Design of SNP markers for Aldabra giant tortoises using low coverage ddRAD-seq

AbstractThe Aldabra giant tortoise (Aldabrachelys gigantea) is one of only two remaining giant tortoise species worldwide. Captive-bred A. gigantea are being used in rewilding projects in the Western Indian Ocean to functionally replace the extinct endemic giant tortoise species and restore degraded island ecosystems. Furthermore, large-scale translocations may become necessary as rising sea levels threaten the only wild population on the low-lying Aldabra Atoll. Critical management decisions would be greatly facilitated by insights on the genetic structure of breeding populations. We used a double-digest restriction-associated DNA sequencing (ddRAD-seq) approach to identify single nucleotide polymorphisms (SNP) among the wild population and two additional captive populations of A. gigantea. A total of 1674 unlinked, putatively neutral genome-wide SNPs were identified. The values of expected heterozygosity ranged from 0.33 to 0.5, whereas the minor allele frequency ranged from 0.20 to 0.5. These novel SNP markers will serve as useful tools for informing the conservation of A. gigantea.

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Design of SNP Markers for Aldabra Giant Tortoises using ddRAD-seq

10.21203/rs.3.rs-498085/v1 ◽

2021 ◽

Author(s):

F. Gözde Çilingir ◽

Dennis Hansen ◽

Arpat Ozgul ◽

Christine Grossen

Keyword(s):

Large Scale ◽

Wild Population ◽

Western Indian Ocean ◽

Snp Markers ◽

Nucleotide Polymorphisms ◽

Sea Levels ◽

Breeding Populations ◽

Captive Populations ◽

Genome Wide ◽

Rising Sea Levels

Abstract The Aldabra giant tortoise ( Aldabrachelys gigantea ) is one of only two remaining giant tortoise species worldwide. Captive-bred A. gigantea are being used in rewilding projects in the Western Indian Ocean to functionally replace the extinct endemic giant tortoise species and restore degraded island ecosystems. Furthermore, large-scale translocations may become necessary as rising sea levels threaten the only wild population on the low-lying Aldabra Atoll. Critical management decisions would be greatly facilitated by insights on the genetic structure of breeding populations. We used a double-digest restriction-associated DNA sequencing (ddRAD-seq) approach to identify single nucleotide polymorphisms (SNP) among the wild population and two additional captive populations of A. gigantea . A total of 149 unlinked, putatively neutral genome-wide SNPs were identified. The values of expected heterozygosity ranged from 0.32 to 0.5, whereas the minor allele frequency ranged from 0.20 to 0.5. These novel SNP markers will serve as useful tools for informing the conservation of A. gigantea .

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Tropical Cyclone-Induced Hazards Caused by Storm Surges and Large Waves on the Coast of China

Geosciences ◽

10.3390/geosciences9030131 ◽

2019 ◽

Vol 9 (3) ◽

pp. 131 ◽

Cited By ~ 2

Author(s):

Zai-Jin You

Keyword(s):

Large Scale ◽

Storm Surges ◽

Chinese Economy ◽

Coastal Hazards ◽

Economic Losses ◽

Sea Levels ◽

The North ◽

Coastal Waves ◽

Storm Wave ◽

Rising Sea Levels

The mainland coast of China is about 18,000 km long and houses about 70% of China’s largest cities and 50% of its population. For the last few decades, the rapid growth of the Chinese economy has resulted in extensive development of the coastal infrastructure and property, large-scale expansion of coastal ports, excessive reclamation of coastal land, and a significant increase in the coastal population. Previous studies have indicated that tropical cyclones (TCs) have struck the coast of China at a higher frequency and intensity, and TC-induced coastal hazards have resulted in heavy human losses and huge losses to the Chinese coastal economy. In analyzing the long-term and most recent coastal hazard data collected on the coast of China, this study has found that TC-induced storm surges are responsible for 88% of the direct coastal economic losses, while TC-induced large coastal waves have caused heavy loss of human lives, and that the hazard-caused losses are shown to increase spatially from the north to south, peak in the southern coastal sector, and well correlate to storm wave energy flux. The frequency and intensity of coastal hazards on the coast of China are expected to increase in response to future changing TC conditions and rising sea levels. A simple two-parameter conceptual model is also presented for the assessment of coastal inundation and erosion hazards on the coast of China.

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De Novo Transcriptomic Resources in the Brain of Vespa velutina for Invasion Control

Insects ◽

10.3390/insects11020101 ◽

2020 ◽

Vol 11 (2) ◽

pp. 101

Author(s):

Miao Wang ◽

Hanyu Li ◽

Huoqing Zheng ◽

Liuwei Zhao ◽

Xiaofeng Xue ◽

...

Keyword(s):

Large Scale ◽

Target Genes ◽

De Novo ◽

Transcriptome Profiling ◽

Molecular Study ◽

Snp Markers ◽

Nucleotide Polymorphisms ◽

Illumina Hiseq ◽

Vespa Velutina ◽

Genes Encoding

The invasion of Vespa velutina presents a great threat to the agriculture economy, the ecological environment, and human health. An effective strategy for this hornet control is urgently required, but the limited genome information of Vespa velutina restricts the application of molecular-genomic tools for targeted hornet management. Therefore, we conducted large-scale transcriptome profiling of the hornet brain to obtain functional target genes and molecular markers. Using an Illumina HiSeq platform, more than 41 million clean reads were obtained and de novo assembled into 182,087 meaningful unigenes. A total of 56,400 unigenes were annotated against publicly available protein sequence databases and a set of reliable Simple Sequence Repeats (SSRs) and Single Nucleotide Polymorphisms (SNP) markers were developed. The homologous genes encoding crucial behavior regulation factors, odorant binding proteins (OBPs), and vitellogenin, were also identified from highly expressed transcripts. This study provides abundant molecular targets and markers for invasive hornet control and further promotes the genetic and molecular study of Vespa velutina.

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Development and Characterization of PCR Markers in Cucumber

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.127.4.545 ◽

2002 ◽

Vol 127 (4) ◽

pp. 545-557 ◽

Cited By ~ 51

Author(s):

Gennaro Fazio ◽

Jack E. Staub ◽

Sang Min Chung

Keyword(s):

Large Scale ◽

Cost Effective ◽

Snp Markers ◽

Yield Component ◽

Nucleotide Polymorphisms ◽

Pcr Markers ◽

Dinucleotide Repeats ◽

Sequence Characterized Amplified Region ◽

Tetranucleotide Repeats ◽

Multiple Lateral Branching

Highly polymorphic microsatellites or simple sequence repeat (SSR), along with sequence characterized amplified region (SCAR) and single nucleotide polymorphisms (SNP), markers are reliable, cost-effective, and amenable for large scale analyses. Molecular polymorhisms are relatively rare in cucumber (Cucumis sativus L.) (3% to 8%). Therefore, experiments were designed to develop SSR, SCAR and SNP markers, and optimize reaction conditions for PCR. A set of 110 SSR markers was constructed using a unique, strategically applied methodology that included the GeneTrapper (Life Technologies, Gaithersburg, Md.) kit to select plasmids harboring microsatellites. Of these markers, 58 (52%) contained dinucleotide repeats (CT, CA, TA), 21 (19%) possessed trinucleotide repeats (CTT, ATT, ACC, GCA), 3 (2.7%) contained tetranucleotide repeats (TGCG, TTAA, TAAA), 4 (3.6%) enclosed pentanucleotide repeat (ATTTT, GTTTT, GGGTC, AGCCC), 3 (2.7%) contained hexanucleotide repeats (CCCAAA, TAAAAA, GCTGGC) and 21 possessed composite repeats. Four SCARs (L18-3 SCAR, AT1-2 SCAR, N6-A SCAR, and N6-B SCAR) and two PCR markers based on SNPs (L18-2H19 A and B) that are tightly linked to multiple lateral branching (i.e., a yield component) were also developed. The SNP markers were developed from otherwise monomorphic SCAR markers, producing genetically variable amplicons. The markers L18-3 SCAR and AT1-2 SCAR were codominant. A three-primer strategy was devised to develop a codominant SCAR from a sequence containing a transposable element, and a new codominant SCAR product was detected by annealing temperature gradient (ATG) PCR. The use of a marker among laboratories can be enhanced by methodological optimization of the PCR. The utility of the primers developed was optimized by ATG-PCR to increase reliability and facilitate technology transfer. This array of markers substantially increases the pool of genetic markers available for genetic investigation in Cucumis.

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Inhabiting the machine

10.26686/wgtn.17011988.v1 ◽

2021 ◽

Author(s):

◽

George Goodwin

Keyword(s):

Financial Management ◽

Urban Poor ◽

Tamil Nadu ◽

Architectural Design ◽

Large Scale ◽

Sea Levels ◽

Civil Society Organisations ◽

Slum Dwellers ◽

Basic Services ◽

Rising Sea Levels

<p>Like many cities across India, Chennai (capital of Tamil Nadu) has two tiers of slums — those with official government recognition and those without. Slums with official government recognition are then further categorised to either be objectionable or unobjectionable. Recognised slums receive government funding to provide new tenements and basic services on site. But recent studies have shown that 4.8 sq km of the Chennai metropolitan area are comprised of either unrecognised or objectionable slums. The current government strategy is to forcibly relocate families from unrecognised or objectionable slums to large-scale, high-rise settlement colonies on the distant outskirts of Chennai. Numerous civil society organisations, however, have documented that eviction and relocation results in extreme trauma for these families. The Transparent Chennai Project at the Institute for Financial Management and Research in Chennai argues that: “A far more reasonable strategy would be to once again implement the Tamil Nadu Slum Clearance Act in the spirit that it was written, and start to recognise slums and improve them in situ” (Raman and Narayan). This thesis proposes that architectural design can improve conditions for Chennai’s urban poor without resorting to forced relocation. It argues that a new framework for slum housing can be designed that is capable of: protecting slum dwellers from environmental disasters such as rising sea levels, storm surge, and tsunamis; mitigating environmental pollution to improve hygiene; and providing economic sources of fresh water and energy through sustainable means. It further argues that this framework can be achieved in a culturally sensitive manner by acknowledging traditional and historically significant regional architectural typologies.</p>

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Genomic insights into adaptive divergence and speciation among malaria vectors of the Anopheles nili group

10.1101/068239 ◽

2016 ◽

Author(s):

Caroline Fouet ◽

Colince Kamdem ◽

Stephanie Gamez ◽

Bradley J. White

Keyword(s):

Population Structure ◽

Large Scale ◽

Incomplete Lineage Sorting ◽

Snp Markers ◽

Malaria Vectors ◽

Adaptive Divergence ◽

Nucleotide Polymorphisms ◽

Lineage Sorting ◽

Interspecific Gene Flow ◽

Scale Control

AbstractOngoing speciation in most African malaria vectors gives rise to cryptic populations, which differ remarkably in their behaviour, ecology and capacity to vector malaria parasites. Understanding the population structure and the drivers of genetic differentiation among mosquitoes is critical for effective disease control because heterogeneity within species contribute to variability in malaria cases and allow fractions of vector populations to escape control efforts. To examine the population structure and the potential impacts of recent large-scale control interventions, we have investigated the genomic patterns of differentiation in mosquitoes belonging to the Anopheles nili group, a large taxonomic group that diverged ∼3-Myr ago. Using 4343 single nucleotide polymorphisms (SNPs), we detected strong population structure characterized by high FST values between multiple divergent populations adapted to different habitats within the Central African rainforest. Delineating the cryptic species within the Anopheles nili group is challenging due to incongruence between morphology, ribosomal DNA and SNP markers consistent with incomplete lineage sorting and/or interspecific gene flow. A very high proportion of loci are fixed (FST = 1) within the genome of putative species, which suggests that ecological and/or reproductive barriers are maintained by strong selection on a substantial number of genes.

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Climate Change and Supply Chain Operations

Climate Change, Supply Chain Management and Enterprise Adaptation ◽

10.4018/978-1-61692-800-1.ch004 ◽

2011 ◽

pp. 93-126

Author(s):

Costas P. Pappis

Keyword(s):

Climate Change ◽

Large Scale ◽

Water Cycle ◽

Well Being ◽

Developed Countries ◽

Sea Levels ◽

The World ◽

Stern Review ◽

Rising Sea Levels

In the previous chapter 3 the focus of the presentation has been on the implications of climate change, as felt globally, for the environment and human societies in developing as well as in developed countries. As noticed there, the Stern Review’s conclusion that “climate change will have increasingly severe impacts on people around the world, with a growing risk of abrupt and large-scale changes at higher temperatures” (Stern Review, 2006) is shared by most scientists and governments. The Review warns that “a warmer world with a more intense water cycle and rising sea levels will influence many key determinants of wealth and well-being, including water supply, food production, human health, availability of land, and the environment” (Stern Review, p. 84).

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Salty Urbanism: Toward an Adaptive Coastal Design Framework to Address Rising Seas and Climate Change

Design for Climate Action ◽

10.35483/acsa.aia.inter.20.6 ◽

2020 ◽

Author(s):

Jeffrey E. Huber

Keyword(s):

Climate Change ◽

Urban Design ◽

Large Scale ◽

Systems Approach ◽

Flood Management ◽

Wildlife Habitat ◽

Sea Levels ◽

Rising Sea Levels ◽

Economic Assets

Over the next 100 years, nothing will radically change thecoastal built environment more than climate change and sea level rise. The coastal zone is home to some of our country’s most valuable ecological and socio-economic assets. Many of these locations are being demonstrably transformed dueto large-scale human and biophysical processes. The result is a potential loss of myriad ecosystem services such as storm protection, wildlife habitat, recreation and aesthetics, among others. Policy and design solutions are not truly consideringthe necessary transformation that will be required to live and work within a saturated coastal environment. The old paradigm of flood management and control will need tochange from prevention to acceptance and population will decline as businesses and individuals decide the costs are too high. The need for developing a long-term urban design and planning framework that adapts to these effects is critical. More specifically, there is a need for a “systems” approach that utilizes urban design and takes into consideration infrastructure impacts, future investments, and insurability of risk as long-term objectives to address potential impacts from both coastal flooding and rising sea levels, while at the same time guiding communities’ future land use and investment plans.

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Sustaining observations of the unsteady ocean circulation

Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences ◽

10.1098/rsta.2013.0335 ◽

2014 ◽

Vol 372 (2025) ◽

pp. 20130335 ◽

Cited By ~ 4

Author(s):

E. Frajka-Williams

Keyword(s):

Ocean Circulation ◽

Large Scale ◽

Measurement Techniques ◽

Warming Trend ◽

Personal Perspective ◽

Sea Levels ◽

Rising Sea Levels ◽

Time Basis ◽

The Uk ◽

Ocean Properties

Sustained observations of ocean properties reveal a global warming trend and rising sea levels. These changes have been documented by traditional ship-based measurements of ocean properties, whereas more recent Argo profiling floats and satellite records permit estimates of ocean changes on a near real-time basis. Through these and newer methods of observing the oceans, scientists are moving from quantifying the ‘state of the ocean’ to monitoring its variability, and distinguishing the physical processes bringing signals of change. In this paper, I give a brief overview of the UK contributions to the physical oceanographic observations, and the role they have played in the wider global observing systems. While temperature and salinity are the primary measurements of physical oceanography, new transbasin mooring arrays also resolve changes in ocean circulation on daily timescales. Emerging technologies permit routine observations at higher-than-ever spatial resolutions. Following this, I then give a personal perspective on the future of sustained observations. New measurement techniques promise exciting discoveries concerning the role of smaller scales and boundary processes in setting the large-scale ocean circulation and the ocean's role in climate. The challenges now facing the scientific community include sustaining critical observations in the case of funding system changes or shifts in government priorities. These long records will enable a determination of the role and response of the ocean to climate change.

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Earth's Amphibious Transformation: Tange Kenzo, Buckminster Fuller, and marine urbanization in global environmental thought (1950s–present)

Modern Asian Studies ◽

10.1017/s0026749x21000251 ◽

2021 ◽

pp. 1-30

Author(s):

Stefan Huebner

Keyword(s):

Communication Networks ◽

Communication Technology ◽

Communication Systems ◽

Large Scale ◽

Land Reclamation ◽

Offshore Structures ◽

Tokyo Bay ◽

Sea Levels ◽

Rising Sea Levels ◽

Post War

Abstract Climate change and rising sea levels, which threaten many Asian and other coastal cities, have returned the question of adaptation to unstable marine surfaces to the global discussions about urbanization, as was illustrated by a recent United Nations (UN) roundtable. As de facto counterproposals to hydroelectric dams and similar regional development projects, floating or elevated structures reject land reclamation and terrestrialization processes. Consequently, the rapidly growing number of offshore structures, which often constitute unconventional settlements, have contributed to an amphibious transformation of Earth's surface in the course of the twentieth and early twenty-first centuries. This amphibious transformation meant that both terrestrial and aquatic places have turned into human habitats. This article asks how and why today's leading environmental-political strand in large-scale marine urbanization emerged from the waters of Tokyo Bay. It investigates Japanese star architect Tange Kenzō's ‘Plan for Tokyo 1960’ (1961) and world-renowned American designer R. Buckminster Fuller's floating design called ‘Tetrahedronal City’ (1966). Emphasizing the important role that Asian cities have played in shaping global urbanization ideas and practices, Tokyo Bay became a node in the global cybernetics revolution that moved urban design into the information age. Tange's and Fuller's evolution-inspired cybernetic designs used the post-war communication technology revolution to replicate, through artificial communication networks, the biological communication systems that enable organisms to interact with their environments. Applying communication technology to recreate, in floating or elevated structures, the biological processes of growth, adaptation, mobility, and autonomy became the central environmental-political strand for large-scale marine urbanization and reducing its ecological footprint.

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