The population demography of Betula maximowicziana, a cool‐temperate tree species in Japan, in relation to the last glacial period: its admixture‐like genetic structure is the result of simple population splitting not admixing

Abstract

Conservation of the local genetic variation and evolutionary integrity of economically and ecologically important trees is a key aspect of studies involving forest genetics, and a population demographic history of the target species provides valuable information for this purpose. Here, the genetic structure of 48 populations of Betula maximowicziana was assessed using 12 expressed sequence tag-simple sequence repeat (EST-SSR) markers. Genetic diversity was lower in northern populations than southern ones and structure analysis revealed three groups: northern and southern clusters and an admixed group. Eleven more genomic-SSR loci were added and the demographic history of these three groups was inferred by approximate Bayesian computation (ABC). The ABC revealed that a simple split scenario was much more likely than isolation with admixture, suggesting that the admixture-like structure detected in this species was due to ancestral polymorphisms. The ABC analysis suggested that the population growth and divergence of the three groups occurred 96 800 (95% CI, 20 500-599 000) and 28 300 (95% CI, 8700-98 400) years ago, respectively. We need to be aware of several sources of uncertainty in the inference such as assumptions about the generation time, overlapping of generations, confidence intervals of the estimated parameters and the assumed model in the ABC. However, the results of the ABC together with the model-based maps of reconstructed past species distribution and palaeoecological data suggested that the modern genetic structure of B. maximowicziana originated prior to the last glacial maximum (LGM) and that some populations survived in the northern range even during the LGM.

Genetic Structure and Population Demographic History of a Widespread Mangrove Plant Xylocarpus granatum J. Koenig across the Indo-West Pacific Region

“…Furthermore, the westward Equatorial Current that bifurcates north and south as it approaches the Indo-Malay Archipelago [54] could be a strong barrier preventing the gene dispersal of haplotype XG2 beyond Palau. Thus, although we need to be cautious about uncertainties in the ABC inferences, such as the generation time of species, overlapping of generations, and wide 95% CI of inferred parameters in the assumed model [16], the present results suggest that genetic differentiation caused by a genetic barrier between the South China Sea and Oceania was generated by episodes of eustatic change in sea levels in relation to ice ages over the past several hundred thousand years. Moreover, population shrinkage was detected in the Oceania group (estimated 128,000 years BP (95% HPD, 8880-292,000)), suggesting that effective population size was reduced following genetic divergence from the South China Sea.…”

“…In addition, as the mean value of F ST among populations within Oceania (0.4090) was significantly higher than within the South China Sea (0.1800), higher genetic isolation within the Oceania group might have also contributed to a decrease in the regional effective population size in Oceania. Regarding the assumed model in the ABC, DIYABC does not consider gene flow after divergence, and it may bias the inferred temporal parameters [16,20]. However, as genetic differentiation between the South China Sea and Oceania is high enough with less gene flow (F' RT = 0.815), this bias may be limited.…”

“…However, as genetic differentiation between the South China Sea and Oceania is high enough with less gene flow (F' RT = 0.815), this bias may be limited. In addition, since no consideration of gene flow after divergence may underestimate divergence times [16], the main discussion here would not be changed with the population split still occurring before the Last Glacial Maximum (LGM). Finally, although the ABC approach in this study revealed the demographic history of the species, the results obtained in this study might be based on the limited sample size in this study.…”

“…To understand the genetic structure of mangroves across the entire IWP region, it is necessary to focus on species that are widespread across the region. Moreover, although coalescent-based population demographic inferences have started to provide a deeper understanding of the genetic diversity and structure of species and their history (e.g., [15][16][17]), this kind of approach has not yet been well conducted in mangrove species. Thus, further inferences of past demographic history of mangrove species can shed new light on not only the population genetics of mangrove species, but also mangrove forest management and conservation, as demonstrated in forest tree species [16,[18][19][20].…”

Vicariance and Oceanic Barriers Drive Contemporary Genetic Structure of Widespread Mangrove Species Sonneratia alba J. Sm in the Indo-West Pacific

“…This corresponded with the lower nucleotide diversity across populations detected in Zhou et al (2011) [12] and Yang et al (2017) [11], both of which attributed this to a demographic history involving recent colonization, migration and local adaptation. Such consistently low level of genetic diversity could also be a character mirrored by long species history [61].…”