The potential of genomics for restoring ecosystems and biodiversity

Breed, Martin F.; Harrison, Peter A.; Blyth, Colette; Byrne, Margaret; Gaget, Virginie; Gellie, Nicholas J. C.; Groom, Scott V. C.; Hodgson, Riley J.; Mills, Jacob G.; Prowse, Thomas A. A.; Steane, Dorothy A.; Mohr, Jakki J.

doi:10.1038/s41576-019-0152-0

Cited by 173 publications

(216 citation statements)

References 138 publications

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“…Fortunately, more species‐specific data, especially involving molecular analyses, are being generated as restoration science progresses (e.g. Breed et al ). When molecular data are available, using population boundaries (i.e.…”

Section: Discussionmentioning

confidence: 99%

Assessment of population genetics and climatic variability can refine climate‐informed seed transfer guidelines

Massatti

Shriver

Winkler

et al. 2020

Restoration Ecology

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Restoration guidelines increasingly recognize the importance of genetic attributes in translocating native plant materials (NPMs). However, when species-specific genetic information is unavailable, seed transfer guidelines use climate-informed seed transfer zones (CSTZs) as an approximation. While CSTZs may improve how NPMs are developed and/or matched to restoration sites, they overlook genetic factors that can diminish restoration success and/or deteriorate natural patterns of genetic diversity and environmental factors that may introduce unexpected variation. Here, we analyze molecular data and geographic patterns of environmental variability across the western United States and demonstrate how they can refine CSTZs. Using genetic data available for 13 relevant plant species, we found that the probability of mixing genetically differentiated individuals (i.e. from different evolutionary lineages, or populations) was approximately 8% when considering locations separated by 50 km and reached nearly 80% by 500 km, which are distances relevant to ecoregionally constrained CSTZs. Furthermore, climate analyses revealed that geographically proximate locations are likely to maintain environmental similarity, regardless of CSTZ or ecoregion assignment. These results suggest constraining CSTZ-informed seed transfer decisions by distance may mitigate the opportunity for negative genetic outcomes. Furthermore, environmental variability and/or specificity of NPMs (depending upon the restoration strategy) should be achieved by sourcing NPMs from geographically proximate locations to avoid introducing excessive genetic differentiation. Our results highlight the utility of combining molecular genetic data with other genetic inferences (i.e. of adaptation) to determine how best to transfer seed across restoration species' ranges and develop new restoration materials.

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Section: Discussionmentioning

confidence: 99%

Assessment of population genetics and climatic variability can refine climate‐informed seed transfer guidelines

Massatti

Shriver

Winkler

et al. 2020

Restoration Ecology

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“…Genomic analyses of single species, although important, do not capture the larger patterns occurring within an interacting community of plants. Trancriptome profiling or genome sequencing of multiple species and individuals within a community will open new, integrative avenues of analyses and allow us to address existing questions that require sampling of floras and communities (Bragg et al, 2015;Fitzpatrick and Keller, 2015;Bowsher et al, 2017;Han et al, 2017;Swenson and Jones, 2017;Zambrano et al, 2017;Matthews et al, 2018;Subrahmaniam et al, 2018;Breed et al, 2019) . This is especially true for understanding responses to climate change where community level analyses are needed to capture the interacting dynamics of different species responses (Liu et al, 2018;Komatsu et al, 2019;Snell et al, 2019) .…”

Section: Introductionmentioning

confidence: 99%

Progress Towards Plant Community Transcriptomics: Pilot RNA-Seq Data from 24 Species of Vascular Plants at Harvard Forest

Marx

Jorgensen

Wisely

et al. 2020

Preprint

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Premise of the study: Large scale projects such as NEON are collecting ecological data on entire biomes to track and understand plant responses to climate change. NEON provides an opportunity for researchers to launch community transcriptomic projects that ask integrative questions in ecology and evolution. We conducted a pilot study to investigate the challenges of collecting RNA-seq data from phylogenetically diverse NEON plant communities, including species with diploid and polyploid genomes.• Methods: We used Illumina NextSeq to generate >20 Gb of RNA-seq for each of 24 vascular plant species representing 12 genera and 9 families at the Harvard Forest NEON site. Each species was sampled twice, in July and August 2016. We used Transrate, BUSCO, and GO analyses to assess transcriptome quality and content. • Results: We obtained nearly 650 Gb of RNA-seq data that assembled into more than 755,000 translated protein sequences across the 24 species. We observed only modest differences in assembly quality scores across a range of k-mer values. On average, transcriptomes contained hits to >70% of loci in the BUSCO

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“…In highly modified landscapes the genetic integrity of many species has been compromised, and local-provenancing can favour the selection of genetically depauperate and maladapted seed (Jones, 2013). Also, local-provenancing gives little consideration to the persistence of plantings under future climates, with growing evidence that genotypes from non-local sources may outperform those sourced locally (Hoffmann et al , 2015; Prober et al , 2015; Breed et al , 2019). In addition, foundation species are especially important during the restoration process because their genetic variation can shape the networks of ecological interaction influencing community assembly, stability, and evolution (Gibson et al , 2012; Lau et al , 2016).…”

Section: Introductionmentioning

confidence: 99%

Spatial, climate, and ploidy factors drive genomic diversity and resilience in the widespread grassThemeda triandra

Ahrens

James

Miller

et al. 2019

Preprint

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24•Fragmented grassland ecosystems, and the species that shape them, are under immense pressure. 25Restoration and management strategies should include genetic diversity and adaptive capacity to 26 improve success but these data are generally unavailable. Therefore, we use the foundational grass, 27Themeda triandra, to test how spatial, environmental, and ploidy factors shape patterns of genetic 28 variation. 29 30•We used reduced-representation genome sequencing on 487 samples from 52 locations to answer 31 fundamental questions about how the distribution of genomic diversity and ploidy polymorphism 32 supports adaptation to harsher climates. We explicitly quantified isolation-by-distance (IBD), 33isolation-by-environment (IBE), and predicted population genomic vulnerability in 2070. 34 35 2 •We found that a majority (54%) of the genomic variation could be attributed to IBD, while 22% of 36 the genomic variation could be explained by four climate variables showing IBE. Results indicate 37 that heterogeneous patterns of vulnerability across populations are due to genetic variation, multiple 38 climate factors, and ploidy polymorphism, which lessened genomic vulnerability in the most 39 susceptible populations. 40 41•These results indicate that restoration and management of T. triandra should incorporate knowledge 42 of genomic diversity and ploidy polymorphisms to increase the likelihood of population persistence 43 and restoration success in areas that will become hotter and more arid. 44 45

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The potential of genomics for restoring ecosystems and biodiversity

Cited by 173 publications

References 138 publications

Assessment of population genetics and climatic variability can refine climate‐informed seed transfer guidelines

Assessment of population genetics and climatic variability can refine climate‐informed seed transfer guidelines

Progress Towards Plant Community Transcriptomics: Pilot RNA-Seq Data from 24 Species of Vascular Plants at Harvard Forest

Spatial, climate, and ploidy factors drive genomic diversity and resilience in the widespread grassThemeda triandra

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