Next‐Gen phylogeography of rainforest trees: exploring landscape‐level cpDNA variation from whole‐genome sequencing

Abstract

Standardized phylogeographic studies across codistributed taxa can identify important refugia and biogeographic barriers, and potentially uncover how changes in adaptive constraints through space and time impact on the distribution of genetic diversity. The combination of next-generation sequencing and methodologies that enable uncomplicated analysis of the full chloroplast genome may provide an invaluable resource for such studies. Here, we assess the potential of a shotgun-based method across twelve nonmodel rainforest trees sampled from two evolutionary distinct regions. Whole genomic shotgun sequencing libraries consisting of pooled individuals were used to assemble species-specific chloroplast references (in silicio). For each species, the pooled libraries allowed for the detection of variation within and between data sets (each representing a geographic region). The potential use of nuclear rDNA as an additional marker from the NGS libraries was investigated by mapping reads against available references. We successfully obtained phylogeographically informative sequence data from a range of previously unstudied rainforest trees. Greater levels of diversity were found in northern refugial rainforests than in southern expansion areas. The genetic signatures of varying evolutionary histories were detected, and interesting associative patterns between functional characteristics and genetic diversity were identified. This approach can suit a wide range of landscape-level studies. As the key laboratory-based steps do not require prior species-specific knowledge and can be easily outsourced, the techniques described here are even suitable for researchers without access to wet-laboratory facilities, making evolutionary ecology questions increasingly accessible to the research community.

From ratites to rats: the size of fleshy fruits shapes species' distributions and continental rainforest assembly

“…For E. globosa, high cpDNA heterogeneity at larger geographical scales (including greater genomic diversity in the tropics) suggests that while dispersal might be sufficient Table 1. A summary of chloroplast genome data for two Endiandra species: reported chloroplast genome length; total number of SNPs (including withinpopulation SNPs and fixed between-population SNPs); Nei's regional genomic diversity (for AWT and NNSW); and genomic distances between regional sites and between regions (calculated following [17] Table 2. Proportions of rainforest trees and vines with different fruit characteristics, including differently sized fleshy fruits and wind-dispersed fruits as non-fleshy comparison (out of a total of 2306 species).…”

tropiTree: An NGS-Based EST-SSR Resource for 24 Tropical Tree Species

“…Multiplexing based on bar-coding is an approach that is being increasingly applied during the next-generation sequencing of plants (see [25] for another example involving multiple tree species). Furthermore, EST-SSRs are the markers of choice for several population genetic applications and show greater transferability across taxonomic boundaries than SSRs derived simply from whole-genome DNA sequencing, which facilitates cross-species comparisons [37].…”

Forest tree genomics: 10 achievements from the past 10 years and future prospects

“…The inferred demographic history has been used as a robust baseline information to detect gene loci under adaptive evolution (Grivet et al 2011;Källman et al 2014). Comparative phylogeographic approaches have given insights into the congruence of demographic history across species through time, first in temperate tree species (e.g., Jaramillo-Correa et al 2010;Petit et al 2003) and more recently in tropical species Heuertz et al 2014;Jones et al 2013;van der Merwe et al 2014). Important predictive power has been gained in phylogeography by integrating species distribution modeling based on spatially interpolated climatic data for different time periods (Carstens and Richards 2007;Cornille et al 2013).…”

“…HTS technologies hold great promise for disentangling evolutionary relationships in complex groups, especially in tropical tree taxa in which botanical knowledge remains limited and cryptic species are common Turchetto-Zolet et al 2013). The first HTS studies reconstructed the complete organellar genomes of tree taxa, which resulted in a higher resolution in phylogeography (McPherson et al 2013;van der Merwe et al 2014), taxonomy, and phylogenetics, particularly for tropical taxa (in Chrysobalanacae, Malé et al 2014;in Malpighiales, Xi et al 2012). HTS studies of the nuclear genome are still rare in phylogenetics and phylogeography of trees (but see Carstens et al 2013;Stölting et al 2013).…”