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.
Diversification of Neotropical Freshwater Fishes Albert, James S; Tagliacollo, Victor A; Dagosta, Fernando
Annual review of ecology, evolution, and systematics,
11/2020, Letnik:
51, Številka:
1
Journal Article
Recenzirano
Odprti dostop
Neotropical freshwater fishes (NFFs) constitute the most diverse continental vertebrate fauna on Earth, with more than 6,200 named species compressed into an aquatic footprint <0.5% of the total ...regional land-surface area and representing the greatest phenotypic disparity and functional diversity of any continental ichthyofauna. Data from the fossil record and time-calibrated molecular phylogenies indicate that most higher taxa (e.g., genera, families) diversified relatively continuously through the Cenozoic, across broad geographic ranges of the South American platform. Biodiversity data for most NFF clades support a model of continental radiation rather than adaptive radiation, in which speciation occurs mainly in allopatry, and speciation and adaptation are largely decoupled. These radiations occurred under the perennial influence of river capture and sea-level oscillations, which episodically fragmented and merged portions of adjacent river networks. The future of the NFF fauna into the Anthropocene is uncertain, facing numerous threats at local, regional, and continental scales.
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.
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•Gymnotiformes includes three lineages: Gymnotidae, Rhamphichthyoidea, and Sinusoidea.•Gymnotidae includes Electrophorus+six Gymnotus species-groups.•Rhamphichthyoidea includes ...Hypopomidae+Rhamphichthyidae (including Steatogenae).•Sinusoidea includes Sternopygidae+Apteronotidae with several new relationships.•“Apteronotus” bonapartii species-group is the sister-group to Porotergus and not the Apteronotus sensu stricto.
This study provides the most comprehensive Model-Based Total Evidence (MBTE) phylogenetic analyses of the clade Gymnotiformes to date, reappraising relationships using a dataset comprised of six genes (5277bp) and 223 morphological characters, and an ingroup taxon sample including 120 of 212 valid species representing 34 of the 35 extant genera. Our MBTE analyses indicate the two main gymnotiform clades are Gymnotidae and Sternopygoidei, the latter comprised of Rhamphichthyoidea (Rhamphichthyidae+Hypopomidae) and Sinusoidea (Sternopygidae+Apteronotidae). Within Gymnotidae, Electrophorus and Gymnotus are sister taxa, and Gymnotus includes the following six clades: (i) G. pantherinus clade, (ii) G. coatesi clade, (iii) G. anguillaris clade, (iv) G. tigre clade, (v) G. cylindricus clade, and (vi) G. carapo clade. Within Rhamphichthyoidea, Steatogenae (Steatogenys+Hypopygus) is a member of Rhamphichthyidae, and Hypopomidae includes the following clades: (i) Akawaio, (ii) Hypopomus, (iii) Microsternarchini, and (iv) Brachyhypopomus. Within Sternopygidae, Sternopygus and Eigenmanninae are sister groups, Rhabdolichops is the sister to other Eigenmanninae, Archolaemus+Distocyclus is the sister to Eigenmannia, and Japigny is nested within Eigenmannia. Within Apteronotidae, Sternarchorhamphinae (Sternarchorhamphus+Orthosternarchus) is the sister to Apteronotinae, Adontosternarchus is the sister group to other Apteronotinae, Sternarchorhynchini (Sternarchorhynchus+Platyurosternarchus) is the sister to Navajini, and species assigned to Apteronotus are members of two separate clades: (i) A. sensu stricto in the Apteronotini, and (ii) the “A.” bonapartii clade in the Navajini.
Identifying habitat characteristics that accelerate organismal evolution is essential to understanding both the origins of life on Earth and the ecosystem properties that are most critical to ...maintaining life into the future. Searching for these characteristics on a large scale has only recently become possible via advances in phylogenetic reconstruction, time-calibration, and comparative analyses. In this study, we combine these tools with habitat and phenotype data for 105 species in a clade of Neotropical suckermouth catfishes commonly known as cascudinhos. Our goal was to determine whether riverine mesohabitats defined by different flow rates (i.e., pools vs. rapids) and substrates (plants vs. rocks) have affected rates of cascudinho cladogenesis and morphological diversification. In contrast to predictions based on general theory related to life in fast-flowing, rocky riverine habitats, Neoplecostomini lineages associated with these habitats exhibited increased body size, head shape diversity, and lineage and phenotype diversification rates. These findings are consistent with a growing understanding of river rapids as incubators of biological diversification and specialization. They also highlight the urgent need to conserve rapids habitats throughout the major rivers of the world.
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•Most species-comprehensive, data-rich phylogeny of the ghost knifefishes to date.•Multi-locus phylogeny based on three mitochondrial and four nuclear ...loci.•Orthosternarchus + Sternarchorhamphus placed sister to all remaining genera.•Substantial polyphyly within Apteronotus.•New suprageneric classification for Apteronotidae.
Ghost knifefishes (Gymnotiformes: Apteronotidae) are weakly electric fishes that possess a high-frequency, neurogenic electric organ discharge. They are found throughout the humid Neotropics from Panama to Argentina and are most diverse and abundant in the channels of large lowland rivers. Apteronotidae is the most species-rich family of Neotropical electric knifefishes with 96 valid species in 15 genera. We present a phylogenetic hypothesis based on molecular sequence data from three mitochondrial genes (16S, coi, cytb) and four nuclear loci (glyt, rag2, ryr3, zic1). Our analysis includes sequence data for 203 samples in 54 species and 14 genera, making it the most densely-sampled and data-rich phylogeny of the Apteronotidae to date. Our results corroborate previous phylogenetic hypotheses with the placement of Orthosternarchus + Sternarchorhamphus sister to all other apteronotids, a non-monophyletic Apterontotus, and a sister relationship between Sternarchorhynchus and the Navajini. We also report several novel relationships, particularly within the Navajini and among several species of the nominal genus Apteronotus not previously included in phylogenetic analyses. We additionally provide a new classification for the family.
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 (ILS) 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 ILS. 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.
Ecological opportunity is often proposed as a driver of accelerated diversification, but evidence has been largely derived from either contemporary island radiations or the fossil record. Here, we ...investigate the potential influence of ecological opportunity on a transcontinental radiation of South American freshwater fishes. We generate a species‐dense, time‐calibrated molecular phylogeny for the suckermouth armored catfish subfamily Hypostominae, with a focus on the species‐rich and geographically widespread genus Hypostomus. We use the resulting chronogram to estimate ancestral geographical ranges, infer historical rates of cladogenesis and diversification in habitat and body size and shape, and test the hypothesis that invasions of previously unoccupied river drainages accelerated evolution and contributed to adaptive radiation. Both the subfamily Hypostominae and the included genus Hypostomus originated in the Amazon/Orinoco ecoregion. Hypostomus subsequently dispersed throughout tropical South America east of the Andes Mountains. Consequent to invasion of the peripheral, low‐diversity Paraná River basin in southeastern Brazil approximately 12.5 Mya, Paraná lineages of Hypostomus, experienced increased rates of cladogenesis and ecological and morphological diversification. Contemporary lineages of Paraná Hypostomus are less species rich but more phenotypically diverse than their congeners elsewhere. Accelerated speciation and morphological diversification rates within Paraná basin Hypostomus are consistent with adaptive radiation. The geographical remoteness of the Paraná River basin, its recent history of marine incursion, and its continuing exclusion of many species that are widespread in other tropical South American rivers suggest that ecological opportunity played an important role in facilitating the observed accelerations in diversification.
Body shape is a fundamental metric of animal diversity affecting critical behavioral and ecological dynamics and conservation status, yet previously available methods capture only a fraction of total ...body-shape variance. Here we use structure-from-motion (SFM) 3D photogrammetry to generate digital 3D models of adult fishes from the Lower Mississippi Basin, one of the most diverse temperate-zone freshwater faunas on Earth, and 3D geometric morphometrics to capture morphologically distinct shape variables, interpreting principal components as growth fields. The mean body shape in this fauna resembles plesiomorphic teleost fishes, and the major dimensions of body-shape disparity are similar to those of other fish faunas worldwide. Major patterns of body-shape disparity are structured by phylogeny, with nested clades occupying distinct portions of the morphospace, most of the morphospace occupied by multiple distinct clades, and one clade (Acanthomorpha) accounting for over half of the total body shape variance. In contrast to previous studies, variance in body depth (59.4%) structures overall body-shape disparity more than does length (31.1%), while width accounts for a non-trivial (9.5%) amount of the total body-shape disparity.
This study aims to investigate relationships between species traits and publication date in the weakly electric osteoglossiform Mormyroidea (African knifefish and elephantfishes) and the ...ostariophysan Gymnotiformes (Neotropical knifefishes). It is investigated whether body size and geographic distribution area are correlated with publication date and whether extinction risk differs between both phylogenetically distant and geographically isolated clades. Statistical modelling indicates that the number of new species described annually is stable in mormyroids and clearly increasing in gymnotiforms. Best‐fitting generalised linear models (GLM) indicate that the newly discovered species are more often of small‐bodied, predominantly narrowly distributed and more likely to be threatened with extinction. These characteristics are more pronounced in mormyroids when compared with gymnotiforms, suggesting that some African electric fishes may live an ephemeral existence after formal description. Despite taxonomic work has been more intense in the Neotropics than in Africa in the recent decades, there is evidence that the African continent represents the next frontier of species descriptions. Taxonomic studies are fundamental for the understanding of richness and distribution and hence extinction risk assessment and conservation, of these remarkable convergent fish clades.
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