Environmental variation shapes genetic variation in Bouteloua gracilis: Implications for restoration management of natural populations and cultivated varieties in the southwestern United States

With the increasing frequency of large‐scale restoration efforts, the need to understand the adaptive genetic structure of natural plant populations and their relation to heavily utilized cultivars is critical. Bouteloua gracilis (blue grama) is a wind‐dispersed, perennial grass consisting of several cytotypes (2n = 2×–6×) with a widespread distribution in western North America. The species is locally dominant and used regularly in restoration treatments. Using amplified fragment length polymorphism (AFLP) and cpDNA analyses, we assessed the genetic variability and adaptive genetic structure of blue grama within and among 44 sampling sites that are representative of the species’ environmental and habitat diversity in the southwestern United States. Five cultivars were also included to investigate genetic diversity and differentiation in natural versus cultivated populations. Three main findings resulted from this study: (a) Ninety‐four polymorphic AFLP markers distinguished two population clusters defined largely by samples on and off the Colorado Plateau; (b) substructure of samples on the Colorado Plateau was indicated by genetic divergence between boundary and interior regions, and was supported by cytotype distribution and cpDNA analysis; and (c) six AFLP markers were identified as “outliers,” consistent with being under selection. These loci were significantly correlated to mean annual temperature, mean annual precipitation, precipitation of driest quarter, and precipitation of wettest quarter in natural populations, but not in cultivated samples. Marker × environment relationships were found to be largely influenced by cytotype and cultivar development. Our results demonstrate that blue grama is genetically variable, and exhibits genetic structure, which is shaped, in part, by environmental variability across the Colorado Plateau. Information from our study can be used to guide the selection of seed source populations for commercial development and long‐term conservation management of B. gracilis, which could include genetic assessments of diversity and the adaptive potential of both natural and cultivated populations for wildland restoration.     

Patterns of Genetic Variation in Swertia przewalskii, an Endangered Endemic Species of the Qinghai-Tibet Plateau

Swertia przewalskii Pissjauk. (Gentianaceae) is a critically endangered and endemic plant of the Qinghai-Tibet Plateau in China. RAPD and ISSR analyses were carried out on a total of 63 individuals to assess the extent of genetic variation in the remaining three populations. Percentage of polymorphic bands was 94% (156 bands) for RAPD and 96% (222 bands) for ISSR. A pairwise distance measure calculated from the RAPD and ISSR data was used as input for analysis of molecular variance (AMOVA). AMOVA indicated that a high proportion of the total genetic variation (52% for RAPD and 56% for ISSR) was found among populations; pairwise Φ _ST comparisons showed that the three populations examined were significantly different (p < 0.001). Significant genetic differentiation was found based on different measures (AMOVA and Hickory θ_B) in S. przewalskii (0.52 on RAPD and 0.56 on ISSR; 0.46 on RAPD and 0.45 on ISSR). The differentiation of the populations corresponded to low average gene flow (0.28 based on RAPD and 0.31 based on ISSR), whereas genetic distance-based clustering and coalescent-based assignment analyses revealed significant genetic isolation among populations. Our results indicate that genetic diversity is independent of population size. We conclude that although sexual reproduction and gene flow between populations of S. przewalskii are very limited, they have preserved high levels of genetic diversity. The main factors responsible for the high level of difference among populations are the isolation and recent fragmentation under human disturbance.     

The response of mycorrhizal colonization to elevated CO2 and climate change in Pascopyrum smithii and Bouteloua gracilis

Large intact soil cores of nearly pure stands of Pascopyrum smithii (western wheatgrass, C₃) and Bouteloua gracilis (blue grama, C₄) were extracted from the Central Plains Experimental Range in northeastern Colorado, USA and transferred to controlled environment chambers. Cores were exposed to a variety of water, temperature and CO₂ regimes for a total of four annual growth cycles. Root subsamples were harvested after the completion of the second and fourth growth cycles at a time corresponding to late winter, and were examined microscopically for the presence of mycorrhizae. After two growth cycles in the growth chambers, 54% of the root length was colonized in P. smithii, compared to 35% in blue grama. Field control plants had significantly lower colonization. Elevation of CO₂ increased mycorrhizal colonization in B. gracilis by 46% but had no effect in P. smithii. Temperatures 4° C higher than normal decreased colonization in P. smithii by 15%. Increased annual precipitation decreased colonization in both species. Simulated climate change conditions of elevated CO₂, elevated temperature and lowered precipitation decreased colonization in P. smithii but had less effect on B. gracilis. After four growth cycles in P. smithii, trends of treatments remained similar, but overall colonization rate decreased.     

Alleviation of salt-induced stress on seed emergence using soil additives in a greenhouse

Use of sodium chloride (NaCl) as a deicing salt results in high concentrations of ions in roadside soils, which decreases seedling emergence in these areas. Greenhouse experiments performed in soil culture tested the efficacy of three soil fertilizers, gypsum (CaSO₄), potash (potassium chloride, KCl) and potassium nitrate (KNO₃), in alleviating NaCl stress on seedling emergence of three grass species exhibiting a range of salt tolerance, Poa pratensis (Kentucky bluegrass), Bouteloua gracilis (blue grama), and Puccinellia distans (alkali grass). Two-factor factorial designs were utilized for each species-fertilizer combination. Treatments of 5000 mg/L (0.086 M) NaCl with or without fertilizer, in concentrations that were equal to 0.5, 1, and 2 times the molar equivalent of 5000 mg/L NaCl were applied biweekly. Salt stress on Poa pratensis emergence was alleviated by all fertilizers with CaSO₄ having the greatest effect in alleviating NaCl stress and potash and potassium nitrate alleviating stress at lower treatment levels. Emergence of Bouteloua gracilis and Puccinellia distans was in most cases negatively effected by soil amendments.     

Stocking may increase mitochondrial DNA diversity but fails to halt the decline of endangered Atlantic salmon populations

Over the last 50 years, Spanish Atlantic salmon (Salmo salar) populations have been in decline. In order to bolster these populations, rivers were stocked with fish of northern European origin during the period 1974–1996, probably also introducing the furunculosis-inducing pathogen, Aeromonas salmonicida. Here we assess the relative importance of processes influencing mitochondrial (mt)DNA variability in these populations from 1948 to 2002. Genetic material collected over this period from four rivers in northern Spain (Cantabria) was used to detect variability at the mtDNA ND1 gene. Before stocking, a single haplotype was found at high frequency (0.980). Following stocking, haplotype diversity (h) increased in all rivers (mean h before stocking was 0.041, and 0.245 afterwards). These increases were due principally to the dramatic increase in frequency of a previously very low frequency haplotype, reported at higher frequencies in northern European populations proximate to those used to stock Cantabrian rivers. Genetic structuring increased after stocking: among-river differentiation was low before stocking (1950s/1960s Φ _ST = –0.00296–0.00284), increasing considerably at the height of stocking (1980s Φ _ST = 0.18932) and decreasing post-stocking (1990s/2002 Φ _ST = 0.04934–0.03852). Gene flow from stocked fish therefore seems to have had a substantial role in increasing mtDNA variability. Additionally, we found significant differentiation between individuals that had probably died from infectious disease and apparently healthy, angled fish, suggesting a possible role for pathogen-driven selection of mtDNA variation. Our results suggest that stocking with non-native fish may increase genetic diversity in the short term, but may not reverse population declines.     

RAPD variation and population genetic structure of Physalaemus cuvieri (Anura: Leptodactylidae) in Central Brazil

Studies about the organization of the genetic variability and population structure in natural populations are used either to understand microevolutionary processes or the effects of isolation by human-inducted landscape modifications. In this paper, we analyzed patterns of genetic population structure using 126 RAPD loci scored for 214 individuals of Physalaemus cuvieri, sampled from 18 local populations. Around 97% of these loci were polymorphic. The among-population variation component (Φ_ST) obtained by AMOVA was equal to 0.101 and θ ^B obtained using a Bayesian approach for dominant markers was 0.103. Genetic divergence, analyzed by Mantel spatial correlogram, revealed only a short-distance significant correlation between genetic and geographic distances. This is expected if low levels of population differentiation, due to high abundance buffering the effect of stochastic processes, are combined with low spatially restricted gene flow. Although this may be consistent with the current knowledge of species’ biology, the spatial distribution of local populations observed in this study also suggest that, at least in part, recent human occupation and habitat fragmentation may also explain part of the interpopulational component of the genetic variation.     

Soil water dynamics,transpiration, and water losses in a crested wheatgrass and native shortgrass ecosystem

The status of water in soil and vegetation was monitored in a stand of crested wheatgrass (Agropyron cristatum) and a nearby shortgrass steppe during a growing season. This was done to determine if water use and losses were similar among two very different communities in a similar climate. Precipitation was similar throughout the study period for both the crested wheatgrass and native shortgrass communities. However, the native shortgrass community with greater root biomass had consistently greater soil water depletion in the deeper soil horizons than was found in the crested wheatgrass community. Greater depletion of soil water by native shortgrass species suggests that they might be more competitive than crested wheatgrass in a water-limited environment.Crested wheatgrass maintained high leaf water potential early in the season, but lower water potential during the latter part of the growing season as compared with the major species of the shortgrass steppe, blue grama (Bouteloua gracilis) and western wheatgrass (Agropyron smithii). Leaf conductance was lower for crested wheatgrass than for the native grasses during the later part of the growing season. Consequently, seasonal transpiration for crested wheatgrass was lower when compared with blue grama or western wheatgrass. Lower conductance allowed crested wheatgrass to maintain relatively high internal water potential and may have accounted for less soil water use at deeper soil depths during the latter part of the growing season.Water loss through transpiration was less for western wheatgrass than for either blue grama or crested wheatgrass because western wheatgrass had less leaf area. However, western wheatgrass was as efficient as the other species in its use of water. Crested wheatgrass transpired more water than blue grama early in the growing season, but less than either native species for the remainder of the growing season. Estimated seasonal transpiration loss was greater in the shortgrass ecosystem than in the established crested wheatgrass stand.     

Genetic transformation of blue grama grass with the <Emphasis Type="BoldItalic">rolA</Emphasis> gene from <Emphasis Type="BoldItalic">Agrobacterium rhizogenes</Emphasis>: regeneration of transgenic plants involves a “hairy embryo” stage

Until recently, information about the effects of transforming plants with the rolA gene of Agrobacterium rhizogenes has been restricted mainly to dicots in which a severely wrinkled phenotype, reduced internode distances, and abnormal reproductive development were commonly observed. In this work, we analyzed the effects associated with the expression of this gene in a new genetic context: the forage grass genome. Transgenic P_35S•rolA plants of blue grama grass (Bouteloua gracilis) were obtained by a biolistic approach employing embryogenic chlorophyllic cells as the target material. Four independent transgenic lines with regeneration capacity were recovered, which showed stable integration of this transgene as demonstrated by polymerase chain reaction and Southern blot hybridization. Growth of the rolA-transformed lines under greenhouse conditions provided evidence for a new biotechnological application for the rolA gene in plants, namely, the improvement of biomass production in forage grasses. Additionally, we described here a new phenotypic marker (referred to here as the “hairy embryo” syndrome) that can be instrumental for the early identification of transformation events when transforming grasses with this gene.     

Genetic Diversity and Geographic Differentiation in the Threatened Species Dysosma pleiantha in China as Revealed by ISSR Analysis

Dysosma pleiantha, an important threatened medicinal plant species, is restricted in distribution to southeastern China. The species is capable of reproducing both sexually and asexually. In this study, inter-simple sequence repeat marker data were obtained and analyzed with respect to genetic variation and genetic structure. The extent of clonality, together with the clonal and sexual reproductive strategies, varied among sites, and the populations under harsh ecological conditions tended to have large clones with relatively low clonal diversity caused by vegetative reproduction. The ramets sharing the same genotype show a clumped distribution. Across all populations surveyed, average within-population diversity was remarkably low (e.g., 0.111 for Nei’s gene diversity), with populations from the nature reserves maintaining relatively high amounts of genetic diversity. Among all populations, high genetic differentiation (AMOVA: Φ_ST = 0.500; Nei’s genetic diversity: G _ST = 0.465, Bayesian analysis: Φ_B = 0.436) was detected, together with an isolation-by-distance pattern. Low seedling recruitment due to inbreeding, restricted gene flow, and genetic drift are proposed as determinant factors responsible for the low genetic diversity and high genetic differentiation observed.     

Detection of Low Genetic Variation in a Critically Endangered Chinese Pine, Pinus squamata, Using RAPD and ISSR Markers

With only 32 individuals in the northeastern corner of Yunnan Province, China, Pinus squamata is one of the most endangered conifers in the world. Using two classes of molecular markers, RAPD and ISSR, its very low genetic variation was revealed. Shannon's index of phenotypic diversity (I) was 0.030, the mean effective number of alleles per locus (A_e) was 1.032, the percentage of polymorphic loci (P) was 6.45, and the expected heterozygosity (H_e) was 0.019 at the species level based on RAPD markers. The results of ISSR were consistent with those detected by RAPD but somewhat higher (I = 0.048, A_e = 1.042, P = 12.3, H_e = 0.029). The genetic variation of the subpopulation on the southwest-facing slope was much higher than that of the subpopulation on the northeast-facing slope, which may be attributed to the more diverse environment on the southwest-facing slope. The genetic differentiation between the two subpopulations was very low. The between-subpopulation variabilities, Φ_ST, calculated from RAPD and ISSR data were 0.011 and 0.024. Because of the lack of fossil records and geological historical data, it was difficult to explain the extremely low genetic diversity of the species. We postulate that this ancient pine might have experienced strong bottlenecks during its long evolutionary history, which caused the loss of genetic variation. Genetic drift and inbreeding in post-bottlenecked small populations may be the major forces that contribute to low genetic diversity. Human activities such as logging may have accelerated the loss of genetic diversity in P. squamata.     

Genetic structure, population size, and seed production of Pulsatilla vulgaris Mill. (Ranunculaceae) in Central Germany

Pulsatilla vulgaris Mill. (Ranunculaceae) is a rare and rapidly declining grassland community species that was once widespread at a time when Central Germany was covered by steppe vegetation. Through the course of this study, the patterns of random-amplified polymorphic DNA (RAPD) variation among 11 populations of varying size were analysed to assess any possible local differentiation, in relation to spatial isolation, resulting from random genetic drift brought on by reduced population size and lack of migration between geographically isolated populations. Following results attained from methods including: multivariate analysis based on asymmetric Soerensen similarity, φ_ST-statistics, and analysis of molecular variance, we were able to conclude that there is a high within-population variability (84.4%) and a weak, but significant, differentiation among populations (φ_ST=0.17). A matrix correlation between genetic and geographical distances revealed that geographical differentiation was reflected in the RAPD profile (Mantel test: r=0.47,p=0.002). Further significant correlations were noted between population size and both percentage of polymorphic loci (p=0.02) and genetic diversity (p=0.03). An additional analysis of seed production showed that mean seed set, seed number, and mean seed mass per population could be attributed to differences in population size, whereas only seed mass was related to genetic variation.     

Genetic analysis of two Portuguese populations of <Emphasis Type="Italic">Ruditapes decussatus</Emphasis> by RAPD profiling

The clam Ruditapes decussatus is commercially important in the south of Portugal. The random amplified polymorphic DNA (RAPD) technique was applied to assess the genetic diversity and population structure of two Portuguese populations occurring in the Ria Formosa (Faro) and the Ria de Alvor, respectively. Twenty-five individuals of each population were investigated by RAPD profiles. Genetic diversity within populations, measured by the percentage of polymorphic loci (%P), varied between 68.57% (Alvor) and 73.88% (Faro). Shannon’s information index (H) and Nei’s gene diversity (h) were 0.281 and 0.176, respectively, for the Alvor population and 0.356 and 0.234 for the Faro population. Overall, genetic variation within R. decussatus populations was high. The total genetic diversity (H _T) was explained by a low variation between populations (G _ST = 0.145), which is consistent with high gene flow (N _m = 2.9). The analysis of molecular variance (AMOVA) showed that 65% of variability is within populations and 35% between populations (Φ_PT = 0.345; P ≥ 0.001). The value of Nei’s genetic distance was 0.0881, showing a low degree of population genetic distance, despite the different geographic origin. This is the first study on the population genetics of R. decussatus by RAPD technique. The results may be useful for restocking programs and aquaculture.     

Genetic Differentiation of Pedunculate Oak Quercus robur L. in the European Part of Russia Based on RAPD Markers

Using randomly amplified polymorphic DNA markers (RAPD), genetic variation and differentiation in four populations of pedunculate oak Quercus robur L. were examined. The populations occupy a large part of the Quercus robur range in the European Russia (Voronezh and Novgorod oblasts; Republics of Mordovia and Bashkortostan). With each of six random primers (A02, A09, A17, B01, B08, B11), 96 DNA samples were analyzed by PCR. In all, 48 putative polymorphic RAPD loci were detected. We failed to reveal population-specific DNA fragments for any primer although the frequencies of 14 fragments were significantly different among populations. The oak populations studied exhibited high variability: 73–90% of genes were polymorphic and the effective allele number was about 1.4. The total genetic variation varied from 0.202 (Vor) to 0.245 (Nov), which corresponded to the estimates for populations of this species from Central and Western Europe. The populations examined showed low among-population differentiation (G _ST = 0.098); gene flow N _e m was 4.61. The proportion of among-population variation of the RAPD loci studied accounted for 7% of the total variability; more than 93% of the total variability was explained by individual and within-population variation.     

Morphological and microsatellite diversity associated with ecological factors in natural populations of Medicago laciniata Mill. (Fabaceae)

Genetic variability in 10 natural Tunisian populations of Medicago laciniata were analysed using 19 quantitative traits and 12 polymorphic microsatellite loci. A large degree of genetic variability within-populations and among-populations was detected for both quantitative characters and molecular markers. High genetic differentiation among populations for quantitative traits was seen, with Q _ST = 0.47, and F _ST = 0.47 for microsatellite markers. Several quantitative traits displayed no statistical difference in the levels of Q _ST and F _ST . Further, significant correlations between quantitative traits and eco-geographical factors suggest that divergence in the traits among populations may track environmental differences. There was no significant correlation between genetic variability at quantitative traits and microsatellite markers within populations. The site-of-origin of eco-geographical factors explain between 18.13% and 23.40% of genetic variance among populations at quantitative traits and microsatellite markers, respectively. The environmental factors that most influence variation in measured traits among populations are assimilated phosphorus (P₂0₅) and mean annual rainfall, followed by climate and soil texture, altitude and organic matter. Significant associations between eco-geographical factors and gene diversity, H _e , were established in five-microsatellite loci suggesting that these simple sequence repeats (SSRs) are not necessarily biologically neutral.     

Antibiotic-resistantArthrobacter sp. andPseudomonas sp. responses in the rhizosphere of blue grama after herbage removal

Summary Streptomycin-resistant Pseudomonas and Arthrobacter were isolated from semi-arid grassland soil and their relative responses in the rhizosphere of blue grama (Bouteloua gracilis) subjected to herbage removal were evaluated. Using plants grown in normal soil, the two bacteria showed differential responses to herbage removal, which were most marked in the rhizoplane, where the Pseudomonas showed a two-log unit increase over a 60 hour period, while Arthrobacter, in contrast, exhibited a one-log unit decrease in viable counts for at least 48 hours after defoliation, responses which are similar to those observed in root exudate medium experiments by earlier workers. These results suggest that the rhizoplane may be a critical environment for interaction of these two types of microorganisms, and that sequential responses of the root-associated soil microorganisms may occur after herbage removal from this important rangeland plant. These responses are most likely associated with increased exudate release following herbage removal, which has been best documented using blue grama grown under sterile conditions.     

Effects of nitrogen availability on competition between Bromus tectorum and Bouteloua gracilis

Exotic plant invasions are a serious concern for land managers and conservationists. There is evidence that increased nitrogen availability favors exotic species and decreased nitrogen availability favors non-weedy native species. This study was conducted to test the effect of nitrogen availability on competition between two grass species with contrasting life histories, cheatgrass (Bromus tectorum), a North American exotic, and blue grama (Bouteloua gracilis), a North American native. We investigated the effects of nitrogen availability and competition on aboveground biomass, belowground biomass, height, and % nitrogen tissue concentrations by growing the two species in the greenhouse under five levels of nitrogen and six levels of competition. Nitrogen availability affected competition between Bromus tectorum and Bouteloua gracilis. At the lowest level of N availability, neither species was affected by competition. As N availability increased, aboveground biomass gain of Bromus was more negatively affected by intraspecific competition relative to interspecific competition while the opposite occurred for Bouteloua. At the competition level at which each species gained the most aboveground biomass, Bromus had a linear response to increasing N availability while the response of Bouteloua was asymptotic. Our results do provide some support for the theory that fast growing exotic species have a rapid response to nutrient enrichment while native non-weedy species do not, and that low N levels can reduce competitive pressure from the exotic on the native.     

Transgenic plants of blue grama grass,Bouteloua gracilis (H.B.K.) Lag. ex Steud., from microprojectile bombardment of highly chlorophyllous embryogenic cells

For the first time, the production of transgenic plants of the forage grass blue grama, Bouteloua gracilis [H.B.K.] Lag. ex Steud., is reported. Transgenic plants containing a gus0nptll fusion driven by a double CaMV35S promoter were obtained by microprojectile bombardment of the highly chlorophyllous embryogenic cell line 'TIANSJ98'. Transformed B. gracilis cell lines resisted a lethal concentration of 160 mg/l of kanamycin for at least 8 months. Chlorophyll development and growth rate were used as useful criteria for discriminating transformed from non-transformed clones. Stable integration of the transgene in the blue grama genome was demonstrated by PCR and Southern-hybridization analysis. Expression of the NPTll protein in transgenic plants grown under greenhouse conditions was confirmed indirectly by spraying kanamycin (150-250 mg/l) on plant foliage, and directly by ELISA immunological tests. Control plants sprayed with kanamycin showed foliar necrosis and reduced growth (tillering) compared to plants containing the transgene. NPTll was found in transgenic plants in levels ranging between 12.6 and 29.6 ng/mg FW of cells, as determined by ELISA reactions.     

Low levels of quantitative and molecular genetic differentiation among natural populations of Medicago ciliaris Kroch. (Fabaceae) of different Tunisian eco-geographical origin

In this paper, we analyze the genetic variability in four Tunisian natural populations of Medicago ciliaris using 19 quantitative traits and six polymorphic microsatellite loci. We investigated the amplification transferability of 30 microsatellites developed in the model legume M. truncatula to M. ciliaris. Results revealed that about 56.66% of analyzed markers are valuable genetic markers for M. ciliaris. The most genetic diversity at quantitative traits and microsatellite loci was found to occur within populations (>80%). Low differentiations among populations at quantitative traits Q _ST  = 0.146 and molecular markers F _ST  = 0.18 were found. The majority of measured traits exhibited no significant difference in the level of Q _ST and F _ST . Furthermore, significant correlations established between these traits and eco-geographical factors suggested that natural selection should be invoked to explain the level of phenotypic divergence among populations rather than drift. There was no significant correlation between population differentiation at quantitative traits and molecular markers. Significant spatial genetic structure consistent with models of isolation by distance was detected within all studied populations. The site-of-origin environmental factors explain about 9.07% of total phenotypic genetic variation among populations. The eco-geographical factors that influence more the variation of measured traits among populations are the soil texture and altitude. Nevertheless, there were no consistent pattern of associations between gene diversity (He) and environmental factors.     

Molecular genetic structure and evolution in native and colonized populations of the Chinese mitten crab, Eriocheir sinensis

Chinese mitten crab (Eriocheir sinensis), a native species in China, has populated Continental Europe and North America since 1912. In this paper, the nucleotide variation in the fragments of mitochondrial COII (693 bp), Cytb (766 bp), and nucleotide ITS (706 bp) was analyzed in native (Yantgze, Yellow, and Liaohe Rivers in China) and colonized (Elbe, Rhine, and Thames Rivers in Europe, and San Francisco Bay in North America) populations of the Chinese mitten crab. The major findings are as follows. First, the genetic variability in the native populations is higher than that in the colonized European and North American populations, with the exception of the Elbe River population, which possesses a similar level of variability with the native populations. Second, a remarkable loss of singletons has been associated with the colonization of Chinese mitten crabs. Third, the AMOVA and F _ST results demonstrate that there are no significant genetic differentiations among the populations from the three continents, but there is a significant differentiation between pairwise populations within and among continents. Fourth, it is found that expansion-drift and gene flow pattern are involved in the European populations. The neutrality test and R ₂ statistics suggest that a moderate founder population exists in the colonized populations, and only the Yangtze River population has undergone a recent population expansion. Finally, the results demonstrate that the European populations originate from multiple rivers in China on multiple occasions. The San Francisco population originates from both the native Chinese populations and the colonized European populations, most likely the Thames population.     

Distribution and genetic structure of the Japanese wood pigeon (Columba janthina) endemic to the islands of East Asia

The Japanese wood pigeon (Columba janthina) is endemic to the islands of East Asia and it is included in the Japanese and Asian Red Lists because of its narrow habitat range that is restricted to mature forests on small islands and because of the destruction of these habitats. We examined the genetic structure of Columba janthina by studying 463 base pairs of the mitochondrial control region sequences. We analyzed 154 samples from eight populations and identified 27 haplotypes. Three population groups were identified based on the pairwise Φ_ST values. A substantial gene flow, as reflected by the low and non-significant Φ_ST values, is maintained among the northern group that includes six populations found on the Okinawa, Tokara, Goto, Setouchi, Oki, and Izu islands. In contrast, the southeastern group found on the Ogasawara Islands had large Φ_ST values with every population from other regions (0.910 < Φ_ST < 0.962). The southwestern group found on the Sakishima Islands also had significant but small Φ_ST values with every population from the northern group (0.081 < Φ_ST < 0.205). The Mantel test showed a highly significant correlation between the Φ_ST values and the route length of the habitat network, as well as the linear distance with correction of the habitat gap effect, indicating the importance of the closely connected structure of the habitats. The three groups mentioned above could be considered as independent management units, and the southeastern group has the highest conservation priority due to its narrow distribution range and small population size. Electronic Supplementary Material The online version of this article (doi: ) contains supplementary material, which is available to authorized users.