Divergent lineages and conserved niches: using ecological niche modeling to examine the evolutionary patterns of the Nile monitor (<Emphasis Type="Italic">Varanus niloticus</Emphasis>)

Ecological niche modeling is a useful tool that can support phylogeographic analyses, offering insight into the evolutionary processes that have generated present-day patterns of biodiversity. Findings of ecological divergence across evolutionary lineages can be utilized to bolster inferences of parapatric or sympatric modes of speciation, and provide support for species-level classifications. Conversely, conserved ecological niches across evolutionary timescales are thought to have facilitated allopatric speciation. Here, we examined the climatic niche of three genetic lineages of the Nile monitor (Varanus niloticus) to better understand the processes involved in generating patterns of genetic variation, and to potentially clarify their taxonomic status. We built ecological niche models using genetically confirmed occurrence points from the three evolutionary lineages of V. niloticus, occupying the western, northern, and southern regions of Africa. Pairwise comparisons of climatic niche overlap provided evidence in support of niche conservatism across all V. niloticus lineages. These findings are consistent with an allopatric mode of differentiation. Furthermore, climatic niche conservatism could have played a role in isolating V. niloticus populations during historic climate oscillations, generating the observed genetic patterns across Africa.     

Pleistocene climatic fluctuations explain the disjunct distribution and complex phylogeographic structure of the Southern Red-backed Salamander, <Emphasis Type="Italic">Plethodon serratus</Emphasis>

The southeastern United States (U.S.) has experienced dynamic climatic changes over the past several million years that have impacted species distributions. In many cases, contiguous ranges were fragmented and a lack of gene flow between allopatric populations led to genetic divergence and speciation. The Southern Red-backed Salamander, Plethodon serratus, inhabits four widely disjunct regions of the southeastern U.S.: the southern Appalachian Mountains, the Ozark Plateau, the Ouachita Mountains, and the Southern Tertiary Uplands of central Louisiana. We integrated phylogenetic analysis of mitochondrial DNA sequences (1399 base pairs) with ecological niche modeling to test the hypothesis that climate fluctuations during the Pleistocene drove the isolation and divergence of disjunct populations of P. serratus. Appalachian, Ozark, and Louisiana populations each formed well-supported clades in our phylogeny. Ouachita Mountain populations sorted into two geographically distinct clades; one Ouachita clade was sister to the Louisiana clade whereas the other Ouachita clade grouped with the Appalachian and Ozark clades but relationships were unresolved. Plethodon serratus diverged from its sister taxon, P. sherando, ~5.4 million years ago (Ma), and lineage diversification within P. serratus occurred ~1.9–0.6 Ma (Pleistocene). Ecological niche models showed that the four geographic isolates of P. serratus are currently separated by unsuitable habitat, but the species was likely more continuously distributed during the colder climates of the Pleistocene. Our results support the hypothesis that climate-induced environmental changes during the Pleistocene played a dominant role in driving isolation and divergence of disjunct populations of P. serratus.     

Phylogeography and historical demography of the orchid bee <Emphasis Type="Italic">Euglossa iopoecila</Emphasis>: signs of vicariant events associated to Quaternary climatic changes

The aim of this study was to investigate whether Pleistocene climatic instability influenced the phylogeographic structure and historical demography of an endemic Atlantic Forest (AF) orchid bee, Euglossa iopoecila Dressler, which shows two main patterns of integument colors over of its geographical distribution. We based our analysis on the concatenated sequence of four mtDNA segments belonging to genes 16S (357 bp), Cytb (651 bp) and COI (1206 bp), totaling 2234 bp. Samples of E. iopoecila populations were collected in 14 AF remnants along its geographic distribution. Median-Joining haplotype networks, SAMOVA and BAPS results indicated three lineages (southern, central and northern clusters) for E. iopoecila, with two important phylogeographic ruptures. We found higher genetic diversity among samples collected in the central region of the AF, which coincides with predicted areas of climatic stability, according to recent AF stability–extinction model. The demographic analysis suggests that only the southern cluster had undergone recent population expansion, which probably started after the last glacial maximum (LGM). Our data suggest that the differentiation observed in the three mitochondrial lineages of E. iopoecila is the result of past disconnections and multiple extinction/recolonization events involving climate fluctuations. In terms of conservation, we would emphasize the importance of considering: (1) the region of the central clade as the location of the highest genetic diversity of mtDNA of E. iopoecila populations; (2) the philopatric behavior of females that tends to restrict mtDNA gene flow in particular, with direct implications for the conservation of the total genetic diversity in euglossine populations.     

Strong genetic differentiation and low genetic diversity of the freshwater pearl mussel (<Emphasis Type="Italic">Margaritifera margaritifera</Emphasis> L.) in the southwestern European distribution range

Genetic diversity of European freshwater pearl mussel, Margaritifera margaritifera (L.), appears exceptional with highest genetic variability found in the northernmost European populations of Scandinavia and lower genetic variability in central and southern Europe. The objective of this study was to investigate genetic diversity and differentiation of 14 southernmost populations on the Iberian Peninsula which greatly differ in terms of life span and habitat conditions from the rest of central and northern European populations. The analyses of ten microsatellite loci revealed a pronounced level of genetic divergence and very low genetic diversity. These results match the expectations of geographically peripheral populations with respect to their genetic composition. The life history strategy, the narrow ecological niche of the species, and anthropogenic habitat modifications have most likely shaped the genetic pattern of Iberian pearl mussel populations. The peripheral position with less optimal habitat conditions may increase the extinction risk of these populations and thus effective conservation strategies for the Iberian M. margaritifera are needed. The successful conservation of the species at its southwestern margin requires inclusion of genetically different conservation units which may reveal local adaptation.     

Conservation genetics of redside dace (<Emphasis Type="Italic">Clinostomus elongatus</Emphasis>): phylogeography and contemporary spatial structure

Redside dace Clinostomus elongatus (Teleostei: Cyprinidae) is a species of conservation concern that is declining throughout its range as a result of habitat fragmentation, degradation and loss. We characterized the genetic structure and diversity of redside dace populations across the species range using mitochondrial and microsatellite data to inform conservation efforts and assess how historical and recent events have shaped genetic structure and diversity within and among populations. Phylogeographic structure among 28 redside dace populations throughout southern Ontario (Canada) and the United States was assessed by sequence analysis of the mitochondrial cytochrome b and ATPase 6 and 8 genes. Populations were also genotyped using ten microsatellite loci to examine genetic diversity within and among populations as well as contemporary spatial structuring. Mitochondrial DNA sequence data revealed three geographically distinct lineages, which were highly concordant with groupings identified by microsatellite analysis. The combined genetic data refute published glacial refugia hypotheses of a single Mississippian refugium or of two lineages associated with Mississippian and Atlantic refugia. Secondary contact between the two eastern groups was documented in the Allegheny River drainage and tributaries to Lake Ontario. With the exception of several allopatric populations within the Allegheny watershed, high genetic structuring among populations suggests their isolation, indicating that recovery efforts should be population-based.     

Phylogeography of rare fern <Emphasis Type="Italic">Polystichum glaciale</Emphasis> endemic to the subnival zone of the Sino-Himalaya

Previous phylogeographical studies of the Sino-Himalaya (SH) regions have mainly focused on seed plants from forest or alpine grassland habitats, whereas the flora of the subnival summits, especially the ferns, has largely been ignored. Here, we report on phylogeographical studies on Polystichum glaciale, a rare fern endemic to the subnival belt of the SH region. Based on cpDNA/nDNA sequences, strikingly rich genetic diversity was detected in P. glaciale. Combined with the lack of ‘isolation by distance’ and the major genetic differentiation among populations revealed by AMOVA, they collectively suggested that P. glaciale exhibited island-like population genetic structure. Phylogeographical structure with two genetic groups (N vs. S) was further identified in P. glaciale by the SAMOVA based on cpDNA data, of which the geographical pattern was mainly associated with the biogeographical boundary between the northern and southern Hengduan Mountains at 29°N latitude. We concluded that extremely complex topography of SH region and highly fragmented subnival habitat have played a critical role in shaping phylogeographical structure and genetic differentiation of P. glaciale. Mismatch distribution analyses and ecological niche modelling suggested P. glaciale has undergone north-westward retreat after the LGM. Predictions of its future distribution indicated the possibility of compression within suitable subnival habitats. We suggest in situ conservation should be urgently implemented to preserve this rare fern. Our results represent a first framework for a comprehensive understanding of the biogeographical history of fern species associated with the subnival belt of the SH region and the effects of historical events on its genetic architecture.     

Genetic structure of Schrenck newt <Emphasis Type="Italic">Salamandrella schrenckii</Emphasis> populations by mitochondrial cytochrome <Emphasis Type="Italic">b</Emphasis> variation

The nucleotide sequence variation of the mitochondrial cytochrome b gene was studied in Schrenck newt Salamandrella schrenckii (Strauch, 1870) from populations of Primorye and the Khabarovsk region. Phylogenetic analysis revealed two haplotype clusters, southern cluster 1 and northern cluster 2, with a divergence of 3%. Analysis of the mtDNA and cytochrome b amino acid sequence variations made it possible to assume that the modern range of Schrenck newt was colonized from south Primorye northwards. In contrast to the southern cluster, the northern one demonstrated all the signs of demographic expansion (a unimodal distribution of pairwise nucleotide differences, specific results of tests for selective neutrality of mtDNA variation, and a good correspondence of genetic parameters to those expected from demographic expansion models).     

Echoes of the whispering land: interacting roles of vicariance and selection in shaping the evolutionary divergence of two <Emphasis Type="Italic">Calceolaria</Emphasis> (Calceolariaceae) species from Patagonia and Malvinas/Falkland Islands

A key to understanding the origin and identity of young species lays on the knowledge of the Quaternary climatic oscillations’ effect on gene flow and vicariance. Even though the effect of climatic fluctuations is relatively well understood for southern hemisphere plant species, little is known about their effect on the evolutionary histories of species from mainland and islands. Thus, we investigated whether Quaternary climate-driven fluctuations translated into lineage divergence and speciation, followed or not by climatic niche differentiation, in two allopatric plant species, Calceolaria uniflora and C. fothergillii from Patagonia and Malvinas/Falkland islands, respectively. We sampled the range of both species, and sequenced two chloroplastic (cpDNA; trnS–trnG and trnH–psbA), and one single copy “anonymous” non-coding nuclear region (nDNA). We performed phylogeographic and dating analyses, and adjusted spatio-temporal diffusion models. We complemented molecular evidence with climatic niche differentiation analyses and species paleo-distribution projections. A species coalescent reconstruction based on multi-locus data retrieved both species as monophyletic. Estimates from cpDNA indicated the species diverged during the Great Patagonian Glaciation. Chloroplast and nuclear DNA showed east–west distribution of the main genetic groups but with contrasting spatial genetic diversity. The spatio-temporal diffusion analyses showed that between 1–0.8 Mya and 570 Kya the lineage leading to C. fothergillii diverged from C. uniflora and arrived to the islands. Climatic niche projections hindcasted range expansions during glaciations, and contractions during the interglacial periods. Comparisons of climatic niches between the two study species indicated that temperature variables show evidence of niche conservatism while precipitation regimes supported niche divergence, even when considering the background environmental divergence. Our study indicates that glacial fluctuations affected the mainland/islands connections favouring speciation mediated not only by isolation, but also by climatic niche differentiation.     

Molecular data reveal the hybrid nature of an introduced population of banded newts (<Emphasis Type="Italic">Ommatotriton</Emphasis>) in Spain

The three species of banded newt (genus Ommatotriton) are endemic to the Near East. Recently an introduced banded newt population was discovered in Catalonia, Spain. To determine the species involved and the geographical source, we genotyped 11 individuals for one mitochondrial and two nuclear genetic markers, and compared the observed haplotypes to a range-wide phylogeography of Ommatotriton. All haplotypes identified in Spain are identical to haplotypes known from the native range. The mitochondrial haplotypes derive from O. ophryticus and were originally recorded in northeast Turkey. The nuclear haplotypes reveal that all individuals are genetically admixed between O. ophryticus and O. nesterovi. While the geographical resolution for the nuclear markers is low, the source of the O. nesterovi ancestry must be Turkey, as this species is a Turkish endemic. Species distribution models suggest a large potential distribution for the two Ommatotriton species, extending over northern Iberia and southern France. The ecology of hybrids can differ substantially from that of the parent species, making the impact of the Spanish hybrid banded newt population difficult to predict.     

Nuclear genetic variation of <Emphasis Type="Italic">Rosa odorata</Emphasis> var. <Emphasis Type="Italic">gigantea</Emphasis> (Rosaceae): population structure and conservation implications

Rosa odorata var. gigantea is one of the most important ancestors of modern roses, which owns many merit traits including large flower, early flowering, and tea scent. Due to habitat loss and fragmentation, it has been listed as a rare and endangered species in China. In this study, a total of 424 accessions from 27 locations across its major distribution range were sampled. Its genetic diversity and population structure were assessed using a combination of seven nuclear microsatellite markers and one single-copy nuclear gene. Moderate to high within-population genetic diversity and moderate differentiation among populations were revealed despite its narrow distribution. The sampled 27 populations were resolved into two genetic clusters with limited contemporary and historical gene flows. The Red River Fault Zone was inferred to be a physical or geographical barrier to gene flow between these two genetic clusters. Genetic distances were significantly associated with geographic distances, indicating the isolation-by-distance model. Our ecological niche modeling indicated that R. odorata var. gigantea had high current potential areas in the central Yunnan province and substantial losses of high potential distribution areas in the western Yunnan in the future. Two detected clusters showed significant genetic differentiation and represented two separate evolutionary lineages, which should be recognized as two evolutionary significant units (ESUs) for conservation concerns. These results could be applied for the decision-making and conservation planning for this important species.     

RAPD-PCR Analysis of Ground Squirrels from the Tobol-Ishim Interfluve: Evidence for Interspecific Hybridization between Ground Squirrel Species <Emphasis Type="Italic">Spermophilus major</Emphasis> and <Emphasis Type="Italic">S. erythrogenys</Emphasis>

Populations of two ground squirrel species, Spermophilus major and S. erythrogenys, from the interfluvial area of the Tobol and Ishim rivers, where their ranges overlap, have been examined using RAPD-PCR. We have identified 253 loci, which included taxon-specific markers for S. major and S. erythrogenys as well as markers for geographic populations. Estimation of genetic diversity and construction of phylogenetic relationships were performed using software programs POPGENE, TEPGA, and TREECON. In all, based on morphological traits, animals from the Tobol-Ishim interfluve were assigned to the two parental morphotypes and showed similar levels of genetic variability (H, n_a, n_e). However, the total polymorphism level proved to be higher in ground squirrels with the major morphotype (P = 40.32%,P₉₅ = 27.27%) than in animals with the erythrogenys morphotype (P = 32%,P₉₅ = 22.13%). Nevertheless, the number of rare alleles was high in both cases, constituting about 70% of the total number. Interpopulation differentiation was considerably higher in S. major δ = 0.50) than in S. erythrogenys δ = 0.41). The genetic differentiation between local samples from the Tobol-Ishim interfluvial area was lower than that between the parental species. A significant part of the genetic diversity of the species examined and animals from the zone of overlapping ranges was accounted for by intrapopulation variability. Animals from the northern and southern parts of the Tobol-Ishim interfluve were charac-terized by the core traits of S. major and S. erythrogenys, respectively, falling into two distinct clusters in the UPGMA and NJ reconstructions. In addition to three hybrid individuals, identified by the bioacoustic method, three hybrid animals were distinguished using RAPD analysis. These animals earlier were thought to be “pure” species and formed their own clusters in phylogenetic reconstructions. Thus, the RAPD-PCR results directly showed the existence of stable hybridization (20% genetic hybrids) between S. major and S. erythrogenys in the Tobol-Ishim interfluvial area, which is more extensive than inferred previously from morphological and bioacoustic data.     

Genetic diversity and population structure of common walnut (<Emphasis Type="Italic">Juglans regia</Emphasis>) in China based on EST-SSRs and the nuclear gene phenylalanine ammonia-lyase (<Emphasis Type="Italic">PAL</Emphasis>)

Common walnut (Juglans regia L.) is an economically important temperate tree species valued for both its nut and wood. We investigated the genetic diversity and population structure of J. regia germplasm from 13 locations in China using 10 markers derived from expressed sequences (EST-SSR) and sequence polymorphisms within the phenylalanine ammonia-lyase (PAL) gene. Analysis of the population genetic structure based on EST-SSRs showed distinct populations in northern versus southern China that were not reflected in the spatial distribution of PAL haplotypes. High levels of population differentiation were probably the result of reproductive isolation and in southern China, hybridization with Juglans sigillata. The results indicate the possible presence of distinct evolutionary lineages of J. regia in the Qinling and Daba Mountains of China and in Yunnan province that may require ecological management if they are to be retained as in situ resources.     

A mountain range is a strong genetic barrier between populations of <Emphasis Type="Italic">Afzelia quanzensis</Emphasis> (pod mahogany) with low genetic diversity

Understanding patterns of genetic diversity of plants is important in guiding conservation programs. The aim of our study was to characterize genetic diversity in Afzelia quanzensis, an economically important African tree species. We genotyped 192 individuals at 10 nuclear microsatellite loci. Samples were collected from nine sites in Zimbabwe, five in the north and four in the south, separated by a mountain range, the Kalahari-Zimbabwe axis. Overall, genetic diversity was relatively low across all sites (expected heterozygosity (H _E)?=?0.452, mean number of alleles (A)?=?4.367, allelic richness (A _R)?=?2.917, effective number of alleles (A _E)?=?2.208, and private allelic richness (PA_R)?=?0.197). Genetic diversity estimates, H _E, A, A _R, and PA_R, were not significantly different between northern and southern sites. Allelic richness was significantly higher in southern sites. Significant population differentiation was observed among all sites (F _ST ?=?0.0936, G′ _ST ?=?0.1982, G _ST ?=?0.1001, D _JOST?=?0.0598). STRUCTURE analysis and principal components analysis identified two gene pools, one predominantly made up of southern individuals, and the other of northern individuals. A Monmonier’s function detected a genetic barrier that coincided with the Kalahari-Zimbabwe axis. The relatively low level of genetic diversity in A. quanzensis may reduce adaptability and limit future evolutionary responses. All sites should be monitored for deleterious effects of low genetic diversity, and genetic resource management should take into consideration the existence of the distinct gene pools to capture the entire extant genetic variation.     

Climatic Similarity of Extant and Extinct <Emphasis Type="Italic">Dasypus</Emphasis> Armadillos

The similar geographic distributions of an extinct (Dasypus bellus) and an extant (D. novemcinctus) armadillo species have long been of interest to scholars because of the unresolved phylogeny. The relationship between the two species has been investigated through morphological and phylogenetic studies, whereas the ecological perspective has been overlooked, the importance of which is more and more acknowledged in speciation events. Here, we used ecological niche models to study the climatic niche similarity of three species of Dasypus (D. bellus, D. novemcinctus, and D. kappleri) and provide new insights on the relationship among them. The climatic niche similarity was compared in two ways: hindcast of ecological niche models based on occurrences and climatic layers, and direct niche boundary comparison along bioclimatic axes. The fossil records of D. bellus were not predicted suitable by the ecological niche models of the two extant armadillos. The direct comparison of niche boundary showed that D. bellus lived in colder and relative dryer climates, with high temperature variation and low precipitation variation. Our results did not support the previously assumed ecological similarity of D. bellus and D. novemcinctus based on their geographic distributions and emphasized the possibility of a cold adapted characteristic of the life history of D. bellus.     

Genetic variability of wildlife-derived <Emphasis Type="Italic">Sarcoptes scabiei</Emphasis> determined by the ribosomal ITS-2 and mitochondrial 16S genes

Infestation by the ectoparasitic mite Sarcoptes scabiei (Acari: Sarcoptidae) has important implications for global wildlife conservation and both animal and human health. Ribosomal and mitochondrial DNA sequences of parasites are useful to determine genetic diversity and to describe their likely dynamic evolution. In this study, we described the genetic diversity of S. scabiei individuals collected from wild animals in China by sequencing the ribosomal ITS-2 and mitochondrial 16S rRNA genes. A total of 13 Sarcoptes isolates of wildlife, coupled with one of rabbit origin, were subjected to genetic characteristics. After cloning and sequencing, 14 ITS-2 sequences and 12 16S rRNA sequences were obtained and analyzed. Further analysis of haplotype network and population genetic structure revealed that there were 79 haplotypes in ITS-2 (main haplotype H2) and 31 haplotypes in 16S rRNA (main haplotype C10). The phylogenetic trees showed some partial clustering by location and host, and the analysis of gene polymorphism may prompt that all isolates of S. scabiei have a similar origin. We speculate that the genetic evolution of S. scabiei may be related with that of the hosts, but more research is necessary to better understand the host-parasite co-evolutionary relationship in S. scabiei. These results provide new insights into understanding the population genetics and evolutionary biology of S. scabiei and therefore a better understanding of controlling its infestation pathways worldwide.     

Climate-induced shifts in the niche similarity of two related spadefoot toads (genus <Emphasis Type="Italic">Pelobates</Emphasis>)

Of the four species encompassing the genus Pelobates, only two overlap along a narrow contact zone, i.e., Pelobates fuscus and Pelobates syriacus. Our study investigated the shifts in niche similarity of these two closely related species from the Last Interglacial towards the end of the twenty-first century. We computed climatic suitability models using Maxent and projected them onto future and past climates. We used fossil occurrences to test the predictive accuracy of past projections. Niche similarity was assessed between the studied species using Schoener’s D index and a background similarity test. Finally, we evaluated niche differentiation by contrasting the species occurrences using a logistic regression analysis. The ecological niches are slightly extended outside the present geographical ranges in the Caucasus and the Balkans, south for P. fuscus and north and west for P. syriacus, suggesting that their present distribution is not at equilibrium with the climate. The Last Interglacial distribution of P. fuscus included British Isles and broad areas in western, central, and northern Europe, while P. syriacus extended northwards in the Balkans. The validation with fossil records revealed good predictive performance (omission error?=?4.1 % for P. fuscus and 16.6 % for P. syriacus). During the Last Glacial Maximum, climatic suitability persisted in refugia in southern Europe, Pannonian Basin, and Caucasus for P. fuscus, and Israel, southern Balkans, and Caucasus for P. syriacus. Present potential distributions revealed a low similarity of species’ ecological niches, comparable with Last Interglacial, but projections towards 2080 revealed a sharp increase.     

Investigating the genetic diversity and differentiation patterns in the <Emphasis Type="Italic">Penstemon scariosus</Emphasis> species complex under different sample sizes using AFLPs and SSRs

Habitat fragmentation due to anthropogenic activities is the major cause of biodiversity loss. Endemic and narrowly distributed species are the most susceptible to habitat degradation. Penstemon scariosus is one of many species whose natural habitat is vulnerable to industrialization. All varieties of P. scariosus (P. scariosus var. albifluvis, P. scariosus var. cyanomontanus, P. scariosus var. garrettii, P. scariosus var. scariosus) have small distribution ranges, but only P. scariosus var. albifluvis is being considered for listing under the Endangered Species Act. We used eight microsatellites or simple sequence repeats (SSRs) loci and two amplified fragment length polymorphism (AFLP) primer combinations to investigate the population genetic structure and diversity of P. scariosus varieties. Moreover, we compared the utility of the two marker systems in conservation genetics and estimated an appropriate sample size in population genetic studies. Genetic differentiation among populations based on F_st ranged from low to moderate (F_st?=?0.056–0.157) and from moderate to high when estimated with D_es (D_es?=?0.15–0.32). Also, AMOVA analysis shows that most of the genetic variation is within populations. Inbreeding coefficients (F_is) were high in all varieties (0.20–0.56). The Bayesian analysis, STRUCTURE, identified three clusters from SSR data and four clusters from AFLPs. Clusters were not consistent between marker systems and did not represent the current taxonomy. MEMGENE revealed that a high proportion of the genetic variation is due to geographic distance (R²?=?0.38, P?=?0.001). Comparing the genetic measurements from AFLPs and SSRs, we found that AFLP results were more accurate than SSR results across sample size when populations were larger than 25 individuals. As sample size decreases, the estimates become less stable in both AFLP and SSR datasets. Finally, this study provides insight into the population genetic structure of these varieties, which could be used in conservation efforts.     

Geographic patterns of genetic variation in nuclear and chloroplast genomes of two related oaks (<Emphasis Type="Italic">Quercus aliena</Emphasis> and <Emphasis Type="Italic">Q. serrata</Emphasis>) in Japan: implications for seed and seedling transfer

In this study, we assessed geographic patterns of genetic variations in nuclear and chloroplast genomes of two related native oaks in Japan, Quercus aliena and Q. serrata, in order to facilitate development of genetic guidelines for transfer of planting stocks for each species. A total of 12 populations of Q. aliena and 44 populations of Q. serrata were analyzed in this study. Genotyping of nuclear microsatellites in Q. aliena was done with only nine populations (n = 212) due to limited numbers of individuals in two populations, while all 12 populations (n = 89) were used in sequencing chloroplast DNA (cpDNA). In Q. serrata, 43 populations (n = 1032) were genotyped by nuclear microsatellite markers, while cpDNA of 44 populations (n = 350) was sequenced. As anticipated, geographic patterns detected in the variations of Q. aliena’s nuclear genome and its chloroplast haplotype distribution clearly distinguished northern and southern groups of populations. However, those of Q. serrata were inconsistent. The geographic distribution of its chloroplast haplotypes tends to show the predicted differentiation between northern and southern lineages, but geographic signals in the genetic structure of its nuclear microsatellites are weak. Therefore, treating northern and southern regions of Japan as genetically distinct transferrable zones for planting stocks is highly warranted for Q. aliena. For Q. serrata, the strong NE-SW geographic structure of cpDNA should be considered.