scholarly journals Whole genome approach in conservation biology and its perspectives

2021 ◽  
Vol 19 (3) ◽  
pp. 281-298
Author(s):  
Sergei F. Kliver
Keyword(s):  
Conservation Biology ◽  
Conservation Planning ◽  
Biological Diversity ◽  
Demographic History ◽  
National Level ◽  
Whole Genome ◽  
Total Abundance ◽  
Conservation Genomics ◽  
Reliable Assessment ◽  
The Status

Conservation biology aims to maintain biological diversity and to defend species from extinction. The number of endangered species is constantly increasing from year to year, reflecting both a deteriorating situation and an increasing number of studied species. In order to obtain a reliable assessment of the status and conservation planning of threatened species, not only an estimate of current total abundance, but also data on population structure, demographic history, and genetic diversity are needed. The development of new approaches and lower costs of sequencing have made it possible to solve these problems at a level previously inaccessible and have led to the formation of conservation genomics. This review discusses the opportunities and prospects offered by the use of whole genome sequencing in conservation biology, features of sample gathering for sequencing, as well as some features of planning whole genome studies. In addition, emphasis is placed on the importance of the formation of open biobanks of samples and cell cultures at the national level.

scholarly journals Maisematason geodiversiteetti Suomessa

Terra ◽  
2021 ◽  
Vol 133 (2) ◽  
Author(s):  
Helena Tukiainen ◽  
Jan Hjort
Keyword(s):  
Nature Conservation ◽  
National Parks ◽  
Conservation Planning ◽  
Land Surface ◽  
Management Practices ◽  
Biological Diversity ◽  
National Level ◽  
Landscape Scale ◽  
Conservation Areas ◽  
Conservation And Management

The diversity of nature consists of two complementary components: biological diversity (biodiversity) and abiotic diversity (geodiversity). Biodiversity is widely acknowledged in both research, and conservation and management practices, whereas geodiversity (the variety of abiotic features and processes of the land surface and subsurface) is just emerging as a research and practical issue. In this study, we introduce the geodiversity concept in Finnish context and explore how landscape-scale geodiversity varies in Finland and between Finnish municipalities. In addition, we study how geodiversity varies between nature areas and human impacted areas and how Finnish strict nature reserves and national parks succeed in capturing geodiversity. According to the results, there is distinct geographical variation in geodiversity in Finland. The geodiversity of municipalities varies through the country but, on average, municipalities in the southern and northern parts of the country have especially high geodiversity values. Interestingly, human impacted areas have slightly higher geodiversity than nature areas. Nature conservation areas manage especially well in capturing geomorphological richness. This study emphasizes the need for the investigation of geodiversity on a national and sub-national level. Study of geodiversity provides information on nature beyond current biodiversity-focused perspectives, which can be further utilized in e.g., land-use and nature conservation planning.

scholarly journals Whole genome sequences from non-invasively collected caribou faecal samples

2021 ◽  
Author(s):  
Rebecca S. Taylor ◽  
Micheline Manseau ◽  
Bridget Redquest ◽  
Sonesinh Keobouasone ◽  
Patrick Gagné ◽  
...  
Keyword(s):  
Demographic History ◽  
Primate Species ◽  
Whole Genome ◽  
Faecal Dna ◽  
Conservation Genomics ◽  
High Coverage ◽  
Tissue Samples ◽  
Non Invasive ◽  
Faecal Samples ◽  
Whole Genomes

AbstractConservation genomics is an important tool to manage threatened species under current biodiversity loss. Recent advances in sequencing technology mean that we can now use whole genomes to investigate demographic history, local adaptation, inbreeding, and more in unprecedented detail. However, for many rare and elusive species only non-invasive samples such as faeces can be obtained, making it difficult to take advantage of whole genome data. We present a method to extract DNA from the mucosal layer of faecal samples to re-sequence high coverage whole genomes using standard laboratory techniques. We use wild collected faecal pellets collected from caribou (Rangifer tarandus), a species undergoing declines in many parts of its range in Canada and subject to comprehensive conservation and population monitoring measures. We compare four faecal genomes to two tissue genomes sequenced in the same run. Quality metrics were similar between faecal and tissue samples with the main difference being the alignment success of raw reads to the reference genome due to differences in low quality and endogenous DNA content, affecting overall coverage. One of our faecal genomes was only re-sequenced at low coverage (1.6 ×), however the other three obtained between 7 and 15 ×, compared to 19 and 25 × for the tissue samples. We successfully re-sequenced high-quality whole genomes from faecal DNA and are one of the first to obtain genome-wide data from wildlife faecal DNA in a non-primate species. Our work represents an important advancement for non-invasive conservation genomics.

scholarly journals Regional scalable priorities for national biodiversity and carbon conservation planning in Asia

2021 ◽  
Vol 7 (35) ◽  
pp. eabe4261
Author(s):  
Li Zhu ◽  
Alice C. Hughes ◽  
Xiao-Qian Zhao ◽  
Li-Jing Zhou ◽  
Ke-Ping Ma ◽  
...  
Keyword(s):  
Conservation Planning ◽  
Biological Diversity ◽  
National Level ◽  
Convention On Biological Diversity ◽  
Stepwise Approach ◽  
Terrestrial Vertebrates ◽  
Asian Region ◽  
Global Biodiversity ◽  
Funding Mechanisms

To achieve the goals of the post-2020 global biodiversity framework, we must identify representative targets that effectively protect biodiversity and can be implemented at a national level. We developed a framework to identify synergies between biodiversity and carbon across the Asian region and proposed a stepwise approach based on scalable priorities at regional, biome, and national levels that can complement potential Convention on Biological Diversity targets of protecting 30% land in the post-2020 global biodiversity framework. Our targets show that 30% of Asian land could effectively protect over 70% of all assessed species relative to only 11% now (based on analysis of 8932 terrestrial vertebrates), in addition to 2.3 to 3.6 hundred billion metric tons of carbon. Funding mechanisms are needed to ensure such targets to support biodiversity-carbon mutually beneficial solutions at the national level while reflecting broader priorities, especially in hyperdiverse countries where priorities exceed 30% of land.

scholarly journals A Regional Review of Genetic Resource Access and Benefit Sharing – Key Issues and Research Gaps

2021 ◽  
pp. 1-24
Author(s):  
Clare Morrison ◽  
Fran Humphries ◽  
Charles Lawson
Keyword(s):  
Intellectual Property ◽  
Traditional Knowledge ◽  
Biological Diversity ◽  
National Level ◽  
Sustainable Use ◽  
Benefit Sharing ◽  
Comparative Approach ◽  
Future Research ◽  
Access And Benefit Sharing ◽  
Legal Mechanism

Countries are increasingly using access and benefit sharing (ABS) as a legal mechanism to support the conservation and sustainable use of the world’s biological diversity. ABS regulates collection and/or use of genetic resources/traditional knowledge and sharing benefits from their use with the provider. The purpose of this review is to assess the trends, biases and gaps of ABS literature using a regional comparative approach about the key topics of concern between each region. It analyses four key topic groupings: (1) implementation of international, regional and national ABS policy and law; (2) intellectual property and ABS; (3) traditional knowledge; and (4) research, development and commercialisation. Findings included gaps in: (1) analysing effectiveness of national level implementation; (2) addressing apparent conflicts between support for intellectual property promoting exclusivity for traditional knowledge and challenges to intellectual property exclusivity for patents; (3) examining traditional knowledge of local communities (in contrast to Indigenous Peoples); and (4) lack of practical examples that quantify benefit sharing from research and commercialisation outcomes. We conclude that future research addressing the identified gaps and biases can promote more informed understanding among stakeholders about the ABS concept and whether it is capable of delivering concrete biological conservation, sustainable use and equity outcomes.

Present Status of Musculoskeletal Radiology in Europe: International Survey by the European Society of Musculoskeletal Radiology

2020 ◽  
Vol 24 (03) ◽  
pp. 323-330
Author(s):  
Timea Hebar ◽  
Žiga Snoj ◽  
Luca Maria Sconfienza ◽  
Filip Maria H.M. Vanhoenacker ◽  
Maryam Shahabpour ◽  
...  
Keyword(s):  
European Society ◽  
Interventional Procedures ◽  
National Level ◽  
International Survey ◽  
Online Questionnaire ◽  
Musculoskeletal Radiology ◽  
Radiological Society ◽  
The Status ◽  
Structure Relationship ◽  
Academic Radiology

No official data exist on the status of musculoskeletal (MSK) radiology in Europe. The Committee for National Societies conducted an international survey to understand the status of training, subspecialization, and local practice among the European Society of Musculoskeletal Radiology (ESSR) partner societies. This article reports the results of that survey. An online questionnaire was distributed to all 26 European national associations that act as official partner societies of the ESSR. The 24 questions were subdivided into six sections: society structure, relationship with the national radiological society, subspecialization, present radiology practice, MSK interventional procedures, and MSK ultrasound. The findings of our study show a lack of standardized training and/or accreditation methods in the field of MSK radiology at a national level. The European diploma in musculoskeletal radiology is directed to partly overcome this problem; however, this certification is still underrecognized. Using certification methods, a more homogeneous European landscape could be created in the future with a view to subspecialist training. MSK ultrasound and MSK interventional procedures should be performed by a health professional with a solid knowledge of the relevant imaging modalities and sufficient training in MSK radiology. Recognition of MSK radiology as an official subspecialty would make the field more attractive for younger colleagues as well as attracting the brightest and best, an important key to further development of both clinical and academic radiology. Key Points

Adapting environmental conservation legislation for an enlarged European Union: experience from the Habitats Directive

2013 ◽  
Vol 40 (2) ◽  
pp. 97-107 ◽  
Author(s):  
DOUGLAS EVANS ◽  
ANDRÁS DEMETER ◽  
PETER GAJDOŠ ◽  
ĽUBOŠ HALADA
Keyword(s):  
Native Species ◽  
Biological Diversity ◽  
National Level ◽  
Environmental Conservation ◽  
Habitats Directive ◽  
Scientific Support ◽  
Union Experience ◽  
Biodiversity Governance ◽  
The Eu ◽  
Initial Base

SUMMARYThe European Union's (EU's) Habitats Directive includes annexes listing the habitats and species requiring protection. As new countries join the EU these lists need to be amended to remain pertinent. In 2004 and 2007, 12 countries, mostly in central Europe, joined the EU and were asked to propose native species or habitats that required protection; this formed an initial base for negotiations with the European Commission in consultation with the existing member states and with scientific support from the European Topic Centre on Biological Diversity. The 12 countries made 831 proposals, resulting in the addition of 191 species and 33 habitats, and geographical exemptions for eight species. Although the Directive provided definitions, these needed to be supplemented with additional criteria to permit assessments of the proposals. The process involved many actors at both European and national level. This illustrates the development of biodiversity governance and provides potential lessons for future activities, including the need for scientific guidance and the importance of involving all relevant actors.

Demographic history and patterns of molecular evolution from whole genome sequencing in the radiation of Galapagos giant tortoises

2021 ◽  
Author(s):  
Evelyn L. Jensen ◽  
Stephen J. Gaughran ◽  
Ryan C. Garrick ◽  
Michael A. Russello ◽  
Adalgisa Caccone
Keyword(s):  
Molecular Evolution ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Demographic History ◽  
Whole Genome

Recent Developments

2004 ◽  
Vol 48 (2) ◽  
pp. 268-270 ◽  
Author(s):  
Jon C. Lovett
Keyword(s):  
Biological Diversity ◽  
National Policy ◽  
Plant Conservation ◽  
Global Strategy ◽  
Convention On Biological Diversity ◽  
International Botanical ◽  
International Botanical Congress ◽  
The Status ◽  
Recent Developments ◽  
Essential Resource

At the 1999 International Botanical Congress held in St Louis, Missouri, the President of the Congress, Dr Peter Raven, presented a keynote address emphasizing the importance of plants to human existence and underlined concerns that the Earth is undergoing a human-induced extinction crisis. One of the resolutions of the congress was to establish a new co-ordinating body associated with the United Nations to monitor the status of plants throughout the world and take steps to conserve them. The resolutions were followed up with a meeting in Gran Canaria on 3–4 April, 2000 when leading botanists met to formulate a declaration which could be taken forward to the fifth Conference of the Parties (CoP5) to the Convention on Biological Diversity held in Nairobi in May 2000. CoP5 recognized that plant diversity is a common concern of humankind and an essential resource for the planet, with as many as two-thirds of the world's plant species in danger of extinction, and proposed that at the sixth meeting of the Conference of the Parties (CoP6) the establishment of a global strategy for plant conservation should be considered. A strategy with 16 targets was presented and adopted at the CoP6 meeting held in The Hague in April 2002. These targets differ from the normal approach adopted in the Convention on Biological Diversity of using general principles that can be interpreted by national policy, in that they are quantified.

scholarly journals Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Fan Jiang ◽  
Ruiyi Lin ◽  
Changyi Xiao ◽  
Tanghui Xie ◽  
Yaoxin Jiang ◽  
...  
Keyword(s):  
Gene Flow ◽  
South Asia ◽  
South Asian ◽  
Demographic History ◽  
Nervous System Development ◽  
Chromosome 1 ◽  
Whole Genome ◽  
Chinese Populations ◽  
Asian Populations ◽  
History Of

Abstract Background The most prolific duck genetic resource in the world is located in Southeast/South Asia but little is known about the domestication and complex histories of these duck populations. Results Based on whole-genome resequencing data of 78 ducks (Anas platyrhynchos) and 31 published whole-genome duck sequences, we detected three geographic distinct genetic groups, including local Chinese, wild, and local Southeast/South Asian populations. We inferred the demographic history of these duck populations with different geographical distributions and found that the Chinese and Southeast/South Asian ducks shared similar demographic features. The Chinese domestic ducks experienced the strongest population bottleneck caused by domestication and the last glacial maximum (LGM) period, whereas the Chinese wild ducks experienced a relatively weak bottleneck caused by domestication only. Furthermore, the bottleneck was more severe in the local Southeast/South Asian populations than in the local Chinese populations, which resulted in a smaller effective population size for the former (7100–11,900). We show that extensive gene flow has occurred between the Southeast/South Asian and Chinese populations, and between the Southeast Asian and South Asian populations. Prolonged gene flow was detected between the Guangxi population from China and its neighboring Southeast/South Asian populations. In addition, based on multiple statistical approaches, we identified a genomic region that included three genes (PNPLA8, THAP5, and DNAJB9) on duck chromosome 1 with a high probability of gene flow between the Guangxi and Southeast/South Asian populations. Finally, we detected strong signatures of selection in genes that are involved in signaling pathways of the nervous system development (e.g., ADCYAP1R1 and PDC) and in genes that are associated with morphological traits such as cell growth (e.g., IGF1R). Conclusions Our findings provide valuable information for a better understanding of the domestication and demographic history of the duck, and of the gene flow between local duck populations from Southeast/South Asia and China.

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