Evolution News - Chimpanzees Diversifying Into Subspecies

Chimpanzee dung samples were collected across Africa to determine if populations were recently connected despite historical barriers to gene flow.

© PanAf

Chimpanzees without borders | Max-Planck-Gesellschaft

Unlike humans who also occupy diverse habitats and have marked cultural differences but whose genetics form a gradient between groups, chimpanzees form much more sharply delineated difference to the extent that they form four subspecies. However, there are signs of a recent remixing of these groups, accelerated by human interference with their habitats. This is the conclusion of an international research team led by scientists from the Max Planck Institute for Evolutionary Anthropology.

Pan spp. range map showing modern bonobo and chimpanzee geographic distribution.

User:Cody.pope, Public domain, via Wikimedia Commons

There is evidence that through our evolutionary history, humans probably also began to diversify into distinct subspecies or regional varieties, only to merge and remix later, in much the same way that we interbred with the much more diversified species of humans when we emerged from Africa and met the descendants of a first wave of migration by archaic hominins.

With chimpanzees, the divergence was less pronounced amongst the Pan troglodytes species than by the early extra-African humans, although the Pan genus did diverge into P. troglodytes (common chimpanzee) and P. paniscus (bonobo) in geographical isolation. The belief is that as the climate changed and the West African forests split up, chimpanzees became isolated in fragmented refugia and began to speciate.

Then when the climate began to change again and as humans destroyed the forest habitats, the subspecies came back into contact and genes began to flow between them.

The press release by Jack Lester, first author of the study, of the Max Planck Institute for Evolutionary Anthropology, Leipzig, explains:

A new large-scale study uncovers recent genetic connectivity between chimpanzee subspecies despite past isolation events

Much like us, chimpanzees, occupy diverse habitats and exhibit extensive behavioural variation. Human genetic variation however changes along a gradient, with no races and some areas of local genetic adaptation. Chimpanzees, on the other hand, are divided into four subspecies separated by geographic barriers like rivers. Previous studies attempting to understand chimpanzee population histories have been limited either by a poor geographic distribution of samples, samples of uncertain origin or different types of genetic markers. Due to these obstacles, some studies have shown clear separations between chimpanzee subspecies while others suggest a genetic gradient across the species as in humans.

We used rapidly-evolving genetic markers that reflect the recent population history of species and, in combination with the dense sampling from across their range, we show that chimpanzee subspecies have been connected, or, more likely, reconnected, for extended periods during the most recent maximal expansion of African forests...

Although not unforeseen, we were disheartened to already find the influence of human impacts at some field sites where genetic diversity was markedly lower than what we expected.

Jack D Lester, first author
Max Planck Institute for Evolutionary Anthropology (MPI EVAN),
Leipzig, Germany

To resolve this dichotomy, researchers from the Pan African Programme: The Cultured Chimpanzee (PanAf) at the Max Planck Institute for Evolutionary Anthropology and a team of international researchers, collected over 5000 fecal samples from 55 sites in 18 countries across the chimpanzee range over 8 years. This is by far the most complete sampling of the species to date, with a known location of origin for every sample, thus addressing the sampling limitations of previous studies. “Collecting these samples was often a daunting task for our amazing field teams. The chimpanzees were almost all unhabituated to human presence, so it took a lot of patience, skill and luck to find chimpanzee dung at each of the sites,” explains Mimi Arandjelovic, co-director of the PanAf and senior author of the study.

It is widely thought that chimpanzees persisted in forest refugia during glacial periods, which has likely been responsible for isolating groups of populations which we now recognize as subspecies. Our results from fast-evolving microsatellite DNA markers however indicate that genetic connectivity in the most recent millennia mainly mirrors geographic distance and local factors, masking the older subspecies subdivisions.

Paolo Gratton, co-author
Researcher,
Università degli Studi di Roma "Tor Vergata"

So although chimpanzees were separated into different subspecies in their distant past, prior to the rise of recent anthropogenic disturbances, the proposed subspecies-specific geographic barriers were permeable to chimpanzee dispersal. Paolo Gratton, co-author of the study and researcher at the Università di Roma “Tor Vergata” adds: “It is widely thought that chimpanzees persisted in forest refugia during glacial periods, which has likely been responsible for isolating groups of populations which we now recognize as subspecies. Our results from fast-evolving microsatellite DNA markers however indicate that genetic connectivity in the most recent millennia mainly mirrors geographic distance and local factors, masking the older subspecies subdivisions.”

[T]hese results suggest that the great behavioural diversity observed in chimpanzees are therefore not due to local genetic adaptation but that they rely on behavioural flexibility, much like humans, to respond to changes in their environment

Hjalmar Kuehl, Co-author

Furthermore, “these results suggest that the great behavioural diversity observed in chimpanzees are therefore not due to local genetic adaptation but that they rely on behavioural flexibility, much like humans, to respond to changes in their environment,” notes Hjalmar Kuehl, co-director of the PanAf and researcher at the German Centre for Integrative Biodiversity Research.

The team also observed signals of reductions in diversity at some sites that appeared to be associated with recent anthropogenic pressures. In fact, at some locations PanAf teams visited no, or few, chimpanzees were detected despite recordings of their presence within the last decades. “Although not unforeseen, we were disheartened to already find the influence of human impacts at some field sites where genetic diversity was markedly lower than what we expected,” says Jack Lester.

The research is published open access today in Communications Biology:

Abstract

Much like humans, chimpanzees occupy diverse habitats and exhibit extensive behavioural variability. However, chimpanzees are recognized as a discontinuous species, with four subspecies separated by historical geographic barriers. Nevertheless, their range-wide degree of genetic connectivity remains poorly resolved, mainly due to sampling limitations. By analyzing a geographically comprehensive sample set amplified at microsatellite markers that inform recent population history, we found that isolation by distance explains most of the range-wide genetic structure of chimpanzees. Furthermore, we did not identify spatial discontinuities corresponding with the recognized subspecies, suggesting that some of the subspecies-delineating geographic barriers were recently permeable to gene flow. Substantial range-wide genetic connectivity is consistent with the hypothesis that behavioural flexibility is a salient driver of chimpanzee responses to changing environmental conditions. Finally, our observation of strong local differentiation associated with recent anthropogenic pressures portends future loss of critical genetic diversity if habitat fragmentation and population isolation continue unabated.

Lester, Jack D.; Vigilant, Linda; Gratton, Paolo; McCarthy, Maureen S.; Barratt, Christopher D.; Dieguez, Paula; Agbor, Anthony; Álvarez-Varona, Paula; Angedakin, Samuel; Ayimisin, Emmanuel Ayuk; Bailey, Emma; Bessone, Mattia; Brazzola, Gregory; Chancellor, Rebecca; Cohen, Heather; Danquah, Emmanuel; Deschner, Tobias; Egbe, Villard Ebot; Eno-Nku, Manasseh; Goedmakers, Annemarie; Granjon, Anne-Céline; Head, Josephine; Hedwig, Daniela; Hernandez-Aguilar, R. Adriana; Jeffery, Kathryn J.; Jones, Sorrel; Junker, Jessica; Kadam, Parag; Kaiser, Michael; Kalan, Ammie K.; Kehoe, Laura; Kienast, Ivonne; Langergraber, Kevin E.; Lapuente, Juan; Laudisoit, Anne; Lee, Kevin; Marrocoli, Sergio; Mihindou, Vianet; Morgan, David; Muhanguzi, Geoffrey; Neil, Emily; Nicholl, Sonia; Orbell, Christopher; Ormsby, Lucy Jayne; Pacheco, Liliana; Piel, Alex; Robbins, Martha M.; Rundus, Aaron; Sanz, Crickette; Sciaky, Lilah; Siaka, Alhaji M.; Städele, Veronika; Stewart, Fiona; Tagg, Nikki; Ton, Els; van Schijndel, Joost; Vyalengerera, Magloire Kambale; Wessling, Erin G.; Willie, Jacob; Wittig, Roman M.; Yuh, Yisa Ginath; Yurkiw, Kyle; Zuberbuehler, Klaus; Boesch, Christophe; Kühl, Hjalmar S.; Arandjelovic, Mimi
Recent genetic connectivity and clinal variation in chimpanzees
Commun Biol 4, 283 (2021). doi: 10.1038/s42003-021-01806-x

Copyright: © 2021 The authors, Published by Springer Nature
Open Access
Reprinted under a Creative Commons Attribution 4.0 International License(CC BY 4.0)

What we have here then is a record of the evolutionary history of the Pan genus written away in its DNA and readable by anyone with the right skills and knowledge of evolution and how this is affected by environmental change. Chimpanzees, because of their more restricted range compared to humans have been more affected by the local environmental changes and so the genus has undergone more diversification with sharper delineations between subspecies in the past compared to Homo sapiens which never achieved subspecies status anywhere across their range because there was always dynamic gene flow between groups which were never isolated for long enough or with sufficient natural barriers to prevent it.

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