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

Tagliacollo/PartitionUCE: PartitionUCE

First release of PartitionUC

Supplementary Figures-Caribbean Plate

Molecular phylogenies and Ancestral area estimates of Poeciliidae and Cichlida

Data from: Molecular phylogeny of Aphyocharacinae (Characiformes, Characidae) with morphological diagnoses for the subfamily and recognized genera

The subfamily Aphyocharacinae was recently redefined to comprise eight genera: Aphyocharax, Prionobrama, Paragoniates, Phenagoniates, Leptagoniates, Xenagoniates, Rachoviscus and Inpaichthys. This new composition, however, is partly incongruent with results of published molecular studies especially with regards to the positions of Rachoviscus and Inpaichthys. Our goal was to investigate the monophyly of Aphyocharacinae and its interrelationships using three distinct phylogenetic methodologies: Maximum–likelihood and Bayesian analyses of molecular data, and also Parsimony analysis of a concatenated molecular and morphological dataset. All tree topologies recovered herein suggest that Rachoviscus, Inpaichthys and Leptagoniates pi do not belong to the Aphyocharacinae. The remaining aphyocharacin taxa analyzed do form a monophyletic group, which is itself composed of two subgroups being one comprised of Paragoniates, Phenagoniates, Leptagoniates and Xenagoniates, and the other comprised of Aphyocharax and Prionobrama. Internal relationships among these genera are statistically well supported and morphological synapomorphies are presented at the generic level. All tree topologies also indicate that Aphyocharacidium is closely related to Aphyocharacinae suggesting that it should be included in this subfamily. As recognized in the present study, the Aphyocharacinae is diagnosed by a single morphological synapomorphy: two dorsal-fin rays articulating with the first dorsal pterygiophore

Existing protected areas provide a poor safety-net for threatened Amazonian fish species

Freshwater ecosystems represent less than 0.01% of Earth's surface water but proportionately encompass the most species-rich environment on the planet, including nearly one-third of all vertebrate species. Even though inland continental waters are widely regarded as highly endangered ecosystems, their species assemblages are mostly ignored in conservation plans, largely because spatial patterns of freshwater species remain poorly understood. This is particularly severe throughout the Neotropics, most notably in the Amazon superbasin, where the sheer biotic diversity is coupled with a severe lack of biodiversity knowledge at several levels. Spatial patterns of Neotropical freshwater fishes focusing mainly on the Amazon superbasin were investigated. First, Endemic Amazonian Fish Areas (EAFAs) representing central units for the conservation of continental fishes were delimited. Interpolated maps were then analysed using alternative methodologies to delimit spatial patterns of diversity and endemicity across the Amazon superbasin. Several biogeographical analyses used a comprehensive dataset of species and geographical coordinates of Amazonian fishes. The results reveal well-defined spatial patterns of species richness and endemicity in the Amazonian fish fauna, showing that most protected areas are concentrated in a single bioregion (Amazon lowlands). Those areas are incongruent and insufficient to protect endemic and threatened species, which are mostly distributed in upland regions. Effective conservation of the Amazonian fish fauna should include EAFAs within protected areas, especially those undergoing deforestation and hydropower development pressure and containing a high concentration of threatened species. The following EAFAs should be considered as conservation priorities: Upper Araguaia, Upper Tocantins, Lower Teles Pires/Serra do Cachimbo, Chapada dos Parecis and Upper Marañon. These regions should be urgently protected to avert the loss of important trophic relationships and unique elements of the Amazonian fish fauna

Phylogenetic revision of Gymnotidae (Teleostei: Gymnotiformes), with descriptions of six subgenera.

The diversity of gymnotid electric fishes has been intensely studied over the past 25 years, with 35 species named since 1994, compared to 11 species in the previous 236 years. Substantial effort has also been applied in recent years to documenting gymnotid interrelationships, with seven systematic studies published using morphological and molecular datasets. Nevertheless, until now, all gymnotids have been assigned to one of just two supraspecific taxa, the subfamily Electrophorinae with one genus Electrophorus and three valid species and the subfamily Gymnotine also with one genus Gymnotus and 43 valid species. This simple classification has obscured the substantial phenotypic and lineage diversity within the subfamily Gymnotine and hampered ecological and evolutionary studies of gymnotid biology. Here we present the most well-resolved and taxon-complete phylogeny of the Gymnotidae to date, including materials from all but one of the valid species. This phylogeny was constructed using a five-gene molecular dataset and a 115-character morphological dataset, enabling the inclusion of several species for which molecular data are still lacking. This phylogeny was time-calibrated using biogeographical priors in the absence of a fossil record. The tree topology is similar to those of previous studies, recovering all the major clades previously recognized with informal names. We propose a new gymnotid classification including two subfamilies (Electrophorinae and Gymnotinae) and six subgenera within the genus Gymnotus. Each subgenus exhibits a distinctive biogeographic distribution, within which most species have allopatric distributions and the subgenera are diverged from one another by an estimated 5-35 million years. We further provide robust taxonomic diagnoses, descriptions and identification keys to all gymnotid subgenera and all but four species. This new taxonomy more equitably partitions species diversity among supra-specific taxa, employing the previously vacant subgenus and subfamily ranks. This new taxonomy renders known gymnotid diversity more accessible to study by highlighting the deep divergences (chronological, geographical, genetic and morphological) among its several clades

Data from: Coordinated dispersal and pre-Isthmian assembly of the Central American ichthyofauna

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 (POA) river. Ancestral area estimation places the earliest colonizations of the Greater Antilles and Central America (GACA) during the Paleocene-Eocene (c. 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) plate margin did not serve as a dispersal corridor until the Late Neogene (12-0 Ma), and contributed relatively little to the formation of modern distributions

Data from: Biogeography of curimatid fishes reveals multiple lowland-upland river transitions and differential diversification in the Neotropics (Teleostei, Curimatidae)

The Neotropics harbors a megadiverse ichthyofauna comprising over 6300 species with approximately 80% in just three taxonomic orders within the clade Characiphysi. This highly diverse group has evolved in tropical South America over tens to hundreds of millions of years influenced mostly by re‐arrangements of river drainages in lowland and upland systems. In this study, we investigate patterns of spatial diversification in Neotropical freshwater fishes in the family Curimatidae, a species‐rich clade of the order Characiformes. Specifically, we examined ancestral areas, dispersal events, and shifts in species richness using spatially explicit biogeographic and macroevolutionary models to determine whether lowlands–uplands serve as museums or cradles of diversification for curimatids. We used fossil information to estimate divergence times in BEAST, multiple time‐stratified models of geographic range evolution in BioGeoBEARS, and alternative models of geographic state‐dependent speciation and extinction in GeoHiSSE. Our results suggest that the most recent common ancestor of curimatids originated in the Late Cretaceous likely in lowland paleodrainages of northwestern South America. Dispersals from lowland to upland river basins of the Brazilian and Guiana shields occurred repeatedly across independently evolving lineages in the Cenozoic. Colonization of upland drainages was often coupled with increased rates of net diversification in species‐rich genera such as Cyphocharax and Steindachnerina. Our findings demonstrate that colonization of novel aquatic environments at higher elevations is associated with an increased rate of diversification, although this pattern is clade‐dependent and driven mostly by allopatric speciation. Curimatids reinforce an emerging perspective that Amazonian lowlands act as a museum by accumulating species along time, whereas the transitions to uplands stimulate higher net diversification rates and lineage diversification.Funding provided by: Fundação de Amparo à Pesquisa do Estado de São PauloCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001807Award Number: 11/08374-1Funding provided by: Conselho Nacional de Desenvolvimento Científico e TecnológicoCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100003593Award Number: 200159/2020-8Funding provided by: American Museum of Natural HistoryCrossref Funder Registry ID: http://dx.doi.org/10.13039/100005835Award Number: Stiassny AMNH Axelrod Research CuratorshipFunding provided by: Fundação de Amparo à Pesquisa do Estado de São PauloCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001807Award Number: 17/09321-5Funding provided by: Fundação de Amparo à Pesquisa do Estado de São PauloCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001807Award Number: 18/20806-3Funding provided by: Conselho Nacional de Desenvolvimento Científico e TecnológicoCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100003593Award Number: 404991/2018-1Funding provided by: Conselho Nacional de Desenvolvimento Científico e TecnológicoCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100003593Award Number: 405643/2018-7Data collection and analyses were performed by all authors of the paper