, simple explanations were advocated as the causes of the significant incongruences detected. The analysis of multiple gene partitions showed unprecedented phylogenetic resolution within the genus Septoria that supported the results from previously published single gene phylogenies. Specifically, we have delimited distinct but closely related species representing monophyletic groups that frequently correlated with their respective host families. Conversely, the occurrence of well-supported groups including closely related but distinct molecular taxa sampled on unrelated host-plants allowed us to reject, in these particular cases, the co-evolutionary concept expected between a parasite and its host and to discuss alternative evolutionary models recently proposed for these pathogens.     

An early divergence of KhoeSan ancestors from those of other modern humans is supported by an ABC-based analysis of autosomal resequencing data

Sub-Saharan Africa has consistently been shown to be the most genetically diverse region in the world. Despite the fact that a substantial portion of this variation is partitioned between groups practicing a variety of subsistence strategies and speaking diverse languages, there is currently no consensus on the genetic relationships of sub-Saharan African populations. San (a subgroup of KhoeSan) and many Pygmy groups maintain hunter-gatherer lifestyles and cluster together in autosomal-based analysis, whereas non-Pygmy Niger-Kordofanian speakers (non-Pygmy NKs) predominantly practice agriculture and show substantial genetic homogeneity despite their wide geographic range throughout sub-Saharan Africa. However, KhoeSan, who speak a set of relatively unique click-based languages, have long been thought to be an early branch of anatomically modern humans based on phylogenetic analysis. To formally test models of divergence among the ancestors of modern African populations, we resequenced a sample of San, Eastern, and Western Pygmies and non-Pygmy NKs individuals at 40 nongenic (～2 kb) regions and then analyzed these data within an Approximate Bayesian Computation (ABC) framework. We find substantial support for a model of an early divergence of KhoeSan ancestors from a proto-Pygmy-non-Pygmy NKs group ～110 thousand years ago over a model incorporating a proto-KhoeSan-Pygmy hunter-gatherer divergence from the ancestors of non-Pygmy NKs. The results of our analyses are consistent with previously identified signals of a strong bottleneck in Mbuti Pygmies and a relatively recent expansion of non-Pygmy NKs. We also develop a number of methodologies that utilize "pseudo-observed" data sets to optimize our ABC-based inference. This approach is likely to prove to be an invaluable tool for demographic inference using genome-wide resequencing data.     

Methods for selecting fixed-effect models for heterogeneous codon evolution,with comments on their application to gene and genome data

Background

Models of codon evolution have proven useful for investigating the strength and direction of natural selection. In some cases, a priori biological knowledge has been used successfully to model heterogeneous evolutionary dynamics among codon sites. These are called fixed-effect models, and they require that all codon sites are assigned to one of several partitions which are permitted to have independent parameters for selection pressure, evolutionary rate, transition to transversion ratio or codon frequencies. For single gene analysis, partitions might be defined according to protein tertiary structure, and for multiple gene analysis partitions might be defined according to a gene's functional category. Given a set of related fixed-effect models, the task of selecting the model that best fits the data is not trivial.

Results

In this study, we implement a set of fixed-effect codon models which allow for different levels of heterogeneity among partitions in the substitution process. We describe strategies for selecting among these models by a backward elimination procedure, Akaike information criterion (AIC) or a corrected Akaike information criterion (AICc). We evaluate the performance of these model selection methods via a simulation study, and make several recommendations for real data analysis. Our simulation study indicates that the backward elimination procedure can provide a reliable method for model selection in this setting. We also demonstrate the utility of these models by application to a single-gene dataset partitioned according to tertiary structure (abalone sperm lysin), and a multi-gene dataset partitioned according to the functional category of the gene (flagellar-related proteins of Listeria).

Conclusion

Fixed-effect models have advantages and disadvantages. Fixed-effect models are desirable when data partitions are known to exhibit significant heterogeneity or when a statistical test of such heterogeneity is desired. They have the disadvantage of requiring a priori knowledge for partitioning sites. We recommend: (i) selection of models by using backward elimination rather than AIC or AICc, (ii) use a stringent cut-off, e.g., p = 0.0001, and (iii) conduct sensitivity analysis of results. With thoughtful application, fixed-effect codon models should provide a useful tool for large scale multi-gene analyses.

     

Dynamically heterogenous partitions and phylogenetic inference: an evaluation of analytical strategies with cytochrome b and ND6 gene sequences in cranes

ki ctes over whether molecular sequence data should be partitioned for phylogenetic analysis often confound two types of heterogeneity among partitions. We distinguish historical heterogeneity (i.e., different partitions have different evolutionary relationships) from dynamic heterogeneity (i.e., different partitions show different patterns of sequence evolution) and explore the impact of the latter on phylogenetic accuracy and precision with a two-gene, mitochondrial data set for cranes. The well-established phylogeny of cranes allows us to contrast tree-based estimates of relevant parameter values with estimates based on pairwise comparisons and to ascertain the effects of incorporating different amounts of process information into phylogenetic estimates. We show that codon positions in the cytochrome b and NADH dehydrogenase subunit 6 genes are dynamically heterogenous under both Poisson and invariable-sites + gamma-rates versions of the F84 model and that heterogeneity includes variation in base composition and transition bias as well as substitution rate. Estimates of transition-bias and relative-rate parameters from pairwise sequence comparisons were comparable to those obtained as tree-based maximum likelihood estimates. Neither rate-category nor mixed-model partitioning strategies resulted in a loss of phylogenetic precision relative to unpartitioned analyses. We suggest that weighted-average distances provide a computationally feasible alternative to direct maximum likelihood estimates of phylogeny for mixed-model analyses of large, dynamically heterogenous data sets.     

Assessing the phylogenetic utility of four mitochondrial genes and a nuclear intron in the asian pit viper genus,Trimeresurus: separate,simultaneous, and conditional data combination analyses

A number of methods have been proposed for addressing how to optimize the analysis of multiple data sets from diverse mitochondrial and nuclear gene partitions in the pursuit of robust organismal phylogenies. The present study used separate, simultaneous, and conditional data combination methods to analyze 3,135 bp of data from four mitochondrial partitions and the seventh intron of the beta fibrinogen gene in the Asian pit viper genus, Trimeresurus sensu stricto. The phylogenetic utility and homogeneity of all partitions were estimated via a combination of homogeneity partition tests, homoplasy indices, and partitioned Bremer support. Despite the detection of significant heterogeneity of phylogenetic signal between the mitochondrial and nuclear partitions, the simultaneous analysis represented the best-supported topology of all the data. The relatively slow rate (approximately one quarter of the rate of mtDNA) and functionally unconstrained molecular evolution of the intron resulted in much lower levels of homoplasy compared with the mitochondrial partitions. This was further shown via partitioned Bremer support, which, when considered throughout hierarchical clade levels, highlighted the phylogenetic strength and limitations of the intron at deeper and shallower phylogenetic levels, respectively. The simultaneous analysis helped to resolve the phylogenetic relationships of taxa that were unresolved throughout all individual gene trees and tentatively supports the existence of morphologically and genetically distinct clades within the genus. Topological appraisals of the mitochondrial gene partitions suggest that the cytochrome b and the NADH subunit 4 gene partitions are better estimators of phylogenetic relationships than are the 12S and 16S ribosomal RNA partitions at the taxonomic levels under consideration.     

Combined mitochondrial and nuclear sequences support the monophyly of forcipulatacean sea stars

Previous molecular phylogenetic analyses of forcipulatacean sea stars (Echinodermata: Asteroidea) have reconstructed a non-monophyletic order Forcipulatida, provided that two or more forcipulate families are included. This result could mean that one or more assumptions of the reconstruction method was violated, or else the traditional classification could be erroneous. The present molecular phylogenetic analysis included 12 non-forcipulatacean and 39 forcipulatacean sea stars, with multiple representatives of all but one of the forcipulate families and/or subfamilies. Bayesian analysis of approximately 4.2kb of sequence data representing seven partitions (nuclear 18S rRNA and 28S rRNA, mitochondrial 12S rRNA, 16S rRNA, 5 tRNAs and cytochrome oxidase I with first and second codon positions analyzed separately from third codon positions) recovered a consensus tree with three well-supported clades (78%-100% bootstrap support) that corresponded at least approximately to traditional taxonomic ranks: the superorder Forcipulatacea (Forcipulatida + Brisingida) + Pteraster, the Brisingida/Brisingidae and Asteriidae + Rathbunaster + Pycnopodia. When a molecular clock was enforced, the partitioned Bayesian analysis recovered the traditional Forcipulatacea. Five of six genera represented by two or more species were monophyletic with 100% bootstrap support. Most of the traditional subfamilial and familial groupings within the Forcipulatida were either unresolved or non-monophyletic. The separate partitions differed considerably in estimates of model parameters, mainly between nuclear sequences (with high GC content, low rates of sequence substitution and high transition/transversion rate ratios) and mitochondrial sequences.     

Remarkable phylogenetic resolution of the most complex clade of Cyprinidae (Teleostei: Cypriniformes): A proof of concept of homology assessment and partitioning sequence data integrated with mixed model Bayesian analyses

Despite many efforts to resolve evolutionary relationships among major clades of Cyprinidae, some nodes have been especially problematic and remain unresolved. In this study, we employ four nuclear gene fragments (3.3 kb) to infer interrelationships of the Cyprinidae.A reconstruction of the phylogenetic relationships within the family using maximum parsimony, maximum likelihood, and Bayesian analyses is presented. Among the taxa within the monophyletic Cyprinidae, Rasborinae is the basal-most lineage; Cyprinine is sister to Leuciscine. The monophyly for the subfamilies Gobioninae, Leuciscinae and Acheilognathinae were resolved with high nodal support. Although our results do not completely resolve relationships within Cyprinidae, this study presents novel and significant findings having major implications for a highly diverse and enigmatic clade of East-Asian cyprinids. Within this monophyletic group five closely-related subgroups are identified. Tinca tinca, one of the most phylogenetically enigmatic genera in the family, is strongly supported as having evolutionary affinities with this East-Asian clade; an established yet remarkable association because of the natural variation in phenotypes and generalized ecological niches occupied by these taxa.Our results clearly argue that the choice of partitioning strategies has significant impacts on the phylogenetic reconstructions, especially when multiple genes are being considered. The most highly partitioned model (partitioned by codon positions within genes) extracts the strongest phylogenetic signals and performs better than any other partitioning schemes supported by the strongest 2Δln Bayes factor. Future studies should include higher levels of taxon sampling and partitioned, model-based analyses.     

Testing heterogeneous base composition as potential cause for conflicting phylogenetic signal between mitochondrial and nuclear DNA in the land snail genus <Emphasis Type="Italic">Theba</Emphasis> Risso 1826 (Gastropoda: Stylommatophora: Helicoidea)

Several pitfalls can mislead phylogenetic analyses based on molecular data, including heterogeneous base composition. Previous work has revealed conflicting topologies in analyses of the land snail genus Theba Risso 1826 based on mitochondrial cytochrome oxidase subunit I (COI) and nuclear AFLP data, respectively. However, the third codon positions of COI had heterogeneous base composition, prompting the present investigation asking specifically if this was the cause for the mito-nuclear discordance. For a potentially better resolution of the mitochondrial data, we also sequenced a fragment of 16S rRNA, the loop sections of which proved to have inhomogeneous base frequencies as well. In partitioned phylogenetic analyses, we compared topologies generated from the original data to those based on alignments in which the heterogeneous partitions were RY-coded and to a LogDet transformed distance analysis. In addition, we tested whether conventional Bayesian analyses would reconstruct the original topology from inhomogeneous data simulated based on this original topology. All our analyses, regardless of whether we accounted for heterogeneous base frequencies or not, revealed very similar topologies, confirming previous findings. Thus, the phylogenetic signal of mtDNA in the land snail genus Theba appeared to be robust despite considerable inhomogeneity of base composition. Therefore, the discordance of mitochondrial and nuclear topologies is probably real and most likely a consequence of incomplete lineage sorting.     

Inferences of biogeographical histories within subfamily Hyacinthoideae using S-DIVA and Bayesian binary MCMC analysis implemented in RASP (Reconstruct Ancestral State in Phylogenies)

Background and Aims

Subfamily Hyacinthoideae (Hyacinthaceae) comprises more than 400 species. Members are distributed in sub-Saharan Africa, Madagascar, India, eastern Asia, the Mediterranean region and Eurasia. Hyacinthoideae, like many other plant lineages, show disjunct distribution patterns. The aim of this study was to reconstruct the biogeographical history of Hyacinthoideae based on phylogenetic analyses, to find the possible ancestral range of Hyacinthoideae and to identify factors responsible for the current disjunct distribution pattern.

Methods

Parsimony and Bayesian approaches were applied to obtain phylogenetic trees, based on sequences of the trnL-F region. Biogeographical inferences were obtained by applying statistical dispersal-vicariance analysis (S-DIVA) and Bayesian binary MCMC (BBM) analysis implemented in RASP (Reconstruct Ancestral State in Phylogenies).

Key Results

S-DIVA and BBM analyses suggest that the Hyacinthoideae clade seem to have originated in sub-Saharan Africa. Dispersal and vicariance played vital roles in creating the disjunct distribution pattern. Results also suggest an early dispersal to the Mediterranean region, and thus the northward route (from sub-Saharan Africa to Mediterranean) of dispersal is plausible for members of subfamily Hyacinthoideae.

Conclusions

Biogeographical analyses reveal that subfamily Hyacinthoideae has originated in sub-Saharan Africa. S-DIVA indicates an early dispersal event to the Mediterranean region followed by a vicariance event, which resulted in Hyacintheae and Massonieae tribes. By contrast, BBM analysis favours dispersal to the Mediterranean region, eastern Asia and Europe. Biogeographical analysis suggests that sub-Saharan Africa and the Mediterranean region have played vital roles as centres of diversification and radiation within subfamily Hyacinthoideae. In this bimodal distribution pattern, sub-Saharan Africa is the primary centre of diversity and the Mediterranean region is the secondary centre of diversity. Sub-Saharan Africa was the source area for radiation toward Madagascar, the Mediterranean region and India. Radiations occurred from the Mediterranean region to eastern Asia, Europe, western Asia and India.     

Data partitions and complex models in Bayesian analysis: the phylogeny of Gymnophthalmid lizards

Phylogenetic studies incorporating multiple loci, and multiple genomes, are becoming increasingly common. Coincident with this trend in genetic sampling, model-based likelihood techniques including Bayesian phylogenetic methods continue to gain popularity. Few studies, however, have examined model fit and sensitivity to such potentially heterogeneous data partitions within combined data analyses using empirical data. Here we investigate the relative model fit and sensitivity of Bayesian phylogenetic methods when alternative site-specific partitions of among-site rate variation (with and without autocorrelated rates) are considered. Our primary goal in choosing a best-fit model was to employ the simplest model that was a good fit to the data while optimizing topology and/or Bayesian posterior probabilities. Thus, we were not interested in complex models that did not practically affect our interpretation of the topology under study. We applied these alternative models to a four-gene data set including one protein-coding nuclear gene (c-mos), one protein-coding mitochondrial gene (ND4), and two mitochondrial rRNA genes (12S and 16S) for the diverse yet poorly known lizard family Gymnophthalmidae. Our results suggest that the best-fit model partitioned among-site rate variation separately among the c-mos, ND4, and 12S + 16S gene regions. We found this model yielded identical topologies to those from analyses based on the GTR+I+G model, but significantly changed posterior probability estimates of clade support. This partitioned model also produced more precise (less variable) estimates of posterior probabilities across generations of long Bayesian runs, compared to runs employing a GTR+I+G model estimated for the combined data. We use this three-way gamma partitioning in Bayesian analyses to reconstruct a robust phylogenetic hypothesis for the relationships of genera within the lizard family Gymnophthalmidae. We then reevaluate the higher-level taxonomic arrangement of the Gymnophthalmidae. Based on our findings, we discuss the utility of nontraditional parameters for modeling among-site rate variation and the implications and future directions for complex model building and testing.     

Monophyly, phylogenetic position and inter-familial relationships of the Alepocephaliformes (Teleostei) based on whole mitogenome sequences

Recent mitogenomic studies suggest a new position for the deep-sea fishes of the order Alepocephaliformes, placing them within the Otocephala in contrast to their traditional placement within the Euteleostei. However, these studies included only two alepocephaliform taxa and left several questions unsolved about their systematics. Here we use whole mitogenome sequences to reconstruct phylogenetic relationships for 11 alepocephaliform taxa, sampled from all five nominal families, and a large selection of non-alepocephaliform teleosts, to address the following three questions: (1) is the Alepocephaliformes monophyletic, (2) what is its phylogenetic position within the Teleostei and (3) what are the relationships among the alepocephaliform families? Our character sets, including unambiguously aligned, concatenated mitogenome sequences that we have divided into four (first and second codon positions, tRNA genes, and rRNA genes) or five partitions (same as before plus the transversions at third codon positions, using "RY" coding), were analyzed by the partitioned maximum likelihood and Bayesian methods. Our result strongly supported the monophyly of the Alepocephaliformes and its close relationship to the Clupeiformes and Ostariophysi. Altogether, these three groups comprise the Otocephala. Statistical comparison using likelihood-based SH test confidently rejected the monophyly of the Euteleostei when including the Alepocephaliformes. However, increasing the taxonomic sampling within the Alepocephaliformes did not resolve its position relative to the Clupeiformes and Ostariophysi. Within the Alepocephaliformes, our results strongly supported the monophyly of the platytroctid genera but not that of the remaining taxa. From one analysis to other, platytroctids were either the sister group of the remaining taxa or nested within the alepocephalids. Inferred relationships among alepocephaliform taxa were not congruent with any of the previously published phylogenetic hypotheses based on morphological characters.     

Sources of incongruence among mammalian mitochondrial sequences: COII, COIII, and ND6 genes are main contributors

To investigate the origins of incongruence among mammalian mitochondrial protein-coding genes, we compiled a matrix that included 13 protein-coding-genes for 41 mammals from 14 different orders. This matrix was examined for congruence using different partitioning strategies. The incongruence length difference test showed significant incongruence among the 13 gene partitions used simultaneously, and the result was not affected by third codon or transversion weighting. In the pair-wise comparisons, significant incongruence was detected between NADH:ubiquinone oxidoreductase subunit 6 gene (ND6), cytochrome oxidase subunit II (COII), or cytochrome oxidase subunit III (COIII) gene partitioned individually against the rest of the genes. Omission of any of the 14 mammalian orders alone or in combinations from the matrix did not result in a statistically significant improvement of congruence, suggesting that taxonomic sampling will not improve congruence among the data sets. However, omission of the ND6, COII, and COIII significantly improved congruence in our data matrix. Possible origins of unusual phylogenetic properties of the three genes are discussed.     

From Africa via Europe to South America: migrational route of a species‐rich genus of Neotropical lowland rain forest trees (Guatteria,Annonaceae)

Aim Several recent studies have suggested that a substantial portion of today’s plant diversity in the Neotropics has resulted from the dispersal of taxa into that region rather than by vicariance. In general, three routes have been documented for the dispersal of taxa onto the South American continent: (1) via the North Atlantic Land Bridge, (2) via the Bering Land Bridge, or (3) from Africa directly onto the continent. Here a species‐rich genus of Neotropical lowland rain forest trees (Guatteria, Annonaceae) is used as a model to investigate these three hypotheses. Location The Neotropics. Methods The phylogenetic relationships within the long‐branch clade of Annonaceae were reconstructed (using maximum parsimony, maximum likelihood and Bayesian inference) in order to gain insight in the phylogenetic position of Guatteria. Furthermore, Bayesian molecular dating and Bayesian dispersal–vicariance (Bayes‐DIVA) analyses were undertaken. Results Most of the relationships within the long‐branch clade of Annonaceae were reconstructed and had high support. However, the relationship between the Duguetia clade, the Xylopia–Artabotrys clade and Guatteria remained unclear. The stem node age estimate of Guatteria ranged between 49.2 and 51.3 Ma, whereas the crown node age estimate ranged between 11.4 and 17.8 Ma. For the ancestral area of Guatteria and its sister group, the area North America–Africa was reconstructed in 99% of 10,000 DIVA analyses, while South America–North America was found just 1% of the time. Main conclusions The estimated stem to crown node ages of Guatteria in combination with the Bayes‐DIVA analyses imply a scenario congruent with an African origin followed by dispersal across the North Atlantic Land Bridge in the early to middle Eocene and further dispersal into North and Central America (and ultimately South America) in the Miocene. The phylogenetically and morphologically isolated position of the genus is probably due to extinction of the North American and European stem lineages in the Tertiary.     

Molecular phylogenetics of the allodapine bee genus Braunsapis: A-T bias and heterogeneous substitution parameters

Extreme AT bias in Hymenopteran mitochondrial genes have created difficulties for molecular phylogenetic analyses, especially for older divergences where multiple substitutions can erode signal. Heterogeneity in the evolutionary rates of different codon positions and different genes also appears to have been a major problem in resolving ancient divergences in allodapine bees. Here we examine the phylogeny of relatively recent divergences in the allodapine bee genus Braunsapis. We examined heterogeneity in nucleotide substitution parameters for one nuclear gene and codon positions in two mitochondrial genes, exploring various phylogenetic analyses for recovering relationships among species from Africa, Madagascar, southern Asia, and Australia. We explored maximum parsimony, maximum likelihood, Log determinant and Bayesian analyses. Broad topological features of best fit trees tended to be similar for equivalent data sets (e.g., total, or with 3rd mt positions excluded), regardless of the analytic method used (e.g., maximum likelihood or Bayesian). Analyses that used the total data set without modelling partitions separately gave unlikely results, indicating that the Malagasy species was most closely related to Australian species. However, analyses that excluded 3rd mitochondrial positions, or modelled partitions separately, suggested that the Malagasy species falls within the African clade. The unlikely topologies apparently result from long branch attraction, and this problem is ameliorated where modelling allows more realistic estimates of base composition and evolutionary rates for 3rd mitochondrial positions. However, we found that even when codon positions are modelled separately, estimated evolutionary rates for 3rd mitochondrial positions are likely to underestimate true rates. Long branch attraction and multiple substitutions are likely to be much more difficult to circumvent in analyses that explore older, generic-level, divergences in allodapine bees where overwriting is expected to be much more extreme. Our results indicate an African origin for Braunsapis, followed by a single, very early, dispersal event into Asia and then by a later dispersal event into Australia. The Malagasy species is derived from within the African clade.     

Genomic ancestry of North Africans supports back-to-Africa migrations

North African populations are distinct from sub-Saharan Africans based on cultural, linguistic, and phenotypic attributes; however, the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood. Here, we interrogate the multilayered history of North Africa by characterizing the effect of hypothesized migrations from the Near East, Europe, and sub-Saharan Africa on current genetic diversity. We present dense, genome-wide SNP genotyping array data (730,000 sites) from seven North African populations, spanning from Egypt to Morocco, and one Spanish population. We identify a gradient of likely autochthonous Maghrebi ancestry that increases from east to west across northern Africa; this ancestry is likely derived from "back-to-Africa" gene flow more than 12,000 years ago (ya), prior to the Holocene. The indigenous North African ancestry is more frequent in populations with historical Berber ethnicity. In most North African populations we also see substantial shared ancestry with the Near East, and to a lesser extent sub-Saharan Africa and Europe. To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the distribution of migrant tracts. In order to first identify migrant tracts, we assign local ancestry to haplotypes using a novel, principal component-based analysis of three ancestral populations. We estimate that a migration of western African origin into Morocco began about 40 generations ago (approximately 1,200 ya); a migration of individuals with Nilotic ancestry into Egypt occurred about 25 generations ago (approximately 750 ya). Our genomic data reveal an extraordinarily complex history of migrations, involving at least five ancestral populations, into North Africa.     

Global relationships of Bemisia tabaci (Hemiptera: Aleyrodidae) revealed using Bayesian analysis of mitochondrial COI DNA sequences

Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a species complex that is one of the most devastating agricultural pests worldwide and affects a broad range of food, fiber and ornamental crops. Unfortunately, using parsimony and neighbor joining methods, global phylogenetic relationships of the major races/biotypes of B. tabaci remain unresolved. Aside from the limitations of these methods, phylogenetic analyses have been limited to only small subsets of the global collection of B. tabaci, and thus limited taxon sampling has confounded the analyses. To improve our understanding of global B. tabaci phylogenetic relationships, a Bayesian phylogenetic technique was utilized to elucidate the relationships among all COI DNA sequence data available in GenBank for B. tabaci worldwide (366 specimens). As a result, the first well-resolved phylogeny for the B. tabaci species complex was produced showing 12 major well-resolved (0.70 posterior probability or above) genetic groups: B. tabaci (Mediterranean/Asia Minor/Africa), B. tabaci (Mediterranean), B. tabaci (Indian Ocean), B. tabaci (sub-Saharan Africa silverleafing), B. tabaci (Asia I), B. tabaci (Australia), B. tabaci (China), B. tabaci (Asia II), B. tabaci (Italy), B. tabaci (New World), B. tabaci (sub-Saharan Africa non-silverleafing) and B. tabaci (Uganda sweet potato). Further analysis of this phylogeny shows a close relationship of the New World B. tabaci with Asian biotypes, and characteristics of the major sub-Saharan Africa non-silverleafing clade strongly supports an African origin of B. tabaci due to its position at the base of the global phylogeny, and the diversity of well-resolved sub-clades within this group. Bayesian re-analyses of B. tabaci ITS, COI, and a combined dataset from a previous study resulted in seven major well-resolved races with high posterior probabilities, also showing the utility of the Bayesian method. Relationships of the 12 major B. tabaci genetic groups are discussed herein.