Conservation and the Genomics of Populations

Oxford University Press eBooks, Journal Year: 2022, Volume and Issue: unknown

Published: Feb. 10, 2022

Abstract Loss of biodiversity is among the greatest problems facing world today. Conservation and Genomics Populations gives a comprehensive overview essential background, concepts, tools needed to understand how genetic information can be used conserve species threatened with extinction, manage ecological or commercial importance. New molecular techniques, statistical methods, computer programs, principles, methods are becoming increasingly useful in conservation biological diversity. Using balance data theory, coupled basic applied research examples, this book examines phenotypic variation natural populations, principles mechanisms evolutionary change, interpretation from these conservation. The includes examples plants, animals, microbes wild captive populations. This third edition has been thoroughly revised include advances genomics contains new chapters on population genomics, monitoring, genetics practice, as well sections climate emerging diseases, metagenomics, more. More than one-third references were published after previous edition. Each 24 Appendix end Guest Box written by an expert who provides example presented chapter their own work. for advanced undergraduate graduate students genetics, resource management, biology, professional biologists policy-makers working wildlife habitat management agencies. Much will also interest nonprofessionals curious about role

Language: Английский

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Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: March 14, 2022

Northern Hemisphere forests changed drastically in the early Eocene with diversification of oak family (Fagaceae). Cooling climates over next 20 million years fostered spread temperate biomes that became increasingly dominated by oaks and their chestnut relatives. Here we use phylogenomic analyses nuclear plastid genomes to investigate timing pattern major macroevolutionary events ancient genome-wide signatures hybridization across Fagaceae. Innovation related seed dispersal is implicated triggering waves continental radiations beginning rapid lineages resulting unparalleled transformation forest dynamics within 15 following K-Pg extinction. We detect introgression at multiple time scales, including predating origination genus-level diversity. As moved into newly available habitats Miocene, secondary contact between previously isolated species occurred. This resulted adaptive introgression, which may have further amplified white Eurasia.

Language: Английский

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Genome-wide analyses of introgression between two sympatric Asian oak species

Nature Ecology & Evolution, Journal Year: 2022, Volume and Issue: 6(7), P. 924 - 935

Published: May 5, 2022

Language: Английский

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Modern Strategies to Assess and Breed Forest Tree Adaptation to Changing Climate

Frontiers in Plant Science, Journal Year: 2020, Volume and Issue: 11

Published: Oct. 21, 2020

Studying the genetics of adaptation to new environments in ecologically and industrially important tree species is currently a major research line fields plant science genetic improvement for tolerance abiotic stress. Exploring genomic basis local imperative assessing conditions under which trees will successfully adapt situ global climate change. However, this knowledge has scarcely been used conservation forest because woody perennials face limitations such as their outcrossing reproductive systems, long juvenile phase, huge genome sizes. Therefore, review we discuss predictive approaches that promise increasing selection accuracy shortening generation intervals. They may also assist detection novel allelic variants from germplasm, disclose potential different environments. For instance, natural populations allow using tools population genomics field study signatures adaptation. Conventional markers whole sequencing both help identifying genes diverge between more than expected neutrality, exhibit unique diversity indicative 'selective sweeps'. Ultimately, these efforts inform breeding status capable pivoting health, ecosystem services, sustainable production. Key long-term perspectives include understanding how trees' phylogeographic history affect adaptive relevant variation available environmental Encouraging 'big data' (machine learning –ML) comprehensively merging heterogeneous ecological datasets becomes imperative, too.

Language: Английский

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Medicinal Uses, Phytochemistry, and Pharmacological Activities of Quercus Species

Evidence-based Complementary and Alternative Medicine, Journal Year: 2020, Volume and Issue: 2020(1)

Published: Jan. 1, 2020

Quercus species, also known as oak, represent an important genus of the Fagaceae family. It is widely distributed in temperate forests northern hemisphere and tropical climatic areas. Many its members have been used traditional medicine to treat prevent various human disorders such asthma, hemorrhoid, diarrhea, gastric ulcers, wound healing. The multiple biological activities including anti‐inflammatory, antibacterial, hepatoprotective, antidiabetic, anticancer, gastroprotective, antioxidant, cytotoxic ascribed presence bioactive compounds triterpenoids, phenolic acids, flavonoids. This paper aimed provide available information on medicinal uses, phytochemicals, pharmacology species from . However, further investigation needed fully clarify mode action evaluate vivo chronic toxicity, before exploring their potential use a supplement functional foods natural pharmaceutics.

Language: Английский

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Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus)

New Phytologist, Journal Year: 2019, Volume and Issue: 226(4), P. 1158 - 1170

Published: April 9, 2019

Botanists have long recognised interspecific gene flow as a common occurrence within white oaks (Quercus section Quercus). Historical allele exchange, however, has not been fully characterised and the complex genomic signals resulting from combination of vertical horizontal transmission may confound phylogenetic inference obscure our ability to accurately infer deep evolutionary history oaks. Using anchored enrichment, we obtained phylogenomic dataset consisting hundreds single-copy nuclear loci. Concatenation, species-tree network analyses were carried out in an attempt uncover signal ancient introgression divergent topology for oak clade. Locus site-level likelihood comparisons then conducted further explore introgressed dataset. Historical, intersectional is suggested occurred between ancestor Eurasian Roburoid lineage Quercus pontica North American Dumosae Prinoideae lineages. Despite extensive time past, approach proved successful detecting signature introgression. Our results, highlight importance sampling use plurality analytical tools methods sufficiently datasets, this signal, history.

Language: Английский

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High-quality genome and methylomes illustrate features underlying evolutionary success of oaks

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: April 19, 2022

Abstract The genus Quercus , which emerged ∼55 million years ago during globally warm temperatures, diversified into ∼450 extant species. We present a high-quality de novo genome assembly of California endemic oak, lobata revealing features consistent with oak evolutionary success. Effective population size remained large throughout history despite declining since early Miocene. Analysis 39,373 mapped protein-coding genes outlined copious duplications genetic and phenotypic diversity, both by retention created the ancient γ whole hexaploid duplication event tandem within families, including numerous resistance very block duplicated DUF247 genes, have been found to be associated self-incompatibility in grasses. An additional surprising finding is that subcontext-specific patterns DNA methylation transposable elements reveal broadly-distributed heterochromatin intergenic regions, similar Collectively, these promote variation would facilitate adaptability changing environments.

Language: Английский

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A chromosome‐scale genome assembly of the Mongolian oak (Quercus mongolica)

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 22(6), P. 2396 - 2410

Published: April 4, 2022

Mongolian oak (Quercus mongolica Fisch.) is an ecologically and economically important white species native to widespread in the temperate zone of East Asia. Here, we present a chromosome-scale reference genome assembly Q. mongolica, representative species, by combining Illumina PacBio data with Hi-C mapping technologies that first created for Asian oak. Our results showed draft size was 809.84 Mb, BUSCO complete gene percentage 92.71%. scaffolding anchored 774.59 Mb contigs (95.65% assembly) onto 12 pseudochromosomes. The contig N50 scaffold were 2.64 66.74 respectively. Of 36,553 protein-coding genes predicted study, approximately 95% had functional annotations public databases. A total 435.34 (53.75% genome) repetitive sequences assembled genome. Genome evolution analysis closely related robur from Europe, they shared common ancestor ~11.8 million years ago (Ma). Gene family revealed nucleotide-binding site (NBS)-encoding disease resistance significantly contracted, whereas ECERIFERUM 1 (CER1) homologous cuticular wax biosynthesis expanded. This pioneering resource represents supplement genomics community will improve our understanding biology evolution.

Language: Английский

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Tracing the origin of Oriental beech stands across Western Europe and reporting hybridization with European beech – Implications for assisted gene flow

Forest Ecology and Management, Journal Year: 2023, Volume and Issue: 531, P. 120801 - 120801

Published: Jan. 26, 2023

The benefits and risks of human-aided translocation individuals within the species range, assisted gene flow (AGF), depend on genetic divergence, rate direction hybridization, climate transfer distance between host donor populations. In this study, we explored use Oriental beech (Fagus sylvatica subsp. orientalis), growing from Iran to Balkans, for AGF into European populations (F. sylvatica) that increasingly suffer warming. Using samples natural microsatellite loci, identified 5 distinct clusters in with a divergence (FST) 0.15 0.25 beech. knowledge, traced origin 11 stands Western Europe established during 20th century. two Greater Caucasus origin, found evidence extensive 18% 41% offspring having hybrid status. Climate data revealed higher seasonality warmer drier summers across native sites comparison planting Europe. Accordingly, bud burst occurred four days earlier than Overall, our results suggest could increase diversity may foster introgression variants adapted expected future climatic conditions. Our study showcases evaluation call similar studies other tree species.

Language: Английский

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A global synthesis of the patterns of genetic diversity in endangered and invasive plants

Biological Conservation, Journal Year: 2024, Volume and Issue: 291, P. 110473 - 110473

Published: Feb. 28, 2024

Language: Английский

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