Modelling evolutionary tempo and mode using formal morphological spaces and Markov chain principles.

Evolutionary tempo and mode summarize ancient and controversial subjects of theoretical biology such as gradualism, convergence, contingence, trends, and entrenchment. We employed an integrative methodological approach to explore the evolutionary tempo and mode of Lepidosaurian phalangeal formulae (PFs). This approach involves quantifying the frequencies of morphological changes along an evolutionary trajectory. The five meristic characters encoded by PFs are particularly valuable in revealing evolutionary patterns, owing to their discrete nature and extensive documentation in the literature. Based on a pre-existing dataset of PFs from 649 taxa (35 Lepidosauria families, including fossils), from which there exists a unique repertoire of 53 formulations, our approach simultaneously considers phenetic and phylogenetic data. This culminates in a diagram accounting for the phylogenetic dynamic of evolution traversing across different regions of morphospace. The method involves enumerating phenotypical options, reconstructing phenotypes across the phylogeny, projecting phenotypes onto a morphospace, and constructing a flow network from the frequency of evolutionary transitions between unique phenotypic conditions. This approach links Markovian chains and evolutionary trajectories to formally define parameters that describe the underlying transitions of morphological change. Among other results, we found that (a) PF evolution exhibits a clear trend towards reduction in the phalangeal count and that (b) evolutionary change tends to occur significantly between morphologically similar PFs. Notwithstanding, although minor but not trivial, transitions between distant formulas -jumps- occur. Our results support a pluralistic view including stasis, gradualism, and saltationism discriminating their prevalence in a target character evolution.

Insights on the evolution of Coronavirinae in general, and SARS-CoV-2 in particular, through innovative biocomputational resources.

The structural proteins of coronaviruses portray critical information to address issues of classification, assembly constraints, and evolutionary pathways involving host shifts. We compiled 173 complete protein sequences from isolates belonging to the four genera of the subfamily Coronavirinae. We calculate a single matrix of viral distance as a linear combination of protein distances. The minimum spanning tree (MST) connecting the individuals captures the structure of their similarities. The MST re-capitulates the known phylogeny of Coronovirinae. Hosts were mapped onto the MST and we found a non-trivial concordance between host phylogeny and viral proteomic distance. We also study the chimerism in our dataset through computational simulations. We found evidence that structural units coming from loosely related hosts hardly give rise to feasible chimeras in nature. This work offers a fresh way to analyze features of SARS-CoV-2 and related viruses.

Network architecture associated with the highly specialized hindlimb of frogs.

Network analyses have been increasingly used in the context of comparative vertebrate morphology. The structural units of the vertebrate body are treated as discrete elements (nodes) of a network, whose interactions at their physical contacts (links) determine the phenotypic modules. Here, we use the network approach to study the organization of the locomotor system underlying the hindlimb of frogs. Nodes correspond to fibrous knots, skeletal and muscular units. Edges encode the ligamentous and monoaxial tendinous connections in addition to joints. Our main hypotheses are that: (1) the higher centrality scores (measured as betweenness) are recorded for fibrous elements belonging to the connective system, (2) the organization of the musculoskeletal network belongs to a non-trivial modular architecture and (3) the modules in the hindlimb reflect functional and/or developmental constraints. We confirm all our hypotheses except for the first one, since bones overpass the fibrous knots in terms of centrality. Functionally, there is a correlation between the proximal-to-distal succession of modules and the progressive recruitment of elements involved with the motion of joints during jumping. From a developmental perspective, there is a correspondence between the order of the betweenness scores and the ontogenetic chronology of hindlimbs in tetrapods. Modular architecture seems to be a successful organization, providing of the building blocks on which evolution forges the many different functional specializations that organisms exploit.

Biogeography and areas of endemism of Prepops Reuter (Heteroptera: Miridae)

Resumen Miridae (Hemiptera: Heteroptera) es una de las familias de insectos más ricas en especies, con alrededor de 11 100 especies descritas. Mirinae es la mayor subfamilia y sus endemismos se hacen evidentes desde el nivel de tribu hacia abajo. La tribu Restheniini (Mirinae) se encuentra en América, con la mayor parte de su diversidad en el Neotrópico. Prepops Reuter es el mayor género de Restheniini con 198 especies, con un rango de distribución similar al de la tribu. Los estudios sobre distribución y áreas de endemismo en Miridae son escasos, y no existen para Prepops. Aquí se analizan todos los registros geográficos de Prepops (707 registros de 181 especies) con el objetivo de identificar patrones de diversidad y áreas de endemismo, usando análisis de redes. Los datos de localidad se asignaron usando especímenes de museo y registros geográficos en la literatura. Además usamos datos de distribución para proponer preferencias de hábitat y variables geoclimáticas importantes para cada grupo de especies co-ocurrentes. Los resultados indican una alta riqueza específica en las regiones subtropicales, mientras que la faja tropical y las altas latitudes aparecen empobrecidas. La región Neotropical presenta 86 % de las especies, la Neártica alrededor del 11 % (pero con mayores rangos específicos de distribución). La región Andina casi no posee registros del género. Veintitrés áreas de endemismo (y dos díadas), formadas por 2 o más especies endémicas se encuentran en la región Neártica (3), la zona de transición Mexicana/subregión Caribe (5), y la zona de transición Sudamericana/ subregiones Amazónica, Chaqueña y Paranaense (15). La superposición de algunas áreas indica regiones con elevada riqueza específica y con una historia compleja. La falta de registros en la región Andina (excepto para P. nigrus en el sur de Patagonia) y la dominancia de especies estrictamente neotropicales (86 %) apoyan la hipótesis del origen neotropical para la tribu Restheniini. La conformación general de los grupos de especies co-ocurrentes de Prepops muestra una estrecha correlación con las regiones y subregiones biogeográficas conocidas. Entre las características ecofisiográficas más comunmente asociadas con los registros geográficos de Prepops se encuentran, en orden de importancia: bosques de hoja ancha (húmedos y secos), pastizales y hábitats xéricos.

AbstractThe Miridae (Hemiptera: Heteroptera) are one of the most species rich families of insects, with about 11 100 described species. Mirinae is the largest subfamily and its endemism becomes evident at the tribal level and below. Mirines of the tribe Restheniini are found throughout America, with most of the diversity confined to the Neotropics. Prepops Reuter is the largest genus in Restheniini with 198 described species and its geographical range is similar to that of the tribe. The study of the distribution and areas of endemism in Miridae are scarce and non-existent for Prepops. We analyzed all the geographic records of Prepops (707 records for 181 species) in order to identify diversity patterns and areas of endemism, using network analysis. Locality data were assigned using museum specimens and geographic records in the literature. Additionally we used spatial data to propose habitat preferences and geoclimatic variables important for each group of co-occurring species. The results indicate high species richness in subtropical regions, while the tropical belt and high latitudes appear impoverished. The Neotropical region contains 86% of the species, and the Nearctic about 11 % (but with larger species ranges); the Andean region is sparingly represented. Twenty-three areas of endemism (and two diads), formed by 2 or more endemic species, are distributed in the Nearctic (3), Mexican Transition Zone and Caribbean subregion (5), South American Transition Zone and Amazonian, Chacoan and Paranaense subregions (15). Overlap between some of the areas indicates regions with high species richness and complex history. The lack of records from the Andean region (except for P. nigrus in Southern Patagonia) and dominance of strictly Neotropical species (86 %) supports the hypothesis of a Neotropical origin for the tribe Restheniini. The general arrangement of the units of co-occurrence of Prepops species shows a close correlation with known biogeographic regions and subregions. Broad physiographic characteristics most commonly associated with Prepops geographical records are, in order of importance: broad leaf forests (wet and dry), grasslands and xeric habitats. Rev. Biol. Trop. 64(1): 17-31. Epub 2016 March 01.

Biogeography and areas of endemism of Prepops Reuter (Heteroptera: Miridae).

The Miridae (Hemiptera: Heteroptera) are one of the most species rich families of insects, with about 11 100 described species. Mirinae is the largest subfamily and its endemism becomes evident at the tribal level and below. Mirines of the tribe Restheniini are found throughout America, with most of the diversity confined to the Neotropics. Prepops Reuter is the largest genus in Restheniini with 198 described species and its geographi- cal range is similar to that of the tribe. The study of the distribution and areas of endemism in Miridae are scarce and non-existent for Prepops. We analyzed all the geographic records of Prepops (707 records for 181 species) in order to identify diversity patterns and areas of endemism, using network analysis. Locality data were assigned using museum specimens and geographic records in the literature. Additionally we used spatial data to propose habitat preferences and geoclimatic variables important for each group of co-occurring species. The results indicate high species richness in subtropical regions, while the tropical belt and high latitudes appear impover- ished. The Neotropical region contains 86% of the species, and the Nearctic about 11 % (but with larger species ranges); the Andean region is sparingly represented. Twenty-three areas of endemism (and two diads), formed by 2 or more endemic species, are distributed in the Nearctic (3), Mexican Transition Zone and Caribbean sub- region (5), South American Transition Zone and Amazonian, Chacoan and Paranaense subregions (15). Overlap between some of the areas indicates regions with high species richness and complex history. The lack of records from the Andean region (except for P. nigrus in Southern Patagonia) and dominance of strictly Neotropical spe- cies (86 %) supports the hypothesis of a Neotropical origin for the tribe Restheniini. The general arrangement of the units of co-occurrence of Prepops species shows a close correlation with known biogeographic regions and subregions. Broad physiographic characteristics most commonly associated with Prepops geographical records are, in order of importance: broad leaf forests (wet and dry), grasslands and xeric habitats.

Co-authorship networks (and other contextual factors) behind the growth of taxonomy of South American Ephemeroptera: a scientometric approach.

Science carried out in South America has experienced a major rise in the levels of productivity and impact during the last decade. The continuity of this process depends upon strong policy decisions of personnel training and of increasing investments. We study the effects of a new regional paradigm, specifically, an increasing international visibility through knowledge support, using the particular case of taxonomy of an ancient group of insects (Ephemeroptera) in South America. We tracked the number of new species described in scholarly papers along a period of two centuries. We have also mined patterns of connections from the respective co-authorship network. A quantitative framework to analyze historical sequences of scientific output is also proposed. Our results point out three stages of taxonomic development: (i) a pioneering stage (1800's-1970's) where foreign authors coming from Europe and North America account for almost the totality of described species, (ii) a transitional stage (1980's-1990's) where new species are described by both foreign and regional authors, and (iii) an autonomous stage (1999-present) where the bulk of scientific output is performed by regional authors. Remarkably, the transitional stage coincides with the advent of democracy in the region. We hypothesize that conjunction of funding and interactions between researchers act synergistically to foster an autochthonous taxonomy in South America.