Population genetics and conservation of the Philippine crocodile : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Conservation Biology at Massey University, Manawatu, New Zealand.

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The endemic Philippine crocodile (Crocodylus mindorensis) is considered to be one of the most highly threatened crocodilians in the world. Historically known to occur throughout the Philippine archipelago, wild populations are now confined to small and isolated populations on the islands of Luzon and Mindanao. Reintroduction is seen as an important element in the recovery of this species. Successful captive breeding programmes initiated in the 1980‟s increased the number to hundreds of captive Philippine crocodiles, many of which are candidates for reintroduction to suitable habitats. Preliminary genetic studies based on mtDNA found Crocodylus porosus-C. mindorensis hybrids in the biggest captive population which raises concerns on species integrity and suitability of the captive population for the reintroduction programme. In addition, unresolved issues on the extent of genetic differentiation among extant populations hampered recovery plans for many years. To resolve these issues, a total of 618 wild and captive Philippine crocodiles were genotyped at 11 microsatellite loci to investigate genetic diversity and population structure. In addition, information from an existing mtDNA study was combined with the results from a Bayesian assignment test based on microsatellite loci to find evidence of hybridisation. A high degree of genetic differentiation across all populations was observed (FST = 0.29. Genetic differentiation reflected geographic structuring, with the highest FST values recorded between populations from the northern Philippines (Luzon) and southern Philippines (Mindanao). Moderate levels of genetic diversity were seen in all captive and wild populations included in the sampling, except for one captive population in Abra. A total of 92 hybrids were identified from two captive facilities. Three of the identified hybrids in this study were part of the group released into the wild during the first reintroduction programme in 2009. These three individuals did not exhibit obvious morphological anomalies and were thought to be pure C. mindorensis. The results of this study have important conservation implications and will influence the management of captive and wild populations of Philippine crocodiles and the design of future reintroductions.
Philippine crocodile, Crocodylus mindorensis