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Peñafiel Loaiza N, Chafe AH, Moraes R M, Oleas NH, Roncal J. Genotyping-by-sequencing informs conservation of Andean palms sources of non-timber forest products. Evol Appl 2024; 17:e13765. [PMID: 39091352 PMCID: PMC11291087 DOI: 10.1111/eva.13765] [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: 04/06/2023] [Revised: 06/30/2024] [Accepted: 07/18/2024] [Indexed: 08/04/2024] Open
Abstract
Conservation and sustainable management of lineages providing non-timber forest products are imperative under the current global biodiversity loss. Most non-timber forest species, however, lack genomic studies that characterize their intraspecific variation and evolutionary history, which inform species' conservation practices. Contrary to many lineages in the Andean biodiversity hotspot that exhibit high diversification, the genus Parajubaea (Arecaceae) has only three species despite the genus' origin 22 million years ago. Two of the three palm species, P. torallyi and P. sunkha, are non-timber forest species endemic to the Andes of Bolivia and are listed as IUCN endangered. The third species, P. cocoides, is a vulnerable species with unknown wild populations. We investigated the evolutionary relationships of Parajubaea species and the genetic diversity and structure of wild Bolivian populations. Sequencing of five low-copy nuclear genes (3753 bp) challenged the hypothesis that P. cocoides is a cultigen that originated from the wild Bolivian species. We further obtained up to 15,134 de novo single-nucleotide polymorphism markers by genotyping-by-sequencing of 194 wild Parajubaea individuals. Our total DNA sequencing effort rejected the taxonomic separation of the two Bolivian species. As expected for narrow endemic species, we observed low genetic diversity, but no inbreeding signal. We found three genetic clusters shaped by geographic distance, which we use to propose three management units. Different percentages of missing genotypic data did not impact the genetic structure of populations. We use the management units to recommend in situ conservation by creating new protected areas, and ex situ conservation through seed collection.
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Affiliation(s)
- Nicolás Peñafiel Loaiza
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
- Present address:
Chone y BabahoyoLojaEcuador
| | - Abigail H. Chafe
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
| | - Mónica Moraes R
- Herbario Nacional de Bolivia, Instituto de EcologíaUniversidad Mayor de San AndrésLa PazBolivia
| | - Nora H. Oleas
- Centro de Investigación de la Biodiversidad y Cambio Climático – BioCamb e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio AmbienteUniversidad IndoaméricaQuitoEcuador
| | - Julissa Roncal
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
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Fuchs EJ, Cascante-Marín A, Madrigal-Brenes R, Quesada M. Genetic diversity and phylogeographic patterns of the dioecious palm Chamaedorea tepejilote (Arecaceae) in Costa Rica: the role of mountain ranges and possible refugia. AOB PLANTS 2023; 15:plac060. [PMID: 36654989 PMCID: PMC9840212 DOI: 10.1093/aobpla/plac060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Gene flow connects populations and is necessary to sustain effective population sizes, and genetic diversity. In the Lower Central American (LCA) region, the complex topographic and climatic history have produced a wide variety of habitats resulting in high biodiversity. Phylogeographic studies of plants from this area are scarce, and to date none have been conducted on palms. We used SSR and chloroplast DNA (cpDNA) markers to study the genetic diversity and structure of populations of the understory palm Chamaedorea tepejilote in Costa Rica. We found that populations of C. tepejilote have moderate to high nuclear simple sequence repeat (SSR) genetic diversity, likely due to large population sizes and its outcrossing mating system. Habitat loss and fragmentation may have contributed to increased genetic structure within slopes. High-elevation mountain ranges appeared to be a significant barrier for gene flow among populations in the Caribbean and Pacific slopes; however, ranges are permeable through low-elevation passes. In contrast, most populations had a single distinct cpDNA haplotype, supporting the hypothesis of several isolated populations that experienced decline that likely resulted in eroded cytoplasmic genetic diversity within populations. The haplotype network and Bayesian analysis linked populations in the Caribbean and the southern Pacific coast, suggesting that gene flow between Pacific and Caribbean populations may have occurred through the southern extreme of the Talamanca Mountain range in Panama, a colonization pathway not previously suggested for LCA plants. This is one of the first phylogeographic studies conducted on tropical palms in the LCA region and the first in the genus Chamaedorea, which sheds light on possible gene flow and dispersal patterns of C. tepejilote in Costa Rica. Our results also highlight the importance of mountain ranges on shaping gene flow patterns of Neotropical plants.
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Affiliation(s)
- Eric J Fuchs
- Escuela de Biología, Universidad de Costa Rica, Ciudad Universitaria Rodrigo Facio, San Pedro Montes de Oca 11501-2060, Costa Rica
- Laboratorio Nacional de Análisis y Síntesis Ecológica, Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia, Michoacán, 58190, México
- Laboratorio Binacional de Análisis y Síntesis Ecológica, UNAM-UCR, México–Costa Rica
| | - Alfredo Cascante-Marín
- Escuela de Biología, Universidad de Costa Rica, Ciudad Universitaria Rodrigo Facio, San Pedro Montes de Oca 11501-2060, Costa Rica
- Laboratorio Binacional de Análisis y Síntesis Ecológica, UNAM-UCR, México–Costa Rica
| | - Ruth Madrigal-Brenes
- Escuela de Biología, Universidad de Costa Rica, Ciudad Universitaria Rodrigo Facio, San Pedro Montes de Oca 11501-2060, Costa Rica
- Laboratorio Nacional de Análisis y Síntesis Ecológica, Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia, Michoacán, 58190, México
- Laboratorio Binacional de Análisis y Síntesis Ecológica, UNAM-UCR, México–Costa Rica
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Genetic Diversity and Population Structure of Jubaea chilensis, an Endemic and Monotype Gender from Chile, Based on SNP Markers. PLANTS 2022; 11:plants11151959. [PMID: 35956437 PMCID: PMC9370131 DOI: 10.3390/plants11151959] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/12/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022]
Abstract
Jubaea chilensis (Molina) Baill., also named Chilean palm, is an endemic species found in the coastal area of Mediterranean sclerophyllous forest in Chile. It has a highly restricted and fragmented distribution along the coast, being under intense exploitation and anthropogenic impact. Based on 1038 SNP markers, we evaluated the genetic diversity and population structure among six J. chilensis natural groups encompassing 96% of the species distribution. We observed low levels of genetic diversity, a deficit of heterozygotes (mean HE = 0.024; HO = 0.014), and high levels of inbreeding (mean FIS = 0.424). The fixation index (FST) and Nei’s genetic distance pairwise comparisons indicated low to moderate structuring among populations. There was no evidence of isolation by distance (r = −0.214, p = 0.799). In the cluster analysis, we observed a closer relationship among Culimo, Cocalán, and Candelaria populations. Migration rates among populations were low, except for some populations with moderate values. The K value that best represented the spatial distribution of genetic diversity was ∆K = 3. Habitat fragmentation, deterioration of the sclerophyllous forest, lack of long-distance dispersers, and a natural regeneration deficit may have driven inbreeding and low levels of genetic diversity in the palm groves of J. chilensis. Although extant populations are not at imminent risk of extinction, the rate of inbreeding could increase and migration could decrease if the effects of climate change and human impact become more acute.
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Pinanga palms revisited 20 years on: what can changes in Pinanga species populations tell us about rainforest understory palm persistence? JOURNAL OF TROPICAL ECOLOGY 2022. [DOI: 10.1017/s0266467422000256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Borneo is the centre of diversity of the palm genus Pinanga. At least 13 understory species have been recorded in the Ulu Temburong National Park in Brunei, but little is known of their persistence. Changes in populations of Pinanga understory palms may be indicative of more widespread changes due to climate change, such as changes in rainfall, which may be important for the palm diversity in the protected area. However, we know little about the population dynamics of these palms, how persistent their populations are or if they behave similarly over long time frames. In 1998, populations of five co-occurring species of Pinanga at several locations in the Ulu Temburong National Park were documented. This project aimed to undertake a comprehensive resurvey of the original five Pinanga palm species populations in order to assess if they showed similar population changes across sites and species after two decades. Overall, most species maintained their population size in the surveyed region but not consistently among sites, and one species significantly declined in abundance. There was considerable variation in population growth rate (R) within and among species and sites that was significantly correlated with density and the percentage of multi-stemmed plants. There was evidence of pulsed recruitment in some species and or sites rather than steady or exponential patterns of population growth.
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Shapcott A, James H, Simmons L, Shimizu Y, Gardiner L, Rabehevitra D, Letsara R, Cable S, Dransfield J, Baker WJ, Rakotoarinivo M. Population modelling and genetics of a critically endangered Madagascan palm Tahina spectabilis. Ecol Evol 2020; 10:3120-3137. [PMID: 32211182 PMCID: PMC7083664 DOI: 10.1002/ece3.6137] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/26/2020] [Accepted: 02/07/2020] [Indexed: 11/10/2022] Open
Abstract
Madagascar is home to 208 indigenous palm species, almost all of them endemic and >80% of which are endangered. We undertook complete population census and sampling for genetic analysis of a relatively recently discovered giant fan palm, the Critically Endangered Tahina spectablis in 2008 and 2016. Our 2016 study included newly discovered populations and added to our genetic study. We incorporated these new populations into species distribution niche model (SDM) and projected these onto maps of the region. We developed population matrix models based on observed demographic data to model population change and predict the species vulnerability to extinction by undertaking population viability analysis (PVA). We investigated the potential conservation value of reintroduced planted populations within the species potential suitable habitat. We found that the population studied in 2008 had grown in size due to seedling regeneration but had declined in the number of reproductively mature plants, and we were able to estimate that the species reproduces and dies after approximately 70 years. Our models suggest that if the habitat where it resides continues to be protected the species is unlikely to go extinct due to inherent population decline and that it will likely experience significant population growth after approximately 80 years due to the reproductive and life cycle attributes of the species. The newly discovered populations contain more genetic diversity than the first discovered southern population which is genetically depauperate. The species appears to demonstrate a pattern of dispersal leading to isolated founder plants which may eventually lead to population development depending on local establishment opportunities. The conservation efforts currently put in place including the reintroduction of plants within the species potential suitable habitat if maintained are thought likely to enable the species to sustain itself but it remains vulnerable to anthropogenic impacts.
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Affiliation(s)
- Alison Shapcott
- Genecology Research Centre School of Science and Engineering University of the Sunshine Coast Maroochydore Qld Australia
| | - Heather James
- Genecology Research Centre School of Science and Engineering University of the Sunshine Coast Maroochydore Qld Australia
| | - Laura Simmons
- Genecology Research Centre School of Science and Engineering University of the Sunshine Coast Maroochydore Qld Australia
| | - Yoko Shimizu
- Genecology Research Centre School of Science and Engineering University of the Sunshine Coast Maroochydore Qld Australia
| | - Lauren Gardiner
- Cambridge University Herbarium Department of Plant Sciences University of Cambridge Cambridge UK
| | | | - Rokiman Letsara
- Parc Botanique et Zoologique deTsimbazaza Antananarivo Madagascar
| | | | | | | | - Mijoro Rakotoarinivo
- Département de Biologie et Ecologie Végétales Faculté des Sciences Université d'Antananarivo Antananarivo Madagascar
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Peñaloza-Ramírez JM, Aguilar-Amezquita B, Núñez-Farfán J, Pérez-Nasser N, Albarrán-Lara AL, Oyama K. Consequences of habitat fragmentation on genetic structure of Chamaedorea alternans (Arecaceae) palm populations in the tropical rain forests of Los Tuxtlas, Veracruz, Mexico. REV MEX BIODIVERS 2016. [DOI: 10.1016/j.rmb.2016.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Hernández-Barrios JC, Anten NPR, Martínez-Ramos M. Sustainable harvesting of non-timber forest products based on ecological and economic criteria. J Appl Ecol 2014. [DOI: 10.1111/1365-2664.12384] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Juan C. Hernández-Barrios
- Centro de Investigaciones en Ecosistemas; Campus Morelia; Universidad Nacional Autonóma de México; Antigua Carretera a Pátzcuaro 8701 58190 Morelia Michoacán México
| | - Niels P. R. Anten
- Centre for Crop System Analysis; Wageningen University; PO Box 430 6700 AK Wageningen The Netherlands
| | - Miguel Martínez-Ramos
- Centro de Investigaciones en Ecosistemas; Campus Morelia; Universidad Nacional Autonóma de México; Antigua Carretera a Pátzcuaro 8701 58190 Morelia Michoacán México
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Pauls SU, Nowak C, Bálint M, Pfenninger M. The impact of global climate change on genetic diversity within populations and species. Mol Ecol 2012; 22:925-46. [DOI: 10.1111/mec.12152] [Citation(s) in RCA: 392] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 10/22/2012] [Accepted: 10/25/2012] [Indexed: 12/16/2022]
Affiliation(s)
- Steffen U. Pauls
- Biodiversity and Climate Research Centre (BiK‐F) by Senckenberg Gesellschaft für Naturforschung and Goethe University Senckenberganlage 25 D‐60325 Frankfurt/Main Germany
| | - Carsten Nowak
- Biodiversity and Climate Research Centre (BiK‐F) by Senckenberg Gesellschaft für Naturforschung and Goethe University Senckenberganlage 25 D‐60325 Frankfurt/Main Germany
- Conservation Genetics Group Senckenberg Research Institute and Natural History Museum Frankfurt Clamecystraße 12 D‐63571 Gelnhausen Germany
| | - Miklós Bálint
- Biodiversity and Climate Research Centre (BiK‐F) by Senckenberg Gesellschaft für Naturforschung and Goethe University Senckenberganlage 25 D‐60325 Frankfurt/Main Germany
- Molecular Biology Center, Babes‐Bolyai University Str. Treboniu Laurian 42 400271 Cluj Romania
| | - Markus Pfenninger
- Biodiversity and Climate Research Centre (BiK‐F) by Senckenberg Gesellschaft für Naturforschung and Goethe University Senckenberganlage 25 D‐60325 Frankfurt/Main Germany
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Simmons CL, Auld TD, Hutton I, Baker WJ, Shapcott A. Will climate change, genetic and demographic variation or rat predation pose the greatest risk for persistence of an altitudinally distributed island endemic? BIOLOGY 2012; 1:736-65. [PMID: 24832517 PMCID: PMC4009823 DOI: 10.3390/biology1030736] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 10/29/2012] [Accepted: 11/16/2012] [Indexed: 11/24/2022]
Abstract
Species endemic to mountains on oceanic islands are subject to a number of existing threats (in particular, invasive species) along with the impacts of a rapidly changing climate. The Lord Howe Island endemic palm Hedyscepe canterburyana is restricted to two mountains above 300 m altitude. Predation by the introduced Black Rat (Rattus rattus) is known to significantly reduce seedling recruitment. We examined the variation in Hedyscepe in terms of genetic variation, morphology, reproductive output and demographic structure, across an altitudinal gradient. We used demographic data to model population persistence under climate change predictions of upward range contraction incorporating long-term climatic records for Lord Howe Island. We also accounted for alternative levels of rat predation into the model to reflect management options for control. We found that Lord Howe Island is getting warmer and drier and quantified the degree of temperature change with altitude (0.9 °C per 100 m). For H. canterburyana, differences in development rates, population structure, reproductive output and population growth rate were identified between altitudes. In contrast, genetic variation was high and did not vary with altitude. There is no evidence of an upward range contraction as was predicted and recruitment was greatest at lower altitudes. Our models predicted slow population decline in the species and that the highest altitude populations are under greatest threat of extinction. Removal of rat predation would significantly enhance future persistence of this species.
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Affiliation(s)
- Catherine Laura Simmons
- Faculty of Science Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD 4558, Australia.
| | - Tony D Auld
- Office of Environment and Heritage (NSW), P.O. Box 1967 Hurstville, NSW 2220, Australia.
| | - Ian Hutton
- Box 157, Lord Howe Island, NSW 2898, Australia.
| | | | - Alison Shapcott
- Faculty of Science Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD 4558, Australia.
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Namoff S, Veloz A, Jiménez F, Rodríguez-Peña RA, Peguero B, Lewis C, Moynihan J, Abdo M, Maunder M, Von Wettberg E, Meerow AW, Griffith MP, Francisco-Ortega J. Sweet drinks are made of this: conservation genetics of an endemic palm species from the Dominican Republic. J Hered 2011; 102:1-10. [PMID: 21172825 DOI: 10.1093/jhered/esq118] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Pseudophoenix ekmanii is a threatened palm species endemic to the Dominican Republic. Sap from trees is extracted to make a local drink; once they are tapped the individual usually dies. Plants are also illegally harvested for the nursery trade and destroyed by poachers hunting the endemic and threatened Hispaniolan parrot. We used 7 DNA microsatellite markers to assist land managers in developing conservation strategies for this palm. We sampled 4 populations along the known distribution range of this species (3 populations from the mainland and 1 from the small island of Isla Beata), for a total sample of n = 104. We found strong evidence for genetic drift, inbreeding, and moderate gene flow (i.e., all populations had at least 4 loci that were not in Hardy-Weinberg equilibrium, at least 9 loci pairs were in linkage disequilibrium, the pairwise F(ST) values ranged from 0.069 to 0.266, and had positive F(IS) values). Data supported an isolation-by-distance model, and cluster analyses based on genetic distances resolved 2 groups that match a north-south split. The population from Isla Beata had the lowest levels of genetic diversity and was the only one in which we found pairs of individuals with identical shared multilocus genotypes.
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Affiliation(s)
- Sandra Namoff
- Center for Tropical Plant Conservation, Fairchild Tropical Botanic Garden, Coral Gables, Miami, FL 33156, USA
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