Phylogenetic Analysis of South American Mammals

South America hosts one of the richest mammalian faunas on Earth, shaped by a complex interplay of geological upheaval, climatic oscillations and biotic interchange. Phylogenetic analysis has become a central tool to unravel the evolutionary history of these mammals, combining DNA sequence data with fossil calibrations and biogeographical modelling. Studies employ both mitochondrial and nuclear markers to reconstruct branching patterns, estimate divergence times and infer ancestral distributions. Key lineages such as sigmodontine rodents, caviomorph hystricognaths, marsupials and native carnivorans reveal contrasting tempos of diversification in relation to the uplift of the Andes, the Great American Biotic Interchange and Pleistocene refugia in Amazonia and the Dry Diagonal. Integrative approaches now harness genome-scale data, museum specimens and environmental DNA to resolve deep and recent splits, detect cryptic species and assess rates of speciation and extinction. This work not only clarifies taxonomic boundaries but also informs conservation priorities by identifying centres of endemism, regions acting as evolutionary cradles or museums, and the legacy of past climatic shifts on contemporary genetic diversity.

Research from Nature Portfolio

Recent studies have produced the most comprehensive phylogeny to date for the sigmodontine rodents, the most diverse Neotropical mammal clade. By integrating thousands of occurrences with mitochondrial and nuclear gene trees, researchers have shown that Andean orogenesis acted as both cradle and pump of diversity, with multiple dispersal events from the Northern and Central-Southern Andes into adjacent lowlands. Speciation and turnover rates in montane regions exceed those elsewhere, underlining the Andes’ dual role in generating new lineages and distributing them across the Neotropics. This work highlights the dynamic interplay between mountain building and lineage radiation over the Miocene and Pliocene epochs.

Phylogenetic Analysis of South American Mammals publication trend

The graph below shows the total number of articles in phylogenetic analysis of south american mammals across all publications each year (not limited to Nature Index journals).

Technical terms

Phylogeny: A diagrammatic hypothesis of evolutionary relationships among species or populations.

Mitochondrial genome: The complete set of DNA contained within the mitochondria, often used as a marker in evolutionary studies.

Ultraconserved elements (UCEs): Highly conserved nuclear DNA regions used for resolving deep and shallow phylogenetic divergences.

Monophyly: A group of organisms that forms a clade, containing an ancestor and all its descendants.

Genome skimming: Low-coverage whole-genome sequencing used to recover high-copy regions such as organelle genomes.

References

1. The importance of the Andes in the evolutionary radiation of Sigmodontinae (Rodentia, Cricetidae), the most diverse group of mammals in the Neotropics. Scientific Reports (2023).
2. Rapid mitochondrial genome sequencing based on Oxford Nanopore Sequencing and a proxy for vertebrate species identification. Ecology and Evolution (2020).
3. Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul. BMC Ecology and Evolution (2020).
4. Ancient DNA From Museum Specimens and Next Generation Sequencing Help Resolve the Controversial Evolutionary History of the Critically Endangered Puebla Deer Mouse. Frontiers in Ecology and Evolution (2020).