Title: Population Genetic Structure and Reproductive Ecology of Crocodylus across Local and Regional scales
Description: New world crocodilians constitute a monophyletic group comprising four species: Crocodylus rhombifer (Cuban crocodile), Crocodylus acutus (American crocodile), Crocodylus intermedius (Orinoco crocodile), and Crocodylus moreletii (Morelet’s crocodile). All of these are in the IUCN Red list of Threatened Species and exhibit geographic distributions covering small to widespread ranges across the Americas and insular Caribbean. With the overarching goal of generating relevant information for the conservation of endangered new world crocodilians, this dissertation integrates genetic and ecological information to provide a context spanning a scale from the species level to specific populations, to analyses of mating systems and breeding strategies in Crocodylus. In addition, my research applies tools of ecological inference to model the influence of environmental factors and natural habitat disturbances in the reproductive success of Crocodylus using a long-term dataset. This work uses C. intermedius and C. acutus as model species to explore four focal questions organized in distinct chapters related to the biology and ecology of crocodilians.

In Chapter I, I compare previously reported reproductive traits among C. acutus populations across its geographic range. This comparative analysis reveals a high degree of variability in reproductive traits across C. acutus range and provides potential adaptive explanations for the patterns observed. Crocodylus acutus appears to be one of the most adaptable of crocodilians in terms of nesting requirements, total nests per breeding season, nest mode (hole vs. mound), timing of egg-laying, female minimum reproductive size, clutch size, female nest defence behavior, and female parental care. Besides regional comparisons, this chapter focuses on the largest nesting population of C. acutus located in southeastern Cuba, where the species still occurs at its natural population numbers. In Chapter II, I use molecular tools to elucidate the mating system of the Orinoco crocodile in a reintroduced population in the Llanos of Venezuela. Analyzing 17 polymorphic microsatellite loci from 20 clutches I found multiple paternity in C. intermedius, with half of the clutches fathered by two or three males.

Sixteen mothers and 14 fathers were inferred by reconstruction of multilocus parental genotypes. Results showed skewed paternal contributions to multiple-sired clutches in four of the clutches (40%), leading to an overall unequal contribution of offspring among fathers with six of the 14 inferred males fathering 90% of the total offspring, and three of those six males fathering more than 70% of the total offspring. Results of this chapter provide the first evidence of multiple paternity occurring in the Orinoco crocodile and confirm the success of reintroduction efforts of this critically endangered species in Venezuela. In Chapter III, I apply generalized linear mixed models to infer the effect of tropical cyclones and environmental variability on the nesting success of C. acutus in the largest nesting population of the species in southeastern Cuba for a period of 21 years. Results of this chapter report the highest-density nesting for the species documented to date, and one of the highest densities of nesting in relation to other crocodilian species, with an average of 164 nests per year and a density of 17 nests per hectare.

Two of the five analyzed nesting sites had consistently higher nests and higher nesting success for the whole 21-year period. Much of the temporal variation in nesting success could be explained by the occurrence of tropical cyclones. I found that occurrence of tropical cyclones within a nesting season negatively affected nesting success, whereas the occurrence of tropical cyclones one or two years before the nesting season positively affected nesting success. Additionally, results of this chapter suggest that higher ambient temperature negatively affected nesting success. Higher-intensity tropical cyclones are expected to strike the coasts of Cuba due to climate change, potentially devastating C. acutus nests if they occur during the nesting season. As the recruitment of C. acutus populations in Cuba heavily rely on nesting success, we propose incorporating information on crocodilian’s nesting success and density, as well as the impact of tropical cyclones on the latter, as key components of coastal resilience when designing plans for coastal adaptation in the context of climate change.

In the last chapter, I employed data on mitochondrial DNA (mtDNA) control region and 12 nuclear polymorphic microsatellite loci to assess the degree of population structure of C. acutus between and among localities in South America, North America, Central America and the Greater Antilles. All analyses for both mtDNA and nuclear markers show evidence of strong population genetic structure in the American crocodile, with unique populations in each of the sampling localities. My research results reinforce previous findings showing the greatest degree of genetic differentiation between the continental C. acutus and the Greater Antillean C. acutus. Three new haplotypes unique to Venezuela were reported. These were considerably less distant from Central and North American haplotypes than Greater Antillean haplotypes. Overall evidence of this chapter suggests that Cuban and Jamaican C. acutus share a mtDNA haplotype but currently represent at least two different genetic populations when using nuclear, faster evolving, microsatellite markers.

Findings of this chapter offer the first evidence of genetic differentiation among the populations of Greater Antillean C. acutus, the first ever reported haplotypes for the species in Venezuela, and provide important information for the regional planning and in-situ conservation of the species. In conclusion, research findings of my dissertation are the product of combining ecological data collected in the field, genetic data generated in the lab, and the use of a suite of classic and inference-based methodological approaches to gain a better understanding of the behavior and evolution of crocodilians. The dissertation presents the first genetic research on C. intermedius, shows the importance of coastal mangrove conservation for the persistence of C. acutus in Cuba, and depicts phylogeographic linkages among distinct C. acutus populations across the Americas and Greater Antilles. The outcomes of this research provide science-based information to influence decision-making processes for the conservation of threatened crocodilians and their habitats across the study areas.