Pseudocongruent phylogeographic patterns in forest-living herpetofauna

Similar phylogeographic patterns do not necessarily imply similar evolutionary histories. Instead, environmental factors like the formation of rivers, ancient climatic cycles and climatic gradients could collectively interact with the unique life histories species to strengthen dispersal barriers at different times and generate complex biogeographic patterns.

Above: Isolated forest fragment in the Eastern Cape Province of South Africa.

Climatic and geological changes play important roles in shaping species distributions over evolutionary time. Ancient climatic fluctuations have particularly impacted habitat structure and composition, resulting in numerous contractions and expansion events that often led to extinction or diversification of organisms associated with these habitats. Understanding how past environmental changes impacted individual species or regional patterns of diversity is important for developing effective conservation strategies for the future.

Editors’ choice article: (Free to read online for two years.)
Busschau, T., Jordaan, A., Conradie, W., & Daniels, S. R. (2022). Pseudocongruent phylogeography reflects unique responses to environmental perturbations in a biodiversity hotspot. Journal of Biogeography, 49, 445–459. 

In my masters (MSc) research I wanted to understand more about the population structure and genetic diversity of three codistributed forest-living reptile species, two snakes and a gecko, considering the fragmented nature of forest habitats in South Africa (Busschau, Conradie, & Daniels, 2019; Busschau, 2019; Busschau, Conradie, & Daniels, 2021). I generally found a high degree of genetic diversity and some populations were isolated long enough that they can be regarded as separate species, suggesting forests may hold a higher degree of biodiversity than previously recognized. In the meantime, other studies uncovered high levels of genetic diversity in a forest associated frog (Kushata, Conradie, Cherry, & Daniels, 2021; Tolley, Conradie, Harvey, Measey, & Blackburn, 2018) and a lizard (Zhao et al., 2019). Comparisons among these studies revealed that the five species share congruent phylogeographic patterns along the east coast of South Africa, i.e., the genetic breaks between populations were similar. The most obvious pattern was a phylogeographic break between populations in the northern region and those in the south. This raised two intriguing questions – do similar phylogeographic patterns mean these species with different life histories responded similarly to past environmental changes, and what environmental factors shaped the genetic diversity we see today? Notably, most of the east coast of South Africa falls within a biodiversity hotspot. So, answering these questions could provide clues to the factors generating and maintaining diversity in the region.

Map of the study region, Maputoland-Pondoland-Albany biodiversity hotspot along the eastern escarpment of South Africa. Shading depicts the northern and southern phylogeographic regions deduced from previous phylogeographic studies. The three rivers coinciding with the transitional zone between regions are shown.

To answer these questions, we used a comparative phylogeographic approach that makes statistical comparisons among the five species groups and then correlates the genetic patterns with a set of environmental factors that could be driving these patterns. First, we confirmed that the observed patterns were generally comparable among species and statistically supported. The next important step was to test whether the observed patterns of genetic divergence happened at the same time. This was not so straightforward. Genetic data can be used to estimate the time populations or species diverged, but to do this we need either reliable fossil calibration points or know the gene mutation rates, neither of which were available for the study species. So, we searched the literature for mutation rates of other snakes, lizards, frogs, etc., and realized that even within each of these groups the mutation rates can sometimes be very different. Basing our mutation rates on other studies could therefore introduce errors in our analyses. To overcome this issue, we decided to take a reasonably conservative approach and estimate our gene mutation rates with a broad range of possible values deduced from other studies. This resulted in large confidence intervals around the times populations diverged in each species, yet there was still no overlap among some species. This provided evidence that although the study species show similar genetic patterns, they do not necessarily share the same evolutionary histories.

Two codistributed species that revealed pseudocongruent phylogeographic patterns along the east coast of South Africa. Left Afroedura pondolia. Right Macrelaps microlepidotus.

How is it possible for multiple species to share the same phylogeographic patterns if they do not share the same history in response to past events such as climate change and/or forest fragmentation? In an attempt to answer this question, we tested how well rivers, past climatic changes or climatic gradients could explain the patterns we see. Although we detected some genetic variation explained by the rivers, they do not correlate with genetic patterns across all species. Niche modeling revealed that only one species had a fragmented distribution in past climates, and one species had a significantly reduced distribution while the rest remained relatively stable. Lastly, current climatic variables explained the genetic patterns across all species reasonably well. Multiple climatic variables were significantly different among populations in each species group and significantly correlated with latitude. While this list of environmental factors is certainly not exhaustive, these results indicate that latitudinal climatic gradients may have been persistent drivers of genetic diversity throughout the unique evolutionary histories of species along the east coast of South Africa. We ultimately conclude that additional factors like the formation of rivers or ancient climatic cycles, would collectively have interacted with climatic gradients and the unique life histories of the study species to strengthen dispersal barriers at different times and generate complex biogeographic patterns in the region.

Our study highlights the utility of comparative phylogeographic studies to uncover drivers of biodiversity. Interestingly, our niche modeling also identified a small region that was climatically stable for all species throughout past climatic changes, emphasizing the importance of this region for forest conservation in the face of climate change. This is the first study of its kind in South Africa and we believe similar studies in the future could uncover even higher levels of hidden diversity and previously unrecognized biogeographical processes.

Written by:
Theo Busschau
Current: PhD student in Biology at New York University Abu Dhabi
This study stems from my MSc work at Stellenbosch University, South Africa

Additional information:

I would like to thank my MSc supervisors, Prof. Savel Daniels and Werner Conradie, for their support and guidance throughout my research career, and of course their patience, and thank you to my friend and mega niche modeler, Adriaan Jordaan, for his help and major contribution to this study.


Busschau, T., Conradie, W., & Daniels, S. R. (2019). Evidence for cryptic diversification in a rupicolous forest-dwelling gecko (Gekkonidae: Afroedura pondolia) from a biodiversity hotspot. Molecular Phylogenetics and Evolution, 139, 106549.

Busschau, T. (2019). Phylogeographic patterning of three co-distributed forest-dwelling reptile species along the east coast of South Africa. MSc Thesis, Stellenbosch Uniiversity.

Busschau, T., Conradie, W., & Daniels, S. R. (2021). One species hides many: Molecular and morphological evidence for cryptic speciation in a thread snake (Leptotyphlopidae: Leptotyphlops sylvicolus Broadley & Wallach, 1997). Journal of Zoological Systematics and Evolutionary Research, 59, 195–221.

Kushata, J. N. T., Conradie, W., Cherry, M. I., & Daniels, S. R. (2021). Comparison of the mitochondrial phylogeographical structure of a generalist and two specialist frog species reveals contrasting patterns in the Eastern and Western Cape provinces of South Africa. Biological Journal of the Linnean Society, 130, 783–799.

Tolley, K. A., Conradie, W., Harvey, J., Measey, J., & Blackburn, D. C. (2018). Molecular phylogenetics reveals a complex history underlying cryptic diversity in the bush squeaker frog (Arthroleptis wahlbergii) in Southern Africa. African Zoology, 53, 83–97.

Zhao, Z., Verdú-Ricoy, J., Mohlakoana, S., Jordaan, A., Conradie, W., & Heideman, N. (2019). Unexpected phylogenetic relationships within the world’s largest limbless skink species (Acontias plumbeus) highlight the need for a review of the taxonomic status of Acontias poecilus. Journal of Zoological Systematics and Evolutionary Research, 57, 445–460.

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