Fábio F. Roxo

Bio: Fábio F. Roxo is an academic researcher from Sao Paulo State University. The author has contributed to research in topics: Loricariidae & Hypoptopomatinae. The author has an hindex of 13, co-authored 55 publications receiving 679 citations.

Molecular phylogeny and biogeographic history of the armored neotropical catfish subfamilies hypoptopomatinae, neoplecostominae and otothyrinae (siluriformes: loricariidae).

Abstract: The main objectives of this study are estimate a species-dense, time-calibrated molecular phylogeny of Hypoptopomatinae, Neoplecostominae, and Otothyrinae, which together comprise a group of armoured catfishes that is widely distributed across South America, to place the origin of major clades in time and space, and to demonstrate the role of river capture on patterns of diversification in these taxa. We used maximum likelihood and Bayesian methods to estimate a time-calibrated phylogeny of 115 loricariid species, using three mitochondrial and one nuclear genes to generate a matrix of 4,500 base pairs, and used parametric biogeographic analyses to estimate ancestral geographic ranges and to infer the effects of river capture events on the geographic distributions of these taxa. Our analysis recovered Hypoptopomatinae, Neoplecostominae, and Otothyrinae as monophyletic with strong statistical support, and Neoplecostominae as more closely related to Otothyrinae than to Hypoptopomatinae. Our time-calibrated phylogeny and ancestral-area estimations indicate an origin of Hypoptopomatinae, Neoplecostominae, and Otothyrinae during the Lower Eocene in the Atlantic Coastal Drainages, from which it is possible to infer several dispersal events to adjacent river basins during the Neogene. In conclusion we infer a strong influence of river capture in: (1) the accumulation of modern clade species-richness values; (2) the formation of the modern basin-wide species assemblages, and (3) the presence of many low-diversity, early-branching lineages restricted to the Atlantic Coastal Drainages. We further infer the importance of headwater stream capture and marine transgressions in shaping patterns in the distributions of Hypoptopomatinae, Neoplecostominae and Otothyrinae throughout South America.

Biogeographical signature of river capture events in Amazonian lowlands

Abstract: Aim To investigate the effects of river capture on the biogeographical history of South American freshwater fishes. Location Western Amazon and La Plata basins, and adjacent river drainages. Methods We used a species-dense time-calibrated phylogeny of long-whiskered catfishes (Siluriformes, Pimelodidae) to calculate likelihoods for 16 biogeographical scenarios of river capture, each differing in details of (1) landscape evolution and/or (2) models of species range evolution. We designed eight alternative landscape evolution models (LEMs) to represent distinct palaeogeographical river capture histories between the Western Amazon and La Plata drainages during the formation of the Central Andean (Bolivian) orocline (43.0–15.0 Ma). The LEMs differed only in patterns of area-connectivity constraints through time, and otherwise had the same geographical areas, time durations and dispersal probabilities. We used the DEC and DECj models of species range evolution under these eight LEM constraints to calculate likelihood values for ancestral area estimates. Results Divergence time estimates indicated that crown-group pimelodids emerged during the Late Cretaceous or Palaeogene (c. 72.9 ± 20 Ma) and model-selection recovered a best-fit palaeogeographical scenario with (1) a LEM with three river capture events, and (2) a DECj model of species range evolution. These results were quantitatively replicated using Lagrange and BayArea-like methods. Main conclusions The taxon–area chronogram of pimelodids exhibits the characteristic biogeographical signature of river capture; i.e. several non-monophyletic regional (basin-wide) species assemblages coupled with the presence of many species inhabiting more than one basin. These phylogenetic and biogeographical patterns are consistent with the effects of three large-scale river capture events during the formation of the Bolivian orocline.

Using Different Methods to Access the Difficult Task of Delimiting Species in a Complex Neotropical Hyperdiverse Group.

Abstract: The genus Rineloricaria is a Neotropical freshwater fish group with a long and problematic taxonomic history, attributed to the large number of species and the pronounced similarity among them. In the present work, taxonomic information and different molecular approaches were used to identify species boundaries and characterize independent evolutionary units. We analyzed 228 samples assembled in 53 distinct morphospecies. A general mixed yule-coalescent (GMYC) analysis indicated the existence of 70 entities, while BOLD system analyses showed the existence of 56 distinct BINs. When we used a new proposed integrative taxonomy approach, mixing the results obtained by each analysis, we identified 73 OTUs. We suggest that Rineloricaria probably has some complexity in the known species and several species not formally described yet. Our data suggested that other hyperdiverse fish groups with wide distributions can be further split into many new evolutionary taxonomic units.

Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times

Abstract: The estimation of phylogenetic divergence times from sequence data is an important component of many molecular evolutionary studies. There is now a general appreciation that the procedure of divergence dating is considerably more complex than that initially described in the 1960s by Zuckerkandl and Pauling (1962, 1965). In particular, there has been much critical attention toward the assumption of a global molecular clock, resulting in the development of increasingly sophisticated techniques for inferring divergence times from sequence data. In response to the documentation of widespread departures from clocklike behavior, a variety of local- and relaxed-clock methods have been proposed and implemented. Local-clock methods permit different molecular clocks in different parts of the phylogenetic tree, thereby retaining the advantages of the classical molecular clock while casting off the restrictive assumption of a single, global rate of substitution (Rambaut and Bromham 1998; Yoder and Yang 2000).

Lessons from the Past: Biotic Recoveries from Mass Extinctions

Abstract: Although mass extinctions probably account for the disappearance of less than 5% of all extinct species, the evolutionary opportunities they have created have had a disproportionate effect on the history of life. Theoretical considerations and simulations have suggested that the empty niches created by a mass extinction should refill rapidly after extinction ameliorates. Under logistic models, this biotic rebound should be exponential, slowing as the environmental carrying capacity is approached. Empirical studies reveal a more complex dynamic, including positive feedback and exponential growth phase during recoveries. Far from a model of refilling ecospace, mass extinctions appear to cause a collapse of ecospace, which must be rebuilt during the recovery. Other generalities include the absence of a clear correlation between the magnitude of extinction and the pace of recovery, or the resulting ecological and evolutionary disruption; the presence of a survival interval, with few originations, immediately following an extinction and preceding the recovery phase; and the presence of many lineages which persist through an extinction event only to disappear during the subsequent recovery. Several recoveries encompass numerous missing lineages, groups which are found before the extinction, then later in the recovery, but are missing during the initial survival-recovery phase. The limited biogeographic studies of recoveries suggest considerable variability between regions.

Can DNA barcoding accurately discriminate megadiverse Neotropical freshwater fish fauna

Abstract: The megadiverse Neotropical freshwater ichthyofauna is the richest in the world with approximately 6,000 recognized species. Interestingly, they are distributed among only 17 orders, and almost 80% of them belong to only three orders: Characiformes, Siluriformes and Perciformes. Moreover, evidence based on molecular data has shown that most of the diversification of the Neotropical ichthyofauna occurred recently. These characteristics make the taxonomy and identification of this fauna a great challenge, even when using molecular approaches. In this context, the present study aimed to test the effectiveness of the barcoding methodology (COI gene) to identify the mega diverse freshwater fish fauna from the Neotropical region. For this purpose, 254 species of fishes were analyzed from the Upper Parana River basin, an area representative of the larger Neotropical region. Of the 254 species analyzed, 252 were correctly identified by their barcode sequences (99.2%). The main K2P intra- and inter-specific genetic divergence values (0.3% and 6.8%, respectively) were relatively low compared with similar values reported in the literature, reflecting the higher number of closely related species belonging to a few higher taxa and their recent radiation. Moreover, for 84 pairs of species that showed low levels of genetic divergence ( 2%), pointing to at least 23 strong candidates for new species. Our study is the first to examine a large number of freshwater fish species from the Neotropical area, including a large number of closely related species. The results confirmed the efficacy of the barcoding methodology to identify a recently radiated, megadiverse fauna, discriminating 99.2% of the analyzed species. The power of the barcode sequences to identify species, even with low interspecific divergence, gives us an idea of the distribution of inter-specific genetic divergence in these megadiverse fauna. The results also revealed hidden genetic divergences suggestive of reproductive isolation and putative cryptic speciation in some species (23 candidates for new species). Finally, our study constituted an important contribution to the international Barcoding of Life (iBOL.org) project, providing barcode sequences for use in identification of these species by experts and non-experts, and allowing them to be available for use in other applications.

Peixes da planície de inundação do alto rio Paraná e áreas adjacentes: revised, annotated and updated

Abstract: The book “Peixes da planicie de inundacao do alto rio Parana e areas adjacentes” represents the most cohesive data compilation for the rio Parana floodplain. However, considering the dynamicity of the taxonomy of freshwater fishes, several new records and taxonomic changes occurred along the past years. Therefore, the results of that publication were revisited, providing an update of the species list, their taxonomic status, records and geographic distribution, and also new keys for genera and species. The species included were those recorded in the rio Parana basin, from the mouth of the rio Paranapanema to the Itaipu Reservoir, following the general methodology presented in the book. A total of 10 orders, 41 families, 126 genera, and 211 species were registered, with an increase of one order, six families, 14 genera, and 29 species when compared to the book. Additionally, four new genera recently described, five synonymization proposals, 14 new identifications, four new combinations, 12 new species recently described, 34 new records, and nine misidentified species were recorded. These results are associated with the redirection of human and financial resources to that area, which enabled monitoring and intensive exploration of its watercourses; as well as training of taxonomists, and new taxonomic resolutions.