Fluctuations in Evolutionary Integration Allow for Big Brains and Disparate Faces

In theory, evolutionary modularity allows anatomical structures to respond differently to selective regimes, thus promoting morphological diversification. These differences can then influence the rate and direction of phenotypic evolution among structures. Here we use geometric morphometrics and phenotypic matrix statistics to compare rates of craniofacial evolution and estimate evolvability in the face and braincase modules of a clade of teleost fishes (Gymnotiformes) and a clade of mammals (Carnivora), both of which exhibit substantial craniofacial diversity. We find that the face and braincase regions of both clades display different degrees of integration. We find that the face and braincase evolve at similar rates in Gymnotiformes and the reverse in Carnivora with the braincase evolving twice as fast as the face. Estimates of evolvability and constraints in these modules suggest differential responses to selection arising from fluctuations in phylogenetic integration, thus influencing differential rates of skull-shape evolution in these two clades

New species of glass knifefish Eigenmannia loretana (Gymnotiformes: Sternopygidae) from the Western Amazon

Waltz, Brandon T., Albert, James S. (2018): New species of glass knifefish Eigenmannia loretana (Gymnotiformes: Sternopygidae) from the Western Amazon. Zootaxa 4399 (3): 399-411, DOI: https://doi.org/10.11646/zootaxa.4399.3.

A new species of the Eigenmannia trilineata (Gymnotiformes: Sternopygidae) species group from the río Orinoco basin, Venezuela

ABSTRACT A new species of the Eigenmannia trilineata species group is described from the río Orinoco basin, Venezuela. The new species is distinguished from congeners by a unique set of characters including an ossified basibranchial 1; 198-217 anal-fin rays; suborbital depth, 21.3-26.1% HL; length of anterodorsal process of maxilla equal to the width of the posterior nostril; premaxilla with 17 teeth distributed in three rows; hyaline pectoral and anal fins; and number of scale series above lateral line, 9-10. It raises the number of species allocated to the Eigenmannia trilineata species group to 13 and the number of species within the genus to 18

A new species of Hisonotus (Siluriformes: Otothyrinae) from the upper rio Paraná and rio São Francisco basins, Brazil

Roxo, Fábio F., Silva, Gabriel S. C., Waltz, Brandon T., Melo, Jorge E. G. (2016): A new species of Hisonotus (Siluriformes: Otothyrinae) from the upper rio Paraná and rio São Francisco basins, Brazil. Zootaxa 4109 (2): 227-238, DOI: http://doi.org/10.11646/zootaxa.4109.2.

pruned_gene_trees

All gene trees (best and bootstrapped) inferred in RAxML for all the filtered datasets. Contents in README

Data from: Resolving deep nodes in an ancient radiation of neotropical fishes in the presence of conflicting signals from incomplete lineage sorting

Resolving patterns of ancient and rapid diversifications is one of the most challenging tasks in evolutionary biology. These difficulties arise from confusing phylogenetic signals that are associated with the interplay of incomplete lineage sorting and homoplasy. Phylogenomic analyses of hundreds, or even thousands, of loci offer the potential to resolve such contentious relationships. Yet, how much useful phylogenetic information these large data sets contain remains uncertain and often goes untested. Here, we assess the utility of different data filtering approaches to maximize phylogenetic information and minimize noise when reconstructing an ancient radiation of Neotropical electric knifefishes (Order Gymnotiformes) using ultraconserved elements. We found two contrasting hypotheses of gymnotiform evolutionary relationships depending on whether phylogenetic inferences were based on concatenation or coalescent methods. In the first case, all analyses inferred a previously—and commonly—proposed hypothesis, where the family Apteronotidae was found as the sister group to all other gymnotiform families. In contrast, coalescent-based analyses suggested a novel hypothesis where families producing pulse-type (viz., Gymnotidae, Hypopomidae and Rhamphichthyidae) and wave-type electric signals (viz., Apteronotidae, Sternopygidae) were reciprocally monophyletic. Nodal support for this second hypothesis increased when analyzing loci with the highest phylogenetic information content and further increased when data were pruned using targeted filtering methods that maximized phylogenetic informativeness at the deepest nodes of the Gymnotiformes. Bayesian concordance analyses and topology tests of individual gene genealogies demonstrated that the difficulty of resolving this radiation was likely due to high gene-tree incongruences that resulted from incomplete lineage sorting. We show that data filtering reduces gene tree heterogeneity and increases nodal support and consistency of species trees using coalescent methods; however, we failed to observe the same effect when using concatenation methods. Furthermore, the targeted filtering strategies applied here support the use of “gene data interrogation” rather than “gene genealogy interrogation” approaches in phylogenomic analyses, to extract phylogenetic signal from intractable portions of the Tree of Life

all_gene_trees

All gene trees (best and bootstrapped) inferred in RAxML for each individual UCE locus for the full and reduced taxon sets. Contents in README

Data from: Resolving deep nodes in an ancient radiation of neotropical fishes in the presence of conflicting signals from incomplete lineage sorting

Resolving patterns of ancient and rapid diversifications is one of the most challenging tasks in evolutionary biology. These difficulties arise from confusing phylogenetic signals that are associated with the interplay of incomplete lineage sorting and homoplasy. Phylogenomic analyses of hundreds, or even thousands, of loci offer the potential to resolve such contentious relationships. Yet, how much useful phylogenetic information these large data sets contain remains uncertain and often goes untested. Here, we assess the utility of different data filtering approaches to maximize phylogenetic information and minimize noise when reconstructing an ancient radiation of Neotropical electric knifefishes (Order Gymnotiformes) using ultraconserved elements. We found two contrasting hypotheses of gymnotiform evolutionary relationships depending on whether phylogenetic inferences were based on concatenation or coalescent methods. In the first case, all analyses inferred a previously—and commonly—proposed hypothesis, where the family Apteronotidae was found as the sister group to all other gymnotiform families. In contrast, coalescent-based analyses suggested a novel hypothesis where families producing pulse-type (viz., Gymnotidae, Hypopomidae and Rhamphichthyidae) and wave-type electric signals (viz., Apteronotidae, Sternopygidae) were reciprocally monophyletic. Nodal support for this second hypothesis increased when analyzing loci with the highest phylogenetic information content and further increased when data were pruned using targeted filtering methods that maximized phylogenetic informativeness at the deepest nodes of the Gymnotiformes. Bayesian concordance analyses and topology tests of individual gene genealogies demonstrated that the difficulty of resolving this radiation was likely due to high gene-tree incongruences that resulted from incomplete lineage sorting. We show that data filtering reduces gene tree heterogeneity and increases nodal support and consistency of species trees using coalescent methods; however, we failed to observe the same effect when using concatenation methods. Furthermore, the targeted filtering strategies applied here support the use of “gene data interrogation” rather than “gene genealogy interrogation” approaches in phylogenomic analyses, to extract phylogenetic signal from intractable portions of the Tree of Life