Genetic barcoding facilitates captive and wild management of three cryptic African crocodile species complexes

Central African dwarf crocodiles found in syntopy are comparably divergent to South American dwarf caimans

Recent molecular taxonomic advancements have expanded our understanding of crocodylian diversity, revealing the existence of previously overlooked species, including the Congo dwarf crocodile (Osteolaemus osborni) in the central Congo Basin rainforests. This study explores the genomic divergence between O. osborni and its better-known relative, the true dwarf crocodile (Osteolaemus tetraspis), shedding light on their evolutionary history. Field research conducted in the northwestern Republic of the Congo uncovered a locality where both species coexist in sympatry/syntopy. Genomic analysis of sympatric individuals reveals a level of divergence comparable to that between ecologically similar South American dwarf caimans (Paleosuchus palpebrosus and Paleosuchus trigonatus), suggesting parallel speciation in the Afrotropics and Neotropics during the Middle to Late Miocene, 10-12 Ma. Comparison of the sympatric and allopatric dwarf crocodiles indicates no gene flow between the analysed sympatric individuals of O. osborni and O. tetraspis. However, a larger sample will be required to answer the question of whether or to what extent these species hybridize. This study emphasizes the need for further research on the biology and conservation status of the Congo dwarf crocodile, highlighting its significance in the unique biodiversity of the Congolian rainforests and thus its potential as a flagship species.

Global conservation prioritization areas in three dimensions of crocodilian diversity

Crocodilians are a taxonomic group of large predators with important ecological and evolutionary benefits for ecosystem functioning in the face of global change. Anthropogenic actions affect negatively crocodilians' survival and more than half of the species are threatened with extinction worldwide. Here, we map and explore three dimensions of crocodilian diversity on a global scale. To highlight the ecological importance of crocodilians, we correlate the spatial distribution of species with the ecosystem services of nutrient retention in the world. We calculate the effectiveness of global protected networks in safeguarding crocodilian species and provide three prioritization models for conservation planning. Our results show the main hotspots of ecological and evolutionary values are in southern North, Central and South America, west-central Africa, northeastern India, and southeastern Asia. African species have the highest correlation to nutrient retention patterns. Twenty-five percent of the world's crocodilian species are not significantly represented in the existing protected area networks. The most alarming cases are reported in northeastern India, eastern China, and west-central Africa, which include threatened species with low or non-significant representation in the protected area networks. Our highest conservation prioritization model targets southern North America, east-central Central America, northern South America, west-central Africa, northeastern India, eastern China, southern Laos, Cambodia, and some points in southeastern Asia. Our research provides a global prioritization scheme to protect multiple dimensions of crocodilian diversity for achieving effective conservation outcomes.

Phylogenetic analysis of a new morphological dataset elucidates the evolutionary history of Crocodylia and resolves the long-standing gharial problem

First appearing in the latest Cretaceous, Crocodylia is a clade of semi-aquatic, predatory reptiles, defined by the last common ancestor of extant alligators, caimans, crocodiles, and gharials. Despite large strides in resolving crocodylian interrelationships over the last three decades, several outstanding problems persist in crocodylian systematics. Most notably, there has been persistent discordance between morphological and molecular datasets surrounding the affinities of the extant gharials, Gavialis gangeticus and Tomistoma schlegelii. Whereas molecular data consistently support a sister taxon relationship, in which they are more closely related to crocodylids than to alligatorids, morphological data indicate that Gavialis is the sister taxon to all other extant crocodylians. Here we present a new morphological dataset for Crocodylia based on a critical reappraisal of published crocodylian character data matrices and extensive firsthand observations of a global sample of crocodylians. This comprises the most taxonomically comprehensive crocodylian dataset to date (144 OTUs scored for 330 characters) and includes a new, illustrated character list with modifications to the construction and scoring of characters, and 46 novel characters. Under a maximum parsimony framework, our analyses robustly recover Gavialis as more closely related to Tomistoma than to other extant crocodylians for the first time based on morphology alone. This result is recovered regardless of the weighting strategy and treatment of quantitative characters. However, analyses using continuous characters and extended implied weighting (with high k-values) produced the most resolved, well-supported, and stratigraphically congruent topologies overall. Resolution of the gharial problem reveals that: (1) several gavialoids lack plesiomorphic features that formerly drew them towards the stem of Crocodylia; and (2) more widespread similarities occur between species traditionally divided into tomistomines and gavialoids, with these interpreted here as homology rather than homoplasy. There remains significant temporal incongruence regarding the inferred divergence timing of the extant gharials, indicating that several putative gavialids ('thoracosaurs') are incorrectly placed and require future re-appraisal. New alligatoroid interrelationships include: (1) support for a North American origin of Caimaninae in the latest Cretaceous; (2) the recovery of the early Paleogene South American taxon Eocaiman as a 'basal' alligatoroid; and (3) the paraphyly of the Cenozoic European taxon Diplocynodon. Among crocodyloids, notable results include modifications to the taxonomic content of Mekosuchinae, including biogeographic affinities of this clade with latest Cretaceous-early Paleogene Asian crocodyloids. In light of our new results, we provide a comprehensive review of the evolutionary and biogeographic history of Crocodylia, which included multiple instances of transoceanic and continental dispersal.

Use of continuous cranial shape variation in the identification of divergent crocodile species of the genus Mecistops

The discovery of cryptic biodiversity has blossomed under the advancements of genetic techniques, but species identification via morphology remains crucial to effective conservation efforts. In this study, we tested the use of continuous cranial shape variation in distinguishing the two living species of Mecistops: the West African slender-snouted crocodile (M. cataphractus) and the Central African slender-snouted crocodile (M. leptorhynchus). Using a combination of geometric morphometric characters and ratios of linear measurements, we identified statistically significant variation in cranial bone and overall skull shape of mature individuals that corroborates existing molecular and discrete morphological evidence for two distinct, extant species within Mecistops. Specifically, variation in the shape of the nasal appears particularly diagnostic, while ratios involving metrics of snout length to snout width at the premaxillary notch offer distinguishing features easily measured in the field. Because of the complementary results and applications of the morphometric and cranial ratio analyses, we argue that both methodologies remain relevant to species identification. Moreover, we recommend continued cooperation between geneticists and morphologists in diagnosing species of conservation concern.

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

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.

Modern cryptic species and crocodylian diversity in the fossil record

Advances in molecular biology and genetics are revealing that many recognized crocodylian species are complexes of two or more cryptic species. These discoveries will have a profound impact on interpretation of the crocodyliform fossil record. Our understanding of ranges of intraspecific variation in modern crocodylian morphology may be based on multiple species and thus express both intraspecific and interspecific variation. This raises questions about our ability to recognize modern species in the fossil record, and it also indicates that specimens from disparate localities or horizons may represent not single widespread species, but multiple related species. Ranges of variation in modern species require a thorough re-evaluation, and we may have to revisit previous perceptions of past crocodyliform diversity, rates of evolution or anagenetic lineages in stratigraphic succession. These challenges will not be unique to those studying crocodyliforms and will require sophisticated approaches to variation among modern and fossil specimens.

Crocodylian conservation and evolution insights from an anatomical and histological examination of phalli from male false gharial (Tomistoma schlegelii)

As wild population threats for the endangered false gharial (Tomistoma schlegelii) persist, conservation breeding programs, including developing semen collection techniques for subsequent artificial insemination, are becoming important species conservation measures. Developing reproductive biology understanding of a species is important to developing best practices and hopefully maximizing reproductive successes. However, information on crocodylians functional copulatory anatomy in general is lacking. To that end, zoological facilities and conservation centres have the exceptional opportunity to contribute new understandings that may not otherwise be attainable regarding crocodylian reproductive anatomy, particularly during routine physical examinations or post-mortem necropsies. Therefore, to better understand T. schlegelii reproductive biology, to contribute knowledge in support of zoo breeding conservation efforts and to contribute to what is known overall about crocodylian reproduction, we investigated phallic anatomy of adult male Tomistoma from two zoological populations, the St. Louis Zoo, USA and Sungai Dusun Wildlife Reserve, Peninsular Malaysia. Here, we present the gross anatomical features and histological analysis of underlying tissue-level details in pursuit of a better understanding of copulatory function and associated gamete transfer mechanisms. While much of the overall Tomistoma phallic morphology and inferred function corresponds to that of other crocodylian species and speaks to conserved aspects of functional anatomy across taxa, species-specific aspects of glans and glans tip morphology are also identified. These novelties are discussed in a general function and overall broader evolutionary contexts.

Use of molecular data in zoo and aquarium collection management: Benefits, challenges, and best practices

The global zoo and aquarium community widely recognizes that its animal collections and cooperative breeding programs are facing a sustainability crisis. It has become commonly accepted that numerous priority species cannot be maintained unless new management strategies are adopted. While molecular data have the potential to greatly improve management across a range of scenarios, they have been generally underutilized by the zoo and aquarium community. This failure to effectively apply molecular data to collection management has been due, in part, to a paucity of resources within the community on which to base informed decisions about when the use of such data is appropriate and what steps are necessary to successfully integrate data into management. Here, we identify three broad areas of inquiry where molecular data can inform management: 1) taxonomic identification; 2) incomplete or unknown pedigrees; and 3) hereditary disease. Across these topics, we offer a discussion of the advantages, limitations, and considerations for applying molecular data to ex situ animal populations in a style accessible to zoo and aquarium professionals. Ultimately, we intend for this compiled information to serve as a resource for the community to help ensure that molecular projects directly and effectively benefit the long-term persistence of ex situ populations.

Did Late Pleistocene climate change result in parallel genetic structure and demographic bottlenecks in sympatric Central African crocodiles, Mecistops and Osteolaemus?

The mid-Holocene has had profound demographic impacts on wildlife on the African continent, although there is little known about the impacts on species from Central Africa. Understanding the impacts of climate change on codistributed species can enhance our understanding of ecosystem dynamics and for formulating restoration objectives. We took a multigenome comparative approach to examine the phylogeographic structure of two poorly known Central African crocodile species-Mecistops sp. aff. cataphractus and Osteolaemus tetraspis. In addition, we conducted coalescent-based demographic reconstructions to test the hypothesis that population decline was driven by climate change since the Last Glacial Maximum, vs. more recent anthropogenic pressures. Using a hierarchical Bayesian model to reconstruct demographic history, we show that both species had dramatic declines (>97%) in effective population size in the 'period following the Last Glacial Maximum 1,500-18,000 YBP. Identification of genetic structuring showed both species have similar regional structure corresponding to major geological features (i.e., hydrologic basin) and that small observed differences between them are best explained by the differences in their ecology and the likely impact that climate change had on their habitat needs. Our results support our hypothesis that climatic effects, presumably on forest and wetland habitat, had a congruent negative impact on both species.

Fine scale patterns of genetic partitioning in the rediscovered African crocodile, Crocodylus suchus (Saint-Hilaire 1807)

Landscape heterogeneity, phylogenetic history, and stochasticity all influence patterns of geneflow and connectivity in wild vertebrates. Fine-scale patterns of genetic partitioning may be particularly important for the sustainable management of widespread species in trade, such as crocodiles. We examined genetic variation within the rediscovered African crocodile, Crocodylus suchus, across its distribution in West and Central Africa. We genotyped 109 individuals at nine microsatellite loci from 16 sampling localities and used three Bayesian clustering techniques and an analysis of contemporary gene flow to identify population structure across the landscape. We identified up to eight genetic clusters that largely correspond to populations isolated in coastal wetland systems and across large distances. Crocodile population clusters from the interior were readily distinguished from coastal areas, which were further subdivided by distance and drainage basin. Migration analyses indicated contemporary migration only between closely positioned coastal populations. These findings indicate high levels of population structure throughout the range of C. suchus and we use our results to suggest a role for molecular tools in identifying crocodile conservation units for this species. Further research, including additional sampling throughout the Congo and Niger drainages, would clarify both the landscape connectivity and management of this species.

Co-occurring cryptic species pose challenges for conservation: a case study of the African dwarf crocodile (Osteolaemusspp.) in Cameroon

The conservation status of threatened taxa may be obfuscated by the detection of cryptic species complexes, in both vertebrate and invertebrate species. African dwarf crocodiles (Osteolaemusspp.) are hunted throughout their range but their conservation status is unknown. Few population assessments have been carried out and there has been a taxonomic revision of the number of species in the genus. The similar morphologies ofOsteolaemus tetraspisandOsteolaemus osbornipose a challenge for conservation in Cameroon, where they are still managed as a single species. Nocturnal spotlight surveys were conducted in three regions during August–November 2010 and December 2011–February 2012 to provide population assessments ofO. tetraspisandO. osborniand raise awareness of the two species in Cameroon. The mean encounter rates ofO. tetraspisandO. osborniwere 1.02 ± SD 1.34 (65 individuals in 39 surveys) and 0.61 ± SD 0.38 (three in four surveys) crocodiles per km, respectively. TheO. tetraspispopulation comprised juveniles predominantly and had a male-biased sex ratio. The fewO. osbornidetected comprised both adults and juveniles. Both species are threatened in Cameroon, based on low encounter rates, young population structures and the threats of habitat loss and hunting pressure. This study provides distribution maps and serves as a baseline to quantify population trends and inform conservation strategies.