Implications of past and present genetic connectivity for management of the saltwater crocodile (Crocodylus porosus).

Effective management of protected species requires information on appropriate evolutionary and geographic population boundaries and knowledge of how the physical environment and life-history traits combine to shape the population structure and connectivity. Saltwater crocodiles (Crocodylus porosus) are the largest and most widely distributed of living crocodilians, extending from Sri Lanka to Southeast Asia and down to northern Australia. Given the long-distance movement capabilities reported for C. porosus, management units are hypothesised to be highly connected by migration. However, the magnitude, scale, and consistency of connection across managed populations are not fully understood. Here we used an efficient genotyping method that combines DArTseq and sequence capture to survey ≈ 3000 high-quality genome-wide single nucleotide polymorphisms from 1176 C. porosus sampled across nearly the entire range of the species in Queensland, Australia. We investigated historical and present-day connectivity patterns using fixation and diversity indices coupled with clustering methods and the spatial distribution of kin pairs. We inferred kinship using forward simulation coupled with a kinship estimation method that is robust to unspecified population structure. The results demonstrated that the C. porosus population has substantial genetic structure with six broad populations correlated with geographical location. The rate of gene flow was highly correlated with spatial distance, with greater differentiation along the east coast compared to the west. Kinship analyses revealed evidence of reproductive philopatry and limited dispersal, with approximately 90% of reported first and second-degree relatives showing a pairwise distance of <50 km between sampling locations. Given the limited dispersal, lack of suitable habitat, low densities of crocodiles and the high proportion of immature animals in the population, future management and conservation interventions should be considered at regional and state-wide scales.

Population assessment of the American crocodile, Crocodylus acutus (Crocodilia: Crocodylidae) on the Pacific coast of Costa Rica.

The American crocodile, Crocodylus acutus, is widely distributed in the American neotropics. It is endangered throughout most of its range and is listed as vulnerable by the International Union for the Conservation of Natural Fauna and Flora (IUCN) and on Appendix I of the Convention for the International Trade in Endangered Species of Wild Flora and Fauna (CITES). Despite this listing, there are few published reports on population status throughout most of its range. We investigated the status of the C. acutus, at several locations along the Pacific coast of Costa Rica. We carried out spotlight and nesting surveys from 2007-2009 along the Costa Rican Pacific coast in four distinct areas, coastal areas of Las Baulas (N=40) and Santa Rosa (N=9) National Parks and the Osa Conservation Area (N=13), and upriver in Palo Verde National Park (N=11). We recorded crocodile locations and standard environmental data at each observation. Encounter rates, population structure, distribution within each area and data on successful nesting (presence of hatchlings, nests, etc) were determined. We attempted to capture all crocodiles to record standard morphometrics. A total of 586 crocodiles were observed along 185.8km of survey route. The majority of animals encountered (54.9%) were either hatchlings (<0.5m) or juveniles (0.5-1.25m). The average non-hatchling encounter rate per survey for the Pacific coast was 3.1 crocodiles/km, with individual encounter rates ranging from 1.2 crocodiles/km to 4.3 crocodiles/ km in Las Baulas National Park and the Osa Conservation Area respectively. Distribution of size classes within the individual locations did not differ with the exception of Santa Rosa and Las Baulas National Parks, where hatchlings were found in water with lower salinities. These were the first systematic surveys in several of the areas studied and additional work is needed to further characterize the American crocodile population in Costa Rica.

Ontogenetic comparisons of standard metabolism in three species of crocodilians.

Due in part to their large size, aggressive temperament, and difficulty in handling, there are few physiological studies of adult crocodilians in the literature. As a result, studies comparing individuals across an ontogenetic series and comparisons among species are also lacking. We addressed this gap in knowledge by measuring standard metabolic rates (SMR) of three species of crocodilians (Crocodylus porosus, C. johnsoni, and Alligator mississippiensis), and included individuals that ranged from 0.22 to 114 kg. Allometric scaling of SMR with body mass was similar among the species, but C. porosus had significantly higher SMR than did C. johnsoni or A. mississippiensis. Differences in SMR among species are potentially related to behavioural differences in levels of aggression; C. porosus are the most aggressive of the crocodilians measured, and have rates of standard metabolism that are approximately 36% higher at the grand mean body size than those measured for C. johnsoni or A. mississippiensis, which are among the least aggressive crocodilians.

The relationship between early growth and survival of hatchling saltwater crocodiles (Crocodylus porosus) in captivity.

Hatchling fitness in crocodilians is affected by "runtism" or failure to thrive syndrome (FTT) in captivity. In this study, 300 hatchling C. porosus, artificially incubated at 32°C for most of their embryonic development, were raised in semi-controlled conditions, with growth criteria derived for the early detection of FTT (within 24 days). Body mass, four days after hatching (BM4d), was correlated with egg size and was highly clutch specific, while snout-vent length (SVL4d) was much more variable within and between clutches. For the majority of hatchlings growth trajectories within the first 24 days continued to 90 days and could be used to predict FTT affliction up to 300 days, highlighting the importance of early growth. Growth and survival of hatchling C. porosus in captivity was not influenced by initial size (BM4d), with a slight tendency for smaller hatchlings to grow faster in the immediate post-hatching period. Strong clutch effects (12 clutches) on affliction with FTT were apparent, but could not be explained by measured clutch variables or other factors. Among individuals not afflicted by FTT (N = 245), mean growth was highly clutch specific, and the variation could be explained by an interaction between clutch and season. FTT affliction was 2.5 times higher among clutches (N = 7) that hatched later in the year when mean minimum air temperatures were lower, compared with those clutches (N = 5) that hatched early in the year. The results of this study highlight the importance of early growth in hatchling C. porosus, which has implications for the captive management of this species.

The good, the bad, and the ugly: agonistic behaviour in juvenile crocodilians.

We examined agonistic behaviour in seven species of hatchling and juvenile crocodilians held in small groups (N = 4) under similar laboratory conditions. Agonistic interactions occurred in all seven species, typically involved two individuals, were short in duration (5-15 seconds), and occurred between 1600-2200 h in open water. The nature and extent of agonistic interactions, the behaviours displayed, and the level of conspecific tolerance varied among species. Discrete postures, non-contact and contact movements are described. Three of these were species-specific: push downs by C. johnstoni; inflated tail sweeping by C. novaeguineae; and, side head striking combined with tail wagging by C. porosus. The two long-snouted species (C. johnstoni and G. gangeticus) avoided contact involving the head and often raised the head up out of the way during agonistic interactions. Several behaviours not associated with aggression are also described, including snout rubbing, raising the head up high while at rest, and the use of vocalizations. The two most aggressive species (C. porosus, C. novaeguineae) appeared to form dominance hierarchies, whereas the less aggressive species did not. Interspecific differences in agonistic behaviour may reflect evolutionary divergence associated with morphology, ecology, general life history and responses to interspecific conflict in areas where multiple species have co-existed. Understanding species-specific traits in agonistic behaviour and social tolerance has implications for the controlled raising of different species of hatchlings for conservation, management or production purposes.

Scaling of standard metabolic rate in estuarine crocodiles Crocodylus porosus.

Standard metabolic rate (SMR, ml O2 min(-1)) of captive Crocodylus porosus at 30 °C scales with body mass (kg) according to the equation, SMR = 1.01 M(0.829), in animals ranging in body mass of 3.3 orders of magnitude (0.19-389 kg). The exponent is significantly higher than 0.75, so does not conform to quarter-power scaling theory, but rather is likely an emergent property with no single explanation. SMR at 1 kg body mass is similar to the literature for C. porosus and for alligators. The high exponent is not related to feeding, growth, or obesity of captive animals. The log-transformed data appear slightly curved, mainly because SMR is somewhat low in many of the largest animals (291-389 kg). A 3-parameter model is scarcely different from the linear one, but reveals a declining exponent between 0.862 and 0.798. A non-linear model on arithmetic axes overestimates SMR in 70% of the smallest animals and does not satisfactorily represent the data.

Combining rapid bioassessment and field-based microcosms for identifying impacts in an urban river.

Rapid bioassessment indices based on macroinvertebrates are the most commonly used tools for assessing stream condition. However, once stream degradation has been detected, it is often difficult to identify which environmental stressors are most important because of changes in multiple correlated factors. In this study, we examined eight sites in an urban river watershed using a field-based microcosm experiment and the rapid bioassessment-based biotic index, SIGNAL. The experiment assessed the effects of polluted river sediment by examining the macroinvertebrate taxa that colonized sediments at an unpolluted wetland. Results were compared with an assessment of field-collected macroinvertebrates using SIGNAL, a biotic index that assigns pollution sensitivity scores to macroinvertebrate families, and environmental data, to determine whether sediment pollution or other factors such as habitat deterioration were likely to be influencing riverine macroinvertebrate communities. The microcosm results indicated that common species (Tanytarsus fuscithorax, Procladius paludicola, and Ablabesmyia notabilis) and the overall macroinvertebrate assemblage did not significantly change among sediments from different sites, with the exception of local effects on a few uncommon taxa (Chironomus pseudoppositus, Kiefferulus martini, Cladotanytarsus australomancus, Chaoboridae, Polypedilum "S1," and Tanytarsus belairensis). In contrast, SIGNAL showed a gradual trend of deterioration from upstream to downstream, decreasing from a score of 6.5 in upstream areas (unimpacted) to a score of 4.4 in the downstream sites (moderately impacted). This result combined with a significant correlation of SIGNAL scores to habitat data suggested that habitat deterioration rather than polluted sediment was likely to be responsible for the declining stream condition detected with the rapid bioassessment approach. The addition of the microcosms to other monitoring approaches could be useful for determining whether sediment pollution is influencing degraded urban streams.

Population assessment of the American crocodile, Crocodylus acutus (Crocodilia: Crocodylidae) on the Pacific coast of Costa Rica

The American crocodile, Crocodylus acutus, is widely distributed in the American neotropics. It is endangered throughout most of its range and is listed as vulnerable by the International Union for the Conservation of Natural Fauna and Flora (IUCN) and on Appendix I of the Convention for the International Trade in Endangered Species of Wild Flora and Fauna (CITES). Despite this listing, there are few published reports on population status throughout most of its range. We investigated the status of the C. acutus, at several locations along the Pacific coast of Costa Rica. We carried out spotlight and nesting surveys from 2007-2009 along the Costa Rican Pacific coast in four distinct areas, coastal areas of Las Baulas (N=40) and Santa Rosa (N=9) National Parks and the Osa Conservation Area (N=13), and upriver in Palo Verde National Park (N=11). We recorded crocodile locations and standard environmental data at each observation. Encounter rates, population structure, distribution within each area and data on successful nesting (presence of hatchlings, nests, etc) were determined. We attempted to capture all crocodiles to record standard morphometrics. A total of 586 crocodiles were observed along 185.8km of survey route. The majority of animals encountered (54.9%) were either hatchlings (<0.5m) or juveniles (0.5-1.25m). The average non-hatchling encounter rate per survey for the Pacific coast was 3.1 crocodiles/km, with individual encounter rates ranging from 1.2 crocodiles/km to 4.3 crocodiles/ km in Las Baulas National Park and the Osa Conservation Area respectively. Distribution of size classes within the individual locations did not differ with the exception of Santa Rosa and Las Baulas National Parks, where hatchlings were found in water with lower salinities. These were the first systematic surveys in several of the areas studied and additional work is needed to further characterize the American crocodile population in Costa Rica.

El cocodrilo americano, Crocodylus acutus, se encuentra ampliamente distribuido en el neotrópico Americano y hay pocos estudios publicados sobre el estado de sus poblaciones en la mayor parte de su rango de distribución. Investigamos el estado del Cocodylus acutus en varias ubicaciones a lo largo de la costa del Pacífico de Costa Rica. Se realizaron muestreos nocturnos y de anidación a lo largo de la Costa Pacífica de Costa Rica en cuatro áreas en particular desde 2007-2009,’áreas costeras en los Parque Nacionales de Las Baulas (N=40) y Santa Rosa (N=9), y en el Área de Conservación de la Osa (N=13) y en el curso alto del Parque Nacional de Palo Verde (N=11). Se registraron datos de la ubicación de los cocodrilos y datos ambientales estándar en cada observación. Se determinó la tasa de encuentros, estructura de la población, distribución dentro de cada área y evidencia de anidación exitosa (presencia de neonatos, nidos, etc.). Intentamos capturar todos los cocodrilos para registrar información morfométrica estándar. En total, se observaron 586 cocodrilos a lo largo de 185.8km de ruta de muestreo. La mayoría de los animales encontrados (54.9%) fueron neonatos (<0.5m) o juveniles (0.5-1.25m). La tasa promedio de encuentros por muestreo de no-neonatos en la costa del Pacífico fue de 3.1 cocodrilos/km; con rangos de encuentro de individuos de entre 1.2 a 4.3 cocodrilos/km en el Parque Nacional de Las Baulas y el Área de Conservación Osa. La distribución por clases de tamaño no varió, a excepción de los Parques Nacionales de Santa Rosa y Las Baulas, donde se encontró a los neonatos en aguas con bajas salinidades. Estos fueron los primeros muestreos sistemáticos en varias de las áreas estudiadas y son necesarios trabajos adicionales para caracterizar las poblaciones de cocodrilo Americano en Costa Rica.