Hypervariable minisatellite DNA sequences in the Indian peafowl Pavo cristatus

Morphological variation in leatherback (Dermochelys coriacea) hatchlings at Sandy Point National Wildlife Refuge, US Virgin Islands

Understanding species’ mating systems provides important information about their ecology, life history, and behavior. Direct observations of mating behaviors can be challenging, but molecular techniques can reveal information about mating systems and paternal identity in difficult-to-observe species such as sea turtles. Genetic markers can be used to assess the paternity of a clutch and to assign hatchlings to a father. Leatherback turtles Dermochelys coriacea sometimes mate with multiple individuals, resulting in clutches with mixed paternity; however, the effects of multiple paternity on hatchling quality are unclear. Leatherback hatchlings at Sandy Point National Wildlife Refuge, St. Croix, US Virgin Islands, exhibit visible variation in individual body size, sometimes within the same clutch. We collected morphometrics and tissue samples from hatchlings across multiple nesting seasons (2009, 2012, 2013, 2015, and 2016) and found that hatchlings exhibited small but statistically significant differences in morphometrics between years. We used maternal and hatchling microsatellite genotypes to reconstruct paternal genotypes, assigning fathers to each hatchling. We found multiple paternity in 5 of 17 clutches analyzed and compared differences in morphometrics between full-siblings with differences between half-siblings. We found no significant differences between morphometrics of hatchlings from the same mother but different fathers. We compared within-clutch variances in morphometrics for clutches with and without multiple paternity and found no significant difference in morphological variation between them. Therefore, we could not attribute differences in hatchling size within a clutch to paternal contribution. Understanding other factors affecting hatchling morphology, and other possible fitness metrics, may reveal insights into the benefits, or lack thereof, of polyandry in sea turtles.

Breeding sex ratios in adult leatherback turtles (Dermochelys coriacea) may compensate for female-biased hatchling sex ratios

For vertebrates with temperature-dependent sex determination, primary (or hatchling) sex ratios are often skewed, an issue of particular relevance to concerns over effects of climate change on populations. However, the ratio of breeding males to females, or the operational sex ratio (OSR), is important to understand because it has consequences for population demographics and determines the capacity of a species to persist. The OSR also affects mating behaviors and mate choice, depending on the more abundant sex. For sea turtles, hatchling and juvenile sex ratios are generally female-biased, and with warming nesting beach temperatures, there is concern that populations may become feminized. Our purpose was to evaluate the breeding sex ratio for leatherback turtles at a nesting beach in St. Croix, USVI. In 2010, we sampled nesting females and later sampled their hatchlings as they emerged from nests. Total genomic DNA was extracted and all individuals were genotyped using 6 polymorphic microsatellite markers. We genotyped 662 hatchlings from 58 females, matching 55 females conclusively to their nests. Of the 55, 42 females mated with one male each, 9 mated with 2 males each and 4 mated with at least 3 males each, for a multiple paternity rate of 23.6%. Using GERUD1.0, we reconstructed parental genotypes, identifying 47 different males and 46 females for an estimated breeding sex ratio of 1.02 males for every female. Thus we demonstrate that there are as many actively breeding males as females in this population. Concerns about female-biased adult sex ratios may be premature, and mate choice or competition may play more of a role in sea turtle reproduction than previously thought. We recommend monitoring breeding sex ratios in the future to allow the integration of this demographic parameter in population models.

Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping

Background

The publication of the first draft chicken sequence assembly became available in 2004 and was updated in 2006. However, this does not constitute a definitive and complete sequence of the chicken genome, since the microchromosomes are notably under-represented. In an effort to develop maps for the microchromosomes absent from the chicken genome assembly, we developed radiation hybrid (RH) and genetic maps with markers isolated from sequence currently assigned to "chromosome Unknown" (chrUn). The chrUn is composed of sequence contigs not assigned to named chromosomes. To identify and map sequence belonging to the microchromosomes we used a comparative mapping strategy, and we focused on the small linkage group E26C13.

Results

In total, 139 markers were analysed with the chickRH6 panel, of which 120 were effectively assigned to the E26C13 linkage group, the remainder mapping elsewhere in the genome. The final RH map is composed of 22 framework markers extending over a 245.6 cR distance. A corresponding genetic map was developed, whose length is 103 cM in the East Lansing reference population. The E26C13 group was assigned to GGA25 (Gallus gallus chromosome 25) by FISH (fluorescence in situ hybridisation) mapping.

Conclusion

The high-resolution RH framework map obtained here covers the entire chicken chromosome 25 and reveals the existence of a high number of intrachromosomal rearrangements when compared to the human genome. The strategy used here for the characterization of GGA25 could be used to improve knowledge on the other uncharacterized small, yet gene-rich microchromosomes.

Microsatellite markers for standardized genetic management of captive colonies of rhesus macaques (Macaca mulatta)

To preserve genetic variability and minimize genetic subdivision among captive Macaca mulatta at each of the U.S. National Institutes of Health (NIH)-sponsored regional research colonies, the genetic structure of each colony must be characterized. To compare population genetic and demographic parameters across colonies and generations, one standard panel of highly informative genetic markers is required. We assembled a core marker set of four multiplex polymerase chain reaction (PCR) panels comprising 15 autosomal short tandem repeat (STR) loci with high information content selected from existing panels of well-characterized markers that are currently used for parentage assessment and genetic management of rhesus macaques. We then assessed the effectiveness of these loci for providing high probabilities of individual identification and parentage resolution, and for estimating population genetic parameters that are useful for genetic management.

Multiple Paternity and Breeding System in the Gopher Tortoise, Gopherus polyphemus

Little is known about the reproductive behaviors and the actual outcomes of mating attempts in the gopher tortoise (Gopherus polyphemus). We examined the mating system and reproductive behaviors of a population of gopher tortoises in central Florida. Using microsatellite markers, we assigned fathers to the offspring of seven clutches and determined that multiple fathers were present in two of the seven clutches examined. We found that gopher tortoises exhibited a promiscuous mating system with larger males fertilizing the majority of clutches. The advantage of larger males over smaller males in fertilizing females may be a result of larger males winning access to females in aggressive bouts with other males or larger males may be more attractive to females. Clutches produced by larger females tended to be sired by a single male, whereas clutches of smaller females tended to be sired by multiple males.

Multiple paternity and population genetic structure in natural populations of the poeciliid fish, Heterandria formosa

Heterandria formosa Agassiz, exhibits internal fertilization, internal brooding of embryos, sperm storage and an extreme level of superfetation. In this study we used microsatellite markers to examine variation among seven populations that exhibited significant variance in their histories of population density. We found that the populations were genetically distinct and that the heterozygosity increased as population density increased. We also examined paternity in three of those populations and found that the number of sires per female and the number of sires per brood increased with population density. Overall, the rates of multiple paternity are quite low relative to other species. The correlations with population density suggest that contact rates play a critical role in the breeding system in this species but the low rates of multiple paternity suggest that females may exert control over fertilization of their ova.

The leatherback turtle, Dermochelys coriacea, exhibits both polyandry and polygyny

The leatherback turtle (Dermochelys coriacea) is an endangered species, and world-wide populations are declining. To understand better the mating structure of this pelagic and fragile species, we investigated paternity in nearly 1000 hatchlings from Playa Grande in Parque Marino Nacional Las Baulas, Costa Rica. We collected DNA samples from 36 adult female leatherbacks and assessed allele frequency distributions for three microsatellite loci. For 20 of these 36 females, we examined DNA from hatchlings representing multiple clutches, and in some cases assessed up to four successive clutches from the same female. We inferred paternal alleles by comparing maternal and hatchling genotypes. We could not reject the null hypothesis of single paternity in 12 of 20 families (31 of 50 clutches), but we did reject the null hypothesis in two families (eight of 50 clutches). In the remaining six families, the null hypothesis could not be accepted or rejected with certainty because the number of hatchlings exhibiting extra nonmaternal alleles was small, and could thus be a result of mutation or sample error. Successive clutches laid by the same female had the same paternal allelic contribution, indicating sperm storage or possibly monogamy. None of 20 females shared the same three-locus genotype whereas there were two instances of shared genotypes among 17 inferred paternal three-locus genotypes. We conclude that both polyandry and polygyny are part of the mating structure of this leatherback sea turtle population.

Multiple paternity and female-biased mutation at a microsatellite locus in the olive ridley sea turtle (Lepidochelys olivacea)

Multiple paternity in the olive ridley sea turtle (Lepidochelys olivacea) population nesting in Suriname was demonstrated using two microsatellite loci, viz., Ei8 and Cm84. The large number of offspring sampled per clutch (70 on average, ranging from 15 to 103) and the number of alleles found at the two loci (18 and eight alleles, respectively) enabled unambiguous assessment of the occurrence of multiple paternity. In two out of 10 clutches analysed, the offspring had been sired by at least two males, which was confirmed at both loci. In both clutches, unequal paternity occurred: 73% and 92% of the offspring had been sired by the primary male. The probability of detecting multiple paternity was 0.903, and therefore there is a small chance that multiple paternity occurred but remained undetected in some of the eight clutches that appeared to be singly sired. Analysis of 703 offspring revealed a high mutation rate for locus Ei8 (micro = 2.3 x 10(-2)) with all 33 mutations occurring in maternal alleles. In particular, one allele of 274 bp mutated at a high frequency in a clutch to which the mother contributed the allele, but in another clutch where the father contributed the same allele, no such mutations were observed. Inferred allele-specific mutation rates for Ei8 and expected numbers of mutations per clutch confirmed that maternal alleles for Ei8 are more likely to mutate in the olive ridley sea turtle than paternal alleles. Possible explanations are discussed.

Multiple paternity and mating patterns in the American alligator,Alligator mississippiensis

Eggs were sampled from 22 wild American alligator nests from the Rockefeller Wildlife Refuge in south-west Louisiana, along with the females guarding the nests. Three nests were sampled in 1995 and 19 were sampled in 1997. Females and offspring from all clutches were genotyped using five polymorphic microsatellite loci and the three nests from 1995 were also genotyped using one allozyme locus. Genotypes of the hatchlings were consistent with the guarding females being the mothers of their respective clutches. Multiple paternity was found in seven of the 22 clutches with one being fathered by three males, and the remaining six clutches having genotypes consistent with two males per clutch. Paternal contributions of multiply sired clutches were skewed. Some males sired hatchlings of more than one of the 22 clutches either as one of two sires of a multiple paternity clutch, as the sole sire of two different clutches, or as the sole sire of one clutch and one of two sires of a multiply sired clutch. There was no significant difference between females that had multiple paternity clutches and those that had singly sired clutches with respect to female total length (P = 0.844) and clutch size (P = 0.861). Also, there was no significant correlation between genetic relatedness of nesting females and pairwise nest distances (r2 = 0.003, F1,208 = 0.623, P = 0.431), indicating that females in this sample that nested close to one another were no more related than any two nesting females chosen at random. Eleven mutations were detected among hatchlings at the five loci over the 22 clutches. Most of these mutations (eight of 11) occurred at Ami(mu)-17, the only compound microsatellite locus of the five used in this study, corresponding to a mutation rate of 1.7 x 10-3. Finally, most of the mutations (82%) were homoplasious, i.e., mutating to an allelic state already present in this Louisiana population.

Amplified fragment length polymorphism (AFLP) markers reveal extra-pair parentage in a bird species: the bluethroat (Luscinia svecica)

We tested the use of amplified fragment length polymorphism (AFLP) to assess the frequency of extra-pair parentage in a bluethroat (Luscinia svecica namnetum) population. Thirty-six families totalling 162 nestlings were analysed. Using a combination of three primer pairs, we reached an exclusion probability of 93% for the population. This probability can reach 99% considering families independently. We revealed that extra-pair fertilizations are very common: 63.8% of all broods contain at least one extra-pair young, totalling 41.9% of all young analysed. However, with the technique and the three primer pairs used it was not possible to attribute the parentage exclusions to extra-pair paternity, maternity or both. As brood parasitism has never been reported in this species, it seems likely that the exclusions are due to extra-pair males. This study shows that dominant AFLP markers can be useful for studying the mating system of taxa for which no microsatellite primers are available. This technique allows the approximate estimation of parentage exclusions despite the fact that it is not possible to know which parent has to be excluded.

Single paternity of clutches and sperm storage in the promiscuous green turtle (Chelonia mydas)

Paternity of 22 green turtle (Chelonia mydas) clutches from 13 females of the southern Great Barrier Reef breeding population was determined through microsatellite analyses at five loci, including the analysis of successive clutches for nine of the females. A large number of alleles per locus (10-40) provided probabilities of detecting multiple paternity that were quite high, particularly at all loci combined (99.9%). Although green turtles are promiscuous breeders and there was an expectation of finding extensive multiple paternity, only two clutches were multiply sired and, in these, very few eggs had been fertilized by a secondary male. The rarity of multiple paternity may reflect either a low proportion of multiple matings by females in this population, or sperm competition, possibly resulting from a first-male sperm preference. Additionally, the analysis of > 900 offspring provided data on mutations, which included 20 mutation events that were observed in 27 offspring and involved both maternal and paternal lineages. Most mutations (n = 16) occurred at a single highly variable locus and their presence emphasizes the need to use multiple loci in paternity studies.

Genetic markers linked to quantitative traits in poultry

This study utilized DNA fingerprints and crosses of two genetically distinct lines of layer-type chickens to identify genetic markers linked to quantitative trait loci (QTL). In phase I, backcross (BC1) hens were separately ranked for each of eight traits and then blood pools were produced in groups along each phenotypic distribution. The DNA was isolated from the blood pools and used in a gradient analysis to screen for DNA fingerprint bands that exhibited intensity gradients associated with the phenotypic traits. To identify linkage of bands with QTL and to estimate band effects, F2 progeny were produced in phase II from the phase I BC1 population. A single-trait animal model was used for analysis of associations of all individual DNA fingerprint bands of sires and their progeny phenotypic performance. Twenty fingerprint bands, only two of which had shown trait-associated gradients in phase I, were identified by the animal model analysis of the progeny test as QTL linked (P < or = 0.05) to specific traits of growth, reproduction and egg quality. These 20 bands warrant further study as potentially valuable molecular markers for QTL.

Nucleotide sequence and genomic organization of cichlid fish minisatellites

We have cloned, sequenced, and determined the genomic organization of minisatellites from the African cichlid fish, Oroechromis niloticus. We estimate that minisatellites related in sequence to the Jeffreys' core probes 33.6 and 33.15 occur approximately every 1000 kilobase pairs in the cichlid fish genome. Sequencing of three minisatellites revealed that the size of the monomer units of the tandem arrays ranged from 7 to 24 base pairs (bp). One minisatellite appeared to contain a higher ordered periodicity of 90-120 bp superimposed on the apparent 15 bp monomer repeat, indicating a particularly large unit of homogenization for a minisatellite array. Sequence heterogeneity of repeat units within tandem arrays varied considerably from one minisatellite to another. Hybridization of cloned minisatellites to genomic DNA of cichlid fishes generated, in most instances, multilocus fingerprint patterns, indicating that families of minisatellites related by sequence exist in the cichlid genome. Two minisatellite clones, however, generated polymorphic single locus fingerprints, suggesting that these loci are conserved in closely related African cichlids. The cross hybridization of these cichlid minisatellites within and between related taxa, as well as to unrelated fish species such as Atlantic salmon (Salmo salar), complement the human minisatellite sequences for the study of genetic relationships among individuals from a wide range of fish species.

Minisatellite DNA markers in the chicken genome. II. Isolation and characterization of minisatellite loci

The isolation of chicken minisatellites is reported. Two charomid libraries were constructed from fractions of size-selected MboI-digested genomic DNA. A total of 5985 colonies were screened with the multilocus probes 33.6 and 33.15; 137 positives were obtained (2.35%). A total of 55 clones were tested against four unrelated chickens; 30 revealed variable single locus patterns. More detailed characterization was made of 15 probes, which were tested against four families comprising a total of 53 offspring. Of parent/offspring comparisons 51% were informative for segregation. No mutations were detected. Three minisatellites were linked on the same autosome, implying that these loci may occur in clusters, and one was Z chromosome-linked. Heterozygosity and allelic variability were measured in 67 individuals from several different strains and breeds. Mean heterozygosity ranged from 50 to 84%. Minisatellite loci appear to be highly variable in the chicken and should provide highly informative markers in intraspecific crosses in genome mapping studies.

Identification, isolation and characterization of canine minisatellite sequences

A Charomid ordered-array library containing a 2-16 Kb size fraction of MboI-digested canine genomic DNA has been screened with the Jeffreys multilocus probes, 33.6 and 33.15, to identify and isolate canine minisatellite sequences. Of the 48 positive clones identified, 7 were found to contain polymorphic minisatellites with heterozygosities in the range 20-88%. The majority of the remainder were either monomorphic or dimorphic in the animals tested. Analysis of intrabreed variation in Bedlington Terriers using two polymorphic minisatellites has shown that a significant reduction occurs in the number of alleles seen compared to an agglomerated population sample, correlating with the high level of inbreeding within this breed. Flanking DNA sequence and partial repeat sequence is presented for the most polymorphic minisatellite thus far identified, cCfaMP5. The variable region in this minisatellite is similar to human minisatellites which show a distinct purine or pyrimidine strand bias.

Multilocus DNA fingerprints in gallinaceous birds: general approach and problems

Multilocus profiles were investigated in five different species of Galliformes (ring-necked pheasant Phasianus colchicus, Indian peafowl Pavo cristatus, Japanese quail Coturnix coturnix japonica, domestic chicken Gallus gallus, and red grouse Lagopus lagopus scoticus) using two human multilocus probes (33.6 and 33.15) in combination with each of four restriction enzymes (AluI, DdeI, HaeIII or HinfI). All the species show a DNA fingerprint-like pattern using at least one restriction enzyme in combination with each multilocus probe. The number of bands detected and the value of the index of similarity for each species differ significantly between the profiles obtained with each multilocus probe. Some enzyme/probe combinations reveal strong cross-hybridization of the multilocus probes with satellite or satellite-like DNA sequences in pheasant, peacock, quail and chicken, which partially or completely prevented scoring of the profile. The choice of restriction enzyme was found to influence the number of bands, the value of the index of similarity and the probability of obtaining an identical fingerprint between unrelated individuals. The Mendelian inheritance and independent segregation of the fragments detected using AluI was investigated in three species (ring-necked pheasant, Indian peafowl and red grouse). Some bands were shown to be tightly linked. An extreme case was encountered in the red grouse, where 12 of the 15 bands scored in one parent represented only two, apparently allelic, haplotypes and so derived from a single locus. However, fingerprint patterns will often be adequate for use in paternity analyses, such as in behavioural studies, despite the occurrence of haplotypic sets of bands. Identical DNA multilocus profiles were sometimes observed between captive-bred siblings in one species. These results emphasize the desirability of determining, in each new species, the optimal experimental conditions as a preliminary to any behavioural or population genetic studies that use the multilocus DNA fingerprinting methodology.

Multilocus and single locus minisatellite analysis in population biological studies

In this review we describe the situations in which minisatellite analysis is of value to studies of population and evolutionary biology. Evolutionary and population biologists need to be able to quantify genetic relationships among individual organisms at many different levels, from close familial relationships to evolutionarily distant phylogenetic ones. The use of minisatellite markers is put into this context and compared with the other molecular biological techniques. Examples of the use of multilocus minisatellite analysis in population biology are described. The limitations of multilocus fingerprinting are presented, together with the potential advantages of locus-specific probes. The use of locus-specific probes in population biology is now often feasible due to the recent development of a cloning system which allows their efficient isolation. The availability of locus-specific probes should significantly expand the role of minisatellite markers in population biology.