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Laface VLA, Cavallini M, Di Iorio A, Lombardo G, Binelli G, Sorgonà A, Musarella CM, Spampinato G. Genetic structure of populations of Salvia ceratophylloides endemic to southern Calabria (southern Italy). Heliyon 2024; 10:e35875. [PMID: 39247277 PMCID: PMC11379574 DOI: 10.1016/j.heliyon.2024.e35875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 07/29/2024] [Accepted: 08/05/2024] [Indexed: 09/10/2024] Open
Abstract
Assessing the degree of genetic diversity and differentiation of rare or endangered endemic species is essential to evaluate the conservation status of populations and successively implement appropriate conservation strategies. We investigated the population structure of Salvia ceratophylloides Ard., a scapose hemicryptophyte endemic to Calabria (southern Italy), both to answer questions about its genetic structure and to determine whether the actual population size has undergone significant demographic changes in the near past. The data obtained from the census showed that the populations are characterised by a greater number of adult individuals than juveniles and are on declining. The genetic analysis carried out on 99 individuals from four populations of the species under study, shows a mean expected heterozygosity value of 0.50 and an overall differentiation value of 0.083. The population structure shows that the four studied populations are distinct genetic units, genetically linked to four different ancestral gene pools. Bayesian analysis based on ABC models indicates that the present populations underwent a significant reduction in size in the past. This corresponds to the demographic decline at the end of the 19th century, which according to the literature, was due to the strong anthropic pressure (agriculture, grazing, fire and plantations) of Reggio Calabria suburbs. We can therefore conclude that populations are not affected by inbreeding and low genetic diversity and that there is no immediate danger of genetic erosion, and that the problems associated with population decline, past and present, are exclusively due to anthropogenic causes.
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Affiliation(s)
| | - Marta Cavallini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Antonino Di Iorio
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Gianluca Lombardo
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Giorgio Binelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Agostino Sorgonà
- Department of AGRARIA, University "Mediterranea" of Reggio Calabria, Feo di Vito, 89124, Reggio Calabria, Italy
| | - Carmelo Maria Musarella
- Department of AGRARIA, University "Mediterranea" of Reggio Calabria, Feo di Vito, 89124, Reggio Calabria, Italy
| | - Giovanni Spampinato
- Department of AGRARIA, University "Mediterranea" of Reggio Calabria, Feo di Vito, 89124, Reggio Calabria, Italy
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Cavallini M, Lombardo G, Cantini C, Gerosa M, Binelli G. Genetic Insights into the Historical Attribution of Variety Names of Sweet Chestnut ( Castanea sativa Mill.) in Northern Italy. Genes (Basel) 2024; 15:866. [PMID: 39062645 PMCID: PMC11276188 DOI: 10.3390/genes15070866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
The sweet chestnut (Castanea sativa Mill.) is subject to the progressive disappearance of its traditional chestnut groves. In the northern part of Italy, where distribution of the sweet chestnut is fragmented, many local varieties continue to be identified mostly by oral tradition. We characterised by SSRs eleven historically recognised varieties of sweet chestnut in the area surrounding Lake Como, with the goal of giving a genetic basis to the traditional classification. We performed classical analysis about differentiation and used Bayesian approaches to detect population structure and to reconstruct demography. The results revealed that historical and genetic classifications are loosely linked when chestnut fruits are just "castagne", that is, normal fruits, but increasingly overlap where "marroni" (the most prized fruits) are concerned. Bayesian classification allowed us to identify a homogeneous gene cluster not recognised in the traditional assessment of the varieties and to reconstruct possible routes used for the propagation of sweet chestnut. We also reconstructed ancestral relationships between the different gene pools involved and dated ancestral lineages whose results fit with palynological data. We suggest that conservation strategies based on a genetic evaluation of the resource should also rely on traditional cultural heritage, which could reveal new sources of germplasm.
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Affiliation(s)
- Marta Cavallini
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, 21100 Varese, Italy; (M.C.); (G.L.)
| | - Gianluca Lombardo
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, 21100 Varese, Italy; (M.C.); (G.L.)
| | - Claudio Cantini
- Institute of Bioeconomy (IBE), Consiglio Nazionale Ricerche (CNR), 58022 Follonica, Italy;
| | - Mauro Gerosa
- Associazione Castanicoltori Lario Orientale, 23851 Sala al Barro, Italy;
| | - Giorgio Binelli
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, 21100 Varese, Italy; (M.C.); (G.L.)
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Gargiulo R, Decroocq V, González‐Martínez SC, Paz‐Vinas I, Aury J, Lesur Kupin I, Plomion C, Schmitt S, Scotti I, Heuertz M. Estimation of contemporary effective population size in plant populations: Limitations of genomic datasets. Evol Appl 2024; 17:e13691. [PMID: 38707994 PMCID: PMC11069024 DOI: 10.1111/eva.13691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 03/22/2024] [Accepted: 04/03/2024] [Indexed: 05/07/2024] Open
Abstract
Effective population size (N e) is a pivotal evolutionary parameter with crucial implications in conservation practice and policy. Genetic methods to estimate N e have been preferred over demographic methods because they rely on genetic data rather than time-consuming ecological monitoring. Methods based on linkage disequilibrium (LD), in particular, have become popular in conservation as they require a single sampling and provide estimates that refer to recent generations. A software program based on the LD method, GONE, looks particularly promising to estimate contemporary and recent-historical N e (up to 200 generations in the past). Genomic datasets from non-model species, especially plants, may present some constraints to the use of GONE, as linkage maps and reference genomes are seldom available, and SNP genotyping is usually based on reduced-representation methods. In this study, we use empirical datasets from four plant species to explore the limitations of plant genomic datasets when estimating N e using the algorithm implemented in GONE, in addition to exploring some typical biological limitations that may affect N e estimation using the LD method, such as the occurrence of population structure. We show how accuracy and precision of N e estimates potentially change with the following factors: occurrence of missing data, limited number of SNPs/individuals sampled, and lack of information about the location of SNPs on chromosomes, with the latter producing a significant bias, previously unexplored with empirical data. We finally compare the N e estimates obtained with GONE for the last generations with the contemporary N e estimates obtained with the programs currentNe and NeEstimator.
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Affiliation(s)
| | | | | | - Ivan Paz‐Vinas
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- CNRS, ENTPE, UMR5023 LEHNAUniversité Claude Bernard Lyon 1VilleurbanneFrance
| | - Jean‐Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris‐SaclayEvryFrance
| | | | | | - Sylvain Schmitt
- AMAPUniv. Montpellier, CIRAD, CNRS, INRAE, IRDMontpellierFrance
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Assessment of the Diversity, Distinctiveness and Conservation of Australia’s Central Queensland Coastal Rainforests Using DNA Barcoding. DIVERSITY 2023. [DOI: 10.3390/d15030378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Globally threatened dry rainforests are poorly studied and conserved when compared to mesic rainforests. Investigations of dry rainforest communities within Australia are no exception. We assessed the community diversity, distinctiveness and level of conservation in Central Queensland coastal dry rainforest communities. Our three-marker DNA barcode-based phylogeny, based on rainforest species from the Central Queensland Coast, was combined with the phylogeny from Southeast Queensland. The phylogenetic tree and Central Queensland Coast (CQC) community species lists were used to evaluate phylogenetic diversity (PD) estimates and species composition to pinpoint regions of significant rainforest biodiversity. We evaluated the patterns and relationships between rainforest communities of the biogeographical areas of Central Queensland Coast and Southeast Queensland, and within and between Subregions. Subsequently, we identified areas of the highest distinctiveness and diversity in phylogenetically even rainforest communities, consistent with refugia, and areas significantly more related than random, consistent with expansion into disturbed or harsher areas. We found clear patterns of phylogenetic clustering that suggest that selection pressures for moisture and geology were strong drivers of rainforest distribution and species diversity. These results showed that smaller dry rainforests in Central Queensland Coast (CQC) represented areas of regional plant migration but were inadequately protected. To sustain species diversity and distribution under intense selection pressures of moisture availability and substrate type throughout this dry and geologically complex region, the future conservation of smaller patches is essential.
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Genetic Variability and Admixture Zones in the Italian Populations of Turkey Oak ( Quercus cerris L.). LIFE (BASEL, SWITZERLAND) 2022; 13:life13010018. [PMID: 36675965 PMCID: PMC9863001 DOI: 10.3390/life13010018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/02/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
The Turkey oak (Quercus cerris L.) is widely distributed in Italy, where it is the ecologically dominant oak on sandy and acidic soil. In this work, we analysed 23 natural populations by means of eight SSR (microsatellite) markers, to obtain the first synthetic map of genetic variability for this species and to study its dispersion during the Holocene, due to the possibility that at least one refugium during the Last Glacial Maximum was in Italy. The analyses showed a good amount of genetic variability together with fair differentiation between populations, as indicated by FST = 0.059. A Bayesian analysis of the amount of admixture among populations revealed the presence of four putative gene pools of origin and a rough subdivision of the populations according to their geographic location, as confirmed by the spatial analysis. No evidence for the existence of putative refugial populations was found; however, this study paves the way for the planning of conservation strategies also with regard to the relationship between Turkey oak and other oak species in Italy.
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Assessing the Genetic Identity of Tuscan Sweet Chestnut (Castanea sativa Mill.). FORESTS 2022. [DOI: 10.3390/f13070967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The sweet chestnut (Castanea sativa Mill.) is an important species of European trees, studied for both ecological and economic reasons. Its cultivation in the Italian peninsula can be linked to the Roman period and has been documented, especially in the Tuscan region, for centuries. We sampled 131 grafted trees from three separate areas to determine the genetic variability between populations and assess genetic identity for different varieties of trees, which is useful for future breeding programs and propagation efforts. Molecular analyses were performed using eight microsatellite loci. A total of 98 alleles was detected with an average of 12.3 alleles per locus. We found high levels of genetic diversity within the varieties of the same area, ranging between He = 0.682–0.745. Of the eight loci, seven were found to be at Hardy-Weinberg equilibrium. (FST values Differentiation between cultivation areas was significant between 0.052–0.147) with the two Southern Tuscan areas showing the closest relationship as also indicated by Bayesian inference of the population structure, which revealed the existence of three ancestral gene pools of origin. Demographic events were detected by a coalescent-based approximate Bayesian computation in two of the homogeneous clusters. This work is a step forward for the conservation of this iconic species, albeit at a regional level, as chestnut varieties have never received the full attention of breeders.
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López-Barrera G, Ochoa-Zavala M, Quesada M, Harvey N, Núñez-Farfán J, González-Rodríguez A, Rocha-Ramírez V, Oyama K. Genetic imprints of Brosimum alicastrum Sw. in Mexico. AMERICAN JOURNAL OF BOTANY 2021; 108:1793-1807. [PMID: 34519027 DOI: 10.1002/ajb2.1725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/10/2021] [Accepted: 04/14/2021] [Indexed: 06/13/2023]
Abstract
PREMISE The mechanisms generating the geographical distributions of genetic diversity are a central theme in evolutionary biology. The amount of genetic diversity and its distribution are controlled by several factors, including dispersal abilities, physical barriers, and environmental and climatic changes. We investigated the patterns of genetic diversity and differentiation among populations of the widespread species Brosimum alicastrum in Mexico. METHODS Using nuclear DNA microsatellite data, we tested whether the genetic structure of B. alicastrum was associated with the roles of the Trans-Mexican Volcanic Belt and the Isthmus of Tehuantepec as geographical barriers to gene flow and to infer the role of past events in the genetic diversity patterns. We further used a maximum-likelihood population-effects mixed model (MLPE) to identify the main factor affecting population differentiation in B. alicastrum. RESULTS Our results suggested that Mexican B. alicastrum is well differentiated into three main lineages. Patterns of the genetic structure at a finer scale did not fully correspond to the current geographical barriers to gene flow. According to the MLPE mixed model, isolation by distance is the best model for explaining the genetic differentiation of B. alicastrum in Mexico. CONCLUSIONS We propose that the differentiation patterns might reflect (1) an ancient differentiation that occurred in Central and South America, (2) the effects of past climatic changes, and (3) the functions of some physical barriers to gene flow. This study provides insights into the possible mechanisms underlying the geographic genetic variation of B. alicastrum along a moisture gradient in tropical lowland forests.
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Affiliation(s)
- Gabriela López-Barrera
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro no. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, Michoacán 58190, México
| | - Maried Ochoa-Zavala
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro no. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, Michoacán 58190, México
| | - Mauricio Quesada
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro no. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, Michoacán 58190, México
- Laboratorio Nacional de Análisis y Síntesis Ecológica (LANASE), UNAM, Antigua Carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, Michoacán 58190, México
| | - Nick Harvey
- Genetic Marker Services, 7 Windlesham Road, Brighton BN1 3AG, England
| | - Juan Núñez-Farfán
- Laboratorio de Genética Ecológica y Evolución, Instituto de Ecología, UNAM, Av. Universidad 3000, Coyoacán, Cd. de México 04510, Mexico
| | - Antonio González-Rodríguez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, UNAM, Antigua Carretera a Pátzcuaro no. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, Michoacán 58190, México
| | - Víctor Rocha-Ramírez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, UNAM, Antigua Carretera a Pátzcuaro no. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, Michoacán 58190, México
| | - Ken Oyama
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro no. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, Michoacán 58190, México
- Laboratorio Nacional de Análisis y Síntesis Ecológica (LANASE), UNAM, Antigua Carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, Michoacán 58190, México
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Scotti‐Saintagne C, Boivin T, Suez M, Musch B, Scotti I, Fady B. Signature of mid-Pleistocene lineages in the European silver fir ( Abies alba Mill.) at its geographic distribution margin. Ecol Evol 2021; 11:10984-10999. [PMID: 34429896 PMCID: PMC8366861 DOI: 10.1002/ece3.7886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/11/2021] [Accepted: 06/22/2021] [Indexed: 11/25/2022] Open
Abstract
In a conservation and sustainable management perspective, we identify the ecological, climatic, and demographic factors responsible for the genetic diversity patterns of the European silver fir (Abies alba Mill.) at its southwestern range margin (Pyrenees Mountains, France, Europe). We sampled 45 populations throughout the French Pyrenees and eight neighboring reference populations in the Massif Central, Alps, and Corsica. We genotyped 1,620 individuals at three chloroplast and ten nuclear microsatellite loci. We analyzed within- and among-population genetic diversity using phylogeographic reconstructions, tests of isolation-by-distance, Bayesian population structure inference, modeling of demographic scenarios, and regression analyses of genetic variables with current and past environmental variables. Genetic diversity decreased from east to west suggesting isolation-by-distance from the Alps to the Pyrenees and from the Eastern to the Western Pyrenees. We identified two Pyrenean lineages that diverged from a third Alpine-Corsica-Massif Central lineage 0.8 to 1.1 M years ago and subsequently formed a secondary contact zone in the Central Pyrenees. Population sizes underwent contrasted changes, with a contraction in the west and an expansion in the east. Glacial climate affected the genetic composition of the populations, with the western genetic cluster only observed in locations corresponding to the coldest past climate and highest elevations. The eastern cluster was observed over a larger range of temperatures and elevations. All demographic events shaping the current spatial structure of genetic diversity took place during the Mid-Pleistocene Transition, long before the onset of the Holocene. The Western Pyrenees lineage may require additional conservation efforts, whereas the eastern lineage is well protected in in situ gene conservation units. Due to past climate oscillations and the likely emergence of independent refugia, east-west oriented mountain ranges may be important reservoir of genetic diversity in a context of past and ongoing climate change in Europe.
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Affiliation(s)
| | - Thomas Boivin
- INRAEEcologie des Forêts Méditerranéennes (URFM)AvignonFrance
| | - Marie Suez
- INRAEEcologie des Forêts Méditerranéennes (URFM)AvignonFrance
| | | | - Ivan Scotti
- INRAEEcologie des Forêts Méditerranéennes (URFM)AvignonFrance
| | - Bruno Fady
- INRAEEcologie des Forêts Méditerranéennes (URFM)AvignonFrance
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Binelli G, Montaigne W, Sabatier D, Scotti‐Saintagne C, Scotti I. Discrepancies between genetic and ecological divergence patterns suggest a complex biogeographic history in a Neotropical genus. Ecol Evol 2020; 10:4726-4738. [PMID: 32551056 PMCID: PMC7297752 DOI: 10.1002/ece3.6227] [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: 02/26/2020] [Accepted: 03/04/2020] [Indexed: 11/19/2022] Open
Abstract
Phylogenetic patterns and the underlying speciation processes can be deduced from morphological, functional, and ecological patterns of species similarity and divergence. In some cases, though, species retain multiple similarities and remain almost indistinguishable; in other cases, evolutionary convergence can make such patterns misleading; very often in such cases, the "true" picture only emerges from carefully built molecular phylogenies, which may come with major surprises. In addition, closely related species may experience gene flow after divergence, thus potentially blurring species delimitation. By means of advanced inferential methods, we studied molecular divergence between species of the Virola genus (Myristicaceae): widespread Virola michelii and recently described, endemic V. kwatae, using widespread V. surinamensis as a more distantly related outgroup with different ecology and morphology-although with overlapping range. Contrary to expectations, we found that the latter, and not V. michelii, was sister to V. kwatae. Therefore, V. kwatae probably diverged from V. surinamensis through a recent morphological and ecological shift, which brought it close to distantly related V. michelii. Through the modeling of the divergence process, we inferred that gene flow between V. surinamensis and V. kwatae stopped soon after their divergence and resumed later, in a classical secondary contact event which did not erase their ecological and morphological differences. While we cannot exclude that initial divergence occurred in allopatry, current species distribution and the absence of geographical barriers make complete isolation during speciation unlikely. We tentatively conclude that (a) it is possible that divergence occurred in allopatry/parapatry and (b) secondary contact did not suppress divergence.
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Affiliation(s)
| | - William Montaigne
- UMR EcoFoGUniversité des Antilles et de la GuyaneKourouFrench Guiana
| | - Daniel Sabatier
- AMAPIRDCIRADCNRSINRAEUniversité de MontpellierMontpellierFrance
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Bourguiba H, Scotti I, Sauvage C, Zhebentyayeva T, Ledbetter C, Krška B, Remay A, D’Onofrio C, Iketani H, Christen D, Krichen L, Trifi-Farah N, Liu W, Roch G, Audergon JM. Genetic Structure of a Worldwide Germplasm Collection of Prunus armeniaca L. Reveals Three Major Diffusion Routes for Varieties Coming From the Species' Center of Origin. FRONTIERS IN PLANT SCIENCE 2020; 11:638. [PMID: 32523597 PMCID: PMC7261834 DOI: 10.3389/fpls.2020.00638] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/24/2020] [Indexed: 05/22/2023]
Abstract
The characterization of the largest worldwide representative data set of apricot (Prunus armeniaca L.) germplasm was performed using molecular markers. Genetic diversity and structure of the cultivated apricot genetic resources were analyzed to decipher the history of diffusion of this species around the world. A common set of 25 microsatellite markers was used for genotyping a total of 890 apricot accessions in different collections from the center of origin to the more recent regions of apricot culture. Using a Bayesian model-based clustering approach, the apricot genotypes can be structured into five different genetic clusters (FST = 0.174), correlated with the geographical regions of origin of the accessions. Accessions from China and Central Asia were clustered together and exhibited the highest levels of diversity, confirming an origin in this region. A loss of genetic diversity was observed from the center of origin to both western and eastern zones of recent apricot culture. Altogether, our results revealed that apricot spread from China and Central Asia, defined as the center of origin, following three major diffusion routes with a decreasing gradient of genetic variation in each geographical group. The identification of specific alleles outside the center of origin confirmed the existence of different secondary apricot diversification centers. The present work provides more understanding of the worldwide history of apricot species diffusion as well as the field of conservation of the available genetic resources. Data have been used to define an apricot core collection based on molecular marker diversity which will be useful for further identification of genomic regions associated with commercially important horticultural traits through genome-wide association studies to sustain apricot breeding programs.
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Affiliation(s)
- Hedia Bourguiba
- LR99ES12, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Ivan Scotti
- INRA Centre PACA, UR 629 URFM, Avignon, France
| | | | - Tetyana Zhebentyayeva
- Schatz Center for Tree Molecular Genetics, The Pennsylvania State University, University Park, PA, United States
| | - Craig Ledbetter
- San Joaquin Valley Agricultural Sciences Center, Crop Diseases, Pests & Genetics, Parlier, CA, United States
| | - Boris Krška
- Department of Fruit Growing, Faculty of Horticulture, Mendel University, Lednice, Czechia
| | | | - Claudio D’Onofrio
- Dipartimento di Scienze Agrarie, Alimentari e Agro-Ambientali, Università di Pisa, Pisa, Italy
| | - Hiroyuki Iketani
- National Agriculture and Food Research Organization (NARO) Institute of Fruit Tree Science, Tsukuba, Japan
| | - Danilo Christen
- Département Fédéral de L’économie DFE, Station de Recherche Agroscope Changins-Wädenswil ACW, Centre de Recherche Conthey, Conthey, Switzerland
| | - Lamia Krichen
- LR99ES12, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Neila Trifi-Farah
- LR99ES12, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Weisheng Liu
- Liaoning Institute of Pomology, Yingkou City, China
| | - Guillaume Roch
- INRA Centre PACA, UR 1052 GAFL, Montfavet, France
- CEP Innovation, Lyon, France
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Sheu Y, Zurano JP, Ribeiro‐Junior MA, Ávila‐Pires TC, Rodrigues MT, Colli GR, Werneck FP. The combined role of dispersal and niche evolution in the diversification of Neotropical lizards. Ecol Evol 2020; 10:2608-2625. [PMID: 32185006 PMCID: PMC7069304 DOI: 10.1002/ece3.6091] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 01/23/2023] Open
Abstract
Ecological requirements and environmental conditions can influence diversification across temporal and spatial scales. Understanding the role of ecological niche evolution under phylogenetic contexts provides insights on speciation mechanisms and possible responses to future climatic change. Large-scale phyloclimatic studies on the megadiverse Neotropics, where biomes with contrasting vegetation types occur in narrow contact, are rare. We integrate ecological and biogeographic data with phylogenetic comparative methods, to investigate the relative roles of biogeographic events and niche divergence and conservatism on the diversification of the lizard genus Kentropyx Spix, 1825 (Squamata: Teiidae), distributed in South American rainforests and savannas. Using five molecular markers, we estimated a dated species tree, which recovered three clades coincident with previously proposed species groups diverging during the mid-Miocene. Biogeography reconstruction indicates a role of successive dispersal events from an ancestral range in the Brazilian Shield and western Amazonia. Ancestral reconstruction of climatic tolerances and niche overlap metrics indicates a trend of conservatism during the diversification of groups from the Amazon Basin and Guiana Shield, and a strong signal of niche divergence in the Brazilian Shield savannas. Our results suggest that climatic-driven divergence at dynamic forest-savanna borders might have resulted in adaptation to new environmental niches, promoting habitat shifts and shaping speciation patterns of Neotropical lizards. Dispersal and ecological divergence could have a more important role in Neotropical diversification than previously thought.
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Affiliation(s)
- Yumi Sheu
- Programa de Pós‐Graduação em GenéticaConservação e Biologia EvolutivaInstituto Nacional de Pesquisas do AmazôniaManausBrasil
- Programa de Pós‐Graduação em Genética e MelhoramentoUniversidade Federal do Espírito SantoEspírito SantoBrasil
| | - Juan P. Zurano
- Departamento de Sistemática e EcologiaUniversidade Federal da ParaíbaJoão PessoaBrasil
| | | | | | - Miguel T. Rodrigues
- Departamento de ZoologiaInstituto de BiociênciasUniversidade de São PauloSão PauloBrasil
| | - Guarino R. Colli
- Departamento de ZoologiaInstituto de Ciências BiológicasUniversidade de BrasíliaBrasíliaBrasil
| | - Fernanda P. Werneck
- Programa de Coleções Científicas BiológicasCoordenação de BiodiversidadeInstituto Nacional de Pesquisas da AmazôniaManausBrasil
- Department of Organismic and Evolutionary BiologyMuseum of Comparative BiologyHarvard UniversityCambridgeMAUSA
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Dick CW, Pennington RT. History and Geography of Neotropical Tree Diversity. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2019. [DOI: 10.1146/annurev-ecolsys-110617-062314] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Early botanical explorers invoked biogeographic history to explain the remarkable tree diversity of Neotropical forests. In this context, we review the history of Neotropical tree diversity over the past 100 million years, focusing on biomes with significant tree diversity. We evaluate hypotheses for rain forest origins, intercontinental disjunctions, and models of Neotropical tree diversification. To assess the impact of biotic interchange on the Amazon tree flora, we examined biogeographic histories of trees in Ecuador's Yasuní Forest, which suggest that nearly 50% of its species descend from immigrant lineages that colonized South America during the Cenozoic. Long-distance and intercontinental dispersal, combined with trait filtering and niche evolution, are important factors in the community assembly of Neotropical forests. We evaluate the role of pre-Columbian people on Neotropical tree diversity and discuss the future of Neotropical forests in the Anthropocene.
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Affiliation(s)
- Christopher W. Dick
- Department of Ecology and Evolutionary Biology and Herbarium, University of Michigan, Ann Arbor, Michigan 48109, USA
- Smithsonian Tropical Research Institute, Balboa, Ancon, Panama
| | - R. Toby Pennington
- Department of Geography, University of Exeter, Exeter EX4 4QE, United Kingdom
- Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, United Kingdom
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Odonne G, van den Bel M, Burst M, Brunaux O, Bruno M, Dambrine E, Davy D, Desprez M, Engel J, Ferry B, Freycon V, Grenand P, Jérémie S, Mestre M, Molino JF, Petronelli P, Sabatier D, Hérault B. Long-term influence of early human occupations on current forests of the Guiana Shield. Ecology 2019; 100:e02806. [PMID: 31257578 DOI: 10.1002/ecy.2806] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 05/29/2019] [Accepted: 06/13/2019] [Indexed: 11/08/2022]
Abstract
To decipher the long-term influences of pre-Columbian land occupations on contemporary forest structure, diversity, and functioning in Amazonia, most of the previous research focused on the alluvial plains of the major rivers of the Amazon basin. Terra firme, that is, nonflooded forests, particularly from the Guiana Shield, are yet to be explored. In this study, we aim to give new insights into the subtle traces of pre-Columbian influences on present-day forests given the archaeological context of terra firme forests of the Guiana Shield. Following archaeological prospects on 13 sites in French Guiana, we carried out forest inventories inside and outside archaeological sites and assessed the potential pre-Columbian use of the sampled tree species using an original ethnobotanical database of the Guiana Shield region. Aboveground biomass (320 and 380 T/ha, respectively), basal area (25-30 and 30-35 m2 /ha, respectively), and tree density (550 and 700 stem/ha, respectively) were all significantly lower on anthropized plots (As) than on nonanthropized plots (NAs). Ancient human presence shaped the species composition of the sampled forests with Arecaceae, Burseraceae, and Lauraceae significantly more frequent in As and Annonaceae and Lecythidaceae more frequent in NAs. Although alpha diversity was not different between As and NAs, the presence of pre-Columbian sites enhances significantly the forest beta diversity at the landscape level. Finally, trees with edible fruits are positively associated with pre-Columbian sites, whereas trees used for construction or for their bark are negatively associated with pre-Columbian sites. Half a millennium after their abandonment, former occupied places from the inner Guiana Shield still bear noticeable differences with nonanthropized places. Considering the lack of data concerning archaeology of terra firme Amazonian forests, our results suggest that pre-Columbian influences on the structure (lower current biomass), diversity (higher beta diversity), and composition (linked to the past human tree uses) of current Amazonian forests might be more important than previously thought.
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Affiliation(s)
- Guillaume Odonne
- LEEISA (Laboratoire Ecologie, Evolution, Interactions des Systèmes Amazoniens), CNRS, Université de Guyane, IFREMER, 97300, Cayenne, French Guiana
| | - Martijn van den Bel
- Institut National de Recherches Archéologiques Préventives, 97300, Cayenne, French Guiana
| | - Maxime Burst
- UMR 1434 Silva, Faculté des Sciences et Technologies, Université de Lorraine-AgroParisTech-INRA, 54506, Vandoeuvre-les-Nancy Cedex, France
| | - Olivier Brunaux
- ONF-Guyane, Réserve de Montabo, 97307, Cayenne, French Guiana
| | - Miléna Bruno
- LEEISA (Laboratoire Ecologie, Evolution, Interactions des Systèmes Amazoniens), CNRS, Université de Guyane, IFREMER, 97300, Cayenne, French Guiana
| | - Etienne Dambrine
- Univ. Savoie Mont Blanc, INRA, CARRTEL, 74200, Thonon-les-Bains, France
| | - Damien Davy
- LEEISA (Laboratoire Ecologie, Evolution, Interactions des Systèmes Amazoniens), CNRS, Université de Guyane, IFREMER, 97300, Cayenne, French Guiana
| | - Mathilde Desprez
- Cirad, UMR Écologie des Forêts de Guyane (AgroParisTech, CNRS, INRA, Université des Antilles, Université de Guyane), 97310, Kourou, France
| | - Julien Engel
- Department of Biological Sciences, International Center for Tropical Botany, Florida International University, Miami, Florida, 33199, USA.,AMAP, IRD, Cirad, CNRS, INRA, Université de Montpellier, 34000, Montpellier, France
| | - Bruno Ferry
- Institut National de Recherches Archéologiques Préventives, 97300, Cayenne, French Guiana
| | - Vincent Freycon
- Cirad, UR Forests and Societies, Université Montpellier, 34000, Montpellier, France
| | - Pierre Grenand
- LEEISA (Laboratoire Ecologie, Evolution, Interactions des Systèmes Amazoniens), CNRS, Université de Guyane, IFREMER, 97300, Cayenne, French Guiana
| | - Sylvie Jérémie
- Institut National de Recherches Archéologiques Préventives, 97300, Cayenne, French Guiana
| | - Mickael Mestre
- Institut National de Recherches Archéologiques Préventives, 97300, Cayenne, French Guiana
| | - Jean-François Molino
- AMAP, IRD, Cirad, CNRS, INRA, Université de Montpellier, 34000, Montpellier, France
| | - Pascal Petronelli
- Cirad, UMR Écologie des Forêts de Guyane (AgroParisTech, CNRS, INRA, Université des Antilles, Université de Guyane), 97310, Kourou, France
| | - Daniel Sabatier
- AMAP, IRD, Cirad, CNRS, INRA, Université de Montpellier, 34000, Montpellier, France
| | - Bruno Hérault
- Cirad, UR Forests and Societies, Université Montpellier, 34000, Montpellier, France.,Institut National Polytechnique Félix Houphouet-Boigny (INP-HB), Yamoussoukro, Ivory Coast
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Ferreira M, Fernandes AM, Aleixo A, Antonelli A, Olsson U, Bates JM, Cracraft J, Ribas CC. Evidence for mtDNA capture in the jacamar Galbula leucogastra/chalcothorax species-complex and insights on the evolution of white-sand ecosystems in the Amazon basin. Mol Phylogenet Evol 2018; 129:149-157. [DOI: 10.1016/j.ympev.2018.07.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 06/21/2018] [Accepted: 07/11/2018] [Indexed: 01/09/2023]
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Denis T, Hérault B, Brunaux O, Guitet S, Richard-Hansen C. Weak environmental controls on the composition and diversity of medium and large-sized vertebrate assemblages in neotropical rain forests of the Guiana Shield. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12790] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Thomas Denis
- Office National de la Chasse et de la Faune Sauvage; UMR EcoFoG (AgroParisTech, Cirad, CNRS, INRA, Université des Antilles, Université de Guyane); Kourou French Guiana France
- Université de Guyane; UMR EcoFoG; Kourou French Guiana France
| | - Bruno Hérault
- Cirad; Université de Montpellier; UR Forests & Societies; Montpellier France
- INPHB; Institut National Polytechnique Félix Houphouët-Boigny; Yamoussoukro Ivory Coast
| | - Olivier Brunaux
- Office National des Forêts; R&D, Réserve de Montabo; Cayenne French Guiana France
| | - Stéphane Guitet
- Office National des Forêts; R&D, Réserve de Montabo; Cayenne French Guiana France
- IRD; UMR AMAP (Cirad, CNRS, INRA, Université de Montpellier); Montpellier France
| | - Cécile Richard-Hansen
- Office National de la Chasse et de la Faune Sauvage; UMR EcoFoG (AgroParisTech, Cirad, CNRS, INRA, Université des Antilles, Université de Guyane); Kourou French Guiana France
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Torroba-Balmori P, Budde KB, Heer K, González-Martínez SC, Olsson S, Scotti-Saintagne C, Casalis M, Sonké B, Dick CW, Heuertz M. Altitudinal gradients, biogeographic history and microhabitat adaptation affect fine-scale spatial genetic structure in African and Neotropical populations of an ancient tropical tree species. PLoS One 2017; 12:e0182515. [PMID: 28771629 PMCID: PMC5542443 DOI: 10.1371/journal.pone.0182515] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/08/2017] [Indexed: 01/08/2023] Open
Abstract
The analysis of fine-scale spatial genetic structure (FSGS) within populations can provide insights into eco-evolutionary processes. Restricted dispersal and locally occurring genetic drift are the primary causes for FSGS at equilibrium, as described in the isolation by distance (IBD) model. Beyond IBD expectations, spatial, environmental or historical factors can affect FSGS. We examined FSGS in seven African and Neotropical populations of the late-successional rain forest tree Symphonia globulifera L. f. (Clusiaceae) to discriminate the influence of drift-dispersal vs. landscape/ecological features and historical processes on FSGS. We used spatial principal component analysis and Bayesian clustering to assess spatial genetic heterogeneity at SSRs and examined its association with plastid DNA and habitat features. African populations (from Cameroon and São Tomé) displayed a stronger FSGS than Neotropical populations at both marker types (mean Sp = 0.025 vs. Sp = 0.008 at SSRs) and had a stronger spatial genetic heterogeneity. All three African populations occurred in pronounced altitudinal gradients, possibly restricting animal-mediated seed dispersal. Cyto-nuclear disequilibria in Cameroonian populations also suggested a legacy of biogeographic history to explain these genetic patterns. Conversely, Neotropical populations exhibited a weaker FSGS, which may reflect more efficient wide-ranging seed dispersal by Neotropical bats and other dispersers. The population from French Guiana displayed an association of plastid haplotypes with two morphotypes characterized by differential habitat preferences. Our results highlight the importance of the microenvironment for eco-evolutionary processes within persistent tropical tree populations.
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Affiliation(s)
- Paloma Torroba-Balmori
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, Madrid, Spain
- Sustainable Forest Management Research Institute, University of Valladolid - INIA, Palencia, Spain
| | | | - Katrin Heer
- Institute of Experimental Ecology, University of Ulm, Ulm, Germany
- Conservation Biology and Ecology, University of Marburg, Marburg, Germany
| | - Santiago C. González-Martínez
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, Madrid, Spain
- Sustainable Forest Management Research Institute, University of Valladolid - INIA, Palencia, Spain
- UMR BIOGECO, INRA, University of Bordeaux, Cestas, France
| | - Sanna Olsson
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, Madrid, Spain
| | | | | | - Bonaventure Sonké
- Ecole Normale Supérieure, Université de Yaoundé I, Yaoundé, Cameroon
- Evolutionary Biology and Ecology, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
| | - Christopher W. Dick
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Smithsonian Tropical Research Institute, Republic of Panama
| | - Myriam Heuertz
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, Madrid, Spain
- UMR BIOGECO, INRA, University of Bordeaux, Cestas, France
- Evolutionary Biology and Ecology, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
- * E-mail:
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