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The riverine barrier hypothesis is a central concept in Amazonian biogeography. It states that large rivers limit species distributions and trigger vicariant speciation. Although the hypothesis has explanatory power, many recent biogeographical observations addressing it have produced conflicting results. We propose that the controversies arise because tributary arrangements in the Amazon river system have changed in geologically recent times, such that large tracts of forest that were on the same side of a river at one time got separated to different sides at another. Based on topographical data and sediment dating, we map about 20 major avulsion and river capture events that have rearranged the river network in central Amazonia during the late Pleistocene and Holocene. We identify areas where past riverine barrier effects might still linger in the absence of a major river, as well as areas where such effects may not yet have accumulated across an existing river. These results call for a reinterpretation of previous biogeographical studies and a reorientation of future works to take into account the idiosyncratic histories of individual rivers.

Diversification processes acting across geographically continuous populations have been rarely documented in Amazonia, because of the lack of fine-scale sampling over extensive areas. We aimed to determine the geographic effects of an environmental transition zone and large rivers on the intraspecific population structure of the Manaus slender-legged tree frog (Osteocephalus taurinus) along a ~ 900 km transect of tropical rain forest. Using one mitochondrial (16S), two nuclear genes (TYR, POMC) and three microsatellites, we estimated the population structure, phylogenetic relationships and geographic variation of 262 O. taurinus and 5 O. oophagus (a close relative) along the Purus–Madeira interfluve (PMI) and opposite banks of the central Amazon and upper Madeira rivers, at central-southern Amazonia, Brazil. Six genetic clusters were identified: two corresponding to sympatric populations of O. taurinus and O. oophagus from their type locality, north of Amazon river. Within PMI, there were three distinct O. taurinus genetic clusters distributed along the geographic gradient with one main phylogeographic break found (concordant between 16S and TYR), that corresponds to a transition zone (ecotone) between dense and open rain forest ecotypes. The sixth cluster was an O. taurinus population isolated at the east bank of the upper Madeira river. In addition, restricted haplotype sharing was identified from the west to east banks at upper Madeira river. Within PMI, parapatric genetic structure is explained by a potential association of the genetic clusters to the different forest ecotypes they inhabit coupled with isolation by distance, thus supporting the gradient hypothesis for diversification. Differentiation of populations that are external to the PMI is most likely explained by the barrier effect of the Madeira and Amazon rivers. Our findings provide new evidence on diversification processes across continuous Amazonian landscapes; however, the specific mechanisms underlying the origin and maintenance of the identified phylogeographic break need to be further studied.

Aim: We describe patterns of skull size and shape variation in an Atlantic forest endemic rodent to test the influence of genetic structure, historical and environmental variables upon intraspecific morphological variability. Location: South America, Brazil, Atlantic forest. Methods: We analyse subtle differences in skull morphology of Akodon cursor through geometric morphometrics applied to 324 individuals from 12 localities distributed throughout the species range. Using cytochrome-b gene (cyt-b) sequences from 125 individuals (38 localities), we describe underlying patterns of genetic structure and transform them into distance measures that are included in our morphological analyses. We estimate the relative importance of genetic structure, historical variables and environmental variables on skull size and shape through mixed model selection and Akaike's information criterion. Results: Geographical patterns in skull size are mainly explained by non-random factors related to primary productivity and precipitation, whereas spatial shifts in shape correlate with mitochondrial divergence. Cytochrome-b data revealed a phylogeographic break around the Jequitinhonha River, yet striking morphological shifts were observed further south. Differences in palaeostability between regions, and the configuration of rivers, appear as secondary sources of explanation for observed patterns. Main conclusions: Multiple forces explain morphological variation within A. cursor. Teasing apart the effects of local adaptation and gene flow may be difficult, but is a key to improve our understanding of the drivers of intraspecific morphological variation. Our findings support the view that size is a more labile feature than shape, and that it may more easily break away from constraints imposed by gene flow. The combination of random and non-random factors, together with documented breaks in the distribution of the Atlantic forest over the Late Quaternary, accounts for the majority of morphological differences observed in A. cursor.

Aim This study aims to reconstruct the evolutionary history of the African rodent genus Malacomys and to identify factors driving diversification within this genus.Location African tropical lowland forest.Methods Analyses were based on sampling representatives from most of the known geographical range of the genus. We assessed genetic structure and historical biogeography using a combination of mitochondrial and nuclear markers. Morphological differences between lineages were analysed using a geometric morphometric approach.Results Three species of Malacomys are recognized within the genus. Two are endemic to West Africa, and one is endemic to Central Africa. Our analyses reveal a strong phylogeographical structure with 13 lineages, most of them allopatric or parapatric. A complex biogeographical history, including dispersal–vicariance events, explains the current genetic structure of Malacomys. Discrete divergence events within the genus are dated to the mid-Pliocene (3.7 Ma, 95% range: 2.4–5.2 Ma) and the Pleistocene (less than 1.9 Ma, with most events less than 1 Ma). Morphological variation is partly congruent with genetic structure and may indicate local adaptations.Main conclusions Climatic oscillations, which led to periodic fragmentation of the forest habitat, seem to be the major driver of diversification within this genus. Our results support the existence of multiple small, rather than a few large, forest refugia during glacial maxima. Rivers have played a significant role in shaping boundaries of several regional haplogroups, either by promoting diversification or by preventing secondary contact between previously isolated lineages.

Among those few hypotheses of Amazonian diversification amenable to falsification by phylogenetic and population genetics methods, three can be singled out because of their general application to vertebrates: the riverine barrier, the refuge, and the Miocene marine incursion hypotheses. I used phylogenetic and population genetics methods to reconstruct the diversification history of the upland (terra‐firme) forest superspecies Xiphorhynchus spixii/elegans (Aves: Dendrocolaptidae) in Amazonia, and to evaluate predictions of the riverine barrier, refuge, and Miocene marine incursion hypotheses. Phylogeographic and population genetics analyses of the X. spixiilelegans superspecies indicated that the main prediction of the riverine barrier hypothesis (that sister lineages occur across major rivers) hold only for populations separated by “clear‐water” rivers located on the Brazilian shield, in central and eastern Amazonia; in contrast, “white‐water” rivers located in western Amazonia did not represent areas of primary divergence for populations of this superspecies. The main prediction derived from the refuge hypothesis (that populations of the X. spixiilelegans superspecies would show signs of past population bottlenecks and recent demographic expansions) was supported only for populations found in western Amazonia, where paleoecological data have failed to support past rainforest fragmentation and expansion of open vegetation types; conversely, populations from the eastern and central parts of Amazonia, where paleoecological data are consistent with an historical interplay between rainforest and open vegetation types, did not show population genetics attributes expected under the refuge hypothesis. Phylogeographic and population genetics data were consistent with the prediction made by the Miocene marine incursion hypothesis that populations of the X. spixii/elegans superspecies found on the Brazilian shield were older than populations from other parts of Amazonia. In contrast, the phylogeny obtained for lineages of this superspecies falsified the predicted monophyly of Brazilian shield populations, as postulated by the Miocene marine incursion hypothesis. In general, important predictions of both riverine barrier and Miocene marine incursion hypotheses were supported, indicating that they are not mutually exclusive; in fact, the data presented herein suggest that an interaction among geology, sea level changes, and hydrography created opportunities for cladogenesis in the X. spixii/elegans superspecies at different temporal and geographical scales.

AIM: The roles of dispersal limitation and environmental heterogeneity in structuring tropical species composition can be better understood by accounting for dispersal barriers and possible niche differentiation effects. We make ecological and historical interpretations of dissimilarity in avian species composition across a riverine dispersal boundary in the light of environmental characteristics, species and subspecies range limits, and geographical distances. LOCATION: Lowland rain forest, western Amazon River Basin, Peru. METHODS: We surveyed all birds and one plant family, collected soil samples and measured forest structural characteristics and fragmentation in surrounding landscapes, at sites to the north and south of the Amazon River flood plain. We used Mantel tests, multiple regression on distance matrices, indicator species analysis and ordination methods to assess the relationships among dissimilarities in species composition, geographical distance, position relative to the river and environmental characteristics. We examined compositional variation for all bird species, for only species without range limits between sites, and for species with and without subspecies limits at the Amazon River. RESULTS: Dissimilarity in avian species composition across the river was large, despite a lack of environmental differences. Most of this dissimilarity was accounted for by species and subspecies range limits at the river. Plant species composition did not show any dissimilarity across the river. Plant species composition and forest fragmentation explained additional components of avian compositional dissimilarity not associated with the riverine boundary and involving different bird species. MAIN CONCLUSIONS: The riverine dispersal boundary, floristic heterogeneity and forest fragmentation were associated with distinctive components of avian species compositional dissimilarity, collectively explaining three‐quarters of the total dissimilarity among sites. Compositional dissimilarity was consistent with historical and continuing isolation of avian populations on opposite sides of the river, and may be partly driven by niche differentiation between subspecies. Geographical distance as a measure of dispersal limitation would not have accounted for these relationships. The use of rivers in biogeographical region delineation should address their variable importance for different taxa.

Aim This study aims to elucidate the phylogeography of the murid rodent Praomys misonnei and to document whether or not rain forest refugia and rivers structure patterns of diversity within this species. Location Tropical Africa, from Ghana to Kenya. Methods Patterns of genetic structure and signatures of population history (cytochrome b gene) were assessed in a survey of 229 individuals from 54 localities. Using maximum likelihood, Bayesian, network and genetic structure analyses, we inferred intra-specific relationships and tested hypotheses for historical patterns of gene flow within P. misonnei. Results Our phylogenetic analyses reveal a strong phylogeographical structure. We identified four major geographical clades within P. misonnei: one clade in Ghana and Benin, a Nigerian clade, a West Central African clade and a Central and East African clade. Several subclades were identified within these four major clades. A signal of population expansion was detected in most clades or subclades. Coalescence within all of the major clades of P. misonnei occurred during the Middle Pleistocene and/or the beginning of Late Pleistocene. Main conclusions Our results suggest a role for both Pleistocene refugia and rivers in structuring genetic diversity in P. misonnei. This forest-dwelling rodent may have been isolated in a number of forest fragments during arid periods and expanded its range during wetter periods. Potential forest refugia may have been localized in Benin–Ghana, south-western Cameroon, southern Gabon, northern Gabon and eastern Democratic Republic of Congo–western Uganda. The Niger and/or the Cross Rivers, the Oubangui-Congo, Sanaga, Ogooue and/or Ivindo Rivers probably stopped the re-expansion of the species from relict areas.

Aim: Subterranean rodents of the genus Ctenomys are widespread in open habitats; the collared tuco-tuco, C. torquatus, has a wide range crossed by large watercourses.Based on a phylogeographical approach to investigate the riverine barrier hypothesis, we evaluated the strength of a river as a barrier and characterized the effect of large rivers in structuring distinct populations of the collared tuco-tuco. Location: Grasslands of southern Brazil. Methods: Sampling included 294 individuals from 33 localities throughout the geographical range of C. torquatus, especially around the main rivers. Phylogeographical patterns were estimated through two mitochondrial DNA sequences (control region and COI). Additionally, 22 microsatellite loci were surveyed to estimate the effect of rivers on population divergence through the FST index of genetic differentiation and AMOVAs. Spatial autocorrelation analyses were performed for both molecular markers. Molecular rates of change for mitochondrial DNA were estimated using fossil records and applied to Bayesian demographic analysis to test the relationship with the river geological data. Results: Molecular-dock analysis estimated the time to most recent common ancestor (TMRCA) to be c. 200 kyr and indicated a pattern of recent demographic expansion for torquatus. Fu's FS neutrality test was significant and negative (— 13.7). High and significant FST and AMOVA among-population comparisons (FSC) revealed highly differentiated populations, although no AMOVA groupings considering rivers as a segregating factor were significant. Spatial autocorrelation analysis revealed that isolation by distance was detected over approximately 200 km. Main conclusions: The effect of the river was not proportionally larger from the headwaters to the mouth, and no population differentiation was observed after the later events of dispersal over the river or the formation of a water channel.This finding could result from the recent history of the occupation of C. torquatus in that region, combined with a dry Pleistocene climate and lower river levels.

AIM: In this study, we reconstructed the biogeographical history of species within the sister‐genera Thylamys and Lestodelphys, Neotropical marsupials that primarily inhabit open biomes. We used this reconstruction to test the extent to which physical geography (e.g. mountains and rivers) and habitat type (e.g. biomes) shaped patterns of diversification. LOCATION: Central and southern South America. METHODS: A fossil‐calibrated ultrametric tree for all species within Thylamys and Lestodelphys, along with relevant marsupial outgroups, was reconstructed using sequences from 23 nuclear loci and three mitochondrial loci. Using two biogeographical area schemes (based on biomes and physical barriers, respectively), the biogeographical history of this clade was reconstructed using Lagrange, a maximum‐likelihood approach. RESULTS: Thylamys and Lestodelphys originated during the Pliocene in the lowland areas east of the Andes and later expanded their range into and across the Andes. Rivers are implicated in speciation events that occurred in the lowlands, whereas differentiation among habitat types may have led to increased in situ speciation within the Andes. MAIN CONCLUSIONS: Biogeographical area schemes based on biomes and physical geographical barriers offered largely complementary results, supporting the hypothesis that both physical geography and ecological differences among habitats drive speciation in continental fauna. Invasion of high‐elevation grasslands may have been the impetus for further diversification in montane habitats, eventually seeding the adjacent lowland areas with additional species.

Rivers can act as both islands of mesic refugia for terrestrial organisms during times of aridification and barriers to gene flow, though evidence for long-term isolation by rivers is mixed. Understanding the extent to which riverine barrier effects can be heightened for populations trapped in mesic refugia can help explain maintenance and generation of diversity in the face of Pleistocene climate change. Herein, we implement phylogenetic and population genetic approaches to investigate the phylogeographic structure and history of the ground skink, Scincella lateralis, using mtDNA and eight nuclear loci. We then test several predictions of a river-refugia model of diversification. We recover 14 well-resolved mtDNA lineages distributed east–west along the Gulf Coast with a subset of lineages extending northward. In contrast, ncDNA exhibits limited phylogenetic structure or congruence among loci. However, multilocus population structure is broadly congruent with mtDNA patterns and suggests that deep coalescence rather than differential gene flow is responsible for mtDNA–ncDNA discordance. The observed patterns suggest that most lineages originated from population vicariance due to riverine barriers strengthened during the Plio–Pleistocene by a climate-induced coastal distribution. Diversification due to rivers is likely a special case, contingent upon other environmental or biological factors that reinforce riverine barrier effects.