Molecular diversity among domestic guinea-pigs (Cavia porcellus) and their close phylogenetic relationship with the Andean wild species Cavia tschudii.
Revista Chilena de Historia Natural 77: 243-250
To investigate the origin and diversity of domestic guinea-pigs Cavia porcellus (Linnaeus, 1758; Rodentia, Caviidae), we sequenced the mitochondrial cytochrome b gene of 12 domestic and 10 wild specimens from six species, including the two presumed as ancestral to the domestic one: Cavia tschudii and Cavia aperea. All maximum parsimony and maximum likelihood analyses grouped C. porcellus with C. tschudii (mean K2P distance = 3.2 %); best trees had 609 steps (CI = 0.796; Bremer support Index (SI) = 28), and a –Ln = 4419.52, with 100 % and 97 % bootstrap support respectively. This clade, supported by three substitutions and 96 % bootstrap, is also obtained in the cladistic analysis of corresponding amino acids. When the C. aperea node was forced to join C. porcellus, these trees were consistently longer, less likely and robust, and with less defining characters than the optimal one. All C. porcellus sequences also clustered in a node defined by 15 substitutions. The sub-node containing animals from city markets, pet shops and laboratories was characterized by four substitutions (one non-silent, SI = 7, and 91 % bootstrap). Some South American C. porcellus, called “criollos” (creoles) by local breeders, were more diverse. Probably, a particular clade from southern Peru and Chile may represent a pre-Columbian lineage. Mean K2P distance between C. tschudii and C. aperea was rather large, 7.7 %. Cavia appeared as a robust node (100 % bootstrap). These results indicate that C. tschudii is the species most closely related to C. porcellus.
Conservation genetics of native and European-introduced Chinese water deer (Hydropotes inermis).
Zoological Journal of the Linnean Society 191(4): 1181–1191.
Sufficient genetic variation is vital for the long-term survival of a population. The adaptive potential and reproductive fitness of a population is generally enhanced by greater levels of genetic diversity, while loss of genetic variation in small populations may increase extinction risk due to disease susceptibility and decreased reproductive fitness. Determining levels of genetic diversity in threatened species can, therefore, help inform conservation strategies. The Chinese water deer (Hydropotes inermis) is classified as Vulnerable in its native range on the IUCN Red List, and populations in Korea and mainland China have declined drastically in recent years. However, the species was introduced to Europe about a century ago and populations there now make up over 40% of global numbers. To infer the population genetic structure and genetic diversity of Chinese water deer both in their native China and in populations introduced to the UK and France, variation in mitochondrial DNA was investigated for over 100 individuals (92 cytochrome b and 106 control region sequences). Our results reveal lower levels of genetic diversity in the British populations, differentiation between native and introduced populations, and that the source population of British deer is likely to be extinct. Recommendations are made for the conservation of populations.
Extended and continuous decline in effective population size results in low genomic diversity in the world's rarest hyena species, the brown hyena..
Molecular Biology and Evolution, 35(5): 1225–1237. doi.org/10.1093/molbev/msy037
Hyenas (family Hyaenidae), as the sister group to cats (family Felidae), represent a deeply diverging branch within the cat-like carnivores (Feliformia). With an estimated population size of <10,000 individuals worldwide, the brown hyena (Parahyaena brunnea) represents the rarest of the four extant hyena species and has been listed as Near Threatened by the IUCN. Here, we report a high-coverage genome from a captive bred brown hyena and both mitochondrial and low-coverage nuclear genomes of 14 wild-caught brown hyena individuals from across southern Africa. We find that brown hyena harbor extremely low genetic diversity on both the mitochondrial and nuclear level, most likely resulting from a continuous and ongoing decline in effective population size that started ∼1 Ma and dramatically accelerated towards the end of the Pleistocene. Despite the strikingly low genetic diversity, we find no evidence of inbreeding within the captive bred individual and reveal phylogeographic structure, suggesting the existence of several potential subpopulations within the species.
Population genetics and abundance of the Endangered grey-headed lemur Eulemur cinereiceps in south-east Madagascar: assessing risks for fragmented and continuous populations.
ORYX 46(2): 298–307. doi:10.1017/S003060531100015
Knowledge of both population size and genetic diversity is critical for assessing extinction risk but few studies include concurrent estimates of these two components of population biology. We conducted an investigation of population density and size, and genetic variation and past demographic events, of the Endangered grey-headed lemur Eulemur cinereiceps in south-east Madagascar. We estimated lemur density using line-transect surveys and used satellite imagery to calculate forest fragment area in three localities. We collected tissue samples from 53 individuals and used 26 polymorphic microsatellite loci to obtain measures of population structure (divergence and diversity) across these localities. We tested the probability of past bottleneck events using three models. Contrary to expectation, there were no significant differences in population density across localities. Genetic diversity decreased, but not significantly, with decreasing habitat area and population size. We found a higher likelihood of past bottleneck events in the fragmented coastal populations. The low population size and prior decline in diversity in coastal patches are consistent with their isolation, anthropogenic disturbance, and exposure to cyclone activity. The similarities in the estimates of density between continuous and fragmented sites may indicate recent population growth in the fragments but these populations nevertheless remain at risk from reduced levels of genetic variation. These patterns should be confirmed with more extensive sampling across the limited range of E. cinereiceps.
Japanese Ornamental Koi Carp: Origin, Variation and Genetics.
In: PIETSCH, C. & HIRSCH, P. (eds., 2015) Biology and Ecology of Carp. Kapitel 2: 27-53. DOI:10.1201/b18547-4.
The ornamental form of the carp, Cyprinus carpio L., provides a rich source of investigation for science and commercial possibilities alike. For researchers, however, there is also the challenge of cultural and language barriers that add a dimension of the mystic. On the other hand, many koi hobbyists and professionals are not familiar with published scientific information on koi genetics. This chapter intends to better equip all kinds of readers with an understanding of the origin, variationand genetics of koi.This chapter was written collectively by a koi professional and writer, who has run a large koi farm and authored several books on koi keeping (De Kock and Watt 2006), and a fish geneticist, who has studied inheritance of different traits in koi for 20 years.
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.