Open Access Method Article

Extrapolation of the Species Accumulation Curve for Incomplete Species Samplings: A New Nonparametric Approach to Estimate the Degree of Sample Completeness and Decide when to Stop Sampling

Jean Béguinot

Annual Research & Review in Biology, Page 1-9
DOI: 10.9734/ARRB/2015/22351

Incomplete species samplings are deemed to remain the common practice in those groups of animals, such as small or micro- invertebrates, with numerous species that often are more or less difficult to detect in the field. Thus, extrapolating the Species Accumulation Curve as far as possible beyond the actual sample size may thus serve as a useful (although imperfect) surrogate to the desired, but practically inaccessible, complete samplings. In this context, several kinds of theoretical or empirical models for the Species Accumulation Curve and also a lot of estimators of the asymptotic limit of the Curve (i.e. total species richness) have been proposed. The practical issue is now to select appropriately among these numerous, different propositions. Here, I show that realistic Species Accumulation Curves are constrained to respect a general mathematical relationship, which, in turn, may serve to discriminate and select among the available models of Species Accumulation Curves and, as well, among the different formulations of the estimators of species richness that are commonly referred to.

As a result of the application of this screening approach, it follows that, for the generality of cases (i.e. ratio singletons/doubletons larger than 0.6), a specific formulation of the Species Accumulation Curve (bi-hyperbolic with exponents -1 and -2 for sample size) complies at best. Accordingly, the more appropriate estimator of total species richness is Jackknife-2. Only when the ratio singletons/doubletons happens to fall beneath 0.6, Chao estimator may then be preferred. This is the case when samplings closely approach exhaustivity or when they address assemblages with unusually homogeneous abundances of species.

Open Access Commentary

NGS and Male Infertility: Biomarkers Wanted

Rute Pereira, Mário Sousa

Annual Research & Review in Biology, Page 1-4
DOI: 10.9734/ARRB/2015/20263

Male factor abnormalities account for 30 to 50% of all infertility cases [1]. Nowadays it is clear that genetic abnormalities are a significant cause of male infertility, with about 20% of patients with sperm defects presenting gene mutations [2]. Next-generation sequencing (NGS) technologies allowed the exponential increase in knowledge of new genes involved in male infertility, offering an enormous amount of data in a fast way [3]. Currently, whole exome sequencing (WES) is the most used approach to study the genetics of infertility. Although WES covers only the coding regions of the genome, it is cost-effective and the data are easy to interpret. Also, there is a high likelihood of identifying significant variants, since approximately 85% of disease-causing mutations are thought to occur in gene coding regions [4]. On the other hand, whole genome sequencing (WGS) analysis provides the most complete information of the genetic variants in an individual, but there are still regions (repetitive or satellite) that cannot be sequenced by WGS. Also, WGS is too pricey (too time and labour consuming) for most research and clinical laboratories, the data produced are technically demanding, and their functional interpretation is challenging, with most of the information gathered having an unknown meaning [5]. Nevertheless, it is becoming clear that non-coding regions of the genome also play crucial roles in normal physiology and development, namely in testis and epididymis development and in spermatogenesis [6,7]. Non-coding regions of the genome were already found to be useful for disease diagnosis (e.g. expression profiles of micro RNA are able to accurately identify the origin of some tumours, enabling their classification), prognosis (in some tumours), and therapies (RNA-based and RNA-targeted therapies) [8]. Thus, non-coding regions of the genome should not be forgotten in the biomedical research and, consequently, WES is not enough: There is an urgent need that WGS becomes the standard approach. For that to happen, the inherent costs should decrease, and extremely high-performance computing and intensive bioinformatics support have to be developed.

Open Access Original Research Article

African Continent a Likely Origin of Family Combretaceae (Myrtales). A Biogeographical View

Jephris Gere, Kowiyou Yessoufou, Barnabas H. Daru, Olivier Maurin, Michelle Van Der Bank

Annual Research & Review in Biology, Page 1-20
DOI: 10.9734/ARRB/2015/17476

Aim: The aim of this study was to estimate divergence ages and reconstruct ancestral areas for the clades within Combretaceae.

Methods: We utilized a comprehensive dataset of 144 species of Combretaceae with a worldwide sampling to reconstruct a dated phylogeny based on a Bayesian analysis of five gene regions (ITS, rbcL, matK, psaA-yf3 and trnH-psbA). Bayesian phylogenetic tree was generated using a Bayesian MCMC approach implemented in BEAST v.1.7.5 to generate lineage dating. Two fossils Dilcherocarpon Combretoides (93.5-112 mya) and Terminalioxylon (28 mya) were used for calibration. S-DIVA and DEC model analysis were used to estimate ancestral area ranges.

Results: Our results indicate that the earliest diversification of Combretaceae occured ca. 110 mya. This was followed by the splitting of the family into two subfamilies, Combretoideae and Strephonematoideae during the Late Cretaceous period. This event followed the radiation of Combretoideae, ca 105.6 mya to give rise to two tribes, Combretaeae and Laguncularieae which diverged around 60.9 mya and 52.9 mya, respectively. The two main subtribes Combretineae and Terminaliinae, radiated at ca. 48.3 and 46.4 mya respectively. African continent is inferred as the origin of Combretaceae, with dispersal as the major event responsible for the intercontinental disjunct distribution observed in the tropical and subtropical regions.

Main Conclusions: Our results revealed that the crown age of Combretaceae is ca.110 mya, a time hypothesised to be marked by high angiosperm diversification. Two largest subtribes Combretineae and Terminaliinae, split occurred in the Late Cretaceous period with divergence estimated at the commencement of Eocene epoch. The African continent is hypothesised to have emerged from the split of the super continent Gondwana. Long distance dispersal is postulated as the major modeller, with vicariance and extinction playing marginal roles in shaping the current intercontinental disjunct distribution of Combretaceae in the tropical and subtropical regions of the world.

Open Access Original Research Article

Analysis of Tissue Alterations and Quantitative Histopathological Indices in Rhamdia quelen (Quoy & Gaimard, 1824) and Metynnis maculatus (Kner, 1858) During Treatment of Ichthyophthiriasis

Thayzi de Oliveira Zeni, Aline Horodesky, Gisela Geraldine Castilho-Westphal, Antonio Ostrensky

Annual Research & Review in Biology, Page 1-10
DOI: 10.9734/ARRB/2015/21944

Aims: The present study aimed to describe the histological alterations observed in gills of Rhamdia quelen and Metynnis maculatus during treatment of white spot disease and to compare three quantitative indices of gill alterations originally developed by other authors for this type of evaluation.

Study Design: Animals were collected and analysed on days zero, 10, 20, 30, 40 and 100 in relation to the beginning of treatment of ichthyophthiriasis.

Place and Duration of Study: Integrated Group for Aquaculture and Environmental Studies, Department of Animal Sciences, Federal University of Paraná, between January and April 2014.

Methodology: For the analyses, animals presenting clinical signs of a ciliate Ichthyophthirius multifiliis infestation were maintained in a laboratory. Immediately after disease identification, the fish were medicated and monitored for the occurrence and evolution of gill histological alterations.  For histopathology, 15 sick fishes (presence of white spot) of each species were collected from each tank on day zero. On days 10, 20, 30 and 40 after diagnosis, 10 individuals of each species were collected. After collection, the fish were subjected to spinal cord section and subsequent biometric analysis. Next a gill arch from the right side of each fish were collected and fixed in Davidson solution for 48 hours (ALFAC) [1]. The biological material was then subjected to a routine histotechnical procedure. Animals were observed daily for behavioural analysis, and the mortality was recorded.

Results: Twelve histological alterations were identified and described throughout the collections. However, it was not possible to establish an unequivocal causal relationship between the observed alterations and the parasitic disease. The application of the different indices suggests that the dynamics of the gill alterations occurred differently for R. quelen and M. maculatus.

Conclusion: The robustness and suitability of the indices as a tool for assessing the severity of the damage caused by the parasitic disease to gill tissue in the two species allow us to better understand of the temporal evolution of the disease are discussed and questioned.

Open Access Original Research Article

Response of the Gene Actions Governing Grain Yield and Quality Traits in Wheat Parents and Their F1 Progenies to Decreasing Soil-N Rate

A. M. M. Al-Naggar, R. Shabana, M. M. Abd El-Aleem, Zainab El-Rashidy

Annual Research & Review in Biology, Page 1-16
DOI: 10.9734/ARRB/2015/21939

To start an accurate wheat breeding program for improving low-N tolerance, information on the type of gene action controlling the inheritance of grain yield and quality traits under contrasting N environments should be available, which is the objective of the present investigation. The diallel crosses (except reciprocals) among six divergent parents in low-N tolerance were made. Parents and F1 crosses were evaluated in two seasons under two N environments; namely 0 kg N/fed (low-N) and 75 kg N/fed (high-N) in two separate experiments using a randomized complete block design with 3 replications. Results of analysis of combining ability across seasons showed that variances due to both general (GCA) and specific (SCA) combining ability were significant for all studied yield and quality traits, indicating the involvement of additive and non-additive types of genes in controlling these traits. Parents and F1 crosses thus have different GCA and SCA effects, respectively. The best general combiners with positive effects for improvement of low-N tolerance were L26, L27 and L25 parents. Under low–N conditions, the best specific combinations for improvement of low-N tolerance were L25 x Gz168, Gem9 x Gz168 and Gem7 x Gem 9. Hayman analysis of variance indicated that spikes/plant (SPP), grains/spike (GPS), harvest index (HI) and grain yield/plant (GYPP) were controlled by additive and non-additive types of gene action, while 100 grain weight (100 GW) was controlled by an additive type of gene action. A high narrow sense heritability estimate was observed for GYPP (66.32%), SPP (42.52%), 100 GW (33.11%) and GPS (21.80%) under low-N.

Open Access Original Research Article

Effect of Flooding on Trypanosome Infection Rates in Trade Cattle at Central Abattoir, Makurdi Metropolis, Benue State, North Central Nigeria

J. N. Abenga

Annual Research & Review in Biology, Page 1-6
DOI: 10.9734/ARRB/2015/15757

Aim: The aim of the study was to determine trypanosome infection rates in cattle brought to Makurdi central abattoir during a devastating flooding of 2012.

Study Design: Cattle of mixed sexes and breeds were randomly sampled three times a week.

Place and Duration of Study: The investigation which covered the months of September and October was carried out at the Wurrukum central abattoir, South Bank, Makurdi, administrative headquarters of Benue state, North Central Nigeria.

Methodology: Blood samples collected into plastic sample bottles containing EDTA anticoagulant were used for parasitological diagnosis using concentration methods and haematological investigation.

Results: Trypanosome infection rate in cattle was 13.1% which was adjudged three times higher than the average national trypanosome prevalence rate and the result of previous larger surveys obtained from within this area. The dominant infecting trypanosome specie was Trypanosoma vivax (42.4%), followed by T. brucei (28.6%). Infected cattle had lower PCV(28.2±1.6%) compared to those of apparently negative animals (38.1±4.7%).

Conclusion: Previous data had associated wet or rainy seasons with increased tsetse fly density and trypanosomosis outbreaks in sub-Saharan Africa. It was therefore concluded that extended wet season associated with flooding might have created a conducive environment for breeding of tsetse and other haematophagous flies thereby increasing fly-animal contacts and trypanosome infection rates in the cattle.

Open Access Review Article

Molecular Genetic Markers for Assessing the Genetic Variation and Relationships in Lactuca Germplasm

Mohamed A. El-Esawi

Annual Research & Review in Biology, Page 1-13
DOI: 10.9734/ARRB/2015/20647

The genus Lactuca L. belonging to the Asteraceae family, is widely distributed in different geographical and ecological areas. Lettuce and most of the other species of the genus Lactuca L. have been cultivated for their economic and medicinal importance. This review summarizes recent knowledge of the application of biochemical (isozymes) and molecular technologies (restriction fragment length polymorphism; random amplified polymorphic DNA; amplified fragment length polymorphism; microsatellites or simple sequence repeats; single nucleotide polymorphism) in Lactuca germplasm in order to better understand the genetic variation, interspecific relationships, taxonomy and breeding as a basis for further research studies. Undoubtedly, this would in turn provide a better platform for germplasm improvement, utilization and conservation.