The Amazon at sea: Onset and stages of the Amazon River from a marine record, with special reference to Neogene plant turnover in the drainage basin

Aim Present Amazonian diversity patterns can result from many different mechanisms and, consequently, the factors contributing to divergence across regions and/or taxa may differ. Nevertheless, the river‐barrier hypothesis is still widely invoked as a causal process in divergence of Amazonian species. Here we use model‐based phylogeographic analyses to test the extent to which major Amazonian rivers act similarly as barriers across time and space in two broadly distributed Amazonian taxa. Local Amazon rain forest. Taxon The lizard Gonatodes humeralis (Sphaerodactylidae) and the tree frog Dendropsophus leucophyllatus (Hylidae). Methods We obtained RADseq data for samples distributed across main river barriers, representing main Areas of Endemism previously proposed for the region. We conduct model‐based phylogeographic and genetic differentiation analyses across each population pair. Results Measures of genetic differentiation (based on FST calculated from genomic data) show that all rivers are associated with significant genetic differentiation. Parameters estimated under investigated divergence models showed that divergence times for populations separated by each of the 11 bordering rivers were all fairly recent. The degree of differentiation consistently varied between taxa and among rivers, which is not an artifact of any corresponding difference in the genetic diversities of the respective taxa, or to amounts of migration based on analyses of the site‐frequency spectrum. Main conclusions Taken together, our results support a dispersal (rather than vicariance) history, without strong evidence of congruence between these species and rivers. However, once a species crossed a river, populations separated by each and every river have remained isolated—in this sense, rivers act similarly as barriers to any further gene flow. This result suggests differing degrees of persistence and gives rise to the seeming contradiction that the divergence process indeed varies across time, space and species, even though major Amazonian rivers have acted as secondary barriers to gene flow in the focal taxa.

Section: Introductionmentioning

confidence: 99%

Testing main Amazonian rivers as barriers across time and space within widespread taxa

Pirani

Werneck

Thomaz

et al. 2019

“…The putative extension of the Pebas wetland into the Orinoco region (as suggested by the occurrence of estuarine, water‐dispersed plants) is in light green and the onset of the Amazon River at c . 9 Ma is shown with a blue line (Hoorn et al., ). Below the phylogeny, six known periods of marine events are depicted with an ‘M’ (Jaramillo et al., ; Salamanca et al., ).…”

Section: Molecular Phylogeneticsmentioning

confidence: 99%

“…Our hypothesis is that these candidate plant species growing in western Amazonia are, in a sense, living fossils that can help us to understand the interactions between landscape changes and biodiversity. The current distribution of candidate species and their patterns of richness underscore the interplay between biota and landscape processes, including Andean mountain building and marine incursions (Eakin, Lithgow‐Bertelloni, & Dávila, ; Hoorn, Wesselingh, ter Steege, et al., ; Hoorn et al., ; Shepard, Müller, Liu, & Gurnis, ; van Soelen et al., ).…”

Section: Plants As Relicts Of Marine Incursions?mentioning

confidence: 99%

Could coastal plants in western Amazonia be relicts of past marine incursions?

Bernal

Bacon

Balslev

et al. 2019

Self Cite

The rainforests of Amazonia comprise some of the most biologically diverse ecosystems on Earth. Despite this high biodiversity, little is known about how landscape changes that took place in deep history have affected the assembly of its species, and whether the impact of such changes on biodiversity can still be observed. Here, we present a hypothesis to explain our observation that plants typical of Neotropical coastal habitats also occur in western Amazonia, in some cases thousands of kilometres away from the coast. Evidence on their current distribution, dispersal biology and divergence times estimated from molecular phylogenies suggest that these plants may be the legacy of the large marine‐influenced embayment that dominated the area for millions of years in the Neogene. We hypothesize that coastal plants dispersed along the shores of this embayment and persisted as inland relicts after the marine incursion(s) retreated, probably with the aid of changes in soil conditions caused by the deposition of marine sediments. This dispersal corridor may also have facilitated the colonization of coastal environments by Amazonian lineages. These scenarios could imply an unexpected coastal source that has contributed to Amazonia's high floristic diversity and led to disjunct distributions across the Neotropics. We highlight the need for future studies and additional evidence to validate and shed further light on this potentially important pattern.

“…Additionally, new lines of evidence suggest that river configuration within the Amazon Basin was far more dynamic in the Neogene than previously thought (e.g. Hoorn et al, ;Hoorn et al, ;Rossetti et al, ;Ruokolainen, Moulatlet, Zuquim, Hoorn, & Tuomisto, ), potentially mixing up populations from opposite banks over thousands of generations.…”

Section: Introductionmentioning

confidence: 98%

Hidden in the DNA: How multiple historical processes and natural history traits shaped patterns of cryptic diversity in an Amazon leaf‐litter lizard Loxopholis osvaldoi (Squamata: Gymnophthalmidae)

Marques‐Souza

Pellegrino

Brunes

et al. 2019

Aim To investigate the cryptic diversity and diversification timing in the putatively low‐dispersal Amazonian leaf‐litter lizard Loxopholis osvaldoi, and to ask how geography (rivers, isolation by distance, IBD), ecological drivers (isolation by environment, IBE) and historical factors (climatic refugia) explain intraspecific genetic variation. Location Central Amazonia, Brazil. Taxon Squamata; Gymnophthalmidae; Loxopholis osvaldoi. Methods We sequenced two mitochondrial and two nuclear markers in 157 individuals. Phylogeographic structure and the occurrence of independent evolving lineages where explored through phylogenetic and coalescent analyses. A species tree and divergence dates of lineages were inferred with *BEAST, employing multiple DNA substitution rates. The potential genetic impacts of geographical distance among localities, the environment and the position of localities in relation to main rivers were tested by redundancy analysis (RDA). Results We detected 11 independently evolving and largely divergent intraspecific lineages. Lineage distribution patterns are complex and do not match any conspicuous barrier to gene flow, except for the Amazon River. Most lineages appear to have originated in the lower Miocene and Pliocene, in disagreement with the Pleistocene refuge hypothesis. IBD, IBE and rivers appear to have acted in concert establishing and maintaining genetic structure. However, when controlling for other explanatory variables, IBD explains significantly more variation than rivers, IBE or historical factors. Main Conclusions Our results strongly suggest that L. osvaldoi is a species complex. Future taxonomic work should use an integrative approach to explore whether morphological variation is present and congruent with the genetic data. While the use of a sensitive dating analysis allowed us to better describe the diversification history of L. osvaldoi, the lack of a spatial model of Neogene river dynamics prevents the test of specific, more informative river barrier hypotheses. The data suggest that nonlinear correlation analyses (e.g. RDA) should be preferred to detect factors that affect phylogeographic patterns in the Amazon, instead of linear multiple regressions (e.g. Mantel tests). Given the high level of cryptic diversity detected within this and other Amazonian species, we caution against hypothesis tests based solely on the distribution of nominal taxa, which can provide a rather incomplete view of the processes behind Amazonian diversity.