A map of copy number variations in Chinese populations

It has been shown that the human genome contains extensive copy number variations (CNVs). Investigating the medical and evolutionary impacts of CNVs requires the knowledge of locations, sizes and frequency distribution of them within and between populations. However, CNV study of Chinese minorities, which harbor the majority of genetic diversity of Chinese populations, has been underrepresented considering the same efforts in other populations. Here we constructed, to our knowledge, a first CNV map in seven Chinese populations representing the major linguistic groups in China with 1,440 CNV regions identified using Affymetrix SNP 6.0 Array. Considerable differences in distributions of CNV regions between populations and substantial population structures were observed. We showed that ～35% of CNV regions identified in minority ethnic groups are not shared by Han Chinese population, indicating that the contribution of the minorities to genetic architecture of Chinese population could not be ignored. We further identified highly differentiated CNV regions between populations. For example, a common deletion in Dong and Zhuang (44.4% and 50%), which overlaps two keratin-associated protein genes contributing to the structure of hair fibers, was not observed in Han Chinese. Interestingly, the most differentiated CNV deletion between HapMap CEU and YRI containing CCL3L1 gene reported in previous studies was also the highest differentiated regions between Tibetan and other populations. Besides, by jointly analyzing CNVs and SNPs, we found a CNV region containing gene CTDSPL were in almost perfect linkage disequilibrium between flanking SNPs in Tibetan while not in other populations except HapMap CHD. Furthermore, we found the SNP taggability of CNVs in Chinese populations was much lower than that in European populations. Our results suggest the necessity of a full characterization of CNVs in Chinese populations, and the CNV map we constructed serves as a useful resource in further evolutionary and medical studies.     

Allozyme variation of African and Iberian populations of the genus Cobitis

African and Iberian populations of the genus Cobitis exhibit high morphological polymorphism and their taxonomy is unclear. In seven such populations the percentage of polymorphic loci ranged between _ P =0.08–0.48 and mean heterozygosity per locus H =0.005–0.073. The lowest Nei genetic distance between African and Iberian populations of Cobitis was D =0.250. The populations separated with the formation of the Gibraltar strait 5 million years ago. C. calderoni is a well-differentiated branch from the rest of the Iberian populations of the genus. Our analysis supports the concept that C. paludica populations and C. maroccana are referable to the subgenus Iberocobitis . These African and Iberian populations represent two taxa, C. maroccana Pellegrin, 1929 and C. paludica De Buen, 1930. C. maroccana and C. paludica populations are monophyletic and the African population is the most differentiated genetically. The Arrago population of C. paludica is genetically the most differentiated of the Iberian populations. Our allozyme data do not support the previous consideration of the Albufera lagoon population as a different species from C. paludica .     

Population structuring of the ubiquitous stingless bee Tetragonisca angustula in southern Brazil as revealed by microsatellite and mitochondrial markers

Tetragonisca angustula is one of the most widespread stingless bees in the Neotropics. This species swarms frequently and is extremely successful in urban environments. In addition, it is one of the most popular stingless bee species for beekeeping in Latin America, so nest transportation and trading is common. Nest transportation can change the genetic structure of the host population, reducing inbreeding and increasing homogenization. Here, we evaluate the genetic structure of 17 geographic populations of T. angustula in southern Brazil to quantify the level of genetic differentiation between populations. Analyses were conducted on partially sequenced mitochondrial genes and 11 microsatellite loci of 1002 workers from 457 sites distributed on the mainland and on 3 islands. Our results show that T. angustula populations are highly differentiated as demonstrated by mitochondrial DNA (mtDNA) and microsatellite markers. Of 73 haplotypes, 67 were population‐specific. MtDNA diversity was low in 9 populations but microsatellite diversity was moderate to high in all populations. Microsatellite data suggest 10 genetic clusters and low level of gene flow throughout the studied area. However, physical barriers, such as rivers and mountain ranges, or the presence or absence of forest appear to be unrelated to population clusters. Factors such as low dispersal, different ecological conditions, and isolation by distance are most likely shaping the population structure of this species. Thus far, nest transportation has not influenced the general population structure in the studied area. However, due to the genetic structure we found, we recommend that nest transportation should only occur within and between populations that are genetically similar.     

Variability of sexual organ possession rates and phylogenetic analyses of a parthenogenetic Japanese earthworm, Amynthas vittatus (Oligochaeta: Megascolecidae)

Although earthworms are hermaphroditic animals with biparental sexual reproduction, some parthenogenetic species have been found. Evolutionary trends in parthenogenetic earthworms revealed a reduction in the reproductive organs. To clarify the phylogenetic relationships of parthenogenetic earthworms with different degree of degraded reproductive organs, we conducted a morphological analysis of the reproductive organs and molecular phylogenetic analyses of Amynthas vittatus which usually degraded a part of reproductive organs. Morphological analysis revealed that almost all individuals collected around Mt. Aobayama, Sendai city of northeastern Japan, possessed male pores, while individuals collected from areas located across Hirose River did not. Phylogenetic analysis using mitochondrial DNA sequences of 48 individuals representing 20 populations indicated that almost all individuals collected around Mt. Aobayama belonged to a different lineage from the other populations collected around Sendai, and that almost all individuals collected from across Japan belonged to the latter lineage. We suggest that the difference in the male pore possession rate was caused by histories of each population, but the A. vittatus population found on Mt. Aobayama belongs to a different lineage as compared to the other Japanese populations and not the primitive population. Thus, the parthenogenetic earthworm A. vittatus has undergone at least two morphological evolutionary processes.     

Unparallel diversification in bacterial microcosms

Adaptive speciation has gained popularity as a fundamental process underlying the generation of diversity. We tested whether populations respond to similar forms of disruptive selection by diversifying in similar or parallel ways by investigating diversified populations of Escherichia coli B evolved in glucose and glucose-acetate environments. In both environments, the populations have differentiated into two phenotypes, named for their characteristic colony morphologies: large (L) and small (S). Each type is heritable and this polymorphism (or 'diversified pair') appears to be maintained by negative frequency dependence. The L and S phenotypes from different environments are convergent in their colony morphology and growth characteristics. We tested whether diversification was parallel by conducting competition experiments between L and S types from different environments. Our results indicate that replicate diversified pairs from different environments have not diversified in parallel ways and suggest that subtle differences in evolutionary environment can crucially affect the outcome of adaptive diversification.     

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

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

Unraveling the journey of cancer stem cells from origin to metastasis

Cancer biology research over recent decades has given ample evidence for the existence of self-renewing and drug-resistant populations within heterogeneous tumors, widely recognized as cancer stem cells (CSCs). However, a lack of clear understanding about the origin, existence, maintenance, and metastatic roles of CSCs limit efforts towards the development of CSC-targeted therapy. In this review, we describe novel avenues of current CSC biology. In addition to cell fusion and horizontal gene transfer, CSCs are originated by mutations in somatic or differentiated cancer cells, resulting in de-differentiation and reprogramming. Recent studies also provided evidence for the existence of distinct or heterogeneous CSC populations within a single heterogeneous tumor. Our analysis of the literature also opens the doors for a novel hypothesis that CSC populations with specific phenotypes, metabolic profiles, and clonogenic potential metastasize to specific organs.     

Selection promotes organ compartmentalization in HIV-1: evidence from gag and pol genes

The existence of organ-specific human immunodeficiency virus type 1 (HIV-1) populations within infected hosts has been long lasting studied. Previous work established that population subdivision by organs occurs at the envelope env gene, but less is known about other genomic regions. Here, we used a population genetics approach to detect organ compartmentalization in proviral sequences of HIV-1 gag and pol genes. Significant population structure was found in pol (100% of cases) and gag (33%) pair-wise organ comparisons. The degree of compartmentalization positively correlated with the ratio of nonsynonymous to synonymous substitutions, and codons showing organ compartmentalization were more likely to be under significantly positive selection. This suggests that HIV-1 populations dynamically adapt to locally variable intra-host environments. In the case of pol gene, differential penetration of antiretroviral drugs might account for the observed pattern, whereas for gag gene, local selective pressures remain unexplored.     

Inferring admixture proportions from molecular data: extension to any number of parental populations

The relative contribution of two parental populations to a hybrid group (the admixture proportions) can be estimated using not only the frequencies of different alleles, but also the degree of molecular divergence between them. In this paper, we extend this possibility to the case of any number of parental populations. The newly derived multiparental estimator is tested by Monte Carlo simulations and by generating artificial hybrid groups by pooling mtDNA samples from human populations. The general properties (including the variance) of the two-parental estimator seem to be retained by the multiparental estimator. When mixed human populations are considered and hypervariable single-locus data are analyzed (mtDNA control region), errors in the estimated contributions appear reasonably low only when highly differentiated parental populations are involved. Finally, the method applied to the hybrid Canary Island population points to a much lower female contribution from Spain than has previously been estimated.     

Assessment of the genetic diversity among Glyptosternum maculatum, an endemic fish of Yarlung Zangbo River, Tibet, China using SSR markers

The genetic diversity of Glyptosternum maculatum populations from Nyang River, Lhasa River, and Shetongmon Reach of Yarlung Zangbo River was assessed using six microsatellite markers. Overall, the genetic diversity across the three populations was low. The Shetongmon population exhibited the highest level of genetic diversity in terms of number of alleles and effective alleles, heterozygosity, and polymorphic information content value, followed by the Nyang population and Lhasa population. The analysis of molecular variance demonstrated that almost the variation (86.64%) occurred within populations. The differentiation among populations was not significant, and population structure was weak. These results revealed that three natural populations of G. maculatum are not genetically differentiated and the large disparity of living altitude did not caused genetic differentiation between different populations. Our observations will help identify the genetic relationship among populations to understand the genetic diversity of G. maculatum.     

青藏高原特有植物露蕊乌头（毛茛科）从冰期避难所扩张后繁殖资源分配的变化

物种分布范围的形成是进化生态学研究的基本问题之一。但植物的资源分配策略是否与物种边界形成有关一直没有相关研究。青藏高原特有植物露蕊乌头在末次最大冰期时有4个避难所,但冰期后只有一个避难所的种群发生了扩张并最终形成了现代分布格局。以露蕊乌头的避难所种群（同仁种群）和扩张后邻近分布区边缘的两个种群（兴海种群和海北种群）为研究对象,通过比较避难所种群和边缘种群的资源分配方式,探讨露蕊乌头的资源分配与该植物分布区及边界形成的关系。结果发现：1）兴海和海北种群的营养结构（包括根、植株高度和茎叶生物量）均显著低于同仁种群．海北种群的繁殖结构（花数量和花生物量）显著低于同仁和兴海种群,但海北和兴海的繁殖分配均显著高于同仁种群;2）3个种群的繁殖资源与个体大小呈现显著的正相关关系,投入到繁殖资源的比例（繁殖分配）与个体大小呈显著的负相关关系。对露蕊乌头的研究结果一方面进一步证明了个体大小依赖的繁殖分配,但不符合“植物开始繁殖必须达到一定的大小（阈值）”这一结论,这可能与露蕊乌头的生活史特征有关：而另一方面,露蕊乌头在扩张过程中逐渐增加了对繁殖资源投资的比例,说明胁迫生境中有性繁殖对该植物具有更为重要的意义,且露蕊乌头在扩张过程中可能逐渐实现繁殖产出最大化,并可能在边缘种群实现最优繁殖分配进而最终形成该物种分布区的边界,但这一结论仍需在更多的植物类群中验证。     

Human Races: A Genetic and Evolutionary Perspective

Race is generally used as a synonym for subspecies , which traditionally is a geographically circumscribed, genetically differentiated population. Sometimes traits show independent patterns of geographical variation such that some combination will distinguish most populations from all others. To avoid making "race" the equivalent of a local population, minimal thresholds of differentiation are imposed. Human "races" are below the thresholds used in other species, so valid traditional subspecies do not exist in humans. A "subspecies" can also be defined as a distinct evolutionary lineage within a species. Genetic surveys and the analyses of DNA haplotype trees show that human "races" are not distinct lineages, and that this is not due to recent admixture; human "races" are not and never were "pure." Instead, human evolution has been and is characterized by many locally differentiated populations coexisting at any given time, but with sufficient genetic contact to make all of humanity a single lineage sharing a common evolutionary fate.     

Circulating Virus Load Determines the Size of Bottlenecks in Viral Populations Progressing within a Host

For any organism, population size, and fluctuations thereof, are of primary importance in determining the forces driving its evolution. This is particularly true for viruses—rapidly evolving entities that form populations with transient and explosive expansions alternating with phases of migration, resulting in strong population bottlenecks and associated founder effects that increase genetic drift. A typical illustration of this pattern is the progression of viral disease within a eukaryotic host, where such demographic fluctuations are a key factor in the emergence of new variants with altered virulence. Viruses initiate replication in one or only a few infection foci, then move through the vasculature to seed secondary infection sites and so invade distant organs and tissues. Founder effects during this within-host colonization might depend on the concentration of infectious units accumulating and circulating in the vasculature, as this represents the infection dose reaching new organs or “territories”. Surprisingly, whether or not the easily measurable circulating (plasma) virus load directly drives the size of population bottlenecks during host colonization has not been documented in animal viruses, while in plants the virus load within the sap has never been estimated. Here, we address this important question by monitoring both the virus concentration flowing in host plant sap, and the number of viral genomes founding the population in each successive new leaf. Our results clearly indicate that the concentration of circulating viruses directly determines the size of bottlenecks, which hence controls founder effects and effective population size during disease progression within a host.     

Bottlenecks, drift and differentiation: the population structure and demographic history of sika deer (Cervus nippon) in the Japanese archipelago

We assessed genetic differentiation and diversity in 14 populations of sika deer (Cervus nippon) from Japan and four populations of sika deer introduced to the UK, using nine microsatellite loci. We observed extreme levels of differentiation and significant differences in diversity between populations. Our results do not support morphological subspecies designations, but are consistent with previous mitochondrial DNA analyses which suggest the existence of two genetically distinct lineages of sika deer in Japan. The source of sika introduced to the UK was identified as Kyushu. The underlying structure of Japanese populations probably derives from drift in separate glacial refugia and male dispersal limited by distance. This structure has been perturbed by bottlenecks and habitat fragmentation, resulting from human activity from the mid-nineteenth century. Most current genetic differentiation and differences in diversity among populations probably result from recent drift. Coalescent model analysis suggests sika on each of the main Japanese islands have experienced different recent population histories. Hokkaido, which has large areas of continuous habitat, has maintained high levels of gene flow. In Honshu the population is highly fragmented and is likely to have been evolving by drift alone. In Kyushu there has been a balance between gene flow and drift but all the populations have experienced high levels of drift. Habitat fragment size was not significantly associated with genetic diversity in populations but there was a significant correlation between habitat fragment size and effective population size.     

Genome scale assessment of a species translocation program

Despite increased use of species translocations, controversy remains regarding the efficacy and efficiency of the strategy in obtaining conservation goals. Much of this controversy results from vague program objectives, unclear definitions of success, and lack of follow-up monitoring. We used the translocation program initiated by Zoo Knoxville for the federally threatened Bog Turtle (Glyptemys muhlenbergii) as a case study to demonstrate how genomic assessments not only assess the success of program objectives, but also allow managers to quickly obtain baseline data from which program objectives and explicit definitions of ‘success’ can be determined. Here we used 7030 SNP markers derived from RADseq data to confirm the premise that different source populations are genetically differentiated. Then we tested whether the release population has enhanced genetic diversity, as expected from a deliberate admixture. Although the release population had greater diversity than any source population, variation was lower than expected from modeling admixture with equal source contribution. Our results support the premise that genetic diversity can be maximized by including representatives from as many natural populations as possible. But failure to achieve the expected level of diversity could result from nonrandom success of founders from different sources or unrecorded bias in the implementation of the release program. Many existing and future translocation programs would benefit from genetic assessment similar to that conducted here with Bog Turtles.     

Cytochrome b sequence divergence in the European sea bass (Dicentrarchus labrax) and phylogenetic relationships among some Perciformes species

The entire cytochrome b (cyt b ) gene has been sequenced in eight Mediterranean populations of the European sea bass, Dicentrarchus labrax and in one of D. punctatus . Our data indicate that both eastern (Greece and Egypt) and northwestern (French coast) populations of D. labrax were genetically differentiated from the Tyrrhenian ones, which were nearly indistinguishable from each other at the cyt b level. The D. labrax population from the Atlantic coast (Portugal) was genetically quite distinct from all the Mediterranean ones. These results strongly confirm the conclusions from previous studies where the same populations were screened for allozymes, random amplified polymorphic DNA (RAPD) and mitochondrial DNA (mtDNA) d -loop variation. Seven other species of Perciformes belonging to five different families (Sparidae, Serranidae, Carangidae, Pomatomidae, Sciaenidae) were sequenced to explore the usefulness of the cyt b gene for inferring evolutionary relationships at different hierarchical levels. The data were analysed together with other published cyt b sequences from Perciformes fishes. Our data suggest that the superfamily Percoidea is not monophyletic. At the family level, the Sparidae and Moronidae seem to be monophyletic. The evolutionary relationships among families were not resolved. Possible causes for this lack of resolution are discussed.     

Distinguishing between primary and secondary intergradation among morphologically differentiated populations of Anolis marmoratus

Distinguishing between primary and secondary intergradation among differentiated populations, and the relative importance of drift and selection, are persistent problems in evolutionary biology. An historical perspective on population interactions can provide insight into the nature of contacts, and thus help resolve these questions. Continuously distributed populations of Anolis marmoratus from the island of Basse Terre in the Guadeloupean archipelago of the Lesser Antilles show a striking degree of geographic variation in morphology. Initial surveys of mtDNA variation from throughout the Guadeloupean Archipelago revealed one case where levels of sequence difference and phylogenetic relationships of alleles from morphologically differentiated populations from the east coast of Basse Terre were consistent with primary intergradation. In this paper, I examine the genetic population structure of a series of populations spanning this north-south cline in morphological variation to test the hypothesis of primary intergradation. Sequences of the mitochondrial cytochrome-b gene from 50 individuals representing five populations spanning the cline were obtained and fourteen unique haplotypes (differing by 2% or less) were detected. Patterns of nucleotide substitution among haplotypes do not deviate from neutral expectation indicating no effect of selection at the level of mtDNA sequences. Estimates of population structure and gene flow were made using both summary statistics for nucleotide diversity (N_at) and cladistic methods. The results are sensitive to the choice of gene flow model, and this is discussed in detail. Mitochondrial variation in the northern populations may not be at equilibrium, and the phylogeny of alleles is consistent with a recent increase in effective population size. Estimates of nucleotide diversity, gene flow, and the phylogenetic relationships of haplotypes indicate that the southern-most population (representing the extreme of morphological variation along this cline) has been relatively isolated from populations to the north and has experienced a reduced effective population size. The apparent clinal variation between the southern population and the others may therefore reflect secondary contact and introgression rather than primary intergradation.     

Isolation by distance in the spore-forming soil bacterium Myxococcus xanthus

Genetic differentiation between spatially separated populations within a species is commonly observed in plants and animals, but its existence in microbes has long been a contentious issue. Traditionally, many microbial ecologists have reasoned that microbes are not limited by dispersal as a result of their immense numbers and microscopic size. In this view, the absence of barriers to gene flow between populations would prevent differentiation of populations by genetic drift and hinder local adaptation. Myxococcus xanthus is a globally distributed, spore-forming bacterium that offers a robust test for genetic differentiation among populations because sporulation is expected to enhance dispersal. Using multi-locus sequence data, we show here that both diversity and the degree of differentiation between populations increase as a function of distance in M. xanthus. Populations are consistently differentiated at scales exceeding 10(2)-10(3) km, and isolation by distance, the divergence of populations by genetic drift due to limited dispersal, is responsible. Our results provide new insights into how genetic diversity within species of free-living microbes is distributed from centimeter to global scales.     

Population structure of common juniper in the Cis-Urals and Southern Urals

The population structure of common juniper (Juniperus communis L.) growing in the Cis-Urals and Southern Urals has been studied using 17 morphological traits of generative and vegetative organs. A multivariate analysis of ten coenopopulations has recognized three phenotypically different local populations: Cis-Ural, forest Cis-Ural forest-steppe, and Southern Ural mountain populations. The Cis-Ural forest population is strictly associated with lowland pine forests of the northwestern part of the Bashkir Cis-Urals. The Cis-Ural forest-steppe population is located in the northwestern part of the Bashkir Cis-Urals and the southeastern part of the Udmurt Cis-Urals. The Southern Ural mountain population is located in the central part of the Southern Urals and is associated mainly with mountain pine and dark coniferous forests. The last population is divided into forest and forest-edge subpopulations; the first one is represented by typical undergrowth locations, whereas the second is associated with open steppelike slopes and forest edges. In general, based on morphological traits of generative organs, the revealed local subpopulations hold an intermediate position between the Eastern European and Siberian populations of common juniper. Based on the morphological traits of vegetative organs, Cis-Ural populations are considered related to the populations of the European part of Russia, whereas the mountain Southern Ural population resemble Siberian populations. Concerning morphological traits of generative organs, the intrapopulation phenotypic diversity of common juniper is higher for mountain habitats; in the case of vegetative organs, the maximum diversity is observed for lowland habitats. The character of phenotypic differentiation determines the need to conserve the gene pool of common juniper of the Cis-Urals and southern Urals on a population basis.     

Diversity among peripheral populations: genetic and evolutionary differentiation of Salamandra atra at the southern edge of the Alps

Separate populations at the edge of a species range are receiving great attention and have been shown to be often different from populations in the core area. However, it has rarely been tested whether neighboring peripheral populations are genetically and evolutionarily similar to each other, as expected for their geographical proximity and similar ecological conditions, or differ due to historical contingency. We investigated isolation and differentiation, within‐population genetic diversity and evolutionary relationships among multiple peripheral populations of a cold‐adapted terrestrial salamander, Salamandra atra, at the southern edge of the species core range. We carried out population genetic, phylogeographic, and phylogenetic analyses on various molecular markers (10 autosomal microsatellite loci, three mitochondrial loci with total length >2,100 bp, two protein‐coding nuclear genes) sampled from more than 100 individuals from 13 sites along the southern Prealps. We found at least seven isolated peripheral populations, all highly differentiated from the remaining populations and differentiated from each other at various levels. The within‐population genetic diversity was variable in the peripheral populations, but consistently lower than in the remaining populations. All peripheral populations along the southern Prealps belong to an ancient lineage that is also found in the Dinarides but did not contribute to the postglacial recolonization of the inner and northern Alps. All fully melanistic populations from the Orobian mountains to the southern Dinarides represent a single clade, to the exclusion of the two yellow‐patched populations inhabiting the Pasubio massif and the Sette Comuni plateau, which are distinguished as S. atra pasubiensis and S. atra aurorae, respectively. In conclusion, multiple populations of S. atra at the southern edge of the species core area have different levels of differentiation, different amount of within‐population genetic diversity, and different evolutionary origin. Therefore, they should be regarded as complementary conservation targets to preserve the overall genetic and evolutionary diversity of the species.