Molecular phylogeny and timing of diversification in South American Cynolebiini seasonal killifishes

Geoclimatic drivers of diversification in the largest arid and semi-arid environment of the Neotropics: Perspectives from phylogeography

The South American Dry Diagonal, also called the Diagonal of Open Formations, is a large region of seasonally dry vegetation extending from northeastern Brazil to northern Argentina, comprising the Caatinga, Cerrado, and Chaco subregions. A growing body of phylogeography literature has determined that a complex history of climatic changes coupled with more ancient geological events has produced a diverse and endemic-rich Dry Diagonal biota. However, the exact drivers are still under investigation, and their relative strengths and effects are controversial. Pleistocene climatic fluctuations structured lineages via vegetation shifts, refugium formation, and corridors between the Amazon and Atlantic forests. In some taxa, older geological events, such as the reconfiguration of the São Francisco River, uplift of the Central Brazilian Plateau, or the Miocene inundation of the Chaco by marine incursions, were more important. Here, we review the Dry Diagonal phylogeography literature, discussing each hypothesized driver of diversification and assessing degree of support. Few studies statistically test these hypotheses, with most support drawn from associating encountered phylogeographic patterns such as population structure with the timing of ancient geoclimatic events. Across statistical studies, most hypotheses are well supported, with the exception of the Pleistocene Arc Hypothesis. However, taxonomic and regional biases persist, such as a proportional overabundance of herpetofauna studies, and the under-representation of Chaco studies. Overall, both Pleistocene climate change and Neogene geological events shaped the evolution of the Dry Diagonal biota, though the precise effects are regionally and taxonomically varied. We encourage further use of model-based analyses to test evolutionary scenarios, as well as interdisciplinary collaborations to progress the field beyond its current focus on the traditional set of geoclimatic hypotheses.

Phylogeny and historical biogeography of neotropical catfishes Trichomycterus (Siluriformes: Trichomycteridae) from eastern Brazil

The catfish subfamily Trichomycterinae is widely distributed in South America inhabiting several habitats, but specially mountain streams. Trichomycterus is the most speciose trichomycterid genus and recently due to his paraphyletic condition has been restricted to a clade from eastern Brazil called Trichomycterus sensu stricto comprising around 80 valid species distributed in seven areas of endemism of eastern Brazil. This paper aims to analyse the biogeographical events responsible for the distribution of Trichomycterus s.s., by reconstructing the ancestral data based on a time-calibrated multigene phylogeny. A multi-gene phylogeny was generated using 61 species of Trichomycterus s.s. and 30 outgroups, with divergence events calculated based on the estimated origin of Trichomycteridae. Two event-based analyses were applied to investigate the biogeographical events responsible the present distribution of Trichomycterus s.s. and suggest that the modern distribution of the group is a result of different vicariance and dispersal events. The diversification of Trichomycterus s.s. subgenera occurred in the Miocene, except for Megacambeva, with different biogeographical events shaping its distribution in eastern Brazil. An initial vicariant event split up the Fluminense ecoregion from the Northeastern Mata Atlantica + Paraíba do Sul + Fluminense + Ribeira do Iguape + Upper Paraná ecoregions. Dispersal events occurred mainly between Paraíba do Sul and neighboring river basins, with additional dispersal events from Northeastern Mata Atlantica to Paraíba do Sul, from São Francisco to Northeastern Mata Atlântica, and from Upper Paraná to São Francisco.

Multilocus phylogeny and historical biogeography of Hypostomus shed light on the processes of fish diversification in La Plata Basin

Distribution history of the widespread Neotropical genus Hypostomus was studied to shed light on the processes that shaped species diversity. We inferred a calibrated phylogeny, ancestral habitat preference, ancestral areas distribution, and the history of dispersal and vicariance events of this genus. The phylogenetic and distribution analyses indicate that Hypostomus species inhabiting La Plata Basin do not form a monophyletic clade, suggesting that several unrelated ancestral species colonized this basin in the Miocene. Dispersal to other rivers of La Plata Basin started about 8 Mya, followed by habitat shifts and an increased rate of cladogenesis. Amazonian Hypostomus species colonized La Plata Basin several times in the Middle Miocene, probably via the Upper Paraná and the Paraguay rivers that acted as dispersal corridors. During the Miocene, La Plata Basin experienced marine incursions, and geomorphological and climatic changes that reconfigured its drainage pattern, driving dispersal and diversification of Hypostomus. The Miocene marine incursion was a strong barrier and its retraction triggered Hypostomus dispersal, increased speciation rate and ecological diversification. The timing of hydrogeological changes in La Plata Basin coincides well with Hypostomus cladogenetic events, indicating that the history of this basin has acted on the diversification of its biota.

Diversification of Neotropical Freshwater Fishes

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.

Transcriptome-Based SNP Discovery and Validation in the Hybrid Zone of the Neotropical Annual Fish Genus Austrolebias

The genus Austrolebias (Cyprinodontiformes: Rivulidae) represents a specious group of taxa following annual life cycles in the neotropical ichthyofauna. They live in temporary ponds and each generation must be completed in a few months, depending on environmental stochasticity. Annual fish survive the dry season through diapausing eggs buried in the substrate of these ponds. A hypothesized bimodal hybrid zone between two taxa of the genus, A. charrua and A. reicherti from Dos Patos Merin lagoon system, was recently proposed based on genetics and morphological analyses. However, hundreds of additional nuclear molecular markers should be used to strongly support this hypothesized bimodal pattern. In the present paper, we conducted RNA-seq-based sequencing of the transcriptomes from pools of individuals of A. charrua, A. reicherti and their putative natural hybrids from the previously characterized hybrid zone. As a result, we identified a set of 111,725 SNP (single nucleotide polymorphism) markers, representing presumably fixed allelic differences among the two species. The present study provided the first panel of 106 SNP markers as a single diagnostic multiplex assay and validated their capacity to reconstruct the patterns of the hybrid zone between both taxa. These nuclear markers combined with Cytb gene and morphological analyses detected a population structure in which some groups among the hybrid swarms showed different level of introgression towards one or the other parental species according to their geographic distribution. High-quality transcriptomes and a large set of gene-linked SNPs should greatly facilitate functional and population genomics studies in the hybrid zone of these endangered species.

Diversity and conservation of seasonal killifishes of the Hypsolebias fulminantis complex from a Caatinga semiarid upland plateau, São Francisco River basin, northeastern Brazil (Cyprinodontiformes, Aplocheilidae)

A high concentration of endemic species of seasonal killifishes has been recorded for a small area encompassing the highland plateaus associated with the upper section of the Carnaúba de Dentro River drainage and adjacent drainages of the middle section of the São Francisco River basin, northeastern Brazil. The present study is primarily directed to the taxonomy of theH.fulminantisspecies complex in this region, and describes habitat decline and extirpation of natural killifish populations recorded in field studies between 1993 and 2017. Both morphological characters and molecular species delimitation methods using single-locus models (GMYC and bPTP) support recognition of two closely related endemic species,H.fulminantisandH.splendissimusCosta,sp. n.The new species is distinguished from other congeners of theH.fulminantiscomplex by having a red pectoral fin in males, well-developed filamentous rays on the tips of the dorsal and anal fins in adult males, and the second proximal radial of the dorsal fin between the neural spines of the 8thand 9thvertebrae in males. Most recent field inventories indicated possible local extinction of populations ofH.fulminantisandH.splendissimusin the studied area, but additional field studies should be made in other parts of the upper Carnaíba de Dentro River basin to evaluate the current conservation status of these species.

Cryptic species diversity in the Hypsolebiasmagnificus complex, a clade of endangered seasonal killifishes from the São Francisco River basin, Brazilian Caatinga (Cyprinodontiformes, Aplocheilidae)

A great diversity of animal species adapted to life in the semi-arid Caatinga of northeastern Brazil, including seasonal killifishes, has been reported in the last three decades. More recently, field and molecular data have shown a high occurrence of cryptic species. The killifish group herein analysed, the Hypsolebiasmagnificus species complex, is endemic to the middle and southern portion of the Caatinga, occupying about 120 km along the floodplains of the middle São Francisco River and some adjacent tributaries. Species of this complex are rare and presently considered threatened with extinction, being uniquely found in pools protected by trees and bushes. Single-locus delimitation methods were used to test species limits of populations displaying different colour patterns along the whole distribution of the complex. All analyses consistently supported the three nominal species and two new, herein described: H.gardneri Costa, sp. n., from the floodplains of the middle São Francisco River and H.hamadryades Costa, sp. n., from the Gorotuba River floodplains. The phylogenetic analysis highly supports H.hamadryades as sister to a clade comprising H.gardneri and H.harmonicus. Our field observations suggest that H.hamadryades is a miniature species. This study indicates that the H.magnificus complex comprises cryptic species apparently endemic to small areas and extremely vulnerable to environmental changes, deserving high concern.

A new miniature cryptic species of the seasonal killifish genus Spectrolebias from the Tocantins River basin, central Brazil (Cyprinodontiformes, Aplocheilidae)

The miniature seasonal killifish Spectrolebiascostae, first described for the middle Araguaia River basin, has been also recorded from two areas in the middle Tocantins River basin, from where male specimens exhibit some differences in their colour pattern. Analyses directed to species delineation (GMYC and bPTP), using a fragment of the mitochondrial gene COI, strongly support two species, S.costae from the Araguaia River basin and a new species from the Tocantins River basin. Spectrolebiasgracilis sp. n. is described on the basis of specimens collected from two localities separated by about 530 km, Canabrava River floodplains near Alvorada do Tocantins and Tocantins River floodplains near Palmeirante. Field inventories were unsuccessful in finding additional populations in the region, which is attributed to the high environmental degradation, including several large dams that have permanently inundated typical killifish habitats. Spectrolebiasgracilis is member of a clade also including S.costae, S.inaequipinnatus, and S.semiocellatus, diagnosed by having the dorsal and anal fins in males with iridescent dots restricted to their basal portion, caudal fin in males hyaline, and caudal-fin base with two pairs of neuromasts. Within this clade, a single miniaturisation event is supported for the most recent common ancestor of the subclade comprising S.costae and S.gracilis, which differ from other congeners by reaching only about 20 mm standard length as maximum adult size.

Three new species of the ‘ Geophagus’ brasiliensis species group from the northeast Brazil (Cichlidae, Geophagini)

Morphological characters and phylogenetic trees generated by analyses of segments of two mitochondrial genes cytochrome b and cytochrome c oxidase I support recognition of three new species of the ‘Geophagus’ brasiliensis species group from coastal basins of northeast Brazil. All new species were diagnosed by exclusive morphological characters and exclusive nucleotide transformations. Geophagusrufomarginatus sp. n., from the Rio Buranhém Basin, is distinguished from all other species of the group by dorsal-fin lappets with red edges, the presence of longitudinal series of small light blue spots between the anal-fin spines and rays, and non-denticulated gill-rakers; it is closely related to G.brasiliensis and G.iporangensis. Geophagusmultiocellus sp. n., from the Rio de Contas Basin, is distinguished from all other species of the group by having small pale blue spots with minute bright blue dots at their centres, that are often vertically coalesced to form short bars on the caudal fin. Geophagussantosi sp. n., from the Rio Mariana Basin, is distinguished from all other species of the group by having blue stripes parallel to the dorsal and anal fin rays on their longest portions. Geophagusmultiocellus and G.santosi belong to the same clade of G.itapicuruensis. The clade composed by the Rio Paraguaçu Basin species was recovered as the sister group of the other species of the ‘G.’ brasiliensis species group.

An endangered new species of seasonal killifish of the genus Austrolebias (Cyprinodontiformes: Aplocheiloidei) from the Bermejo river basin in the Western Chacoan Region

Austrolebias wichi, new species, is herein described from seasonal ponds of the Bermejo river basin in the Western Chacoan district in northwestern Argentina. This species was found in a single pond, a paleochannel of the Bermejo River, which is seriously disturbed by soybean plantations surrounding it. Despite intensive sampling in the area, this species was only registered in this pond where it was relatively scarce. Therefore, we consider this species as critically endangered. This species is the sister species of A. patriciae in our phylogenetic analyses and is similar, in a general external aspect, to A. varzeae and A. carvalhoi. It can be distinguished among the species of Austrolebias by its unique color pattern in males. Additionally, from A. varzeae by presenting a supraorbital band equal or longer than the infraorbital band (vs. shorter) and from A. patriciae by the convex dorsal profile of head (vs. concave). Further diagnostic characters and additional comments on its ecology and reproduction are provided.

Synchronic historical patterns of species diversification in seasonal aplocheiloid killifishes of the semi-arid Brazilian Caatinga

The Caatinga is the largest nucleus of seasonally dry tropical forests in South America, but little is known about the evolutionary history and biogeography of endemic organisms. Evolutionary diversification and distribution of terrestrial vertebrates endemic to the Caatinga have been explained by palaeogeographical Neogene episodes, mostly related to changes in the course of the São Francisco River, the largest river in the region. Our objective is to estimate the timing of divergence of two endemic groups of short-lived seasonal killifishes inhabiting all ecoregions of the Caatinga, testing the occurrence of synchronic events of spatial diversification in light of available data on regional palaeogeography. We performed independent time-calibrated phylogenetic molecular analyses for two clades of sympatric and geographically widespread seasonal killifishes endemic to the Caatinga, the Hypsolebias antenori group and the Cynolebias alpha-clade. Our results consistently indicate that species diversification took place synchronically in both groups, as well as it is contemporary to diversification of other organisms adapted to life in the semi-arid Caatinga, including lizards and small mammals. Both groups originated during the Miocene, but species diversification started between the Late Miocene and Early Pliocene, when global cooling probably favoured the expansion of semi-arid areas. Synchronic diversification patterns found are chronologically related to Tertiary palaeogeographical reorganizations associated to continental drift and to Quaternary climatic changes, corroborating the recent proposal that South American biodiversity has been continuously shaped between the Late Paleogene and Pleistocene.

Review of the family Rivulidae (Cyprinodontiformes, Aplocheiloidei) and a molecular and morphological phylogeny of the annual fish genus Austrolebias Costa 1998

ABSTRACT The family Rivulidae is the fourth most diverse clade of Neotropical fishes. Together with some genera of the related African family Nothobranchiidae, many rivulids exhibit a characteristic annual life cycle, with diapausing eggs and delayed embryonic development, which allows them to survive in the challenging seasonal ponds that they inhabit. Rivulidae also includes two species known as the only the self-fertilizing vertebrates and some species with internal fertilization. The first goal of this article is to review the systematics of the family considering phylogenetic relationships and synapomorphies of subfamilial clades, thus unifying information that is dispersed throughout the literature. From this revision, it is clear that phylogenetic relationships within Rivulidae are poorly resolved, especially in one of the large clades that compose it, the subfamily Rivulinae, where conflicting hypotheses of relationships of non-annual and annual genera are evident. The second goal of this work is to present an updated phylogenetic hypothesis (based on mitochondrial, nuclear, and morphological information) for one of the most speciose genus of Rivulidae, Austrolebias. Our results confirm the monophyly of the genus and of some subgeneric clades already diagnosed, but propose new relationships among them and their species composition, particularly in the subgenus Acrolebias.