ORBi: Detailled Reference

Article (Scientific journals)

Phylogenetic diversity of two geographically overlapping lichens: isolation by distance, environment, or fragmentation?

Moncada, Bibiana; Mercado-Diaz, Joel A.; Magain, Nicolas et al.

2021 • In Journal of Biogeography

Peer Reviewed verified by ORBi

Permalink
https://hdl.handle.net/2268/256337

DOI
10.1111/jbi.14033

Files (1)Send to Details Statistics Bibliography Similar publications

Files

Full Text

jbi.14033.pdf

Publisher postprint (3.35 MB)

All documents in ORBi are protected by a user license.

Send to

RIS BibTex APA Chicago Permalink X Linkedin

Details

Keywords :

Brazil; drift; Galapagos; Mexico; Puerto Rico

Abstract :

[en] Aim Phylogenetic diversification is a precursor to speciation, but the underlying patterns and processes are not well‐studied in lichens. Here we investigate what factors drive diversification in two tropical, morphologically similar macrolichens that occupy a similar range but differ in altitudinal and habitat preferences, testing for isolation by distance (IBD), environment (IBE), and fragmentation (IBF). Location Neotropics, Hawaii, Macaronesia. Taxon Sticta andina, S. scabrosa (Peltigeraceae). Methods We analysed 395 specimens from 135 localities, using the fungal ITS barcoding marker to assess phylogenetic diversification, through maximum likelihood tree reconstruction, TCS haplotype networks, and Tajima's D. Mantel tests were employed to detect structure in genetic vs. geographic, environmental, and fragmentation distances. Habitat preferences were quantitatively assessed by statistical analysis of locality‐based BIOclim variables. Results Sticta andina exhibited high phenotypic variation and reticulate phylogenetic diversity across its range, whereas the phenotypically uniform S. scabrosa contained two main haplotypes, one unique to Hawaii. Sticta andina is restricted to well‐preserved andine forests and paramos, naturally fragmented habitats due to disruptive topology, whereas S. scabrosa thrives in lowland to lower montane zones in exposed or disturbed microsites, representing a continuous habitat. Sticta scabrosa showed IBD only across its full range (separating the Hawaiian population) but not within continental Central and South America, there exhibiting a negative Tajima's D. Sticta andina did not exhibit IBD but IBE at continental level and IBF in the northern Andes. Main conclusions Autecology, particularly preference for either low or high altitudes, indirectly drives phylogenetic diversification. Low diversification in the low altitude species, S. scabrosa, can be attributed to rapid expansion and effective gene flow across a more or less continuous niche due to disturbance tolerance. In contract, high diversification in the high altitude species, S. andina, can be explained by niche differentiation (IBE) and fragmentation (IBF) caused by the Andean uplift.

Disciplines :

Phytobiology (plant sciences, forestry, mycology...)

Author, co-author :

Moncada, Bibiana

Mercado-Diaz, Joel A.

Magain, Nicolas ; Université de Liège - ULiège > Département de Biologie, Ecologie et Evolution > Biologie de l'évolution et gestion de la biodiversité

Hodkinson, Brendan P.

Smith, Clifford W.

Bungartz, Frank

Perez-Perez, Rosa-Emilia

Gumboski, Emerson

Sérusiaux, Emmanuël ; Université de Liège - ULiège > Département de Biologie, Ecologie et Evolution > Océanographie biologique

Lumbsch, H. Thorsten

Lücking, Robert

Language :

English

Title :

Phylogenetic diversity of two geographically overlapping lichens: isolation by distance, environment, or fragmentation?

Publication date :

January 2021

Journal title :

Journal of Biogeography

ISSN :

0305-0270

eISSN :

1365-2699

Publisher :

Blackwell, Oxford, United Kingdom

Peer reviewed :

Peer Reviewed verified by ORBi

Available on ORBi :

since 02 February 2021

Statistics

Number of views

74 (9 by ULiège)

Number of downloads

113 (9 by ULiège)

More statistics

Scopus citations^®

11

Scopus citations^®
without self-citations

7

OpenCitations

6

OpenAlex citations

15

Bibliography

Allen, J. L., Mckenzie, S. K., Sleith, R. S., & Alter, S. E. (2018). First genome-wide analysis of the endangered, endemic lichen Cetradonia linearis reveals isolation by distance and strong population structure. American Journal of Botany, 105, 1556–1567.
Baldwin, B. G., Kyhos, D. W., Dvorak, J., & Carr, G. D. (1991). Chloroplast DNA evidence for a North American origin of the Hawaiian silversword alliance (Asteraceae). Proceedings of the National Academy of Sciences, 88, 1840–1843. https://doi.org/10.1073/pnas.88.5.1840
Baldwin, B. G., & Sanderson, M. J. (1998). Age and rate of diversification of the Hawaiian silversword alliance (Compositae). Proceedings of the National Academy of Sciences, 95, 9402–9406. https://doi.org/10.1073/pnas.95.16.9402
Barrier, M., Robichaux, R. H., & Purugganan, M. D. (2001). Accelerated regulatory gene evolution in an adaptive radiation. Proceedings of the National Academy of Sciences, 98, 10208–10213. https://doi.org/10.1073/pnas.181257698
Bonnet, E., & Van de Peer, Y. (2002). zt: A software tool for simple and partial Mantel tests. Journal of Statistical Software, 7(10), 1–12.
Boucher, F. C., Zimmermann, N. E., & Conti, E. (2016). Allopatric speciation with little niche divergence is common among alpine Primulaceae. Journal of Biogeography, 43, 591–602. https://doi.org/10.1111/jbi.12652
Branco, S., Gladieux, P., Ellison, C. E., Kuo, A., LaButti, K., Lipzen, A., Grigoriev, I. V., Liao, H.-L., Vilgalys, R., Peay, K. G., Taylor, J. W., & Bruns, T. D. (2015). Genetic isolation between two recently diverged populations of a symbiotic fungus. Molecular Ecology, 24, 2747–2758. https://doi.org/10.1111/mec.13132
Buschbom, J. (2007). Migration between continents: Geographical structure and long-distance gene flow in Porpidia flavicunda (lichen-forming Ascomycota). Molecular Ecology, 16, 1835–1846. https://doi.org/10.1111/j.1365-294X.2007.03258.x
Cañedo-Argüelles, M., Gutiérrez-Cánovas, C., Acosta, R., Castro-López, D., Cid, N., Fortuño, P., Munné, A., Múrria, C., Pimentão, A. R., Sarremejane, R., & Soria, M. (2020). As time goes by: 20 years of changes in the aquatic macroinvertebrate metacommunity of Mediterranean river networks. Journal of Biogeography, 47, 1861–1874.
Cannon, C. H., Morley, R. J., & Bush, A. B. (2009). The current refugial rainforests of Sundaland are unrepresentative of their biogeographic past and highly vulnerable to disturbance. Proceedings of the National Academy of Sciences, 106, 11188–11193. https://doi.org/10.1073/pnas.0809865106
Carlquist, S., Baldwin, B. G., & Carr, G. D. (Eds.) (2003). Tarweeds & Silverswords: Evolution of the Madiinae (Asteraceae). Missouri Botanical Garden Press.
Clement, M., Snell, Q., Walker, P., Posada, D., & Crandall, K. (2002). TCS: Estimating gene genealogies. IPDPS, 2, 184.
Coyne, J. A., & Orr, H. A. (2004). Speciation. Sinauer.
Crabot, J., Clappe, S., Dray, S., & Datry, T. (2019). Testing the Mantel statistic with a spatially-constrained permutation procedure. Methods in Ecology and Evolution, 10, 532–540. https://doi.org/10.1111/2041-210X.13141
Drummond, A. J., & Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214. https://doi.org/10.1186/1471-2148-7-214
Felsenstein, J. (1993). PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics. University of Washington.
Felsenstein, J. (2008). Dnadist – Program to Compute Distance Matrix from Nucleotide Sequences. http://evolution.genetics.washington.edu/phylip/doc/dnadist.htmlaccessed. Accessed December 10, 2018
Fernández-Mendoza, F., Domaschke, S., García, M. A., Jordan, P., Martín, M. P., & Printzen, C. (2011). Population structure of mycobionts and photobionts of the widespread lichen Cetraria aculeata. Molecular Ecology, 20, 1208–1232. https://doi.org/10.1111/j.1365-294X.2010.04993.x
Fick, S. E., & Hijmans, R. J. (2017). WorldClim 2: New 1-km spatial resolution climate surfaces for global land areas. International Journal of Climatology, 37, 4302–4315. https://doi.org/10.1002/joc.5086
Galloway, D. J. (1994). Studies on the lichen genus Sticta (Schreber) Ach.: I. Southern South American Species. Lichenologist, 26, 223–282.
Galloway, D. J. (1998a). Studies on the lichen genus Sticta (Schreber) Ach.: V. Australian Species. Tropical Bryology, 15, 117–160.
Galloway, D. J. (1998b). Edvard Vainio and the family Lobariaceae, with special reference to the taxonomic history of Sticta. In M. P. Marcelli, & T. Ahti (eds.). Recollecting Edvard August Vainio (pp. 61–84).: CETESB – Companhia de Tecnologia de Saneamento Ambiental.
Galloway, D. J. (2007). Flora of New Zealand Lichens. Revised Second Edition Including Lichen-Forming and Lichenicolous Fungi. Manaaki Whenua Press. Volumes 1 and 2.
Ghazoul, J., & McLeish, M. (2001) Reproductive ecology of tropical forest trees in logged and fragmented habitats in Thailand and Costa Rica. In K. E. Linsenmair, A. J. Davis, B. Fiala, & M. R. Speight (eds). Tropical Forest Canopies: Ecology and Management (pp. 335–345).: Springer.
Givnish, T. J. (2010). Ecology of plant speciation. Taxon, 59, 1326–1366. https://doi.org/10.1002/tax.595003
Givnish, T. J., Barfuss, M. H. J., Ee, B. V., Riina, R., Schulte, K., Horres, R., Gonsiska, P. A., Jabaily, R. S., Crayn, D. M., Smith, J. A. C., Winter, K., Brown, G. K., Evans, T. M., Holst, B. K., Luther, H., Till, W., Zizka, G., Berry, P. E., & Sytsma, K. J. (2014). Adaptive radiation, correlated and contingent evolution, and net species diversification in Bromeliaceae. Molecular Phylogenetics and Evolution, 71, 55–78. https://doi.org/10.1016/j.ympev.2013.10.010
Givnish, T. J., Millam, K. C., Mast, A. R., Paterson, T. B., Theim, T. J., Hipp, A. L., Henss, J. M., Smith, J. F., Wood, K. R., & Sytsma, K. J. (2009). Origin, adaptive radiation, and diversification of the Hawaiian lobeliads (Asterales: Campanulaceae). Proceedings of the Royal Society B: Biological Sciences, 276, 407–416. https://doi.org/10.1098/rspb.2008.1204
Givnish, T. J., Spalink, D., Ames, M., Lyon, S. P., Hunter, S. J., Zuluaga, A., & Endara, L. (2015). Orchid phylogenomics and multiple drivers of their extraordinary diversification. Proceedings of the Royal Society, 282, 20151553.
Guillot, G., & Rousset, F. (2013). Dismantling the Mantel tests. Methods in Ecology and Evolution, 4, 336–344. https://doi.org/10.1111/2041-210x.12018
Hagen, K. V., & Kadereit, J. W. (2003). The diversification of Halenia (Gentianaceae): Ecological opportunity versus key innovation. Evolution, 57, 2507–2518.
Hall, T. A. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95–98.
Heard, S. B., & Hauser, D. L. (1995). Key evolutionary innovations and their ecological mechanisms. Historical Biology, 10, 151–173. https://doi.org/10.1080/10292389509380518
Hijmans, R. J., Cameron, S. E., Parra, J. L., Jones, P. G., & Jarvis, A. (2005). Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology, 25, 1965–1978. https://doi.org/10.1002/joc.1276
Hoorn, C., Wesselingh, F. P., ter Steege, H., Bermudez, M. A., Mora, A., Sevink, J., Sanmartin, I., Sanchez-Meseguer, A., Anderson, C. L., Figueiredo, J. P., Jaramillo, C., Riff, D., Negri, F. R., Hooghiemstra, H., Lundberg, J., Stadler, T., Sarkinen, T., & Antonelli, A. (2010). Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity. Science, 330, 927–931. https://doi.org/10.1126/science.1194585
Hughes, C. E., & Atchison, G. W. (2015). The ubiquity of alpine plant radiations: From the Andes to the Hengduan Mountains. New Phytologist, 207, 275–282. https://doi.org/10.1111/nph.13230
Hutchison, D. W., & Templeton, A. R. (1999). Correlation of pairwise genetic and geographic distance measures: Inferring the relative influences of gene flow and drift on the distribution of genetic variability. Evolution, 53, 1898–1914. https://doi.org/10.1111/j.1558-5646.1999.tb04571.x
Katoh, K., Asimenos, G., & Toh, H. (2009). Multiple alignment of DNA sequences with MAFFT. Methods in Molecular Biology, 537, 39–64.
Katoh, K., Misawa, K., Kuma, K., & Miyata, T. (2002). MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30, 3059–3066. https://doi.org/10.1093/nar/gkf436
Kisel, Y., & Barraclough, T. G. (2010). Speciation has a spatial scale that depends on levels of gene flow. American Naturalist, 175, 316–334. https://doi.org/10.1086/650369
Kraichak, E., Lücking, R., Aptroot, A., Beck, A., Dornes, P., John, V., Lendemer, J. C., Nelsen, M. P., Neuwirth, G., Nutakki, A., Parnmen, S., Sohrabi, M., Tønsberg, T., & Lumbsch, H. T. (2015). Hidden diversity in the morphologically variable script lichen (Graphis scripta) complex (Ascomycota, Ostropales, Graphidaceae). Organisms Diversity & Evolution, 15, 447–458. https://doi.org/10.1007/s13127-015-0219-5
Küper, W., Kreft, H., Nieder, H., Köster, N., & Barthlott, W. (2004). Large-scale diversity patterns of vascular epiphytes in neotropical montane rain forests. Journal of Biogeography, 31, 1477–1487. https://doi.org/10.1111/j.1365-2699.2004.01093.x
Leigh, J. W., & Bryant, D. (2015). Popart: Full-feature software for haplotype network construction. Methods in Ecology and Evolution, 6, 1110–1116.
Liti, G., Carter, D. M., Moses, A. M., Warringer, J., Parts, L., James, S. A., Davey, R. P., Roberts, I. N., Burt, A., Koufopanou, V., Tsai, I. J., Bergman, C. M., Bensasson, D., O’Kelly, M. J. T., van Oudenaarden, A., Barton, D. B. H., Bailes, E., Nguyen, A. N., Jones, M., … Louis, E. J. (2009). Population genomics of domestic and wild yeasts. Nature, 458, 337–341. https://doi.org/10.1038/nature07743
Little, E. L., & Skolmen, R. G. (1989). Common Forest Trees of Hawaii (Native and Introduced). Agricultural Handbook No. 679. US Department of Agriculture, Forest Service, Washington.
Losos, J. B., & Ricklefs, R. E. (2009). Adaptation and diversification on islands. Nature, 457, 830–836. https://doi.org/10.1038/nature07893
Lücking, R., & Hawksworth, D. L. (2018). Formal description of sequence-based voucherless Fungi: Promises and pitfalls, and how to resolve them. IMA Fungus, 9, 143–166. https://doi.org/10.5598/imafungus.2018.09.01.09
Lücking, R., Moncada, M., & Smith, C. W. (2017). The genus Lobariella (Ascomycota: Lobariaceae) in Hawaii: Late colonization, high inferred endemism, and three new species. Lichenologist, 49, 673–691.
Madriñán, S., Cortés, A. J., & Richardson, J. E. (2013). Páramo is the world's fastest evolving and coolest biodiversity hotspot. Frontiers in Genetics, 4, 192. https://doi.org/10.3389/fgene.2013.00192
Magain, N., & Sérusiaux, E. (2015). Dismantling the treasured flagship lichen Sticta fuliginosa (Peltigerales) into four species in Western Europe. Mycological Progress, 14, 97. https://doi.org/10.1007/s11557-015-1109-0
Malhi, Y., Adu-Bredu, S., Asare, R. A., Lewis, S. L., & Mayaux, P. (2013). African rainforests: Past, present and future. Philosophical Transactions of the Royal Society B: Biological Sciences, 368, 20120312. https://doi.org/10.1098/rstb.2012.0312
Milá, B., Warren, B. H., Heeb, P., & Thébaud, C. (2010). The geographic scale of diversification on islands: Genetic and morphological divergence at a very small spatial scale in the Mascarene grey white-eye (Aves: Zosterops borbonicus). BMC Evolutionary Biology, 10, 158. https://doi.org/10.1186/1471-2148-10-158
Miller, M. A., Pfeiffer, W., & Schwartz, T. (2010). Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Proceedings of the Gateway Computing Environments Workshop (GCE): 1–8. New Orleans.
Moncada, B. (2012). El Género Sticta en Colombia, Taxonomía, Ecogeografía e Importancia. PhD Thesis,: Universidad Nacional de Colombia.
Moncada, B., Lücking, R., & Suárez, A. (2014). Molecular phylogeny of the genus Sticta (lichenized Ascomycota: Lobariaceae) in Colombia. Fungal Diversity, 64, 205–231. https://doi.org/10.1007/s13225-013-0230-0
Moncada, B., Mercado-Díaz, J. A., Smith, C. W., Bungartz, F., Sérusiaux, E., Lumbsch, H. T., & Lücking, R. (2020). Two new common, previously unrecognized species in the Sticta weigelii morphodeme (Ascomycota: Peltigeraceae). Willdenowia, (in press).
Moncada, B., Reidy, B., & Lücking, R. (2014). A phylogenetic revision of Hawaiian Pseudocyphellaria (lichenized Ascomycota: Lobariaceae) reveals eight new species and a high degree of inferred endemism. Bryologist, 117, 119–160.
Morley, R. J. (2011). Cretaceous and Tertiary climate change and the past distribution of megathermal rainforests. In M. B. Bush, & J. R. Flenley (eds.). Tropical Rainforest Responses to Climatic Change (pp. 1–34).: Springer.
Morse, S. (2011). Batch Distance Computations based on Latitude/Longitude in One Step. https://stevemorse.org/nearest/distancebatch.htmlaccessed. Accessed December 10, 2018
Purvis, O. W., & James, P. W. (1993). Studies in the lichens of the Azores. Part 1 – Caldeira do Faial [Estudo dos líquenes dos Açores. Parte 1 – Caldeira do Faial]. Arquipélago, 11A, 1–15.
Ranft, H., Moncada, B., De Lange, P. J., Lumbsch, H. T., & Lücking, R. (2018). The Sticta filix morphodeme (Ascomycota: Lobariaceae) in New Zealand, with the newly recognized species S. dendroides and S. menziesii: Indicators of forest health in a threatened island biota? Lichenologist, 50, 185–210.
Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J. C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S. E., & Sánchez-Gracia, A. (2017). DnaSP v6: DNA sequence polymorphism analysis of large datasets. Molecular Biology and Evolution, 34, 3299–3302.
Ryan, P. G., Bloomer, P., Moloney, C. L., Grant, T. J., & Delport, W. (2007). Ecological speciation in South Atlantic island finches. Science, 315, 1420–1423. https://doi.org/10.1126/science.1138829
Saeki, I., Hirao, A. S., Kenta, T., Nagamitsu, T., & Hiura, T. (2018). Landscape genetics of a threatened maple, Acer miyabei: Implications for restoring riparian forest connectivity. Biological Conservation, 220, 299–307. https://doi.org/10.1016/j.biocon.2018.01.018
Schluter, D. (2000). The Ecology of Adaptive Radiation. Oxford University Press.
Schoch, C. L., Seifert, K. A., Huhndorf, S., Robert, V., Spouge, J. L., Levesque, C. A., Chen, W., Bolchacova, E., Voigt, K., Crous, P. W., Miller, A. N., Wingfield, M. J., Aime, M. C., An, K.-D., Bai, F.-Y., Barreto, R. W., Begerow, D., Bergeron, M.-J., Blackwell, M., … … Fungal Barcoding Consortium. (2012). Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences, 109, 6241–6246. https://doi.org/10.1073/pnas.1117018109
Sexton, J. P., Hangartner, S. B., & Hoffmann, A. A. (2014). Genetic isolation by environment or distance: Which pattern of gene flow is most common? Evolution, 68, 1–15. https://doi.org/10.1111/evo.12258
Shimizu-Kimura, Y., Accad, A., & Shapcott, A. (2017). The relationship between climate change and the endangered rainforest shrub Triunia robusta (Proteaceae) endemic to southeast Queensland. Australia Sci Rep, 7, 46399.
Simon, A., Goffinet, B., Magain, N., & Sérusiaux, E. (2018). High diversity, high insular endemism and recent origin in the lichen genus Sticta (lichenized Ascomycota, Peltigerales) in Madagascar and the Mascarenes. Molecular Phylogenetics and Evolution, 122, 15–28. https://doi.org/10.1016/j.ympev.2018.01.012
Stamatakis, A. (2015). Using RAxML to Infer Phylogenies. Unit 6.14, Current Protocols in Bioinformatics. John Wiley & Sons Inc.
Stamatakis, A., Hoover, P., & Rougemont, J. (2008). A rapid bootstrap algorithm for the RAxML web servers. Systematic Biology, 57, 758–771. https://doi.org/10.1080/10635150802429642
Tripp, E. A., Lendemer, J. C., Barberán, A., Dunn, R. R., & Fierer, N. (2016). Biodiversity gradients in obligate symbiotic organisms: Exploring the diversity and traits of lichen propagules across the United States. Journal of Biogeography, 43, 1667–1678. https://doi.org/10.1111/jbi.12746
Verboom, G. A., Bergh, N. G., Haiden, S. A., Hoffmann, V., & Britton, M. N. (2015). Topography as a driver of diversification in the Cape Floristic Region of South Africa. New Phytologist, 207, 368–376.
von Humboldt, A., & Bonpland, A. (1805). Essai sur la Géographie des Plantes Accompagné d'un Tableau Physique des Régions Équinoxiales.
Walser, J. C., Holderegger, R., Gugerli, F., Hoebee, S. E., & Scheidegger, C. (2005). Microsatellites reveal regional population differentiation and isolation in Lobaria pulmonaria, an epiphytic lichen. Molecular Ecology, 14, 457–467. https://doi.org/10.1111/j.1365-294x.2004.02423.x
Wiens, J. J., & Graham, C. H. (2005). Niche conservatism: Integrating evolution, ecology, and conservation biology. Annual Review of Ecology Evolution and Systematics, 36, 519–539. https://doi.org/10.1146/annurev.ecolsys.36.102803.095431
Wright, S. (1943). Isolation by distance. Genetics, 28, 114–138.

Similar publications