Model-based analysis supports interglacial refugia over long-dispersal events in the diversification of two South American cactus species

Abstract

Pilosocereus machrisii and P. aurisetus are cactus species within the P. aurisetus complex, a group of eight cacti that are restricted to rocky habitats within the Neotropical savannas of eastern South America. Previous studies have suggested that diversification within this complex was driven by distributional fragmentation, isolation leading to allopatric differentiation, and secondary contact among divergent lineages. These events have been associated with Quaternary climatic cycles, leading to the hypothesis that the xerophytic vegetation patches which presently harbor these populations operate as refugia during the current interglacial. However, owing to limitations of the standard phylogeographic approaches used in these studies, this hypothesis was not explicitly tested. Here we use Approximate Bayesian Computation to refine the previous inferences and test the role of different events in the diversification of two species within P. aurisetus group. We used molecular data from chloroplast DNA and simple sequence repeats loci of P. machrisii and P. aurisetus, the two species with broadest distribution in the complex, in order to test if the diversification in each species was driven mostly by vicariance or by long-dispersal events. We found that both species were affected primarily by vicariance, with a refuge model as the most likely scenario for P. aurisetus and a soft vicariance scenario most probable for P. machrisii. These results emphasize the importance of distributional fragmentation in these species, and add support to the hypothesis of long-term isolation in interglacial refugia previously proposed for the P. aurisetus species complex diversification.

The xeric side of the Brazilian Atlantic Forest: The forces shaping phylogeographic structure of cacti

“…The species tree was obtained after 100 million MCMC generations, with a 25% burn‐in, and sampling trees every 5,000 steps. Divergence time for each node was estimated using a uniform prior distribution for the plastid marker trnS‐trnG including the minimum and maximum substitution rates observed in the chloroplast sequences of angiosperms, that is, 0.29% and 0.11% of substitution per million years (Bonatelli et al., ; Wolfe et al., ), respectively, and using a wide prior for PHYC evolutionary rate following Perez, Bonatelli, Moraes, and Carstens ().…”

Genetic differentiation and historical demography of wood stork populations in Brazilian wetlands: Implications for the conservation of the species and associated ecosystems

“…Initially, five demographic scenarios were simulated, with different combinations of colonization events followed by either population stability or exponential population growth, and different migration parameters, totalling 14 candidate models. Data simulations (100 000 for each model) were performed with the scripts given in Perez, Bonatelli, Moraes, and Carstens (), using empirical sample sizes. Priors for the parameters were drawn from simulated uniform distributions: divergence time ( τ ) was drawn from a distribution of 11 000 to 25 000 years and the effective population size of the ancient population ( N e ) was drawn from a distribution of 50 to 10 000 individuals.…”

“…From the empirical and simulated mtDNA sequence data, a set of summary statistics ( SuSts ) was computed: the proportion of polymorphic sites (π), the number of segregating sites ( S ), Tajima's D and θ H statistic (Fay & Wu, ) using a custom PERL script written by N. Takebayashi (available at: http://raven.iab.alaska.edu/~ntakebay/teaching/programming/coalsim/scripts/msSS.pl). The simulated nuclear data were converted into microsatellite alleles using ‘microsat’ (available at: http://massey.genomicus.com/software.html#microsat) and further formatted using a script from Perez et al () to compute the number of alleles ( A ), expected heterozygozity ( H E ) and a modified version of Garza and Williamson's M (mM) (Excoffier, Laval, & Schneider, ; Garza & Williamson, ) in Arlequin (Excoffier & Lischer, ). Pairwise F ST values were computed between populations for both the simulated and empirical data.…”

“…Initially, five demographic scenarios were simulated, with different combinations of colonization events followed by either population stability or exponential population growth, and different migration parameters, totalling 14 candidate models. Data simulations (100 000 for each model) were performed with the scripts given in Perez, Bonatelli, Moraes, and Carstens (2016), using empirical sample sizes.…”

Paleodistribution of Neotropical species of Erythroxylum (Erythroxylaceae) in humid and dry environments

“…During the LIG, E. buxus was the only species that occurred throughout the country, while E. deciduum was displaced, and showed a more restricted distribution along the southern coast. According to Perez et al (2016), the LIG was the most favorable period for the formation of small refuges of diversity for tropical dry vegetation due to increased rainfall. This fragmentation was more evident with E. daphinites than with E. deciduum.…”