Phylogeography and Genetic Diversity of Reptilian Lineages

Phylogeography investigates how historical processes such as climatic oscillations, geological change and habitat fragmentation have shaped the spatial distribution of genetic lineages within reptile groups. Research over the last decade has revealed that many snakes and lizards harbour deep genetic subdivisions that often correspond to Pleistocene refugia and older Miocene radiations. Advances in multilocus sequencing, whole mitogenome assembly and genome-wide data have uncovered patterns of allopatric divergence, secondary contact and hybridisation, producing mosaic genomes in island endemics and continental forms alike. These insights illuminate how topographic complexity, thermal niches and past sea-level changes have driven diversification, with direct implications for species delimitation, conservation priorities and predictions of climate-driven range shifts.

Research from Nature Portfolio

One study has described a previously unknown mountain snake lineage in the Southern Levant, revealing four deeply divergent clades within a well-known snake complex and dating their basal split to the Late Miocene. Complete mitogenomes, mitochondrial and nuclear markers, together with detailed morphology, supported the recognition of this new species and emphasised the Levant as a hotspot of endemism vulnerable to land-use change. Another investigation of Mediterranean wall lizards used genome sequencing of multiple lineages to reconstruct an 11-million-year-old evolutionary history. This work showed that hybridisation has been prevalent throughout their diversification, resulting in highly reticulated relationships and mosaic genomes that facilitated rapid adaptation on islands. A third contribution examined genome-wide substitution rates and physiological traits in temperate lacertid lizards, finding that global cooling drove niche disparity and a slowdown in molecular evolution among temperate species compared with their tropical relatives, with implications for resilience under ongoing climate warming.

Phylogeography and Genetic Diversity of Reptilian Lineages publication trend

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

Technical terms

Phylogeography: The study of the historical processes influencing the geographic distribution of genetic lineages within species.

Refugium: A location where populations persist during periods of unfavourable climate, serving as a source for later expansion.

Mosaic genome: A genome composed of genetic segments derived from two or more ancestral lineages due to hybridisation.

Introgression: The incorporation of genetic material from one lineage into another through hybridisation and backcrossing.

Mitogenome: The complete mitochondrial genome, often used for reconstructing maternal lineage history.

References

1. A new, rare, small-ranged, and endangered mountain snake of the genus Elaphe from the Southern Levant. Scientific Reports (2023).
2. Environmental temperatures shape thermal physiology as well as diversification and genome-wide substitution rates in lizards. Nature Communications (2019).
3. Persistence across Pleistocene ice ages in Mediterranean and extra-Mediterranean refugia: phylogeographic insights from the common wall lizard. BMC Ecology and Evolution (2013).
4. Extensive introgression and mosaic genomes of Mediterranean endemic lizards. Nature Communications (2021).
5. Phylogeography and demographic history of Lacerta lepida in the Iberian Peninsula: multiple refugia, range expansions and secondary contact zones. BMC Ecology and Evolution (2011).