Biogeography and Phylogeography

Biogeography investigates the distribution of species and ecosystems across space, while phylogeography combines this spatial perspective with genetic data to infer the historical processes shaping intraspecific lineages. At broad scales, geological events—such as mountain uplift, continental drift and sea-level change—create barriers and corridors that promote vicariance or dispersal. Climatic fluctuations, notably glacial–interglacial cycles, have repeatedly fragmented habitats, creating refugia where isolated populations accrued genetic divergence. Upon recolonisation, secondary contact may yield admixture zones. Modern phylogeography employs multilocus and genomic markers, time-calibrated molecular clocks and coalescent models to reconstruct demographic histories, migration routes and divergence times. These approaches clarify how landscape dynamics, oceanic currents and climatic gradients have driven speciation, gene flow and endemism. By integrating palaeogeography, palaeoclimate reconstructions and population genomics, researchers can predict future shifts in biodiversity under global change, identify evolutionarily significant units for conservation and refine our understanding of Earth’s biotic assembly over millions of years.

Research from Nature Portfolio

Fresh insights into Amazonian fish diversity demonstrate that Andean mountain building since the Late Cretaceous has been the principal driver of freshwater fish diversification in western Amazonia. By coupling reconstructions of palaeoriver networks over an 80-million-year timescale with mechanistic simulations of dispersal, speciation and extinction, researchers revealed that repeated small river-capture events generated a highly dynamic habitat mosaic, fuelling exceptional in situ lineage splitting. Marine incursions and mega-wetland phases played a subordinate role. This model reconciles current richness hotspots with palaeohydrographic evolution and refines the biogeographic narrative of South American freshwater fauna.

In temperate forests of the Northern Hemisphere, phylogenomic analyses of oak and chestnut relatives have traced continental radiations following the end-Cretaceous clearance of forests. Genome-scale sequencing of nuclear and plastid loci uncovers waves of diversification linked to innovations in seed morphology and dispersal modes, which facilitated colonisation of emerging temperate biomes. Ancient and recurrent hybridisation events are evident, with adaptive introgression amplifying white oak diversity across Eurasia. These findings highlight the interplay of climatic cooling, biome emergence and genome dynamics in shaping the macroevolution of Fagaceae.

Global mapping of wildlife trade reveals that tropical regions concentrate the highest losses of phylogenetic and functional diversity among traded birds and mammals. Analyses of trade data against phylogenetic and trait trees show that deep-branch taxa with distinctive ecological roles are disproportionately targeted. Standardised effect sizes of traded evolutionary history pinpoint epicentres of risk in the Amazon, Central Africa and Southeast Asia, signalling urgent priorities for regulation and community-based stewardship to avert cascading ecosystem impacts.

Biogeography and Phylogeography publication trend

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

Technical terms

Biogeography: The study of patterns and processes governing the geographic distribution of organisms.

Phylogeography: The analysis of the spatial distribution of genetic lineages within and among species to infer historical population processes.

Vicariance: The splitting of a once-continuous range by the formation of a barrier, leading to genetic divergence.

Dispersal: The movement of organisms or propagules across existing barriers into new habitats.

Refugium: A geographically restricted area where populations persist through adverse climatic periods.

Molecular clock: A method that estimates divergence times based on the rate of genetic mutations.

Coalescent model: A retrospective framework for inferring demographic history from genetic data.

Phylogenomic: The use of genome-scale data to resolve evolutionary relationships and divergence events.

Adaptive introgression: The transfer of beneficial alleles between species or lineages through hybridisation.

References

1. What Is Evolutionary Biogeography?.
2. Freshwater fish diversity in the western Amazon basin shaped by Andean uplift since the Late Cretaceous. Nature Ecology & Evolution (2023).
3. Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere. Nature Communications (2022).
4. Global hotspots of traded phylogenetic and functional diversity. Nature (2023).
5. Speciation in Coastal Basins Driven by Staggered Headwater Captures: Dispersal of a Species Complex, Leporinus bahiensis, as Revealed by Genome-wide SNP Data. Systematic Biology (2023).
6. Historical and contemporary processes driving the origin and structure of an admixed population within a contact zone between subspecies of a north temperate diadromous fish. Molecular Ecology (2024).
7. Phylogeny, Distribution, and Biology of Pygmy Whitefish (Prosopium coulterii) in the Beringia Region (Chukotka). Diversity (2023).