A Phylogenetic and Environmental Analysis of Brazilian Placosoma Lizards
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City University of New York (CUNY) CUNY Academic Works Dissertations and Theses City College of New York 2017 A Phylogenetic and Environmental Analysis of Brazilian Placosoma Lizards Kai A. Farje-Van Vlack CUNY City College How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/cc_etds_theses/707 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] 1 2 3 4 A Phylogenetic and Environmental Analysis of Brazilian Placosoma Lizards 5 6 7 8 9 10 11 12 Kai A. Farje-Van Vlack 13 14 15 16 The City College of New York, 160 Convent Ave., New York, NY, 10031 17 18 19 Masters Dissertation Committee 20 Dr. Ana Carolina Carnaval 21 Dr. Amy Berkov 22 Dr. David J. Lohman 1 23 Abstract. Placosoma is a genus comprised of the Brazilian spectacled lizards P. champsonotus , 24 P. cipoense , P. cordylinum , P. glabellum , and P. limaverdorum . While P. champsonotus , P. 25 cordylinum , and P. glabellum occupy the southern coast of Brazil, P. cipoense is found in the 26 montane grasslands north of that range, and P. limaverdorum was recently discovered in forest 27 isolates that persist within the semi-arid Caatinga. This study elucidates the ecological and 28 evolutionary relationships among these morphologically similar lizards. Using mitochondrial and 29 nuclear gene sequences, genus-wide phylogenies were inferred through Bayesian inference and a 30 species tree approach, and reconciled with geographical and climate data. I generated DNA 31 sequences for the nuclear markers DNAH3, PRLR, and SINCAIP, and the mitochondrial 32 markers ND4 and 16S for all species but P. limaverdorum (for which tissues are unavailable. 33 Results of the phylogenetic analyses were then compared to an environmental Principle 34 Component Analysis of the range of Placosoma to characterize differences in the environments 35 that each species occupies. Each sampled species of Placosoma was recovered as a monophyletic 36 clade, but discordance was observed between the species tree and non-coalescent-based Bayesian 37 trees. In the environmental PCA, P. champsonotus , P. cordylinum , and P. glabellum occupy 38 similar environmental spaces, while the geographically isolated P. cipoense and P. limaverdorum 39 are each similarly isolated in environmental space, albeit along different climatic variables. Both 40 phylogenetic and environmental analyses suggest that P. champsonotus and its sister species P. 41 glabellum may have diverged recently. 42 Keywords. Atlantic Forest, genetic structure, phylogeography, Placosoma , lizards 43 44 45 2 46 Introduction. 47 Identifying and understanding the processes that influence species distributions is of 48 paramount importance, particularly in threatened areas of the world with high rates of endemism. 49 As anthropogenic climate change progresses, endemics with restricted ranges - and the biomes 50 they occupy - may experience rates of extinction that exceed our ability to study them (Ferrier, 51 Pressey, & Barrett, 2000). Climate, in particular, is known to strongly determine species ranges 52 (Cracraft & Prum, 1988, Elith et al., 2006; Graham et al ., 2004). When tied to information about 53 phylogenetic relationships and divergence times, studies that map the distribution of narrow 54 endemics provide insight into conservation and biological discovery (Faith, 1992, Myers et al ., 55 2000). For instance, the similarity of the climatic tolerances of closely related lineages, or niche 56 conservatism, has been identified as a driver of allopatric speciation and concomitant rapid 57 diversification, explaining several of the patterns of lineage distribution in space (Kozak & 58 Weins, 2006). The assumption of pervasive niche conservatism among closely related taxa 59 across the tree of life underlie current standard analytical methods (Anderson, 2013; Peterson & 60 Nyari, 2008; Phillips & Dudík, 2008; Warren, Glor, & Turelli, 2008, and Wiens & Graham, 61 2005). 62 I verify the extent to which realized climatic niches differ across closely related species 63 of endemics in a species-rich biome while reconstructing the phylogeny of Placosoma , a genus 64 of Neotropical spectacled lizards. Of the five lizard species that comprise the genus Placosoma , 65 three are found in the montane forests of eastern Brazil (Bérnils & Costa, 2012), particularly in 66 the southern Atlantic Forest (AF) domain (Carnaval et al., 2014), and two are endemic to high 67 elevation sites further north (Fig. 1). Placosoma glabellum inhabits low to high-altitude 68 rainforests along the Atlantic Coast of Brazil from Santa Catarina to Espírito Santo, P. 3 69 champsonotus is found from Santa Catarina to Rio de Janeiro, and P. cordylinum appears 70 restricted to the high-altitude areas of Rio de Janeiro state (Uzzell, 1959 and 1962). Placosoma 71 cipoense is found in the rockier montane grasslands of the relictual Atlantic Forest fragments 72 known as the “Brejos de Altitude” in Serra do Cipó in Minas Gerais (Cunha, 1966). Finally, P. 73 limaverdorum was recently described from an isolated high-altitude forest refugium at Ceará 74 (Borges-Nojosa et al., 2016; Fig. 1). Placosoma cipoense , known for only a handful of 75 specimens, is the only species in the genus that is considered endangered (Rodrigues, 2005). 76 The Brazilian coastal forests are a species rich, yet critically threatened environment. In 77 the Atlantic Forest domain, species turnover has been closely linked to regional climatic 78 conditions, and species occupying distinct climatic spaces of the forest seem to have responded 79 differently to past environmental shifts (Carnaval et al., 2014). Multiple species are co- 80 distributed along the lowlands and northern coastal region of the forest, many exhibiting signs of 81 population contractions under the cool conditions of the Last Glacial Maximum (LGM), and 82 post-LGM expansions (Carnaval et al., 2009, 2014). In contrast, phylogeographic studies and 83 environmental analyses indicate that the Southern Atlantic Forest and the highland sites further 84 north are populated by cold-associated species, which have experienced contractions in their 85 ranges after the LGM (Amaro, Rodrigues, Yassuda, and Carnaval, 2014; Batalha-Filho, 86 Cabanne, and Miyaki, 2012; Carnaval et al., 2014; Thomé et al ., 2010). This pattern of 87 historical range contraction, coupled with habitat threats from anthropogenic causes, make cold- 88 associated endemic species important targets for biodiversity conservation and prediction 89 (Morellato & Haddad, 2000). Placosoma lizards are one such group. 90 Here, I ask whether different species within this cold-associated genus further partition 91 the available climatic space and explore distinct environmental envelopes within the Southern 4 92 Atlantic Forest domain, or if, alternatively, they all share similar climatic niches and hence have 93 responded, and should be expected to respond, similarly to environmental shifts. To that end, I 94 reconstruct the phylogeny of Placosoma and assess the differences in the environmental spaces 95 occupied by its species. While morphological records exist for the species that comprise 96 Placosoma , no phylogenetic analyses exist and, consequently, evolutionary relationships have 97 not been inferred between species. Utilizing multilocus DNA sequence data from P. cipoense , P. 98 champsonotus , P. cordylinum , and P. glabellum (tissues of P. limaverdorum are not yet available 99 for sequencing), this study contributes to the biogeography of the Atlantic Forest by addressing 100 the following questions: (1) What are the evolutionary relationships among the species of 101 Placosoma , and (2) are Placosoma species structured in geographic and environmental space? 102 To answer these questions, I sample broadly and infer phylogenies using coalescent methods, 103 which have been useful in delimiting species in morphologically cryptic taxa (Blair et al ., 2014), 104 as well as Bayesian inference. Using climatic data from our collection sites and occurrence 105 points of Placosoma limaverdorum from Borges-Nojosa et al. (2016), I then compare the 106 climatic envelopes occupied by all five species of Placosoma . 107 108 Materials and Methods 109 DNA extraction, amplification, and sequencing 110 I sampled 30 Placosoma individuals of four species from the Brazilian States of Minas 111 Gerais, Rio de Janeiro, and São Paulo (Fig. 1, Appendix 1). Samples of Placosoma cipoense 112 were obtained from Serra do Cipó in Minas Gerais. Placosoma champsonotus, Placosoma 113 cordylinum, and Placosoma glabellum were obtained from various national parks in São Paulo 114 and Rio de Janeiro. A specimen of Colobodactylus taunayi (MTR 15549), a gymnophthalmid 5 115 lizard, was included as an outgroup given its basal position relative to Placosoma in a previous 116 phylogenetic study of the Gymnophthalmidae (Pellegrino, et al ., 2001). Collection sites were 117 either assigned geographic coordinates in the field using Global Positioning System equipment 118 or geo-referenced using collection notes. Tissues were obtained from the University of São Paulo 119 under the following collection codes: CTMZ (tissue collection of the Museu de Zoologia), LG 120 (cytogenetic laboratory at the University of São Paulo), MCL and MTR (herpetological 121 collection of Miguel Trefaut-Rodrigues), and MZUSP (specimen collection of the Museu de 122