Some problems in the study of the origin of neotropical biodiversity using palaeoecological and molecular phylogenetic evidence

Strong Fuzzy EHLFS: A General Conceptual Framework to Address Past Records of Environmental, Ecological and Cultural Change

Although the interpretation of Quaternary records of interrelated environmental–ecological–human processes is necessarily complex, it is often addressed using too-simple deterministic approaches. This paper suggests a holistic framework called EHLFS (Environmental–Human–Landscape Feedbacks and Synergies) to tackle Quaternary complexity. The EHLFS scheme is a multiple-working-hypotheses framework, able to account for the particular nature of Quaternary research, and is used in combination with the strong inference method of hypothesis testing. The resulting system is called the strong fuzzy EHLFS approach. This approach is explained in some detail and compared with the more extended simplistic determinisms—namely the environmental determinism and the human determinism—as well as with dual determinisms or deterministic approaches based on two contrasting and apparently contradictory and excluding hypotheses or theories. The application of the strong EHLFS methodology is illustrated using the Late Holocene ecological and cultural history of Easter Island since its initial human settlement, a topic that has traditionally been addressed using simplistic and dual deterministic approaches. The strong fuzzy EHLFS approach seems to be a robust framework to address past complex issues where environment, humans and landscape interact, as well as an open system able to encompass new challenging evidence and thorough changes in fundamental research questions.

Speciation with gene flow in whiptail lizards from a Neotropical xeric biome

Two main hypotheses have been proposed to explain the diversification of the Caatinga biota. The riverine barrier hypothesis (RBH) claims that the São Francisco River (SFR) is a major biogeographic barrier to gene flow. The Pleistocene climatic fluctuation hypothesis (PCH) states that gene flow, geographic genetic structure and demographic signatures on endemic Caatinga taxa were influenced by Quaternary climate fluctuation cycles. Herein, we analyse genetic diversity and structure, phylogeographic history, and diversification of a widespread Caatinga lizard (Cnemidophorus ocellifer) based on large geographical sampling for multiple loci to test the predictions derived from the RBH and PCH. We inferred two well-delimited lineages (Northeast and Southwest) that have diverged along the Cerrado-Caatinga border during the Mid-Late Miocene (6-14 Ma) despite the presence of gene flow. We reject both major hypotheses proposed to explain diversification in the Caatinga. Surprisingly, our results revealed a striking complex diversification pattern where the Northeast lineage originated as a founder effect from a few individuals located along the edge of the Southwest lineage that eventually expanded throughout the Caatinga. The Southwest lineage is more diverse, older and associated with the Cerrado-Caatinga boundaries. Finally, we suggest that C. ocellifer from the Caatinga is composed of two distinct species. Our data support speciation in the presence of gene flow and highlight the role of environmental gradients in the diversification process.

Genomic variation in a widespread Neotropical bird (Xenops minutus) reveals divergence, population expansion, and gene flow

The demographic and phylogeographic histories of species provide insight into the processes responsible for generating biological diversity, and genomic datasets are now permitting the estimation of species histories with unprecedented accuracy. We used a genomic single nucleotide polymorphism (SNP) dataset generated using a RAD-Seq method to investigate the historical demography and phylogeography of a widespread lowland Neotropical bird (Xenops minutus). As expected, we found that prominent landscape features that act as dispersal barriers, such as Amazonian rivers and the Andes Mountains, are associated with the deepest phylogeographic breaks, and also that isolation by distance is limited in areas between these barriers. In addition, we inferred positive population growth for most populations and detected evidence of historical gene flow between populations that are now physically isolated. Although we were able to reconstruct the history of Xenops minutus with unprecedented resolution, we had difficulty conclusively relating this history to the landscape events implicated in many Neotropical diversification hypotheses. We suggest that even if many traditional diversification hypotheses remain untestable, investigations using genomic datasets will provide greater resolution of species histories in the Neotropics and elsewhere.