Unexpected diversity in the catfishPseudancistrus brevispinisreveals dispersal routes in a Neotropical center of endemism: the Guyanas Region

Exploring hidden diversity: Molecular insights into the Leporinus species of the rivers of the Brazilian states of Maranhão and Piauí

The present study delved into the world of hidden diversity by examining specimens identified as Leporinus piau from the river basins of the northern Brazilian states of Maranhão and Piauí. Using genetic analyses that combined data from three mitochondrial markers and one nuclear marker, the study identified two well-supported groups, reinforcing the findings of previous publications. The first group, found in samples from the Itapecuru, Mearim, Turiaçu, and Pericumã basins, in Maranhão, appears to represent a relatively ancient diversification and the possibility of concealed cryptic diversity. The second group, comprising specimens from the Parnaíba (Piauí) and Mearim (Maranhão) basins, appears to have resulted from a more recent process of diversification and has a close relationship with Leporinus friderici from the type locality. Our findings not only confirm the existence of a complex scenario of cryptic diversity in the genus Leporinus from the study basins but also underscore the taxonomic inconsistencies within this group of fish. This study offers a comprehensive analysis of the species diversity of the Maranhão and Piauí basins, which are critical regions for the conservation of Amazonian fish, providing valuable insights for the sustainable management and conservation of these fish.

Applying convolutional neural networks to speed up environmental DNA annotation in a highly diverse ecosystem

High-throughput DNA sequencing is becoming an increasingly important tool to monitor and better understand biodiversity responses to environmental changes in a standardized and reproducible way. Environmental DNA (eDNA) from organisms can be captured in ecosystem samples and sequenced using metabarcoding, but processing large volumes of eDNA data and annotating sequences to recognized taxa remains computationally expensive. Speed and accuracy are two major bottlenecks in this critical step. Here, we evaluated the ability of convolutional neural networks (CNNs) to process short eDNA sequences and associate them with taxonomic labels. Using a unique eDNA data set collected in highly diverse Tropical South America, we compared the speed and accuracy of CNNs with that of a well-known bioinformatic pipeline (OBITools) in processing a small region (60 bp) of the 12S ribosomal DNA targeting freshwater fishes. We found that the taxonomic labels from the CNNs were comparable to those from OBITools, with high correlation levels for the composition of the regional fish fauna. The CNNs enabled the processing of raw fastq files at a rate of approximately 1 million sequences per minute, which was about 150 times faster than with OBITools. Given the good performance of CNNs in the highly diverse ecosystem considered here, the development of more elaborate CNNs promises fast deployment for future biodiversity inventories using eDNA.

DNA barcoding and phylogeography of the Hoplias malabaricus species complex

Hoplias malabaricus (Bloch, 1794) is a carnivorous fish species widely distributed from northern to southern South America. This taxon is believed to be a good model for the investigation of biogeographic events that shape the ichthyofauna evolution in the Neotropical freshwater systems. However, many studies have revealed that H. malabaricus hides a species complex that hampers its taxonomic identity and limit its practical value for evolutionary and biogeographic studies. In this paper, we used the mitochondrial gene cytochrome c oxidase subunit I (COI) to delimit cryptic species and explore the phylogeography of H. malabaricus sensu stricto. We found genetic evidence for putative new species in the genus Hoplias and showed that H. malabaricus (Bloch, 1794) is a major clade assigned to barcode index number (BIN) BOLD:ABZ3047. This species is structured in six subpopulations differentiated by high Fst values and restricts gene flow. The subpopulations of the São Francisco/East Atlantic/Eastern Northeast Atlantic/Parnaíba/Itapecuru River basins and Tapajós River Basin were the most differentiated and showed demographic fluctuations. The present distributional pattern is most likely explained through a scenario from the Pleistocene.

Genetic landscape clustering of a large DNA barcoding data set reveals shared patterns of genetic divergence among freshwater fishes of the Maroni Basin

The Maroni is one of the most speciose basins of the Guianas and hosts a megadiverse freshwater fish community. Although taxonomic references based on morphological identification exist for both the Surinamese and Guianese parts of the basin, there are still taxonomic uncertainties concerning the status of several species. We used COI sequences of 1284 fish in conjunction with morphological and biogeographical evidence to assist with species delineation and discovery in order to validate and standardize the current taxonomy. This resulted in a final DNA barcode data set of 199 fish species (125 genera, 36 families and eight orders; 68.86% of strictly freshwater fishes from the basin), among which 25 are new putative candidate species flagged as requiring taxonomic update. DNA barcoding delineation through Barcode Index Numbers (BINs) revealed further cryptic diversity (230 BINs in total). To explore global genetic patterns across the basin, genetic divergence landscapes were computed for 128 species, showing a global trend of high genetic divergence between the Surinamese southwest (Tapanahony and Paloemeu), the Guianese southeast (Marouini, Litany, Tampok, etc.), and the river outlet in the north. This could be explained by lower levels of connectivity between these three main areas and/or the exchange of individuals between these areas and the neighbouring basins. A new method of ordination of genetic landscapes successfully assigned species into cluster groups based on their respective pattern of genetic divergence across the Maroni Basin: genetically homogeneous species were effectively discriminated from species showing high spatial genetic fragmentation and possible lower capacity for dispersal.

A new species of Bryconops (Characiformes: Iguanodectidae) from Atlantic coastal drainages of Suriname and French Guiana

ABSTRACT A new species of Bryconops is described based on its unique caudal-fin color pattern, with a dark blotch occupying the mid-basal region of the caudal-fin dorsal lobe, and a combination of 29-32 branched anal-fin rays, 44-47 perforated scales in the lateral line, six rows of scales above the lateral line, and a deep body (30.3-31.7 % SL). The new species belongs to the subgenus Bryconops based on its edentulous and short maxilla, with the posterior extension of that bone not reaching the junction between the second and third infraorbitals. The new species was previously reported in the literature as B. caudomaculatus. However, these species differ from each other in morphometric and meristic characters, as well as in color pattern. Comments on distribution of Bryconops species in coastal drainages of Suriname and French Guiana additional support for biogeographic hypotheses in this area.

The distribution of Cteniloricaria (Siluriformes: Loricariidae): known and new records in Brazil suggest headwater captures as drivers of disjoint distribution

Abstract Cteniloricaria is a genus of Neotropical armored catfishes belonging to the Loricariinae, currently including two valid species: C. platystoma and C. napova. Cteniloricaria platystoma is presently recorded across the main coastal drainages of the Guiana Shield, from the Sinnamary River, French Guiana, to the Essequibo River basin, Guyana, and is considered to be restricted to the region. Cteniloricaria napova is only known from its type locality at the headwaters of the Paru de Oeste River, Amazon basin, Sipaliwini Savannah, Trio Amerindian territory in Suriname, close to the Brazilian border. Based on a specimen of C. napova, captured in the Cuminapanema River, a tributary to the Curuá River, within Brazilian territory, the geographic distribution of the species and the genus is extended, representing the first record of Cteniloricaria in Brazil. The genus shows a disjoint distribution, and divergence between populations in the north-flowing coastal rivers of the Guianas and the south-flowing Amazon tributaries, and more recent headwater capture between south-flowing Amazon tributaries, may have played a key role in shaping its current distribution. Illustrations, diagnostic characters, morphometrics, description of the habitat where the new specimen was captured, extinction risk assessment, and a discussion of the distribution of the genus are provided.

Evolutionary units delimitation and continental multilocus phylogeny of the hyperdiverse catfish genus Hypostomus

With 149 currently recognized species, Hypostomus is one of the most species-rich catfish genera in the world, widely distributed over most of the Neotropical region. To clarify the evolutionary history of this genus, we reconstructed a comprehensive phylogeny of Hypostomus based on four nuclear and two mitochondrial markers. A total of 206 specimens collected from the main Neotropical rivers were included in the present study. Combining morphology and a Bayesian multispecies coalescent (MSC) approach, we recovered 85 previously recognized species plus 23 putative new species, organized into 118 'clusters'. We presented the Cluster Credibility (CC) index that provides numerical support for every hypothesis of cluster delimitation, facilitating delimitation decisions. We then examined the correspondence between the morphologically identified species and their inter-specific COI barcode pairwise divergence. The mean COI barcode divergence between morphological sisters species was 1.3 ± 1.2%, and only in 11% of the comparisons the divergence was ≥2%. This indicates that the COI barcode threshold of 2% classically used to delimit fish species would seriously underestimate the number of species in Hypostomus, advocating for a taxon-specific COI-based inter-specific divergence threshold to be used only when approximations of species richness are needed. The phylogeny of the 108 Hypostomus species, together with 35 additional outgroup species, confirms the monophyly of the genus. Four well-supported main lineages were retrieved, hereinafter called super-groups: Hypostomus cochliodon, H. hemiurus, H. auroguttatus, and H. plecostomus super-groups. We present a compilation of diagnostic characters for each super-group. Our phylogeny lays the foundation for future studies on biogeography and on macroevolution to better understand the successful radiation of this Neotropical fish genus.

Phylogeny and biogeography of the Brazilian–Guiana Shield endemic Corymbophanes clade of armoured catfishes (Loricariidae)

Numerous rivers, interrupted by large waterfalls and extensive rapids, drain the geologically ancient Guiana Shield Highlands. We describe a new armoured catfish genus and two new species endemic to the upper Ireng and Kuribrong rivers, respective tributaries of the Amazon and Essequibo basins in western Guiana. Corymbophanes ameliae sp. nov. is distinguished by having vermiculations on the abdomen, bands on the caudal fin, the anal fin i,5 and narrow caudal peduncle. Yaluwak primus gen. & sp. nov. is distinguished by having evertible cheek odontodes, a plated snout, a tall caudal peduncle and absence of adipose fin and iris operculum. We present a new molecular phylogenetic analysis inclusive of these and several related genera that suggests that the Corymbophanes clade (Araichthys, Corymbophanes, Cryptancistrus, Guianancistrus, Hopliancistrus and Yaluwak) originated in the Guiana Shield with secondary dispersal to the Brazilian Shield. Within the Guiana Shield, relationships among Corymbophanes and Yaluwak are consistent with geodispersal between drainages via headwater capture, although an uplift-mediated relictual distribution cannot be ruled out. ND2 haplotype structure among C. ameliae populations suggests that ichthyofaunal diversity on the Guiana Shield escarpment is shaped not only by inter-, but also intrafluvial barriers to gene flow.

Evidence of cryptic lineages within a small South American crocodilian: the Schneider's dwarf caiman Paleosuchus trigonatus (Alligatoridae: Caimaninae)

Schneider’s dwarf caiman Paleosuchus trigonatus is one of the smallest living crocodilians. Due to its broad distribution, cryptic behavior, and small home range, the species is well suited for the study of phylogeographic patterns on a continental scale. Additionally, this species is under threat due to habitat loss, trade and harvest, but is considered at low conservation risk by the IUCN. In the present study we test the hypothesis that P. trigonatus is comprised of geographically structured lineages. Phylogenetic reconstructions of the mitochondrial cytochrome b gene and single locus species discovery methods revealed the existence of two well-supported lineages within P. trigonatus—an Amazonian and Guianan lineage. Fossil calibrated divergence of these lineages was estimated to have occurred in the Late Miocene (7.5 Ma). The hypothesis that the Atlantic coast drainages might have been colonized from the southeast or central Amazon is supported by demographic metrics and relatively low genetic diversity of the Coastal and upper Branco populations when compared to the Amazon basin populations. The Amazon basin lineage is structured along an east-west gradient, with a sharp transition in haplotype frequencies to the east and west of the Negro and Madeira rivers. These lineages are already under anthropogenic threat and, therefore, are conservation dependent. Recognition of these lineages will foster discussion of conservation future of P. trigonatus and these lineages.

A continental-wide molecular approach unraveling mtDNA diversity and geographic distribution of the Neotropical genus Hoplias

With an estimate of around 9,000 species, the Neotropical region hosts the greatest diversity of freshwater fishes of the world. Genetic surveys have the potential to unravel isolated and unique lineages and may result in the identification of undescribed species, accelerating the cataloguing of extant biodiversity. In this paper, molecular diversity within the valuable and widespread Neotropical genus Hoplias was assessed by means of DNA Barcoding. The geographic coverage spanned 40 degrees of latitude from French Guiana to Argentina. Our analyses revealed 22 mitochondrial lineages fully supported by means of Barcode Index Number, Automatic Barcode Gap Discovery and phylogenetic analyses. This mtDNA survey revealed the existence of 15 fully supported mitochondrial lineages within the once considered to be the continentally distributed H. malabaricus. Only four of them are currently described as valid species however, leaving 11 mitochondrial lineages currently "masked" within this species complex. Mean genetic divergence was 13.1%. Barcoding gap analysis discriminated 20 out of the 22 lineages tested. Phylogenetic analyses showed that all taxonomically recognized species form monophyletic groups. Hoplias malabaricus sensu stricto clustered within a large clade, excluding the representatives of the La Plata River Basin. In the H. lacerdae group, all species but H. curupira showed a cohesive match between taxonomic and molecular identification. Two different genetic lineages were recovered for H. aimara. Given the unexpected hidden mitochondrial diversity within H. malabaricus, the COI sequence composition of specimens from Suriname (the type locality), identified as H. malabaricus sensu stricto, is of major importance.

An integrative framework to reevaluate the Neotropical catfish genus Guyanancistrus (Siluriformes: Loricariidae) with particular emphasis on the Guyanancistrus brevispinis complex

Characterizing and naming species becomes more and more challenging due to the increasing difficulty of accurately delineating specific bounderies. In this context, integrative taxonomy aims to delimit taxonomic units by leveraging the complementarity of multiple data sources (geography, morphology, genetics, etc.). However, while the theoretical framework of integrative taxonomy has been explicitly stated, methods for the simultaneous analysis of multiple data sets are poorly developed and in many cases different information sources are still explored successively. Multi-table methods developed in the field of community ecology provide such an intregrative framework. In particular, multiple co-inertia analysis is flexible enough to allow the integration of morphological, distributional, and genetic data in the same analysis. We have applied this powerfull approach to delimit species boundaries in a group of poorly differentiated catfishes belonging to the genus Guyanancistrus from the Guianas region of northeastern South America. Because the species G. brevispinis has been claimed to be a species complex consisting of five species, particular attention was paid to taxon. Separate analyses indicated the presence of eight distinct species of Guyanancistrus, including five new species and one new genus. However, none of the preliminary analyses revealed different lineages within G. brevispinis, and the multi-table analysis revealed three intraspecific lineages. After taxonomic clarifications and description of the new genus, species and subspecies, a reappraisal of the biogeography of Guyanancistrus members was performed. This analysis revealed three distinct dispersals from the Upper reaches of Amazonian tributaries toward coastal rivers of the Eastern Guianas Ecoregion. The central role played by the Maroni River, as gateway from the Amazon basin, was confirmed. The Maroni River was also found to be a center of speciation for Guyanancistrus (with three species and two subspecies), as well as a source of dispersal of G. brevispinis toward the other main basins of the Eastern Guianas.

Multifactorial genetic divergence processes drive the onset of speciation in an Amazonian fish

Understanding the processes that drive population genetic divergence in the Amazon is challenging because of the vast scale, the environmental richness and the outstanding biodiversity of the region. We addressed this issue by determining the genetic structure of the widespread Amazonian common sardine fish Triportheus albus (Characidae). We then examined the influence, on this species, of all previously proposed population-structuring factors, including isolation-by-distance, isolation-by-barrier (the Teotônio Falls) and isolation-by-environment using variables that describe floodplain and water characteristics. The population genetics analyses revealed an unusually strong structure with three geographical groups: Negro/Tapajós rivers, Lower Madeira/Central Amazon, and Upper Madeira. Distance-based redundancy analyses showed that the optimal model for explaining the extreme genetic structure contains all proposed structuring factors and accounts for up to 70% of the genetic structure. We further quantified the contribution of each factor via a variance-partitioning analysis. Our results demonstrate that multiple factors, often proposed as individual drivers of population divergence, have acted in conjunction to divide T. albus into three genetic lineages. Because the conjunction of multiple long-standing population-structuring processes may lead to population reproductive isolation, that is, the onset of speciation, we suggest that the multifactorial population-structuring processes highlighted in this study could account for the high speciation rate characterising the Amazon Basin.

Biogeography of Amazonian fishes: deconstructing river basins as biogeographic units

ABSTRACT Biogeography of Amazonian fishes (2,500 species in vastly disjunct lineages) is complex and has so far been approached only partially. Here, we tackle the problem on the basis of the largest database yet on geographical distribution and phylogenetic relationships of Amazonian fishes, including all information available. Distributions of 4,095 species (both Amazonian and outgroups) and 84 phylogenetic hypotheses (comprising 549 phylogenetically-informative nodes) were compiled, qualified and plotted onto 46 areas (29 Amazonian and 17 non-Amazonian). The database was analyzed with PAE, CADE, BPA and BPA0, yielding largely congruent results and indicating that biogeographic signal is detectable on multiple dimensions of fish distribution, from single species ranges to cladistic congruence. Agreement is especially pronounced in deeper components, such as Trans-Andean, Cis-Andean, Western Amazon and Orinoco basins. Results show that all major Amazonian tributaries, as well as the Amazon basin itself, are non-monophyletic and constitute hybrid sets of heterogeneous biotic partitions. Amazonian drainages should not be assumed a priori as historically cohesive areas, contrary to widespread practice. Our hypothesis allows re-evaluation of broader issues in historical biogeography, such as the predictive power of biogeographic hypotheses, the vicariant/dispersal duality, the significance of widely distributed taxa, and the need for temporal dimension in biogeographic patterns.

New species of the Pseudancistrus barbatus group (Siluriformes, Loricariidae) with comments on its biogeography and dispersal routes

A new species of Pseudancistrus is described from the Tapajós Basin, and assigned to the P. barbatus group by having hypertrophied odontodes along the snout and lacking evertible cheek plates. The new species is distinguished from other species in that group (P. barbatus, P. corantijniensis, P. depressus and P. nigrescens) by its pattern of spots, length and color of snout odontodes, greater head depth, cleithral width, anal-fin spine length, peduncle depth and internares width. Molecular phylogenetic results corroborate placement of the new species in the Pseudancistrus barbatus group which is otherwise distributed in the Xingu Basin and rivers draining the Guyana Shield into the Atlantic Ocean. Topology tests strongly reject alternative hypotheses supporting close relationships with Guyanancistrus, Lithoxancistrus or the species Pseudancistrus pectegenitor, P. sidereus and P. genisetiger. Additionally, we propose two hypotheses on the distribution of the new species in the rio Tapajós, a Brazilian Shield drainage. The first one proposes that ancestral stock of the P. barbatus group was widely distributed throughout rivers draining the Guyana and Brazilian shields, and the species P. zawadzkii and Pseudancistrus sp. L17 are in the limit of the distribution for the group in Tapajós and Xingu rivers. The second hypothesis proposes that ancestral stock of the P. barbatus group was restricted to Guyana Shield rivers, and that headwater capture events permitted several dispersal routs through Guyana and Amazon rivers, permitted that the ancestral lineages of Pseudancistrus sp. L17 and P. zawadzkii reached the rivers of Amazon basin.

Phylogeographical patterns shed light on evolutionary process in South America

The South American continent is composed of several biogeographical regions harbouring the highest biodiversity on the globe, encompassing five of the world's biodiversity 'hot spots'. Nonetheless, the patterns and processes responsible for shaping its astonishing species diversity are largely unknown. Here, we present a review of current South American phylogeographical knowledge based on published articles on this topic. An appraisal of the literature reveals emerging phylogeographical patterns in the biota of South America. The striking phylogeographical divergence observed among organism lineages in South American studies is suggestive of high levels of undocumented species diversity. The interplay between Pleistocene climatic oscillations and Pliocene/Miocene orogenic events has contributed to shaping the current diversity and distribution of modern lineages in both the tropical and temperate regions of South America. Although older divergence times were observed for a range of species, most herpetofauna underwent an intraspecific lineage split much earlier than other organisms. The geographical ranges of species associated with forest habitats were reduced mainly during glacial cycles, whereas species associated with open vegetation domains have shown variable responses to climatic oscillations. The results suggest a highly complex mosaic of phylogeographical patterns in South America. We suggest future research directions to promote a better understanding of the origin and maintenance of the South American biota.

A young clade repeating an old pattern: diversity in Nothonotus darters (Teleostei: Percidae) endemic to the Cumberland River

Hypotheses of diversification in eastern North American freshwater fishes have focused primarily on allopatric distributions of species between disjunct highland areas and major river systems. However, these hypotheses do not fully explain the rich diversity of species within highland regions and river systems. Relatively old diversification events at small geographic scales have been observed in the Barcheek Darter subclade that occurs in the Cumberland River drainage (CRD) in Kentucky and Tennessee, United States of America, but it is unknown if this pattern is consistent in other darter subclades. We explored phylogeographic diversity in two species of Nothonotus darters, N. microlepidus and N. sanguifluus, endemic to the CRD to compare phylogenetic patterns between Barcheek Darters and species of Nothonotus. We collected sequence data for a mitochondrial gene (cytb) and three nuclear genes (MLL, S7 and RAG1) from 19 N. microlepidus and 35 N. sanguifluus specimens. Gene trees were estimated using maximum likelihood and Bayesian methods, and a 'species tree' was inferred using a Bayesian method. These trees indicate that species diversity in Nothonotus is underestimated. Five distinct lineages were evident, despite retained ancestral polymorphism and unsampled extirpated populations. Comparison of chronograms for Barcheek Darters and Nothonotus revealed that microendemism resulting from species diversification at small geographic scales in the CRD is a consistent pattern in both old and young darter subclades. Our analyses reveal that geographic isolating mechanisms that result in similar phylogeographic patterns in the CRD are persistent through long expanses of evolutionary time.

Transcriptome screen for fast evolving genes by Inter-Specific Selective Hybridization (ISSH)

Background

Fast evolving genes are targets of an increasing panel of biological studies, from cancer research to population genetics and species specific adaptations. Yet, their identification and isolation are still laborious, particularly for non-model organisms. We developed a method, named the Inter-Specific Selective Hybridization (ISSH) method, for generating cDNA libraries enriched in fast evolving genes. It utilizes transcripts of homologous tissues of distinct yet related species. Experimental hybridization conditions are monitored in order to discard transcripts that do not find their homologous counterparts in the two species sets as well as transcripts that display a strong complementarity between the two species. Only heteroduplexes that disanneal at low stringency are used for constructing the resulting cDNA library.

Results

We demonstrate the efficiency of the ISSH method by generating a brain cDNA library enriched in fast evolving transcripts of a non-model catfish species as well as a control, non-enriched library. Our results indicate that the enriched library contains effectively more fast evolving sequences than the control library. Gene annotation analyses also indicate enrichment in genes with low expression levels and non-ubiquitously expressed genes, both categories encompassing the majority of fast evolving genes. Furthermore, most of the identified transcripts show higher sequence divergence between two closely related catfish species as compared to recognized fast evolving DNA markers.

Conclusions

The ISSH method offers a simple, inexpensive and efficient way to screen the transcriptome for isolating fast evolving genes. This method opens new opportunities in the investigation of biological mechanisms that include fast evolving genes, such as the evolution of lineage specific processes and traits responsible for species adaptation to their environment.