Non-adaptive evolutionary processes governed the diversification of a temperate conifer lineage after its migration into the tropics

Constructing phylogenetic relationships among closely related species is a recurrent challenge in evolutionary biology, particularly for long-lived taxa with large effective population sizes and uncomplete reproductive isolation, like conifers. Conifers further have slow evolutionary rates, which raises the question of whether adaptive or non/adaptive processes were predominantly involved when they rapidly diversified after migrating from temperate regions into the tropical mountains. Indeed, fine-scale phylogenetic relationships within several conifer genus remain under debate. Here, we studied the phylogenetic relationships of endemic firs (Abies, Pinaceae) discontinuously distributed in the montane forests from the Southwestern United States to Guatemala, and addressed several hypotheses related to adaptive and non-adaptive radiations. We derived over 80K SNPs from genotyping by sequencing (GBS) for 45 individuals of nine Mesoamerican species to perform phylogenetic analyses. Both Maximum Likelihood and quartets-inference phylogenies resulted in a well-resolved topology, showing a single fir lineage divided in four subgroups that coincided with the main mountain ranges of Mesoamerica; thus having important taxonomic implications. Such subdivision fitted a North-South isolation by distance framework, in which non-adaptive allopatric processes seemed the rule. Interestingly, several reticulations were observed within subgroups, especially in the central-south region, which may explain past difficulties for generating infrageneric phylogenies. Further evidence for non-adaptive processes was obtained from analyses of 21 candidate-gene regions, which exhibited diminishing values of πa/πs and Ka/Ks with latitude, thus indicating reduced efficiency of purifying selection towards the Equator. Our study indicates that non-adaptive allopatric processes may be key generators of species diversity and endemism in the tropics.Readme.txt describes each file. Funding provided by: Consejo Nacional de Ciencia y TecnologíaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100003141Award Number: CB-2016-284457Funding provided by: Consejo Nacional de Ciencia y TecnologíaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100003141Award Number: 278987Funding provided by: Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de MéxicoCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100006087Award Number: PAPIIT-IN208416Sample We sampled foliage from 45 individuals of genus Abies (Pinaceae) collected in 33 natural fir populations (1-2 indivs/pop) along a latitudinal gradient between the Southwestern USA and Guatemala. To root our networks and phylogenies, we used an individual of A. lasiocarpa as outgroup. We extracted DNA from frozen needles with either a DNeasy Plant Mini Kit (Qiagen) or a modified CTAB protocol. We double-digested individual DNA samples (200 ng) with enzymes MspI (C|CGG) and PstI (TGCA|G), and ligated unique barcodes and adapters to digestion products. Single end sequencing (100x1) was done in an Illumina Hiseq 2500 lane. Both library preparation and sequencing were performed at the Institute of Integrative Biology and Systems at Université Laval (http://www.ibis.ulaval.ca/en/services-2/genomic-analysis-platform/). We used a pyRAD (Eaton, 2014) pipeline (https://github.com/dereneaton/ipyrad) to process raw sequence reads