Abstract
Magnolias are characteristic tree species of the Tropical Montane Cloud Forest (TMCF) in Mexico, an ecosystem that is highly threatened by habitat fragmentation and climate change. In this study, based on DNA sequences from five regions (chloroplast: trnT-trnL, trnK5-matK, trnS-trnG, rpl32-trnL, nuclear: ITS) and seven nuclear microsatellite markers, we aimed to delineate species boundaries between two-endemic species of the TMCF, Magnolia pedrazae and Magnolia schiedeana, and to estimate levels of genetic structure and diversity among populations. Phylogenetic and haplotype network analyses for the chloroplast and ITS regions did not support genetic differentiation as two distinctive species. Results from Bayesian and multivariate cluster analyses based on microsatellite loci showed high genetic differentiation across most populations, which was consistent with a strong and significant pattern of isolation by geographical distance. We found moderate to high levels of population genetic diversity, but it was lower in small populations relative to large populations. Our results suggest a contemporary decrease of genetic connectivity among populations, likely as a consequence of the current decline of suitable TMCF habitat. Managing landscape connectivity among remnant Magnolia populations within protected natural parks and surroundings, and with emphasis of small populations, would be key for the species conservation.
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References
Aguilar R, Quesada M, Ashworth L et al (2008) Genetic consequences of habitat fragmentation in plant populations: susceptible signals in plant traits and methodological approaches. Mol Ecol 17:5177–5188. https://doi.org/10.1111/j.1365-294X.2008.03971.x
Auffret AG, Rico Y, Bullock JM et al (2017) Plant functional connectivity—integrating landscape structure and effective dispersal. J Ecol. https://doi.org/10.1111/1365-2745.12742
Azuma H, García-Franco JG, Rico-Gray V, Thien LB (2001) Molecular phylogeny of the Magnoliaceae: the biogeography of tropical and temperate disjunctions. Am J Bot 88:2275–2285. https://doi.org/10.2307/3558389
Azuma H, Figlar RB, Del Tredici P et al (2011) Intraspecific sequence variation of cpDNA shows two distinct groups within Magnolia virginiana L. of Eastern North America and Cuba. Castanea 76:118–123
Budd C, Zimmer E, Freeland JR (2015) Conservation genetics of Magnolia acuminata, an endangered species in Canada: can genetic diversity be maintained in fragmented, peripheral populations? Conserv Genet. https://doi.org/10.1007/s10592-015-0746-9
Caye K, Deist TM, Martins H et al (2016) TESS3: fast inference of spatial population structure and genome scans for selection. Mol Ecol Resour 16:540–548. https://doi.org/10.1111/1755-0998.12471
Cires E, Smet Y, De Cuesta C, Goetghebeur P (2013) Gap analyses to support ex situ conservation of genetic diversity in Magnolia, a flagship group. Biodivers Conserv 22:567–590. https://doi.org/10.1007/s10531-013-0450-3
CONABIO (2010) El bosque mesófilo de montaña en México: amenazas y oportunidades para su conservación y manejo sostenible. Comisión Nacional para el Conocimiento y Uso de la Biodiversidad, México Distrito Federal, Mexico
Cruz-Durán R, Vega-Flores K, Jiménez-Ramírez J (2008) Magnolia Vazquezii (Magnoliaceae), una especie nueva del estado de Guerrero, Mexico. Novon: J Bot Nomencl 18:21–24. https://doi.org/10.3417/2005096
Cué-Bar E, Villaseñor JL, Arrendondo-Amezcua L et al (2006) La flora arbórea de Michoacán, México. Bot Sci 78:47–81
Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772. https://doi.org/10.1038/nmeth.210
Díaz-Cárdenas B, Ruiz-Sanchez E, Castro-Felix P, Castañeda-Gaytán G, Ruiz-Santana S, Gadsden H (2017) Species delimitation of the blue-spotted spiny lizard within a multilocus, multispecies coalescent framework, results in the recognition of a new Sceloporus species. Mol Phylogenetics Evol 111:185–195. https://doi.org/10.1016/j.ympev.2017.04.004
Dieringer G, Espinosa SJE (1994) Reproductive ecology of Magnolia schiedeana (Magnoliaceae) a threatened cloud forest tree species in Veracruz, Mexico. Bull Torrey Bot Club 121:154–159
DiLeo MF, Rico Y, Boehmer HJ, Wagner HH (2017) An ecological connectivity network maintains genetic diversity of a flagship wildflower, Pulsatilla vulgaris. Biol Conserv. https://doi.org/10.1016/j.biocon.2017.05.026
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15
Earl DA, vonHoldt BM (2012) Structure harvester: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361. https://doi.org/10.1007/s12686-011-9548-7
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797. https://doi.org/10.1093/nar/gkh340
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol 14:2611–2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x
Excoffier L, Lischer H (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567. https://doi.org/10.1111/j.1755-0998.2010.02847.x
Farwig N, Braun C, Böhning-Gaese K (2008) Human disturbance reduces genetic diversity of an endangered tropical tree, Prunus africana (Rosaceae). Conserv Genet 9:317–326. https://doi.org/10.1007/s10592-007-9343-x
Frankham R (2005) Genetics and extinction. Biol Conserv 126:131–140. https://doi.org/10.1016/j.biocon.2005.05.002
Fuchs EJ, Hamrick JL (2010) Spatial genetic structure within size classes of the endangered tropical tree Guaiacum sanctum (Zygophyllaceae). Am J Bot 97:1200–1207. https://doi.org/10.3732/ajb.0900377
García D, Chacoff NP (2007) Scale-dependent effects of habitat fragmentation on hawthorn pollination, frugivory, and seed predation. Conserv Biol 21:400–411. https://doi.org/10.1111/j.1523-1739.2006.00593.x
González-Espinosa M, Meave JA, Lorea-Hernández FG, Ibarra-Manriquez G, Newton AC (2011) The red list of Mexican Cloud Forest trees. Fauna andFlora International, Cambridge
Gottsberger G, Silberbauer-Gottsberger I, Seymour RS, Dötterl S (2012) Pollination ecology of ovata may explain the overall large flower size of the genus. Flora—morphology, distribution. Funct Ecol Plants 207:107–118. https://doi.org/10.1016/J.FLORA.2011.11.003
Goudet J (1995) FSTAT (Version 1.2): a computer program to calculate F-statistics. J Hered 86:485–486. https://doi.org/10.1371/journal.pone.0026694
Guindon S, Lethiec F, Duroux P, Gascuel O (2005) PHYML online—a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res 33:W557–W559. https://doi.org/10.1093/nar/gki352
Huelsenbeck JP, Ronquist F (2001) MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755. https://doi.org/10.1093/bioinformatics/17.8.754
Isagi Y, Kanazashi T, Suzuki W et al (1999) Polymorphic microsatellite DNA markers for Magnolia obovata Thunb. and their utility in related species. Mol Ecol 8:698–700
Isagi Y, Tateno R, Matsuki Y et al (2007) Genetic and reproductive consequences of forest fragmentation for populations of Magnolia obovata. Ecol Res 22:382–389. https://doi.org/10.1007/s11284-007-0360-5
Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806. https://doi.org/10.1093/bioinformatics/btm233
Jiménez-Ramírez J, Vega-Flores K, Cruz-Durán R, Vázquez-García JA (2007) Una nueva especie del bosque mesofilo de montaña del estado de Guerrero, México. Bot Sci 80:73–76
Jombart T, Devillard S, Dufour a-B, Pontier D (2008) Revealing cryptic spatial patterns in genetic variability by a new multivariate method. Heredity 101:92–103. https://doi.org/10.1038/hdy.2008.34
Kalinowski ST (2005) HP-RARE 1.0: a computer program for performing rarefaction on measures of allelic richness. Mol Ecol Notes 5:187–189. https://doi.org/10.1111/j.1471-8286.2004.00845.x
Kikuchi S, Isagi Y (2002) Microsatellite genetic variation in small and isolated populations of Magnolia sieboldii ssp. japonica. Heredity. 88:313–321. https://doi.org/10.1038/sj/hdy/6800047
Kohn C, Von Conrad K, Kramer M, Pooler M (2018) Genetic diversity of Magnolia ashei characterized by SSR markers. Conserv Genet. https://doi.org/10.1007/s10592-018-1065-8
Kumar S, Stecher G, Li M et al (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096
Leigh JW, Bryant D (2015) Popart: full-feature software for haplotype network construction. Methods Ecol Evol 6:1110–1116. https://doi.org/10.1111/2041-210X.12410
Leimu R, Mutikainen P, Koricheva J, Fischer M (2006) How general are positive relationships between plant population size, fitness and genetic variation? J Ecol 94:942–952. https://doi.org/10.1111/j.1365-2745.2006.01150.x
Liu F, Wang M, Damm U, Crous P, Cai L (2016) Species boundaries in plant pathogenic fungi: a Colletotrichum case study. BMC Evolutionary Biol 16:81. https://doi.org/10.1186/s12862-016-0649-5
Newton AC, Robertson A, Williams-Linera G, Rámirez-Marcial N, González-Espinosa M, Allnutt TR, Ennos R (2007) Genetic variation in two rare endemic mexican trees, Magnolia sharpii and Magnolia schiedeana. Silvae Genetica 57:348–356
Noreen AME, Webb EL (2013) High genetic diversity in a potentially vulnerable tropical tree species despite extreme habitat loss. PLoS One 8:e82632. https://doi.org/10.1371/journal.pone.0082632
Oksanen J, Blanchet F, Kindt R et al (2013) vegan: Community ecology package. R package version 2.0–10. R package version 1. https://doi.org/10.4135/9781412971874.n145
Peakall R, Smouse PE (2012) GenALEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28:2537–2539. https://doi.org/10.1093/bioinformatics/bts460
Postaire B, Magalon H, Bourmard CA, Bruggemann JH (2016) Molecular species delimitation methods and population genetics data reveal extensive lineage diversity and cryptic species in Aglaopheniidae (Hydrozoa). Mol Phylogenet Evol 105:36–49. https://doi.org/10.1016/j.ympev.2016.08.013
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959. https://doi.org/10.1111/j.1471-8286.2007.01758.x
R Core Team (2018) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. https://www.R-project.org
Raymond M, Rousset F (1995) GENEPOP (Version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249. https://doi.org/10.1093/oxfordjournals.jhered.a111573
Rivers M, Beech E, Murphy L, Oldfield S (2016) The red list of magnoliaceae, revised and extended. BGCI, Richmond
Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138. https://doi.org/10.1046/j.1471-8286.2003.00566.x
Rousset F (1997) Genetic Differentiation and Estimation of Gene Flow from F-Statistics Under Isolation by Distance. Genet 145:1219–1228
SEMARNAT (Secretaría de Medio Ambiente y Recursos Naturales) (2010) NOM-059-SEMARNAT-2010 de protección ambiental—especies nativas de México de flora y fauna silvestres—categorías de riesgo, especificaciones para su inclusión, exclusión o cambio-lista de especies en riesgo. Diario Oficial de la Federación. 30 de Diciembre del 2010. Segunda sección, México
Setsuko S, Ueno S, Tsumura Y, Tomaru N (2005) Development of microsatellite markers in Magnolia stellata (Magnoliaceae), a threatened Japanese tree. Conserv Genet 6:317–320. https://doi.org/10.1007/s10592-004-7826-6
Setsuko S, Nagamitsu T, Tomaru N (2013) Pollen flow and effects of population structure on selfing rates and female and male reproductive success in fragmented Magnolia stellata populations. BMC Ecol 13:10
Shaw J, Lickey EB, Beck JT et al (2005) The tortoiseand the hare II: relative utility of 21noncoding chloroplast DNA sequences forphylogenetic analysis. Am J Bot 92:142–166
Thioulouse J, Dray S (2007) Interactive multivariate data analysis in R with the ade4 and ade4TkGUI Packages. J Stat Softw 22:1–14. https://doi.org/10.18637/jss.v022.i05
Toledo-Aceves T, Meave JA, González-Espinosa M, Ramírez-Marcial N (2011) Tropical montane cloud forests: current threats and opportunities for their conservation and sustainable management in Mexico. J Environ Manag 92:974–981. https://doi.org/10.1016/J.JENVMAN.2010.11.007
Vaidya G, Lohman DJ, Meier R (2011) SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Cladistics 27:171–180. https://doi.org/10.1111/j.1096-0031.2010.00329.x
Van Oosterhout C, Hutchinson WF, Derek PM, Willis PM (2004) Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538. https://doi.org/10.1111/j.1471-8286.2004.00684.x
Vásquez-Morales SG, Sánchez-Velásquez LR (2011) Seed ecology and pre-germinative treatments in Magnolia schiedeana Schlecht, an endangered species from Mexico. J Food Agric Environ 9:604–608
Vásquez-Morales SG, Tellez-Valdés O, Pineda-López MR et al (2014) Effect of climate change on the distribution of Magnolia schiedeana: a threatened species. Bot Sci 92:575–585
Vásquez-Morales SG, Sánchez-Velásquez LR, Pineda-lópez R et al (2017) Moderate anthropogenic disturbance does not affect the demography of Magnolia schiedeana, an endangered species from Mexico. Flora 234:77–83. https://doi.org/10.1016/j.flora.2017.07.005
Vázquez-García JA (1994) Magnolia (Magnoliaceae) in Mexico and Central America: a synopsis. Brittonia 46:1-23. https://doi.org/10.2307/2807454
Vázquez-García JA, De Castro-Arce E, Muñiz-Castro MA, Cházaro-Basáñez M, De J (2012) Magnolia zoquepopolucae (subsection Talauma, Magnoliaceae), a new species from Sierra de Santa Marta. Veracruz Mexico Phytotaxa 57:51–55
Vázquez-García JA, Muñiz-Castro MA, Arroyo F, Pérez AI, Serna M, Cuevas-Guzmán R, Domínguez-Yescas R, de Castro-Arce E, Gurrola-Diaz CM (2013a) Novelties of the neotropical Magnolia and addendum proposal the IUCN red list of Magnoliaceae. In: Salcedo-Pérez E, Hernández-Álvarez E, Vázquez-García JA, Escoto-García T, Díaz-Echavarría N (eds) Recursos Forestales en el Occidente de Mexico, Diversidad, Manejo, Aprovechamiento y Conservación. Universidad de Guadalajara. ISBN 978-607-8072-73-6
Vázquez-García JA, Pérez-Farrera MA, Martínez-Camilo R, Muñiz-Castro MA, Martínez-Meléndez N (2013b) Magnolia lacandonica (subsection Talauma, Magnoliaceae), a new rainforest species from Chiapas, Mexico. Phytotaxa 79:30–36
Vázquez-García JA, Domínguez-Yescas R, Velazco-Macías C et al (2016) Magnolia nuevoleonensis sp. nov. (Magnoliaceae) from northeastern Mexico and a key to species of section Macrophylla. Nordic J Bot 34:48–53
White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR Protocols: a guide to methods and applications. Academic Press, New York, pp 315–322
Whitlock R, Hipperson H, Thompson DBA, Butlin RK, Burke T (2016) Consequences of in-situ strategies for the conservation of plant genetic diversity. Biol Conserv 203:134–142. https://doi.org/10.1016/j.biocon.2016.08.006
Wu FQ, Shen SK, Zhang XJ et al (2015) Genetic diversity and population structure of an extremely endangered species: the world’s largest Rhododendron. AoB Plants. https://doi.org/10.1093/aobpla/plu082
Acknowledgements
We thank Jose Antonio Vázquez García and Miguel Ángel Muñiz Castro for providing location information of M. pedrazae sites in Querétaro. We are especially grateful with Roberto Pedraza from the Grupo Ecológico Sierra Gorda for the authorization and guidance to sample in JH and YE. Likewise, to Pedro and Maximino Cruz Ponce and Rosalío Garay Galván from the community of La Trinidad and Coronel Castillo in San Luis Potosí for their authorization and guidance to sample leaves in FO, SI, and CS. We thank Sergio Zamudio, Brenda Bedolla, María Magdalena Salinas Rodríguez, and Hugo Castillo Gómez for their assistance in sampling collection, Cristina Barcenas for her assistance in the optimization of microsatellite markers and Maria Luisa Herrera Arroyo for processing a subset of DNA extractions.
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Rico, Y., Gutiérrez Becerril, B.A. Species delimitation and genetic structure of two endemic Magnolia species (section Magnolia; Magnoliaceae) in Mexico. Genetica 147, 57–68 (2019). https://doi.org/10.1007/s10709-019-00052-8
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DOI: https://doi.org/10.1007/s10709-019-00052-8