bioRxiv preprint doi: https://doi.org/10.1101/2020.09.28.317602; this version posted September 29, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 2 3 4 Understanding the genetic diversity of the guayabillo (Psidium galapageium), an 5 endemic plant of the Galapagos Islands 6 7 8 9 10 11 Diego Urquia a*, Gabriela Pozo a, Bernardo Gutierrez a, b , Jennifer K. Rowntree c, Maria 12 de Lourdes Torres a, d# 13 14 15 16 17 a Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito (USFQ), 18 Diego de Robles y Via Interoceanica s/n, Quito,170157, Ecuador 19 b Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, 20 United Kingdom 21 c Ecology & Environment Research Centre, Department of Natural Sciences, 22 Manchester Metropolitan University, Oxford Road, Manchester M15 6BH, United 23 Kingdom 24 d Galapagos Science Center, Universidad San Francisco de Quito and University of 25 North Carolina at Chapel Hill, Alsacio Northia s/n, Isla San Cristobal 200150, 26 Galapagos, Ecuador 27 28 29 30 # Corresponding author: 31 Prof. Maria de Lourdes Torres 32 Universidad San Francisco de Quito, 33 Diego de Robles y Via Interoceanica s/n, Quito,170157, Ecuador 34 Email: [email protected] 35 36 37 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.09.28.317602; this version posted September 29, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 38 39 40 41 ABSTRACT 42 43 Oceanic archipelagos are known to host a variety of endemic plant species. The genetic 44 diversity and structure of these species is an important indicator of their evolutionary 45 history and can inform appropriate conservation strategies that mitigate the risks to which 46 they’re exposed, including invasive species and environmental disturbances. A 47 comprehensive consideration of the role of their natural history, as well as the landscape 48 features and the geological history of the islands themselves is required to adequately 49 understand any emerging patterns. Such is the case for the guayabillo (Psidium 50 galapageium), an understudied endemic plant from the Galapagos Islands with important 51 ecological and economic roles. In this study we designed and evaluated 13 informative 52 SSR markers and used them to investigate the genetic diversity, population structure and 53 connectivity of the guayabillo populations from San Cristobal, Isabela and Santa Cruz 54 islands. A total of 208 guayabillo individuals were analyzed, revealing a strong 55 population structure between islands and two distinct genetic lineages for the Santa Cruz 56 population. Overall, the guayabillo genetic diversity is relatively high, an unusual pattern 57 for an insular endemic species which is possibly explained by its polyploidy and the 58 geographical features of the islands. These include their broad altitudinal ranges and 59 habitat heterogeneity. For populations displaying a lower genetic diversity such as San 60 Cristobal, the history of human disturbance could be an important factor explaining these 61 observations. Some similarities between individuals in Santa Cruz and the San Cristobal 62 population could be explained by population differentiation or distinct natural histories 63 of separate lineages. Our findings highlight the complex population dynamics that shape 64 the genetic diversity of species like the guayabillo and emphasize the need to explore the 65 currently unresolved questions about this Galapagos endemic plant. 66 67 68 69 70 71 Keywords: 72 Galapagos Islands; endemic species; insular species; genetic diversity; Psidium 73 galapageium; microsatellites 74 75 76 77 78 79 80 81 82 83 84 85 86 87 2 bioRxiv preprint doi: https://doi.org/10.1101/2020.09.28.317602; this version posted September 29, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 88 89 1. Introduction 90 91 Oceanic islands are home to unique species which have emerged as a product of 92 their evolutionary histories being driven by geographical isolation and distinct topological 93 and climatic conditions. This makes them ideal study cases for evolutionary and 94 ecological processes (Carlquist, 1974; Emerson, 2002; Shaw and Gillespie, 2016). 95 Studying these species has been an important step in addressing evolutionary biology 96 questions about key processes such as adaptation, speciation, radiation, and the link 97 between evolution and geography (Geist et al., 2014; Rumeu et al., 2016; Shaw and 98 Gillespie, 2016). Among these, insular endemics are an interesting case of species that 99 comprise distinct gene pools compared to their counterparts in mainland ecosystems. The 100 genetic diversity patterns observed for insular organisms are driven by factors that include 101 founder events and genetic bottlenecks, phenomena that island species usually experience 102 at some point in their history (Mayr, 1954; Hagenblad et al., 2015; Stuessy et al., 2014). 103 The characteristics of the island inhabited by specific plant populations or species, 104 including their size, age and habitat heterogeneity, are also major factors that determine 105 their genetic diversity (MacArthur and Wilson, 1967; Stuessy et al., 2014). 106 107 The Galapagos Islands are a prime example of these oceanic archipelagos; they 108 are conformed by 13 main islands and more than 100 minor islets of volcanic origin. The 109 archipelago is located in the Pacific Ocean, ~1000 km off the coast of South America. 110 Thanks to their tropical location and oceanographic situation, the Galapagos harbor a 111 great variety of unique species, as well as rich ecosystems which remain relatively 112 undisturbed compared to other insular systems (Gillespie and Clague, 2009; Jaramillo et 113 al., 2011). Moreover, the overall young age of the archipelago and the coexistence of 114 islands of different ages provide a real-time observation window of evolutionary 115 processes (Jaramillo et al., 2011). 116 117 The endemic species of the Galapagos have been extensively studied in the 118 context of their evolution and conservation. However, most research has been focused on 119 animal species (Geist et al., 2014; Shaw and Gillespie, 2016). Few studies explore the 120 genetic diversity and population structure of endemic plant species, both being key 121 properties for understanding the evolutionary history and assessing the vulnerability and 3 bioRxiv preprint doi: https://doi.org/10.1101/2020.09.28.317602; this version posted September 29, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 122 responsiveness to environmental change of the archipelago’s endemic flora (Fridley et 123 al., 2007; Jump et al., 2009; Stuessy et al., 2014). In fact, insular endemic species are 124 valuable genetic resources for scientific development in fields such as bioprospection and 125 plant breeding (e.g. Guezennec et al., 2006; Pailles et al., 2017). Unfortunately, endemic 126 insular species are intrinsically vulnerable to threats which include environmental change, 127 disease, invasive species, human perturbation and habitat loss due to their isolation, 128 relatively small population sizes and restricted distribution (Whittaker, 1998; Sakai et al., 129 2001). Thus, it is not surprising that in 2016, 40% of all recognized endangered species 130 were found in island ecosystems (Island Conservation, 2016). The identification of 131 factors that promote or disfavor genetic diversity, and the assessment of genetic structure, 132 also assist in the establishment of conservation areas, the prioritization of populations for 133 conservation action and the adequate evaluation of such strategies (Bensted-Smith, 2002; 134 Wallis and Trewick, 2009; Moritz, 2002; Gitzendanner et al., 2012). 135 136 Multiple driving forces have been associated with the evolution and genetic 137 diversity of the endemic species in the Galapagos Islands. For instance, Scalesia affinis 138 presents a higher genetic diversity in Isabela island compared to Floreana island, partially 139 explained by the former having a much larger landmass and a broader altitudinal gradient 140 (Nielsen, 2004). Other factors pertaining to the evolutionary history of the species, 141 including speciation mechanisms (anagenesis vs. cladogenesis) and other events such as 142 past hybridization and polyploidization, should also be considered for interpreting genetic 143 diversity patterns (Soltis and Soltis, 2000; Stuessy et al., 2006; Stuessy et al., 2014). It 144 has been proposed, for example, that the Galapagos endemic shrub Galvezia leucantha 145 harbors high levels of genetic diversity in part due to populations from different islands 146 maintaining some gene flow (Guzmán et al., 2016); thus, all these populations still 147 conform a single species (as observed in anagenesis) (Stuessy et al.,