The Genetic Integrity of the Ex Situ Population of the European Wildcat (Felis silvestris silvestris) Is Seriously Threatened by Introgression from Domestic Cats (Felis silvestris catus).
PLoS ONE 9(8): e106083. https://doi.org/10.1371/journal.pone.0106083
Studies on the genetic diversity and relatedness of zoo populations are crucial for implementing successful breeding programmes. The European wildcat, Felis s. silvestris, is subject to intensive conservation measures, including captive breeding and reintroduction. We here present the first systematic genetic analysis of the captive population of Felis s. silvestris in comparison with a natural wild population. We used microsatellites and mtDNA sequencing to assess genetic diversity, structure and integrity of the ex situ population. Our results show that the ex situ population of the European wildcat is highly structured and that it has a higher genetic diversity than the studied wild population. Some genetic clusters matched the breeding lines of certain zoos or groups of zoos that often exchanged individuals. Two mitochondrial haplotype groups were detected in the in situ populations, one of which was closely related to the most common haplotype found in domestic cats, suggesting past introgression in the wild. Although native haplotypes were also found in the captive population, the majority (68%) of captive individuals shared a common mtDNA haplotype with the domestic cat (Felis s. catus). Only six captive individuals (7.7%) were assigned as wildcats in the STRUCTURE analysis (at K = 2), two of which had domestic cat mtDNA haplotypes and only two captive individuals were assigned as purebred wildcats by NewHybrids. These results suggest that the high genetic diversity of the captive population has been caused by admixture with domestic cats. Therefore, the captive population cannot be recommended for further breeding and reintroduction.
Genetic structure of the high dispersal Atlanto-Mediterreanean sea star Astropecten aranciacus revealed by mitochondrial DNA sequences and microsatellite loci.
Marine Biology 156(4): 597-610
To investigate the impact of potential marine barriers on gene flow in high dispersal marine invertebrates, we assessed the population genetic structure of the sea star Astropecten aranciacus. Samples were obtained from nine locations within the Atlantic and the Mediterranean Sea including populations east of the Siculo-Tunisian Strait. We obtained both DNA sequence data of the mitochondrial control region and genotype data at four microsatellite loci. Both markers were highly polymorphic and showed a great level of genetic diversity. Genetic differentiation between populations (FST) was in general low, particularly for nuclear data, as is often the case in high dispersal marine invertebrates. Nevertheless, both marker sets indicated a significant genetic differentiation of the population from the island of Madeira to most other populations. Our results also demonstrate a clear pattern of isolation-by-distance supported by both mitochondrial and nuclear markers. Therefore, we conclude that larval dispersal of A. aranciacus is somewhat limited even within the basins of the Atlantic, the west Mediterranean and the east Mediterranean. Microsatellite loci further revealed genetic differentiation between the three basins; however, it is not clear whether this is truly caused by marine barriers. Genetic differentiation between basins might also be a result of isolation-by-distance allowing for any grouping to be significant as long as geographical neighbors are clustered together. Although levels of genetic differentiation were less pronounced in microsatellite data, both datasets were coherent and revealed similar patterns of genetic structure in A. aranciacus.
Speciation with gene flow in equids despite extensive chromosomal plasticity.
Proc. Natl. Acad. Sci. U S A. 2014 Dec 30; 111(52): 18655–18660.
Published online 2014 Dec 1. doi: 10.1073/pnas.1412627111
Horses, asses, and zebras belong to a single genus, Equus, which emerged 4.0–4.5 Mya. Although the equine fossil record represents a textbook example of evolution, the succession of events that gave rise to the diversity of species existing today remains unclear. Here we present six genomes from each living species of asses and zebras. This completes the set of genomes available for all extant species in the genus, which was hitherto represented only by the horse and the domestic donkey. In addition, we used a museum specimen to characterize the genome of the quagga zebra, which was driven to extinction in the early 1900s. We scan the genomes for lineage-specific adaptations and identify 48 genes that have evolved under positive selection and are involved in olfaction, immune response, development, locomotion, and behavior. Our extensive genome dataset reveals a highly dynamic demographic history with synchronous expansions and collapses on different continents during the last 400 ky after major climatic events. We show that the earliest speciation occurred with gene flow in Northern America, and that the ancestor of present-day asses and zebras dispersed into the Old World 2.1–3.4 Mya. Strikingly, we also find evidence for gene flow involving three contemporary equine species despite chromosomal numbers varying from 16 pairs to 31 pairs. These findings challenge the claim that the accumulation of chromosomal rearrangements drive complete reproductive isolation, and promote equids as a fundamental model for understanding the interplay between chromosomal structure, gene flow, and, ultimately, speciation.
Pooling strategy and chromosome painting characterize a living zebroid for the first time.
PLoS ONE 12(7): e0180158. https://doi.org/10.1371/journal.pone.0180158
We have investigated the complex karyotype of a living zebra-donkey hybrid for the first time using chromosome-specific painting probes produced from flow-sorted chromosomes from a zebra (Equus burchelli) and horse (Equus caballus). As the chromosomes proved difficult to distinguish from one another, a successful new strategy was devised to resolve the difficulty and characterize each chromosome. This was based on selecting five panels of whole chromosome painting probes that could differentiate zebra and donkey chromosomes by labelling the probes with either FITC or Cy3 fluorochromes. Each panel was hybridized sequentially to the same G-Q-banded metaphases and the results combined so that every zebra and donkey chromosome in each suitable metaphase could be identified. A diploid number of 2n = 53, XY was found, containing haploid sets of 22 chromosomes from the zebra and 31 chromosomes from the donkey, without evidence of chromosome rearrangement. This new strategy, developed for the first time, may have several applications in the resolution of other complex hybrid karyotypes and chromosomal aberrations.
Zootierhaltung - Tiere in menschlicher Obhut: Grundlagen.
478 Seiten, mit s/w-Abbildungen.
Verlag Harri Deutsch, Frankfurt /Main. ISBN13: 078-3-8171-1813-7.
Die Haltung und Pflege von Wildtieren steht heute auf einem gesicherten FundamentJahrzehntelange Erfahrungen in den Zoologischen Gärten, gesammelt aber auch von Tierliebhabern, vor allem jedoch die Ergebnisse mehrerer naturwissenschaftlicher Disziplinen lieferten die Voraussetzung, Wildtieren artgemäße Haltungsbedingungen zu schaffen. Für Tierhalter und Tierpfleger bedeutet dies jedoch, über eine kaum nochüberschaubare Fülle von einschlägigen Informationen und Daten verfügen zu müssen. Im vorliegenden Band haben in der Haltung von Wildtieren erfahrene Spezialisten wissenschaftlicher Disziplinen und erfolgreiche Autoren einen Abriss des Wissens zusammengestellt, das die Grundlage der Wildtierhaltung bildet. Das Buch hat gleichermaßen den Charakter eines Lehrbuches wie eines Nachschlagewerkes und ist leicht verständlich geschrieben. Zahlreiche instruktive Zeichnungen erläuterndie beschriebenen Zusammenhänge. Diese neubearbeitete und auf sechs Bände erweiterte Auflage von "Wildtiere in Menschenhand" ist vor allem für Zootierpfleger und Mitarbeiter von Tierparks geschrieben. Erkenntnisse über Pflege, Ernährung, Verhalten etc.in Zoologischen Gärten werden aufbereitet und so für den Tierpfleger zugänglich gemacht. Das Werk ist aber auch für Hobby-Tierhalter, Biologen und Veterinärmediziner von Interesse.
Microsatellite analysis of genetic diversity of the Vietnamese sika deer (Cervus nippon pseudaxis).
J Hered. 2004 Jan-Feb; 95(1):11-8.
The Vietnamese sika deer (Cervus nippon pseudaxis) is an endangered subspecies of economic and traditional value in Vietnam. Most living individuals are held in traditional farms in central Vietnam, others being found in zoos around the world. Here we study the neutral genetic diversity and population structure of this subspecies using nine microsatellite loci in order to evaluate the consequences of the limited number of individuals from which this population was initiated and of the breeding practices (i.e., possible inbreeding). Two hundred individuals were sampled from several villages. Our data show both evidence for limited local inbreeding and isolation by distance with a mean F(ST) value of 0.02 between villages. This suggests that exchange of animals occurs at a local scale, at a rate such that highly inbred mating is avoided. However, the genetic diversity, with an expected heterozygosity (H(e)) of 0.60 and mean number of alleles (k) of 5.7, was not significantly larger than that estimated from zoo populations of much smaller census size (17 animals sampled; H(e) = 0.65, k = 4.11). Our results also suggest that the Vietnamese population might have experienced a slight bottleneck. However, this population is sufficiently variable to constitute a source of individuals for reintroduction in the wild in Vietnam.
Genetic diversity analysis of captive populations : the Vietnamese sika deer (Cervus nippon pseudaxis) in zoological parks.
Zoo Biology 22: 465-475.
The Vietnamese sika deer (Cervus nippon pseudaxis) is an endangered subspecies; it has disappeared in the wild, but is being bred in zoological parks. We studied the neutral genetic diversity and population structure of herds kept in different European zoos, using nine microsatellite loci. The goal was to evaluate the consequences of founding effects and breeding practices on the level and structure of genetic variability. The level of genetic diversity within the European zoos is not lower than that of the populations kept in Vietnamese farms. Strong differences among zoological parks and between the European group and the Vietnamese population were detected. This is probably due to founding effects, genetic drift, and possibly hybridization in both Europe and Vietnam. We expected to find a much lower level of genetic diversity in Europe. The current overall level of genetic diversity is probably due to the recent introduction of Cuc Phuong individuals, and to important differences among the populations of different zoological parks, which increase the total genetic variability. Although the current level of genetic variability is not particularly low, future levels are probably threatened by the current herd sizes and structure. Based on these results, management guidelines are proposed.
Captive breeding of squirrel monkeys, Saimiri sciureus and Saimiri boliviensis: The problem of hybrid groups.
Zoo Biology 17 (2): 95-109
The electrophoretic variability of blood proteins coding for up to 32 genetic loci was analyzed in 108 squirrel monkeys (Saimiri sciureus, Saimiri boliviensis, hybrids) from two captive colonies. Twelve polymorphic loci with 31 alleles are reported. The biallelic Ada* locus, G‐statistics and Hardy‐Weinberg genotype equilibria are useful for recognizing hybrids between S. sciureus and S. boliviensis. Backcrosses in hybrid stocks and gene flow in a natural hybrid belt, however, complicate the taxonomic diagnosis of captive specimens: S. sciureus phenotypes imported from Peru possessed the allele Ada*132, which generally characterizes S. boliviensis (or species hybrids). The complex taxonomy of Saimiri spp. Requires careful planning of captive breeding. We suggest a genetic analysis of the founder individuals before their inclusion in the European studbook population and to breed S. sciureus from Guyana separately from Peruvian imports, because the latter bear a greater risk of being taxonomically heterogeneous.
Cryptic, Sympatric Diversity in Tegu Lizards of the Tupinambis teguixin Group (Squamata, Sauria, Teiidae) and the Description of Three New Species.
PLoS ONE 11(8): e0158542. https://doi.org/10.1371/journal.pone.0158542
Tegus of the genera Tupinambis and Salvator are the largest Neotropical lizards and the most exploited clade of Neotropical reptiles. For three decades more than 34 million tegu skins were in trade, about 1.02 million per year. The genus Tupinambis is distributed in South America east of the Andes, and currently contains four recognized species, three of which are found only in Brazil. However, the type species of the genus, T. teguixin, is known from Bolivia, Brazil, Colombia, Ecuador, French Guyana, Guyana, Peru, Suriname, Trinidad and Tobago, and Venezuela (including the Isla de Margarita). Here we present molecular and morphological evidence that this species is genetically divergent across its range and identify four distinct clades some of which are sympatric. The occurrence of cryptic sympatric species undoubtedly exacerbated the nomenclatural problems of the past. We discuss the species supported by molecular and morphological evidence and increase the number of species in the genus Tupinambis to seven. The four members of the T. teguixin group continue to be confused with Salvator merianae, despite having a distinctly different morphology and reproductive mode. All members of the genus Tupinambis are CITES Appendix II. Yet, they continue to be heavily exploited, under studied, and confused in the minds of the public, conservationists, and scientists.
STOW, A. J. & SUNNUCKS, P. (2004a)
High mate and site fidelity in Cunningham's skinks (Egernia cunninghami) in natural and fragmented habitat.
Molecular Ecology 13 (2): 419-430. 10.1046/j.1365-294X.2003.02061.x
While habitat alteration has considerable potential to disrupt important within-population processes, such as mating and kin structure, via changed patterns of dispersal, this has rarely been tested. We are investigating the impact of anthropogenic habitat alteration on the population biology of the rock-dwelling Australian lizard Egernia cunninghami on the Central Tablelands of New South Wales, Australia, by comparing deforested and adjacent naturally vegetated areas. The novel analyses in this paper, and its companion, build on previous work by adding a new replicate site, more loci and more individuals. The additional microsatellite loci yield sufficient power for parentage analysis and the sociobiological inferences that flow from it. Genetic and capture–mark–recapture techniques were used to investigate mate and site fidelity and associated kin structure. Analyses of the mating system and philopatry using 10 microsatellite loci showed high levels of site fidelity by parents and their offspring in natural and deforested habitats. Parentage assignment revealed few individuals with multiple breeding partners within seasons and fidelity of pairs across two or more breeding seasons was typical. Despite reduced dispersal, increased group sizes and significant, dramatic increases in relatedness among individuals within rock outcrops in deforested areas, no significant differences between deforested and natural areas were evident in the degree of multiple mating or philopatry of breeding partners within and across seasons. With the exception that there was a significantly higher proportion of unmated males in the deforested area, the social and mating structure of this species has so far been surprisingly robust to substantial perturbation of dispersal and relatedness structure. Nonetheless, approximately 10-fold elevation of mean pairwise relatedness in the deforested areas has great potential to increase inbred matings, which is investigated in the companion paper.
STOW, A. J. & SUNNUCKS, P. (2004b)
Inbreeding avoidance in Cunningham's skinks (Egernia cunninghami) in natural and fragmented habitat.
Molecular Ecology 13 (2): 443-447. 10.1046/j.1365-294X.2003.02060.x
Habitat fragmentation/alteration has been proposed as a distinct process threatening the viability of populations of many organisms. One expression of its impact may be the disruption of core population processes such as inbreeding avoidance. Using the experimental design outlined in our companion paper, we report on the impact of habitat alteration (deforestation) on inbreeding in the rock-dwelling Australian lizard Egernia cunninghami. Ten microsatellite loci were used to calculate relatedness coefficients of potential and actual breeding pairs, and to examine mate-choice and heterozygosity. Despite significantly less dispersal and higher within-group relatedness between potential mates in deforested than in natural habitats, this did not result in significantly more inbred matings. Average relatedness amongst breeding pairs was low, with no significant difference between natural and fragmented populations in relatedness between breeding pairs, or individual heterozygosity. Active avoidance of close kin as mates was indicated by the substantially and significantly lower relatedness in actual breeding pairs than potential ones. These facts, and heterozygote excesses in all groups of immature lizards from both habitats, show that E. cunninghami maintained outbreeding in the face of increased accumulation of relatives.