Analysis Of The Molecular Variance Research Articles

Genotypic Variation in Agronomic Traits and Molecular Markers among Chinese Luobuma (Apocynum spp.) Germplasm Accessions

Apocynum spp., known as Chinese Luobuma species, are perennial herbaceous plants that not only have good ecological characteristics, such as drought resistance, salt resistance, freezing resistance, high-temperature resistance and wind sand resistance, but also have good medicinal and textile value. However, studies on the genetic variation in Chinese Luobuma are rare. In this study, the genotypic variation in the agronomic traits and molecular markers among eight germplasm accessions (referred to as genotypes) of Apocynum spp. was investigated. The accessions were evaluated at two locations in China, Altay and Yuzhong, during a three-year period. Analysis of the variance in yield-related traits revealed significant genotypic variation (p < 0.05) among the eight genotypes at the early flowering and full flowering stages. There were also significant (p < 0.05) genotype × year and genotype × location × year interactions for all the traits except leaf dry weight. In comparison to those evaluated at Yuzhong, the plant height, number of branches, leaf dry weight and stem dry weight at the early flowering stage were greater in Altay, with averages of 991.0 mm, 5.52, 26.41 g and 25.35 g, respectively. There were significant (p < 0.05) differences among genotypes in terms of the quality traits measured at the early and full flowering stages. The crude protein and crude fat content for each genotype at different locations at the early flowering stage in different years ranged from 8.64 to 10.07%. The average flavone (FLA) content was 2.31 mg/100 g. Principal component analysis (PCA) revealed that the G1 genotype in Altay had a higher neutral detergent fiber content and leaf dry weight, and the G2 genotype had a larger stem thickness, branch number and stem-to-leaf ratio. Five DNA sequences, ITS, matK, psbA-trnH, rbcL and trnL-F, were selected for analysis of the molecular variance in Chinese Luobuma. Analyses of molecular variance (AMOVA) based on the nuclear DNA sequences and chloroplast DNA sequences showed that most of the variation occurred within species. Our study indicated the significant genetic variation in Chinese Luobuma for future cultivar domestication. Genotypes with high leaf dry weights and many branches are beneficial for tea production, while tall plants with long internode lengths are valuable for the production of hemp.

The Grasshopper Paradigm in damselflies: evidence for phalanx-like postglacial recolonization of Europe from a Balkan refugium in Platycnemis pennipes Pallas (Odonata: Zygoptera: Platycnemidae)

We explore haplotype diversity, phylogeography and phylogenetic relationships of the damselfly Platycnemis pennipes in Europe based on 618 bp DNA from the mitochondrial gene COI. A haplotype network analysis shows that the species is divided into two haplotype groups. One is restricted to the Italian Peninsula, while the other is found from the Black Sea region across eastern and central Europe to Scandinavia, England, and southwestern France. This pattern is recovered in a Bayesian phylogenetic analysis. Genetic distance (K2P) between the two groups is approximately 1.5%, while within-group variation is an order of magnitude lower. An analysis of the molecular variance (AMOVA) shows that variation between the two groups account for more than 96% of the total variation within the dataset, adding to the evidence that they have been isolated for a considerable amount of time. The pattern we find is similar to the so-called Grasshopper Paradigm in European phylogeography, where a species has recolonized Europe after the last glaciation from a glacial refugium in the southeast, while other refugial populations in the Iberian and Italian peninsulas have remained isolated to this day. In P. pennipes there is only an isolated refugial population in Italy as the species does not have current populations in the Iberian Peninsula. By comparing the genetic distance between the two groups to a previously published divergence time analysis of European Odonata we estimate that they have likely been isolated since the onset of the Saale Glaciation ca 400 ky ago.

Analysis of genetic diversity and population structure of Moroccan date palm (Phoenix dactylifera L.) using SSR and DAMD molecular markers

BackgroundDate palm, oasis pivot, plays a vital socio-economic part in the southern area of Morocco. However, with climate change and drought intensity and frequency increasing, the Moroccan palm grove is threatened with significant genetic degradation. Genetic characterization of this resource is key element for the development of effective conservation and management strategies in the current circumstances of climate change and various biotic and abiotic stresses. To evaluate the genetic diversity of date palm populations collected from different Moroccan oases, we used simple sequence repeats (SSR) and directed amplification of mini-satellite DNA (DAMD) markers. Our results showed that used markers could efficiently assess genetic diversity in Phoenix dactylifera L. ResultsA total of 249 and 471 bands were respectively scored for SSR and DAMD, of which 100% and 92.9% were polymorphic. The polymorphic information content (PIC = 0.95), generated by the SSR primer was nearly identical to that generated by the DAMD primer (PIC = 0.98). The resolving power (Rp) was higher in DAMD than SSR (29.46 and 19.51, respectively). Analysis of the molecular variance (AMOVA) based on the combined data sets for both markers revealed a higher variance within populations (75%) than among populations (25%). Principal coordinate analysis (PCoA) and the ascendant hierarchical classification showed that the population of Zagora and Goulmima regions were the closest populations. The STRUCTURE analysis clustering of the 283 tested samples into seven clusters based on their genetic composition. ConclusionThe results drawn from this study will orient genotypes selection strategies for a successful future breeding and conservation program, particularly under climate change context.

Distribution of Genetic Diversity in Beta patula Aiton Populations from Madeira Archipelago, Portugal

Beta patula Aiton is a crop wild relative (CWR) which belongs to the Gene Pool 1b and is considered a Critically Endangered species, and is present in very specific environments, such as the Desembarcadouro islet (DI) in Ponta de São Lourenço or Chão islet (CI) in the Desertas Islands. The ISOPlexis Center (University of Madeira) has been providing continuous support for its in situ conservation by keeping a management plan of wild populations and an ex situ conservation strategy through the storage of accessions in the ISOPlexis GeneBank. The present work intends to present the spatial distribution of genetic variability and diversity in these B. patula populations using eight polymorphic Simple Sequence Repeat (SSR) markers. The overall results lead to the identification of three spots with a high genetic diversity. CI with a small cluster of individuals shows a genetic footprint different from DI, having unique alleles present in its population. DI has two distinct areas: the western area, with a higher individual density but with a lower genetic diversity and higher allele fixation; and the central area, with a lower individual count but with a higher genetic diversity and with the presence of unique alleles. Despite some genetic differences, the comparison of the two islets’ DI and CI populations shows that they have more similarities than differences. Analysis of the Molecular Variance, based on the hierarchical cluster, showed a 9% diversity between populations, 68% among individuals, and 23% within individuals. This data will be used for the establishment of a protocol to monitor and manage B. patula genetic diversity under a genetic reserve, subsequently contributing to the European Genetic Reserve network implementation and the protection of this important CWR.

Analyses of the Global Multilocus Genotypes of the Human Pathogenic Yeast Cryptococcus neoformans Species Complex.

Cryptococcus neoformans species complex (CNSC) is a globally distributed human opportunistic yeast pathogen consisting of five major molecular types (VNI, VNII, VNB, VNIII and VNIV) belonging to two species, C. neoformans (VNI, VNII and VNB, collectively called serotype A) and C. deneoformans (VNIV, commonly called serotype D), and their hybrids (VNIII, serotype AD). Over the years, many studies have analyzed the geographical distribution and genetic diversity of CNSC. However, the global population structure and mode of reproduction remain incompletely described. In this study, we analyze the published multilocus sequence data at seven loci for CNSC. The combined sequences at the seven loci identified a total of 657 multilocus sequence types (STs), including 296 STs with known geographic information, representing 4200 non-redundant isolates from 31 countries and four continents. Among the 296 STs, 78 and 52 were shared among countries and continents, respectively, representing 3643 of the 4200 isolates. Except for the clone-corrected serotype D sample among countries, our analysis of the molecular variance of the 4200 isolates revealed significant genetic differentiations among countries and continents in populations of CNSC, serotype A, and serotype D. Phylogenetic analyses of the concatenated sequences of all 657 STs revealed several large clusters corresponding to the major molecular types. However, several rare but distinct STs were also found, representing potentially novel molecular types and/or hybrids of existing molecular types. Phylogenetic incompatibility analyses revealed evidence for recombination within all four major molecular types-VNI, VNII, VNIV and VNB-as well as within two VNB subclades, VNBI and VNBII, and two ST clusters around the most common STs, ST5 and ST93. However, linkage disequilibrium analyses rejected the hypothesis of random recombination across most samples. Together, our results suggest evidence for historical differentiation, frequent recent gene flow, clonal expansion and recombination within and between lineages of the global CNSC population.

Genetic Diversity and Population Structure of Local Chicken Ecotypes in Burkina Faso Using Microsatellite Markers.

The objective of this study was to investigate the genetic diversity and population structure of local chicken ecotypes from Burkina Faso using microsatellite markers. A total of 71 individuals representing local chicken populations from the Centre-East (18), Centre-North (17), Sahel (18) and South-West (18) were used to estimate genetic diversity indices, population structure and phylogenetic relationships using 20 selected polymorphic microsatellite markers. The number of alleles, mean number of alleles, mean of observed and expected heterozygosity and polymorphic information content were 127, 6.35, 0.391, 0.521, 0.539 and 0.541, respectively. The estimated overall fixation index between loci (F), among populations (FIS) and inbreeding coefficient within chicken ecotypes were 0.239, 0.267 and 0.243, respectively. Analysis of the molecular variance revealed that 77% of the total genetic diversity was attributed to within-population variation and the remaining 1% and 22% were attributed to among-regions differentiation (FST) and among-individual differentiation (FIT), respectively. The highest pairwise genetic distance (0.026) was found between the local Konde ecotype and those from the Centre-North region while the lowest distance was observed between local chickens from the Sahel and the Centre-North regions (0.003). Neighbour-joining phylogenetic tree and principal component discriminant analyses confirmed the observed genetic distances between populations. The results show that local chickens in Burkina Faso have a rich genetic diversity with little differentiation between the studied populations. This study provides important information on measures of genetic diversity that could help in the design and implementation of future genetic improvement and conservation programs for local chickens in Burkina Faso.

Molecular Characterization of a New Ecotype of Holoparasitic Plant Orobanche L. on Host Weed Xanthium spinosum L.

A species of Orobanche was observed on spiny cocklebur (Xanthium spinosum) for the first time in Iran and tentatively was named IR-Iso.This study was conducted to make a phylogenetic analysis of the Orobanche using 5.8S rRNA region sequences, and also to better understand its sequence pattern. The full-length ITS1-ITS2 region of the new Orobanche isolate was PCR-amplified from the holoparasitic plant parasitizing X. spinosum. Sequences of the amplicons from the isolate were 100% identical but differed by 5.6–6.7% from most homologous GenBank accessions to 37.9% divergence from distant species. The analysis of the molecular variance showed that variation between-population (61.9%, SE = 0.04) was larger than within-population. Neighbor-joining analysis placed the Iranian isolate in the same clade as most of the Orobanche and Phelipanche species. The isolate was more closely related to Orobanche aegyptiaca (from China), and this was confirmed by using a structure analysis. However, complementary analyses showed that the Iranian isolate has a unique nucleotide substitution pattern, and hence it was considered as an ecotype of O. aegyptiaca (ecotype Alborzica). In this paper we report on the association between this new ecotype of Orobanche and X. spinosum.

ISSR markers and morphometry determine genetic diversity and population structure in Hedera helix L.

Hedera helix L. is an invasive, but medicinally important plant. In Iran, there is no available study on the H. helix population to reveal the genetic diversity and population structure. Fifty-six individual plants belonging to nine geographical populations were collected in four provinces of Iran. High genetic diversity, polymorphisms, and a Shannon diversity index of 0.269 were detected in Mazandaran, Kandovan (Population 3). Analysis of the molecular variance indicated 40% of total genetic variation of the whole population was present in the subpopulation. A high genetic similarity (0.922) between plant Populations 5 (Kermanshah; Islamabad) and 6 (Kermanshah; Paveh) was noted. On the other hand, a low genetic similarity was observed between plant Populations 1 (Tehran; Darband) and 8 (Ardabil; Hur). The Mantel test revealed a correlation between the genetic and geographical distances. Furthermore, it demonstrated the isolation mechanism responsible for the population structure in the H. helix plant populations. The principal component analysis explained the majority of the variation in the morphological characteristics. Three components explained 87% of the variation, and the first component explained 60% of the variation. For instance, the leaf morphology showed a correlation of > 0.7 between leaf morphological and floral characters. The plant leaves and quantitative flower characteristics separated the plant populations according to the differences in length. The current results have implications for plant conservation and management.

The Genetic Differences and Structure of Selected Important Populations of the Endangered Taxus baccata in the Czech Republic

Taxus baccata L. (common yew) is an endangered tree species in the Czech Republic. However, its natural occurrence has not been adequately protected in all areas of the country. The aim of this study is to determine whether the yew population in the newly established Mařeničky seed orchard (TS_L) enables mixing with other Czech yew populations. Using a set of nuclear microsatellites, the genetic diversity in the Lužické Mountains (TS_L) and in selected wild-provenance populations from the Czech Republic (Jílovské yews, TS_J; Březinské yews, TS_B, and yews from Moravský Karst, TS_M) was studied, as they could be donor sources for potential translocation activities. We observed that the level of genetic diversity within the four Czech yew units that were investigated was high. An analysis of the molecular variance (AMOVA) showed 7% variation among populations, and the genetic differentiation values were low to moderate (FST = 0.042–0.108). According to a STRUCTURE analysis, high genetic similarity was observed between the TS_L and TS_B units. Our results provide important genetic suggestions on how conservation management can be designed to maximize its success.

Genetic variability and population structure of Leucinodes orbonalis (Guenée), a severe insect pest of brinjal in India

Aim: The present study was undertaken to provide valuable insights regarding population genetic structure of Leucinodes orbonalis from diverse agro-ecologies of India. Methodology: Molecular characterization of L. orbonalis populations collected from five major agro-climatic zones of India was carried out using mitochondrial cytochrome oxidase I (COI) gene. Collected specimens were subjected to DNA extractions, partial PCR amplification and sequencing of the target gene, and multiple sequence alignments. Results: The results showed very less diversity in the nucleotide positions of the COI sequences of 79 studied specimens, with a low number of segregating sites (30), nucleotide diversity (0.00438) and overall mean genetic distance (0.004 ± 0.001). The significant negative values of neutrality tests and unimodal mismatch distribution supported the demographic expansion theory in Indian L. orbonalis. Analysis of the molecular variance revealed that 93.13% of the genetic variation was within populations, and the variation among populations was only 6.87%. The pairwise genetic differentiation was also found to be low to moderate between most of the populations. Multiple haplotypes were recorded from all the populations, and both neighbour-joining tree as well as the haplotype network showed that clustering of the haplotypes was independent of the geographical location. Interpretation: Thus, it can be inferred that Indian populations of L. orbonalis have very low genetic variation levels concerning the COI gene. There is a possible occurrence of stable inherited gene flow among populations, thereby reducing genetic variation in India.

Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS).

Olives are one of the most important fruit and woody oil trees cultivated in many parts of the world. Olive oil is a critical component of the Mediterranean diet due to its importance in heart health. Olives are believed to have been brought to the United States from the Mediterranean countries in the 18th century. Despite the increase in demand and production areas, only a few selected olive varieties are grown in most traditional or new growing regions in the US. By understanding the genetic background, new sources of genetic diversity can be incorporated into the olive breeding programs to develop regionally adapted varieties for the US market. This study aimed to explore the genetic diversity and population structure of 90 olive accessions from the USDA repository along with six popular varieties using genotyping-by-sequencing (GBS)-generated SNP markers. After quality filtering, 54,075 SNP markers were retained for the genetic diversity analysis. The average gene diversity (GD) and polymorphic information content (PIC) values of the SNPs were 0.244 and 0.206, respectively, indicating a moderate genetic diversity for the US olive germplasm evaluated in this study. The structure analysis showed that the USDA collection was distributed across seven subpopulations; 63% of the accessions were grouped into an identifiable subpopulation. The phylogenetic and principal coordinate analysis (PCoA) showed that the subpopulations did not align with the geographical origins or climatic zones. An analysis of the molecular variance revealed that the major genetic variation sources were within populations. These findings provide critical information for future olive breeding programs to select genetically distant parents and facilitate future gene identification using genome-wide association studies (GWAS) or a marker-assisted selection (MAS) to develop varieties suited to production in the US.

Revealing the genetic diversity of maize (Zea mays L.) populations by phenotypic traits and DArTseq markers for variable resistance to fall armyworm

The fall armyworm (FAW) is a gregarious insect pest causing substantial yield losses and crop failures in maize and related cereal crops in sub-Saharan Africa due to a lack of resistant varieties and integrated control options. Genetic variation for economic traits including resistance to the FAW damage is a prerequisite in maize improvement programs. The objective of this study was to determine the genetic diversity of 59 maize genotypes of diverse genetic background with variable resistance to fall armyworm, using phenotypic traits and SNP-based DArT markers. The test genotypes were profiled using agro-morphological traits, FAW damage parameters, and Diversity Array Technology Sequencing-derived single nucleotide polymorphism (SNP) markers. Significant (p < 0.001) differences were observed among the genotypes for 13 phenotypic traits with phenotypic coefficient of variation ranging from 2.19 to 51.79%. Notable phenotypic variation was observed for ear position, grain yield, FAW induced leaf and cob damage. The mean gene diversity and polymorphic information content were 0.29 and 0.23, respectively, reflecting a moderate level of genetic variation among the test genotypes when assessed using SNP markers. Analysis of the molecular variance revealed greater genetic variance within a population rather than between populations. Population structure and cluster analysis grouped the test populations into two main clusters. The following genetically divergent open pollinated varieties were selected with favourable agronomic performance and FAW resistance for population improvement or hybrid breeding: Pool 16, ZM 4236 and ZM 7114. The genetic diversity detected within and among the tested populations will facilitate the breeding of maize varieties incorporating farmer-preferred agronomic traits and FAW resistance in Zambia and related agro-ecologies.

Multivariate Statistical Methods Used in Population Genetics

Several multivariate statistical methods are used in population genetics but there are very few studies that have revealed the strengths and weaknesses of different methods. Thus, this study aims to reveal the strengths and weaknesses of the different multivariate statistical methods used in population genetics through the world. This synthesis is carried out according to the methodology "Preferred Reporting Items for Systematic Reviews and Meta-Analyzes" (PRISMA). This study shown that various statistical methods or combination of multivariate statistical methods are used in population genetics. It emerges that there is no a priori a better method, so it is necessary to determine the method adapted to both the data collected and the research objective. This study identified the most commonly used multivariate statistical methods in genetics such as: Ordination methods (52.50%) are methods that summarize the information contained in the data matrix by minimizing wastage. This are: principal components analysis (by 32.0% of the articles), principal coordinates analysis (by 7.50% of the articles), discriminant analysis of principal component, factorial correspondence analysis, factorial discriminant analysis, factorial analysis on distance table. Clustering methods (35%) that aim to form groups of individuals that are as similar as possible, including the hierarchical ascending clustering (17.50% of articles), neighbor-joining, and Bayesian clustering model (by 15% of the articles). The analysis of the molecular variance (7.50%) which consists of studying the intra and inter-population variation and the Mantel test (5%) which aims to test the correlation between the matrix of genetic distances and other distance matrices (environmental causes of genetic variability).

Effect of pelleted high-grain total mixed ration on rumen morphology, epithelium-associated microbiota and gene expression of proinflammatory cytokines and tight junction proteins in Hu sheep

This study evaluated the effects of a pelleted high-grain total mixed ration (TMR) on rumen fermentation, epithelium-associated microbiota and rumen epithelium health of Hu sheep. Fifteen (15) male lambs were allocated to three (3) dietary groups (n = 5 for each). The first group (CON) received a low-grain non-pelleted TMR; (300 g/kg diet) concentrate, the second group (HG) received a high-grain non-pelleted TMR; (700 g/kg diet) concentrate, while the third group (HP) also received a high-grain TMR in a pelleted form. As compared with the HG group, rumen pH of the HP group was lower (P = 0.012), while lactate concentration was observed to be higher (P = 0.024). The analysis of the molecular variance revealed that all the three (3) groups clustered separately from each other. The alpha diversity estimators (OUT numbers, ACE and Chao) were decreased in the HG group compared with the CON group as well as in the HP group compared with the HG group. Bacteroidetes and Firmicutes were found to be the predominant phyla in all the groups. At the genus level, Prevotella showed a significant increase in the HG group compared with the CON group (P = 0.009) while showing no significant difference between the HP group and HG group. In contrast, the unclassified Lachnospiraceae showed a significant decrease in the HG group compared with the CON group (P = 0.009). Compared with the HG group, Megasphaera (P = 0.008), Rumincoccus (P = 0.016), Olsenella (P = 0.007) and Sharpea (P = 0.005) were significantly increased in the HP group. While, the predominant OTUs that belonged to Prevotella and unclassified Prevotellaceae increased in the HG group as compared with the CON group.The up-regulation of TNF-α and IL-6 in the HG group coupled with the disruption of the stratum corneum as shown in the histological examination indicate the presence of inflammation. In summary, this study showed that feeding of pelleted high-grain TMR to Hu sheep altered the rumen fermentation and epithelium associated microbiome which resulted in rumen epithelial injuries thereby affecting animal production.

Genetic structure and variation in Iranian licorice (Glycyrrhiza glabra L.) populations based on morphological, phytochemical and simple sequence repeats markers

Licorice (Glycyrrhiza glabra L.) as a strategic and highly valuable medicinal plant in Iran with numerous beneficial pharmaceutical properties contributes substantially to Iranian herbs exports. In the present study, variation of cultivated licorice populations was assessed via morphological, phytochemical and simple sequence repeats (SSRs) markers. A remarkable variation among cultivated populations of G. glabra in terms of morphological and phytochemical characteristics was found. Maximum coefficient of variance was observed in leaf attributes such as leaf width (CV = 34.6 %) and leaf length (CV = 32.7 %) among different populations. Minimum (11.7 mg/g Dry Weight (DW)) and maximum (74.0 mg/g DW) amount of glycyrrhizic acid were observed in Haji Abad and Eghlid populations, respectively. High levels of glabridin content were allocated to Kashmar (4.0 mg/g DW), Ahar (3.0 mg/g DW) and Ilam (2.9 mg/g DW) populations. Nine EST-SSR primers were applied to analyze the genetic variation of 162 individuals of 28 licorice populations. In total 46 bands were obtained from 9 SSR markers with 24 bands being polymorphic (52.2 %). The polymorphic information content (PIC) for markers ranged from 0.32 (SSR-25053) to 0.61 (SSR-20631), with an average of 0.50. The analysis of the molecular variance (AMOVA) of the licorice populations demonstrated that 82.0 % of variability was related to the intra-population level, while the diversity among populations amounted to 18.0 %. Ultimately, the results of this investigation create guidelines such as the identification of glycyrrhizic acid/glabridin rich-clones and genetically separated clones for deliberate interbreeding and further examinations as a subset of breeding programs.

Comparison of the rumen bacterial community, rumen fermentation and growth performance of fattening lambs fed low-grain, pelleted or non-pelleted high grain total mixed ration

This study aimed to compare the rumen bacterial community, rumen fermentation and growth performance of fattening lambs fed non-pelleted low grain, non-pelleted high grain or pelleted high-grain total mixed ration (TMR) in Hu sheep. Fifteen male lambs were allocated into 3 groups (n = 5 for each). One group (CON) received a low-grain non pelleted TMR (30% concentrate), the second group (HG) received a high-grain non-pelleted TMR (70% concentrate), while the third group (HP) received the same high-grain TMR in a pelleted form. The composition and CowPI predicted function of ruminal digesta-associated microbiome, rumen fermentation parameters and growth performance were examined. The animals of the HG group showed a significantly higher average daily gain (P = 0.032) and body weight gain compared to the CON group (P = 0.032). While there was no significant difference between HG and HP in any of the growth performance parameters. As compared with the HG group, rumen pH of the HP group was lower (P = 0.012), while lactate concentration was higher (P = 0.024). The unweighted unifractional principle coordinates analysis and the analysis of the molecular variance (AMOVA) revealed that all groups clustered separately from each other. All the alpha diversity estimators were decreased in HG compared to CON as well as in HP compared to HG. Bacteroidetes and Firmicutes were the predominant phyla in all groups and the abundance of Fibrobacteres was significantly decreased in the HP group compared to the HG group (P = 0.047). At the genus level, as compared with the HG group, pelleting resulted in a decrease in the percentage of unclassified BS11 gut group and Succiniclasticum, while it led to an increase in the abundance of some simple sugar fermenters like Megasphaera (P = 0.008), Olsenella (P = 0.007), Dialister (P = 0.009) and Sharpea (P = 0.019). Among the predominant OTUs, the proportion of some OTUs belonging to the Prevotella species increased in the HG group with a severe decrease in the HP group. The CowPI predicted functional profile of the rumen microbiome revealed the enrichment of the pentose phosphate pathway in the HP group only. In summary, this study showed that pelleting the high-grain TMR altered the rumen fermentation and amplified the ruminal microbiome simple sugar utilization.

Assessment of genetic diversity and population structure of the common littoral shrimp Palaemon serratus (Pennant, 1777) by microsatellites: Towards a sustainable management

Abstract The common littoral shrimp Palaemon serratus is an ecologically and economically important decapod crustacean. Understanding the spatial structure of its populations is crucial to implement effective management strategies. In this study, 17 polymorphic microsatellite nuclear markers were examined in 252 individuals to explore the genetic diversity and the population structure underlying the geographical distribution of this crustacean in European waters. Basic genetic descriptors, population genetic analyses based on FST, analysis of the molecular variance (AMOVA), Bayesian clustering and the Mantel test were performed. Genetic differentiation was significant among sampling sites. AMOVAs and Bayesian assignment tests showed genetic differentiation among localities from the Atlantic coast and those belonging to the area of the Strait of Gibraltar and the Mediterranean Sea. The Guadalquivir estuary was significantly different from the remaining localities. A biogeographical break was detected to the west of the Strait of Gibraltar, and evidence of isolation by distance was obtained. Localities on both sides of the English Channel showed genetic differentiation with the rest of the Atlantic sampling sites, indicating a biogeographical break in this area. These results will contribute towards the better understanding of the biology and ecology of this shrimp and management of the valuable fishery. Two priority areas were delimited: the Atlantic and the Gibraltar–Mediterranean. The Guadalquivir estuary, Anglesey and Calais should also be considered as different genetic stocks.

Asexual reproduction and heterozygote selection in an Antarctic demosponge (Stylocordyla chupachus, Suberitida)

Antarctic bottoms harbor stable, benthic communities, subjected to low temperatures. Environmental stability may promote the asexual (clonal) reproduction of sponges to maintain adapted genotypes to those particular conditions. Stylocordyla chupachups forms patchy populations across the Antarctic continental shelf. Individuals are mostly similar in size without distinct cohorts, which indicates fast growth of the new recruits. Settlement of incubated (clonal?) functional sponges may accelerate sponge growth and success at early colonization phases. To analyze the weight of clonal reproduction in the species, a genetic study was performed on three close populations using eight polymorphic microsatellite loci that were designed from massive sequencing. The three study populations showed a relatively low genetic diversity and low loci polymorphism (from 2 to 6 alleles). The estimators of genetic structure, the Analysis of the Molecular Variance (AMOVA), and the presence of private alleles indicated low but significant structure between the populations. A relatively high rate of asexual reproduction (ca. 25% of the individuals) was detected. The program MLGsim found five identical multilocus genotypes (MLGs) with an asexual origin. An excess of heterozygotes (in five out of the eight loci genotyped) was found, which suggests a positive selection mechanism for heterozygotes. The relatively high rates of asexual reproduction may be the result of adaptation to the environmental stability, while heterozygote selection would help maintain some genetic diversity in the populations. S. chupachups has been reported to be one of the first sponge species recolonizing bare areas resulting from iceberg scouring, which indicates a high species fitness and adaptation to Antarctic bottoms. Two out of the three study populations showed bottleneck, which may indicate a recent founder effect and supports the pioneer nature of this species.

Genetic diversity of the habitat-forming red alga Gracilaria vermiculophylla along Chinese coasts

As a habitat-forming species, the red alga Gracilaria vermiculophylla has been noted to play an essential role in shaping coastal marine communities and maintaining intertidal ecosystems along Chinese coasts. However, few studies have been conducted that analyze the genetic structure of the population and the distribution patterns of genetic variation. In this study, we compiled partial mitochondrial DNA cytochrome c oxidase subunit I gene (cox1) of 19 G. vermiculophylla populations (461 individuals) and performed phylogenetic analysis and population genetic surveys. A total of 461 mt-DNA cox1 sequences were obtained and edited into 641 bp, which contained 21 polymorphic sites and yielded 15 haplotypes. Phylogenetic inferences, haplotype networking, and principal coordinate analysis consistently indicated that G. vermiculophylla populations diverged into two groups: the northern group is comprised of specimens from the Yellow-Bohai Sea and the Shengsi Islands, while the southern group is comprised of specimens from six locations south to Xiamen, Fujian Province. Analysis of the molecular variance and Nei’s genetic distances indicated low genetic differentiation between populations in each group while group-level genetic divergence is comparable to the degree of subspecies differentiation. •研究报告• 782 生 物 多 样 性 Biodiversity Science 第 24 卷

Assessment of population genetic diversity of Derris elliptica (Fabaceae) in China using microsatellite markers

Derris elliptica (Fabaceae) is one of the most important sources of the insecticide rotenone. This plant was first introduced from different Southeast Asian countries to China in the early decades of last century. The purpose of this study is to assess genetic diversity of D. elliptica in China for the conservation of its germplasm resources and for future breeding programs. Genetic diversity and population structure of 14 cultivated populations of D. elliptica in China were detected using 25 microsatellite markers. A moderate level of genetic diversity was found across the whole sample (expected heterozygosity, He=0.529), indicating a history of multiple sources of introduction and a broad genetic base for the crop cultivated by cuttings. The genetic diversity at the population level (Mean He=0.31) was relatively lower. Repeated bottlenecks or founder effects in its short cultivated history and also its vegetative reproduction mode may explain the results. FST (Wright F-statistic) values and AMOVA (analysis of the molecular variance) indicated large genetic differentiation among populations (FST=0.461; 44.1%, AMOVA), while the cluster analysis showed that the collections belong to two major groups of genotypes. The initial difference in the introduced germplasm from the primary center of origin and the limited gene flows among populations may have played important roles in shaping the genetic variation pattern in D. elliptica of China.