Genetic structure of captive and free-ranging okapi (Okapia johnstoni) with implications for management

Breeding programs for endangered species increasingly use molecular genetics to inform their management strategies. Molecular approaches can be useful for investigating relatedness, resolving pedigree uncertainties, and for estimating genetic diversity in captive and wild populations. Genetic data can also be used to evaluate the representation of wild population genomes within captive population gene-pools. Maintaining a captive population that is genetically representative of its wild counterpart offers a means of conserving the original evolutionary potential of a species. Okapi, an even-toed ungulate, endemic to the Democratic Republic of Congo, have recently been reclassified as Endangered by the IUCN. We carried out a genetic assessment of the ex-situ okapi (Okapia johnstoni) population, alongside an investigation into the genetic structure of wild populations across their geographic range. We found that while levels of nuclear (12 microsatellite loci) genetic variation in the wild, founder and captive okapi populations were similar, mitochondrial (833 bp of Cyt b, CR, tRNA-Thr and tRNA-Pro) variation within captive okapi was considerably reduced compared to the wild, with 16 % lower haplotype diversity. Further, both nuclear and mitochondrial alleles present in captivity provided only partial representation of those present in the wild. Thirty mitochondrial haplotypes found in the wild were not found in captivity, and two haplotypes found in captivity were not found in the wild, and the patterns of genetic variation at microsatellite loci in our captive samples were considerably different to those of the wild samples. Our study highlights the importance of genetic characterisation of captive populations, even for well-managed ex-situ breeding programs with detailed studbooks. We recommend that the captive US population should be further genetically characterised to guide management of translocations between European and US captive population

Залежність стану тканин пародонта від поведінкових факторів ризику в дітей шкільного віку м. Полтави, виявлених із застосуванням європейських індикаторів

The aim of the work was the definition of informativeness of European indicators in a comprehensive assessment of the state of periodontal tissues in children of school age and identification possible relationships with behavioral risk factors for periodontal disease. Analytical dental epidemiology was employed, using the EGOHID-2005 system. Oral hygiene and dental caries were assessed in 12- 15-year-old children in Poltava city. The main determinants of periodontal tissue diseases were non-observance of children a recommended regime of brushing teeth and unhealthy habits. Systematic monitoring of major dental diseases allows to determine their tendencies and, using European system of indicators of dental health, allows to identify the risk factors to be eliminated in order to prevent periodontal tissue diseases.Целью работы было определение информативности европейских индикаторов в комплексной оценке состояния тканей пародонта у детей школьного возраста и выявление возможных взаимосвязей с поведенческими факторами риска возникновения заболеваний тканей пародонта. Аналитическая эпидемиология состояния тканей пародонта у детей двух ключевых возрастных групп 12 и 15 лет по 100 человек в г. Полтаве. Использование Международной системы EGOHID – 2005 и методов, рекомендованных ВОЗ–2013. Основными детерминантами заболеваний тканей пародонта было несоблюдение детьми рекомендованного режима чистки зубов и нездоровые привычки. Систематический мониторинг основных стоматологических заболеваний позволяет определить их тенденции и с помощью системы европейских индикаторов стоматологического здоровья выявить факторы риска, подлежащие устранению с целью профилактики заболеваний тканей пародонта.Метою роботи було визначення інформативності європейських індикаторів у комплексній оцінці стану тканин пародонта в дітей шкільного віку та виявлення можливих взаємозв’язків з поведінковими чинниками ризику виникнення захворювань тканин пародонта. Аналітична епідеміологія стану тканин пародонта у дітей двох ключових вікових груп 12 і 15 років по 100 осіб в м. Полтаві. Використання Міжнародної системи EGOHID – 2005 і методів, рекомендованих ВООЗ–2013. Основними детермінантами захворювань тканин пародонта були недотримання дітьми рекомендованого режиму чищення зубів і нездорові звички. Систематичний моніторинг основних стоматологічних захворювань дозволяє визначити їх тенденції і за допомогою системи європейських індикаторів стоматологічного здоров’я виявити фактори ризику, які підлягають усуненню з метою профілактики захворювань тканин пародонта

In the name of the rose: a roadmap for rose research in the genome era

The recent completion of the rose genome sequence is not the end of a process, but rather a starting point that opens up a whole set of new and exciting activities. Next to a high-quality genome sequence other genomic tools have also become available for rose, including transcriptomics data, a high-density single-nucleotide polymorphism array and software to perform linkage and quantitative trait locus mapping in polyploids. Rose cultivars are highly heterogeneous and diverse. This vast diversity in cultivated roses can be explained through the genetic potential of the genus, introgressions from wild species into commercial tetraploid germplasm and the inimitable efforts of historical breeders. We can now investigate how this diversity can best be exploited and refined in future breeding work, given the rich molecular toolbox now available to the rose breeding community. This paper presents possible lines of research now that rose has entered the genomics era, and attempts to partially answer the question that arises after the completion of any draft genome sequence: ‘Now that we have “the” genome, what’s next?’. Having access to a genome sequence will allow both (fundamental) scientific and (applied) breeding-orientated questions to be addressed. We outline possible approaches for a number of these questions

A high-quality sequence of Rosa chinensis to elucidate genome structure and ornamental traits

Rose is the worlds most important ornamental plant with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Rose has a complex genome with high heterozygosity and various ploidy levels. Our objectives were (i) to develop the first high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short read sequencing, and anchoring to a high-density genetic map and (ii) to study the genome structure and the genetic basis of major ornamental traits. We produced a haploid rose line from R. chinensis "Old Blush" and generated the first rose genome sequence at the pseudo-molecule scale (512 Mbp with N50 of 3.4 Mb and L75 of 97). The sequence was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features including the pericentromeric regions through annotation of TE families and positioned centromeric repeats using FISH. Genetic diversity was analysed by resequencing eight Rosa species. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and number of flower petals. A rose APETALA2 homologue is proposed to be the major regulator of petals number in rose. This reference sequence is an important resource for studying polyploidisation, meiosis and developmental processes as we demonstrated for flower and prickle development. This reference sequence will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae

Synchronous diversification of Sulawesi’s iconic artiodactyls driven by recent geological events

The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back 40 Myr ago. Recent studies, however, suggest that much of Sulawesi’s fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification, and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric data sets derived from Sulawesi’s three largest mammals: the Babirusa, Anoa, and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Myr ago to 2-3 Myr ago), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (~1–2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years

A Sensitive Assay for Virus Discovery in Respiratory Clinical Samples

In 5–40% of respiratory infections in children, the diagnostics remain negative, suggesting that the patients might be infected with a yet unknown pathogen. Virus discovery cDNA-AFLP (VIDISCA) is a virus discovery method based on recognition of restriction enzyme cleavage sites, ligation of adaptors and subsequent amplification by PCR. However, direct discovery of unknown pathogens in nasopharyngeal swabs is difficult due to the high concentration of ribosomal RNA (rRNA) that acts as competitor. In the current study we optimized VIDISCA by adjusting the reverse transcription enzymes and decreasing rRNA amplification in the reverse transcription, using hexamer oligonucleotides that do not anneal to rRNA. Residual cDNA synthesis on rRNA templates was further reduced with oligonucleotides that anneal to rRNA but can not be extended due to 3′-dideoxy-C6-modification. With these modifications >90% reduction of rRNA amplification was established. Further improvement of the VIDISCA sensitivity was obtained by high throughput sequencing (VIDISCA-454). Eighteen nasopharyngeal swabs were analysed, all containing known respiratory viruses. We could identify the proper virus in the majority of samples tested (11/18). The median load in the VIDISCA-454 positive samples was 7.2 E5 viral genome copies/ml (ranging from 1.4 E3–7.7 E6). Our results show that optimization of VIDISCA and subsequent high-throughput-sequencing enhances sensitivity drastically and provides the opportunity to perform virus discovery directly in patient material

The status of the world's land and marine mammals: diversity, threat, and knowledge

Knowledge of mammalian diversity is still surprisingly disparate, both regionally and taxonomically. Here, we present a comprehensive assessment of the conservation status and distribution of the world's mammals. Data, compiled by 1700+ experts, cover all 5487 species, including marine mammals. Global macroecological patterns are very different for land and marine species but suggest common mechanisms driving diversity and endemism across systems. Compared with land species, threat levels are higher among marine mammals, driven by different processes (accidental mortality and pollution, rather than habitat loss), and are spatially distinct (peaking in northern oceans, rather than in Southeast Asia). Marine mammals are also disproportionately poorly known. These data are made freely available to support further scientific developments and conservation action

The mammals of Angola

Scientific investigations on the mammals of Angola started over 150 years ago, but information remains scarce and scattered, with only one recent published account. Here we provide a synthesis of the mammals of Angola based on a thorough survey of primary and grey literature, as well as recent unpublished records. We present a short history of mammal research, and provide brief information on each species known to occur in the country. Particular attention is given to endemic and near endemic species. We also provide a zoogeographic outline and information on the conservation of Angolan mammals. We found confirmed records for 291 native species, most of which from the orders Rodentia (85), Chiroptera (73), Carnivora (39), and Cetartiodactyla (33). There is a large number of endemic and near endemic species, most of which are rodents or bats. The large diversity of species is favoured by the wide range of habitats with contrasting environmental conditions, while endemism tends to be associated with unique physiographic settings such as the Angolan Escarpment. The mammal fauna of Angola includes 2 Critically Endangered, 2 Endangered, 11 Vulnerable, and 14 Near-Threatened species at the global scale. There are also 12 data deficient species, most of which are endemics or near endemics to the countryinfo:eu-repo/semantics/publishedVersio