Implications of social dominance and multiple paternity for the genetic diversity of a captive-bred reptile population (tuatara)

Captive breeding is an integral part of many species recovery plans. Knowledge of the genetic mating system is essential for effective management of captive stocks and release groups, and can help to predict patterns of genetic diversity in reintroduced populations. Here we investigate the poorly understood mating system of a threatened, ancient reptile (tuatara) on Little Barrier Island, New Zealand and discuss its impact on the genetic diversity. This biologically significant population was thought to be extinct, due to introduced predators, until 8 adults (4 males, 4 females) were rediscovered in 1991/92. We genotyped these adults and their 121 captively-bred offspring, hatched between 1994 to 2005, at five microsatellite loci. Multiple paternity was found in 18.8% of clutches. Male variance in reproductive success was high with one male dominating mating (77.5% of offspring sired) and one male completely restricted from mating. Little Barrier Island tuatara, although clearly having undergone a demographic bottleneck, are retaining relatively high levels of remnant genetic diversity which may be complemented by the presence of multiple paternity. High variance in reproductive success has decreased the effective size of this population to approximately 4 individuals. Manipulation to equalize founder representation was not successful, and the mating system has thus had a large impact on the genetic diversity of this recovering population. Although population growth has been successful, in the absence of migrants this population is likely at risk of future inbreeding and genetic bottleneck.     

Focusing and accommodation in tuatara (Sphenodon punctatus)

Summary Photorefraction and photokeratometry were performed on two juvenile tuatara (Sphenodon punctatus, 7 years of age, total length approx. 27 cm). Sphenodon is the only surviving genus of the Rhynchocephalia, an order of reptiles. Both existing species are endangered and are found only in New Zealand. Even though Walls (1942) has stated that the ciliary muscle is relatively weak in tuataras, we observed 8 D of accommodation. The eyes were found to focus independently and we could induce an anisometropia of 6 D. The average corneal power of the tuatara was found to be 101 D.     

Seasonal monogamy and multiple paternity in a wild population of a territorial reptile (tuatara)

Investigating the mating system of a population provides insight into the evolution of reproductive patterns, and can inform conservation management of threatened or endangered species. Combining behavioural and genetic data is necessary to fully understand the mating system and factors affecting male reproductive success, yet behavioural data are often difficult to collect for threatened species. In the present study, we use behavioural data and paternity analyses to characterize the mating system of a high density population of a long-lived, ancient reptile (tuatara, Sphenodon punctatus ). We further investigate the phenotypic traits (including body size, body condition, tail length, and ectoparasite load) that affect male reproductive success. Our behavioural data reflect a seasonally monogamous system with low levels of polyandry and polygyny that are consistent with male mate guarding. Male reproduction is highly skewed (only 25–30% of males are successful), and body size is the primary predictor of male reproductive success. Based on the genetic data, multiple paternity was found in only 8% of clutches, and the results of the paternity analyses showed monandrous clutches from socially polyandrous females. Our behavioural and genetic results revealed complexities in female mating patterns that support the potential for cryptic female choice or sperm competition. This warrants further experimental investigation into the mechanisms underlying reptile fertilization and the disparities between social and genetic polyandry in wild populations.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 161–170.     

Identification of a 130-kDa albumin in tuatara (Sphenodon) and detection of a novel albumin polymorphism

Electrophoretic, immunochemical, and protein sequence analyses were performed on plasma albumin of the tuatara (Sphenodon), a rare reptile endemic to New Zealand. The analyses revealed that, unlike other terrestrial vertebrates, tuatara do not seem to possess a 60- to 75-kDa plasma albumin. The common form of plasma albumin in this genus has an apparent molecular mass of 130 kDa, making it by far the largest albumin reported for any terrestrial vertebrate. Starch gel electrophoresis of samples from tuatara on 24 of the 30 islands inhabited by this genus resolved two forms of the 130-kDa albumin (albumins A and C). A third albumin of approximately 170 kDa (albumin B), reflecting a novel alloalbuminemia, was found in tuatara in three geographically isolated populations. Albumin A appears to be restricted to populations at the southern extremity of the tuatara's distribution, while albumin C was found in all but four (southern) populations. Possible explanations for the origin and distribution of these albumins are discussed.     

Genetic variation in island populations of tuatara (<Emphasis Type="Italic">Sphenodon</Emphasis> spp) inferred from microsatellite markers

Tuatara (Sphenodon spp) populations are restricted to 35 offshore islands in the Hauraki Gulf, Bay of Plenty and Cook Strait of New Zealand. Low levels of genetic variation have previously been revealed by allozyme and mtDNA analyses. In this new study, we show that six polymorphic microsatellite loci display high levels of genetic variation in 14 populations across the geographic range of tuatara. These populations are characterised by disjunct allele frequency spectra with high numbers of private alleles. High F _ST (0.26) values indicate marked population structure and assignment tests allocate 96% of all individuals to their source populations. These genetic data confirm that islands support genetically distinct populations. Principal component analysis and allelic sequence data supplied information about genetic relationships between populations. Low numbers of rare alleles and low allelic richness identified populations with reduced genetic diversity. Little Barrier Island has very low numbers of old tuatara which have retained some relictual diversity. North Brother Island’s tuatara population is inbred with fixed alleles at 5 of the 6 loci.     

Differences in dietary and plasma fatty acids between wild and captive populations of a rare reptile, the tuatara (Sphenodon punctatus)

Tuatara (Sphenodon) are rare reptiles endemic to New Zealand. Wild tuatara on Stephens Island (study population) prey on insects as well as the eggs and chicks of a small nesting seabird, the fairy prion (Pachyptila turtur). Tuatara in captivity (zoos) are fed diets containing different insects and lacking seabirds. We compared the fatty acid composition of major dietary items and plasma of wild and captive tuatara. Fairy prions (eaten by tuatara in the wild) were rich in C20 and C22 polyunsaturated fatty acids (PUFA), especially the n-3 fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). In contrast, items from the diet of captive tuatara contained no C20 and C22 PUFA and were higher in medium-chain and less unsaturated fatty acids. Plasma from wild tuatara was higher in n-3 PUFA [including alpha-linoleic acid (C18:3n-3), EPA and DHA], and generally lower in oleic acid (C18:1) and palmitic acid (C16:0), than plasma from captive tuatara in the various fractions (phospholipid, triacylglycerol, cholesterol ester and free fatty acids). Plasma from wild adult tuatara showed strong seasonal variation in fatty acid composition, reflecting seasonal consumption of fairy prions. Differences in the composition of diets and plasma between wild and captive tuatara may have consequences for growth and reproduction in captivity. Accepted: 3 August 1998     

DNA evidence for multiple origins of intergeneric allopolyploids in annualMicroseris (Asteraceae)

Seventy populations of North American annualMicroseris, Stebbinsoseris, andUropappus species were examined for chloroplast and nuclear ribosomal DNA restriction site variability to determine the origin of the allotetraploid speciesS. heterocarpa andS. decipiens. Previously identified chloroplast DNA restriction site variants were used in concert with restriction site variation forNco I in the nuclear-encoded ribosomal DNA repeat. The presence of two, mutually exclusive restriction site gains were observed in diploid populations ofM. douglasii; these same variants were also found in populations of allotetraploidS. heterocarpa, indicating mutiple origins of this species from different maternal diploid populations ofM. douglasii. Variation in the rDNA repeat between the diploid annual species and the putative paternal genome ofU. lindleyi was found to be additive inS. heterocarpa. A similar relationship was observed for the origin ofS. decipiens; cpDNA restriction site variants found inM. bigelovii andM. douglasii were present inS. decipiens. The rDNANco I variants also were additive in this purported allotetraploid. These results confirm the reticulate evolutionary pattern inStebbinsoseris and provide another example of multiple origins of intergeneric allopolyploids.     

Polymorphic microsatellite loci and low-invasive DNA sampling inMacaca cyclopis

Polymorphic genetic markers and methods for DNA sampling in the field are the basic requirements for studies on population and conservation genetics of wildMacaca cyclopis. In this paper we screened microsatellites for their polymorphism and accessed the validity in paternity identification and gene typing of DNA samples from various sources. Among the 36 primer sets tested, 21 are polymorphic with an average observed heterozygosity 0.56. All theeight loci examined for a parent-offspring triad followed Medelian inheritance. Application of the two most polymorphic loci in paternity identification of a daptive group showed that the top-ranking male sired all the juveniles. DNA samples from wound and menstrual bleeding, or from ejaculates and hairs produced concordant microsatellite banding patterns for specific individuals. The success in DNA extraction from samples collected low-invasively and the polymorphic loci screened in this study can be applied in future studies on population and conservation genetics of natural primate populations.     

Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence-tagged sites (STSs)

Microsatellite repeat sequences were investigated as sequenced-tagged site (STS) DNA markers to determine the potential for genetic analysis of the grapevine genome. The PCR-generated markers detect codominant alleles at a single locus or site in the genome. The marker type is very informative detecting high heterozygosity (69%–88%) within individual grapevine cultivars and high genetic variation between cultivars, making it a useful marker type for plant genome mapping and genome typing. For five loci a screening of 26 V. vinifera cultivars found 13, 12, 8, 5, and 4 different length alleles respectively with some alleles more common than others. The genomic DNA sequences surrounding microsatellite sequences were conserved within the genus permitting STS primers to amplify STSs from other Vitis species. These Vitis species were found to have some unique alleles not present in V. vinifera.     

Microsatellite evidence for sperm storage and multiple paternity in the marine gastropod Crepidula coquimbensis

In gregarious species with copulation and internal fertilization, male-male competition and female cryptic choice may affect reproductive success of both sexes. We carried out a molecular analysis to study paternity and sperm use by females in the protandrous marine brooding gastropod Crepidula coquimbensis. In the field, a single female inhabits an empty hosting shell with up to six males. This gregarious behavior may promote intra-brood multiple paternity if females can store sperm from several consecutive copulations with the surrounding males. To study female sperm usage, the males sharing shelters with five different adult females were collected and preserved for paternity analysis. Females were transported alive to the laboratory and isolated for six months. After that, an additional male was offered to each of the five study females. Once the females had laid capsules, a total of 528 embryos from the five females were assigned paternity based on five microsatellite loci. Paternity analysis showed that every male sharing the empty hosting shell of a female as well as the additional male were assigned fatherhood of embryos laid by this specific female. Females can thus use sperms from multiple males including sperms stored for at least six months. In addition, in four out of the five offspring arrays, a similar contribution of each male to the brood was observed, a pattern associated with the close relationship between the number of fathers observed and the effective paternity index calculated. These results contrast with those of paternity analyses carried out in another species of the same genus, C. fornicata which is characterized by a stacking behavior in which the closest male to the female achieves the highest reproductive success. Male reproductive success may be largely influenced by the aggregation pattern and male mating opportunities in the Crepidula complex, a hypothesis to be examined further by studying other species exhibiting different grouping behavior.     

Microsatellite DNA loci from the typical halophyte <Emphasis Type="Italic">Thellungiella salsuginea</Emphasis> (Brassicaceae)

Thellungiella salsuginea (Brassiaceae) is a typical halophyte which can tolerate extreme cold, drought, and salinity. In order to understand the adaptive evolution of this species in the arid habitats, it is important to know its genetic structure. In this study, 17 polymorphic microsatellite loci were isolated and characterized from an enrichment genomic library of this species. We further assessed the polymorphisms of each locus in 18 individuals from nine geographically distant populations. The number of alleles per locus ranged from six to fourteen. The observed and expected heterozygosity ranged from 0.17 to 0.28 and 0.32 to 0.45, respectively. These markers have been crossly checked in another congeneric species, T. halophila. These microsatellite markers will be useful for investigating population genetics and adaptive evolution of this species and morphological divergence between and it and the closely related species.     

Social network structure and parasite infection patterns in a territorial reptile, the tuatara (Sphenodon punctatus)

We investigated whether the parasite load of an individual could be predicted by its position in a social network. Specifically, we derived social networks in a solitary, territorial reptile (the tuatara, Sphenodon punctatus), with links based on the sharing of space, not necessarily synchronously, in overlapping territories. Tuatara are infected by ectoparasitic ticks (Amblyomma sphenodonti), mites (Neotrombicula spp.) and a blood parasite (Hepatozoon tuatarae) which is transmitted by the tick. We recorded the location of individual tuatara in two study plots twice daily during the mating season (March) in 2 years (2006 and 2007) on Stephens Island, New Zealand. We constructed weighted, directed networks to represent pathways for parasite transmission, where nodes represented individual tuatara and edges connecting the nodes represented the extent of territory overlap among each pair of individuals. We considered a network-based hypothesis which predicted that the in-strength of individuals (the sum of edge weights directed towards a node) in the derived network would be positively related to their parasite load. Alternatively, if the derived social network did not reflect actual parasite transmission, we predicted other factors such as host sex, size or territory size may better explain variation in parasite infection patterns. We found clear positive relationships between the in-strength of tuatara and their tick loads, and infection patterns with tick-borne blood parasites. In particular, the extent that individuals were connected to males in the network consistently predicted tick loads of tuatara. However, mite loads of tuatara were significantly related to host sex, body size and territory size, and showed little association with network measures. The results suggest that the pathway of transmission of parasites through a population will depend on the transmission mechanism of the parasite, but that social networks provide a powerful predictive tool for some parasites.     

Polymorphic microsatellite DNA amplification customized for chimpanzee paternity testing

DNA segments containing GT/AC dinucleotide repeats in the chimpanzee (Pan troglodytes) genome were screened. Thirteen transformedE. coli colonies were identified with the (GT)₁₀ probe to have chimpanzee DNA fragments containing (GT)_n repeats. These potentially polymorphic (variable n) DNA segments were sequenced. Primers for the polymerase chain reaction (PCR) amplifying these DNA segments were designed. Six pairs of primers yielded polymorphic PCR products. Three of them revealed considerable length polymorphisms and heterozygosities in a group of captive chimpanzees. For studies on chimpanzees in the wild and in captivity, these primers should be useful for paternity testing, for investigating genetic variations, and for improving the genetic maintenance of breeding colonies. The strategy adopted in the present study to obtain PCR primers amplifying polymorphic microsatellite DNA segments may well be applicable to almost all eukaryotic organisms.     

Captive breeding, paternity determination, and genetic variation in chimpanzees (Pan troglodytes) in the Australasian region

DNA “fingerprinting” using polymorphic (CA)-repeat microsatellite markers was used to quantify the level of genetic variation present in chimpanzees (Pan troglodytes) in the Australasian region. These markers were also used to determine the paternity of chimpanzees born at Taronga Zoo over a 20-year period. The results suggested that the dominant male in the colony was responsible for siring most, but not all, of the offspring. Where the dominant male was excluded from paternity, the sire was identifiable if all candidate males were available for typing. This enabled us to prove the captive origin of offspring born in the colony during this period. Thus, microsatellite analysis was a useful tool for assignment of familial relationships and improving genetic management of breeding colonies.     

Paternity testing of wild black rockfish <Emphasis Type="Italic">Sebastes inermis</Emphasis> (brownish type) from the Seto Inland Sea of Japan

We developed four microsatellite DNA loci to test for multiple paternity of black rockfish, Sebastes inermis, from the Seto Inland Sea of Japan. All loci showed a high degree of polymorphism (number of alleles per locus = 10–14, expected heterozygosity = 0.80) and discriminating power (probability of identity index = 3.71 × 10⁻⁶, exclusion probability = 0.999) in unrelated wild specimens (n = 32). Genotypic assignment of five dams (109–220 mm in total length) and 50 embryos from each dam (n = 50) indicated that four dams were mated with a single sire. Only for one dam and three of her embryos we could not exclude multiple paternity.     

Non-invasive sampling and DNA amplification for paternity exclusion,community structure,and phylogeography in wild chimpanzees

Genetic studies of free-ranging primates have been seriously impeded by difficulties of sampling tissues, including the undesirability of bleeding habituated animals, of transporting frozen samples to the laboratory, and of the inherent inadequacies of accessible variation including allozymes, mtDNA RFLP patterns and DNA fingerprints. We have developed methods of non-invasive DNA sampling and DNA-level genotyping which, when combined with a hierarchical analysis of mtDNA sequences and hypervariable nDNA simple sequence repeat (microsatellite) loci size length polymorphisms, facilitate the resolution of most questions at the individual, social group (community), population, and species (phylogenetic) levels. This approach, based on DNA amplified from shed hair, represents an important new tool for the acquisition of genetic information and will facilitate the study and management of both captive and free-ranging chimpanzees (Pan troglodytes). Our hierarchical analysis of population genetics of chimpanzees has revealed high historical levels of gene flow and large effective population sizes, as well as substantial divergence between the West African subspecies and chimpanzees from central and East Africa. At the community level, closer relatedness among philopatric males than among females supports the view that kin selection has been an evolutionary force shaping male-male cooperation in this species. Results from our study of the now relatively isolated Gombe community suggest that habitat fragmentation affects population genetic structure and possibly population viability.     

Microsatellite loci isolation in the endangered Gran Canarian blue chaffinch (Fringilla teydea polatzeki) and their utility in closely related taxa

The blue chaffinch, Fringilla teydea, is an endemic species of the Canary Islands. This species is formed by two subspecies: The Teneriffean blue chaffinch (F. t. teydea), and the endangered Gran Canarian blue chaffinch, (F. t. polatzeki). Here we report the isolation and characterization of nine tetranucleotide microsatellites (AAAG and AAAT) from the Gran Canarian subspecies, using an enrichment protocol. An average of 7.8 alleles per locus and an average observed heterozygosity of 0.773 were found (n = 28). The loci were tested for their ability to cross amplify in the Teneriffean subspecies and in the common chaffinch (Fringilla coelebs). These microsatellites will be used to manage a captive breeding programme for the endangered Gran Canarian subspecies.