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Diversification and historical demography of Rhampholeon spectrum in West-Central Africa - PubMed

  • ️Sat Jan 01 2022

Diversification and historical demography of Rhampholeon spectrum in West-Central Africa

Walter Paulin Tapondjou Nkonmeneck et al. PLoS One. 2022.

Abstract

Pygmy Chameleons of the genus Rhampholeon represent a moderately diverse, geographically circumscribed radiation, with most species (18 out of 19 extant taxa) limited to East Africa. The one exception is Rhampholeon spectrum, a species restricted to West-Central African rainforests. We set out to characterize the geographic basis of genetic variation in this disjunctly distributed Rhampholeon species using a combination of multilocus Sanger data and genomic sequences to explore population structure and range-wide phylogeographic patterns. We also employed demographic analyses and niche modeling to distinguish between alternate explanations to contextualize the impact of past geological and climatic events on the present-day distribution of intraspecific genetic variation. Phylogenetic analyses suggest that R. spectrum is a complex of five geographically delimited populations grouped into two major clades (montane vs. lowland). We found pronounced population structure suggesting that divergence and, potentially, speciation began between the late Miocene and the Pleistocene. Sea level changes during the Pleistocene climatic oscillations resulted in allopatric divergence associated with dispersal over an ocean channel barrier and colonization of Bioko Island. Demographic inferences and range stability mapping each support diversification models with secondary contact due to population contraction in lowland and montane refugia during the interglacial period. Allopatric divergence, congruent with isolation caused by geologic uplift of the East African rift system, the "descent into the Icehouse," and aridification of sub-Saharan Africa during the Eocene-Oligocene are identified as the key events explaining the population divergence between R. spectrum and its closely related sister clade from the Eastern Arc Mountains. Our results unveil cryptic genetic diversity in R. spectrum, suggesting the possibility of a species complex distributed across the Lower Guinean Forest and the Island of Bioko. We highlight the major element of species diversification that modelled today's diversity and distributions in most West-Central African vertebrates.

Copyright: © 2022 Tapondjou Nkonmeneck et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Rhampholeon spectrum.

(Left) Male from Ekona Lelu, Mt. Cameroon. (Right) Female from Mt. Kupe. Photograph credit Luke Welton (right image).

Fig 2
Fig 2. Map of suitable habitat for Rhampholeon spectrum species complex in West-Central Africa.

Present-day suitable habitat was generated using kuenm. Sampling localities are indicated by various-shaded circles.

Fig 3
Fig 3. Maximum likelihood phylogenetic tree inferred from 16S+ND4+RAG1 data set in IQ-TREE.

Node values represent SH-aLRT/Ultrafast bootstrap supports in percentage. Branch colors correspond to key in Fig 2.

Fig 4
Fig 4. Bayesian chronogram of the Pygmy Chameleon genus Rhampholeon inferred from 16S+ND4+RAG1 data.

Nodes with high support (≥ 95%) are denoted by filled circles adjacent to nodes and posterior probabilities (< 95%) are denoted with empty circles. Median ages are provided above nodes and blue bars at nodes represent 95% highest probability densities (HPD). The spatial distribution of populations is presented with the same color scheme in Fig 2. Pli = Pliocene, Pl = Pleistocene, Qu = Quaternary.

Fig 5
Fig 5. Bayesian cluster analysis using the STRUCTURE program for 28 Rhampholeon spectrum.

(a) plot for K = 4, (b) plot for K = 5, (c) delta K from the structure analysis was calculated according to the method of Evanno from POPHELPER, and (d) a discriminant analysis of principal components using the program Adegenet. In (a) and (b), each bar corresponds to one sample of R. spectrum. C = Mt. Cameroon, K = Mt. Kupe, M = Mt. Manengouba, N = Mt. Nlonako, K = Number of populations, CVL = Cameroon Volcanic Line. The color scheme matches the sampling localities depicted in Fig 2.

Fig 6
Fig 6. Results of demographic model comparisons among all four clades.

The best migration and species delimitation model generated from multidimensional site frequency spectrum inferred with FastSimcoal2 implemented in DelimitR. NA: Ancestral population, NL = Lowland population, NM = montane population, Tdiv = Divergence time, Ti = Time since isolation, m = migration.

Fig 7
Fig 7. Results of demographic model comparisons between all populations.

The best migration and species delimitation model generated from multidimensional site frequency spectrum inferred with FastSimcoal2 implemented in DelimitR. NA: Ancestral population, Tdiv = Divergence time, Ti = Time since isolation, m = migration.

Fig 8
Fig 8. Stability map representing regions of persistent suitable habitat for Rhampholeon spectrum species complex across LGM and current climate regimes.

The green color represents the highest habitat stability inferred. 1: Cameroon Volcanic Line; 2: Ngovayang and surrounding massifs; 3: Monts de Cristal; 4: Monts Doudou; 5: Massif du Chaillu; and 6: Congo River.

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