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Geographic isolation reduces opportunities for gene flow within a species. Therefore, genetic differences accumulate across the species’ range and may lead to allopatric speciation. Given that marginal populations of widespread species are more likely than other populations to become isolated, they can play an important role in speciation. Consequently, peripheral speciation might be a common way by which regional endemics originate.
Population dynamics during the Pleistocene, however, had a large influence on evolutionary history. Species that avoided extinction expanded and retreated as a result of environmental changes during the Pleistocene, resulting in their current distribution and genetic structure throughout their range (Avise, 2000; Hewitt, 2000). A simple evolutionary consequence is that range contractions of widespread species have left isolated populations in marginal areas, leading to peripheral speciation of regional endemics. In this case, the population sizes of endemics would be much smaller than those of their ancestral and sister species, and a lack of migration would be observed after speciation (Conye & Orr, 2004). However, Pleistocene population dynamics, such as range expansion, contraction and/or population extinction, could blur distribution patterns and complicate the evolutionary history of a species. Indeed, it is now recognized that introgression may have occurred between species during past Pleistocene range expansions and contractions at times when they were sympatric (Kikuchi et al., 2010) and that, in general, the effects of historical hybridization between species that are currently allopatric might be more frequent than previously thought (Cronn & Wendel, 2004; Pelser et al., 2011). Thus, the speciation process cannot simply be inferred based on the current range of a species. A better understanding of the evolutionary history of regional endemics is likely to provide novel insights into the evolutionary dynamics of species during climatic oscillations.
Here we assess the potential influence of Pleistocene population dynamics on the evolutionary history of a species through an examination of the speciation history of a Japanese alpine endemic, Cardamine nipponica (Brassicaceae). The high mountains in Japan range from 2000 to 3000 m in altitude and 35° to 44° in latitude, and harbor an alpine flora consisting of species that also occur in the Arctic (e.g. Empetrum nigrum, Diapensia lapponica, and Vaccinium vitis-idaea) as well as endemics that appear to be closely related to arctic-alpine species. Specifically, one-third of the Japanese alpine plant species are either endemic to this archipelago, but with closely related arctic species, or are themselves widely distributed in the Arctic (Shimizu, 1982, 1983). C. nipponica, a perennial, mostly autogamous herb with compound leaves (Kitakawa, 1999; H. Ikeda, pers. obv.), is a representative of such endemics. The narrow range of this endemic species is located at the periphery of the range of an apparently closely related, widespread arctic–alpine species, Cardamine bellidifolia, which also is perennial and mostly autogamous, but with simple leaves (Hultén & Fries, 1986; Brochmann & Steen, 1999). The current range of C. bellidifolia extends throughout the entire Circum-Arctic and into the high mountains of North America and East Asia (Fig. 1). Both species are diploid (2n = 16; Kučera et al., 2005; Warwick & Al-Shehbaz, 2006; Y. I. Iwatsubo, pers. obv.). The current distributions of C. nipponica and C. bellidifolia do not overlap, but C. bellidifolia extends southward to Sakhalin Island north of Japan (Fig. 1). Thus, one may reasonably hypothesize that the Japanese endemic C. nipponica is sister to the arctic-alpine C. bellidifolia and has diverged in the periphery of the range of this widespread species. However, a previous study inferred a nonsister relationship between these two species based on internal transcribed spacer (ITS) sequences (Carlsen et al., 2009). That study used DNA extracted from an old herbarium specimen of C. nipponica, and thus the risk of contamination or other errors during experimental procedures may have been high. Therefore, re-evaluating the phylogenetic position of C. nipponica and its relationship with C. bellidifolia would be worthwhile.
Figure 1. (a) Distribution ranges of Cardamine bellidifolia (light gray) and C. nipponica (dark gray). Black squares represent sampling sites for C. bellidifolia. (b) Detailed range (black dots) and sampling sites (dots with arrows) for the Japanese endemic C. nipponica. Detailed information on the localities is given in Supporting Information Table S1.
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In this study, we first re-examined whether the Japanese endemic C. nipponica is sister to the arctic–alpine C. bellidifolia. Initially, we reanalyzed the previously published as well as new ITS sequences of the genus Cardamine. Because phylogenetic relationships inferred between close relatives are sometimes inconsistent across genes as a result of incomplete lineage sorting and/or gene flow, multilocus analyses are necessary to determine a robust sister species relationship. Therefore, using several putative sister species identified in the ITS analysis, further phylogenetic analyses were conducted based on 10 other nuclear genes. Given that C. nipponica and C. bellidifolia were indeed identified as sister taxa in our study, we next explored their speciation history statistically using demographic parameters under the isolation-with-migration (IM) model (Nielsen & Wakeley, 2001; Hey & Nielsen, 2004). Based on these parameters, we attempted to evaluate the potential peripheral speciation between the sister species and infer the evolutionary influence of Pleistocene climatic oscillations.
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Fig. S1 Parsimony networks of alleles at each locus.
Fig. S2 Summaries of the Bayesian clustering implemented by STRUCTURE.
Fig. S3 Summaries of the Bayesian clustering implemented by InStruct.
Fig. S4 Maximum likelihood tree of Cardamine nipponica and its closely related species based on concatenated sequences of all sites of 10 nuclear genes.
Table S1 Locality information for the samples and alleles at each locus
Table S2 Accession numbers of ITS used for phylogenetic analysis
Table S3 Sequences of primers used for PCR and sequencing
Table S4 Maximum likelihood estimates (MLEs) of demographic parameters of the IM model between Cardamine nipponica and C. bellidifolia
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