Phylogenetic and spatial distribution of evolutionary diversification, isolation, and threat in turtles and crocodilians (non-avian archosauromorphs)

Abstract

Background The origin of turtles and crocodiles and their easily recognized body forms dates to the Triassic and Jurassic. Despite their long-term success, extant species diversity is low, and endangerment is extremely high compared to other terrestrial vertebrate groups, with ~ 65% of ~ 25 crocodilian and ~ 360 turtle species now threatened by exploitation and habitat loss. Here, we combine available molecular and morphological evidence with statistical and machine learning algorithms to present a phylogenetically informed, comprehensive assessment of diversification, threat status, and evolutionary distinctiveness of all extant species. Results In contrast to other terrestrial vertebrates and their own diversity in the fossil record, the recent extant lineages of turtles and crocodilians have not experienced any global mass extinctions or lineage-wide shifts in diversification rate or body-size evolution over time. We predict threat statuses for 114 as-yet unassessed or data-deficient species and identify a concentration of threatened turtles and crocodilians in South and Southeast Asia, western Africa, and the eastern Amazon. We find that unlike other terrestrial vertebrate groups, extinction risk increases with evolutionary distinctiveness: a disproportionate amount of phylogenetic diversity is concentrated in evolutionarily isolated, at-risk taxa, particularly those with small geographic ranges. Our findings highlight the important role of geographic determinants of extinction risk, particularly those resulting from anthropogenic habitat-disturbance, which affect species across body sizes and ecologies. Conclusions Extant turtles and crocodilians maintain unique, conserved morphologies which make them globally recognizable. Many species are threatened due to exploitation and global change. We use taxonomically complete, dated molecular phylogenies and various approaches to produce a comprehensive assessment of threat status and evolutionary distinctiveness of both groups. Neither group exhibits significant overall shifts in diversification rate or body-size evolution, or any signature of global mass extinctions in recent, extant lineages. However, the most evolutionarily distinct species tend to be the most threatened, and species richness and extinction risk are centered in areas of high anthropogenic disturbance, particularly South and Southeast Asia. Range size is the strongest predictor of threat, and a disproportionate amount of evolutionary diversity is at risk of imminent extinction.

Evolutionary history of mental glands in turtles reveals a single origin in an aquatic ancestor and recurrent losses independent of macrohabitat

“…We found that generalized hidden Markov models (HMM) better approximate the complexity of MG and macrohabitat evolution in turtles. Turtles make up a relatively small but globally distributed vertebrate clade with divergences between extant families reaching the Upper Mesozoic and early Paleogene 43,[46][47][48][49] . Trait evolution across such large expanses of biodiversity time may be better approximated by models that can accommodate heterogeneous rates among clades 50 .…”

Different solutions lead to similar life history traits across the great divides of the amniote tree of life

“…10 )], we depict the slopes using a Generalized Additive model instead of PGLS as visual examination of scatter plot revealed a non-linear relationship. We used taxonomy-imputed trees from Upham et al [ 149 ] for Mammalia, Tonini et al [ 150 ] for Squamata, Colston et al [ 151 ] for Testudines, and Cooney et al [ 152 ] for Aves to control for phylogenetic autocorrelation. We averaged the life history data of species which are represented by a single synonym in the phylogenetic tree and multiple synonyms in the life history data sets.…”

Cytogenetic Analysis of the Asian Box Turtles of the Genus Cuora (Testudines, Geoemydidae)

“…With 71 described species, the family Geoemydidae is the most diverse turtle family [8,29,30]. Despite their wide geographical range, the cytogenetic characteristics of this family are still poorly studied.…”

“…The Asian box turtles of the genus Cuora are arranged into 13 species distributed in Southeast Asia, including China, Indonesia, and Philippines [8,29,30]. All Cuora species are rapidly declining due to human pressure, including pollution, habitat loss, and unsustainable harvesting for food consumption [4,29,40].…”

“…Distribution of diploid chromosome numbers and topology of rDNA loci and TTAGGG telomeric repeats across the phylogeny of geoemydid species. Phylogenetic branching patterns from Colston et al[30].…”