Estimating Improved Partitioning Schemes for Ultraconserved Elements

Ultraconserved (UCEs) are popular markers for phylogenomic studies. They are relatively simple to collect from distantly-related organisms, and contain sufficient information to infer relationships at almost all taxonomic levels. Most studies of UCEs use partitioning to account for variation in rates and patterns of molecular evolution among sites, for example by estimating an independent model of molecular evolution for each UCE. However, rates and patterns of molecular evolution vary substantially within as well as between UCEs, suggesting that there may be opportunities to improve how UCEs are partitioned for phylogenetic inference. We propose and evaluate new partitioning methods for phylogenomic studies of UCEs: Sliding-Window Site Characteristics (SWSC), and UCE Site Position (UCESP). The first method uses site characteristics such as entropy, multinomial likelihood, and GC content to generate partitions that account for heterogeneity in rates and patterns of molecular evolution within each UCE. The second method groups together nucleotides that are found in similar physical locations within the UCEs. We examined the new methods with seven published data sets from a variety of taxa. We demonstrate the UCESP method generates partitions that are worse than other strategies used to partition UCE data sets (e.g., one partition per UCE). The SWSC method, particularly when based on site entropies, generates partitions that account for within-UCE heterogeneity and leads to large increases in the model fit. All of the methods, code, and data used in this study, are available from https://github.com/Tagliacollo/PartitionUCE. Simplified code for implementing the best method, the SWSC-EN, is available from https://github.com/Tagliacollo/PFinderUCE-SWSC-EN.National Postdoctoral Program (PNPD/CAPES) and Australian Endeavour Program. RL was supported by an Australian Research Council Future Fellowship

Why the short face? Developmental disintegration of the neurocranium drives convergent evolution in neotropical electric fishes

© 2017 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. Convergent evolution is widely viewed as strong evidence for the influence of natural selection on the origin of phenotypic design. However, the emerging evo-devo synthesis has highlighted other processes that may bias and direct phenotypic evolution in the presence of environmental and genetic variation. Developmental biases on the production of phenotypic variation may channel the evolution of convergent forms by limiting the range of phenotypes produced during ontogeny. Here, we study the evolution and convergence of brachycephalic and dolichocephalic skull shapes among 133 species of Neotropical electric fishes (Gymnotiformes: Teleostei) and identify potential developmental biases on phenotypic evolution. We plot the ontogenetic trajectories of neurocranial phenotypes in 17 species and document developmental modularity between the face and braincase regions of the skull. We recover a significant relationship between developmental covariation and relative skull length and a significant relationship between developmental covariation and ontogenetic disparity. We demonstrate that modularity and integration bias the production of phenotypes along the brachycephalic and dolichocephalic skull axis and contribute to multiple, independent evolutionary transformations to highly brachycephalic and dolichocephalic skull morphologies

Coordinated dispersal and pre-isthmian assembly of the central American ichthyofauna

© The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. We document patterns of coordinated dispersal over evolutionary time frames in heroine cichlids and poeciliine live-bearers, the two most species-rich clades of freshwater fishes in the Caribbean basin. Observed dispersal rate (DO) values were estimated from time-calibrated molecular phylogenies in LAGRANGE+, a modified version of the ML-based parametric biogeographic program LAGRANGE. DO is measured in units of wallaces (wa) as the number of biogeographic range-expansion events per million years. DO estimates were generated on a dynamic paleogeographic landscape of five areas over three time intervals from Upper Cretaceous to Recent. Expected dispersal rate (DE) values were generated from alternative paleogeographic models, with dispersal rates proportional to target area and source-river discharge volume, and inversely proportional to paleogeographic distance. Correlations between DO and DE were used to assess the relative contributions of these three biogeographic parameters. DO estimates imply a persistent dispersal corridor across the Eastern (Antillean) margin of the Caribbean plate, under the influence of prevailing and perennial riverine discharge vectors such as the Proto-Orinoco-Amazon river. Ancestral area estimation places the earliest colonizations of the Greater Antilles and Central America during the Paleocene-Eocene (ca. 58-45 Ma), potentially during the existence of an incomplete Paleogene Arc (∼59 Ma) or Lesser Antilles Arc (∼45 Ma), but predating the GAARlandia land bridge (∼34-33 Ma). Paleogeographic distance is the single best predictor of DO. The Western (Central American) platemargin did not serve as a dispersal corridor until the LateNeogene (12-0 Ma), and contributed relatively little to the formation of modern distributions

Using community phylogenetics to assess phylogenetic structure in the fitzcarrald region of Western Amazonia

© 2020 The Authors. Di versity and Distributions Published by SBI. Here we explore the use of community phylogenetics as a tool to document patterns of biodiversity in the Fitzcarrald region, a remote area in Southwestern Amazonia. For these analyses, we subdivide the region into basin-wide assemblages encompassing the headwaters of four Amazonian tributaries (Urubamba, Yuruá, Purús and Las Piedras basins), and habitat types: river channels, terra firme (non-floodplain) streams, and floodplain lakes. We present a robust, well-documented collection of fishes from the region including 272 species collected from 132 field sites over 63 field days and four years, comprising the most extensive collection of fishes from this region to date. We conduct a preliminary community phylogenetic analysis based on this collection and recover results largely statistically indistinguishable from the random expectation, with only a few instances of phylogenetic structure. Based on these results, and of those published in other recent biogeographic studies, we conclude that the Fitzcarrald fish species pool accumulated over a period of several million years, plausibly as a result of dispersal from the larger species pool of Greater Amazonia

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

Landscape dynamics and diversification of the megadiverse South American freshwater fish fauna

Landscape dynamics are widely thought to govern the tempo and mode of continental radiations, yet the effects of river network rearrangements on dispersal and lineage diversification remain poorly understood. We integrated an unprecedented occurrence dataset of 4,967 species with a newly compiled, time-calibrated phylogeny of South American freshwater fishes—the most species-rich continental vertebrate fauna on Earth—to track the evolutionary processes associated with hydrogeographic events over 100 Ma. Net lineage diversification was heterogeneous through time, across space, and among clades. Five abrupt shifts in net diversification rates occurred during the Paleogene and Miocene (between 30 and 7 Ma) in association with major landscape evolution events. Net diversification accelerated from the Miocene to the Recent (c. 20 to 0 Ma), with Western Amazonia having the highest rates of in situ diversification, which led to it being an important source of species dispersing to other regions. All regional biotic interchanges were associated with documented hydrogeographic events and the formation of biogeographic corridors, including the Early Miocene (c. 23 to 16 Ma) uplift of the Serra do Mar and Serra da Mantiqueira and the Late Miocene (c. 10 Ma) uplift of the Northern Andes and associated formation of the modern transcontinental Amazon River. The combination of high diversification rates and extensive biotic interchange associated with Western Amazonia yielded its extraordinary contemporary richness and phylogenetic endemism. Our results support the hypothesis that landscape dynamics, which shaped the history of drainage basin connections, strongly affected the assembly and diversification of basin-wide fish fauna

Associação entre posicionamento do aluno na sala de aula e desempenho escolar

This research was aimed at analyzing whether there is an association between the positioning of the pupil in the classroom and his academic performance, as well as to diagnose the main factors underlying the association. Thus, this study analyzed 4 Elementary School II institutions of both public and private educational systems, in Botucatu, São Paulo, Brazil during a school year bimester. To register the positions students were seated, 29 similar classes (containing 6 rows x 6 columns) were investigated, each one with around 30 students, which resulted in a sampling of 859 students. For the questionnaire application, which objective was to verify the main reason for students’ seat choice, the same 29 classes were investigated. However, the sampling number was reduced to 692 students. In turn, for the collection of school performance and absence percentage of each student for the bimester in question, teachers’ evaluation books were used. As a result, it was found that the lower the percentage of the student's absences, the greater is their performance at school, and the greater their performance at school is, the closer up front to the board they are seated. Finally, the closer up to the board they are seated, the more their motivation and interest in learning increase. Therefore, there is an association between the position of a student in the classroom and his or her academic performance, where the association is conditioned by the motivation and interest in learningEssa pesquisa objetivou analisar se há uma associação entre o posicionamento do aluno na sala de aula e seu desempenho escolar, bem como diagnosticar qual é o principal condicionador dessa associação. Desse modo, essa pesquisa analisou 4 instituições do Ensino Fundamental II da rede pública e privada de Botucatu, SP, Brasil durante um bimestre letivo. Para se registrar a posição de assento dos alunos foram investigadas 29 classes semelhantes (6 linhas x 6 colunas), cada uma com aproximadamente 30 alunos, o que resultou numa amostragem de 859 estudantes. Já para aplicação do questionário, cujo objetivo era constatar qual a principal razão que condicionou a escolha do assento por parte do aluno, investigou-se as mesmas 29 classes, porém reduziu-se o número de amostragem para 692 alunos. Por sua vez, para coleta do desempenho escolar e percentual de ausência de cada aluno para o bimestre em questão, recorreu-se às cadernetas de avaliação dos professores. Como resultado, constatou-se que quanto menor é o percentual de ausência do aluno, maior é seu desempenho escolar, e quanto maior o seu desempenho escolar, mais próximo da lousa é sua posição de assento. Finalmente, quanto mais próximo da lousa é sua posição de assento, maior sua motivação e interesse no aprender. Portanto, conclui-se que existe uma associação entre o posicionamento do aluno na sala de aula e seu desempenho escolar, onde essa associação é condicionada pela motivação e interesse no aprende

Sistema filogenética da subfamília aphyocharacinae (Characiformes, Characidae)

The subfamily Aphyocharacinae comprises the genera Aphyocharax, Prionobrama, Paragoniates, Phenagoniates, Leptagoniates, Xenagoniates, Rachoviscus, and Inpaichthys. This current arrangement based on a morphological analysis is congruent with most proposed morphological phylogenetic analyses, except for the inclusion of Rachoviscus and Inpaichthys which is tenuous and not always supported by data. In this current work the goal was to investigate the monophyly of the subfamily Aphyocharacinae and to recover relationships within it using molecular and morphological analyses. Using separate parsimony and Bayesian analyses of morphological, nuclear and mitochondrial genes, I recover new relationships within Aphyocharacinae. Independent analyses recovered similar topologies for molecular and morphologic datasets. Molecular based topologies showed common generic relationships: Aphyocharacinae, excluding the genus Rachoviscus and Inpaichthys, constitutes a monophyletic group. Moreover, Aphyocharacinae has two well–marked major branches. One composed by (Paragoniates (Phenagoniates (Leptagoniates+Xenagoniates))), while the other includes Aphyocharax and Prionobrama. Also, relationships among the genera were completely resolved and supported by strong statistical indexes. Based on molecular hypotheses, I had a specific monophyletic framework to conduct morphological analysis. This approach suggests that Aphyocharacidium sp. and Microschemobrycon cf. casiquiare are most probably the sister group of Aphyocharacinae. The morphological analysis conducted with 25 unweighted and unordered characters recovers one tree, resolved at generic–species level. A similar hypothesis found using molecular data is recovered with three well–marked... (Complete abstract click electronic access below)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

Tagliacollo/PartitionUCE: PartitionUCE

First release of PartitionUC

Supplementary Figures-Caribbean Plate

Molecular phylogenies and Ancestral area estimates of Poeciliidae and Cichlida