Genome of the panther chameleon decoded

Genome of the panther chameleon decoded

by Alex Laube Science

In recent decades, genetic research has developed rapidly. Since 2009, the so-called high fidelity (HiFi) Pacbio sequencing method has been available for sequencing genomes. Nevertheless, relatively little is being done in the reptile field. There are only about a hundred so-called reference genomes for reptiles, and none at all for chameleons. Scientists from China have now published a reference genome for the panther chameleon (Furcifer pardalis).

For the analysis, a 5-year-old male captive panther chameleon was killed using isoflurane and then dissected. Different tissues were frozen in liquid nitrogen. Skeletal muscle was used for short genome DNA sequencing and HI-C sequencing. Liver was used for HiFi sequencing. RNA from heart, liver, spleen, testis, lung, kidney, and skin were used for transcriptome sequencing.

The genome size of the panther chameleon from the K-mer analysis is 1.61 gigabase pairs (Gbp), containing only 22 so-called contigs, sets of overlapping DNA. The karyotype contains 11 chromosomes, each consisting of one to four contigs. Ten out of eleven chromosomes have repeat sequences (TAACCC). BUSCO analysis demonstrated a high completeness of the genome. The genome can be viewed in the NCBI BioProject under the number PRJNA974816 and in ScienceDataBank.

Efficient and highly continuous chromosome-level genome assembly of the first chameleon genome
Hongxin Xie, Zixuan Chen, Shuai Pang, Weiguo Du
Genome Biology and Evolution 131, 2023
DOI: 10.1093/gbe/evad131

 

Picture: Alex Laube

Karyotypes in chameleons

Karyotypes in chameleons

by Alex Laube Science

Scientists from Great Britain and Italy have now studied the chromosomes of different chameleon species. They examined the karyotype of a total of 83 different chameleon species. Among them were 57 Madagascan chameleon species, of which 32 karyotypes were described for the first time ever. For Calumma brevicorne, Calumma fallax, Calumma parsonii and Furcifer verrucosus, there were even several animals each available for examination. The scientists found out that presumably the fusion of chromosomes has reduced the total number of chromosomes in the course of evolution in chameleons. Presumably, it was mainly microchromosomes (particularly small chromosomes) that fused.

Microchromosome fusions underpin convergent evolution of chameleon karyotypes
Marcello Mezzasalma, Jeffrey W Streicher, Fabio M Guarino, Marc E H Jones, Simon P Loader, Gaetano Odierna, Natalie Cooper
Evolution, Juni 2023
DOI: 10.1093/evolut/qpad097

 

Chameleons at different altitudes of the Amber Mountain (Madagascar)

Chameleons at different altitudes of the Amber Mountain (Madagascar)

by Alex Laube Science

International scientists have intensively studied the different altitudes of the Amber Mountain and the amphibians and reptiles found there. The Amber Mountain (French Montagne d’Ambre) is a former volcanic massif in northern Madagascar. The mountain, which is up to 1475 m high, is mainly covered by rainforest, which belongs to the national park of the same name. To the north of the mountain is a dry forest that belongs to the Forêt d’Ambre Special Reserve. The north-western flank of the mountain has not yet been protected.

In the present work, amphibians and reptiles were observed and sampled over 12 km between 700 and 1470 metres altitude. The western slope of the Montagne d’Ambre at altitudes between 770 and 1290 m was also included in the study for the first time. In addition, animals were sampled in the Forêt d’Ambre from 470 m altitude. All animals found were measured. Cheek swabs, scales as well as live animals that had been euthanised were collected and genetically analysed. A total of 2631 observations of 34 species of amphibians and 48 species of reptiles were made. As expected, different animals occurred at different altitudes. The species richness of the Montagne d’Ambre was greatest at around 1000 m a.s.l. with 41 different species. Above 1100 m, about one third of the species found were locally endemic.

Two genetic clusters of the earth chameleon Brookesia tuberculata have been identified. Group 1 lives on the eastern flank of the Montagne d’Ambre at altitudes of 887 to 1170 m, group 2 at 1260 to 1455 m on the eastern flank and at 956 to 1150 m on the western slope of the Montagne d’Ambre. Group 1 showed a particularly high number of mitochondrial haplotypes, while group 2 had only one haplotype. The scientists assume that due to their small body size and high site fidelity, the species tends to form isolated groups rather than tree-inhabiting chameleons, which can overcome natural barriers more easily and thus move within a much larger environmental radius.

In Calumma linotum, the genetic differences between three groups at different altitudes were rather small. The measurement data of various body dimensions also showed no clear trend for this species at the different altitudes. Although Calumma linotum appeared to be slightly smaller at lower altitudes, this could have been due to subadult individuals misidentified as females. For Calumma amber and Calumma ambreense, body size decreased the higher the chameleons were found in the Montagne d’Ambre. This may be related to the cooler temperatures at higher altitudes, which contribute to slower growth. But it could also be that more younger animals were simply measured.

The study reveals interesting adaptations of different chameleon species to the altitudinal differences of the Montagne d’Ambre. It is possible that these are already the first indications of an early stage of speciation. The work also illustrates how important the different altitudinal levels are for species diversity.

Repeated divergence of amphibians and reptiles across an elevational gradient in northern Madagascar
Mark D. Scherz, Robin Schmidt, Jason L. Brown, Julian Glos, Ella Z. Lattenkamp, Zafimahery Rakotomalala, Andolalao Rakotoarison, Ricky T. Rakotonindrina, Onja Randriamalala, Achille P. Raselimanana, Safidy M. Rasolonjatovo, Fanomezana M. Ratsoavina, Jary H. Razafindraibe, Frank Glaw, Miguel Vences
Ecology and Evolution 13 (3)
DOI: 10.1002/ece3.9914

Genetics: Karyotype in the Veiled Chameleon

Genetics: Karyotype in the Veiled Chameleon

by Alex Laube Science

It has been known for some time that the sex of the Veiled chameleon (Chamaeleo calyptratus) is genetically determined. The species has an XX/XY system. Scientists from Russia, Great Britain, Italy, and Thailand have now studied the karyotype of the species, i.e. the characteristics of the chromosomes.

The probably most original karyotype of all chameleons is 2n= 36. This “primal chameleon” had six pairs of metacentric macrochromosomes and twelve pairs of microchromosomes, particularly small chromosomes. The Veiled chameleon, on the other hand, has a smaller number of chromosomes, namely only 2n=24. Using various genetic investigation methods, the researchers in the present study found that this karyotype probably arose through fusions. Microchromosomes apparently fused with each other twice, and micro- and macrochromosomes fused no less than four times. The latter, the so-called heterogeneous fusion between chromosomes of different sizes, is unusual for vertebrates. Normally, macro- and microchromosomes are located at different locations in the cell nucleus and are transcribed and replicated at different rates. However, this phenomenon is already known from alligators and turtles – for chameleons it is new.

Until now, it was also unclear which pair of chromosomes in the Veiled chameleon is actually responsible for the sex. In Chamaeleo chamaeleon, the second largest chromosome pair codes for sex. However, initial speculation suggests that in the Veiled chameleon the fifth chromosome pair (CCA5) may instead be the sex chromosome pair. The conjecture still needs to be validated by further research. It is also still up for discussion which gene is actually predominantly responsible for the development of the sex organs in the embryo – the researchers identified at least three possible genes on CCA5.

Identification of Iguania ancestral syntenic blocks and putative sex chromosomes in the Veiled Chameleon (Chamaeleo calyptratus, Chamaeleonidae, Iguania)
Katerina V. Tishakova, Dmitry Yu. Prokopov, Guzel I. Davletshina, Alexander V. Rumyantsev, Patricia C. M. O’Brien, Malcolm A. Ferguson-Smith, Massimo Giovannotti, Artem P. Lisachov, Vladimir A. Trifonov
International Journal of Molecular Sciences 23, December 2022
DOI: 10.3390/ijms232415838

Rhampholeon spectrum – not just one species?

Rhampholeon spectrum – not just one species?

by Alex Laube 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

Hidden species within the genus Chamaeleo

Hidden species within the genus Chamaeleo

by Alex Laube Science

Thanks to genetic studies, the identification of species is much more precise today than it was a few decades ago. However, genetics always raises new questions. The genus Chamaeleo currently has 14 species. Scientists from South Africa have now investigated whether there might be other ‘hidden’ species of the genus Chamaeleo. At the same time, they investigated where the origin of the genus Chamaeleo might lie. For this purpose, the genetic material of all 14 species recognised so far was examined. Exciting results came to light: of the fourteen Chamaeleo species, thirteen were confirmed, but one was questioned. In addition, several new candidate species were identified.

The two different populations of Chamaeleo anchietae in western Angola and in south-eastern Congo and Tanzania probably represent two different species. If the animals from the Democratic Republic of Congo and Tanzania were true to be elevated to species status in the future, they would have to be named Chamaeleo vinckei according to taxonomy and a species description from 1950.

Chamaeleo gracilis seems to hide – which would not be surprising due to its wide distribution – at least three independent species. The “real” Chamaeleo gracilis would be found in Liberia, Sierra Leone and Guinea. The other two groups originate from the triangle of countries between Chad, Cameroon and the Central African Republic and from the border between Kenya and Tanzania. Unfortunately, only single specimens of Chamaeleo gracilis have been sampled, so no more far-reaching recommendation on the splitting of species can be made at this point.

The flap-necked chameleon (Chamaeleo dilepis), currently described as a single species, could contain a total of three species. One of the genetically distinct populations occurs in eastern Africa in Tanzania and Rwanda, while a second species is found in southern and eastern Africa, from South Africa through Botswana, Zambia, Namibia, Mozambique and Malawi to southern Tanzania. The third species would be distributed in west central Africa between Angola and the Congo. None of the candidate species matches the eight subspecies described so far purely on the basis of appearance. Therefore, a complete review of the previous subspecies, their status and the species status of the three newly emerged clades is necessary.

The results of the study on Chamaeleo necasi from Benin are also interesting. It turned out that the genetics identified the sampled animal as Chamaeleo gracilis. However, the specimen itself was not examined by the researchers. It could be a Chamaeleo gracilis misclassified by its appearance. In this case, the specimens used for the species description in 2007 would have to be viewed and sampled again in order to obtain more information about the actual species’ status.

In the course of the genetic investigations, the researchers found out that the origin of the genus Chamaeleo probably lies in South Africa. Chamaeleo namaquensis, the only terrestrial chameleon of the genus Chamaeleo, split off from the other Chamaeleo species as early as 40 million years ago in the Eocene. This makes the Namaqua chameleon from the Namib Desert and Damaraland the “oldest” chameleon of the genus Chamaeleo. Chamaeleo anchietae followed about 29 million years ago.

Out of southern Africa: origins and cryptic speciation in Chamaeleo, the most widespread chameleon genus
Devon C. Main, Bettine Jansen van Vuuren, Colin R. Tilbury & Krystal A. Tolley Conceptualisation
Molecular Phylogenetics and Evolution, Volume 175
DOI: 10.1016/j.ympev.2022.107578