Abundance and seasonal migrations of the penaeid shrimp Metapenaeus affinis (H. Milne-Edwards) within Iraqi waters

Migration of Metapenaeus affinis (H. Milne-Edwards) from the Arabian Gulf to nursery grounds in the inland waters of Iraq extends from May/June to January/February. Shrimp ranging in size from 3–125 mm total length were found in inland waters. In the shallow waters of the Al-Assaflya small-sized shrimp only were caught, while in the Marshes large-sized shrimp were abundant. Maximum numbers of recruits were recorded when temperatures reached 23–25 °C. However, the discharge of the Shatt Al-Arab may also be an important factor regulating recruitment.The growth rates of small shrimp were higher than those of large ones. There mostly was, a preponderance of females over males. Spawning at sea appears to occur immediately after emigration. Gonad development was not observed. Commercial landings, at the two main fish markets at Basrah, during September–November 1985 averaged 1000 kg day^–1.     

Sex, size and colour in a semi-terrestrial crab, Heloecius cordiformis (H. Milne Edwards, 1837)

We investigated the relationship between sex, size and colour in the little studied Australian endemic semaphore crab, Heloecius cordiformis, and related it to the crabs' social system with the aim of identifying the potential signalling function of claw colour.Equal sampling of crabs from all size classes revealed a strong relationship between sex, size and claw colour. Purple-clawed males were larger and had larger claws than pink-, orange- or green-clawed males. Male claws showed positive allometric growth: relative to body size, purple-clawed males had larger claws. The largest females had pink claws; the few with purple claws were no larger than immature green-clawed crabs. Female claws grow isometrically with the body so the relative claw size did not differ among the female colour classes. Quantitative measurements of claw colour revealed spectral differences between these subjectively described colours. The purple claws typical of large males also contrasted more strongly against the mudflat background than the other colours.Heloecius copulate outside female-owned burrows and probably within male-owned burrows. The male's waving display, in which both claws are raised and lowered, may feature in both mating strategies: as a territorial display and to attract wandering females. Large males are competitively superior so size, and potentially colour, are important in territorial disputes and may also feature in mate choice.     

Genetic characterization of two hill stream fish species Barilius bendelisis (Ham.1807) and Barilius barna (Ham.1822) using RAPD markers

Genetic structure of four wild populations of two hill stream fishes Barilius bendelisis (Ham.1807) and B. barna (Ham. 1822) from Uttarakhand, India, was studied using RAPD markers. Eight selective primers provided distinct and consistent RAPD profiles in both the species, producing a total of 47 and 35 scorable bands in B. bendelisis and B. barna respectively. The bands in the range 666–4,830?bp were scored for consistent results. The RAPD profiles generated by all the eight primers revealed varying degrees of polymorphism (25.00–50.00?%). The average genetic diversity (h) was estimated as 0.1661 and 0.1606 among the four populations of B. bendelisis and B. barna respectively.     

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.     

Genetic mapping of mutations using phenotypic pools and mapped RAPD markers.

Genetic markers facilitate the study of inheritance and the cloning of genes by genetic approaches. Molecular markers detect differences in DNA sequence, and are thus less ambiguous than phenotypic markers, which require gene expression. We have demonstrated a molecular approach to the mapping of mutant genes using RAPD markers and pooling of individuals based on phenotype. To map genes by phenotypic pooling a strain carrying a mutation is crossed to a strain that is homozygous for the wild-type allele of the corresponding gene. A set of primers corresponding to mapped RAPDs distributed throughout the genome and in coupling phase with respect to the wild type parent is then used to amplify DNA from wild type and mutant pools of F2 individuals. Linkage between the mutant gene and the RAPD markers is visualized by the absence of the corresponding RAPD DNA bands in the mutant pool. We developed a mathematical model for calculating the probability of linkage between RAPDs and target genes and we successfully tested this approach with the model plant Arabidopsis thaliana.     

Genetic diversity in Tanzanian Arabica coffee using random amplified polymorphic DNA (RAPD) markers

DNA from Coffea arabica leaves was used for RAPD analysis and a total of 144 leaf samples collected from 16 provenances in five regions of Tanzania were analysed. Ten arbitrary 10 mer primers were employed in the analysis and they produced a total of 86 fragments. Fragment sizes ranged from 100-1400 bp. The resulting dissimilarity matrix revealed values ranging from 0.11 to 1, while the average was 0.66. The cophenetic matrix and the original dissimilarity matrix showed a significant correlation of 78%. Mean dissimilarity values within provenances showed a fairly uniform trend despite the large range from 0.31 to 0.65. The dendrogram based on genetic distances but showed two clusters with grouping of provenances similar to the dendrogram generated by Jaccard's coefficient. Bootstrap analysis showed low values, despite this, the resulting dendrogram grouped all provenances according to their geographical origin. The standard genetic distances were fairly uniform implying a narrow genetic base in the cultivated Arabica coffee.     

Genetic mapping in Eucalyptus urophylla and Eucalyptus grandis using RAPD markers.

Two single-tree linkage maps were constructed for Eucalyptus urophylla and Eucalyptus grandis, based on the segregation of 480 random amplified polymorphic DNA (RAPD) markers in a F1 interspecific progeny. A mixture of three types of single-locus segregations were observed: 244 1:1 female, 211 1:1 male, and 25 markers common to both, segregating 3:1. Markers segregating in the 1:1 ratio (testcross loci) were used to establish separate maternal and paternal maps, while markers segregating in the 3:1 ratio were used to identify homology between linkage groups of the two species maps. An average of 2.8 polymorphic loci were mapped for each arbitrary decamer primer used in the polymerase chain reaction. The mean interval size beween framework markers on the maps was 14 cM. The maps comprised 269 markers covering 1331 cM and 236 markers covering 1415 cM, in 11 linkage groups, for E. urophylla (2n = 2x = 22) and E. grandis (2n = 2x = 22), respectively. A comparative mapping analysis with two other E. urophylla and E. grandis linkage maps showed that RAPDs could be reliable markers for establishing a consensus species map. RAPD markers were automatically and quantitatively scored with an imaging analyzer. They were classified into four categories based on their optical density. A fragment intensity threshold is proposed to optimize the selection of reliable RAPD markers for future mapping experiments. Key words : genetic linkage map, Eucalyptus urophylla, Eucalyptus grandis, random amplified polymorphic DNA, RAPD, automated data collection.     

Genetic linkage mapping in peach using morphological,RFLP and RAPD markers

We have constructed a genetic linkage map of peach [Prunus persica (L.) Batsch] consisting of RFLP, RAPD and morphological markers, based on 71 F₂ individuals derived from the self-fertilization of four F₁ individuals of a cross between New Jersey Pillar and KV 77119. This progeny, designated as the West Virginia (WV) family, segregates for genes controlling canopy shape, fruit flesh color, and flower petal color, size and number. The segregation of 65 markers, comprising 46 RFLP loci, 12 RAPD loci and seven morphological loci, was analyzed. Low-copy genomic and cDNA probes were used in the RFLP analysis. The current genetic map for the WV family contains 47 markers assigned to eight linkage groups covering 332 centi Morgans (cM) of the peach nuclear genome. The average distance between two adjacent markers is 8 cM. Linkage was detected between Pillar (Pi) and double flowers (Dl) RFLP markers linked to Pi and flesh color () loci were also found. Eighteen markers remain unassigned. The individuals analyzed for linkage were not a random sample of all F₂ trees, as an excess of pillar trees were chosen for analysis. Because of this, Pi and eight other markers that deviated significantly from the expected Mendelian ratios (e.g., 121 or 31) were not eliminated from the linkage analysis. Genomic clones that detect RFLPs in the WV family also detect significant levels of polymorphism among the 34 peach cultivars examined. Unique fingerprint patterns were created for all the cultivars using only six clones detecting nine RFLP fragments. This suggests that RFLP markers from the WV family have a high probability of being polymorphic in crosses generated with other peach cultivars, making them ideal for anchor loci. This possibility was examined by testing RFLP markers developed with the WV family in three other unrelated peach families. In each of these three peach families respectively 43%, 54% and 36% of RFLP loci detected in the WV family were also polymorphic. This finding supports the possibility that these RFLP markers may serve as anchor loci in many other peach crosses.     

Molecular characterization of eight Indian Snakehead species (Pisces: Perciformes Channidae) using RAPD markers

Murrels (Perciformes; Channidei; Channidae) are unique group of freshwater air breathing fishes having a confined distribution to African and Asian continents. The phylogenetic relationship among eight Channid species viz. Channa aurantimaculata, Channa bleheri, Channa diplogramma, Channa gachua, Channa marulius, Channa punctatus, Channa stewartii and Channa striatus were investigated using RAPD markers. Eight random oligodecamers viz. OPAC03, OPAC05, OPAC07, OPAC09, OPAC19, OPA10, OPA11 and OPA16 were used to generate the RAPD profile. Estimates of Nei’s (Genetics, 89:583–590, 1978) unbiased genetic distance (D) demonstrated sufficient genetic divergence to discriminate the samples of different species and the values ranged from 0.3292 to 0.800 The present RAPD analyses strongly substantiate the view of earlier morphological and osteological studies of Channid species, the closer association among species in “gachua” and “marulius” groups.     

Factors influencing the onset and duration of receptivity of female purple rock crabs, Hemigrapsus sexdentatus (H. Milne Edwards, 1837) (Brachyura: Grapsidae)

The effects of males, field, and laboratory conditions on the receptivity of females were tested in the New Zealand purple rock crab Hemigrapsus sexdentatus. Onset and duration of female receptivity is of interest because it influences the time available for mating and therefore the operational sex ratio (OSR), male-male competition, and the extent of sperm competition. Females were receptive once a year for a short time prior to oviposition. The breeding season was highly synchronised and lasted for about 3 weeks (from the end of March to mid-April; southern autumn), after which, almost all females carried eggs. We found few receptive females in the field (0% to 4.9%) during the breeding season despite a large number of crabs examined (935 in 1999 and 555 in 2000), suggesting that females are receptive for less than a day. The onset of the breeding season was the same for the wild crabs and those held in field cages, but the duration of receptivity increased to several days for caged females. The onset of the breeding season of females in the laboratory was earlier compared to females in the field and had, overall, a longer breeding season. Females isolated from males stayed receptive significantly longer (5.5 days) than females caged with males (3.3 days), suggesting that the duration of female receptivity is adjusted according to the presence or absence of males. Our results suggest that females have some control over their receptivity in relation to male presence, and this could influence the outcome of sexual selection.     

Genetic characterization of weedy rice (Oryza sativa L.) based on morpho-physiology, isozymes and RAPD markers

 Weedy rice (Oryza sativa L.) is an important resource for breeding and for studying the evolution of rice. The present study was carried out to identify the genetic basis of the weedy rices distributed in various countries of the world. One hundred and fifty two strains of weedy rice collected from Bangladesh, Brazil, Bhutan, China, India, Japan, Korea, Nepal, Thailand and the USA were tested for variations in six morpho-physiological characteristics and in 14 isozyme loci. Twenty six weedy strains selected from the above materials were assayed for the Est-10 locus, six RAPD loci of the nuclear genome, and one chloroplast locus. From the results of multivariate analysis based on the morpho-physiological characteristics and the isozymes, weedy rice strains were classified into indica and japonica types, and each type was further divided into forms resembling cultivated and wild rice. Thus, four groups designated as I, II, III and IV were identified. Weedy strains of group I (indica-type similar to cultivars) were distributed mostly in temperate countries, group II (indica-type similar to wild rice) in tropical countries, group III (japonica-type similar to cultivars) in Bhutan and Korea, group IV ( japonica-type similar to wild rice) in China and Korea. In group I, classified as indica, several strains showed japonica-specific RAPD markers, while some others had japonica cytoplasm with indica-specific RAPD markers in a heterozygous state at several loci. One weedy strain belonging to group II showed a wild rice-specific allele at the Est-10 locus. However, in groups III and IV, no variation was ound either for the markers on Est-10 or for the RAPD loci tested. Judging from this study, weedy rice of group I might have originated at least partly from gene flow between indica and japonica, whereas that of group II most probably originated from gene flow between wild and cultivated indica rice. Weedy rice of group III is thought to have originated from old rice cultivars which had reverted to a weedy form, and that of group IV from gene flow between japonica cultivars and wild rice having japonica backgrounds. Received: 2 May 1996 / Accepted: 30 August 1996     

Genetic analysis of populations of threatened snake species using RAPD markers

Snakes are a particularly threatened vertebrate taxon, with distributions of many species and populations becoming increasingly fragmented. At present, little is known about the degree of genetic differentiation that exists between isolated populations even though such information may be critical to their survival and conservation. As an example of how recently developed RAPD genetic markers can be used in conservation genetics, we present preliminary results from a study which used these DNA-based markers to assess population divergence in two threatened Canadian snakes, the black rat snake ( Elaphe o. obsoleta ) and the eastern massasauga rattlesnake ( Sistrurus c. catenatus ). We present information on the levels of variation and reliability of amplification for fragments generated from five primers. We then use a recently developed analytical technique to estimate levels of nucleotide diversity within populations and sequence divergence between populations. Our results show that intrapopulation levels of divergence as estimated by the methods of Clark & Lanigan ( Molecular Biology and Evolution 1993, 10 , 1096–1111) approximate those found for mtDNA in vertebrates and that diversity between snake populations is small and non-significant when tested using randomization procedures. Thus, our study provides an example of how RAPDs can be applied to conservation genetic studies of vertebrates and suggest that the snake populations we examined have only recently become isolated and maybe considered genetically equivalent from a conservation perspective, although this conclusion needs to be confirmed with other DNA-based markers.     

Genetic structure of the endangered plant Neolitsea sericea (Lauraceae) from the Zhoushan archipelago using RAPD markers

BACKGROUND AND AIMS: The Zhoushan archipelago is the largest archipelago in China. It separated from the mainland about 9000 years ago due to rising sea levels and climate change. Because of the long-term influences of human activities, the original forest vegetation on the large islands has been badly damaged and its plant diversity reduced. METHODS: Levels and patterns of genetic diversity in 114 individuals from six natural populations and four cultivated populations of the insular endangered plant Neolitsea sericea (Lauraceae) on the Zhoushan archipelago were assessed using random amplified polymorphic DNA (RAPD) markers. KEY RESULTS: A total of 99 discernible loci were obtained for all populations using ten primers, 50.5 % of which were polymorphic [percentage of polymorphic bands (PPB)=50.5 %]. Despite being a woody, long-lived, perennial, outcrossing and insect-pollinated plant, N. sericea exhibited low levels of genetic variation. The cultivated populations (PPB=18.9 %, HE=0.060, S=0.092) were genetically less diverse than the natural populations (PPB=23.1 %, HE=0.082, S=0.123). Based on analysis of molecular variance, a high degree of among-population differentiation was revealed for both natural (0.387) and cultivated populations (0.598). CONCLUSIONS: Removal of plants from the wild for horticulture purposes has eroded the level of genetic variation of N. sericea. Low levels of genetic diversity and a high degree of population differentiation indicate that management strategies should include conservation of natural habitats occupied by all six wild populations, and sampling of germplasm resources from multiple seed sources.     

Genetic mapping of new morphological, isozyme and RAPD markers in Vicia faba L. using trisomics

Thirteen F₂ families of faba bean (Vicia faba L.), descended from plants trisomic for chromosomes 3, 4, 5 and 6, have been analyzed for morphological, isozyme and RAPD markers. This allowed the establishment of linkage relationships among these markers as well as the assignment of some markers and/or linkage groups to their respective chromosomes. The linkage analysis of partially overlapping sets of informative genetic markers for the data pooled from 13 F₂ families has revealed 48 linkage groups, six of which have been precisely assigned to specific chromosomes. A statistical procedure to analyze the data of joint segregation analysis in families derived from trisomic plants has been developed.     

Agonistic Behaviour and Development of Territoriality During Ontogeny of the Sea Anemone Dwelling Crab Allopetrolisthes Spinifrons (H. Milne Edwards, 1837) (Decapoda: Anomura: Porcellanidae)

Allopetrolisthes spinifrons is an ectosymbiotic crab of the sea anemone Phymactis clematis. As a consequence of low host abundance, these represent a scarce and limited resource for the crab. Additionally, the relatively small size of the sea anemone host suggests that few symbiotic crabs can cohabit on one host individual, forcing crabs to adopt a territorial behaviour. In order to examine the potential presence and ontogenetic development of territoriality, the agonistic behaviour between crabs of various ontogenetic stages (adults, juveniles, and recruits) was studied in the laboratory. Laboratory experiments demonstrated that adult or juvenile crabs aggressively defended their sea anemone hosts against adult or juvenile intruders, respectively, but both adult and juvenile crabs tolerated recruits. Adult crabs behaved indifferently towards juvenile crabs, sometimes tolerating them, sometimes expelling them. Recruits never showed agonistic behaviour among themselves. The agonistic interactions observed in the laboratory and the uniform population distribution pattern on sea anemones recently described for A. spinifrons indicate that this species exhibits territorial behaviour, which develops during ontogeny. Territoriality in this species and other symbiotic decapods may function as a density-dependent mechanism of population regulation, being mediated by the availability of hosts. Resource monopolisation behaviours may be common among other symbiotic and free-living marine invertebrates inhabiting discrete habitats that represent a limiting resource.     

Sexing birds using random amplified polymorphic DNA (RAPD) markers

We used random amplified polymorphic DNA (RAPD) markers to sex birds from small tissue (usually blood) samples. Arbitrarily chosen 10-mer PCR primers were screened with DNA from known-sex individuals for the production of a bright female-specific band. Suitable primers were found for seven bird species after screening about 30 primers (range 2–63), and no primer was found for three other species after screening about 50 primers for each species. Investigations into the reliability of RAPD markers for sexing great tits Parus major and oystercatchers Haematopus ostralegus show that: (i) when PCR reaction conditions for great tit DNA are varied, either the presence of the female-specific band correctly predicts the individual's sex or no DNA amplification occurs; (ii) the female-specific band in great tits can be sequenced, and subsequently amplified using specific PCR primers; (iii) null alleles of the female-specific fragment occur at an estimated frequency of 0% ( n = 241 females) in great tits and 0.6% ( n > 290 females) in oystercatchers; (iv) the female-specific fragment in great tits occurs in individuals from a wide geographical range encompassing two subspecies; and (v) the relative intensity of bands in great tit RAPD banding profiles is consistent across individual birds and scorers. The RAPD primers that we have identified are generally species specific, and the consequent time cost of screening for primers is the chief disadvantage of using RAPD markers to sex birds. However, with large sample sizes this disadvantage is outweighed by the relative technical simplicity and low cost of the technique.     

Genetic characterization of Iranian safflower (Carthamus tinctorius) using inter simple sequence repeats (ISSR) markers

Safflower (Carthamus tinctorious L.) is valued as a source of high quality vegetable oil. 20 ISSR primers were used to assess the genetic diversity of 18 accessions of safflower collected from different geographical regions of Iran. The ISSR primers combinations revealed 57.6 % polymorphism, among 338 genetic loci amplified from the accessions. The sum of effective number of alleles and observed number of alleles were 29.76 and 36.77, respectively. To understand genetic relationships among these cultivars, Jacquards’ similarity coefficient and UPGMA clustering algorithm were applied to the ISSR marker data set. ISSR markers grouped accessions into two main clusters and four sub clusters. Also, the principal coordinate analysis (PCoA) supported the cluster analysis results. The results showed these genotypes have high genetic diversity, and can be used for alternative safflower breeding program.     

Agonistic Behaviour and Development of Territoriality During Ontogeny of the Sea Anemone Dwelling Crab Allopetrolisthes Spinifrons (H. Milne Edwards, 1837) (Decapoda: Anomura: Porcellanidae)

Allopetrolisthes spinifrons is an ectosymbiotic crab of the sea anemone Phymactis clematis . As a consequence of low host abundance, these represent a scarce and limited resource for the crab. Additionally, the relatively small size of the sea anemone host suggests that few symbiotic crabs can cohabit on one host individual, forcing crabs to adopt a territorial behaviour. In order to examine the potential presence and ontogenetic development of territoriality, the agonistic behaviour between crabs of various ontogenetic stages (adults, juveniles, and recruits) was studied in the laboratory. Laboratory experiments demonstrated that adult or juvenile crabs aggressively defended their sea anemone hosts against adult or juvenile intruders, respectively, but both adult and juvenile crabs tolerated recruits. Adult crabs behaved indifferently towards juvenile crabs, sometimes tolerating them, sometimes expelling them. Recruits never showed agonistic behaviour among themselves. The agonistic interactions observed in the laboratory and the uniform population distribution pattern on sea anemones recently described for A . spinifrons indicate that this species exhibits territorial behaviour, which develops during ontogeny. Territoriality in this species and other symbiotic decapods may function as a density-dependent mechanism of population regulation, being mediated by the availability of hosts. Resource monopolisation behaviours may be common among other symbiotic and free-living marine invertebrates inhabiting discrete habitats that represent a limiting resource.     

Genetic diversity and relationships among Egyptian Galium (Rubiaceae) and related species using ISSR and RAPD markers

Genetic diversity and phylogenetic analyses of 24 species, representing nine sections of the genus Galium (Rubiaceae), have been made using the Inter Simple Sequence Repeats (ISSR), Randomly Amplified Polymorphic DNA (RAPD), and combined ISSR and RAPD markers. Four ISSR primers and three RAPD primers generated 250 polymorphic amplified fragments. The results of this study showed that the level of genetic variation in Galium is relatively high. RAPD markers revealed a higher level of polymorphism (158 bands) than ISSR (92 bands). Clustering of genotypes within groups was not similar when RAPD and ISSR derived dendrograms were compared. Six clades can be recognized within Galium, which mostly corroborate, but also partly contradict, traditional groupings. UPGMA-based dendrogram showed a close relationship between members of section Leiogalium with G. verum and G. humifusum (sect. Galium), and G. angustifolium (sect. Lophogalium). Principal coordinated analysis, however, showed some minor differences with UPGMA-based dendrograms. The more apomorphic groups of Galium form the section Leiogalium clade including the perennial sections Galium, Lophogalium, Jubogalium, Hylaea and Leptogalium as well as the annual section Kolgyda. The remaining taxa of Galium are monophyletic.