Growth of the Orinoco Caiman (Crocodylus intermedius, Crocodylia: Crocodylidae) under two captivity conditions

Growth of the Orinoco Caiman (Crocodylus intermedius, Crocodylia: Crocodylidae) under two captivity conditions. In order to determine the growth of Caiman of the Orinoco (Crocodylus intermedius) under two conditions of captivity, 40 specimens were raised during 11 months and 15 days in two circular tanks, with 28.3 m2 of surface area and a volume of 62.2 m3 in each tank. The tanks were built with concrete walls and guarded blocks covered internally with sheets of myrrhlike resin, and a roof of galvanized sheets. One tank was covered partially with the galvanized sheets (tank I), the other was totally covered (tank II). Twenty caimans were placed in each tank, and both groups were fed with 85% beef, 10% fresh fish, 5% hen eggs and a mixture of minerals and vitamins. The length and weight differed significantly between the groups (p < 0.001). Mean growth (103.0 +/- 6.81 cm) and weight (3 987 +/- 0.98 g) were higher in tank II, (tank I: 88.9 +/- 7.58 cm; 2 705 +/- 0.69 g). The greater growth in tank II reflects higher air and water temperatures. The survival rate was 97.5%. These results can be used for rearing caimans in captivity for conservation and commercial purposes.     

Hybridization between Crocodylus acutus and Crocodylus moreletii in the Yucatan Peninsula: II. Evidence from microsatellites

Detecting and quantifying hybridization between endangered or threatened taxa can provide valuable information with regards to conservation and management strategies. Hybridization between members of the genus Crocodylus has been known to occur in captivity and in some wild populations. We tested for hybridization among wild populations of American crocodile (C. acutus) and Morelet's crocodile (C. moreletii) in the Yucatan Peninsula by comparing Bayesian assignment tests, based on microsatellite data, to mitochondrial and morphological assignments. Skin clips from 83 individuals were taken for genetic identification, and a total of 32 individuals (38.6%) exhibited some evidence of hybridization by combined morphological, mitochondrial and microsatellite analyses. The majority of hybrids were classified as F(2) hybrids and backcrosses to C. moreletii. Most of the introgression occurs in two national biosphere reserves located on the northern and eastern coasts of the Yucatan Peninsula. Preliminary tests did not find a significant decrease in hybridity across three life stages, thus far indicating a low level of selection against hybrids. Model-based analyses on multilocus genotypes of pure individuals returned little geographic partitioning in both C. acutus and C. moreletii.     

Genetic variability and individual assignment of Chinese indigenous sheep populations (Ovis aries) using microsatellites

The purpose of this study was to assess the genetic characteristics of six breeds of Chinese local sheep using 19 microsatellite loci and to effectively validate statistical methods for individual assignment based on informative microsatellites. All the six breeds deviated from Hardy–Weinberg equilibrium expectations, while the majority of markers complied. The polymorphism information content (PIC) of overall loci for the six populations ranged from 0.283 (SRCRSP5) to 0.852 (OarVH72). Tibetan sheep were the most diverse population with the highest mean allelic richness (6.895), while Ujmuqin (UQ) harboured the lowest allelic richness (6.000). The F‐statistics for the six populations were F_IS = ?0.172, F_IT = ?0.082 and F_ST = 0.077, respectively. Furthermore, the pair‐wise F_IS revealed a moderate genetic differentiation among populations (P < 0.01), indicating that all breeds can be considered genetically independent entities. The lowest genetic differentiation was between Tengchong (TC) and UQ (F_ST = 0.041), and the highest one was between TC and Fat‐tailed Han (F_ST = 0.111). In comparing the three statistical models, we note that the seven microsatellite loci (MAF65, OarJMP58, SRCRSP9, MCM140, OarAE129, BM8125 and SRCRSP5) commonly used for individual assignment will ensure a powerful detection of individual origin, with accuracy up to 91.87%, when the likelihood‐based method is used. Overall, these findings shed light onto the genetic characteristics of Chinese indigenous sheep and offer a set of microsatellite loci that is simple, economic and highly informative for individual assignment of Chinese sheep.     

Genetic characterization of captive Cuban crocodiles (Crocodylus rhombifer) and evidence of hybridization with the American crocodile (Crocodylus acutus)

There is a surprising lack of genetic data for the Cuban crocodile (Crocodylus rhombifer), especially given its status as a critically endangered species. Samples from captive individuals were used to genetically characterize this species in comparison with other New World crocodilians. Partial mitochondrial sequence data were generated from cyt-b (843 bp) and the tRNA(Pro)- tRNA(Phe)-D-loop region (442 bp). Phylogenetic analyses were performed by generating maximum parsimony, maximum likelihood, and Bayesian-based topologies. In addition, in an effort to identify species-specific alleles, ten polymorphic microsatellite loci were genotyped. Distance and model-based clustering analyses were performed on microsatellite data, in addition to a model-based assignment of hybrid types. Both mitochondrial and nuclear markers identified two distinct C. rhombifer genetic sub-clades (alpha and beta); and microsatellite analyses revealed that most admixed individuals were F(2) hybrids between C. rhombifer-alpha and the American crocodile (C. acutus). All individuals in the C. rhombifer-beta group were morphologically identified as C. acutus and formed a distinct genetic assemblage. J. Exp. Zool. 309A:649-660, 2008. (c) 2008 Wiley-Liss, Inc.     

Evidence of multiple paternity in Morelet's Crocodile (Crocodylus moreletii) in Belize, CA, inferred from microsatellite markers

Microsatellite data were generated from hatchlings collected from ten nests of Morelet's Crocodile (Crocodylus moreletii) from New River Lagoon and Gold Button Lagoon in Belize to test for evidence of multiple paternity. Nine microsatellite loci were genotyped for 188 individuals from the 10 nests, alongside 42 nonhatchlings from Gold Button Lagoon. Then mitochondrial control region sequences were generated for the nonhatchlings and for one individual from each nest to test for presence of C. acutus-like haplotypes. Analyses of five of the nine microsatellite loci revealed evidence that progeny from five of the ten nests were sired by at least two males. These data suggest the presence of multiple paternity as a mating strategy in the true crocodiles. This information may be useful in the application of conservation and management techniques to the 12 species in this genus, most of which are threatened or endangered.     

Genetic differentiation of the African dwarf crocodile Osteolaemus tetraspis Cope, 1861 (Crocodylia: Crocodylidae) and consequences for European zoos

The endangered African dwarf crocodile Osteolaemus tetraspis is distributed in Central and Western Africa. Conventionally, two subspecies were distinguished: Osteolaemus tetraspis tetraspis and Osteolaemus tetraspis osborni. The taxonomic significance of diagnostic morphological characters is still being discussed and the existence of additional species in the Osteolaemus group remains unclear. Recent molecular studies suggest the existence of three allopatric species in the genus Osteolaemus. These results supported a division of the dwarf crocodile into a Congo Basin form (O. osborni), an Ogooué Basin form (O. tetraspis), and a third separate evolutionary lineage from Western Africa. Several European zoos host African dwarf crocodiles. For reasons of conservation and possible reintroduction, it is important to clarify provenance of these zoo animals. Therefore, we conducted molecular and phylogenetic analyses of three mitochondrial and two nuclear gene sequences with all available samples from European zoos and museums. We also estimated the origin of the zoo animals by comparing sequences of wild animals and museum samples of known provenance. Our study strongly supports three distinct lineages of Osteolaemus as recently postulated, but also reveals a fourth evolutionary lineage. We demonstrate that, of the European zoo animals sampled, only one dwarf crocodile corresponds to the Congo Basin form (O. osborni) whereas the majority of individuals correspond to the three other forms. Four zoo animals belong to the new fourth group; but their provenance is still unresolved. The origin of these animals is probably located in an African region from which no wild animal samples are currently available. Further investigations and sampling of other regions should be completed to clarify the identity of this fourth lineage. We found potential hybrids from European zoological gardens using nuclear DNA sequences. The European Studbook will use these results for further breeding programmes to keep genetically suitable ex-situ populations as reassurance colonies for prospective reintroduction into African countries.     

Genetic characterization of Colombian Brahman cattle using microsatellites markers

Genetic structure and diversity of 3789 animals of the Brahman breed from 23 Colombian regions were assessed. Considering the Brahman Zebu cattle as a single population, the multilocus test based on the HW equilibrium, shows significant differences (P < 0.001). Genetic characterization made on the cattle population allowed to examine the genetic variability, calculating a H _o = 0.6621. Brahman population in Colombia was a small subdivision wthin populations (F _it = 0.045), a geographic subdivision almost non-existent or low differentiation (F _st = 0.003) and the F _is calculated (0.042) indicates no detriment to the variability in the population, despite the narrow mating takes place or there is a force that causes the variability is sustained without inbreeding actually affect the cattle population. The outcomes of multivariate analyses, Bayesian inferences and interindividual genetic distances suggested that there is no genetic sub-structure in the population, because of the high rate of animal migration among regions.     

Genetic variation (protein markers and microsatellites) in endangered Catalonian donkeys

Genetic variation of the endangered Catalonian donkey breed (Equus asinus) has been analysed at 19 loci including seven protein loci and 12 microsatellite loci isolated from the domestic horse, in 98 individuals of both sexes. Only four protein markers and three microsatellites were polymorphic. Allele frequencies of the analysed loci showed close agreement with Hardy–Weinberg proportions, with the exception of the MPZ002 locus (P<0.01). The within-population inbreeding estimate was not significantly different from zero (as measured by F_IS-statistic). The cumulative-exclusion probability for all polymorphic loci was 82.9%, this value still being very low so that these markers could efficiently be utilised for verification of parentage.     

Genetic variability in a captive herd of Speke's gazelle (Gazella spekei)

A captive herd of Speke' gazelle was screened for genetic variability at 28 enzyme-coding loci, the nuclear ribosomal DNA (rDNA), and the mitochondrial DNA (mtDNA). There is one variable restriction site out of 52 in the rDNA and three variable sites out of 41 in the mtDNA. This amount of mitochondrial diversity is low for a mammal, but is about the maximum to be expected given that the entire herd is derived from three females. However, 14% of the enzymecoding loci were polymorphic, a figure typical for mammals. Hence, despite the fact that the herd was founded by one male and three females, much genetic variation is still present. It is therefore important to continue breeding programs designed to maintain genetic diversity. MtDNA is maternally inherited, so tracing back from the current animals through females allowed us to infer that each founding female had a distinct mtDNA haplotype. Hence, the founding females could not have shared the same mother. The nuclear variability could also be traced back through the pedigrees to the founders. One female was found to have contributed none of the assayed genetic variability to the current herd. “Gene drop” simulations of the herd indicated that this was the only founder for which much genetic variability had already been lost because of breeding decisions made during the early history of the herd. This illustrates the importance of implementing breeding programs designed to preserve genetic variability as soon as possible.     

253 Novel polymorphic microsatellites for the saltwater crocodile (Crocodylus porosus)

Genomic elucidation and mapping of novel organisms requires the generation of large genetic resources. In this study, 253 novel and polymorphic microsatellite loci were isolated and characterized for the saltwater crocodile (Crocodylus porosus) by constructing libraries enriched for microsatellite DNA. All markers were evaluated on animals obtained from Darwin Crocodile Farm in the Northern Territory, Australia, and are intended for future use in the construction of a genetic-linkage map for the saltwater crocodile. The 253 loci yielded an average of 4.12 alleles per locus, and those selected for mapping had an average polymorphic information content (PIC) of 0.425.     

Genetic assessment of captive elephant (Elephas maximus) populations in Thailand

The genetic diversity and population structure of 136 captive Thai elephants (Elephas maximus) with known region of origin were investigated by analysis of 14 highly polymorphic microsatellite loci. We did not detect significant indications of inbreeding and only a low differentiation of elephants from different regions. This is probably explained by the combined effects of isolation by distance and exchange between different regions or between captive and wild elephant populations. Estimates of effective population sizes were in the range of 90–240 individuals, which emphasizes the necessity to guard against inbreeding as caused by the current use of a restricted number of breeding bulls.     

Genetic variability and bottleneck studies in Zalawadi, Gohilwadi and Surti goat breeds of Gujarat (India) using microsatellites

Indian goat breeds are recognized as an invaluable component of the world's goat genetic resources. Microsatellite pairs were chosen from the list suggested by International Society for Animal Genetics (ISAG) and amplified in two multiplexes (Set-I: 7 microsatellites and Set-II: 11 microsatellites) for automated fluorescence genotyping to assess bottleneck and analyze genetic variability and genetic distances within and between three goat breeds viz. Zalawadi, Gohilwadi and Surti. The observed number of alleles ranged from 4 (Oar JMP-29) to 15 (ILSTS-030 and -034) with a total of 178 alleles and mean of 9.89 alleles across the three breeds. The overall heterozygosity, PIC and Shannon index values were 0.61, 0.60 and 1.50 indicating high genetic diversity. The maximum observed heterozygosity was found in Gohilwadi and minimum in Surti goat breed. The Nei's standard genetic distance was minimum between Zalawadi and Gohilwadi, and maximum between Gohilwadi and Surti. Non-significant heterozygote excess on the basis of IAM, TPM and SMM models, as revealed from Wilcoxon sign-rank tests, along with a normal ‘L’-shaped distribution of mode-shift test, indicated no bottleneck in Zalawadi and Gohilwadi goat populations, whereas mild bottleneck in the recent past for Surti breed. This research on goat genetic diversity in Gujarat state provides valuable information on Zalawadi, Gohilwadi and Surti goat genetic resources, and will assist in developing a national plan for the conservation and utilization of indigenous goat breeds.     

Genetic variability in a narrow endemic snapdragon (Antirrhinum subbaeticum,Scrophulariaceae) using RAPD markers

Antirrhinum subbaeticum is an endangered species inhabiting fragmented limestone cliffs. In the last 3 years, a drastic population decline has been observed in three of four known populations and the estimated number of surviving individuals is now close to 400. A RAPD study was conducted to evaluate the levels of genetic variation present in this species to improve conservation guidelines. Thirty-nine polymorphic products identified 66.1% of the samples by unique RAPD multilocus profiles. A cluster analysis grouped the samples into two broad groups corresponding to northern or southern provenances. AMOVA analysis showed that only 17.7% of the genetic diversity was partitioned within populations. These results are in contrast to data available for other Antirrhinum species. This genetic structure could be explained by the predominant selfing behaviour exhibited by A. subbaeticum as opposed to the allogamy of other congeners. Genetic diversity within populations does not seem to be strongly related to population size and historical factors could be responsible for the very low levels of genetic diversity found in one population. Given the low genetic diversity within populations, it is suggested that an extensive sampling of individuals be made for recovering appropriate levels of the gene pool for ex situ preservation. However, translocation of individuals to the genetically weakened Bogarra population from other sources is not recommended.     

Hybridization between Crocodylus acutus and Crocodylus moreletii in the Yucatan Peninsula: I. Evidence from mitochondrial DNA and morphology

The American crocodile (Crocodylus acutus) and the Morelet's crocodile (C. moreletii) are broadly sympatric in Belize and Mexico. The presence of morphologically anomalous individuals in the overlapping range area suggests possible hybridization between these species. Analysis of 477 base pairs of the mitochondrial tRNA(Pro)-tRNA(Phe)-Dloop region revealed the presence of pure C. acutus (N=43) and C. moreletii (N=56), as well as a high proportion of interspecific hybrids (N=17, 14.6%) in the Yucatan Peninsula, Mexico. Although all individuals could be assigned to one species or other based on phenotypic characters, some had been characterized as potential hybrids in the field by anomalous scale counts. The hybridization zone lies along the area of sympatry between C. acutus and C. moreletii investigated in this study, but extends further inland if hybrid localities from Belize are included. Hybridization in the Yucatan Peninsula is bidirectional, which indicates considerably more genetic contact between these species than previously recognized, and is probably more detrimental to the genetic integrity of smaller C. acutus populations. A more intensive study of the pattern of hybridization is warranted and supports continued classification of C. acutus as a critically threatened species in the Yucatan Peninsula.     

Genetic variability in local Brazilian horse lines using microsatellite markers

Genetic variability at 11 microsatellite markers was analyzed in five naturalized/local Brazilian horse breeds or genetic groups. Blood samples were collected from 328 animals of the breeds Campeira (Santa Catarina State), Lavradeira (Roraima State), Pantaneira (Pantanal Mato-Grossense), Mangalarga Marchador (Minas Gerais State), as well as the genetic group Baixadeiro (Maranh?o State), and the exotic breeds English Thoroughbred and Arab. We found significant genetic variability within evaluated microsatellite loci, with observed heterozygosis varying between 0.426 and 0.768 and polymorphism information content values of 0.751 to 0.914. All breeds showed high inbreeding coefficients and were not in Hardy-Weinberg equilibrium. The smallest genetic distance was seen between the Pantaneira and Arab breeds. The principal component analyzes and Bayesian approach demonstrated that the exotic breeds have had a significant influence on the genetic formation of the local breeds, with introgression of English Throroughbred in Pantaneira and Lavradeira, as well as genetic proximity between the Arab, Pantaneira and Mangalarga Marchador populations. This study shows the need to conserve traits acquired by naturalized horse breeds over centuries of natural selection in Brazil due to the genetic uniqueness of each group, suggesting a reduced gene flow between them. These results reinforce the need to include these herds in animal genetic resource conservation programs to maximize the genetic variability and conserve useful allele combinations.     

Genetic variation within the Merino sheep breed: analysis of closely related populations using microsatellites

Genetic relationships among six populations of Merino sheep were investigated using microsatellites. The history of the six populations is relatively well documented, with all being derived from the Spanish Merino breed within the last 400 years. Genetic variation was highest amongst the Spanish and Portuguese populations, although the preservation of genetic diversity within the other populations was high. By a variety of different statistical tests the French Mutton, German Mutton and New Zealand Merino populations could be differentiated from each other and the Iberian Merinos, indicating that microsatellites are able to track relatively recent changes in the population structure of sheep breeds. The dendrograms constructed on the basis of microsatellite allelic frequencies showed that populations that have shared selection criteria (meat vs. wool) tend to cluster together.     

基于SRAP分子标记的海南沼虾种群遗传多样性

为了调查我国海南沼虾(Macrobrachium hainanense)不同地理种群遗传多样性及遗传分化状况,本文采用序列相关扩增多态性(sequence-related amplified polymorphism,SRAP)标记对我国南方瓯江(OJ)、闽江(MJ)、珠江(PR)、万泉河(WQ)、昌化江(CH)等5个海南沼虾种群的遗传多样性进行了研究。共得到255个清晰、稳定的位点,平均多态位点比例为47.05%,由小到大依次为:PR(43.92%)=WQ(43.92%)相似文献   

Assessing genetic diversity among six populations of Gossypium arboreum L. using microsatellites markers

Among the four cultivated cotton species, G. hirsutum (allotetraploid) presently holds a primary place in cultivation. Efforts to further improve this primary cotton face the constraints of its narrow genetic base due to repeated selective breeding and hence demands enrichment of diversity in the gene pool. G. arboreum (diploid species) is an invaluable genetic resource with great potential in this direction. Based on the dispersal and domestication in different directions from Indus valley, different races of G. arboreum have evolved, each having certain traits like drought and disease resistance, which the tetraploid cotton lack. Due to lack of systematic, race wise characterization of G. arboreum germplasm, it  has not been explored fully. During the present study, 100 polymorphic SSR loci were  used to genotype 95 accessions belonging to 6 races of G. arboreum producing 246 polymorphic alleles; mean number of effective alleles was 1.505. AMOVA showed 14 % of molecular variance among population groups, 34 % among individuals and remaining 52 % within individuals. UPGMA dendrogram, based on Nei’s genetic distance, distributed the six populations in two major clusters of 3 populations each; race ‘bengalense’ was found more close to ‘cernuum’ than the others. The clustering of 95 genotypes by UPGMA tree generation as well as PCoA analysis clustered ‘bengalense’ genotypes into one group along with some genotypes of ‘cernuum’, while rest of the genotypes made separate clusters. Outcomes of this research should be helpful in identifying the genotypes for their further utilization in hybridization program to obtain high level of germplasm diversity.

Electronic supplementary material

The online version of this article (doi:10.1007/s12298-015-0326-y) contains supplementary material, which is available to authorized users.     

Genetic variability and diversification process in local pear cultivars from northwestern Spain using microsatellites

This is the first known large-scale molecular study of simple sequence repeats loci based on pear cultivars from the northwestern Iberian Peninsula. Most of the Spanish pear crop (one of the largest in Europe) is based on the Spanish cultivar Blanquilla and various other foreign cultivars. However, local cultivars can still be found in old orchards in northwestern Spain. Between 1978 and 1981, the Centro de Investigaciones Agrarias de Mabegondo (Xunta de Galicia) established a Germplasm Bank of local pear cultivars containing 221 accessions. In the current study, these were analysed and compared with 20 commercial cultivars of Pyrus spp. using 19 microsatellites. We identified 127 genotypes out of 221 accessions with an average of 43% clonality in this collection. Genotypes were analysed using a model-based Bayesian procedure (Structure), factorial correspondence analysis and molecular variance analysis, and Jaccard coefficients were estimated. Four reconstructed populations were identified by Structure, one related to Asian cultivars, two to French and English cultivars and one to Galician cultivars. The four identified groups of pears had evolved independently. This study explains the diversification process in pear cultivars from northwestern cultivars based on hybridization (16%), selection of triploids (38%) and the introgression of commercial cultivars in the collection (4%).