Nuclear DNA microsatellites reveal genetic variation but a lack of phylogeographical structure in an endangered species, Fraxinus mandshurica, across North-east China

Abstract

Background and aims: The widely accepted paradigm that the modern genetic structure of plant species in the northern hemisphere has been largely determined by recolonization from refugia after the last glacial maximum fails to explain the presence of cold-tolerant species at intermediate latitudes. Another generally accepted paradigm is that mountain ridges act as important barriers causing genetic isolation of species, but this too has been challenged in recent studies. The aims of the work reported here were to determine the genetic diversity and distribution patterns of extant natural populations of an endangered cool temperate species, Faxinus mandshurica, and to examine whether these two paradigms are appropriate when applied to this species over a wide geographical scale.

Methods: 1435 adult individuals were sampled from 30 natural populations across the main and central range of the species, covering major mountain ranges across North-east China (NEC). Genetic variation was estimated based on nine polymorphic nuclear microsatellite loci. Phylogeographical analyses were employed using various approaches, including Bayesian clustering, spatial analysis of molecular variance, Monmonier's algorithm, neighbor-joining trees, principal co-ordinate analysis and isolation by distance.

Key results: Genetic diversity within populations was relatively high, and no significant recent bottlenecks were detected in any of the populations. A significant negative correlation between intra-population genetic diversity and latitude was identified. In contrast, genetic differentiation among all the populations examined was extremely low and no clear geographic genetic structure was identified, with the exception of one distinct population.

Conclusions: The modern genetic structure in this species can be explained by extensive gene flow, an absence of mountains acting as barriers, and the presence of a wide refuge across NEC rather than multiple small refugia. Intra-population genetic variation along latitudes is probably associated with the systematically northward shifts of forest biomes in eastern China during the mid-Holocene. To determine important genetic patterns and identify resources for conservation, however, it will be necessary to examine differentially inherited genetic markers exposed to selection pressures (e.g. chloroplast DNA) and to investigate different generations.

Fig. 1.

Geographic locations of the 30 natural populations of Fraxinus mandshurica, focusing on major five mountain ranges across three Provinces in North-east China.

Fig. 2.

Pearson correlation analysis showing that (A) the allele richness (A_S) was significantly correlated with latitude (R = –0·642, P < 0·001), and (B) that the expected heterozygosity (H_e) was also significantly correlated with latitude (R = –0·618, P < 0·001).

Fig. 3.

(A) Fixation indexes (F) as a function of the user-defined number of groups of populations (K) for 30 natural populations of Fraxinus mandshurica using SAMOVA based on the stepwise mutation model (SMM) in terms of 1000 iterations. F_CT, F_ST and F_SC represent genetic differentiation between groups of populations, between populations overall, and between populations within groups, respectively. (B), Barrier analysis based on Monmonier's algorithm and significance tested by means of 1000 bootstrap matrices of D_A (Nei et al., 1983). The first significant barriers (95 %) confirmed that there was only one distinct population: Jianxin (X1) was maximally differentiated from all the others.

Fig. 4.

(A) Isolation by distance (IBD) analysis based on the Mantel test (Mantel, 1967) with 9999 random permutations indicated no significant differences between the 30 Fraxinus mandshurica natural populations (R² = 0·017, P > 0·05); (B) The same data with X1 excluded: there is a weak but significant relationship between the remaining 29 populations (R² = 0·048, P < 0·001).