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Maia UM, Santos Júnior JED, Molina M, Galaschi-Teixeira JS, Carvalho AT, Miranda LDS, Imperatriz-Fonseca VL, Oliveira G, Giannini TC. Evidence for morphological and genetic structuring of Plebeia flavocincta (Apidae: Meliponini) populations in Northeast Brazil. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1057624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Tropical dry forests are increasingly threatened by human activities. In Northeast Brazil, the Caatinga, an area of tropical dry forests surrounded by wetlands, is considered globally unique among these habitats. In this region, the stingless bee Plebeia flavocincta is found in a variety of environmental, ecological, and demographic conditions. We aimed to characterize P. flavocincta populations within its natural range through wing geometric morphometrics and mitochondrial DNA (mtDNA) analyses. The characterization of population variability can clarify whether the species is morphologically and genetically diverse and whether populations are morphologically and genetically structured. We analyzed 673 samples by wing morphometry and 75 by cytochrome-b assays. Our results revealed P. flavocincta is genetically and morphologically diverse and populations are morphologically and genetically structured. Despite the differentiation between the two most morphologically distant populations, we verified a large overlap of morphological variation between all populations. The genetic analysis showed that the haplotypes were geographically structured into six clusters, four of which were located in coastal areas, and the remaining two in the drier inland region. The characterization of P. flavocincta populations is an important step toward decision-making in programs for the protection, management, and sustainable use of this stingless bee in local breeding efforts.
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Genetic diversity and structure of an endangered medicinal plant species (Pilocarpus microphyllus) in eastern Amazon: implications for conservation. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01454-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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3
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Hoban S, Archer FI, Bertola LD, Bragg JG, Breed MF, Bruford MW, Coleman MA, Ekblom R, Funk WC, Grueber CE, Hand BK, Jaffé R, Jensen E, Johnson JS, Kershaw F, Liggins L, MacDonald AJ, Mergeay J, Miller JM, Muller-Karger F, O'Brien D, Paz-Vinas I, Potter KM, Razgour O, Vernesi C, Hunter ME. Global genetic diversity status and trends: towards a suite of Essential Biodiversity Variables (EBVs) for genetic composition. Biol Rev Camb Philos Soc 2022; 97:1511-1538. [PMID: 35415952 PMCID: PMC9545166 DOI: 10.1111/brv.12852] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 12/14/2022]
Abstract
Biodiversity underlies ecosystem resilience, ecosystem function, sustainable economies, and human well‐being. Understanding how biodiversity sustains ecosystems under anthropogenic stressors and global environmental change will require new ways of deriving and applying biodiversity data. A major challenge is that biodiversity data and knowledge are scattered, biased, collected with numerous methods, and stored in inconsistent ways. The Group on Earth Observations Biodiversity Observation Network (GEO BON) has developed the Essential Biodiversity Variables (EBVs) as fundamental metrics to help aggregate, harmonize, and interpret biodiversity observation data from diverse sources. Mapping and analyzing EBVs can help to evaluate how aspects of biodiversity are distributed geographically and how they change over time. EBVs are also intended to serve as inputs and validation to forecast the status and trends of biodiversity, and to support policy and decision making. Here, we assess the feasibility of implementing Genetic Composition EBVs (Genetic EBVs), which are metrics of within‐species genetic variation. We review and bring together numerous areas of the field of genetics and evaluate how each contributes to global and regional genetic biodiversity monitoring with respect to theory, sampling logistics, metadata, archiving, data aggregation, modeling, and technological advances. We propose four Genetic EBVs: (i) Genetic Diversity; (ii) Genetic Differentiation; (iii) Inbreeding; and (iv) Effective Population Size (Ne). We rank Genetic EBVs according to their relevance, sensitivity to change, generalizability, scalability, feasibility and data availability. We outline the workflow for generating genetic data underlying the Genetic EBVs, and review advances and needs in archiving genetic composition data and metadata. We discuss how Genetic EBVs can be operationalized by visualizing EBVs in space and time across species and by forecasting Genetic EBVs beyond current observations using various modeling approaches. Our review then explores challenges of aggregation, standardization, and costs of operationalizing the Genetic EBVs, as well as future directions and opportunities to maximize their uptake globally in research and policy. The collection, annotation, and availability of genetic data has made major advances in the past decade, each of which contributes to the practical and standardized framework for large‐scale genetic observation reporting. Rapid advances in DNA sequencing technology present new opportunities, but also challenges for operationalizing Genetic EBVs for biodiversity monitoring regionally and globally. With these advances, genetic composition monitoring is starting to be integrated into global conservation policy, which can help support the foundation of all biodiversity and species' long‐term persistence in the face of environmental change. We conclude with a summary of concrete steps for researchers and policy makers for advancing operationalization of Genetic EBVs. The technical and analytical foundations of Genetic EBVs are well developed, and conservation practitioners should anticipate their increasing application as efforts emerge to scale up genetic biodiversity monitoring regionally and globally.
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Affiliation(s)
- Sean Hoban
- Center for Tree Science, The Morton Arboretum, 4100 Illinois Rt 53, Lisle, IL, 60532, USA
| | - Frederick I Archer
- Southwest Fisheries Science Center, NOAA/NMFS, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
| | - Laura D Bertola
- City College of New York, 160 Convent Avenue, New York, NY, 10031, USA
| | - Jason G Bragg
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Mrs Macquaries Rd, Sydney, NSW, 2000, Australia
| | - Martin F Breed
- College of Science and Engineering, Flinders University, University Drive, Bedford Park, SA, 5042, Australia
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cathays Park, Cardiff, CF10 3AX, Wales, UK
| | - Melinda A Coleman
- Department of Primary Industries, New South Wales Fisheries, National Marine Science Centre, 2 Bay Drive, Coffs Harbour, NSW, 2450, Australia
| | - Robert Ekblom
- Wildlife Analysis Unit, Swedish Environmental Protection Agency, Blekholmsterrassen 36, Stockholm, SE-106 48, Sweden
| | - W Chris Funk
- Department of Biology, Graduate Degree in Ecology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO, 80523-1878, USA
| | - Catherine E Grueber
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Carslaw Building, Sydney, NSW, 2006, Australia
| | - Brian K Hand
- Flathead Lake Biological Station, 32125 Bio Station Ln, Polson, MT, 59860, USA
| | - Rodolfo Jaffé
- Exponent, 15375 SE 30th Place, Suite 250, Bellevue, WA, 98007, USA
| | - Evelyn Jensen
- School of Natural and Environmental Sciences, Newcastle University, Agriculture Building, Newcastle Upon Tyne, NE1 7RU, UK
| | - Jeremy S Johnson
- Department of Environmental Studies, Prescott College, 220 Grove Avenue, Prescott, AZ, 86303, USA
| | - Francine Kershaw
- Natural Resources Defense Council, 40 West 20th Street, New York, NY, 10011, USA
| | - Libby Liggins
- School of Natural Sciences, Massey University, Ōtehā Rohe campus, Gate 4 Albany Highway, Auckland, Aotearoa, 0745, New Zealand
| | - Anna J MacDonald
- Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
| | - Joachim Mergeay
- Research Institute for Nature and Forest, Gaverstraat 4, 9500, Geraardsbergen, Belgium.,Aquatic Ecology, Evolution and Conservation, KULeuven, Charles Deberiotstraat 32, box 2439, 3000, Leuven, Belgium
| | - Joshua M Miller
- Department of Biological Sciences, MacEwan University, 10700 104 Avenue, Edmonton, AB, T5J 4S2, Canada
| | - Frank Muller-Karger
- College of Marine Science, University of South Florida, 140 7th Avenue South, Saint Petersburg, Florida, 33701, USA
| | - David O'Brien
- NatureScot, Great Glen House, Leachkin Road, Inverness, IV3 8NW, UK
| | - Ivan Paz-Vinas
- Laboratoire Evolution et Diversité Biologique, Université de Toulouse, CNRS, IRD, UPS, UMR-5174 EDB, 118 route de Narbonne, Toulouse, 31062, France
| | - Kevin M Potter
- Department of Forestry and Environmental Resources, North Carolina State University, 3041 Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Orly Razgour
- Biosciences, University of Exeter, Streatham Campus, Hatherly Laboratories, Prince of Wales Road, Exeter, EX4 4PS, UK
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre- Fondazione Edmund Mach, Via E. Mach, 1, San Michele all'Adige, 38010, (TN), Italy
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA
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4
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Westergaard KB, Kyrkjeeide MO, Brandrud MK. Using genomics to guide seed-sourcing at the right taxonomical level for ecological restoration projects: The complex case of Carex bigelowii s.lat. in Norway. Ecol Evol 2021; 11:17117-17131. [PMID: 34938497 PMCID: PMC8668773 DOI: 10.1002/ece3.8350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 11/23/2022] Open
Abstract
There is a growing demand for ecological restoration using suitable seeds following international standards or national legal demands for local seed-sourcing. However, before selecting the appropriate geographic origin of seeds, it is vital to explore taxonomic complexity related to the focal taxa. We used ddRAD-seq to screen genomic diversity within Carex bigelowii s.lat. focussing on Norway. This species complex is considered a candidate for seeding, but presents considerable morphological, ecological, and genetic variation. The genetic structure of 132 individuals of C. bigelowii s.lat., including Carex nigra as an outgroup, was explored using ordinations, clustering analyses, and a genetic barrier algorithm. Two highly divergent clusters were evident, supporting the recognition of two taxonomic units "C. dacica" and C. bigelowii "subsp. bigelowii". Previously defined seed-sourcing regions for C. bigelowii s.lat. did not consider the known taxonomic complexity, and therefore interpreted the overall genetic structure as seed-sourcing regions, not taxa. We estimated genetic neighborhood sizes within each taxon to be 100-150 km and 300 km, respectively, indicating species-specific delimitations of local seed-sourcing regions. Frequent hybrids, local genetic distinctiveness, and suggested ecotypes add complexity to the discussed seed-sourcing regions. Our results show how genomic screening of diversity and structure in a species complex can alleviate the taxonomic impediment, inform practical questions, and legal requirements related to seed-sourcing, and together with traditional taxonomic work provide necessary information for a sound management of biodiversity.
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Dalapicolla J, Alves R, Jaffé R, Vasconcelos S, Pires ES, Nunes GL, Pereira JBDS, Guimarães JTF, Dias MC, Fernandes TN, Scherer D, dos Santos FMG, Castilho A, Santos MP, Calderón EN, Martins RL, da Fonseca RN, Esteves FDA, Caldeira CF, Oliveira G. Conservation implications of genetic structure in the narrowest endemic quillwort from the Eastern Amazon. Ecol Evol 2021; 11:10119-10132. [PMID: 34367563 PMCID: PMC8328431 DOI: 10.1002/ece3.7812] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/01/2021] [Indexed: 02/05/2023] Open
Abstract
The quillwort Isoëtes cangae is a critically endangered species occurring in a single lake in Serra dos Carajás, Eastern Amazon. Low genetic diversity and small effective population sizes (N e) are expected for narrow endemic species (NES). Conservation biology studies centered in a single species show some limitations, but they are still useful considering the limited time and resources available for protection of species at risk of extinction. Here, we evaluated the genetic diversity, population structure, N e, and minimum viable population (MVP) of I. cangae to provide information for effective conservation programs. Our analyses were based on 55 individuals collected from the Amendoim Lake and 35,638 neutral SNPs. Our results indicated a single panmictic population, moderate levels of genetic diversity, and N e in the order of thousands, contrasting the expected for NES. Negative FIS values were also found, suggesting that I. cangae is not under risk of inbreeding depression. Our findings imply that I. cangae contains enough genetic diversity to ensure evolutionary potential and that all individuals should be treated as one demographic unit. These results provide essential information to optimize ex situ conservation efforts and genetic diversity monitoring, which are currently applied to guide I. cangae conservation plans.
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Affiliation(s)
| | | | - Rodolfo Jaffé
- Instituto Tecnológico ValeBelémBrazil
- ExponentBellevueWAUSA
| | | | | | | | | | | | - Mariana C. Dias
- Instituto Tecnológico ValeBelémBrazil
- Programa Interunidades de Pós‐Graduação em BioinformáticaUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | - Daniela Scherer
- VALE S/AGerência de Estudos AmbientaisLicenciamento e EspeleologiaNova LimaBrazil
| | | | - Alexandre Castilho
- VALE S/AGerência de Estudos AmbientaisLicenciamento e EspeleologiaNova LimaBrazil
| | - Mirella Pupo Santos
- Instituto de Biodiversidade e Sustentabilidade NUPEMUniversidade Federal do Rio de JaneiroMacaéBrazil
| | - Emiliano Nicolas Calderón
- Instituto de Biodiversidade e Sustentabilidade NUPEMUniversidade Federal do Rio de JaneiroMacaéBrazil
| | - Rodrigo Lemes Martins
- Instituto de Biodiversidade e Sustentabilidade NUPEMUniversidade Federal do Rio de JaneiroMacaéBrazil
| | - Rodrigo Nunes da Fonseca
- Instituto de Biodiversidade e Sustentabilidade NUPEMUniversidade Federal do Rio de JaneiroMacaéBrazil
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6
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do Amaral TS, Dos Santos JS, Rosa FF, Pessôa MB, Chaves LJ, Ribeiro MC, Collevatti RG. Agricultural Landscape Heterogeneity Matter: Responses of Neutral Genetic Diversity and Adaptive Traits in a Neotropical Savanna Tree. Front Genet 2021; 11:606222. [PMID: 33613620 PMCID: PMC7890196 DOI: 10.3389/fgene.2020.606222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/31/2020] [Indexed: 11/27/2022] Open
Abstract
Plants are one of the most vulnerable groups to fragmentation and habitat loss, that may affect community richness, abundance, functional traits, and genetic diversity. Here, we address the effects of landscape features on adaptive quantitative traits and evolutionary potential, and on neutral genetic diversity in populations of the Neotropical savanna tree Caryocar brasiliense. We sampled adults and juveniles in 10 savanna remnants within five landscapes. To obtain neutral genetic variation, we genotyped all individuals from each site using nine microsatellite loci. For adaptive traits we measured seed size and mass and grown seeds in nursery in completely randomized experimental design. We obtained mean, additive genetic variance (Va) and coefficient of variation (CVa%), which measures evolvability, for 17 traits in seedlings. We found that landscapes with higher compositional heterogeneity (SHDI) had lower evolutionary potential (CVa%) in leaf length (LL) and lower aboveground dry mass (ADM) genetic differentiation (QST). We also found that landscapes with higher SHDI had higher genetic diversity (He) and allelic richness (AR) in adults, and lower genetic differentiation (FST). In juveniles, SHDI was also positively related to AR. These results are most likely due to longer dispersal distance of pollen in landscapes with lower density of flowering individuals. Agricultural landscapes with low quality mosaic may be more stressful for plant species, due to the lower habitat cover (%), higher cover of monocropping (%) and other land covers, and edge effects. However, in landscapes with higher SHDI with high quality mosaic, forest nearby savanna habitat and the other environments may facilitate the movement or provide additional habitat and resources for seed disperses and pollinators, increasing gene flow and genetic diversity. Finally, despite the very recent agriculture expansion in Central Brazil, we found no time lag in response to habitat loss, because both adults and juveniles were affected by landscape changes.
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Affiliation(s)
- Tatiana Souza do Amaral
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Juliana Silveira Dos Santos
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil.,Laboratório de Ecologia Espacial e Conservação (LEEC), Departamento de Biodiversidade, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Fernanda Fraga Rosa
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Marcelo Bruno Pessôa
- Laboratório de Metacomunidades e Paisagem, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Lázaro José Chaves
- Escola de Agronomia, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Milton Cezar Ribeiro
- Laboratório de Ecologia Espacial e Conservação (LEEC), Departamento de Biodiversidade, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Rosane Garcia Collevatti
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil
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7
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Cruzan MB, Hendrickson EC. Landscape Genetics of Plants: Challenges and Opportunities. PLANT COMMUNICATIONS 2020; 1:100100. [PMID: 33367263 PMCID: PMC7748010 DOI: 10.1016/j.xplc.2020.100100] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/03/2020] [Accepted: 07/17/2020] [Indexed: 05/06/2023]
Abstract
Dispersal is one of the most important but least understood processes in plant ecology and evolutionary biology. Dispersal of seeds maintains and establishes populations, and pollen and seed dispersal are responsible for gene flow within and among populations. Traditional views of dispersal and gene flow assume models that are governed solely by geographic distance and do not account for variation in dispersal vector behavior in response to heterogenous landscapes. Landscape genetics integrates population genetics with Geographic Information Systems (GIS) to evaluate the effects of landscape features on gene flow patterns (effective dispersal). Surprisingly, relatively few landscape genetic studies have been conducted on plants. Plants present advantages because their populations are stationary, allowing more reliable estimates of the effects of landscape features on effective dispersal rates. On the other hand, plant dispersal is intrinsically complex because it depends on the habitat preferences of the plant and its pollen and seed dispersal vectors. We discuss strategies to assess the separate contributions of pollen and seed movement to effective dispersal and to delineate the effects of plant habitat quality from those of landscape features that affect vector behavior. Preliminary analyses of seed dispersal for three species indicate that isolation by landscape resistance is a better predictor of the rates and patterns of dispersal than geographic distance. Rates of effective dispersal are lower in areas of high plant habitat quality, which may be due to the effects of the shape of the dispersal kernel or to movement behaviors of biotic vectors. Landscape genetic studies in plants have the potential to provide novel insights into the process of gene flow among populations and to improve our understanding of the behavior of biotic and abiotic dispersal vectors in response to heterogeneous landscapes.
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8
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Andrino CO, Barbosa-Silva RG, Lovo J, Viana PL, Moro MF, Zappi DC. Iron islands in the Amazon: investigating plant beta diversity of canga outcrops. PHYTOKEYS 2020; 165:1-25. [PMID: 33192143 PMCID: PMC7642173 DOI: 10.3897/phytokeys.165.54819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/15/2020] [Indexed: 05/15/2023]
Abstract
The world's largest mineral iron province, Serra dos Carajás, is home to an open vegetation known as canga, found on top of isolated outcrops rising out of the Amazon rainforest. Over one thousand vascular plants species have been recorded in these canga sites, including 38 edaphic endemics. A new survey adds to our investigation of biogeographic relationships between sixteen canga outcrops and the effect of the distance between site pairs on the number of shared species, regional species turnover and species distribution patterns. Plant collecting expeditions to the westernmost site, the Serra de Campos of São Félix do Xingu (SFX), were carried out followed by the identification of all collected specimens and the creation of a species database, built to perform biogeographical analyses. Floristic relationships among the sites were investigated regarding their similarity, using multivariate analyses. The correlation between canga areas and species richness was tested, as well as the geographical distance between pairs of outcrops and their shared species. Vascular plants at SFX total 254 species including 17 edaphic endemics. All canga sites are grouped with 25% of minimum similarity, and the SFX falls within a large subgroup of outcrops. The total species number shared between site pairs does not change significantly with geographical distance but is positively correlated with the area of each outcrop. Meanwhile, shared endemic species numbers between site pairs decline when geographical distance increases, possibly imposed by the barrier of the rainforest. Our data suggest higher shared similarity between the largest and species-richest sites as opposed to geographically nearby sites, and provide useful insight for drafting conservation and compensation measures for canga locations. The size of the canga outcrops is associated to higher floristic diversity but connectivity among islands also plays a role in their similarity.
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Affiliation(s)
- Caroline Oliveira Andrino
- Instituto Tecnológico Vale, Belém, Pará, BrazilInstituto Tecnológico ValeBelémBrazil
- Museu Paraense Emílio Goeldi, Coordenação Botânica, Belém, Pará, BrazilMuseu Paraense Emílio GoeldiBelémBrazil
| | - Rafael Gomes Barbosa-Silva
- Instituto Tecnológico Vale, Belém, Pará, BrazilInstituto Tecnológico ValeBelémBrazil
- Museu Paraense Emílio Goeldi, Coordenação Botânica, Belém, Pará, BrazilMuseu Paraense Emílio GoeldiBelémBrazil
| | - Juliana Lovo
- Instituto Tecnológico Vale, Belém, Pará, BrazilInstituto Tecnológico ValeBelémBrazil
- Museu Paraense Emílio Goeldi, Coordenação Botânica, Belém, Pará, BrazilMuseu Paraense Emílio GoeldiBelémBrazil
| | - Pedro Lage Viana
- Museu Paraense Emílio Goeldi, Coordenação Botânica, Belém, Pará, BrazilMuseu Paraense Emílio GoeldiBelémBrazil
| | - Marcelo Freire Moro
- Instituto de Ciências do Mar (Labomar), Universidade Federal do Ceará, Fortaleza, Ceará, BrazilUniversidade Federal do CearáFortalezaBrazil
| | - Daniela Cristina Zappi
- Instituto Tecnológico Vale, Belém, Pará, BrazilInstituto Tecnológico ValeBelémBrazil
- Museu Paraense Emílio Goeldi, Coordenação Botânica, Belém, Pará, BrazilMuseu Paraense Emílio GoeldiBelémBrazil
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9
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Carvalho CS, Forester BR, Mitre SK, Alves R, Imperatriz-Fonseca VL, Ramos SJ, Resende-Moreira LC, Siqueira JO, Trevelin LC, Caldeira CF, Gastauer M, Jaffé R. Combining genotype, phenotype, and environmental data to delineate site-adjusted provenance strategies for ecological restoration. Mol Ecol Resour 2020; 21:44-58. [PMID: 32419278 DOI: 10.1111/1755-0998.13191] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/23/2020] [Accepted: 05/11/2020] [Indexed: 12/29/2022]
Abstract
Despite the importance of climate-adjusted provenancing to mitigate the effects of environmental change, climatic considerations alone are insufficient when restoring highly degraded sites. Here we propose a comprehensive landscape genomic approach to assist the restoration of moderately disturbed and highly degraded sites. To illustrate it we employ genomic data sets comprising thousands of single nucleotide polymorphisms from two plant species suitable for the restoration of iron-rich Amazonian Savannas. We first use a subset of neutral loci to assess genetic structure and determine the genetic neighbourhood size. We then identify genotype-phenotype-environment associations, map adaptive genetic variation, and predict adaptive genotypes for restoration sites. Whereas local provenances were found optimal to restore a moderately disturbed site, a mixture of genotypes seemed the most promising strategy to recover a highly degraded mining site. We discuss how our results can help define site-adjusted provenancing strategies, and argue that our methods can be more broadly applied to assist other restoration initiatives.
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Affiliation(s)
- Carolina S Carvalho
- Instituto Tecnológico Vale, Belém, Pará, Brazil.,Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo, São Paulo, Brazil
| | | | | | | | | | | | | | - José O Siqueira
- Instituto Tecnológico Vale, Belém, Pará, Brazil.,Departamento de Ciência do Solo, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | | | | | | | - Rodolfo Jaffé
- Instituto Tecnológico Vale, Belém, Pará, Brazil.,Departamento de Ecologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil
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10
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Silva AR, Resende-Moreira LC, Carvalho CS, Lanes ECM, Ortiz-Vera MP, Viana PL, Jaffé R. Range-wide neutral and adaptive genetic structure of an endemic herb from Amazonian Savannas. AOB PLANTS 2020; 12:plaa003. [PMID: 32128104 PMCID: PMC7043808 DOI: 10.1093/aobpla/plaa003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/28/2020] [Indexed: 05/05/2023]
Abstract
Conserving genetic diversity in rare and narrowly distributed endemic species is essential to maintain their evolutionary potential and minimize extinction risk under future environmental change. In this study we assess neutral and adaptive genetic structure and genetic diversity in Brasilianthus carajensis (Melastomataceae), an endemic herb from Amazonian Savannas. Using RAD sequencing we identified a total of 9365 SNPs in 150 individuals collected across the species' entire distribution range. Relying on assumption-free genetic clustering methods and environmental association tests we then compared neutral with adaptive genetic structure. We found three neutral and six adaptive genetic clusters, which could be considered management units (MU) and adaptive units (AU), respectively. Pairwise genetic differentiation (F ST) ranged between 0.024 and 0.048, and even though effective population sizes were below 100, no significant inbreeding was found in any inferred cluster. Nearly 10 % of all analysed sequences contained loci associated with temperature and precipitation, from which only 25 sequences contained annotated proteins, with some of them being very relevant for physiological processes in plants. Our findings provide a detailed insight into genetic diversity, neutral and adaptive genetic structure in a rare endemic herb, which can help guide conservation and management actions to avoid the loss of unique genetic variation.
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Affiliation(s)
- Amanda R Silva
- Universidade Federal Rural da Amazônia/Museu Paraense Emílio Goeldi, Programa de Pós-graduação em Ciências Biológicas - Botânica Tropical, Belém-PA, Brazil
- Museu Paraense Emílio Goeldi, Programa de Capacitação Institucional (PCI), Belém-PA, Brazil
| | | | | | - Eder C M Lanes
- Instituto Tecnológico Vale, Desenvolvimento Sustentável, Belém-PA, Brazil
| | - Mabel P Ortiz-Vera
- Instituto Tecnológico Vale, Desenvolvimento Sustentável, Belém-PA, Brazil
- Universidade Federal do Pará, Instituto de Ciências Biológicas, Programa de Pós-Graduação em Genética e Biologia Molecular, Belém-PA, Brazil
| | - Pedro L Viana
- Universidade Federal Rural da Amazônia/Museu Paraense Emílio Goeldi, Programa de Pós-graduação em Ciências Biológicas - Botânica Tropical, Belém-PA, Brazil
| | - Rodolfo Jaffé
- Instituto Tecnológico Vale, Desenvolvimento Sustentável, Belém-PA, Brazil
- Universidade de São Paulo, Departamento de Ecologia, São Paulo-SP, Brazil
- Corresponding author’s email address:
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