Rigorous approaches to species delimitation have significant implications for African crocodilian systematics and conservation

Abstract

Accurate species delimitation is a central assumption of biology that, in groups such as the Crocodylia, is often hindered by highly conserved morphology and frequent introgression. In Africa, crocodilian systematics has been hampered by complex regional biogeography and confounded taxonomic history. We used rigorous molecular and morphological species delimitation methods to test the hypothesis that the slender-snouted crocodile (Mecistops cataphractus) is composed of multiple species corresponding to the Congolian and Guinean biogeographic zones. Speciation probability was assessed by using 11 mitochondrial and nuclear genes, and cranial morphology for over 100 specimens, representing the full geographical extent of the species distribution. Molecular Bayesian and phylogenetic species delimitation showed unanimous support for two Mecistops species isolated to the Upper Guinean and Congo (including Lower Guinean) biomes that were supported by 13 cranial characters capable of unambiguously diagnosing each species. Fossil-calibrated phylogenetic reconstruction estimated that the species split ± 6.5-7.5 Ma, which is congruent with intraspecies divergence within the sympatric crocodile genus Osteolaemus and the formation of the Cameroon Volcanic Line. Our results underscore the necessity of comprehensive phylogeographic analyses within currently recognized taxa to detect cryptic species within the Crocodylia. We recommend that the community of crocodilian researchers reconsider the conceptualization of crocodilian species especially in the light of the conservation ramifications for this economically and ecologically important group.

Keywords: African biogeography; Mecistops; Osteolaemus; phylogeography; speciation probability.

Figure 1.

Map of molecular sampling localities. The base map is shaded to reflect topographic and elevation features of the landscape across the sampling distribution. Sample points are colour-coded by corresponding clade (grey, west; white, central), and labels correspond to localities detailed in the electronic supplementary material, table S1. The white, dashed line delimits the distribution of Mecistops. The black arrow indicates the Cameroon Volcanic Line. The black, dashed box in the inset map shows the expanded area.

Figure 2.

Molecular and morphological species delimitation results. (a) Bayesian species delimitation results for Mecistops and Osteolaemus assuming a resolved, five-species guide tree. The marginal probabilities for speciation are displayed at each node for each of the three datasets (six, seven and eight loci) and each combination of priors for θ and τ₀: LD, prior means 0.1; LS, prior mean θ = 0.1, prior mean τ₀ = 0.001; SS, prior means 0.001. Results from both rjMCMC algorithm 0 (left of node) and 1 (right of node) are displayed. There was high speciation probability (>0.95) for all nodes under all combinations of dataset, priors and rjMCMC algorithm, providing robust support for recognition of two Mecistops and three Osteolaemus species. (b) Haplotype network from CHA analysis of mtDNA. Two distinct haplogroups are evident (boxes), one representing all Central African samples and the other all West African samples, separated by 116 mutational steps. Circle size is representative of the number of individuals with each haplotype. Hash marks on branches represent single base changes; branches without hash marks represent only a single base difference between connected haplotypes. (c) NMDS results of multivariate analysis of cranial morphological characters in Mecistops. Individuals are colour-coded by group assignment: Central (black) and West (grey). Ellipses represent 95% concentration limits.

Figure 3.

Comparative cranial morphology of Mecistops from Central and West Africa: (a) dorsal view, (b) ventral view, (c) occipital view. Labelled characters correspond to character descriptions in the electronic supplementary material.

Figure 4.

Divergence date estimates within the Crocodylia. This is an updated phylogeny for the crown Crocodylia presenting all seven proposed African species. Median dates are shown as node labels with bars representing the 95% HPD values. Branch labels are Bayesian posterior probability support values for each node following the label. The scale on the bottom is in millions of years before present. This tree topology and displayed dates are from the analysis partitioned by genome. See the electronic supplementary material for all other Beast results. (Online version in colour.)