Description of a new catfish genus (Siluriformes, Loricariidae) from the Tocantins River basin in central Brazil, with comments on the historical zoogeography of the new taxon
TL;DR: The phylogenetic results indicate that the new genus and species from the Tocantins River basin is a sister taxon of all the other members of the Neoplecostominae, originating during the Eocene at 47.5 Mya (32.7–64. 5 Mya 95% HPD).
Abstract: This study presents the description of a new genus of the catfish subfamily Neoplecostominae from the Tocantins River basin. It can be distinguished from other neoplecostomine genera by the presence of (1) three hypertrophied bicuspid odontodes on the lateral portion of the body (character apparently present in mature males); (2) a large area without odontodes around the snout; (3) a post-dorsal ridge on the caudal peduncle; (4) a straight tooth series in the dentary and premaxillary rows; (5) the absence of abdominal plates; (6) a conspicuous series of enlarged papillae just posterior to the dentary teeth; and (7) caudal peduncle ellipsoid in cross section. We used maximum likelihood and Bayesian methods to estimate a time-calibrated tree with the published data on 116 loricariid species using one nuclear and three mitochondrial genes, and we used parametric biogeographic analyses (DEC and DECj models) to estimate ancestral geographic ranges and to infer the colonization routes of the new genus and the other neoplecostomines in the Tocantins River and the hydrographic systems of southeastern Brazil. Our phylogenetic results indicate that the new genus and species is a sister taxon of all the other members of the Neoplecostominae, originating during the Eocene at 47.5 Mya (32.7–64.5 Mya 95% HPD). The present distribution of the new genus and other neoplecostomines may be the result of a historical connection between the drainage basins of the Paraguay and Parana rivers and the Amazon basin, mainly through headwater captures.
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TL;DR: This study lays a strong foundation for future research to focus on relationships among species and the macroevolutionary processes affecting loricariid diversification rates and patterns by generating a genome-scale data set for 140 species spanning 75 genera and five of six previously proposed subfamilies.
62 citations
Cites background or result from "Description of a new catfish genus ..."
...5) were more consistent with the results of previous molecular studies (Chiachio et al., 2008; Cramer et al., 2011; Roxo et al., 2014, 2017; Silva et al., 2016) than results based exclusively on morphological data (Martins et al., 2014; Pereira and Reis, 2017)....
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...Within Ancistrini, the genus Ancistrus was sister to Lasiancistrus forming a clade sister to Pseudolithoxus, corroborating previous morphological and molecular studies (e.g., Armbruster, 2004a, 2008; Covain and Fisch-Muller, 2012; Lujan et al., 2015a; Silva et al., 2016)....
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...Our results corroborate previous molecular studies (Cramer et al., 2011; Roxo et al., 2014, 2017; Silva et al., 2016), which nested additional species of Otothyropsis, Epactionotus and Eurycheilichthys (including the type species E. pantherinus (Reis and Schaefer, 1992)) within Hisonotus....
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...Previous molecular studies have found Otocinclus to be sister to Hypoptopoma (Chiachio et al., 2008) or the currently monotypic genus Lampiella (Roxo et al., 2014; Silva et al., 2016)....
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...2; ML > 95%, BI= 1) corroborating previous molecular (Roxo et al., 2014, 2017; Lujan et al., 2015a; Covain et al., 2016; Silva et al., 2016) and morphological studies (Armbruster, 2004a, 2008)....
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TL;DR: A new species of Parotocinclus is described from tributaries of rio Sao Joao, an Atlantic coastal river of Rio de Janeiro, southeastern Brazil as discussed by the authors, which is distinguished from its congeners by the possession of a triangular patch of dark pigmentation on the anterior portion of the dorsal-fin base, a fully developed adipose fin, complete exposure of the ventral surface of the pectoral girdle and a distinctive pigmentation pattern of the caudal fin.
Abstract: A new species of Parotocinclus is described from tributaries of rio Sao Joao, an Atlantic coastal river of Rio de Janeiro, southeastern Brazil. The new species is distinguished from its congeners by the possession of a triangular patch of dark pigmentation on the anterior portion of the dorsal-fin base, a fully developed adipose fin, complete exposure of the ventral surface of the pectoral girdle, and a distinctive pigmentation pattern of the caudal fin. The caudal fin has a hyaline background with a large black blotch covering its anterior portion, tapering irregularly through distal portions of the ventral lobe with a hyaline rounded area, and a small patch of dark pigmentation on distal portions of the dorsal lobe.
10 citations
TL;DR: A new species of Parotocinclus is described from three small tributaries of the rio Tapajós basin, Mato Grosso State, Brazil, which can be distinguished from its congeners by presenting the following characters.
Abstract: A new species of Parotocinclus is described from three small tributaries of the rio Tapajos basin, Mato Grosso State, Brazil. The new species can be distinguished from its congeners by presenting the following characters: (1) a triangular dark blotch at the anterior base of the dorsal fin, (2) the absence of an adipose fin but presence of one small platelet at typical adipose-fin region, (3) the abdomen completely covered by dermal plates, (4) a pectoral girdle totally exposed, (5) a single series of bicuspid teeth, and (6) the higher number of bicuspid premaxillary and dentary teeth.
8 citations
Cites background from "Description of a new catfish genus ..."
...Recently, as a result of molecular studies, the genus Parotocinclus was recognized as non-monophyletic with several species more related to species assigned to other Otothyrini genera, mainly Hisonotus, than to the type species Parotocinclus maculicauda (e.g. Cramer et al. 2011; Roxo et al. 2014; Silva et al. 2016)....
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...…of molecular studies, the genus Parotocinclus was recognized as non-monophyletic with several species more related to species assigned to other Otothyrini genera, mainly Hisonotus, than to the type species Parotocinclus maculicauda (e.g. Cramer et al. 2011; Roxo et al. 2014; Silva et al. 2016)....
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TL;DR: In this paper , the authors used the most complete datasets of geographic distributions and evolutionary relationships of South American fishes to date, to track the influence of the geological history on the origins, extinctions, and interchanges of these fishes over the past 100 My.
Abstract: Significance South America harbors the most diverse freshwater fish fauna worldwide; however, scientists have few clear answers about the origins of this megadiversity. Here, we used the most complete datasets of geographic distributions and evolutionary relationships of South American fishes to date, to track the influence of the geological history on the origins, extinctions, and interchanges of these fishes over the past 100 My. We found that abrupt increases of species origination coincided in time and place with major mountain uplift and river re-arrangement events. Species in Western Amazonia originated faster and persisted longer than those in other regions. Thus, this region acted as a source of dispersal to other regions, enhancing the exceptional diversity of fishes across the entire continent.
5 citations
TL;DR: In general, the morphological data suggest a subtle variation by river basin, while the genetic data indicates a weak population structuration by hydrographic areas, especially the Chapecó and Passo Fundo rivers.
Abstract: Pareiorhaphis hystrix is a widely distributed species, occurring in the upper and middle Uruguay River and in the Taquari River basin, Patos Lagoon system, southern Brazil. Morphological variation has been detected throughout the distribution of P. hystrix, and this work seeks to test the conspecific nature of populations in several occurrence areas. Specimens from six areas in the Uruguay River basin and three in the Taquari River basin were compared. Variance analysis (ANOVA) was performed for the meristic data, and Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) were conducted for morphometric data. Molecular analyses used coI, cytb, 12S and 16S mitochondrial genes, examining nucleotide diversity, haplotype diversity, genetic distance, and delimitation of possible multiple species through the Generalized Mixed Yule Coalescent (GMYC) method. Phylogenetic relationships of studied populations were also investigated through Bayesian inference. While PCA indicated a tendency of overlap between areas, ANOVA and LDA detected a subtle differentiation between populations from the two hydrographic basins. Yet, both latter analyses recovered the population from Pelotas River, a tributary to Uruguay River, as more similar to populations from Taquari River, which is congruent to morphological observations of anterior abdominal plates. The molecular data indicated a nucleotide diversity lower than the haplotypic diversity, suggestive of recent expansion. The concatenated haplotype network points to slight differentiation between areas, with each locality presenting unique and non-shared haplotypes, although with few mutational steps in general. The species delimitation by coalescence analysis suggested the presence of a variable number of OTUs depending on the inclusion or exclusion of an outgroup. In general, the morphological data suggest a subtle variation by river basin, while the genetic data indicates a weak population structuration by hydrographic areas, especially the Chapeco and Passo Fundo rivers. However, there is still not enough differentiation between the specimens to suggest multiple species. The iterative analyses indicate that Pareiorhaphis hystrix is composed of a single, although variable, species.
4 citations
References
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TL;DR: The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.
Abstract: The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
40,349 citations
"Description of a new catfish genus ..." refers methods in this paper
...Bootstrap (BS) resampling (Felsenstein 1985) was used to evaluate the support for each node, based on 1000 replicates....
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35,309 citations
Proceedings Article•
01 Jan 1973
TL;DR: The classical maximum likelihood principle can be considered to be a method of asymptotic realization of an optimum estimate with respect to a very general information theoretic criterion to provide answers to many practical problems of statistical model fitting.
Abstract: In this paper it is shown that the classical maximum likelihood principle can be considered to be a method of asymptotic realization of an optimum estimate with respect to a very general information theoretic criterion. This observation shows an extension of the principle to provide answers to many practical problems of statistical model fitting.
18,539 citations
"Description of a new catfish genus ..." refers methods in this paper
...DEC and DEC+J models) were compared using the Akaike Information Criterion (AIC) (Akaike 1973) (Suppl....
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...The model that obtained the lowest AIC values was model 2 with the DEC+J model (M2 – DEC + J), which constrained the dispersal rates between adjacent areas at 1.0 and areas separated by one or more intercalated areas at 0.5....
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...The global likelihood of the six biogeographic scenarios found using the two models (i.e. DEC and DEC+J models) were compared using the Akaike Information Criterion (AIC) (Akaike 1973) (Suppl. material 2)....
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01 Jan 1973
TL;DR: In this paper, it is shown that the classical maximum likelihood principle can be considered to be a method of asymptotic realization of an optimum estimate with respect to a very general information theoretic criterion.
Abstract: In this paper it is shown that the classical maximum likelihood principle can be considered to be a method of asymptotic realization of an optimum estimate with respect to a very general information theoretic criterion. This observation shows an extension of the principle to provide answers to many practical problems of statistical model fitting.
15,424 citations
TL;DR: MUSCLE offers a range of options that provide improved speed and / or alignment accuracy compared with currently available programs, and a new option, MUSCLE-fast, designed for high-throughput applications.
Abstract: In a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUSCLE to achieve the highest scores reported to date on four alignment accuracy benchmarks. Here we present a more complete discussion of the algorithm, describing several previously unpublished techniques that improve biological accuracy and / or computational complexity. We introduce a new option, MUSCLE-fast, designed for high-throughput applications. We also describe a new protocol for evaluating objective functions that align two profiles. We compare the speed and accuracy of MUSCLE with CLUSTALW, Progressive POA and the MAFFT script FFTNS1, the fastest previously published program known to the author. Accuracy is measured using four benchmarks: BAliBASE, PREFAB, SABmark and SMART. We test three variants that offer highest accuracy (MUSCLE with default settings), highest speed (MUSCLE-fast), and a carefully chosen compromise between the two (MUSCLE-prog). We find MUSCLE-fast to be the fastest algorithm on all test sets, achieving average alignment accuracy similar to CLUSTALW in times that are typically two to three orders of magnitude less. MUSCLE-fast is able to align 1,000 sequences of average length 282 in 21 seconds on a current desktop computer. MUSCLE offers a range of options that provide improved speed and / or alignment accuracy compared with currently available programs. MUSCLE is freely available at http://www.drive5.com/muscle
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7,617 citations
"Description of a new catfish genus ..." refers methods in this paper
...The sequences were then aligned in MUSCLE (Edgar 2004) using the default parameters, and inspected visually....
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