Phylogenetics of African dwarf chameleons

Phylogenetics of African dwarf chameleons

by Alex Negro Science

The archives of museums and other zoological collections still contain a lot of single-gene fragment data. Although it is now relatively easy to decode entire genomes and prepare material for storage, this was not the case for a long time. Scientists at the University of Johannesburg (South Africa) have now investigated whether and, if so, which components of these single genes in dwarf chameleons can provide information on the entire genome with regard to the creation of phylogenetic family trees.

Samples were taken from 44 dwarf chameleons in the form of cut-off tail tips during various expeditions between 2010 and 2022. The sampled animals were captured and released in the Eastern Cape, KwaZulu-Natal, Limpopo, Mpumalanga, Northern Cape and Western Cape provinces. They belonged to the species Bradypodion barbatulum, caeruleogula, caffrum, damaranum, gutturale, melanocephalum, ngomeense, occidentale, pumilum, setaroi, taeniabronchum, thamnobates, transvaalense, ventrale, venustum as well as candidate species from Greytown, Kamberg. Karkloof Forest and Gilboa Forest in KwaZulu-Natal. An existing mitogenome of a Chamaeleo chamaeleon was used as a reference genome. In addition, the mitogenomes of seven other genera were loaded from GenBank for comparison.

DNA was extracted from all samples and phylogenetically analysed using Geneious Prime and IQ-Tree, among others. A total of 22 different alignments were created: a complete mitogenome alignment (without tRNA), 15 alignments of individual loci, the short fragment of 16S, a frequently used COI fragment, a concatenation of 16S fragment with ND2, a concatenation of ND2 and ND5, a concatenation of the two ribosomal subunits and a concatenation of all protein-coding genes (PCG). A statistical analysis of the data followed.

The results showed that the complete mitogenome topology is largely consistent with the previously published phylogenies of African dwarf chameleons from ND2-16S concatenations. The phylogeny based on the ND2 fragments proved to be more stable and even closer to the mitogenome. These gene fragments are therefore well suited to phylogenetically classify a genome and thus a chameleon species. However, there were also a few differences to the previously published phylogenies. The mitogenome topology considers Bradypodion setaroi and Bradypodion caffrum to be sister taxa. Furthermore, Bradypodion ngomeense possibly belongs genetically to the Bradypodion transvaalense clade instead of being a sister taxon of it.

The efficacy of single mitochondrial genes at reconciling the complete mitogenome phylogeny – a case study on dwarf chameleons
Devon C. Main, Jody M. Taft, Anthony J. Geneva, Bettine Jansen van Vuuren, Krystal A. Tolley
PeerJ 12:e17076, 2024
DOI: 10.7717/peerj.17076

Picture: Bradypodion transvaalense, photographed by Ryan van Huyssteen, Creative Commons Attribution-Share Alike 4.0 International

Rhampholeon spectrum – not just one species?

Rhampholeon spectrum – not just one species?

by Alex Negro Science

The pygmy chameleon genus Rhampholeon is mainly found in East Africa. Rhampholeon viridis, Rhampholeon spinosus, and Rhampholeon temporalis each live in clearly defined and isolated areas of Tanzania. Rhampholeon spectrum, however, seems to be the complete opposite so far: The species has an enormous range in western Africa. It extends from Côte d’Ivoire through Ghana, Togo, and Benin to Nigeria and the outskirts of Niger and Chad, then on through Cameroon, Equatorial Guinea, and Gabon into the Central African Republic as well as the Democratic Republic of Congo and the Republic of Congo. Researchers from the USA and Cameroon have now investigated genetically what is behind the wide distribution.

Samples from an island at the northernmost tip of Equatorial Guinea, several mountains in Cameroon, and samples from two areas in Gabon were examined. To the researchers’ astonishment, it turned out that Rhampoleon spectrum is by no means genetically identical everywhere. Two clades could be identified from the samples: One in the lowlands and one in the montane forest, where the chameleons are found exclusively above 700 m a.s.l. A total of five genetically distinct populations were identified, several of which may represent new, as yet undescribed chameleon species.

The lowland clade includes the population in Gabon, where chameleons were sampled from Ivindo National Park and animals in an area near the town of Mekambo. The second population of the lowland clade occurs at low altitudes on Mount Korup, a mountain of volcanic origin. Mount Korup is located in the protected national park of the same name in Cameroon on the border with Nigeria.

The montane clade of the Rhampholeon spectrum includes three populations. One population occurs on Mount Biao on the island of Bioko, which belongs to Equatorial Guinea. A second population is found on Mount Cameroon, an active volcano in western Cameroon not far from the Gulf of Guinea. The type specimen of Rhampholeon spectrum comes from Mount Cameroon. The locality mentioned in the first description, Mapanja, is only a few kilometres away from one of the places where individuals were collected in the present study. This population is therefore probably the “true” Rhampholeon spectrum, the so-called topotypic group. The third population of the montane clade is found on three neighbouring mountains in Cameroon: Mount Kupe, Mount Mangengouba, and Mount Nlonako. Together with Mount Cameroon and Mount Biao, all three belong to the so-called Cameroon Line, a mountain range of volcanic origin that stretches along the border between Cameroon and Nigeria from the sea to Lake Chad.

The researchers are also looking into the question of how the different populations might have evolved. The separation between Rhampoleon spectrum and the pygmy chameleons in Tanzania can be dated to the late Eocene around 40 million years ago. During this time, the previously continuous rainforests in West, Central, and East Africa broke up into smaller, sometimes isolated fragments. The Rhampoleon spectrum clade then split into lowland and montane populations in the Miocene around 11.1 million years ago. In the Miocene, tectonic movements led to the uplift of a low mountain range that extended from southern Cameroon to the south of the Republic of Congo. Rivers, deserts, and other geographical barriers changed. Somewhat later, about 9.3 million years ago, the population on Bioko Island split off. The island’s pygmy chameleons are thus older than the island itself – the researchers explain this phenomenon by the fact that the island must have been connected to mainland Africa via a land bridge in the past. The chameleons would therefore have colonised the island, found a home on the mountain, and only then became isolated from the mainland. However, the genetically identical population on the mainland could not be found – researchers consider it extinct. In the late Miocene, around 6.9 million years ago, the populations on Mount Korup and in Gabon emerged. Only at the transition from the Miocene to the Pleistocene, 5.2 million years ago, did the populations on Mount Cameroon and Mount Kupe emerge.

Further research on this topic will show whether new species are actually hiding under the name Rhampholeon spectrum – chances are good. It would also be interesting to investigate populations of the species that are not mentioned in this study. Because, of course, the Rhampholeon spectrum from southern and eastern Cameroon, continental Equatorial Guinea, southern Gabon, and the Congo could also be further, independent populations. Science remains exciting!

Diversification and historical demography of Rhampholeon spectrum in West-Central Africa
Walter Paulin, Tapondjou Nkonmeneck, Kaitlin E. Allen, Paul M. Hime, Kristen N. Knipp, Marina M. Kameni, Arnaud M. Tchassem, LeGrand N. Gonwouo, Rafe M. Brown
PLOS One, December 2022
DOI: 10.1371/journal.pone.0277107

Species diversification in chameleons

Species diversification in chameleons

by Alex Negro Science

From earlier studies, we know that the first chameleons evolved in the late Cretaceous, about 90 million years ago, on mainland of Africa. Around the border between the Cretaceous and Tertiary periods, about 65 million years ago, different species began to evolve. It is still unclear today which factors contributed to the diversity of species. Two researchers from Swansea University in Wales have now used various computational models of phylogenetics to investigate what might have influenced diversification (the splitting of chameleons into many different species).

First, they studied the diversification of chameleon species in Madagascar. In terms of evolutionary history, there are two points in time when chameleons apparently spread across the sea from mainland Africa to Madagascar. One is about 65 million years in the past, the other 45 million years. You could now think that the climatically extremely different habitats in Madagascar could have driven the evolution of the species very quickly after the spread across the sea. To the surprise of the researchers, however, no evidence of this was found. The species richness of chameleons on Madagascar must therefore come from the fact that chameleons spread there very early and thus simply had much more time to develop into different species than elsewhere.

Furthermore, the researchers investigated whether switching between two ecomorphs – from ground-dwelling stub-tailed chameleons to tree-dwelling chameleons with longer tails – had an impact on species diversity. Rather surprisingly, this did not seem to be the case. The evolution to tree-dwellers with longer tails occurred relatively early on one or two occasions. No evidence could be found that different ecomorphs accelerated diversification. Instead, speciation rates were found to slow down progressively over the last 60 million years. Only a very early dispersal event of the genus Bradypodion in South Africa around 10 million years ago was accompanied by a two- to fourfold diversification rate.

As a third focus of the study, the researchers examined the genus Bradypodion. During the climate change in the Miocene around 10 million years ago, South Africa changed a lot. Forests disappeared, leaving behind isolated forest habitats and, in between, savannahs, some of which are now so-called hot spots of biodiversity. Two of them, the Cape Floristic Region at the southwestern tip of South Africa and Maputuland-Pondoland-Albany on the east coast of South Africa, are home to a particularly large number of Bradypodion species. Each species is limited to a geographically very clearly defined area. The researchers, therefore, suspect that Bradypodion species have actually evolved faster under the influence of habitat change. It should be noted that the diversification rate of the genus Bradypodion is probably rather underestimated, as there are still many hidden species to be assumed.

Diversification dynamics of chameleons (Chamaeleonidae)
Stephen Giles, Kevin Arbuckle
Journal of Zoology, 2022
DOI: 10.1111/jzo.13019