Landscape Genomics in Tree Conservation Under a Changing Environment

Frontiers in Plant Science, Год журнала: 2022, Номер 13

Опубликована: Фев. 24, 2022

Understanding the genetic basis of how species respond to changing environments is essential conservation species. However, molecular mechanisms adaptation remain largely unknown for long-lived tree which always have large population sizes, long generation time, and extensive gene flow. Recent advances in landscape genomics can reveal signals adaptive selection linking variations characteristics therefore created novel insights into strategies. In this review article, we first summarized methods used elucidated advantages disadvantages these methods. We then highlighted newly developed method “Risk Non-adaptedness,” predict offset or genomic vulnerability via allele frequency change under multiple scenarios climate change. Finally, provided prospects concerning our introduced approaches assist policymaking improve existing strategies ongoing global changes.

Язык: Английский

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Spatial variations of root-associated bacterial communities of alpine plants in the Qinghai-Tibet Plateau

The Science of The Total Environment, Год журнала: 2022, Номер 839, С. 156086 - 156086

Опубликована: Май 21, 2022

Язык: Английский

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Integrating evolutionary genomics of forest trees to inform future tree breeding amidst rapid climate change

Plant Communications, Год журнала: 2024, Номер 5(10), С. 101044 - 101044

Опубликована: Авг. 7, 2024

Global climate change is leading to rapid and drastic shifts in environmental conditions, posing threats biodiversity nearly all life forms worldwide. Forest trees serve as foundational components of terrestrial ecosystems play a crucial role combating mitigating the adverse effects extreme events, despite their own vulnerability these threats. Therefore, understanding monitoring how natural forests respond key priority for conservation. Recent progress evolutionary genomics, driven primarily by cutting-edge multi-omics technologies, offers powerful new tools address several issues. These include precise delineation species units, inference past histories demographic fluctuations, identification environmentally adaptive variants, measurement genetic load levels. As urgency deal with more stresses grows, genomics history, local adaptation, future responses change, conservation restoration forest will be critical research at nexus global population biology. In this review, we explore application assess using approaches discuss outlook breeding climate-adapted trees.

Язык: Английский

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MrIML: Multi‐response interpretable machine learning to model genomic landscapes

Molecular Ecology Resources, Год журнала: 2021, Номер 21(8), С. 2766 - 2781

Опубликована: Авг. 27, 2021

We introduce a new R package "MrIML" ("Mister iml"; Multi-response Interpretable Machine Learning). MrIML provides powerful and interpretable framework that enables users to harness recent advances in machine learning quantify multilocus genomic relationships, identify loci of interest for future landscape genetics studies, gain insights into adaptation across environmental gradients. Relationships between genetic variation environment are often nonlinear interactive; these characteristics have been challenging address using traditional approaches. Our helps capture this complexity offers functions fit interpret wide range highly flexible models routinely used single-locus studies but rarely extended estimate response multiple loci. To demonstrate the package's broad functionality, we test its ability recover relationships from simulated data. also apply two empirical case studies. In first, model North American balsam poplar (Populus balsamifera, Salicaceae) populations second study, host drivers feline immunodeficiency virus bobcats (Lynx rufus). The thousands collectively compare linear regression extreme gradient boosting, within same analytical framework, has potential be transformative. is extendable not limited modelling variation; example, it can microbiomes coinfection dynamics.

Язык: Английский

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Seed sourcing in the genomics era: multispecies provenance delineation for current and future climates

Restoration Ecology, Год журнала: 2022, Номер 30(S1)

Опубликована: Май 5, 2022

Restoration interventions require knowledge on the suitability of seed sources. Provenance delineation for ecological restoration degraded environments has begun to incorporate genome‐wide information adaptive variation, but this only been completed a small number plant species. Rarely is provenance using genomics approach applied species occurring across different habitats, and in context future climate scenarios, despite their potential importance successful long‐term restoration. Here, we use neutral genetic data investigate patterns differentiation landscape model putatively variation under multiple scenarios two co‐occurring predominantly mesic environment, semi‐arid environment. We then determine similarity sourcing locations hypothetical sites, both current scenarios. found that geographical extent provenances amount change required track projected climatic conditions over time differed within pairs species, between habitats. Additionally, had differing effects landscapes indicating differential response changing from arid This implies guidelines can be habitat dependent. discuss how these results utilized design strategies restoration, methods could more broadly delineate other locations.

Язык: Английский

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Association of putatively adaptive genetic variation with climatic variables differs between a parasite and its host

Evolutionary Applications, Год журнала: 2021, Номер 14(7), С. 1732 - 1746

Опубликована: Март 24, 2021

Parasitism is a pervasive phenomenon in nature with the relationship between species driving evolution both parasite and host. Due to their host-dependent lifestyle, parasites may adapt abiotic environment ways that differ from hosts or free-living relatives; yet rarely has this been assessed. Here, we test two competing hypotheses related whether putatively adaptive genetic variation specialist mistletoe associates same, different, climatic variables as its host species. We sampled 11 populations of Amyema gibberula var. tatei (n = 154) 10 associated Hakea recurva subsp. 160). Reduced-representation sequencing was used obtain genome-wide markers detected using genome scan methods. Climate associations were identified generalized dissimilarity modelling, these mapped geographically visualize spatial patterns composition. Our results supported hypothesis responding differently variables. Temperature relatively more important predicting allelic turnover while precipitation for This suggests parasitic plants respond selective pressures, potentially result differing nutrient acquisition strategies. Specifically, mistletoes acquire water (rather than environment), which provide buffer pressure. work deepens complements physiological other ecological studies adaptation provides window into evolutionary processes underlie previously observed phenomena. Applying methods comparative study host-parasite system also highlighted factors affect selection pressure on nonmodel organisms, such rates lack reference genomes.

Язык: Английский

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Talking Mungee – a teacher, provider, connector, exemplar: what’s not to celebrate about the world’s largest mistletoe, Nuytsia floribunda

Plant and Soil, Год журнала: 2023, Номер unknown

Опубликована: Май 17, 2023

Abstract Purpose Endemic to Noongar Country of southwestern Australia, the charismatic and much-loved mistletoe, Nuytsia floribunda (Labill.) R.Br. ex G.Don ( Munjee / Moodjar in language), was subject a 2010 review which explored aspects its cultural importance botanical attributes based largely on early colonial accounts scientific findings. Our purpose apply cross-cultural methods update findings reported by Hopper (2010). Methods We have recently this iconic species through collaborative Elder-led, process, oral contemporary Merningar knowledge holders. Results record previously unpublished insights relating , longheld custom conservation, use multi-faceted relationships with Australia’s First Nations peoples. present Noongar- Western science-derived physiology, ecology evolution species. Conclusion The unique biology, ingenuity physical prominence has been recognised lore for millennia. suggest it as valuable teacher exemplar prosperous survival old, climatically-buffered, infertile landscapes end, should be widely celebrated.

Язык: Английский

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Recently Naturalized Paraserianthes lophantha subsp. lophantha Displays Contrasting Genetic Diversity and Climate Relationships Compared to Native Populations

Diversity, Год журнала: 2020, Номер 12(11), С. 422 - 422

Опубликована: Ноя. 10, 2020

Paraseriantheslophantha subsp. lophantha (Leguminosae) is native to southwestern Australia, but has become naturalized in eastern Australia and countries around the world. Previous studies have investigated introduction sources for P. overseas, here, we expand on knowledge of genetic patterns its range Australia. Genetic were examined using nine nuclear microsatellite loci three chloroplast DNA markers. The populations exhibited phylogeographic patterns, including north-south differentiation, a signal related temperature gradients. Naturalized Australian displayed lower overall variation no patterns. Several separated by large distances (350–650 km) shared multi-locus genotypes, supporting notion source germplasm possible inbreeding due human-mediated introductions from limited number individuals and/or within range. We advocate that management strategies are tailored distinct conservation aims underpinning or populations. Within distribution, should long-term aim replicate historical evolutionary processes, whereas populations, immediate actions may be required reduce abundance minimize invasive impact recipient vegetation.

Язык: Английский

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Range-wide genomic scans and tests for selection identify non-neutral spatial patterns of genetic variation in a non-model amphibian species (Pelobates cultripes)

Conservation Genetics, Год журнала: 2022, Номер 23(2), С. 387 - 400

Опубликована: Янв. 30, 2022

Язык: Английский

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Genome‐wide diversity analysis suggests divergence among Upper Guinea and the Dahomey Gap populations of the Sisrè berry (Syn: miracle fruit) plant ( Synsepalum dulcificum [Schumach. & Thonn.] Daniell) in West Africa

The Plant Genome, Год журнала: 2023, Номер 16(1)

Опубликована: Янв. 20, 2023

Although Synsepalum dulcificum is viewed as one of the most economically promising orphan tree crops worldwide, its genetic improvement and sustainable conservation are hindered by a lack understanding evolutionary history current population structure. Here, we report for first time application genome-wide single nucleotide polymorphism genotyping to diverse panel S. accessions depict diversity structure species in Dahomey Gap (DG) Upper Guinea (UG) regions infer history. Our findings suggest low overall but strong divergence within species. Neighbor-joining analysis detected two groups UG DG regions, while STRUCTURE distinguished three groups, corresponding UG, Western DG, Central regions. Application Monmonier's algorithm revealed existence barrier disrupting connectivity between groups. The group consistently exhibited highest levels haplotype diversities, that lowest. Analyses Tajima's D, Fu's Fs, Achaz Y* statistics both likely experienced recent expansions, at equilibrium. These geographical structuring variation which supports conclusion differential histories among West African dulcificum. results provide foundational insights guide informed breeding development design strategies this

Язык: Английский

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