The Great Wall of China: a physical barrier to gene flow?

Cryptic species conservation: a review

Cryptic species are groups of two or more taxa that were previously classified as single nominal species. Being almost morphologically indistinguishable, cryptic species have historically been hard to detect. Only through modern morphometric, genetic, and molecular analyses has the hidden biodiversity of cryptic species complexes been revealed. Cryptic diversity is now widely acknowledged, but unlike more recognisable, charismatic species, scientists face additional challenges when studying cryptic taxa and protecting their wild populations. Demographical and ecological data are vital to facilitate and inform successful conservation actions, particularly at the individual species level, yet this information is lacking for many cryptic species due to their recent taxonomic description and lack of research attention. The first part of this article summarises cryptic speciation and diversity, and explores the numerous barriers and considerations that conservation biologists must navigate to detect, study and manage cryptic species populations effectively. The second part of the article seeks to address how we can overcome the challenges associated with efficiently and non-invasively detecting cryptic species in-situ, and filling vital knowledge gaps that are currently inhibiting applied conservation. The final section discusses future directions, and suggests that large-scale, holistic, and collaborative approaches that build upon successful existing applications will be vital for cryptic species conservation. This article also acknowledges that sufficient data to implement effective species-specific conservation will be difficult to attain for many cryptic animals, and protected area networks will be vital for their conservation in the short term.

Anthropogenic Change and the Process of Speciation

Anthropogenic impacts on the environment alter speciation processes by affecting both geographical contexts and selection patterns on a worldwide scale. Here we review evidence of these effects. We find that human activities often generate spatial isolation between populations and thereby promote genetic divergence but also frequently cause sudden secondary contact and hybridization between diverging lineages. Human-caused environmental changes produce new ecological niches, altering selection in diverse ways that can drive diversification; but changes also often remove niches and cause extirpations. Human impacts that alter selection regimes are widespread and strong in magnitude, ranging from local changes in biotic and abiotic conditions to direct harvesting to global climate change. Altered selection, and evolutionary responses to it, impacts early-stage divergence of lineages, but does not necessarily lead toward speciation and persistence of separate species. Altogether, humans both promote and hinder speciation, although new species would form very slowly relative to anthropogenic hybridization, which can be nearly instantaneous. Speculating about the future of speciation, we highlight two key conclusions: (1) Humans will have a large influence on extinction and "despeciation" dynamics in the short term and on early-stage lineage divergence, and thus potentially speciation in the longer term, and (2) long-term monitoring combined with easily dated anthropogenic changes will improve our understanding of the processes of speciation. We can use this knowledge to preserve and restore ecosystems in ways that promote (re-)diversification, increasing future opportunities of speciation and enhancing biodiversity.

Genetic structure of an endangered species Ormosia henryi in southern China, and implications for conservation

BACKGROUND

The evergreen broadleaved forest (EBLF) is an iconic vegetation type of East Asia, and it contributes fundamentally to biodiversity-based ecosystem functioning and services. However, the native habitat of EBLFs keeps on decreasing due to anthropogenic activities. Ormosia henryi is a valuable rare woody species in EBLFs that is particularly sensitive to habitat loss. In this study, ten natural populations of O. henryi in southern China were sampled, and then genotyping by sequencing (GBS) was applied to elucidate the standing genetic variation and population structure of this endangered species.

RESULTS

In ten O. henryi populations, 64,158 high-quality SNPs were generated by GBS. Based on these markers, a relatively low level of genetic diversity was found with the expected heterozygosity (He) ranging from 0.2371 to 0.2901. Pairwise F_ST between populations varied from 0.0213 to 0.1652, indicating a moderate level of genetic differentiation. However, contemporary gene flow between populations were rare. Assignment test and principal component analysis (PCA) both supported that O. henryi populations in southern China could be divided into four genetic groups, and prominent genetic admixture was found in those populations located in southern Jiangxi Province. Mantel tests and multiple matrix regression with randomization (MMRR) analyses suggested that isolation by distance (IBD) could be the possible reason for describing the current population genetic structure. In addition, the effective population size (Ne) of O. henryi was extremely small, and showed a continuous declining trend since the Last Glacial Period.

CONCLUSIONS

Our results indicate that the endangered status of O. henryi is seriously underestimated. Artificial conservation measures should be applied as soon as possible to prevent O. henryi from the fate of extinction. Further studies are needed to elucidate the mechanism that leading to the continuous loss of genetic diversity in O. henryi and help to develop a better conservation strategy.

Hawkmoth and bee pollinators impact pollen dispersal at the landscape but not local scales in two species of Oenothera

PREMISE

Animal pollinators play an important role in pollen dispersal. Here, we assessed differences in pollen and seed dispersal and the role of pollinator functional groups with different foraging behaviors in generating patterns of genetic diversity over similar geographic ranges for two closely related taxa. We focused on two members of Oenothera section Calylophus (Onagraceae) that co-occur on gypsum outcrops throughout the northern Chihuahuan Desert but differ in floral phenotype and primary pollinator: Oenothera gayleana (bee) and O. hartwegii subsp. filifolia (hawkmoth).

METHODS

We measured breeding system and floral traits and studied gene flow and population differentiation at the local (<13 km; four populations) and landscape (60-440 km; five populations) scales using 10-11 nuclear (pollen dispersal) and three plastid (seed dispersal) microsatellite markers.

RESULTS

Both taxa were self-incompatible and floral traits were consistent with expectations for different pollinators. Seed and pollen dispersal patterns were distinctly different for both species. We found no evidence of genetic structure at the local scale but did at the landscape scale; O. gayleana showed greater differentiation and significant isolation by distance than in O. hartwegii subsp. filifolia. The plastid data were consistent with gravity dispersal of seeds and suggest that pollen dispersal is the principal driver of genetic structure in both species.

CONCLUSIONS

We demonstrated that pollinator functional groups can impact genetic differentiation in different and predictable ways. Hawkmoths, with larger foraging distances, can maintain gene flow across greater spatial scales than bees.

Ancient Great Wall building materials reveal environmental changes associated with oases in northwestern China

Plant materials used in the construction of segments and beacon towers of the ancient Great Wall in northwestern China contain untapped potential for revealing local paleoclimatic and environmental conditions. For the first time, we characterize the molecular preservation and stable carbon and nitrogen isotope compositions of AMS-dated common reeds (Phragmites) collected from ancient Great Wall fascines in today's Gansu and Xinjiang using a combination of chromatographic techniques and isotope analyses. Our molecular data, along with Scanning Electron Microscopy, demonstrate excellent preservation of these ancient reeds, which were harvested from nearby habitats during periods of significant expansion of Imperial China when climate conditions sustained sizeable oases in the region. Stable isotope data capture differential rates of environmental change along the eastern margin of the Tarim Basin since the Han Dynasty (170 BC), implying that significant surface-water hydrological changes occurred only after the Song Dynasty (1160 AD) due to regional climate change. This study reveals the wealth of environmental and climate information obtainable from these site-specific organic building materials and establishes the foundation for further applications of advanced molecular, biochemical, and isotopic technologies to study these common and widely-distributed organic archaeological materials.

Influence of Prevailing Wind Direction on Sapping Quantity of Rammed Earth Great Wall of the Ming Dynasty

Sapping caused by prevailing wind erosion is one of the most significant factors in the deterioration of earthen sites located in Datong County, Qinghai Province, China. Long-term effects of wind may cause surface erosion, or even serious damage to the Great Wall of Ming Dynasty. Difference of sapping quantity should be attributed to variability of the prevailing wind directions. To better understand the effects of wind direction on erosion, meteorological data in the study area for fifty-two years (from 1961 to 2013) were collected and statistically analyzed. Sapping quantity of earthen structure was measured by field investigation on the Wall along the ridge whose azimuth ranges from 95°–244° and mainly concentrated in 140°–210°. Results showing obvious difference of sapping quantity could be observed at both sides of the Wall under the prevailing wind directions (ESE, SE and SSE). Further, the Wall was divided into small segments with a length of 20 m for comparison and maximum sapping quantity could be found at the Wall whose azimuth is at an angle of 30° to the prevailing wind. The aim of this study is to provide reference for the deterioration of the Wall under long-term wind pressure, and provide a targeted conservation method for earthen structure.

More opportunities more species: Pleistocene differentiation and northward expansion of an evergreen broad-leaved tree species Machilus thunbergii (Lauraceae) in Southeast China

BACKGROUND

The broad continuum between tropical and temperate floras in Eastern Asia (EAS) are thought to be one of the main factors responsible for a prominent species diversity anomaly of temperate plants between EAS and eastern North America (ENS). However, how the broad continuum and niche evolution between tropical and temperate floras in EAS contributes to lineage divergence and species diversity remains largely unknown.

RESULTS

Population genetic structure, demography, and determinants of genetic structure [i.e., isolation-by-distance (IBD), isolation-by-resistance (IBR), and isolation-by-environment (IBE)] of Machilus thunbergii Sieb. et Zucc. (Lauraceae) were evaluated by examining sequence variation of ten low-copy nuclear genes across 43 populations in southeast China. Climatic niche difference and potential distributions across four periods (Current, mid-Holocene, the last glacial maximum, the last interglacial) of two genetic clusters were determined by niche modelling. North and south clusters of populations in M. thunbergii were revealed and their demarcation line corresponds well with the northern boundary of tropical zone in China of Zhu & Wan. The divergence time between the clusters and demographic expansion of M. thunbergii occurred after the mid-Pleistocene climate transition (MPT, 0.8-1.2 Ma). Migration rates between clusters were asymmetrical, being much greater from north to south than the reverse. Significant effects of IBE, but non-significant effects of IBD and IBR on population genetic divergence were detected. The two clusters have different ecological niches and require different temperature regimes.

CONCLUSIONS

The north-south genetic differentiation may be common across the temperate-tropical boundary in southeast China. Divergent selection under different temperature regimes (possibly above and below freezing temperature in winter) could account for this divergence pattern. The broad continuum between tropical and temperate floras in EAS may have provided ample opportunities for tropical plant lineages to acquire freezing tolerance and to colonize the temperate regions during the late-Cenozoic global cooling. Our findings shed deeper insights into the high temperate plant species diversity in EAS.

Evolutionary and phylogenetic analyses of the barcoding region suggest geographical relationships among Blastocystis sp., ST3 in humans

Blastocystis sp., has 21 distinct subtypes of which ST3 thought to be the most prevalent subtype. This study aims to analyze the global variations of ST3. In total, 496 sequences with more than 400 nucleotides from Asia, Europe, Africa, and America were included in this study. Results show that allele 34 was the most prevalent allele in all continents. The lowest and highest allele diversity were observed in Europe and Africa, respectively. The nucleotide diversity ranged from 0.0077 in Europe to 0.02 in Africa, and haplotype diversity ranged from 0.461 in America to 0.6 in Africa. The haplotype network and Bayesian structure showed at least two major clusters including Asia and Europe-Africa-America. Tajima's D values for all continents were negative and statistically significant, indicating an excess of rare nucleotide variants. Similarly, the Fu's FS test showed negative values for all regions, indicating an excess of rare haplotypes. Pairwise F_ST exhibited a high genetic differentiation between Asia and other continents. Mismatch analysis for all populations showed a unimodal distribution. Our findings indicate that there are two probable major clusters of Blastocystis sp. ST3, a cluster which is shared between Europe, Africa, and America, and a cluster which is restricted to Asia.

The Zagros Mountains acting as a natural barrier to gene flow in the Middle East: more evidence from the evolutionary history of spiny-tailed lizards (Uromasticinae: Saara)

We investigated the phylogeographic structure of the genus Saara and studied whether the Zagros Mountain ranges influence the gene flow and dispersal at the landscape scale between the Iranian Saara species, including S. asmussi in the central Iranian plateau and S. loricata in the Mesopotamian lowlands. Phylogenetic analyses clearly show three well-supported species, including S. loricata, S. asmussi and S. hardwickii, that are distinct from Uromastyx species. The S-DIVA and BBM analyses demonstrate that species of Saara originated from an ancestor somewhere in the Iranian Plateau and then dispersed to its current geographical range. Our results indicate that the separation of S. loricata from S. asmussi coincides with the orogenic events of the Zagros Mountains during the Pliocene, and thus it may show a vicariance event. Diversification within populations of S. loricata and S. assmussi are estimated to have occurred during the Pleistocene. The haplotype network indicates one haplogroup for each of the Iranian Saara species. Population genetic analyses shows signals of demographic expansions at the beginning of the Holocene for S. loricata. Our results support the hypothesis that the Zagros Mountains act as a barrier for gene flow and Quaternary climatic oscillations affected intraspecific genetic divergences of S. loricata and S. asmussi.

Identifying Linear Traces of the Han Dynasty Great Wall in Dunhuang Using Gaofen-1 Satellite Remote Sensing Imagery and the Hough Transform

The Han Dynasty Great Wall (GH), one of the largest and most significant ancient defense projects in the whole of northern China, has been studied increasingly not only because it provides important information about the diplomatic and military strategies of the Han Empire (206 B.C.–220 A.D.), but also because it is considered to be a cultural and national symbol of modern China as well as a valuable archaeological monument. Thus, it is crucial to obtain the spatial pattern and preservation situation of the GH for next-step archaeological analysis and conservation management. Nowadays, remote sensing specialists and archaeologists have given priority to manual visualization and a (semi-) automatic extraction approach is lacking. Based on the very high-resolution (VHR) satellite remote sensing imagery, this paper aims to identify automatically the archaeological features of the GH located in ancient Dunhuang, northwest China. Gaofen-1 (GF-1) data were first processed and enhanced after image correction and mathematical morphology, and the M-statistic was then used to analyze the spectral characteristics of GF-1 multispectral (MS) data. In addition, based on GF-1 panchromatic (PAN) data, an auto-identification method that integrates an improved Otsu segmentation algorithm with a Linear Hough Transform (LHT) is proposed. Finally, by making a comparison with visual extraction results, the proposed method was assessed qualitatively and semi-quantitatively to have an accuracy of 80% for the homogenous background in Dunhuang. These automatic identification results could be used to map and evaluate the preservation state of the GH in Dunhuang. Also, the proposed automatic approach was applied to identify similar linear traces of other generations of the Great Wall of China (Western Xia Dynasty (581 A.D.–618 A.D.) and Ming Dynasty (1368 A.D.–1644 A.D.)) in various geographic regions. Moreover, the results indicate that the computer-based automatic identification has great potential in archaeological research, and the proposed method can be generalized and applied to monitor and evaluate the state of preservation of the Great Wall of China in the future.

Development and characterization of EST-SSR markers for Vitex negundo var. heterophylla (Lamiaceae)

PREMISE OF THE STUDY

Vitex negundo var. heterophylla (Lamiaceae) is a dominant shrub in the warm temperate zone of northern China. Expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed to investigate its genetic diversity and structure.

METHODS AND RESULTS

We detected 12,075 SSRs in V. negundo var. heterophylla using transcriptome sequencing. Primer pairs for 100 SSR loci were designed and amplified in three populations of V. negundo var. heterophylla. Sixty loci were amplified, of which 14 were polymorphic. The number of alleles per locus ranged from two to 15, and levels of observed and expected heterozygosity ranged from 0.241 to 0.828 and from 0.426 to 0.873, respectively. All primer pairs amplified PCR products from V. rotundifolia but only four of them amplified products from Leonurus japonicus.

CONCLUSIONS

The identified EST-SSR markers will be useful for future molecular and reproductive ecology studies of V. negundo var. heterophylla and V. rotundifolia.

Morphological and Genetic Diversity of Sea Buckthorn (Hippophae rhamnoides L.) in the Karakoram Mountains of Northern Pakistan

Sea buckthorn (Hippophae rhamnoides L.) is a dioecious, wind-pollinated shrub growing in Eurasia including the Karakoram Mountains of Pakistan (Gilgit-Baltistan territory). Contrary to the situation in other countries, in Pakistan this species is heavily underutilized. Moreover, a striking diversity of berry colors and shapes in Pakistan raises the question: which varieties might be more suitable for different national and international markets? Therefore, both morphological and genetic diversity of sea buckthorn were studied to characterize and evaluate the present variability, including hypothetically ongoing domestication processes. Overall, 300 sea buckthorn individuals were sampled from eight different populations and classified as wild and supposedly domesticated stands. Dendrometric, fruit and leaf morphometric traits were recorded. Twelve EST-SSRs (expressed sequence tags-simple sequence repeats) markers were used for genotyping. Significant differences in morphological traits were found across populations and between wild and village stands. A significant correlation was found between leaf area and altitude. Twenty-two color shades of berries and 20 dorsal and 15 ventral color shades of leaves were distinguished. Mean genetic diversity was comparatively high (He = 0.699). In total, three distinct genetic clusters were observed that corresponded to the populations’ geographic locations. Considering high allelic richness and genetic diversity, the Gilgit-Baltistan territory seems to be a promising source for selection of improved germplasm in sea buckthorn.

Species Boundaries Between Three Sympatric Oak Species: Quercus aliena, Q. dentata, and Q. variabilis at the Northern Edge of Their Distribution in China

Oaks are important timber trees with wide distributions in China, but few genetic studies have been conducted on a fine scale. In this study, we seek to investigate the genetic diversity and differentiation of three sympatric oak species (Quercus aliena Blume, Quercus dentata Thunb. ex Murray, and Quercus variabilis Blume) in their northern distribution in China using 17 bi-parentally inherited nSSRs markers and five maternally inherited chloroplast DNA (cpDNA) fragments. Both the cpDNA and the nSSRs show a high level of genetic differentiation between different oak sections. The chloroplast haplotypes are clustered into two lineages. Clear species boundaries are detected between Q. variabilis and either Q. aliena or Q. dentata. The sharing of chloroplast haplotype H1 between Q. aliena and Q. dentata suggests very recent speciation and incomplete lineage sorting or introgression of H1 from one species to another. The nSSRs data indicate a complete fixation of variation within sites for all three oak species, and that extensive gene flow occurs within species whereas only limited gene flow is detected between Q. aliena and Q. dentata and nearly no gene flow can be detected between Q. aliena and Q. variabilis and between Q. dentata and Q. variabilis. Prezygotic isolation may have contributed to the species boundaries of these three sympatric oak species.

Genetic and epigenetic variations associated with adaptation to heterogeneous habitat conditions in a deciduous shrub

Environmentally induced phenotypic plasticity is thought to play an important role in the adaption of plant populations to heterogeneous habitat conditions, and yet the importance of epigenetic variation as a mechanism of adaptive plasticity in natural plant populations still merits further research. In this study, we investigated populations of Vitex negundo var. heterophylla (Chinese chastetree) from adjacent habitat types at seven sampling sites. Using several functional traits, we detected a significant differentiation between habitat types. With amplified fragment length polymorphisms (AFLP) and methylation-sensitive AFLP (MSAP), we found relatively high levels of genetic and epigenetic diversity but very low genetic and epigenetic differences between habitats within sites. Bayesian clustering showed a remarkable habitat-related differentiation and more genetic loci associated with the habitat type than epigenetic, suggesting that the adaptation to the habitat is genetically based. However, we did not find any significant correlation between genetic or epigenetic variation and habitat using simple and partial Mantel tests. Moreover, we found no correlation between genetic and ecologically relevant phenotypic variation and a significant correlation between epigenetic and phenotypic variation. Although we did not find any direct relationship between epigenetic variation and habitat environment, our findings suggest that epigenetic variation may complement genetic variation as a source of functional phenotypic diversity associated with adaptation to the heterogeneous habitat in natural plant populations.

The Tanggula Mountains enhance population divergence in Carex moorcroftii: a dominant sedge on the Qinghai-Tibetan Plateau

High-altitude mountains are often geographic barriers to gene flow and play important roles in shaping population divergence. The central Qinghai-Tibetan Plateau (QTP) stands the location of the Tanggula Mountains (TM). We use the TM as a case, using Carex moorcroftii, a dominant species on the QTP to test the effects of geographic barriers on plant population divergence. We sampled 18 C. moorcroftii populations along a north-south transect crossing the TM to investigate the correlations of genetic variation and morphological traits with climate variables. The results showed this species holds high genetic diversity (H_e = 0.58) and the surveyed populations can be genetically clustered into two groups: populations from the north face of TM, and the other from the south. Gene flow between populations within groups is higher than those between groups. The traits, number and mass of seeds, mass of root and infructescence significantly varied among populations. Mantel-tests detected a weak but significantly positive correlation between genetic and geographic (R² = 0.107, p = 0.032) and climatic distance (R² = 0.162, p = 0.005), indicating both isolation by distance and isolation by environment. These findings together suggest high-altitude mountains of TM interrupt habitat continuity, result in distinct climatic conditions on both sides, increasing population divergence of plant species.

Testing the effect of the Himalayan mountains as a physical barrier to gene flow in Hippophae tibetana Schlect. (Elaeagnaceae)

Hippophae tibetana is a small, dioecious wind-pollinated shrub endemic to the Tibetan-Qinghai Plateau. It is one of the shrubs that occur at very high elevations (5250 m a.s.l.). The Himalayan mountains provides a significant geographical barrier to the Qinghai-Tibetan Plateau, dividing the Himalayan area into two regions with Nepal to the south and Tibet to the north. There is no information on how the Himalayan mountains influence gene flow and population differentiation of alpine plants. In this study, we analyzed eight nuclear microsatellite markers and cpDNA trnT-trnF regions to test the role of the Himalayan mountains as a barrier to gene flow between populations of H. tibetana. We also examined the fine-scale genetic structure within a population of H. tibetana on the north slope of Mount (Mt.) Everest. For microsatellite analyses, a total of 241 individuals were sampled from seven populations in our study area (4 from Nepal, 3 from Tibet), including 121 individuals that were spatially mapped within a 100 m × 100 m plot. To test for seed flow, the cpDNA trnT-trnF regions of 100 individuals from 6 populations (4 from Nepal, 2 from Tibet) were also sequenced. Significant genetic differentiation was detected between the two regions by both microsatellite and cpDNA data analyses. These two datasets agree about southern and northern population differentiation, indicating that the Himalayan mountains represent a barrier to H. tibetana limiting gene flow between these two areas. At a fine scale, spatial autocorrelation analysis suggests significant genetic structure within a distance of less than 45 m, which may be attributed mainly to vegetative reproduction and habitat fragmentation, as well as limited gene flow.

Effect of Yangtze River on population genetic structure of the relict plant Parrotia subaequalis in eastern China

Parrotia subaequalis (Hamamelidaceae) is a Tertiary relic species endemic in eastern China. We used inter‐simple sequence repeat (ISSR) markers to access genetic diversity and population genetic structure in natural five populations of P. subaequalis. The levels of genetic diversity were higher at species level (H = 0.2031) but lower at population level (H = 0.1096). The higher genetic diversity at species levels might be attributed to the accumulation of distinctive genotypes which adapted to the different habitats after Quaternary glaciations. Meanwhile, founder effects on the early stage, and subsequent bottleneck of population regeneration due to its biological characteristics, environmental features, and human activities, seemed to explain the low population levels of genetic diversity. The hierarchical AMOVA revealed high levels (42.60%) of among‐population genetic differentiation, which was in congruence with the high levels of Nei's genetic differentiation index (G_ST = 0.4629) and limited gene flow (N_m = 0.5801) among the studied populations. Mantel test showed a significant isolation‐by‐distance, indicating that geographic isolation has a significant effect on genetic structure in this species. Unweighted pair‐group method with arithmetic average clustering, PCoA, and Bayesian analyses uniformly recovered groups that matched the geographical distribution of this species. In particular, our results suggest that Yangtze River has served as a natural barrier to gene flow between populations occurred on both riversides. Concerning the management of P. subaequalis, the high genetic differentiation among populations indicates that preserving all five natural populations in situ and collecting enough individuals from these populations for ex situ conservation are necessary.

Comparative genetic structure between Sedum ussuriense and S. kamtschaticum (Crassulaceae), two stonecrops co-occurring on rocky cliffs

• Premise of the study: Geographic isolation due to discontinuities of suitable habitat may have significant effects on the genetic structure of plant populations. Even within a few kilometers, physical barriers to gene flow may lead to considerable genetic differentiation among populations.• Methods: Sedum ussuriense is a boreal species that in Korea occurs only in four valleys separated by mountain ranges in Juwangsan National Park and its vicinity (a range of ∼15 km). Its congener S. kamtschaticum, by contrast, co-occurs in the four valleys but also on the intervening mountains. Using 12 allozyme loci, we comparatively assessed genetic variability and structure in 12 population pairs of the two stonecrops.• Key results: While we found high and comparable levels of within-population genetic variation for the two species, among-population divergence was significantly higher in S. ussuriense (F_ST = 0.261 vs. F_ST = 0.165). Sedum ussuriense also showed a much higher percentage of among-valley variation (19%) than S. kamtschaticum (4%).• Conclusions: High levels of genetic diversity in the two Sedum species are consistent with the previous hypothesis that mountains of the Korean Peninsula served as glacial refugia for many boreal species. Given that the two congeners have similar life-history traits, the lower among-population differentiation in S. kamtschaticum is attributable to its higher abundance and more continuous distribution in the study area. This study confirms the central role of geographic isolation in the genetic structure of plant species even at very small scales.

A platform of high-density INDEL/CAPS markers for map-based cloning in Arabidopsis

Map-based cloning has been widely used to identify genes responsible for mutant phenotypes in Arabidopsis, especially those mutants generated by EMS or fast neutron mutagenesis. The success of map-based cloning relies on the availability of molecular markers that distinguish the polymorphisms between two Arabidopsis ecotypes. So far, most molecular markers in Arabidopsis have been generated by individual laboratories or the Arabidopsis Information Resource (TAIR). However, the TAIR markers, which are distributed unevenly on the five Arabidopsis chromosomes, only cover approximately 25% of the Arabidopsis BACs. Designing and testing molecular markers is still a time-consuming endeavor. Here we report the construction of a high-resolution BAC-based Arabidopsis mapping platform (AMP), using Col-0 and Ler as model ecotypes. The AMP comprises 1346 markers (1073 INDEL and 273 CAPS/dCAPS markers), of which 971 were newly designed and experimentally confirmed, 179 were from published papers and 196 were TAIR markers. These AMP markers cover 1186 BACs, 1121 of which are in non-centromere regions, representing approximately 75% of the Arabidopsis BACs in non-centromere regions. All the marker information is included on the AMP website (http://amp.genomics.org.cn/) for easy access and download, and sets of standard markers for initial chromosomal localization of a particular gene are recommended. The feasibility of using the AMP to map mutated genes is also discussed.

Statistical methods in spatial genetics

The joint analysis of spatial and genetic data is rapidly becoming the norm in population genetics. More and more studies explicitly describe and quantify the spatial organization of genetic variation and try to relate it to underlying ecological processes. As it has become increasingly difficult to keep abreast with the latest methodological developments, we review the statistical toolbox available to analyse population genetic data in a spatially explicit framework. We mostly focus on statistical concepts but also discuss practical aspects of the analytical methods, highlighting not only the potential of various approaches but also methodological pitfalls.

Genetic diversity and spatial genetic structure within a population of an aromatic shrub, Lippia origanoides (Verbenaceae), in the Chicamocha Canyon, northeastern Colombia

The geographical scale of genetic structure in a continuous population is highly dependent on its breeding system and dispersion capabilities, and this knowledge is important for the study of population dynamics as well as for conservation purposes. In the present study, spatial autocorrelation statistics and intersimple sequence repeat (ISSR) markers were used to describe the genetic structure of a natural population of a prominent aromatic plant, Lippia origanoides, native to the Chicamocha Canyon in northeastern Colombia. For this purpose, individuals were sampled from two localities within the Chicamocha Canyon, where the species is abundant and continuously distributed. Cluster (principal coordinate analysis (PCO) and unweighted pair group method using arithmetic averages (UPGMA)), analysis of molecular variance (AMOVA) and Bayesian analyses revealed a low level of genetic differentiation among the two localities, suggesting that they belong to a single population. Genetic diversity levels in this population, described as the percentage of polymorphic loci (P=86.21%) and quantified using Shannon's diversity index (I=0.453) and the average panmictic heterozygosity (HB=0.484), were shown to be comparable to or higher than that in other plant species with allogamous breeding systems and to other related Verbenaceae species. Fine-scale autocorrelation analyses showed a pattern consistent with the classical model of isolation by distance with moderate but significant levels of local spatial structure. Our results suggest that sampling individuals at distances greater than approximately 1.2 km may result in the collection of different genotypes, which could help preserve the levels of genetic diversity in a propagation programme. The causes of this spatial pattern are currently unknown and could be influenced by many contemporary factors such as restricted seed dispersal and/or short-distance pollen movement, among others.

Population genetic structure of the medicinal plant Vitex rotundifolia in China: implications for its use and conservation

Vitex rotundifolia L. is an important plant species used in traditional Chinese medicine. For its efficient use and conservation, genetic diversity and clonal variation of V. rotundifolia populations in China were investigated using inter-simple sequence repeat markers. Fourteen natural populations were included to estimate genetic diversity, and a large population with 135 individuals was used to analyze clonal variation and fine-scale spatial genetic structure. The overall genetic diversity (GD) of V. rotundifolia populations in China was moderate (GD = 0.190), with about 40% within-population variation. Across all populations surveyed, the average within-population diversity was moderate (P = 22.6%; GD = 0.086). A relatively high genetic differentiation (G(st) = 0.587) among populations was detected based on the analysis of molecular variance data. Such characteristics of V. rotundifolia are likely attributed to its sexual/asexual reproduction and limited gene flow. The genotypic diversity (D = 0.992) was greater than the average values of a clonal plant, indicating its significant reproduction through seedlings. Spatial autocorrelation analysis showed a clear within-population structure with gene clusters of approximately 20 m. Genetic diversity patterns of V. rotundifolia in China provide a useful guide for its efficient use and conservation by selecting particular populations displaying greater variation that may contain required medicinal compounds, and by sampling individuals in a population at >20 m spatial intervals to avoid collecting individuals with identical or similar genotypes.

Genetic diversity of five Kobresia species along the eastern Qinghai-Tibet plateau in China

Plants of the genus Kobresia are alpine grass species of high ecological and economic importance. Vegetative growth is the dominant means of reproduction for the Kobresia. Studies suggest that substantial vegetative growth can reduce genetic diversity and renders populations less able to buffer changing and extreme conditions. Kobresia are dominant species in the Qinghai-Tibet plateau in China where they face harsh conditions and frequent disturbance. The genetic diversity of five Kobresia species (K. humilis, K. royleana, K. kansuensis , K. tibetica and K. setchwanensis) from the Qinghai-Tibet plateau was assessed. The results reveal high genetic diversity at the population level for all of the species and there does not appear to be a relationship between altitude and genetic diversity. AMOVA analysis shows that most genetic variability resides among individuals within populations, whereas only a minor portion is found among populations. Of the five species, K. royleana and K. kansuensis have the highest levels of gene flow and the lowest genetic differentiation. While K. setchwanensis has the lowest gene flow and the greatest genetic differentiation. The level of gene flow between populations and the mating system play a critical role in the genetic structure of these Kobresia populations. Despite the predominance of vegetative growth enough sexual reproduction occurs to maintain the relatively high genetic diversity in Kobresia populations.

Genetic diversity of the narrow endemic Astragalus oniciformis (Fabaceae)

Astragalus oniciformis Barneby is a narrow endemic xerophyte of the upper Snake River Plain of central Idaho, USA, where it inhabits stabilized, aeolian sand deposits and previously burned, sandy sites over Quaternary basalt flows. The objective of this study was to determine the levels and distribution of genetic differentiation within and among populations of A. oniciformis. Fifteen individuals from each of eight populations, chosen from throughout the range of the species, were selected based on accessibility, density of individuals, and large population size. Inter-simple sequence repeats were chosen as the marker to assess genetic differentiation. The two primers selected yielded 40 polymorphic loci in A. oniciformis. In an analysis of molecular variance, 88.69% of the variation was significantly attributed to variation within populations. High gene flow (N(m) = 3.91-3.93; SD = 0.01) and a low percentage deviation from Hardy-Weinberg equilibrium due to population subdivision (G(ST) = 0.113-0.1134; SD = 0.0002) were found among sampled populations. These results suggest that current threats to this species, including changing fire patterns and habitat loss from grazing disturbance, have not yet affected the genetic diversity of this species. Preservation of large populations and smaller, intervening, dispersed patches will help preserve the genetic integrity and the genetic diversity found in A. oniciformis.