Phylodynamics unveils invading and diffusing patterns of dengue virus serotype-1 in Guangdong, China from 1990 to 2019 under a global genotyping framework.

BACKGROUND: The strong invasiveness and rapid expansion of dengue virus (DENV) pose a great challenge to global public health. However, dengue epidemic patterns and mechanisms at a genetic scale, particularly in term of cross-border transmissions, remain poorly understood. Importation is considered as the primary driver of dengue outbreaks in China, and since 1990 a frequent occurrence of large outbreaks has been triggered by the imported cases and subsequently spread to the western and northern parts of China. Therefore, this study aims to systematically reveal the invasion and diffusion patterns of DENV-1 in Guangdong, China from 1990 to 2019. METHODS: These analyses were performed on 179 newly assembled genomes from indigenous dengue cases in Guangdong, China and 5152 E gene complete sequences recorded in Chinese mainland. The genetic population structure and epidemic patterns of DENV-1 circulating in Chinese mainland were characterized by phylogenetics, phylogeography, phylodynamics based on DENV-1 E-gene-based globally unified genotyping framework. RESULTS: Multiple serotypes of DENV were co-circulating in Chinese mainland, particularly in Guangdong and Yunnan provinces. A total of 189 transmission clusters in 38 clades belonging to 22 subgenotypes of genotype I, IV and V of DENV-1 were identified, with 7 Clades of Concern (COCs) responsible for the large outbreaks since 1990. The epidemic periodicity was inferred from the data to be approximately 3 years. Dengue transmission events mainly occurred from Great Mekong Subregion-China (GMS-China), Southeast Asia (SEA), South Asia Subcontinent (SASC), and Oceania (OCE) to coastal and land border cities respectively in southeastern and southwestern China. Specially, Guangzhou was found to be the most dominant receipting hub, where DENV-1 diffused to other cities within the province and even other parts of the country. Genome phylogeny combined with epidemiological investigation demonstrated a clear local consecutive transmission process of a 5C1 transmission cluster (5C1-CN4) of DENV-1 in Guangzhou from 2013 to 2015, while the two provinces of Guangdong and Yunnan played key roles in ongoing transition of dengue epidemic patterns. In contextualizing within Invasion Biology theories, we have proposed a derived three-stage model encompassing the stages of invasion, colonization, and dissemination, which is supposed to enhance our understanding of dengue spreading patterns. CONCLUSIONS: This study demonstrates the invasion and diffusion process of DENV-1 in Chinese mainland within a global genotyping framework, characterizing the genetic diversities of viral populations, multiple sources of importation, and periodic dynamics of the epidemic. These findings highlight the potential ongoing transition trends from epidemic to endemic status offering a valuable insight into early warning, prevention and control of rapid spreading of dengue both in China and worldwide.

The genetic structure of populations of Isthmiophora melis (Schrank, 1788) (Digenea: Echinostomatidae). Does the host's diet matter?

BACKGROUND: Here we provide a comparative analysis of the genetic structure of populations (based on nad1 mtDNA) of Isthmiophora melis isolated from the American mink (Neogale vison), an introduced invasive species, commonly occurring in the territory of Poland, and from the striped field mouse (Apodemus agrarius). METHODS: A total of 133 specimens of I. melis were obtained from naturally infected N. vison collected from six localities in Poland (108 samples) and 25 individuals of I. melis from A. agrarius. All sequences of the nad1 gene obtained during the present study were assembled and aligned. The standard statistics for haplotype composition, i.e., the number of haplotypes, haplotype diversity, nucleotide diversity, and average number of nucleotide differences, were calculated. Haplotype analysis and visualization of haplotype frequency among populations were performed using a median-joining network. RESULTS: Based on the samples collected from different localities in Poland, our study revealed that the overall genetic diversity of I. melis isolated from the American mink and of the striped field mouse do not differ significantly. The median-joining network showed that the three main haplotypes are in the centre of a star-like structure, with the remaining haplotypes as the satellites, reflecting the recent expansion of the populations. CONCLUSIONS: The overall genetic diversity of I. melis isolated from the American mink and striped field mouse reveals a high level of homogeneity. Moreover, regional differences in the food composition of the definitive hosts play an important role in shaping the genetic structure of the trematode populations.

Velvet Family Members Regulate Pigment Synthesis of the Fruiting Bodies of Auricularia cornea.

Color is a crucial feature to consider when breeding and improving strains of Auricularia cornea. To uncover the mechanism of white strain formation in A. cornea, this study selected parental strains that were homozygous for the color trait and analyzed the genetic laws of A. cornea color through genetic population construction, such as test-cross, back-cross, and self-cross populations, and the statistical analysis of color trait segregation. Moreover, the study developed SSR molecular markers to construct a genetic linkage map, perform the fine mapping the color-controlling genetic locus, and verify candidate genes using yeast two-hybrid, transcriptome analysis, and different light treatments. The results of the study indicated that the color trait of A. cornea is controlled by two pairs of alleles. When both pairs of loci are dominant, the fruiting body is purple, while when both pairs of loci are recessive or one pair of loci is recessive, the fruiting body is white. Based on the linkage map, the study finely mapped the color locus within Contig9_29,619bp-53,463bp in the A. cornea genome and successfully predicted the color-controlling locus gene A18078 (AcveA), which belongs to the Velvet factor family protein and has a conserved structure domain of the VeA protein. It can form a dimer with the VelB protein to inhibit pigment synthesis in filamentous fungi. Lastly, the study validated the interaction between AcVeA and VelB (AcVelB) in A. cornea at the gene, protein, and phenotype levels, revealing the mechanism of inhibition of pigment synthesis in A. cornea. Under dark conditions, dimerization occurs, allowing it to enter the nucleus and inhibit pigment synthesis, leading to a lighter fruiting body color. However, under light conditions, the dimer content is low and cannot enter the nucleus to inhibit pigment synthesis. In summary, this study clarified the mechanism of white strain formation in A. cornea, which could aid in improving white strains of A. cornea and studying the genetic basis of color in other fungi.

What are Jews: interrogating genetic studies and the reification of race.

Scientific studies on the genetic proximity of Jews undertake to shed light on "who or what Jews really are". However, various scientists and scholars have warned that such studies reify racial thinking. This essay delineates and contextualizes the debate held between various geneticists and social scientists on the danger of reification within the Jewish context. This is mainly a debate about the impact of (traditional, religious, and Zionist) narratives on scientific research as well as on the ethical responsibility of scientists. The paper claims that such genetic studies test Jewish religious narratives against genetic research results and do not necessarily enforce old notions of distinctiveness.

Assessing temporal and geographic contacts across the Adriatic Sea through the analysis of genome-wide data from Southern Italy.

Southern Italy was characterised by a complex prehistory that started with different Palaeolithic cultures, later followed by the Neolithization and the demic dispersal from the Pontic-Caspian Steppe during the Bronze Age. Archaeological and historical evidences point to a link between Southern Italians and the Balkans still present in modern times. To shed light on these dynamics, we analysed around 700 South Mediterranean genomes combined with informative ancient DNAs. Our findings revealed high affinities of South-Eastern Italians with modern Eastern Peloponnesians, and a closer affinity of ancient Greek genomes with those from specific regions of South Italy than modern Greek genomes. The higher similarity could be associated with a Bronze Age component ultimately originating from the Caucasus with high Iranian and Anatolian Neolithic ancestries. Furthermore, extremely differentiated allele frequencies among Northern and Southern Italy revealed putatively adapted SNPs in genes involved in alcohol metabolism, nevi features and immunological traits.

Genetic Diversity and Population Structure of Fusarium commune Causing Strawberry Root Rot in Southcentral China.

Strawberry plants and fruits are vulnerable to infections by a broad range of pathogens and pests. However, knowledge about the epidemiology of pathogens causing strawberry diseases is limited. In this study, we analyzed Fusarium commune, a major fungal pathogen causing strawberry root rot, from diseased strawberry root tissues in southcentral China. A total of 354 isolates were obtained from 11 locations that spanned about 700 km from both south to north and east to west. Multilocus genotypes of all isolates were obtained using seven polymorphic simple sequence repeat markers developed in this study. Our analyses revealed significant genetic diversity within each of the 11 local populations of F. commune. STRUCTURE analysis revealed that the optimal number of genetic populations for the 354 strains was two, with most local geographic populations containing isolates in both genetic clusters. Interestingly, many isolates showed allelic ancestry to both genetic clusters, consistent with recent hybridization between the two genetic clusters. In addition, though alleles and genotypes were frequently shared among local populations, statistically significant genetic differentiations were found among the local populations. However, the observed F. commune population genetic distances were not correlated with geographic distances. Together, our analyses suggest that populations of F. commune causing strawberry root rot are likely endemic to southcentral China, with each local population containing shared and unique genetic elements. Though the observed gene flow among geographic regions was relatively low, human activities will likely accelerate pathogen dispersals, resulting in the generation of new genotypes through mating and recombination.

Population Structure of German Cockroaches (Blattodea: Ectobiidae) in an Urban Environment Based on Single Nucleotide Polymorphisms.

German cockroaches (Blattella germanica L.) harbor and disperse medically important pathogens and are a source of allergens that impact human health and wellbeing. Management of this pest requires an understanding of their distribution and dispersal. In this study, we collected German cockroaches from three apartment buildings in New Jersey, USA. We identified single-nucleotide polymorphisms (SNPs) from DNA extractions using next generation sequencing. We analyzed the SNPs and characterized cockroach population genetic structure using Fst, principal component, phylogenetic, and STRUCTURE analyses. We found significant differences in German cockroach population structure among the buildings. Within buildings, we found variable population structure that may be evidence for multiple colonization events. This study shows that SNPs derived from next generation sequencing provide a powerful tool for analyzing the genetic population structure of these medically important pests.

ddRAD Sequencing Identifies Pesticide Resistance-Related Loci and Reveals New Insights into Genetic Structure of Bactericera cockerelli as a Plant Pathogen Vector.

(1) Background: Many hemipteran insects transmit plant pathogens that cause devastating crop diseases, while pest management frequently relies primarily on insecticide applications. These intense insecticide applications lead to the development of insecticide resistance, as was the case for potato psyllid, Bactericera cockerelli (Hemiptera: Triozidae), a vector of Candidatus Liberibacter solanacearum, which causes zebra chip disease in potato. (2) Methods: Here, we use double-digest restriction site-associated DNA (ddRAD) to genotype eight psyllid populations (one susceptible and seven resistant to neonicotinoid insecticides). (3) Results: Association tests identified over 400 loci that were strongly segregated between susceptible and resistant populations. Several loci were located within genes involved in insecticide resistance, gene regulation, fertility, and development. Moreover, we explored the genetic structure of these eight populations and discovered that routinely utilized haplotyping was not an accurate predictor of population structure. Pairwise comparisons of the fixation index (FST) of populations of the same haplotype were not different from pairwise FST of populations that belonged to different haplotypes. (4) Conclusions: Our findings suggest that neonicotinoid insecticide resistance has a genetic basis, most likely as a result of similar selection pressure. Furthermore, our results imply that using a single maternally inherited gene marker to designate genetic lineages for potato psyllids should be re-evaluated.

Genetic Population Structure of Summer Flounder Paralichthys dentatus using Microsatellite DNA Analysis.

Summer flounder Paralichthys dentatus supports one of the most valuable commercial and recreational fisheries along the Atlantic Coast of the U.S. However, in recent decades the management of this species has proven to be one of the most contentious for any exploited marine resource in the region. A coastwide catch quota is imposed annually for summer flounder of which 60% is allocated to the commercial fishery and 40% to the recreational fishery. The allocation is further divided among the individual coastal states from North Carolina to Massachusetts based on their landings in the 1980s. This process, based on political jurisdictions, does not consider the species' biological stock structure. Previous genetic studies (allozyme, mtDNA, and SNPs) provided contradictory results regarding the possible population structure of summer. To address this issue, we used DNA microsatellite analysis at 9 loci to define the coastwide population structure of summer flounder. In total, 1,182 specimens were analyzed from 18 collection sites. Most collections were from the continental shelf during the fall-winter spawning season. These were supplemented with additional samples from inshore waters from North Carolina to Florida, and inshore sites which support significant recreational fisheries at Nantucket Shoals, Massachusetts and Fire Island, New York. The overall level of genetic differentiation in pairwise comparison between collections was very low, mean F ST = 0.001. There was no evidence of genetic differentiation between collections from north and south of Cape Hatteras. Our microsatellite results are consistent with an earlier SNP study which failed to find significant allelic heterogeneity among coastwide collections of summer flounder. However, a subset of pairwise F ST comparisons between some collections proved statistically significant. Furthermore, in STRUCTURE analysis we found evidence of two genetic clusters within the species' northern landings area, however, this finding was not supported by DPAC analysis. We conclude that summer flounder most likely constitute a single population along their entire Atlantic Coast distribution.

Genetic Population Structure of Wild Boars (Sus scrofa) in Fukushima Prefecture.

We aimed to reveal the dispersal and gene flow of the local wild boar (Sus scrofa) population and find their genetic boundary in Fukushima Prefecture. After the nuclear incident in 2011, the land was considered a difficult-to-return zone, and the increase in the number of wild boars was pronounced. To provide an effective management strategy for the wild boar population, we used multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq) and clarified the genetic structure of wild boars. We obtained 328 single-nucleotide polymorphisms from 179 samples. STRUCTURE analysis showed that the most likely number of population cluster was K = 2. Molecular analysis of variance showed significant genetic differences between groups of wild boars inhabiting in the east and west across the Abukuma River. The migration rate from the eastern population to the western population is higher than in the reverse case based on BayesAss analysis. Our study indicates that both the Abukuma River and anthropogenic urbanization along the river may affect the migration of wild boars and the population in western was established mainly by the migration from other neighboring prefectures.

Genetic population structure of the agaric Blastosporella zonata (Lyophyllaceae) reveals cryptic species and different roles for sexual and asexual spores in dispersal.

Blastosporella zonata is one of the few basidiomycete fungi that produce asexual spores (conidia) on the mushroom. The role of these conidia in the fungal lifecycle is not known. We tested whether conidia are being utilized in local dispersal by looking for signatures of clonality in 21 samples from three localities separated by about three kilometres in Murillo, Colombia. To identify clonally related individuals, we sequenced three polymorphic markers at two unlinked loci (nuclear rRNA: ITS and LSU, and TEFIα) for all collections plus three herbarium samples. We identified two sets of clonally related individuals growing closely together in one of the three localities, and only one pair shared between localities. In all three localities we observed multiple non-clonally related dikaryons showing that sexual reproduction is also important. Our results indicate that the conidia on the mushroom are primarily important for local dispersal. Unexpectedly, our results also indicate two reproductively isolated populations, possibly representing cryptic biological species. Citation: Van de Peppel LJJ, Baroni TJ, Franco-Molano AE, et al. 2022. Genetic population structure of the agaric Blastosporella zonata (Lyophyllacea) reveals cryptic species and different roles for sexual and asexual spores in dispersal. Persoonia 49: 195-200. https://doi.org/10.3767/persoonia.2022.49.06.

Genetic Diversity of the Symbiotic Fungus Epichloë festucae in Naturally Occurring Host Grass Populations.

Epichloë festucae is a common symbiont of the perennial and widely distributed cool season grass, Festuca rubra. The symbiosis is highly integrated involving systemic growth of the fungus throughout above-ground host parts and vertical transmission from plant to its offspring via host seeds. However, the nature of symbiosis is labile ranging from antagonistic to mutualistic depending on prevailing selection pressures. Both the loss of fungus in the maternal host lineage and horizontal transmission through sexual spores within the host population may partly explain the detected variation in symbiosis in wild grass populations. Epichloë species are commonly considered as pathogens when they produce sexual spores and partly castrate their host plant. This is the pathogenic end of the continuum from antagonistic to mutualistic interactions. Here we examined the population genetic structure of E. festucae to reveal the gene flow, importance of reproduction modes, and alkaloid potential of the symbiotic fungus in Europe. Epichloë-species are highly dependent on the host in survival and reproduction whilst benefits to the host are largely linked to defensive mutualism attributable to fungal-origin bioactive alkaloids that negatively affect vertebrate and/or invertebrate herbivores. We detected decreased genetic diversity in previously glaciated areas compared to non-glaciated regions during the last glacial maximum period and found three major genetic clusters in E. festucae populations: southern, northeastern and northwestern Europe. Sexual reproduction may have a higher role than expected in Spanish E. festucae populations due to the predominance of unique genotypes and presence of both mating types in the region. In contrast, asexual reproduction via host seeds predominates in the Faroe Island and Finland in northern Europe due to the presence of biased mating-type ratios and large dominant genotypes in the E. festucae populations within the region. A substantially larger variation of alkaloid genotypes was observed in the fungal populations than expected, although the variability of the alkaloid genotypes within populations is considerably lower in northern than Spanish populations in southern Europe. E. festucae populations consist of different combinations of alkaloid classes from the gene clusters of ergot alkaloid and indole-terpenes, and from pyrrolopyrazine alkaloid gene. We suggest that the postglacial distribution history of the host grass, prevailing reproduction strategies of E. festucae, and local selection pressures likely explain a large part of the genetic variation observed in fungal populations among geographic regions. The identified alkaloid genotypes can be used by turfgrass breeders to improve resistance against herbivores in red fescue varieties and to develop new sustainable cultivars in Europe.

Novel Sources of Tolerance to Aluminium Toxicity in Wild Cicer (Cicer reticulatum and Cicer echinospermum) Collections.

In acid soils, the toxic form of aluminium, Al3+, significantly inhibits root growth and elongation, leading to less water and nutrient uptake. Previous research had shown differential Al toxicity tolerance among cultivated Cicer arietinum L. (chickpea); however, the potential for developing tolerant cultivars is limited by the narrow genetic diversity of cultivated chickpeas. Recent collections from Turkey of wild Cicer species, Cicer reticulatum, and Cicer echinospermum, have increased the available gene pool significantly, but there has been no large-scale screening of wild Cicer for acid tolerance or Al3+ toxicity tolerance. This study evaluated 167 wild Cicer and 17 Australian chickpea cultivars in a series of screenings under controlled growth conditions. The pH of 4.2 and Al concentrations of 15 and 60 µM Al were selected for large-scale screening based on dose response experiments in a low ionic strength nutrient solution. The change in root length showed better discrimination between tolerant and sensitive lines when compared with shoot and root dry weights and was used as a selection criterion. In a large-scale screening, 13 wild Cicer reticulatum accessions had a higher root tolerance index (≥50%), and eight had higher relative change in root length (≥40%) compared with PBA Monarch, which showed greater tolerance among the Australian domestic cultivars screened. In general, C. reticulatum species were found to be more tolerant than C. echinospermum, while genetic population groups Ret_5, Ret_6, and Ret_7 from Diyarbakir and Mardin Province were more tolerant than other groups. Among C. echinospermum, Ech_6 from the Siv-Diyar collection site of the Urfa Province showed better tolerance than other groups. In this first detailed screening of aluminium toxicity tolerance in the new wild Cicer collections, we identified accessions that were more tolerant than current domestic cultivars, providing promising germplasm for breeding programs to expand chickpea adaptation to acid soils.

Genetic Population Structure of Wild Pigs in Southern Texas.

Wild pigs (Sus scrofa) alter ecosystems, affect the economy, and carry diseases that can be transmitted to livestock, humans, and wildlife. Understanding wild pig movements and population structure data, including natural population boundaries and dispersal, may potentially increase the efficiency and effectiveness of management actions. We trapped, conducted aerial shootings, and hunted wild pigs from 2005 to 2009 in southern Texas. We used microsatellites to assist large-scale applied management. We quantify broad-scale population structure among 24 sites across southern Texas by computing an overall Fst value, and a Bayesian clustering algorithm both with and without considering the spatial location of samples. At a broad geographic scale, pig populations displayed a moderate degree of genetic structure (Fst = 0.11). The best partition for number of populations, based on 2nd order rate of change of the likelihood distribution, was K = 10 genetic clusters. The spatially explicit Bayesian clustering algorithm produced similar results, with minor differences in designation of admixed sites. We found evidence of past (and possibly ongoing) translocations; many populations were admixed. Our original goal was to identify landscape features, such as barriers or dispersal corridors, that could be used to aid management. Unfortunately, the extensive admixture among clusters made this impossible. This research shows that large-scale management of wild pigs may be necessary to achieve control and ameliorate damages. Reduction or cessation of translocations is necessary to prevent human-mediated dispersion of wild pigs.

A gene drive does not spread easily in populations of the honey bee parasite Varroa destructor.

Varroa mites (Varroa destructor) are the most significant threat to beekeeping worldwide. They are directly or indirectly responsible for millions of colony losses each year. Beekeepers are somewhat able to control varroa populations through the use of physical and chemical treatments. However, these methods range in effectiveness, can harm honey bees, can be physically demanding on the beekeeper, and do not always provide complete protection from varroa. More importantly, in some populations varroa mites have developed resistance to available acaricides. Overcoming the varroa mite problem will require novel and targeted treatment options. Here, we explore the potential of gene drive technology to control varroa. We show that spreading a neutral gene drive in varroa is possible but requires specific colony-level management practices to overcome the challenges of both inbreeding and haplodiploidy. Furthermore, continued treatment with acaricides is necessary to give a gene drive time to fix in the varroa population. Unfortunately, a gene drive that impacts female or male fertility does not spread in varroa. Therefore, we suggest that the most promising way forward is to use a gene drive which carries a toxin precursor or removes acaricide resistance alleles. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13592-021-00891-5.

Anthropogenic river fragmentation reduces long-term viability of the migratory fish Salminus brasiliensis (Characiformes: Bryconidae) populations

Life-history, geographical barriers, and damming can shape the genetic diversity of freshwater migratory fish, which are particularly vulnerable to anthropogenic impacts. We investigated the genetic diversity of Salminus brasiliensis, a long-distance migratory species that is recognized as an important provider of ecosystem services. We implemented microsatellite analyses to assess genetic diversity and simulate future scenarios for evaluating the long-term viability of dammed and non-dammed populations from the Uruguay River. High levels of genetic diversity were detected for all sampled populations. However, effective population sizes were lower in the uppermost river stretches, where the landscape is highly fragmented. Population structure analysis indicated two spatial genetic populations. It is suggested that this genetic structure preserves populations partially isolated by an ancient natural barrier, instead of being a result of the presence of dams. The simulated genetic scenarios indicated that genetic variability of S. brasiliensis populations from upstream dams could collapse over the years, mainly due to the reduction in the number of alleles. Therefore, besides helping to better understand issues related to the influence of dams on the genetic diversity of migratory fish, our results are especially relevant for driving local fishery policies and management actions for the species conservation.'

História de vida, barreiras geográficas e barramento dos rios podem moldar a diversidade genética de grandes peixes migratórios de água doce, que são particularmente vulneráveis a impactos antrópicos. Nós investigamos a diversidade genética de Salminus brasiliensis, uma espécie migratória de longa distância que é reconhecida como um importante provedor de serviços ecossistêmicos. Realizamos análises de microssatélites para avaliar a diversidade genética e simular cenários futuros, possibilitando estimar a viabilidade em longo prazo de populações situadas em regiões com e sem represas do rio Uruguai. Altos níveis de diversidade genética foram detectados para todas as populações amostradas. Contudo, os tamanhos populacionais efetivos foram menores nos trechos superiores do rio, onde a paisagem é altamente fragmentada. A análise da estrutura populacional indicou duas populações genéticas espaciais. Sugere-se que esta estrutura genética preserva populações parcialmente isoladas por uma antiga barreira natural, ao invés de ser resultado da presença de barragens. Os cenários genéticos simulados indicaram que a variabilidade genética das populações de S. brasiliensis situadas a montante das barragens entraria em colapso ao longo dos anos, principalmente como resultado da redução do número de alelos. Portanto, além de ajudar a entender melhor questões relacionadas à influência de barragens na diversidade genética de peixes migradores, nossos resultados são especialmente relevantes para a condução de políticas pesqueiras locais e ações de manejo para a conservação das espécies.(AU)

Succinate dehydrogenase gene as a marker for studying Blastocystis genetic diversity.

Blastocystis has been reported as the most common eukaryotic microorganism residing in the intestines of both humans and animals, with a prevalence of up to 100% in some populations. Since this is a cryptic species, sequence polymorphism are the single strategy to analyses its genetic diversity, being traditionally used the analysis of ssu rRNA gene sequence to determine alleles and subtypes (STs) for this species. This multicopy gene has shown high diversity among different STs, making necessary to explore other genes to assess intraspecific diversity. This study evaluated the use of a novel genetic marker, succinate dehydrogenase (SDHA), for the typing and evaluation of the genetic diversity and genetic population structure of Blastocystis. In total, 375 human fecal samples were collected and subjected to PCR, subtyped using the ssu rRNA marker, and then the SDHA gene was amplified via PCR for 117 samples. We found some incongruences between tree topologies for both molecular markers. However, the clustering by ST previously established for Blastocystis was congruent in the concatenated sequence. SDHA showed lower reticulation (The origination of a lineage through the partial merging of two ancestor lineages) signals and better intra ST clustering ability. Clusters with geographical associations were observed intra ST. The genetic diversity was lower in the marker evaluated compared to that of the ssu rRNA gene (nucleotide diversity = 0.03344 and 0.16986, respectively) and the sequences analyzed showed population expansion with genetic differentiation principally among STs. The ssu rRNA gene was useful to explore interspecific diversity but together with the SDHA gene the resolution power to evaluate intra ST diversity was higher. These results showed the potential of the SDHA marker for studying the intra ST genetic diversity of Blastocystis related with geographical location and the inter ST diversity using the concatenated sequences.

Pleistocene Ice Ages Created New Evolutionary Lineages, but Limited Speciation in Northeast Pacific Winged Kelp.

The extent that Pleistocene climate variability promoted speciation has been much debated. Here, we surveyed genetic markers in winged kelp Alaria in the Gulf of Alaska, Northeast Pacific Ocean to understand how paleoclimates may have influenced diversity in this kelp. The study included wide geographic sampling over 2800 km and large sample sizes compared to previous studies of this kelp. Mitochondrial 5'-COI (664 bp), plastid rbcL-3' (740 bp) and 8 microsatellite markers in 16 populations resolved 5 well-defined lineages. COI-rbcL haplotypes were distributed chaotically among populations around the Gulf of Alaska. Principal Coordinates Analysis of microsatellite genotypes grouped plants largely by organellar lineage instead of geography, indicating reproductive isolation among lineages. However, microsatellite markers detected hybrids at 3 sites where lineages co-occurred. Local adaptation on various time scales may be responsible for some genetic differences between populations located along wave-energy and salinity gradients, but the chaotic pattern of variability over hundreds of kilometers is likely due to isolations in northern refugia during Pleistocene ice ages. The range of divergences between populations indicates that episodic glaciations led to the creation of new lineages, but population turnover (local extinctions and recolonizations) limited the formation of new species in the Northeastern Pacific Ocean.

Mapping Quantitative Trait Loci for Soybean Seedling Shoot and Root Architecture Traits in an Inter-Specific Genetic Population.

Wild soybean species (Glycine soja Siebold & Zucc.) comprise a unique resource to widen the genetic base of cultivated soybean [Glycine max (L.) Merr.] for various agronomic traits. An inter-specific mapping population derived from a cross of cultivar Williams 82 and PI 483460B, a wild soybean accession, was utilized for genetic characterization of root architecture traits. The objectives of this study were to identify and characterize quantitative trait loci (QTL) for seedling shoot and root architecture traits, as well as to determine additive/epistatic interaction effects of identified QTLs. A total of 16,469 single nucleotide polymorphisms (SNPs) developed for the Illumina beadchip genotyping platform were used to construct a high resolution genetic linkage map. Among the 11 putative QTLs identified, two significant QTLs on chromosome 7 were determined to be associated with total root length (RL) and root surface area (RSA) with favorable alleles from the wild soybean parent. These seedling root traits, RL (BARC_020495_04641 ~ BARC_023101_03769) and RSA (SNP02285 ~ SNP18129_Magellan), could be potential targets for introgression into cultivated soybean background to improve both tap and lateral roots. The RL QTL region harbors four candidate genes with higher expression in root tissues: Phosphofructokinase (Glyma.07g126400), Snf7 protein (Glyma.07g127300), unknown functional gene (Glyma.07g127900), and Leucine Rich-Repeat protein (Glyma.07g127100). The novel alleles inherited from the wild soybean accession could be used as molecular markers to improve root system architecture and productivity in elite soybean lines.