The climatic association of population divergence and future extinction risk of Solanum pimpinellifolium

Abstract

Under intraspecific differentiation driven by differential climatic adaptation, it may be expected that intraspecific genetic groups occur at distinct environments. Populations occupying different niches may therefore differ in their ability to cope with climate change. Here, we addressed this hypothesis with a wild tomato, Solanum pimpinellifolium. This species is distributed from the west side of Andes to the coastal region in Peru and Ecuador and occupies a wide environmental diversity. This environmental diversity is related to the genetic structure of the species providing an ideal material to investigate the isolation by environment hypothesis. While previous hypothesis stated that S. pimpinellifolium originated from northern Peru and migrated northwards and southwards, our results support that S. pimpinellifolium originated from Ecuador and expanded to northern and southern Peru, and during this process, the niche space of S. pimpinellifolium became more associated with cold and drought. We further predicted its fate under anthropogenic climate change. According to our predictions, the northern group will maintain its current extent or even expand to the entire western region of Ecuador. In contrast, we predicted low habitat suitability for the southern group which could potentially lead to the shrinkage of its distribution. In conclusion, we revealed the distinct fates among the differentiated populations driven by environment under global warming conditions.

Keywords: Solanum pimpinellifolium; climate change; isolation by environment; species distribution modelling.

Figure 1.

Phylogenetic tree and the location of S. pimpinellifolium using S. lycopersicum as outgroup. The red labels indicate the northern population; blue for the central population; goldenrod for the southern population; purple for centre-north population (admixture between the northern population and the central population); aquamarine for centre-south population (admixture between the central population and the southern population). The + indicates the accessions which are geographically distant from all other accessions from the same genetic cluster and therefore removed from further analyses, including LA1236, LA1335, LA1466, LA1547 and LA1585. The bars on the right side are the result of ADMIXTURE and ordered by the accessions latitude from north to south (top to bottom).

Figure 2.

The temperature and precipitation per month of the collection site of each accession. The red curves indicate the northern population; blue for the central population; goldenrod for the southern population.

Figure 3.

Species distribution modelling under current climatic condition.

Figure 4.

Principal component analysis of the nine bioclimatic variables. Ellipse means 95 % confidence interval. The BIO codes indicate Isothermality (BIO 3), Temperature Seasonality (BIO 4), Minimum Temperature of Coldest Month (BIO 6), Temperature Annual Range (BIO 7), Annual Precipitation (BIO 12), Precipitation of Driest Month (BIO 14), Precipitation Seasonality (BIO 15), Precipitation of Warmest Quarter (BIO 18) and Precipitation of Coldest Quarter (BIO 19).

Figure 5.

The overall cumulative importance of each bioclimatic variable from gradient forest. BIO 12, 14, 18 and 19 were done with natural log transform. The units of temperature and precipitation were °C * 10 and mm, respectively.

Figure 6.

The projection of future species distribution on the scenario of RCP 8.5 in 2070.

Figure 7.

Genetic offset in a scenario of RCP 8.5 in 2070. High genetic offset (red) means the less association between genetic variation and bioclimatic variables than current environment, implying an extinction risk for the populations in these regions. Since the definition of genetic offset is the genetic mismatch of current populations to future climatic change, one should only focus on the results in geographic regions occupied by current populations (along the coast).