Cross-species amplification of microsatellites in crocodilians: assessment and applications for the future

Microsatellite DNA loci have emerged as the dominant genetic tool for addressing questions associated with genetic diversity in many wildlife species, including crocodilians. Despite their usefulness, their isolation and development can be costly, as well as labour intensive, limiting their wider use in many crocodilian species. In this study, we investigate the cross-species amplification success of 82 existing microsatellites previously isolated for the saltwater crocodile (Crocodylus porosus) in 18 non-target crocodilian species; Alligator sinensis, Caiman crocodylus, Caiman latirostris, Caiman yacare, Melanosuchus niger, Paleosuchus palpebrosus, Crocodylus acutus, Mecistops cataphractus, Crocodylus intermedius, Crocodylus johnstoni, Crocodylus mindorensis, Crocodylus moreletii, Crocodylus niloticus, Crocodylus novaeguineae, Crocodylus palustis, Crocodylus rhombifer, Crocodylus siamensis, and Osteolaemus tetraspis. Our results show a high level of microsatellites cross-amplification making available polymorphic markers for a range of crocodilian species previously lacking informative genetic markers.     

Crocodilian phylogeny inferred from twelve mitochondrial protein-coding genes, with new complete mitochondrial genomic sequences for Crocodylus acutus and Crocodylus novaeguineae

We report complete mitochondrial genomic sequences for Crocodylus acutus and Crocodylus novaeguineae, whose gene orders match those of other crocodilians. Phylogenetic analyses based on the sequences of 12 mitochondrial protein-coding genes support monophyly of two crocodilian taxonomic families, Alligatoridae (genera Alligator, Caiman, and Paleosuchus) and Crocodylidae (genera Crocodylus, Gavialis, Mecistops, Osteolaemus, and Tomistoma). Our results are consistent with monophyly of all crocodilian genera. Within Alligatoridae, genus Alligator is the sister taxon of a clade comprising Caiman and Paleosuchus. Within Crocodylidae, the basal phylogenetic split separates a clade comprising Gavialis and Tomistoma from a clade comprising Crocodylus, Mecistops, and Osteolaemus. Mecistops and Osteolaemus form the sister taxon to Crocodylus. Within Crocodylus, we sampled five Indopacific species, whose phylogenetic ordering is ((C. mindorensis, C. novaeguineae), (C. porosus, (C. siamensis, C. palustris))). The African species C. niloticus and New World species C. acutus form the sister taxon to the Indopacific species, although our sampling lacks three other New World species and an Australian species of Crocodylus.     

Effects of the egg incubation environment on turtle carapace development

Developing organisms are often exposed to fluctuating environments that destabilize tissue-scale processes and induce abnormal phenotypes. This might be common in species that lay eggs in the external environment and with little parental care, such as many reptiles. In turtles, morphological development has provided striking examples of abnormal phenotypic patterns, though the influence of the environment remains unclear. To this end, we compared fluctuating asymmetry, as a proxy for developmental instability, in turtle hatchlings incubated in controlled laboratory and unstable natural conditions. Wild and laboratory hatchlings featured similar proportions of supernumerary scales (scutes) on the dorsal shell (carapace). Such abnormal scutes likely elevated shape asymmetry, which was highest in natural nests. Moreover, we tested the hypothesis that hot and dry environments cause abnormal scute formation by subjecting eggs to a range of hydric and thermal laboratory incubation regimes. Shape asymmetry was similar in hatchlings incubated at five constant temperatures (26–30°C). A hot (30°C) and severely Dry substrate yielded smaller hatchlings but scutes were not overtly affected. Our study suggests that changing nest environments contribute to fluctuating asymmetry in egg-laying reptiles, while clarifying the conditions at which turtle shell development remains buffered from the external environment.     

A survey of osteoderm histology and ornamentation among Crocodylomorpha: A new proxy to infer lifestyle?

Osteoderms of eight extant and extinct species of crocodylomorphs are studied histologically and morphologically. Most osteoderms display the typical “crocodilian” structure with a woven-fibered matrix surrounded by an upper and a lower parallel fibered matrix. The dorsal ornamentation of those specimens consists of a pit-and-ridge structure, with corresponding remodeling mechanisms. However, an osteoderm of Iberosuchus, studied here for the first time, differs in being nearly devoid of ornamentation; moreover, it shows strong bundles of straight Sharpey's fibers perpendicular to the surface in its lateral and dorsal walls, along with a rough plywood-like structure in its basal plate. This suggests that this osteoderm was more deeply anchored within the dermis than the other osteoderms studied hitherto. This peculiar structure might have been linked to a terrestrial ecology and a specific thermoregulation strategy. Some other notosuchians in our sample do not exhibit ornamentation on their osteoderms, as opposed to neosuchians. Considering current interpretations of osteoderm function(s) in crocodilians, our observations are discussed in reference to possible ecophysiological peculiarities of Notosuchia in general, and Iberosuchus in particular.     

Low Levels of Nucleotide Diversity in Crocodylus moreletii and Evidence of Hybridization with C. acutus

Examinations of both population genetic structure and the processes that lead to such structure in crocodilians have been initiated in several species in response to a call by the IUCN Crocodile Specialist Group. A recent study used microsatellite markers to characterize Morelet's crocodile (Crocodylus moreletii) populations in north-central Belize and presented evidence for isolation by distance. To further investigate this hypothesis, we sequenced a portion of the mitochondrial control region for representative animals after including samples from additional locales in Belize, Guatemala and Mexico. While there is limited evidence of subdivision involving other locales, we found that most of the differentiation among populations of C. moreletiican be attributed to animals collected from a single locale in Belize, Banana Bank Lagoon. Furthermore, mitochondrial DNA sequence analysis showed that animals from this and certain other locales display a haplotype characteristic of the American crocodile, C. acutus, rather than C. moreletii. We interpret this as evidence of hybridization between the two species and comment on how these new data have influenced our interpretation of previous findings. We also find very low levels of nucleotide diversity in C. moreletiihaplotypes and provide evidence for a low rate of substitution in the crocodilian mitochondrial control region. Finally, the conservation implications of these findings are discussed.     

Do crocodilians get the flu? Looking for influenza A in captive crocodilians

It is well established that several wild aquatic bird species serve as reservoirs for the influenza A virus. It has also been shown that the influenza A virus can be transmitted to mammalian species such as tigers and domestic cats and dogs through ingestion of infected birds. Another group of animals that should also be considered as potential hosts for the influenza A virus are the crocodilians. Many crocodilian species share aquatic environments with wild birds that are known to harbor influenza viruses. In addition, many large crocodilians utilize birds as a significant food source. Given these factors in addition to the close taxonomic proximity of aves to the crocodilians, it is feasible to ask whether crocodilian species may also harbor the influenza A virus. Here we analyzed 37 captive crocodilians from two locations in Florida (plus 5 wild bird fecal-samples from their habitat) to detect the presence of influenza A virus. Several sample types were examined. Real-time RT-PCR tests targeting the influenza A matrix gene were positive for four individual crocodilians--Alligator sinensis, Paleosuchus trigonatus, Caiman latirostris and Crocodylus niloticus. Of the seven serum samples tested with the avian influenza virus agar gel immunodiffusion assay, three showed a nonspecific reaction to the avian influenza virus antigen-A. sinensis, P. trigonatus and C. niloticus (C. latirostris was not tested). Viable virus could not be recovered from RT-PCR-positive samples, although this is consistent with previous attempts at viral isolation in embryonated chicken eggs with crocodilian viruses.     

Scute’s polymorphism as a source of evolutionary development of the turtle shell

The scute mosaic (pholidosis) of the turtle shell is a complex correlated system of the modular type. Horny scutes are separate morphological elements partially closely connected with each other and partially relatively autonomous in development. The last feature causes high variability of scutes in the shape, size, rate and direction of growth, and provides the basis of transformation of the entire mosaic. In the evolution of turtles, the horny shell changed towards a decrease in the number of elements composing it. The process of oligomerization developed through reduction and fusion of scutes or their anlages. The traces of these transformations are observed in the ontogeny of living turtles. The scutes undergoing reduction display the following developmental deviations: (1) a decrease in size of the scute anlage, (2) the temporal shift in initiation to later embryonic stages, (3) absence of an anlage of a own furrow (the boundaries of the scute are formed by the furrows of neighboring scutes), and (4) a decrease in size of the zone and rate of the scute growth. The fusion of horny scutes follows two patterns: (1) fusion of scute anlages and (2) reduction of horny furrows separating scutes before. Secondary polymerization of the scute mosaic by the appearance of additional elements usually results from abnormal development and is infrequently fixed in evolution. The main mechanism of evolutionary changes in turtle pholidosis was heterochrony, i.e., the time shift in initiation and developmental rate of scutes. The heterotopies, i.e., changes in the position of scute anlages, played a minor role in the evolution of turtles; they usually caused only scute abnormalities, which was frequently asymmetrical.     

Microevolutionary patterns in the common caiman predict macroevolutionary trends across extant crocodilians

Both extinct and extant crocodilians have repeatedly diversified in skull shape along a continuum, from narrow‐snouted to broad‐snouted phenotypes. These patterns occur with striking regularity, although it is currently unknown whether these trends also apply to microevolutionary divergence during population differentiation or the early stages of speciation. Assessing patterns of intraspecific variation within a single taxon can potentially provide insight into the processes of macroevolutionary differentiation. For example, high levels of intraspecific variation along a narrow‐broad axis would be consistent with the view that cranial shapes can show predictable patterns of differentiation on relatively short timescales, and potentially scale up to explain broader macroevolutionary patterns. In the present study, we use geometric morphometric methods to characterize intraspecific cranial shape variation among groups within a single, widely distributed clade, Caiman crocodilus. We show that C. crocodilus skulls vary along a narrow/broad‐snouted continuum, with different subspecies strongly clustered at distinct ends of the continuum. We quantitatively compare these microevolutionary trends with patterns of diversity at macroevolutionary scales (among all extant crocodilians). We find that morphological differences among the subspecies of C. crocodilus parallel the patterns of morphological differentiation across extant crocodilians, with the primary axes of morphological diversity being highly correlated across the two scales. We find intraspecific cranial shape variation within C. crocodilus to span variation characterized by more than half of living species. We show the main axis of intraspecific phenotypic variation to align with the principal direction of macroevolutionary diversification in crocodilian cranial shape, suggesting that mechanisms of microevolutionary divergence within species may also explain broader patterns of diversification at higher taxonomic levels.     

The family liolopidae (Digenea) including a new genus and two new species from crocodilians

Two new species of liolopid digeneans infecting crocodilians are described and the classification of the family slightly revised. Liolope copulans from the salamander Megalobatrachus japonicus in Japan actually possesses an internal rather than external seminal vesicle and tegumental spines, and the generic diagnosis is emended to include those features. Liolopids paratisitizing crocodilians are removed from Harmotrema and placed in a separate new genus characterized by the possession of a relatively short body with gonads in the posterior rather than middle third of the body. Liolopids infecting Neotropical lizards and turtles remain in Helicotrema and those parasitizing freshwater and marine snakes remain in Harmotrema. The first new species, from Alligator mississipiensis in the southeastern United States, most closely resembles the species described as Harmotrema rudolphii from a saltwater crocodile in the Philippines, but differs from it by having a shorter cirrus sac, stouter and shorter cirrus, and slightly smaller eggs; it differs from all crocodilian liolopids by possessing a more extensively folded metraterm. The second new species, from Crocodylus cataphractis in the Congo (Belgian), differs from all others in crocodilians by having a relatively larger pharynx and smaller acetabulum. Diagnoses of all crocodilian liolopids are presented. Harmotrema laticaudae, previously known from Laticauda laticaudata in Okinawa only, is reported from Aipysurus laevis, Hydrophis major, and a ‘black and white-ringed sea snake’ in Queensland, Australia.     

Osteology and myology of the wing of the Emu (Dromaius novaehollandiae), and its bearing on the evolution of vestigial structures

Emus have reduced their wing skeleton to only a single functional digit, but the myological changes associated with this reduction have never been properly described. Moreover, the intraspecific variability associated with these changes has not previously been examined, dissections having been restricted in the past to only one or two individuals. In this paper, the myology and osteology of the Emu wing is described for a sample of five female birds. The Emu showed a marked reduction in the number of muscles in the wing, even compared with other ratites. Many wing muscles showed diversity in structure, origin and insertion sites, number of heads, as well as presence-absence variation. This variability dramatically exceeds that found in flying birds. Evolutionary theory predicts that relaxed selection on vestigial organs should allow more variation to persist in the population, and corresponds to what is observed here. A large amount of fluctuating asymmetry was also detected, indicating reduced canalization of the wing during development.     

Genetic and morphological evidence of a geographically widespread hybrid zone between two crocodile species,Crocodylus acutus and Crocodylus moreletii

Hybrid zones represent natural laboratories to study gene flow, divergence and the nature of species boundaries between closely related taxa. We evaluated the level and extent of hybridization between Crocodylus moreletii and Crocodylus acutus using genetic and morphological data on 300 crocodiles from 65 localities. To our knowledge, this is the first genetic study that includes the entire historic range and sympatric zone of the two species. Contrary to expectations, Bayesian admixture proportions and maximum‐likelihood estimates of hybrid indexes revealed that most sampled crocodiles were admixed and that the hybrid zone is geographically extensive, extending well beyond their historical region of sympatry. We identified a few geographically isolated, nonadmixed populations of both parental species. Hybrids do not appear to be F₁s or recent backcrosses, but rather are more likely later‐generation hybrids, suggesting that hybridization has been going on for several to many generations and is mostly the result of natural processes. Crocodylus moreletii is not the sister species of C. acutus, suggesting that the hybrid zone formed from secondary contact rather than primary divergence. Nonadmixed individuals from the two species were distinguishable based on morphological characters, whereas hybrids had a complex mosaic of morphological characters that hinders identification in the wild. Very few nonadmixed C. acutus and C. moreletii populations exist in the wild. Consequently, the last nonadmixed C. moreletii populations have become critically endangered. Indeed, not only the parental species but also the naturally occurring hybrids should be considered for their potential conservation value.     

Unusual aetosaur armor from the Upper Triassic of West Texas,U.S.A.

We report two unusual aetosaur scutes from the Tecovas Member of the Dockum Formation, Chinle Group (upper Carnian) of Crosby County, Texas, U.S.A. Originally collected by University of Michigan expeditions in the 1920’s, these scutes cannot be assigned with certainty to any known species of aetosaurs known from the American Southwest. One of these scutes may be a cervical horn ofParatypothorax, and if so confirms the similarities of this aetosaur toDesmatosuchus in the possession of horned lateral spikes. The other is a paramedian scute of a new aetosaur taxon inadequately known at present to be assigned a formal name. These scutes indicate that aetosaurs were more diverse in the Chinle Group than currently known, but do not alter the robust Late Triassic biochronology based on aetosaurs.     

Opportunistic top predators partition food resources in a tropical freshwater ecosystem

相似文献   

Molecular identification of crocodile species using novel primers for forensic analysis

All crocodilians are under varying degrees of threat due to over exploitation and these species have been listed in Appendix I or II of CITES. The lack of molecular techniques for the identification of confiscated samples makes it difficult to enforce the law. Conclusive forensic identification of species requires a complete gene sequence which is difficult in case of degraded samples. We have developed two novel sets of primers to amplify two partial cytochrome b gene sequences of six crocodile species i.e. Crocodylus palustris, Crocodylus porosus, Crocodylus siamensis, Crocodylus niloticus, Gavialis gangeticus and Caiman crocodilus. These partial sequences were edited to give a complete cyt b gene sequence, which can be used as an effective tool for forensic authentication of crocodile species. A phylogeny of crocodile species was reconstructed using these sequences. The described primers hold great promise in forensic identification of crocodile species, which can aid in the effective enforcement of law and conservation of these ancient species.     

FLUCTUATING ODONTOMETRIC ASYMMETRY,MORPHOLOGICAL VARIABILITY,AND GENETIC MONOMORPHISM IN THE CHEETAH ACINONYX JUBATUS

The magnitudes of dimensional variability and fluctuating asymmetry in dental dimensions are reported for a sample of South African cheetah Acinonyx jubatus. To test the hypothesis that elevated levels of variability and asymmetry are associated with the increased developmental instability reported for this species, our results were contrasted to those for two other felids: Felis lybica and F. caracal. These findings suggest that dental dimensions in cheetahs are not significantly more variable or asymmetric. Hence, it is concluded that the cheetah may not be as developmentally unstable as was previously supposed.     

Proliferation in the epidermis of chelonians and growth of the horny scutes

The proliferation of the epidermis in soft skin, claws, and scutes of the carapace and plastron in the tortoise (Testudo hermanni) and the turtle (Chrysemys picta) were studied using autoradiographic and immunocytochemical methods. During the growing season, a basal keratinocyte in the epidermis of soft skin and claws takes 5-9 days to migrate into the corneous layer. In the tortoise, during fall/winter (resting season) a few alpha-keratin cells are produced in soft epidermis and hinge regions among scutes and occasional beta-keratin cells in the outer scute surface. When growth is resumed in spring (growing season), cell proliferation is intense, mainly around hinge regions and tips of marginal scutes. No scute shedding occurs and numerous beta-keratin cells are produced around the hinge regions, while alpha-keratin cells disappear. Beta-cells form a new thick corneous layer around the hinge regions, which constitute the growing rings of scutes. Beta-keratin cells produced in more central parts of scutes maintain a homogeneous thickness of the corneous layer along the whole scute surface. In the turtle, a more complicated process of scute growth occurs than in the tortoise. At the end of the growing season (late fall) the last keratinocytes formed beneath the old stratum corneum of the outer scale surface and hinge regions produce more alpha- than beta-keratin. These thin alpha-keratin cells form a scission layer below the old stratum corneum, which extends from the hinge regions toward the center of scutes and the tip of marginal scutes. In the resting season (fall/winter) most cells remain within the germinative layer of the carapace and plastron and a few alpha-cells move in 7-9 days into the corneous layer above hinge regions. In the following spring/summer (growing season) a new generation of beta-keratin cells is produced beneath the scission layer from the hinge region and more central part of the scutes. The epidermis of the inner surface of scutes and hinge regions contains most of the cells incorporating thymidine and histidine, while the remaining outer scute surface is less active. It takes 5-9 days for a newly produced beta-cell to migrate into the corneous layer. These cells form a new corneous layer that extends the whole scute surface underneath the maturing scission layer. The latter contains lipids and eventually flakes off, determining shedding of the above outer corneous layer in late spring or summer.     

Individualization and estimation of relatedness in crocodilians by DNA fingerprinting with a Bkm-derived probe

Individual-specific DNA fingerprints of crocodilians were obtained by the use of Bkm-2(8) probe. Pedigree analyses of Crocodylus palustris, C. porosus and Caiman crocodilus revealed that the multiple bands (22–23 bands with Aludigest) thus obtained were inherited stably in a Mendelian fashion. Unique fingerprints permitted us to identify individuals, assign parentage, and reconstruct the DNA profile of a missing parent. Average band sharing between unrelated crocodiles was found to be 0.37. Band sharing between animals of known pedigrees increased predictably with relatedness and provided a basis for distinguishing relatives from non-relatives. Similar results obtained in other species/genera, using the same probe, suggest that this approach may be applicable to all species of crocodilians, and could facilitate genetic studies of wild and captive populations.     

Dinosaurs: a field guide/The Princeton field guide to dinosaurs

Eggshells from the three extant crocodilian species Crocodylus mindorensis (Philippine Crocodile), Paleosuchus palpebrosus (Cuvier's Smooth-fronted Caiman or Musky Caiman) and Alligator mississippiensis (American Alligator or Common Alligator) were prepared for thin section and scanning electron microscope analyses and are described in order to improve the knowledge on crocodilian eggs anatomy and microstructure, and to find new apomorphies that can be used for identification. Both extant and fossil crocodilian eggs present an ornamentation that vary as anastomo-, ramo- or the here newly described rugosocavate type. The angusticaniculate pore system is a shared character for Crocodylomorpha eggshells and some dinosaurian and avian groups. Previously reported signs of incubated crocodilian eggs were found also on our only fertilised and hatched egg. Paleosuchus palpebrosus presents unique organization and morphology of the three eggshell layers, with a relatively thin middle layer characterised by dense and compact tabular microstructure.     

Morphological and genetic variation in the endangered Sulawesi tortoise Indotestudo forstenii: evidence of distinct lineages?

Limited fieldwork and anecdotal evidence indicate that allopatric populations of the endangered Sulawesi tortoise (Indotestudo forstenii) differ in size and presence/absence of a nuchal scute, suggesting that these may constitute separate evolutionary lineages. We examined morphological and genetic variation to determine if the nuchal scute is correlated with size or genetic divergence. Our results indicate a strong correlation between size and nuchal scute such that turtles lacking a nuchal scute were larger than those possessing a nuchal scute. However, we found no correlation between genetic divergence and presence/absence of nuchal scutes, and thus no evidence of genetically differentiated lineages.     

A meta-analysis of the heritability of developmental stability

The existence of additive genetic variance in developmental stability has important implications for our understanding of morphological variation. The heritability of individual fluctuating asymmetry and other measures of developmental stability have frequently been estimated from parent-offspring regressions, sib analyses, or from selection experiments. Here we review by meta-analysis published estimates of the heritability of developmental stability, mainly the degree of individual fluctuating asymmetry in morphological characters. The overall mean effect size of heritabilities of individual fluctuating asymmetry was 0.19 from 34 studies of 17 species differing highly significantly from zero (P < 0.0001). The mean heritability for 14 species was 0.27. This indicates that there is a significant additive genetic component to developmental stability. Effect size was larger for selection experiments than for studies based on parent-offspring regression or sib analyses, implying that genetic estimates were unbiased by maternal or common environment effects. Additive genetic coefficients of variation for individual fluctuating asymmetry were considerably higher than those for character size per se. Developmental stability may be significantly heritable either because of strong directional selection, or fluctuating selection regimes which prevent populations from achieving a high degree of developmental stability to current environmental and genetic conditions.