Genetic Diversity and Geographic Differentiation of the Giant Tiger Shrimp (Penaeus monodon) in Thailand Analyzed by Mitochondrial COI Sequences

Genetic diversity and geographic differentiation of the giant tiger shrimp, Penaeus monodon, in Thai waters (Satun, Trang, Phangnga, and Ranong in the Andaman Sea and Chumphon and Trat in the Gulf of Thailand) were examined by COI polymorphism (N = 128). We observed 28 COI mitotypes across all investigated individuals. The sequence divergence between pairs of mitotypes was 0.00–20.76%. A neighbor-joining tree clearly indicated lineage separation of Thai P. monodon and large nucleotide divergence between interlineage mitotypes but limited divergence between intralineage mitotypes. High genetic diversity was found (mean sequence divergence = 6.604%, haplotype diversity = 0.716–0.927, π = 2.936–8.532%). F-statistics (F _ST) and an analysis of molecular variance (AMOVA) indicated that the gene pool of Thai P. monodon was not homogeneous but genetically differentiated intraspecifically (P < 0.05). Six samples of P. monodon could be allocated into three different genetic populations: Trat (A), Chumphon (B), and the Andaman samples Satun, Trang, Phangnga, and Ranong (C). Contradictory results regarding patterns of geographic differentiation previously reported by various molecular approaches were clarified by this study.     

Molecular phylogeography of Fagus engleriana (Fagaceae) in subtropical China: limited admixture among multiple refugia

Beech is one of the most important trees in the temperate and subtropical forests of the Northern Hemisphere. Despite Chinese beeches have the particularity that only grow in subtropical areas, they have received few phylogeographic research. In this study, we sampled 25 populations of the northernmost-distributed Chinese beech, Fagus engleriana, and detected six haplotypes across 350 individuals by using sequences of two chloroplast intergenic spacers. The chloroplast genetic diversity was relatively low (h _T?=?0.659), with most genetic variance residing among populations (G _ST?=?0.831, N _ST?=?0.855, G _ST??N _ST). SAMOVA analysis indicated that populations clustered into six groups with little admixture among them (most groups were characterized by a unique hapotype). Pairwise difference among haplotypes and Fu??s Fs statistic indicated that populations of F. engleriana have not experienced recent sudden expansions. Both the phylogeographic and demographic patterns found in this study suggest that F. engleriana remained fragmented in multiple refugia throughout the Pleistocene climatic changes, and experienced limited both glacial and interglacial/postglacial expansion. The results of this study imply that long-term isolation among multiple refugia, coupled with little admixture among populations of different refugia provided numerous opportunities for population divergence and allopatric speciation, which might be a driving factor for the exceptionally broad temperate species diversity in southern China.     

Mitochondrial DNA Diversity of Orchid Bee Euglossa fimbriata (Hymenoptera: Apidae) Populations Assessed by PCR-RFLP

Euglossa fimbriata is a euglossine species widely distributed in Brazil and occurring primarily in Atlantic Forest remnants. In this study, the genetic mitochondrial structure of E. fimbriata from six Atlantic Forest fragments was studied by RFLP analysis of three PCR-amplified mtDNA gene segments (16S, COI-COII, and cyt b). Ten composite haplotypes were identified, six of which were exclusive and represented singleton mitotypes. Low haplotype diversity (0.085–0.289) and nucleotide diversity (0.000–0.002) were detected within samples. AMOVA partitioned 91.13% of the overall genetic variation within samples and 8.87% (?_st = 0.089; P < 0.05) among samples. Pairwise comparisons indicated high levels of differentiation among some pairs of samples (?_st = 0.161–0.218; P < 0.05). These high levels indicate that these populations of E. fimbriata, despite their highly fragmented landscape, apparently have not suffered loss of genetic variation, suggesting that this particular population is not currently endangered.     

Genetic relationships between Atlantic and Pacific populations of the notothenioid fish Eleginops maclovinus: the footprints of Quaternary glaciations in Patagonia

The genetic relationships between the Pacific and the Atlantic populations of marine coastal biota in Southern South America have been analyzed in few studies, most of them relying on a single mitochondrial locus. We analyzed 10 polymorphic microsatellite loci, isolated from a dinucleotide-enriched Eleginops maclovinus genomic library, in a total of 240 individuals (48 from each of 5 sampled sites: 2 Atlantic, 2 Pacific and 1 in Beagle Channel). The results were contrasted against a previous work on the same species with mitochondrial DNA (mtDNA). Observed heterozygosity within localities ranged from 0.85 to 0.88 with the highest overall number of alleles observed at the northernmost locality on the Pacific side (Concepción), but no clear geographic pattern arose from the data. On the other hand, the number of private alleles was negatively correlated with latitude (Spearman''s r_s test, P=0.017). Among-population variance was low but significant (1.35% P<0.0001, analysis of molecular variance (AMOVA)) and low genetic differentiation between populations was observed (pairwise F_ST values ranged from 0 to 0.021). A Mantel test revealed a significant correlation between geographic distances and F_ST (r=0.56, P=0.047). This could be partially accounted by the Atlantic versus Pacific population differentiation detected in three different analyses (STRUCTURE, SAMOVA (Spatial Analysis of MOlecular VAriance) and a population phylogeny). The observed pattern is compatible with a history of separation into two glacial refugia that was better captured by the multilocus microsatellite data than by the mtDNA analysis.     

Quaternary population dynamics of an endemic conifer, Picea omorika, and their conservation implications

Serbian spruce, Picea omorika (Pan?.) Purk., is a cold-adapted conifer confined to an area of c. 10,000 km² within the Balkans. This area, which has not been exposed to severe anthropogenic disturbances in the recent past, represents a long-term cryptic refugium of this species. We studied Quaternary dynamics of fragmentary distributed Serbian spruce populations to uncover genetic and demographic processes accounting for high levels of genetic diversities in this endemic species within its long-term cryptic refugium. Based on our data set [499 trees from ten populations, five nuclear microsatellites (EST-SSRs) and a mitochondrial (mtDNA) locus], we found the following: (i) continuous increase of genetic distinctiveness of populations caused by various genetic and/or demographic processes, (ii) decreasing over generations pollen flow, and (iii) almost complete lack of seed flow, are trends applicable not only for post-glacial but also for glacial populations. As a result, populations distant few kilometers or less were poorly connected and highly differentiated (nuclear DNA: average ρ _ST , Hedrick’s G′ _ST and Jost’s D of 0.165, 0.429 and 0.385, respectively; mtDNA: G _ST  = 0.632). They were characterized as independent gene pools at the nuclear DNA level. Nonetheless, levels of genetic diversity were high at both nuclear (average allelic richness = 16.14; average H _E  = 0.776) and mtDNA (H _T  = 0.231) levels. They were maintained not by pronounced gene flow but rather by frequent admixtures of highly differentiated populations, and also by species longevity and overlapping generations in the populations. However, admixtures had been possible only if populations encountered each other over time. Particular genetic and/or demographic changes of populations, such as fragmentations, admixture, size reductions/expansions and extinctions, could not be associated exclusively neither to the post-glacial nor to the last glacial as they were detected during both periods. In accordance with expectations on range alternations in cold-adapted taxa confined to refugia during warm Quaternary periods, our study species was expanding range during the last glacial and contracting range post-glacially. Recommendations for conservation of this IUCN red-listed, endemic and relict species have been provided.     

Colonization history of Scots pine in Eastern Europe and North Asia based on mitochondrial DNA variation

During Quaternary glaciations, the ranges of Northern Eurasia forest species periodically experienced contraction followed by subsequent re-colonizations in the interglacial intervals. However, unlike the broadleaf trees of temperate forests, taiga species seem not to have retreated fully to southern regions in unfavorable periods and possibly survived at mid-latitudes in multiple refugia. Here, we report a study of genetic variation of three mitochondrial DNA markers in 90 populations of Scots pine (Pinus sylvestris) located from Eastern Europe to Eastern Siberia. The geographic distribution of seven mitotypes demonstrated the split between western and eastern populations approximately along the 38th meridian. Genetic diversity in the western part was significantly higher than in the eastern one. Five mitotypes were western- and one eastern-specific. One mitotype was common in both regions, but in the eastern part it occurred only in the South Urals and adjacent areas. The geographic structure in the mitotype distribution supports a hypothesis of post-glacial re-colonization of the studied territory from the European and Ural refugia.     

Analysis of Geographic and Pairwise Genetic Distances Among Sheep Populations

This study assessed the usefulness of geographic and pairwise genetic distances in the characterization of five sheep populations using 15 microsatellite markers. The average F statistics across loci were F _IT = 0.523 ± 0.140, F _ST = 0.363 ± 0.131, and F _IS = 0.263 ± 0.092. The average heterozygosity was 0.716 ± 0.069, polymorphism information content was 0.691 ± 0.070, and effective number of alleles was 3.736 ± 0.998. Sheep populations clustered into group 1 (Hu and Tong breeds) and group 2 (small-tailed Han, Wadi, and Tan breeds). Reynolds’ distance varied from 0.0062 to 0.0499, and the range of gene flow (N _m) was 4.8834–40.0726 among the sheep populations. The results showed that the genetic structure of the five populations was not consistent with their genetic distances, and the population genetic divergence was not linearly related to geographic distance as indicated by a Mantel test (P = 0.7936).     

Genetic structure of the critically endangered plant Tricyrtis ishiiana (Convallariaceae) in relict populations of Japan

Tricyrtis ishiiana is a relic endemic plant taxon of the Convallariaceae that inhabits two nearby gorges in Kanagawa Prefecture, Japan. The distribution range and number of populations are thought to have been reduced to the present refugial populations during the Quaternary climatic oscillations. Because of its showy flowers, this plant has faced illegal removal from its natural habitats for horticultural use and has been designated a critically endangered species (class IA). In this study, we analyzed the genetic structure of the relict populations of T. ishiiana in order to contribute to the conservation strategies of the prefectural government. Our analyses of nine nuclear microsatellite loci detected high genetic diversity (H _E = 0.704 and H _O = 0.541) for the two populations. The two populations were slightly differentiated (R _ST = 0.032), accompanied by faint substructure across the populations (K = 3). In addition, each population exhibited spatial genetic structuring. The relatively low inbreeding coefficient for both populations together (F _IS = 0.233) and each population separately (F _IS = 0.217?C0.246) may be attributable to crossing among descendants within a population along with occasional gene flow between the populations. These results suggested that the extant populations have not experienced a severe bottleneck. The two extant populations were genetically differentiated at a very low level, accompanied by occasional pollen flow via pollinators and/or seed dispersal by gravity in the mountainous environment. Occasional gene exchange between the populations has allowed T. ishiiana to harbor high genetic diversity despite being a relic plant confined to two small refugial populations.     

Molecular phylogeography and intraspecific divergence of Spiraea alpina (Rosaceae) distributed in the Qinghai-Tibetan Plateau and adjacent regions inferred from nrDNA

The Qinghai-Tibetan plateau (QTP) uplift had a decisive effect on climatic and eco-environmental evolution in East Asia during the Quaternary. In the current study phylogeographic structure and diversification history of Spiraea alpina across the QTP were investigated for the first time based on nuclear internal transcribed spacer. The nuclear internal transcribed spacers (ITS_1a–ITS₄) were generated for a total of 284 individuals distributed within 31 natural populations. A clear phylogeographic structure was found for S. alpina. The results showed that this species colonized in three different glacial refugia during the Quaternary extensive glaciation and expanded during the Interglacial period. Analysis of molecular variance (AMOVA) showed 74.13% genetic diversity among populations and 25.87% genetic variation within populations with distinct phylogeographic structure (F_ST = 0.741*). The estimated divergence time revealed that the main lineages of S. alpina diversified during the Quaternary 1.2–0.6 million years ago. The study concluded that severe climatic oscillations during Quaternary and the uplift of QTP had a profound effect on intraspecific divergence of S. alpina.     

Holocene southward expansion in seasonally dry tropical forests in South America: phylogeography of Ficus bonijesulapensis (Moraceae)

We conducted a phylogeographical and niche modelling study of the tree Ficus bonijesulapensis, endemic to Brazilian seasonally dry tropical forests (SDTFs), in order to evaluate the effects of Quaternary climatic fluctuations on population dynamics. The trnQ–5′rps16 region of plastid DNA was sequenced from 15 populations. Three phylogeographical groups were identified by the median‐joining algorithm network and spatial analysis of molecular variance (SAMOVA) (F_CT = 0.591): a central‐west, a central‐east and a scattered group. The central groups had higher total haplotype and nucleotide diversities than the scattered group. Ecological niche modelling suggested that, since the Last Interglacial (130 kyr bp ), the central and north regions have been relatively stable, whereas the southern region of the species distribution has been less stable. The phylogeographical groups showed concordance with the floristic units described for SDTFs. The low genetic diversity, unimodal mismatch distribution and unfavourable climatic conditions in the southern region suggest a recent southward expansion of the range of the species during the Holocene, supporting the hypothesis of the southward expansion of SDTFs during this period. The central and northern regions of the current distribution of F. bonijesulapensis, which are consistent with arboreal caatinga and rock outcrop floristic units, were potential refugia during Quaternary climatic fluctuations. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 177 , 189–201.     

Genetic diversity of the endangered Chinese endemic herb Saruma henryi Oliv. (Aristolochiaceae) and its implications for conservation

Saruma henryi Oliv., the only representative of the monotypic genus Saruma Oliv. (Aristolochiaceae), is an endangered perennial herb endemic to China. It is a phylogenetically, ecologically, and medicinally important species. In the present study, inter-simple sequence repeat (ISSR) markers were employed to investigate the genetic diversity and differentiation of 14 populations. A total of 16 selected primers yielded 175 bright and discernible bands, with an average of 10.94 per primer. POPGENE analysis showed that the genetic diversity was quite low at the population level (h = 0.0447–0.1243; I = 0.0642–0.1853; PPB = 10.29–36.57%), but pretty high at the species level (h = 0.2603; I = 0.3857; PPB = 73.71%). The hierarchical analysis of molecular variance (AMOVA) revealed a high level of genetic differentiation among populations (67.18% of total variance components, P < 0.001), in line with the gene differentiation coefficient (G _ST = 0.6903) and the limited among-population gene flow (N _m = 0.2243). Both Principal Coordinates Analysis (PCoA) and UPGMA cluster analysis supported the grouping of all 14 populations into three geographic groups, among which there occurred a moderate level of genetic differentiation (33.18% of total variance components, P < 0.001) as shown by AMOVA analysis. In addition, Mantel test revealed a significant correlation between genetic and geographic distances among populations (r = 0.7792, P = 0.001), indicating the role of geographic isolation in shaping its present population genetic structure. The present levels and patterns of genetic diversity of S. henryi were assumed to result largely from its breeding system, geographic isolation, clonal growth, its unique biological traits and evolutionary history. The high genetic differentiation among populations implies that the conservation efforts should aim to preserve all the extant populations of this endangered herb.     

Clear genetic structure of Pinus kwangtungensis (Pinaceae) revealed by a plastid DNA fragment with a novel minisatellite

Background and Aims

Pinus kwangtungensis is a five-needled pine, inhabiting isolated mountain tops, cliffs or slopes in the montane areas of southern China and northern Vietnam. Global warming and long-term deforestation in southern China threaten its existence and genetic integrity, and this species is listed as vulnerable in the China Species Red List. However, the level and distribution of genetic diversity in this vulnerable species are completely unknown. In this paper, the genetic diversity and structure are examined using paternally inherited plastid markers to shed light on its evolutionary history and to provide a genetic perspective for its conservation.

Methods

By means of direct sequencing, a new polymorphic fragment containing a minisatellite site was identified within the plastid genome of P. kwangtungensis. Using the minisatellite site along with five SNPs (one indel and four substitutions) within the same fragment, the population genetic structure and pollen flow were analysed in 17 populations of P. kwangtungensis in southern China.

Key Results

Analysis of 227 individuals from 17 populations revealed ten haplotypes at the minisatellite site. The haplotype diversity at species level was relatively high (0·629). Genetic diversity of each population ranged from 0 to 0·779, and the western populations harboured more genetic variation than the eastern and Hainan populations, although the former appeared to have experienced a bottleneck in recent history. Population subdivision based on this site was high (F_ST = 0·540 under IAM; R_ST = 0·677 under SMM). Three major clusters (eastern, western and Hainan) were identified based on a neighbor-joining dendrogram generated from genetic distances among the populations. The genetic structures inferred from all the polymorphic sites and the SNPs were in concordance with that from the minisatellite site.

Conclusions

The results suggest that there are at least three refugia for P. kwangtungensis and that populations in these refugia should be treated as separate evolutionarily significant units or conservation units. The high diversities in the western populations suggest that these were much larger in the past (e.g. glacial stages) and that the shrinking population size might have been caused by recent events (e.g. deforestation, global warming, etc.). The western populations should be given priority for conservation due to their higher genetic diversity and limited population sizes. It is concluded that the newly found minisatellite may serve as a novel and applicable molecular marker for unravelling evolutionary processes in P. kwangtungensis.Key words: Pinus kwangtungensis, minisatellite, population genetics, conservation     

Regional-scale differentiation and phylogeography of a desert plant <Emphasis Type="Italic">Allium mongolicum</Emphasis> (Liliaceae) inferred from chloroplast DNA sequence variation

Past geological and climatic changes have promoted regional-scale intraspecific differentiation and range contraction/expansion in many temperate plants. However, little is known about how the desert species in central Asia responded to past geological and climatic changes, especially for a few widespread desert plants. In the present study, we aimed to survey the population structure and phylogeographical history of Allium mongolicum, which is widely distributed in the deserts of northwestern China. We sequenced two chloroplast DNA fragments (accD-psaI and psbA-trnH) for 418 individuals from 38 populations across the whole range of the species. Fourteen chlorotypes were identified, and three out of them were dominant. All populations were divided into three larger distinct groups by SAMOVA, which was largely congruent with the geographical division based on the Monmonier’s maximum-difference algorithm. Each of the groups occupied a distinct geographical region with a specific dominant chlorotype. Analysis of molecular variance showed that a high proportion of the total genetic variation (70.05%) existed among the three regions. The demographic dynamic tests indicated that the desert species had experienced a sudden regional-scale range expansion/recolonization in the Quaternary glaciers, which was further identified by the ecological niche modeling. These results suggest that the species has a distinct regional-scale differentiation as well as multiple geographically isolated refugia. Our results further enforce the idea that the environmental changes since the late Miocene greatly promoted differentiation of desert plants in northwestern China, and the Quaternary climatic oscillations played an important role in structuring the current populations of these species.     

Chloroplast microsatellite diversity of Opisthopappus Shih (Asteraceae) endemic to China

The genus Opisthopappus consists of two species, O. longilobus and O. taihangensis. Both of them are important economic and ornamental plants but endangered in China. In this study, genetic variation in four populations of O. longilobus and nine populations of O. taihangensis was estimated by chloroplast microsatellites (cpSSR). Low genetic diversity was detected in O. longilobus and O. taihangensis populations. The percentages of polymorphic loci (PPL), Nei’s gene diversities (h), and Shannon’s indices (I) was 53.56 %, 0.074, and 0.139, respectively, for O. longilobus, while PPL = 44.44 %, h = 0.018, I = 0.048 for O. taihangensis. Thirteen chloroplast haplotypes were identified from 153 individuals analyzed of two species. Ten haplotypes were found in O. longilobus, while seven in O. taihangensis. Haplotype 1 was the common and ancestral one. The level of haplotype diversity was also low (Hd _{O. longilobus}  = 0.4875, Hd _{O. taihangensis}  = 0.3452). AMOVA analysis revealed that the majority of the genetic differences was partitioned within populations of O. longilobus and O. taihangensis, as confirmed by PCoA and cluster analysis. Inter-population genetic distances among population of O. longilobus and O. taihangensis correlated insignificantly with geographic distances (r = 0.286, P = 0.128 for O. longilobus vs. r = 0.356, P = 0.058 for O. taihangensis). The self-compatibility, effective gene flow, narrow geographical distribution, and historical factors may be the main factors causing differentiation in the genetic structure of O. longilobus and O. taihangensis populations.     

Distribution and polymorphism of Mariner-like elements in the Bambusoideae subfamily

Picea omorika (Pan?.) Purk. is a relict from the Arcto-Tertiary flora with its entire current natural range confined to an area of only 10,000 km² within the Balkans, a region well known as a Quaternary refugium. We have amplified the second intron of the mitochondrial NADH dehydrogenase subunit1 gene in 200 trees originating from ten natural populations to assess the phylogeographic structure and history of this conifer. Five haplotypes harbouring different numbers of 34-bp minisatellites were detected, revealing haplotypic richness of 3.007 and gene diversities H _S = 0.075 and H _T = 0.225. More interestingly, despite the very small distribution range of P. omorika and its dispersal by wind, non-random distribution of haplotypes was observed, resulting in an unexpectedly high estimate of population differentiation (G _ST = 0.668), and 56.8% of molecular variation assigned to variation among populations. Those findings suggest substantial isolation of populations and their partitioning into two gene pools characterized by different history and levels of genetic diversity, and very limited seed flow in this species (Nm = 0.25). They support the hypothesised early arrival of P. omorika in the Balkan region, and residence within this refugium during several ice ages at least. We demonstrate that the assessment of genetic diversity and structuring are not straightforward in species confined to refugial regions, and that past microvicariance might bias formal phylogeographic (G _ST = N _ST = 0.668) and isolation-by-distance analysis (r = 0.028, P > 0.05).     

High genetic diversity detected in the endemic Primula apennina Widmer (Primulaceae) using ISSR fingerprinting

Primula apennina Widmer is endemic to the North Apennines (Italy). ISSR were used to detect the genetic diversity within and among six populations representative of the species distribution range. High levels of genetic diversity were revealed both at population percentage of polymorphic band (PPB = 75.92%, H _S = 0.204, H _pop = 0.319) and at species level (PPB = 96.95%, H _T = 0.242, H _sp = 0.381). Nei gene diversity statistics (15.7%), Shannon diversity index (16.3%) and AMOVA (14%) detected a moderate level of interpopulation diversity. Principal coordinate and Bayesian analyses clustered the populations in three major groups along a geographic gradient. The correlation between genetic and geographic distances was positive (Mantel test, r = 0.232). All together, these analyses revealed a weak but significant spatial genetic structure in P. apennina, with gene flow acting as a homogenizing force that prevents a stronger differentiation of populations. Conservation measures are suggested based on the observed pattern of genetic variability.     

Negligence in the Atlantic forest,northern Brazil: a case study of an endangered orchid

Currently, many Brazilian orchids are threatened with extinction resulting from habitat loss and intense harvesting pressure stemming from their value as ornamental plants. Therefore, the genetic diversity in remaining populations is fundamental to the survival of these species in natural environments. In order to inform conservation strategies, this study evaluated the genetic diversity and structure of Cattleya granulosa populations. The sample consisted of 151 individuals from 12 populations in the Atlantic Forest, northeastern Brazil, evaluated using 91 ISSR markers. Genetic variability was assessed through molecular variance, diversity indexes, clusters of genotypes through Bayesian analysis, and tests for genetic bottlenecks. From all polymorphic loci, genetic diversity (H_E) varied between 0.210 and 0.321 and the Shannon index ranged from 0.323 and 0.472. Significant genetic differentiation between populations (Φ_ST = 0.391; P < 0.0001) resulted in the division of the populations into five groups based on the log-likelihood Bayesian analysis. We found significant positive correlation between geographical and genetic distances between populations (r = 0.794; P = 0.017), indicating isolation by distance. Patterns of allelic diversity within populations suggest the occurrence of bottlenecks in most C. granulosa populations (n = 8). Therefore, in order to maintain the genetic diversity of the species, the conservation of spatially distant groups is necessary.     

Molecular phylogeography and paleodistribution modeling of the boreal tree species <Emphasis Type="Italic">Ulmus lamellosa</Emphasis> (T.Wang et S. L. Chang) (Ulmaceae) in China

The uplift of mountains and climatic oscillations are important for understanding of the demographic history and genetic structure of species. We investigated the biogeographic history of the boreal tree species Ulmus lamellosa (Ulmaceae) in China, by using a combined phylogeographic and paleodistribution modeling approach. In this study, 14 populations of endangered U. lamellosa were analyzed by using chloroplast DNA (cpDNA) sequences. A high level of genetic differentiation (Φ _ST = 86.22%) among populations with a significant phylogeographic pattern (N _ST > G _ST, P < 0.05) was found in U. lamellosa. Ten haplotypes were detected by combining chloroplast DNA data, and haplotype 3 (H3) was found to be common and widespread. The intraspecific divergence of all U. lamellosa cpDNA haplotypes (9.27 Ma; 95% HPD 5.17–13.33 Ma) most probably began in the late Miocene. The pairwise difference among haplotypes and neutrality tests (Tajima’s D and Fu’s Fs statistic) indicated that populations of U. lamellosa, except group I, have not experienced recent sudden expansions. Multiple refuge areas were identified across the entire distribution ranges of U. lamellosa. The low level of gene flow (Nm = 0.14) among populations may have resulted from isolation resulting from distance and complex topography during climatic oscillations; this isolation was probably the major process that shaped the present distribution of haplotypes. These results support the hypothesis that U. lamellosa persisted in situ during glaciations and occupied multiple localized glacial refugia, contrary to the hypotheses of large-scale range contraction and long-distance southward migration.     

Phylogeography of the temperate tree species Quercus acutissima in China: Inferences from chloroplast DNA variations

Quercus acutissima is one of the most widespread temperate deciduous tree species in China. To study its phylogeographical pattern and demographic history, three chloroplast DNA fragments (atpB-rbcL, psbA-trnH and trnS-trnG) from 401 individuals representing 30 populations were sequenced. A total of 19 haplotypes were identified, and these showed a weak phylogeographical structure (N_ST = 0.689 > G_ST = 0.630, P > 0.05) at the species level. The Q. acutissima population harboured a high level of genetic diversity (H_T = 0.791), and the genetic variation mainly resided among populations (59.54%). The unimodal mismatch distribution and significantly negative Fu's F_S value indicate that the Q. acutissima population experienced rapid range expansion, which probably occurred between 0.37 and 0.12 Ma. Molecular phylogeography and ecological niche modelling (ENM) data suggest the existence of multiple localized glacial refugia in central China (e.g., the Qinling, Dabashan and Dabieshan mountain ranges) and southwestern China (Yunnan-Guizhou Plateau and its adjacent regions) during the Quaternary glaciations. Our study showed that geographical heterogeneity and climate changes may have shaped the genetic structure and phylogeographical pattern of this tree species in China.     

Genetic variation and population differentiation of the endochitinase gene family in Pinus monticola

In the present study, we characterized nucleotide variations of the Pinus monticola class IV endochitinase (PmCh4) family. Using primers targeting at conserved amino acid motifs of plant class IV endochitinases, genomic DNA was amplified. Sequence data analysis identified five novel genes in the PmCh4 family with one pseudogene. Single nucleotide polymorphisms of the PmCh4 family were surveyed in seven open-pollinated seed lots representing diverse geographical distribution. Variable levels of average pairwise nucleotide diversity (π = 0.00422–0.02079) and relatively high levels of haplotype diversity (H _d = 0.85–0.96) were revealed at PmCh4 loci. Based on nucleotide variation, P. monticola populations were clustered into two main groups by phylogenetic analysis based on Nei’s genetic distance. The Mantel test revealed no correlation between geographical and genetic distances (r = ?0.11, P = 0.59). A further SNP genetic diversity study on more P. monticola populations throughout Western North America may help the design of sampling regimes for tree breeding, genetic conservation and assisted migration under climate change.