EvoLaps: a web interface to visualize continuous phylogeographic reconstructions.

BACKGROUND: Phylogeographic reconstructions serve as a basis to understand the spread and evolution of pathogens. Visualization of these reconstructions often lead to complex graphical representations which are difficult to interpret. RESULT: We present EvoLaps, a user-friendly web interface to visualize phylogeographic reconstructions based on the analysis of latitude/longitude coordinates with various clustering levels. EvoLaps also produces transition diagrams that provide concise and easy to interpret summaries of phylogeographic reconstructions. CONCLUSION: The main contribution of EvoLaps is to assemble known numerical and graphical methods/tools into a user-friendly interface dedicated to the visualization and edition of evolutionary scenarios based on continuous phylogeographic reconstructions. EvoLaps is freely usable at www.evolaps.org .

PastView: a user-friendly interface to explore ancestral scenarios.

BACKGROUND: Ancestral character states computed from the combination of phylogenetic trees with extrinsic traits are used to decipher evolutionary scenarios in various research fields such as phylogeography, epidemiology, and ecology. Despite the existence of powerful methods and software in ancestral character state inference, difficulties may arise when interpreting the outputs of such inferences. The growing complexity of data (trees, annotations), the diversity of optimization criteria for computing trees and ancestral character states, the combinatorial explosion of potential evolutionary scenarios if some ancestral characters states do not stand out clearly from others, requires the design of new methods to explore associations of phylogenetic trees with extrinsic traits, to ease the visualization and interpretation of evolutionary scenarios. RESULT: We developed PastView, a user-friendly interface that includes numerical and graphical features to help users to import and/or compute ancestral character states from discrete variables and extract ancestral scenarios as sets of successive transitions of character states from the tree root to its leaves. PastView provides summarized views such as transition maps and integrates comparative tools to highlight agreements or discrepancies between methods of ancestral annotations inference. CONCLUSION: The main contribution of PastView is to assemble known numerical and graphical methods into a multi-maps graphical user interface dedicated to the computing, searching and viewing of evolutionary scenarios based on phylogenetic trees and ancestral character states. PastView is available publicly as a standalone software on www.pastview.org .

Molecular phylogeny of Macrosiphini (Hemiptera: Aphididae): An evolutionary hypothesis for the Pterocomma-group habitat adaptation.

The aphid tribe Macrosiphini Wilson, 1910 (Hemiptera: Aphididae: Aphidinae) is one of the most controversial groups within Aphididae. We sequenced 2876 bp from one nuclear gene (EF-1α) and four mitochondrial genes (COI, tRNA + COII, 16S) from 107 terminal taxa representing 57 genera of Macrosiphini s.l. (the former Macrosiphini + genera in former Pterocommatini), including all of the recognized major genera and outgroups, and reconstructed the phylogeny using maximum likelihood, maximum parsimony and Bayesian methods. The stepping-stone method was used to evaluate various topological hypotheses regarding Macrosiphini s.l. and related groups. Our findings support both the monophyly of Macrosiphini s.l., and of two subordinate groups (Macrosiphini s.str and the Pterocomma-group), as well as the transfer of Capitophorus, Pleotrichophorus, Liosomaphis and Vesiculaphis to the Pterocomma-group-a result not previously suggested by analyses of molecular data. Ancestral state reconstructions for Macrosiphini and the Pterocomma-group suggest an ancestral primary host association with Rosales and Malpighiales, respectively, and other host associations within the tribe. Host transitions independently occurred more than once in Macrosiphini s.str. Furthermore, host-shifts between Rosales and Malpighiales may have occurred at least once in the Pterocomma-group. Additionally, the Macrosiphini phylogeny indicates that host associations are consistent also with host ecology, with a partitioning of aphid-host relationships into riparian and periaquatic habitats versus drier forest/shrubland habitats.

Combining high-throughput sequencing and targeted loci data to infer the phylogeny of the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae).

Combining high-throughput sequencing data with amplicon sequences allows the reconstruction of robust phylogenies based on comprehensive sampling of characters and taxa. Here, we combine Next Generation Sequencing (NGS) and Sanger sequencing data to infer the phylogeny of the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae), a diverse lineage of Neotropical plants, using Maximum Likelihood and Bayesian approaches. We used NGS to obtain complete or nearly-complete plastomes of members of this clade, leading to a final dataset with 54 individuals, representing 44 members of ingroup and 10 outgroups. In addition, we obtained Sanger sequences of two plastid markers (ndhF and rpl32-trnL) for 44 individuals (43 ingroup and 1 outgroup) and the nuclear PepC for 64 individuals (63 ingroup and 1 outgroup). Our final dataset includes 87 individuals of members of the "Adenocalymma-Neojobertia" clade, representing 66 species (ca. 90% of the diversity), plus 11 outgroups. Plastid and nuclear datasets recovered congruent topologies and were combined. The combined analysis recovered a monophyletic "Adenocalymma-Neojobertia" clade and a paraphyletic Adenocalymma that also contained a monophyletic Neojobertia plus Pleonotoma albiflora. Relationships are strongly supported in all analyses, with most lineages within the "Adenocalymma-Neojobertia" clade receiving maximum posterior probabilities. Ancestral character state reconstructions using Bayesian approaches identified six morphological synapomorphies of clades namely, prophyll type, petiole and petiolule articulation, tendril ramification, inflorescence ramification, calyx shape, and fruit wings. Other characters such as habit, calyx cupular trichomes, corolla color, and corolla shape evolved multiple times. These characters are putatively related with the clade diversification and can be further explored in diversification studies.

Evolution of larval life mode of Oecophoridae (Lepidoptera: Gelechioidea) inferred from molecular phylogeny.

Phylogenetic relationships within family Oecophoridae have been poorly understood. Consequently the subfamily and genus level classifications with this family problematic. A comprehensive phylogenetic analysis of Oecophoridae, the concealer moths, was performed based on analysis of 4444 base pairs of mitochondrial COI, nuclear ribosomal RNA genes (18S and 28S) and nuclear protein coding genes (IDH, MDH, Rps5, EF1a and wingless) for 82 taxa. Data were analyzed using maximum likelihood (ML), parsimony (MP) and Bayesian (BP) phylogenetic frameworks. Phylogenetic analyses indicated that (i) genera Casmara, Tyrolimnas and Pseudodoxia did not belong to Oecophoridae, suggesting that Oecophoridae s. authors was not monophyletic; (ii) other oecophorids comprising two subfamilies, Pleurotinae and Oecophorinae, were nested within the same clade, and (iii) Martyringa, Acryptolechia and Periacmini were clustered with core Xyloryctidae. They appeared to be sister lineage with core Oecophoridae. BayesTraits were implemented to explore the ancestral character states to infer historical microhabitat patterns and sheltering strategy of larvae. Reconstruction of ancestral microhabitat of oecophorids indicated that oecophorids might have evolved from dried plant feeders and further convergently specialized. The ancestral larva sheltering strategy of oecophorids might have used a silk tube by making itself, shifting from mining leaves.

Speciation within Columnea section Angustiflora (Gesneriaceae): islands, pollinators and climate.

Despite many advances in evolutionary biology, understanding the proximate mechanisms that lead to speciation for many taxonomic groups remains elusive. Phylogenetic analyses provide a means to generate well-supported estimates of species relationships. Understanding how genetic isolation (restricted gene flow) occurred in the past requires not only a well-supported molecular phylogenetic analysis, but also an understanding of when character states that define species may have changed. In this study, phylogenetic trees resolve species level relationships for fourteen of the fifteen species within Columnea section Angustiflorae (Gesneriaceae). The distributions of sister species pairs are compared and ancestral character states are reconstructed using Bayesian stochastic mapping. Climate variables were also assessed and shifts in ancestral climate conditions were mapped using SEEVA. The relationships between morphological character states and climate variables were assessed with correlation analyses. These results indicate that species in section Angustiflorae have likely diverged as a result of allopatric, parapatric, and sympatric speciation, with both biotic and abiotic forces driving morphological and phenological divergence.

Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach.

Morphology of Phasmatodea eggs is remarkably diverse and highly valuable in taxonomic research. Two alterative hypotheses have been proposed to describe the phylogenetic relationship of the species from the genus Agathemera Stål. Additionally, descriptions of the egg morphology within Agathemera have been done based on the eggs of two species. This small sample size does not represent the diverse egg morphology along the genus, thus we attempt to describe the eggs from all the known Agathemera species. The main goal of the present study is to determine whether the evolution of the eggs occurred through either divergent or convergent evolution. We based our descriptions on morphometrics, morphology and the ultrastructure. For data analysis, principal component analysis (PCA) was performed on morphometric variables and the characters emerged from the morphological and ultrastructure were mapped over the molecular phylogeny. The results show that it is possible to discriminate among species using the morphology of the different egg structures, and furthermore, a divergent event at the base of the tree, differentiate the overall egg shape and the internal micropylar plate shape. Finally, we conclude that both divergent and convergent evolution are shaping the different structures of the Agathemera eggs.

Evolutionary implications of the distribution and variation of the skeletal muscles of the anuran lymphatic system.

Lymphatic return to the circulation in anurans is dependent upon the interaction of a number of skeletal muscles and lung deflation. We define character states and describe variation of these putative lymphatic skeletal muscles: the M. cutaneus pectoris (CP), M. cutaneus dorsi (CD), M. piriformis (P), M. sphincter ani cloacalis (SAC), and the complex of the M. gracilis minor/M. abdominal crenator (GM/AC). We include examination of over 400 specimens of 377 species belonging to 40 of the 42 currently recognized anuran families. Some muscles show limited variation (P) or are clearly linked to phylogeny (CP; CD) and thus have limited value in the determination of form and function. However, the GM/AC and SAC show a high degree of structural variation that appears in taxa across the phylogenetic spectrum. This allows us to make phylogenetically independent determinations of form and function. We define an ancestral state of the GM and conclude that evolution of the GM/AC and SAC has progressed in two directions from this ancestral state: toward either elaboration or reduction. Where present, the character states of both of these muscle groups were observed in all species examined and the number of states correlated within each family as well. The degree of development of the GM/AC and SAC compliance pump system is strongly correlated with previously determined lymph flux rates in a three species test. Our data suggest there may be a relationship between greater elaboration of the GM/AC and SAC system and terrestriality among the Anura.