Transcontinental dispersal, ecological opportunity and origins of an adaptive radiation in the Neotropical catfish genus Hypostomus (Siluriformes: Loricariidae)

Molecular and morphometric data provide evidence of intraspecific variation in shape and pigmentation pattern in Otocinclus cocama (Siluriformes: Loricariidae) across major river drainages

Otocinclus cocama, a uniquely colored species of the loricariid catfish genus Otocinclus described solely from the type locality in the lower Ucayali River in northern Peru, is reported occurring in the Tigre River, a tributary to the Marañón River that drains a different section of the Andean Mountain range in the western Amazon. Both populations differ in the number of dark bars spanning the flanks of the body, and we investigated whether these morphotypes constitute distinct species. The body shapes of populations from the Tigre and Ucayali rivers were compared using geometric morphometrics. Although principal component analysis detected a broad overlap between populations, multivariate analysis of variance and linear driscriminat analysis revealed a subtle differentiation between the populations of the two hydrographic basins. Average body shape of the Ucayali River population tend to be slightly higher than that of the Tigre River, with the caudal peduncle stretched vertically in the Ucayali population. Multivariate regression of shape and centroid size revealed an allometric effect of 10.7% (p < 0.001), suggesting that the variation between Tigre and Ucayali populations was purely shape variation. Molecular data of coI, cytb, nd2, and 16S mitochondrial genes indicated a nucleotide diversity range from 0.001 to 0.003, and haplotypic diversity range from 0.600 ± 0.11 to 0.79 ± 0.07. The median-joining haplotype network for the concatenated matrix exhibited two divergent haplogroups related to the geographic area and separated by <10 mutational steps. The molecular species delimitation methods based on distance (automatic barcode gap discovery and assemble species by automatic partitioning) recovered two molecular lineages evolving independently, being one of the lineages formed by individuals from both populations. Tree-based methods (generalized mixed Yule coalescent and Bayesian implementation of the Poisson tree process) recovered similar topologies and supported single lineage recognition. Methods of molecular delimitation of species disclosed the high similarity between the two populations of Otocinclus cocama, further supported by the presence of old haplotypes common to both groups which could indicate that the populations still maintain gene flow. Although the morphological data reveal a subtle variation between both river basins, the molecular data suggest a weak population structuration based on hydrographic areas, but not different species lineages, therefore Otocinclus cocama is composed of a single lineage with two distinct morphotypes.

Freshwater fish diversity in the western Amazon basin shaped by Andean uplift since the Late Cretaceous

South America is home to the highest freshwater fish biodiversity on Earth, and the hotspot of species richness is located in the western Amazon basin. The location of this hotspot is enigmatic, as it is inconsistent with the pattern observed in river systems across the world of increasing species richness towards a river's mouth. Here we investigate the role of river capture events caused by Andean mountain building and repeated episodes of flooding in western Amazonia in shaping the modern-day richness pattern of freshwater fishes in South America, and in Amazonia in particular. To this end, we combine a reconstruction of river networks since 80 Ma with a mechanistic model simulating dispersal, allopatric speciation and extinction over the dynamic landscape of rivers and lakes. We show that Andean mountain building and consequent numerous small river capture events in western Amazonia caused freshwater habitats to be highly dynamic, leading to high diversification rates and exceptional richness. The history of marine incursions and lakes, including the Miocene Pebas mega-wetland system in western Amazonia, played a secondary role.

A new tiny-spotted species of Hypostomus (Siluriformes: Loricariidae) from the upper Rio Tocantins basin, Gois State, Brazil

Scientific visits to ichthyological collections revealed a potentially new species of Hypostomus from the Rio Tocantins basin. From there, subsequent ichthyological surveys led us to capture the taxon in the upper portion of this basin and address it to the H. punctatus group. Here, we present it as a new species to science. The new species is distinguished from its congeners, except those from the H. punctatus group, by having bicuspid teeth with elliptic medial cusps, moderate keels on the head and flanks, small spots on the body, and caudal peduncle that are long and low. From the H. punctatus group, except H. subcarinatus and H. commersoni, it differs by having extremely small dark spots; from H. subcarinatus, it differs by having a beige-brown dorsal-fin background color versus blue in live specimens; and from H. commersoni, it differs by having a short to moderate dorsal fin versus a long dorsal fin.

Songbirds of the Americas show uniform morphological evolution despite heterogeneous diversification

Studying the relationship between diversification and functional trait evolution among broadly co-occurring clades can shed light on interactions between ecology and evolutionary history. However, evidence from many studies is compromised because of their focus on overly broad geographic or narrow phylogenetic scales. We addressed these limitations by studying 46 independent, biogeographically delimited clades of songbirds that dispersed from the Eastern Hemisphere into the Americas and assessed (1) whether diversification has varied through time and/or among clades within this assemblage, (2) the extent of heterogeneity in clade-specific morphological trait disparity and (3) whether morphological disparity among these clades is consistent with a uniform diversification model. We found equivalent support for constant rates birth-death and density-dependent speciation processes, with notable outliers having significantly fewer or more species than expected given their age. We also found substantial variation in morphological disparity among these clades, but that variation was broadly consistent with uniform evolutionary rates, despite the existence of diversification outliers. These findings indicate relatively continuous, ongoing morphological diversification, arguing against conceptual models of adaptive radiation in these continental clades. Additionally, they suggest surprisingly consistent diversification among the majority of these clades, despite tremendous variance in colonization history, habitat valences and trophic specializations that exist among continental clades of birds.

Review of the armoured catfish genus Hypostomus (Siluriformes: Loricariidae) from the Parnaíba River basin, Northeastern Brazil, with description of a new species

Abstract The species of Hypostomus from the Parnaíba River basin were reviewed through molecular and morphological analysis. Five species were found in the basin, including a new species herein described. The distribution of H. pusarum was expanded to this basin, and a closely related species was recorded (H. aff. pusarum), also the presence of H. johnii and H. vaillanti was confirmed. The new species is distinguished from most congeners by its large number of premaxillary and dentary teeth, a wide dental angle of 115° to 135°, presence of a rounded dark spots on a lighter background and anteromedial region of the abdomen depleted of plaques (vs. anteromedial region of the abdomen covered by platelets and odontodes in H. johnii, H. pusarum, H. aff. pusarum and H. vaillanti). Furthermore, an identification key of the species from the Maranhão-Piauí ecoregion and maps with the geographic distribution of these species are presented. The species of Hypostomus in the Parnaíba River basin have different geographic distributions, suggesting different niches or geographical barriers, providing an opportunity for ecological and evolutionary studies.

Biogeography of curimatid fishes reveals multiple lowland-upland river transitions and differential diversification in the Neotropics (Teleostei, Curimatidae)

The Neotropics harbors a megadiverse ichthyofauna comprising over 6300 species with approximately 80% in just three taxonomic orders within the clade Characiphysi. This highly diverse group has evolved in tropical South America over tens to hundreds of millions of years influenced mostly by re-arrangements of river drainages in lowland and upland systems. In this study, we investigate patterns of spatial diversification in Neotropical freshwater fishes in the family Curimatidae, a species-rich clade of the order Characiformes. Specifically, we examined ancestral areas, dispersal events, and shifts in species richness using spatially explicit biogeographic and macroevolutionary models to determine whether lowlands-uplands serve as museums or cradles of diversification for curimatids. We used fossil information to estimate divergence times in BEAST, multiple time-stratified models of geographic range evolution in BioGeoBEARS, and alternative models of geographic state-dependent speciation and extinction in GeoHiSSE. Our results suggest that the most recent common ancestor of curimatids originated in the Late Cretaceous likely in lowland paleodrainages of northwestern South America. Dispersals from lowland to upland river basins of the Brazilian and Guiana shields occurred repeatedly across independently evolving lineages in the Cenozoic. Colonization of upland drainages was often coupled with increased rates of net diversification in species-rich genera such as Cyphocharax and Steindachnerina. Our findings demonstrate that colonization of novel aquatic environments at higher elevations is associated with an increased rate of diversification, although this pattern is clade-dependent and driven mostly by allopatric speciation. Curimatids reinforce an emerging perspective that Amazonian lowlands act as a museum by accumulating species along time, whereas the transitions to uplands stimulate higher net diversification rates and lineage diversification.

Two new species of Hypostomus suckermouth-armoured catfishes (Teleostei: Loricariidae) from central Brazil

This study describes two new endemic Hypostomus species from central Brazil, which were previously identified as genetically distinct lineages in a recent genomic study that recommended their testing and potential description based on morphological data. A machine learning classification procedure (random forest) was used to investigate morphological variation and identify putatively diagnostic characters for these candidate species and revealed that each is morphologically distinct. The new species Hypostomus cafuringa is characterized by small size, dark spots under a light background, deeper caudal peduncle and shorter first ray of the pectoral fin and base of the dorsal fin when compared to congeneric species from the region. H. cafuringa is known from the headwaters of the Maranhão River, upper Tocantins River basin, Distrito Federal, Brazil. The second new species, Hypostomus crulsi, is characterized by dark spots under a light background, absence of plates along the abdomen region, shorter first ray of the pelvic fin, shorter first ray of the pectoral fin and smaller body size. H. crulsi is known from the headwaters of the São Bartolomeu River, upper Paraná River basin, Distrito Federal, Brazil. The rapid conversion of natural habitats for agricultural development and the isolation of protected areas represent a serious threat to the continued existence of these two newly described endemic species, which warrant conservation assessment.

Integrative taxonomy reveals the historically poorly defined armoured catfish Hypostomus variipictus (Ihering 1911), from the upper rio Paraná basin, Brazil (Siluriformes, Loricariidae)

In a recent expedition to the rio Grande basin, a tributary of the rio Paraná in southern Brazil, individuals of the armoured catfish genus Hypostomus with a peculiar and beautiful colour pattern composed of pale vermiculations on the head and four to five horizontal stripes on the flanks were collected. Initially, the specimens were identified as a colour morph of the pale-spotted H. margaritifer. However, when we compared their partial cytochrome C oxidase subunit I (COI) mitochondrial gene to sequences of some typically pale-spotted H. margaritifer, the striped specimens were genetically distinct. Further analysis of the striped individuals revealed that they are the poorly known but valid species Hypostomus variipictus, which was described by Ihering in 1911 from the rio Pardo, a tributary of the rio Grande, upper rio Paraná basin, in São Paulo State, Brazil. Since its descriptions, no robust taxonomic work has been published concerning this species. In this study, the newly sampled population was compared to the original description and to the holotype of H. variipictus, providing the foundation for a complete redescription, proper diagnosis, and first live colour illustration and description of the previously hidden H. variipictus.

Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes

The Neotropics harbor the most species-rich freshwater fish fauna on the planet, but the timing of that exceptional diversification remains unclear. Did the Neotropics accumulate species steadily throughout their long history, or attain their remarkable diversity recently? Biologists have long debated the relative support for these museum and cradle hypotheses, but few phylogenies of megadiverse tropical clades have included sufficient taxa to distinguish between them. We used 1,288 ultraconserved element loci (UCE) spanning 293 species, 211 genera and 21 families of characoid fishes to reconstruct a new, fossil-calibrated phylogeny and infer the most likely diversification scenario for a clade that includes a third of Neotropical fish diversity. This phylogeny implies paraphyly of the traditional delimitation of Characiformes because it resolves the largely Neotropical Characoidei as the sister lineage of Siluriformes (catfishes), rather than the African Citharinodei. Time-calibrated phylogenies indicate an ancient origin of major characoid lineages and reveal a much more recent emergence of most characoid species. Diversification rate analyses infer increased speciation and decreased extinction rates during the Oligocene at around 30 million years ago (Ma) during a period of mega-wetland formation in the proto-Orinoco-Amazonas. Three species-rich and ecomorphologically diverse lineages (Anostomidae, Serrasalmidae, and Characidae) that originated more than 60 Ma in the Paleocene experienced particularly notable bursts of Oligocene diversification and now account collectively for 68% of the approximately 2,150 species of Characoidei. In addition to paleogeographic changes, we discuss potential accelerants of diversification in these three lineages. While the Neotropics accumulated a museum of ecomorphologically diverse characoid lineages long ago, this geologically dynamic region also cradled a much more recent birth of remarkable species-level diversity.

When destruction comes first: Two new species of Hypostomus Lacépède, 1803 (Siluriformes: Loricariidae) from a deeply-impacted river in the Rio São Francisco basin in Brazil

Environmental disasters affecting Brazilian rivers have been frequent recently, especially involving mining activities. Two recent dam-rupture events suddenly released millions of cubic meters of iron tailings downstream into two major Brazilian watersheds. These events generated major losses to the environment and human life. Additionally, the biodiversity in both watersheds was still incompletely known. Two new species of the armoured catfish genus Hypostomus were discovered in the Rio Paraopeba and surrounding rivers of the Rio São Francisco Basin. The species share some main characteristics including a depressed body, large dark spots on a clearer background and the absence of keels on flanks. However, while one species (Hypostomus freirei sp. n.) has a large mandibular ramus and numerous slender teeth, the other (Hypostomus guajupia sp. n.) has a shorter mandibular ramus and few robust teeth. The discovery of these two new mid-sized fish species emphasizes the presumption that the effects of major environmental disasters cannot be fully estimated as local biodiversity is not completely known. This discovery in a recently devastated area also shows that tough environmental laws for the protection, supervision and mitigation of major impacts are urgently needed in developing countries.

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.

Hypostomus hermanni redescription and a new species of Hypostomus (Siluriformes: Loricariidae) from Upper Paraná River basin, Brazil

Abstract A redescription of Hypostomus hermanni is presented herein along with the description of a new species of Hypostomus, which is apparently endemic to the Ivaí River basin, a tributary of the Upper Paraná River basin, Brazil. Hypostomus hermanni is diagnosed from congeners mainly by having: usually large black blotches on body and fins; absence of keels on compound pterotic, on pre-dorsal plates, and on lateral series of bony plates; by having parieto-supraoccipital and predorsal region flat; and by having less than 46 teeth per each premaxilla or dentary ramus. The new species is distinguished from congeners mainly for lacking conspicuous blotches, parieto-supraoccipital non-carinate, and villiform bicuspid teeth.

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.

Molecular inferences about the genus Hypostomus Lacépède, 1803 (Siluriformes: Loricariidae): a review

This review compiles and discusses the use of genetic markers applied in the study of the fish genus Hypostomus Lacépède, 1803 (Siluriformes: Loricariidae). The database comprises 51 peer-review articles that were published in the last 52 years (1968-2020) and that approach analysis based on different classes of genetic markers. The use of cytogenetic and enzymatic markers was predominantly especially in population studies with the genus Hypostomus, while mitochondrial markers were the majority in phylogenetic studies. Although significant methodological advances have occurred for molecular evaluation, they are still modestly applied to the study of neotropical fish genera, in which Hypostomus is included. New perspectives, especially on integrative approaches, are needed to improve our knowledge of the genetic functionality of fishes.

Taxonomic revision of Hypostomus albopunctatus (Siluriformes: Loricariidae) reveals a new piece of the Hypostomus jigsaw in the upper Rio Paraná basin

Hypostomus albopunctatus was described from the Rio Piracicaba, a tributary of the Rio Tietê, upper Rio Paraná basin. Nevertheless, specimens attributed to this species are commonly found throughout other river systems in the upper Rio Paraná basin and present varying degrees of morphological variation. A taxonomic review of H. albopunctatus based on large series of specimens from many localities throughout the upper Rio Paraná basin was carried out. Results support H. lexi, H. niger and H. scaphyceps as junior synonyms. Hypostomus albopunctatus differs from all congeners except H. heraldoi by having pectoral-fin spine equal to or shorter than pelvic-fin spine (v. longer); it differs from H. heraldoi by having white or light yellow spots on the body and fins (v. dark brown or black spots). Despite conspicuous variation related to the shape and size of the spots and snout morphology, both spot and snout patterns overlapped among the examined populations, thus this variation was inferred to be intraspecific within a widely distributed H. albopunctatus.

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.

An integrated approach clarifies the cryptic diversity in Hypostomus Lacépède 1803 from the Lower La Plata Basin

Hypostomus commersoni Valenciennes 1836, Hypostomus cordovae (Günther 1880) and Hypostomus laplatae (Eigenmann 1907) have been little studied since their original descriptions. This study shows a comprehensive review of these species from the Lower La Plata Basin, including their taxonomic history, distribution, color patterns, morphology, and ecological and molecular phylogenetic data. Morphological and phylogenetic analyses based on D-loop sequences suggested that H. commersoni can be separated into two subclades, or subgroups. Based on these results and on the non-overlapping distribution range of the two subclades, we conclude that they represent two distinct species, thereby revalidating H. spiniger. The results also suggest that H. paranensis should be considered as species inquirenda and H. cordovae as valid species. This integrated approach provides key information for assessing the conservation status and biogeographic aspects of the genus Hypostomus in the Lower La Plata Basin.

Nuclear and chloroplast DNA phylogeography suggests an Early Miocene southward expansion of Lithocarpus (Fagaceae) on the Asian continent and islands

BACKGROUND

Most genera of Fagaceae are thought to have originated in the temperate regions except for the genus Lithocarpus, the stone oaks. Lithocarpus is distributed in subtropical and tropical Asia, and its ancestral population is hypothesized to be distributed in tropical regions in Borneo and Indochina. Borneo and the nearby islands (the Greater Sunda Islands) were connected to the Malay Peninsula and Indochina prior to the Pliocene epoch and formed the former Sundaland continent. The Southeast Asian Lithocarpus, is thought to have dispersed between continental Asia and the present Sundaland. The drastic climate changes during the Pliocene and Pleistocene epochs which caused periodic sea-level changes is often used to explain the cause of its diversity. The aim of this study was to establish phylogenetic relationships by analyzing nuclear (nrDNA) and chloroplast (cpDNA) DNA in order to describe and analyze the origin, causes of diversification and historical biogeography of Lithocarpus.

RESULTS

Phylogeny reconstructed through the multiple-species coalescent method with nrDNA and cpDNA revealed that the continental-Asian taxa were clustered at the basal lineages. The derived lineages of tropical Lithocarpus, with the inference of a subtropical ancestral state, imply a southward migration in the Early Miocene period with subsequent in situ diversification in the Greater Sunda Islands. The gradual decrease in temperature since the Middle Miocene period is proposed as a cause of the increase in the net diversification rate.

CONCLUSIONS

The historical ancestral origin of Lithocarpus has been suggested to be mainland Asia. Southward migration in the Early Miocene period with subsequent in situ diversification could explain the current diversity of stone oaks in Southeast Asia. This study also considered the multiple origins of stone oaks currently indigenous to the subtropical islands offshore and near mainland China. Our results provide phylogenetic evidence for a subtropical origin of Asian stone oaks and reveal the process of diversification and how it fits into the timeline of major geologic and climatic events rather than local, episodic, rate-shifting events.

Little Divergence Among Mitochondrial Lineages of Prochilodus (Teleostei, Characiformes)

Evidence that migration prevents population structure among Neotropical characiform fishes has been reported recently but the effects upon species diversification remain unclear. Migratory species of Prochilodus have complex species boundaries and intrincate taxonomy representing a good model to address such questions. Here, we analyzed 147 specimens through barcode sequences covering all species of Prochilodus across a broad geographic area of South America. Species delimitation and population genetic methods revealed very little genetic divergence among mitochondrial lineages suggesting that extensive gene flow resulted likely from the highly migratory behavior, natural hybridization or recent radiation prevent accumulation of genetic disparity among lineages. Our results clearly delimit eight genetic lineages in which four of them contain a single species and four contain more than one morphologically problematic taxon including a trans-Andean species pair and species of the P. nigricans group. Information about biogeographic distribution of haplotypes presented here might contribute to further research on the population genetics and taxonomy of Prochilodus.

Barrier Displacement on a Neutral Landscape: Toward a Theory of Continental Biogeography

Macroevolutionary theory posits three processes leading to lineage diversification and the formation of regional biotas: dispersal (species geographic range expansion), speciation (species lineage splitting), and extinction (species lineage termination). The Theory of Island Biogeography (TIB) predicts species richness values using just two of these processes; dispersal and extinction. Yet most species on Earth live on continents or continental shelves, and the dynamics of evolutionary diversification at regional and continental scales are qualitatively different from those that govern the formation of species richness on biogeographic islands. Certain geomorphological processes operating perennially on continental platforms displace barriers to gene flow and organismal dispersal, and affect all three terms of macroevolutionary diversification. For example, uplift of a dissected landscape and river capture both merge and separate portions of adjacent areas, allowing dispersal and larger geographic ranges, vicariant speciation and smaller geographic ranges, and extinction when range sizes are subdivided below a minimum persistence threshold. The TIB also does not predict many biogeographic and phylogenetic patterns widely observed in continentally distributed taxa, including: (i) power function-like species-area relationships; (ii) log-normal distribution of species geographic range sizes, in which most species have restricted ranges (are endemic) and few species have broad ranges (are cosmopolitan); (iii) mid-domain effects with more species toward the geographic center, and more early-branching, species-poor clades toward the geographic periphery; (iv) exponential rates of net diversification with log-linear accumulation of lineages through geological time; and (v) power function-like relationships between species-richness and clade diversity, in which most clades are species-poor and few clades are species-rich. Current theory does not provide a robust mechanistic framework to connect these seemingly disparate patterns. Here we present SEAMLESS (Spatially Explicit Area Model of Landscape Evolution by SimulationS) that generates clade diversification by moving geographic barriers on a continuous, neutral landscape. SEAMLESS is a neutral Landscape Evolution Model (LEM) that treats species and barriers as functionally equivalent with respect to model parameters. SEAMLESS differs from other model-based biogeographic methods (e.g., Lagrange, GeoSSE, BayArea, and BioGeoBEARS) by modeling properties of dispersal barriers rather than areas, and by modeling the evolution of species lineages on a continuous landscape, rather than the evolution of geographic ranges along branches of a phylogeny. SEAMLESS shows how dispersal is required to maintain species richness and avoid clade-wide extinction, demonstrates that ancestral range size does not predict species richness, and provides a unified explanation for the suite of commonly observed biogeographic and phylogenetic patterns listed above. SEAMLESS explains how a simple barrier-displacement mechanism affects lineage diversification under neutral conditions, and is advanced here toward the formulation of a general theory of continental biogeography. [Diversification, extinction, geodispersal, macroevolution, river capture, vicariance.].

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.