Into Africa: How a Single Ancient Lineage Gave Rise to Africa’s Pythons

Pythons are among the most iconic snakes on Earth, yet their global distribution has long puzzled biogeographers. Most of the nine genera and 38 species in the family Pythonidae live in south-east Asia and Australasia, but one genus, Python, also occurs in sub-Saharan Africa. Today, a vast gap separates the African and Asian pythons across northern Africa, the Saharo-Arabian region and the Iranian plateau. A new study published in Frontiers of Biogeography has now resolved this mystery, showing that all four African species descend from a single ancestral lineage that entered the continent roughly 33 million years ago, and that global cooling since the mid-Miocene carved out the enormous distribution gap we see today.

The research team, led by Krystal Tolley and Graham Alexander, constructed a dated phylogeny based on one nuclear gene and two mitochondrial genes, with near-complete sampling of the genus. This was critical because no previous phylogeny had included all African species, leaving their monophyly untested. Earlier studies had suggested conflicting scenarios: some analyses placed the Ball Python, Python regius, at the base of the genus, hinting at a possible African origin, while others supported an Asian origin for the entire family. If the African species were not monophyletic, multiple independent dispersals into Africa would be required to explain current patterns. The new data settle the question decisively.

The phylogenetic analyses, run using both Bayesian and maximum likelihood frameworks and a multi-species coalescent approach in *BEAST, produced identical topologies. All four African species, P. anchietae, P. natalensis, P. regius and P. sebae, form a well-supported monophyletic clade to the exclusion of the Asian species. The genus Python itself diverged from other pythonid genera around 43 million years ago in Asia, and the African and Asian clades split approximately 33 million years ago during the Late Eocene to Early Oligocene transition. Ancestral range reconstruction using a Bayesian Binary MCMC method strongly supported the Oriental biogeographic region as the ancestral area, confirming a single dispersal event into Africa followed by diversification on the continent.

The timing of this dispersal is biogeographically telling. During the Eocene-Oligocene transition, the Afro-Arabian tectonic plates drew closer to Eurasia as the Tethys Sea receded, opening rare opportunities for faunal interchange. Fossil evidence shows that Python once occupied Europe, the Arabian Peninsula and the Iranian plateau, so the ancestral lineage likely arrived in Africa via those regions rather than directly from the Oriental region. Once in Africa, the lineage diversified, with P. regius diverging around 26 million years ago and P. anchietae about 22 million years ago. Species-level diversification ended around 12 million years ago, coinciding with the acceleration of mid-Miocene global cooling.

One of the study’s most striking findings concerns the taxonomic status of the Southern African Python, P. natalensis. Formerly classified as a subspecies of P. sebae, the two taxa are clearly distinct sister species that diverged approximately 12 million years ago. Haplotype networks built from mitochondrial Cyt-b and nuclear c-mos sequences showed no allele or haplotype sharing between the two species, even for individuals sampled from zones of sympatry in East Africa. Given that the slow-evolving c-mos gene showed complete divergence, the evidence strongly supports P. natalensis as a full species, vindicating Broadley’s 1999 elevation.

Body size emerges as a crucial factor shaping python distributions. Of the ten species in the genus, four are giants exceeding five metres in length, and all are restricted to tropical and sub-tropical regions. Fossil vertebrae from species that once occupied the current distribution gap easily exceed 10 millimetres in breadth, correlating with body sizes in excess of four metres. The researchers suggest that large body size may have influenced paleo- and present-day ranges through several mechanisms. Large-bodied snakes warm more slowly while basking, restricting activity in cool environments. Prey size selection and gape limitation drive the evolution of larger bodies where mega-faunal prey is available, and fecundity advantages in larger females may also select for increased size. All these factors tie large pythons to warm climates.

Temperature is a critical threshold for python reproduction. Female pythons actively incubate and protect their eggs, and successful incubation requires environmental temperatures above roughly 20 degrees Celsius. Today, temperatures across much of the distribution gap regularly fall below this threshold. The fossil record shows that pythons occupied the Arabian Peninsula and the Namib region during the early and mid-Miocene, before these areas progressed toward hyper-aridity in the Late Miocene. Hyper-aridity thus joins temperature as a second limiting factor, excluding pythons from the Arabian, Saharan and Namib deserts as well as from temperate Europe and the Iranian plateau.

The absence of pythons from Madagascar, both today and in the fossil record, receives an elegant explanation independent of climate. Most Malagasy reptile fauna colonised the island through overseas dispersal from eastern Africa during the Eocene and early Oligocene, roughly 55 to 35 million years ago, when paleo-currents were optimal. Python arrived in northern Africa after this window had closed, and shifting relative positions of Africa and Madagascar changed oceanic current directions away from the island, making overseas dispersal far less likely. The timing simply did not align.

Africa’s comparatively low python richness, four species from one genus, contrasts sharply with the dramatic adaptive radiation in Australasia, where 27 species from nine genera colonised environmentally diverse regions with novel niches. The researchers attribute Africa’s low speciation rates to its arid climate, reduced topographic and habitat complexity, and long-term geographic isolation through the early Cenozoic. These same features limited niche diversity and reduced opportunities for allopatric speciation, constraining Python to a modest continental radiation.

The study’s conclusions rest on a dataset of few loci, and the authors acknowledge that more detailed genomic datasets could strengthen confidence in their hypotheses. Nevertheless, their topology agrees with recent phylogenomic analyses, so they do not expect their interpretation to change substantially. The broader message is clear: long-term global cooling since the mid-Miocene has presumably driven range contractions, created the distribution gap, and possibly caused extinctions of Python species and populations. What was once a genus spanning Eurasia and Africa is now confined to warm, mesic tropical and sub-tropical refugia at the edges of two continents, a living testament to the power of climate to reshape life’s geography over deep time.

Subject of Research: Biogeography

Article Title: Into Africa: The biogeography of the genus Python in Africa

Article References: Tolley, K. A., & Alexander, G. J. (2025). Into Africa: The biogeography of the genus Python in Africa. Frontiers of Biogeography, 18, Article e146955. https://doi.org/10.21425/fob.18.146955

Image Credits: AI Generated

DOI: 10.21425/fob.18.146955

Keywords: pythons, biogeography, phylogenetics, Africa, Asia, climate change, fossils, snakes, genus, Python, scientific research