Full paper Effects of landscapes and range expansion on population structure and local adaptation Wei Zhao1,2 , Yan-Qiang Sun1, Jin Pan2, Alexis R. Sullivan2 , Michael L. Arnold3 , Jian-Feng Mao1 and Xiao-Ru Wang1,2 1Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, China; 2Department of Ecology and Environmental Science, UPSC, Umea University, SE-901 87, Umea, Sweden; 3Department of Genetics, University of Georgia, Athens, GA 30602-7223, USA Summary Authors for correspondence: Understanding the origin and distribution of genetic diversity across landscapes is critical for Jian-Feng Mao predicting the future of organisms in changing climates. This study investigated how adaptive Tel: +86 13366181735 and demographic forces have shaped diversity and population structure in Pinus densata,a Email: [email protected] keystone species on Qinghai-Tibetan Plateau (QTP). Xiao-Ru Wang We examined the distribution of genomic diversity across the range of P. densata using Tel: +46 907869955 exome capture sequencing. We applied spatially explicit tests to dissect the impacts of allele Email: [email protected] surfing, geographic isolation and environmental gradients on population differentiation and Received: 13 January 2020 forecasted how this genetic legacy may limit the persistence of P. densata in future climates. Accepted: 15 April 2020 We found that allele surfing from range expansion could explain the distribution of 39% of the c. 48 000 genotyped single nucleotide polymorphisms (SNPs). Uncorrected, these allele New Phytologist (2020) 228: 330–343 frequency clines severely confounded inferences of selection. After controlling for demo- doi: 10.1111/nph.16619 graphic processes, isolation-by-environment explained 9.2–19.5% of the genetic structure, with c. 4.0% of loci being affected by selection. Allele surfing and genotype–environment associations resulted in genomic mismatch under projected climate scenarios. Key words: allele frequency cline, exome We illustrate that significant local adaptation, when coupled with reduced diversity as a sequences, genomic mismatch, local adaptation, nucleotide diversity, Pinus result of demographic history, constrains potential evolutionary response to climate change. densata, Qinghai-Tibetan Plateau. The strong signal of genomic vulnerability in P. densata may be representative for other QTP endemics. allow alleles to ‘surf’ to very high or low frequencies, which may Introduction leave a molecular signature similar to selection (Edmonds et al., The ability of a species to sustain environmental change is primar- 2004; Klopfstein et al., 2006; Excoffier & Ray, 2008). Clines ily determined by its genetic reservoir, which is shaped over the produced by allele surfing can overlap with those produced by course of history through demography and selection. Dissecting IBD, but surfing can also result in strong differentiation between the effects of demography, geography and selection on population geographically proximate populations. Until now, the impact of diversity helps us to understand how genetic variation is dis- range expansion on allele frequency clines (AFCs) has been tributed across a landscape, as well as the evolutionary potential of obtained mostly from theoretical simulations (Klopfstein et al., species under climate change (Sork et al., 1999; Lee & Mitchell- 2006; Lotterhos & Whitlock, 2015; Hoban et al., 2016), with Olds, 2011; Manel & Holderegger, 2013; Orsini et al.,2013). few empirical studies in natural populations, especially in plants Sources of genetic differentiation can be broadly classified into (but see Gonzalez-Martınez et al., 2017; Ruiz Daniels et al., adaptive and dispersal-demographic factors. Among the later, iso- 2018). Detecting adaptive sources of genetic differentiation is lation by distance (IBD; Wright, 1943), a neutral process where often confounded by dispersal-demographic factors including gene flow is increasingly limited between more distant or isolated IBD and allele surfing, but natural populations are widely populations, is a well-studied source of clinal variation. More expected to experience isolation by environment (IBE; Orsini recently, the importance of density-dependent effects during et al., 2013; Wang & Bradburd, 2014), in which gene flow range expansion in producing strong clines or even discrete among populations inhabiting different ecological habitats is lim- genetic sectors has been illustrated by microbial experiments and ited by selection (Nosil et al., 2009; Feder et al., 2012a). simulation studies (Excoffier & Ray, 2008; Excoffier et al., 2009; Although methods exist to control for the ubiquitous autocorrela- Waters et al., 2013; Peischl et al., 2016). Repeated founder effects tion of IBE and IBD, distinguishing selection from dispersal-de- combined with density-dependent competitive exclusion can mographic effects during range expansion remains a challenge. 330 New Phytologist (2020) 228: 330–343 Ó 2020 The Authors www.newphytologist.com New Phytologist Ó 2020 New Phytologist Trust This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. New Phytologist Research 331 Patterns of IBE can be used to identify relationships between Materials and Methods genomic and environmental variation, which can be projected onto future climate models to estimate the vulnerability of extant Sampling and exome capture sequencing populations to extinction (Manel & Holderegger, 2013; Fitz- patrick & Keller, 2015; Bay et al., 2018). Understanding the We sampled 23 populations across the distribution of P. densata genomic mismatch between modern and future environments is (Fig. 1a). The name, location and sample size of each population necessary for assessing the ability of populations to persist. Popu- are listed in Table 1. Because of its hybrid history, we included lations with high genomic mismatch are likely to suffer popula- two and four representative populations of P. tabuliformis and tion decline if de novo mutations and migration cannot P. yunnanensis, respectively, to better polarize the genetic compo- compensate for the required diversity (Bay et al., 2018; Ruegg nents in P. densata. Populations from the eastern margin of et al., 2018). Moreover, the potential for populations to adapt P. densata (group E populations in this study) have a mix of mito- interacts with demographic history, and range expansions may chondrial DNA (mtDNA) haplotypes found in the two parental constrain viability by reducing both the pool of genetic diversity species, reflecting heterogeneous maternal lineages, but predomi- and the effectiveness of selection to purge deleterious alleles. nately P. tabuliformis chloroplast DNA (cpDNA) haplotypes as a Pinus densata forms extensive forests on the southeastern Qing- result of pollen-mediated introgression (cpDNA is paternally hai-Tibetan Plateau (QTP) at elevations ranging from 2700 to inherited in pines; Wang et al., 2011). The frequency of haplo- 4200 m above sea level (Mao & Wang, 2011). Previous genetic types unique to P. densata for both organelles increases westward, analyses suggest that P. densata originated from hybridization which supports the eastern margin as the ancient hybrid zone between Pinus tabuliformis and Pinus yunnanensis in the late where P. densata originated (Wang et al., 2011; Gao et al., 2012). Miocene (Wang & Szmidt, 1994; Wang et al., 2011; Gao et al., Despite their organelle haplotype overlap, P. densata populations 2012). An ancient hybrid zone has been identified in the north- in the east are distinct from the two parental species in cone and eastern edge of the current distribution of P. densata, from where seed morphometric traits (Mao et al., 2008). the hybrid lineage successfully colonized new habitats by step- Needles or cones were collected from four to 12 randomly wise, westward migration (Wang et al., 2011; Gao et al., 2012). selected trees in each stand. Genomic DNA was extracted from This demographic history could produce significant AFCs along needles or seedlings using a Plant Genomic DNA kit (Tian- the expansion route as a result of genetic surfing. Reciprocal gen, Beijing, China). Forty thousand exome probes (each 120 nt) transplant experiments revealed pronounced differences in sur- were designed from Pinus taeda UniGenes (Neves et al., 2013). vival among P. densata populations, suggesting extensive local The majority were aligned to c. 29 000 genes, while 9800 probes adaptation (Zhao et al., 2014). These lines of evidence suggest were aligned to intergenic regions. Library preparation, probe that demographic events and local adaptation have played impor- hybridization, and sequencing were conducted by RAPiD tant roles in the evolution of P. densata. However, until now it Genomics (Gainesville, FL, USA; Neves, et al., 2013). In total, has been difficult to fully address the relative contribution of 208 trees were genotyped. these forces because of the lack of genomic resources and meth- ods to adequately distinguish between AFCs generated by disper- Reduced reference genome preparation, mapping and sal-demographic effects and IBE. variant calling In this study, we used spatially explicit tests to identify the sig- nature of allele surfing, IBD and IBE and forecasted how this Genomes