Nuclear DNA Variation Research Articles

Comparative systematics and phylogeography of Quercus Section Cerris in western Eurasia: inferences from plastid and nuclear DNA variation.

Oaks (Quercus) comprise more than 400 species worldwide and centres of diversity for most sections lie in the Americas and East/Southeast Asia. The only exception is the Eurasian sect. Cerris that comprises about 15 species, most of which are confined to western Eurasia. This section has not been comprehensively studied using molecular tools. Here, we assess species diversity and provide a first comprehensive taxonomic and phylogeographic scheme of western Eurasian members of sect. Cerris using plastid (trnH-psbA) and nuclear (5S-IGS) DNA variation with a dense intra-specific and geographic sampling. Chloroplast haplotypes primarily reflected phylogeographic patterns originating from interspecific cytoplasmic gene flow within sect. Cerris and its sister section Ilex. We identified two widespread and ancestral haplotypes, and locally restricted derived variants. Signatures shared with Mediterranean species of sect. Ilex, but not with the East Asian Cerris oaks, suggest that the western Eurasian lineage came into contact with Ilex only after the first (early Oligocene) members of sect. Cerris in Northeast Asia had begun to radiate and move westwards. Nuclear 5S-IGS diversification patterns were more useful for establishing a molecular-taxonomic framework and to reveal hybridization and reticulation. Four main evolutionary lineages were identified. The first lineage is comprised of Q. libani, Q. trojana and Q. afares and appears to be closest to the root of sect. Cerris. These taxa are morphologically most similar to the East Asian species of Cerris, and to both Oligocene and Miocene fossils of East Asia and Miocene fossils of western Eurasia. The second lineage is mainly composed of the widespread Q. cerris and the narrow endemic species Q. castaneifolia, Q. look, and Q. euboica. The third lineage comprises three Near East species (Q. brantii, Q. ithaburensis and Q. macrolepis), well adapted to continental climates with cold winters. The forth lineage appears to be the most derived and comprises Q. suber and Q. crenata. Q. cerris and Q. trojana displayed high levels of variation; Q. macrolepis and Q. euboica, previously treated as subspecies of Q. ithaburensis and Q. trojana, likely deserve independent species status. A trend towards inter-specific crosses was detected in several taxa; however, we found no clear evidence of a hybrid origin of Q. afares and Q. crenata, as currently assumed.

Genetic structure of Octopus minor around Chinese waters as indicated by nuclear DNA variations (Mollusca, Cephalopoda).

Octopus minor is an economically important resource commonly found in Chinese coastal waters. The nuclear gene (RD and ODH) approach of investigation has not reported in this species. Rhodopsin (RD) and octopine dehydrogenase (ODH) genes were used to elaborate the genetic structure collected from eight localities ranging from the northern to the southern coast of China. In total, 118 individuals for the RD gene and 108 for the ODH were sequenced. Overall (RD and ODH) genes resulted in high (0.741±0.032; 0.805±0.038) haplotype and low nucleotide (0.01261±0.00165; 0.00747±0.00086) diversity. Molecular variance displayed higher values among the populations and lower values within the population where the fixation index FST denoted 0.880 and 0.584 in RD and ODH genes respectively. The Dongshan population clustered separately in a phylogenetic tree as in the haplotype networking assessment. The current data suggests that the Dongshan population needs separate management.

Analysis of retrotransposon abundance, diversity and distribution in holocentric Eleocharis (Cyperaceae) genomes.

Background and AimsLong terminal repeat-retrotransposons (LTR-RTs) comprise a large portion of plant genomes, with massive repeat blocks distributed across the chromosomes. Eleocharis species have holocentric chromosomes, and show a positive correlation between chromosome numbers and the amount of nuclear DNA. To evaluate the role of LTR-RTs in karyotype diversity in members of Eleocharis (subgenus Eleocharis), the occurrence and location of different members of the Copia and Gypsy superfamilies were compared, covering interspecific variations in ploidy levels (considering chromosome numbers), DNA C-values and chromosomal arrangements.MethodsThe DNA C-value was estimated by flow cytometry. Genomes of Eleocharis elegans and E. geniculata were partially sequenced using Illumina MiSeq assemblies, which were a source for searching for conserved proteins of LTR-RTs. POL domains were used for recognition, comparing families and for probe production, considering different families of Copia and Gypsy superfamilies. Probes were obtained by PCR and used in fluorescence in situ hybridization (FISH) against chromosomes of seven Eleocharis species.Key ResultsA positive correlation between ploidy levels and the amount of nuclear DNA was observed, but with significant variations between samples with the same ploidy levels, associated with repetitive DNA fractions. LTR-RTs were abundant in E. elegans and E. geniculata genomes, with a predominance of Copia Sirevirus and Gypsy Athila/Tat clades. FISH using LTR-RT probes exhibited scattered and clustered signals, but with differences in the chromosomal locations of Copia and Gypsy. The diversity in LTR-RT locations suggests that there is no typical chromosomal distribution pattern for retrotransposons in holocentric chromosomes, except the CRM family with signals distributed along chromatids.ConclusionsThese data indicate independent fates for each LTR-RT family, including accumulation between and within chromosomes and genomes. Differential activity and small changes in LTR-RTs suggest a secondary role in nuclear DNA variation, when compared with ploidy changes.

Isolation by environment in the highly mobile olive ridley turtle (Lepidochelys olivacea) in the eastern Pacific.

Spatial and temporal scales at which processes modulate genetic diversity over the landscape are usually overlooked, impacting the design of conservation management practices for widely distributed species. We examine processes shaping population divergence in highly mobile species by re-assessing the case of panmixia in the iconic olive ridley turtle from the eastern Pacific. We implemented a biophysical model of connectivity and a seascape genetic analysis based on nuclear DNA variation of 634 samples collected from 27 nesting areas. Two genetically distinct populations largely isolated during reproductive migrations and mating were detected, each composed of multiple nesting sites linked by high connectivity. This pattern was strongly associated with a steep environmental gradient and also influenced by ocean currents. These findings relate to meso-scale features of a dynamic oceanographic interface in the eastern tropical Pacific (ETP) region, a scenario that possibly provides different cost-benefit solutions and selective pressures for sea turtles during both the mating and migration periods. We reject panmixia and propose a new paradigm for olive ridley turtles where reproductive isolation due to assortative mating is linked to its environment. Our study demonstrates the relevance of integrative approaches for assessing the role of environmental gradients and oceanographic currents as drivers of genetic differentiation in widely distributed marine species. This is relevant for the conservation management of species of highly mobile behaviour, and assists the planning and development of large-scale conservation strategies for the threatened olive ridley turtles in the ETP.

The curious case of Bradypus variegatus sloths: populations in threatened habitats are biodiversity components needing protection

Studying Neotropical wild populations is of particular interest. While this region is facing an escalating habitat degradation, it also has remarkable biodiversity levels, whose origin we are only beginning to understand. A myriad of processes might have had idiosyncratic effects on its numerous species. Within the hottest Neotropical biodiversity hotspot, the Atlantic Forest (AF), species and genetic diversities are organized latitudinally, with decreasing diversity levels southwards. Bradypus variegatus, the brown-throated three-toed sloth, was one of the first species observed to present such pattern. Moreover, within AF, B. variegatus populations seem to be geographically isolated and genetically differentiated. Whether AF B. variegatus isolation, differentiation, and loss of genetic diversity are historical or contemporary (anthropogenic-driven), result from species-specific or general historical events, and if this is of conservation concern remains unclear. Here, we combine micro-evolutionary, multilocus, and high-throughput sequencing approaches to detail the processes responsible for the patterns of genetic diversity on B. variegatus populations in AF, and further understand AF biogeographic history. Few studies made use of similar approaches on Neotropical biodiversity. Our results agree with recent re-interpretations on the AF refugia model and support a species-specific refugium in southern AF, characterized by a metapopulation formation. Finally, we present compelling evidences of the need for conservation actions on AF B. variegatus populations, by comparing genetic diversity levels between populations of different Bradypus species. As far as we know, this is the most comprehensive assessment on Bradypus nuclear DNA diversity.

The origin of wild populations of Toxicodendron succedaneum on mainland Japan revealed by genetic variation in chloroplast and nuclear DNA.

Toxicodendron succedaneum: (L.) Kuntze is a tree cultivated for the production of sumac wax, which is extracted from the mesocarp. There are several hypotheses regarding the origin of T. succedaneum on mainland Japan. In this study, the geographical distribution of genetic variation in 13 wild populations on Honshu, Shikoku, Kyushu, and Ryukyu Islands, Japan was investigated and compared with that of individuals from continental Asia. Seven chloroplast DNA haplotypes of T. succedaneum were observed in Japan and could be divided into three lineages based on relatedness between haplotypes. One of these lineages was also observed in continental Asia, and the others were genetically distant from the haplotypes that originated on the continent, with one considered to have originated on the Ryukyu Islands, and the other on mainland Japan. The genetic diversity of both chloroplast and nuclear DNA was lower in populations from Ryukyu Islands than in populations from mainland Japan. Bayesian clustering based on nuclear genotypes showed a clear difference between the groups from Ryukyu Islands and mainland Japan. Based on approximate Bayesian computation analysis of polymorphic data for both genomes, it was inferred that wild populations of T. succedaneum on mainland Japan consist of both lineages with natural distribution on mainland Japan and those introduced from Ryukyu Islands and continental Asia.

Genetic assessment of an isolated endemic Samango monkey (Cercopithecus albogularis labiatus) population in the Amathole Mountains, Eastern Cape Province, South Africa.

The endemic Samango monkey subspecies (Cercopithecus albogularis labiatus) inhabits small discontinuous Afromontane forest patches in the Eastern Cape, KwaZulu-Natal midlands and southern Mpumalanga Provinces in South Africa. The subspecies is affected by restricted migration between forest patches which may impact on gene flow resulting in inbreeding and possible localized extinction. Current consensus, based on habitat quality, is that C.a.labiatus can be considered as endangered as the small forest patches they inhabit may not be large enough to sustain them. The aim of this study was to conduct a molecular genetic investigation to determine if the observed isolation has affected the genetic variability of the subspecies. A total of 65 Samango monkeys (including juveniles, subadults and adults) were sampled from two localities within the Hogsback area in the Amathole Mountains. Nuclear and mitochondrial DNA variation was assessed using 17 microsatellite markers and by sequencing the hypervariable 1 region (HVR1). Microsatellite data generated was used to determine population structure, genetic diversity and the extent of inbreeding. Sequences of the HVR1 were used to infer individual origins, haplotype sharing and haplotype diversity. No negative genetic factors associated with isolation such as inbreeding were detected in the two groups and gene flow between groups can be regarded as fairly high primarily as a result of male migration. This was in contrast to the low nuclear genetic diversity observed (H o=0.45). A further reduction in heterozygosity may lead to inbreeding and reduced offspring fitness. Translocations and establishment of habitat corridors between forest patches are some of the recommendations that have emerged from this study which will increase long-term population viability of the subspecies.

Cell-free mitochondrial DNA copy number variation in head and neck squamous cell carcinoma: A study of non-invasive biomarker from Northeast India.

Head and neck squamous cell carcinoma is the most commonly diagnosed cancer worldwide. The lifestyle, food habits, and customary practices manifest the Northeast Indian population toward higher susceptibility to develop head and neck squamous cell carcinoma. Here, we have investigated the association of smoke and smokeless tobacco, and alcohol with copy number variation of cell-free mitochondrial DNA and cell-free nuclear DNA in cases and controls. Cell-free DNA from plasma was isolated from 50 head and neck squamous cell carcinoma cases and 50 controls with informed written consent using QIAamp Circulating Nucleic Acid Kit. Real-time polymerase chain reaction was done for copy number variation in cell-free mitochondrial DNA and cell-free nuclear DNA. Receiver operating characteristic curve analysis was performed to evaluate the diagnostic application between the two study groups using clinicopathological parameters. The levels of cell-free nuclear DNA and cell-free mitochondrial DNA of cases in association with smoke and smokeless tobacco, alcohol with smoking (p < 0.05) were significantly higher (p < 0.01 and p < 0.001, respectively) than controls. Using receiver operating characteristic curve analysis between head and neck squamous cell carcinoma cases and controls, we distinguished cell-free mitochondrial DNA (cutoff: 19.84 raw Ct; sensitivity: 84%; specificity: 100%; p < 0.001) and cell-free nuclear DNA (cutoff: 463,282 genomic equivalent/mL; sensitivity: 53%; specificity: 87%; p < 0.001). The copy number variation in cases (cell-free nuclear DNA: 5451.66 genomic equivalent/mL and cell-free mitochondrial DNA: 29,103,476.15 genomic equivalent/mL) and controls (cell-free nuclear DNA: 1650.9 genomic equivalent/mL and cell-free mitochondrial DNA: 9,189,312.54 genomic equivalent/mL), respectively. Our result indicates that the cell-free mitochondrial DNA content is highly associated with smoke and smokeless tobacco, betel quid chewing, and alcohol which shows greater promises, holding the key characteristics of diagnostic biomarkers, that is, minimal invasiveness, high specificity, and sensitivity.

Tsugaru Strait hybrid zone between two Japanese marine sculpins (genus Cottiusculus)

Mitochondrial and nuclear DNA variations in the marine sculpin sister species Cottiusculus schmidti and C. nihonkaiensis, distributed along the Pacific coast of northern Japan and in the Sea of Japan, respectively, indicated a ca. 250-km-wide hybrid zone across the Tsugaru Strait, connecting the Pacific Ocean and Sea of Japan. In addition to incomplete postzygotic isolation between the two species, the hybrid zone may have been shaped and formed by reduced dispersal, the preferred habitat of Cottiusculus being generally deeper than Tsugaru Strait (maximum depth ca. 140 m).

Perpendicular axes of differentiation generated by mitochondrial introgression.

Differential introgression of mitochondrial vs. nuclear DNA generates discordant patterns of geographic variation and can promote population divergence and speciation. We examined a potential case of mitochondrial introgression leading to two perpendicular axes of differentiation. The Eastern Yellow Robin Eopsaltria australis, a widespread Australian bird, shows a deep mitochondrial split that is perpendicular to north-south nuclear DNA and plumage colour differentiation. We propose a scenario to explain this pattern: (i) first, both nuclear and mitochondrial genomes differentiated in concert during north-south population divergence; (ii) later, their histories disconnected after two mitochondrial introgression events resulting in a deep mitochondrial split perpendicular to the nuclear DNA structure. We explored this scenario by coalescent modelling of ten mitochondrial genes and 400 nuclear DNA loci. Initial mitochondrial and nuclear genome divergences were estimated to have occurred in the early Pleistocene, consistent with the proposed scenario. Subsequent climatic transitions may have driven later mitochondrial introgression. We consider neutral introgression unlikely and instead propose that the evidence is more consistent with adaptive mitochondrial introgression and selection against incompatible mitochondrial-nuclear combinations. This likely generated an axis of coastal-inland mitochondrial differentiation in the face of nuclear gene flow, perpendicular to the initial north-south axis of differentiation (reflected in genomewide nuclear DNA and colour variation).

Genetic variations related to maternal whole blood mitochondrial DNA copy number: a genome-wide and candidate gene study

We conducted genome-wide (GWAS) and candidate gene association studies of maternal mitochondrial DNA copy number. Maternal peripheral blood was collected during labor and delivery admission from 471 participants of a placental abruption case-control study conducted in Lima, Peru. Single nucleotide polymorphism (SNP) genotyping was performed using the Illumina Cardio-Metabo Chip. Whole blood mitochondrial DNA (mtDNA) copy number was measured using qRT-PCR techniques. We evaluated 119,629 SNPs in the GWAS and 161 SNPs (in 29 mitochondrial biogenesis and oxidative phosphorylation genes) in the candidate association study. Top hits from GWAS and the candidate gene study were selected to compute weighted genetic risk scores (wGRS). Linear regression models were used to calculate effect size estimates and related nominal p values. The top hit in our GWAS was chr19:51063065 in FOXA3 (empirical p values = 2.20e − 6). A total of 134 SNPs had p values < 0.001 including rs17111633 in CNNM1 (p values = 6.32e − 6) and chr19:51083059 in MYPOP (p values = 3.23e − 5). In the candidate association study, several SNPs in PPARG, PRKCA, SP1 and THRB were associated with mtDNA copy number (p values < 0.05). mtDNA copy number was significantly associated with wGRS based on top GWAS hits (β = 0.49, 95% CI:0.38–0.60, p < 0.001). Variations in nuclear DNA are potentially associated with maternal mtDNA copy number.

Genetic structure in chloroplast and nuclear microsatellites in Rosa rugosa around sea straits in northern Japan

Sea‐strait geological history and seawater dispersal patterns can affect the genetic structure of coastal plants. We investigated microsatellite (simple sequence repeat, SSR) variations in chloroplast (cp) and nuclear (n) DNA of the coastal shrub R osa rugosa, native to northeastern Asia, and three species closely related to it. In northern Japan, we sampled R. rugosa along coasts around the Soya and Tsugaru straits with different histories of the Quaternary land formation as a result of different water depths. Both cpSSR and nSSR variations suggest rare hybridization between R . rugosa and the closely related species. Variations in one of two cpSSRs showed genetic differentiation between eastern and western Hokkaido. This genetic structure may result from introgression from R. davurica in eastern Hokkaido and/or isolation between the eastern and western coastlines of Hokkaido as a result of the Quaternary land formation in the Soya Strait. On the other hand, variations in 10 nSSRs were geographically homogeneous with weak isolation by distance along coastlines. These results suggest that extensive gene flow has been homogenizing the genetic structure of R . rugosa in northern Japan.

Short tandem repeat (STR) based genetic diversity and relationship of domestic sheep breeds with primitive wild Punjab Urial sheep (Ovis vignei punjabiensis)

In this study, short tandem repeat (STR) genotypes of 466 sheep from eleven domestic breeds located in Asia, Africa, Europe and Latin America were compared with wild Asian Urial sheep and captive Mouflon type sheep to assess genetic diversity and relationship among them. Analysis of sheep breeds at 19 short tandem repeat (STR) loci revealed higher diversity in wild Punjab Urial sheep and domestic sheep from West Asia followed by Europe and Latin America as compared to South Asia, consistent with the history of sheep domestication. The average inter-individual allele sharing distance within breed was found to be lowest in South Asian sheep as compared to West Asian, European and Latin American sheep populations. The estimated global FST revealed 15.9% of total variation attributable to between breed differences. Investigation of genetic relationship by phylogeny revealed four distinct clusters; the first cluster formed by four South Asian sheep breeds, the second cluster formed by Iraqi and Bulgarian sheep breeds; the third cluster formed by Iranian, Austrian, Burkina Faso and Peruvian sheep breeds and the fourth cluster formed by Punjab Urial and captive mouflon type sheep. Principal components analysis revealed individuals from Punjab Urial sheep population being distributed close to the cluster of West Asian and East European sheep (Hamdani-Karakachanska-West Palminska) while being distinct from the cluster of four Indian breeds. Analysis of molecular variance (AMOVA) was performed to assess the distribution of STR variation as a function of both breed membership and geographic origin, the results of which revealed the structure based on phylogeny to be evidently stronger than the structure based on geographic origin. Bayesian clustering of individuals without prior population information revealed the most appropriate K with nine genetic clusters. In conclusion, the present study showed the Punjab Urial sheep being genetically closer to West Asian and East European sheep breeds as compared to South Asian sheep breeds. The microsatellite based nuclear DNA variations, thus confirmed the wild Punjab Urial sheep did not share any recent common ancestry with Asian domestic sheep, as reported earlier based on mitochondrial sequence variations.

Mitonuclear Interactions Mediate Transcriptional Responses to Hypoxia in Drosophila.

Among the major challenges in quantitative genetics and personalized medicine is to understand how gene × gene interactions (G × G: epistasis) and gene × environment interactions (G × E) underlie phenotypic variation. Here, we use the intimate relationship between mitochondria and oxygen availability to dissect the roles of nuclear DNA (nDNA) variation, mitochondrial DNA (mtDNA) variation, hypoxia, and their interactions on gene expression in Drosophila melanogaster. Mitochondria provide an important evolutionary and medical context for understanding G × G and G × E given their central role in integrating cellular signals. We hypothesized that hypoxia would alter mitonuclear communication and gene expression patterns. We show that first order nDNA, mtDNA, and hypoxia effects vary between the sexes, along with mitonuclear epistasis and G × G × E effects. Females were generally more sensitive to genetic and environmental perturbation. While dozens to hundreds of genes are altered by hypoxia in individual genotypes, we found very little overlap among mitonuclear genotypes for genes that were significantly differentially expressed as a consequence of hypoxia; excluding the gene hairy. Oxidative phosphorylation genes were among the most influenced by hypoxia and mtDNA, and exposure to hypoxia increased the signature of mtDNA effects, suggesting retrograde signaling between mtDNA and nDNA. We identified nDNA-encoded genes in the electron transport chain (succinate dehydrogenase) that exhibit female-specific mtDNA effects. Our findings have important implications for personalized medicine, the sex-specific nature of mitonuclear communication, and gene × gene coevolution under variable or changing environments.

Nuclear and Chloroplast DNA Variation Provides Insights into Population Structure and Multiple Origin of Native Aromatic Rices of Odisha, India.

A large number of short grain aromatic rice suited to the agro-climatic conditions and local preferences are grown in niche areas of different parts of India and their diversity is evolved over centuries as a result of selection by traditional farmers. Systematic characterization of these specialty rices has not been attempted. An effort was made to characterize 126 aromatic short grain rice landraces, collected from 19 different districts in the State of Odisha, from eastern India. High level of variation for grain quality and agronomic traits among these aromatic rices was observed and genotypes having desirable phenotypic traits like erect flag leaf, thick culm, compact and dense panicles, short plant stature, early duration, superior yield and grain quality traits were identified. A total of 24 SSR markers corresponding to the hyper variable regions of rice chromosomes were used to understand the genetic diversity and to establish the genetic relationship among the aromatic short grain rice landraces at nuclear genome level. SSR analysis of 126 genotypes from Odisha and 10 genotypes from other states revealed 110 alleles with an average of 4.583 and the Nei’s genetic diversity value (He) was in the range of 0.034–0.880 revealing two sub-populations SP 1 (membership percentage-27.1%) and SP 2 (72.9%). At the organelle genomic level for the C/A repeats in PS1D sequence of chloroplasts, eight different plastid sub types and 33 haplotypes were detected. The japonica (Nipponbare) subtype (6C7A) was detected in 100 genotypes followed by O. rufipogon (KF428978) subtype (6C6A) in 13 genotypes while indica (93–11) sub type (8C8A) was seen in 14 genotypes. The tree constructed based on haplotypes suggests that short grain aromatic landraces might have independent origin of these plastid subtypes. Notably a wide range of diversity was observed among these landraces cultivated in different parts confined to the State of Odisha.

Geography has a greater effect than Wolbachia infection on population genetic structure in the spider mite, Tetranychus pueraricola.

Wolbachia is an intracellular symbiotic bacterium that infects various spider mite species and is associated with alterations in host reproduction, which indicates the potential role in mite evolution. However, studies of Wolbachia infections in the spider mite Tetranychus pueraricola, a major agricultural pest, are limited. Here, we used multilocus sequence typing to determine Wolbachia infection status and examined the relationship between Wolbachia infection status and mitochondrial diversity in T. pueraricola from 12 populations in China. The prevalence of Wolbachia ranged from 2.8 to 50%, and three strains (wTpue1, wTpue2, and wTpue3) were identified. We also found double infections (wTpue1 + wTpue3) within the same individuals. Furthermore, the wTpue1 strain caused weak cytoplasmic incompatibility (CI) (egg hatchability ~55%), whereas another widespread strain, wTpue3, did not induce CI. There was no reduction in mitochondrial DNA (mtDNA) or nuclear DNA diversity among infected individuals, and mtDNA haplotypes did not correspond to specific Wolbachia strains. Phylogenetic analysis and analysis of molecular variance revealed that the distribution of mtDNA and nuclear DNA haplotypes were significantly associated with geography. These findings indicate that Wolbachia infection in T. pueraricola is complex, but T. pueraricola genetic differentiation likely resulted from substantial geographic isolation.

Micropropagation of Eryngium campestre L. via Shoot Culture Provides Valuable Uniform Plant Material with Enhanced Content of Phenolic Acids and Antimicrobial Activity

AbstractAn efficient micropropagation protocol for production of genetically uniform clones ofEryngium campestreL. was developed. To determine the effect of nutritional and hormonal factors on shoot and root development and bioactive compounds production, three variants of media differing in the content of macro- and micronutrients, as well as plant growth regulators of various types and concentrations were tested. The highest regeneration (100%), with over 13 shoots per explant, was induced on Murashige and Skoog (MS) medium with 1.0 mg l−1benzyladenine (BA) and 0.1 mg l−1indole-3-acetic acid (IAA). The in vitro derived shoots multiplied through axillary bud formation were rooted and transferred to an experimental plot with 78% frequency of survival. Flow cytometry showed no variation in nuclear DNA between the seedlings and micropropagated plants. Preliminary thin layer chromatography (TLC) analysis indicated that phenolic acids, saponins, flavonoids and acetylenes were present in plant biomass. Ultra high performance liquid chromatography (UHPLC) analysis revealed that shoots and roots from in vitro derived plants and root cultures maintained the ability to produce rosmarinic acid (RA), rosmarinic acid hexoside (RA-HEX) and chlorogenic acid (CGA). The highest phenolic acid content was detected in roots of in vitro regenerated plants. The extract from those roots expressed the highest inhibitory effect against bacteriaStaphylococcus aureus, as well as dermatophytesTrichophyton mentagrophytesandT. rubrum.

The diversity of mycorrhizal fungi in Japanese Cephalanthera species

AbstractThe diversity of mycorrhizal fungi among four Japanese Cephalanthera (Orchidaceae) species was examined at a total of seven sites, based on sequence variation in nuclear ribosomal DNA. This is the first report to detect mycorrhizal fungi in C. subaphylla. Two patterns of mycorrhizal associations were confirmed from our results. C. falcata has lower fungal specificity, associating with Russulaceae, Sebacinales and Thelephoraceae. By contrast, the three Cephalanthera species C. erecta, C. subaphylla, and C. longifolia were associated mainly with Thelephoraceae fungi. There is no large difference found in mycobionts between green and albino individuals of C. falcata and no distinct preference of Japanese Cephalanthera species for a specific fungal group of Thelephoraceae.

Rise (and demise?) of subspecies in the Galah (Eolophus roseicapilla), a widespread and abundant Australian cockatoo

The Galah (Eolophus roseicapilla) is a widespread Australian bird. Its geographical variation and subspecies remain poorly understood. We sampled 192 specimens from across the entire range of the species to assess its phylogeographical structure using the mitochondrially encoded NADH dehydrogenase 2 (MT-ND2) gene. A subset of specimens was examined for nuclear DNA diversity using the Amplified Fragment Length Polymorphism (AFLP) method. Weakly defined structure was evident in the mitochondrial DNA (mtDNA) data, which suggested three geographically defined haplogroups that broadly coincide with the three conventionally recognised subspecies: E. r. roseicapilla—western haplogroup; E. r. albiceps—eastern haplogroup; and E. r. kuhli—northern haplogroup. The three haplogroups all overlap and intersect broadly across the centre of the Australian continent. Geographical expansions of each haplogroup appear to have occurred before and after the Last Glacial Maximum (~20 000 years ago), the species itself probably having undergone an earlier expansion at c. 60 000 years ago. The preliminary nuclear AFLP data suggest very little structure though they likely track more recent processes of gene flow and population admixture. Expansion of the species since European settlement represents another, later expansion uncoupled from what is tracked in the mtDNA data. Future quantitative analyses of phenotypic variation will enhance the precision of how geographical variation in all datasets in this species should be interpreted.

Ecological traits shape genetic diversity patterns across the Mediterranean Sea: a quantitative review on fishes

AbstractAimWe set out to identify the determinants of the variation in genetic diversity among fish species and test whether multi‐species genetic diversity is randomly distributed in space.LocationMediterranean Sea.MethodsWe collected genetic diversity data from 39 published studies on Mediterranean fishes (31 species) along with the spatial coordinates of the sampling sites. We focused on microsatellite heterozygosity (151 data points) and mitochondrial haplotype diversity (201 data points). We used linear regressions to link genetic diversity and 11 ecological traits. We also tested for spatial autocorrelation and trends in the residuals.ResultsAmong‐species variation in microsatellite heterozygosity was explained by three ecological traits: vertical distribution, migration type and body length. Variation in mitochondrial haplotype diversity was also explained by vertical distribution and migration type, and by reproductive strategy (semelparity). However, vertical distribution and migration type showed opposite effects on microsatellites and mitochondrial diversity. After accounting for the effects of ecological traits, no spatial pattern was detected, except for one of the species considered.Main conclusionsEcological factors explain an important proportion of the among‐species genetic diversity. These results suggest that life history strategies of the species influence the variation of microsatellite diversity indirectly through their effect on effective population size, while the spatial variations of genetic diversity seem to be too complex to be identified in our analysis. We found very different effects of traits on mitochondrial and nuclear DNA diversity, which can be explained by the specificities of mitochondrial DNA (absence of recombination, maternal inheritance and non‐neutrality).