Phylogeography and Genetic Diversity in Neotropical Forests

Phylogeography in Neotropical forests combines spatial analysis of genetic lineages with palaeoclimatic and geological history to reveal how past events shaped the remarkable biodiversity of Central and South American woodlands. Through multilocus sequencing of mitochondrial and nuclear markers, researchers have documented patterns of isolation, dispersal and admixture across a mosaic of biomes, including Amazonia, the Atlantic Forest and the Cerrado. Climate fluctuations during the Pleistocene drove cycles of expansion and contraction, creating refugia—areas of long-term habitat stability—that promoted lineage divergence. Vicariance caused by mountain uplift, riverine barriers and sea-level changes further partitioned populations, while periodic corridors facilitated gene flow. Integrative approaches now combine demographic inference, ecological niche modelling and coalescent simulations to distinguish scenarios of panmixia, stepwise colonisation and secondary contact. This wealth of phylogeographic insight not only illuminates the origins of endemic taxa—from bats and ants to frogs and plants—but also underpins strategies for conserving genetic diversity under ongoing climate change and habitat fragmentation.

Research from Nature Portfolio

Analyses of two sympatric social-wasp species in the Brazilian Atlantic Forest have revealed idiosyncratic patterns of genetic structure shaped by both historical refugia and neotectonic barriers. One species exhibited deep chromosomal clines and pronounced population subdivision despite climatic suitability during the last glaciation, whereas the other showed evidence of demographic expansion without strong genetic breaks. Climatic niche reconstructions and multilocus data indicated that sea-level fluctuations influenced demographic histories but did not uniformly determine population structure. These findings underscore the need to integrate organismal life-history traits, chromosomal variation and palaeoclimate models to disentangle the roles of refugia, barriers and eustatic changes in driving diversification across the Atlantic Forest biome.

Phylogeography and Genetic Diversity in Neotropical Forests publication trend

The graph below shows the total number of articles in phylogeography and genetic diversity in neotropical forests across all publications each year (not limited to Nature Index journals).

Technical terms

Phylogeography: The study of the historical processes governing the geographic distributions of genetic lineages.

Refugia: Long-term stable habitats where populations persist through adverse climatic periods.

Vicariance: Fragmentation of a species’ range caused by the emergence of a barrier, leading to lineage divergence.

Panmixia: A population structure in which all individuals are potential mates, indicating unrestricted gene flow.

Haplotype: A specific combination of alleles at adjacent loci that are inherited together.

Ecological Niche Modelling: Computational prediction of species’ past, present or future geographic distributions based on environmental variables.

Coalescent Simulation: A statistical framework for modelling the genealogical history of sampled alleles under different demographic scenarios.

References

1. The roles of barriers, refugia, and chromosomal clines underlying diversification in Atlantic Forest social wasps. Scientific Reports (2017).
2. Potential mammalian species for investigating the past connections between Amazonia and the Atlantic Forest. PLOS ONE (2021).
3. Local adaptation in mainland anole lizards: Integrating population history and genome–environment associations. Ecology and Evolution (2018).