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PubMed2002

Methodologies for conservation assessments of the genetic biodiversity of aquatic macro-organisms.

International organizations and biodiversity scientists recognize three levels of biodiversity: genetic, species, and ecosystem. However, most studies with the goal of assessing biodiversity collect data at only a single level--that of the species. Even when multiple levels of biodiversity are considered, usually only ecosystem diversity is also evaluated. Genetic diversity is virtually never considered. Yet, genetic diversity is essential for the maintenance of populations and species over ecological and evolutionary time periods. Moreover, because components of genetic diversity are independent of either species or ecosystem diversity, genetic diversity can provide a unique measure by which to assess the value of regions for conservation. Regions can be valuable for conservation of their genetic resources regardless of their levels of species or ecosystem uniqueness or diversity. In general, the same methods and statistical programs that are used to answer questions about population genetics and phylogenetics are applicable to conservation genetics. Thus, numerous genetic techniques, laboratory methods, and statistical programs are available for assessing regional levels of genetic diversity for conservation considerations. Here, we provide the rationale, techniques available, field and laboratory protocols, and statistical programs that can be used to estimate the magnitude and type of genetic diversity in regions. We also provide information on how to obtain commonly utilized statistical programs and the type of analyses that they include. The guide that we present here can be used to conduct investigations of the genetic diversity of regions under consideration for conservation of their natural resources.

Animals↗
PubMed2005

A note on the measurement of genetic diversity within genebank accessions of lettuce (Lactuca sativa L.) using AFLP markers.

This paper discusses a statistical approach for measuring genetic diversity within genebank accessions of a self-fertilising species. This approach is applied to lettuce (Lactuca sativa L.), using AFLP marker data on a set of 1,390 accessions, representing six different lettuce types. Knowledge of the within-accession genetic diversity is important for decisions about the way accessions have to be maintained by genebanks. It is argued that if the within-accession diversity is small, as can be expected for a self-fertilising species like L. sativa, the best approach is to sample as many accessions as possible with only two plants per accession and estimate the within-accession diversity by the proportion of accessions of which the individuals are different.

DNA, Plant↗
PubMed2025

RAD-Seq-derived SNPs reveal no local population structure in the commercially important deep-sea queen snapper (Etelis oculatus) in Puerto Rico.

UNLABELLED: The queen snapper (Etelis oculatus Valenciennes in Cuvier & Valenciennes, 1828) is a deep-sea snapper whose commercial importance continues to increase in the US Caribbean. However, little is known about the biology and ecology of this species. In this study, the presence of a fine-scale population structure and genetic diversity of queen snapper from Puerto Rico was assessed through 16,188 SNPs derived from the Restriction site Associated DNA Sequencing (RAD-Seq) technique. Summary statistics estimated low genetic diversity (HO = 0.333-0.264) and did not reveal population differentiation within our samples (F ST = - 0.001-0.025). Principal component analysis and a model-based clustering method did not detect a fine-scale subpopulation structure among sampling sites, however, there was genetic variability within regions and sites. Our results have revealed comparable genetic and dispersal patterns to those observed in other shallow-water snapper species in Puerto Rico waters. It is crucial to further enhance our understanding of the ecological and biological aspect of the queen snapper to effectively manage and conserve this species as fishing pressure has been extended to deep water species in the US Caribbean. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00289-7.

Caribbean Fisheries↗
PubMed1989

Molecular population genetics of mtDNA size variation in crickets.

Nucleotide sequence analysis of a region of cricket (Gryllus firmus) mtDNA showing discrete length variation revealed tandemly repeated sequences 220 base pairs (bp) in length. The repeats consist of 206 bp sequences bounded by the dyad symmetric sequence 5'GGGGGCATGCCCCC3'. The sequence data showed that mtDNA size variation in this species is due to variation in the number of copies of tandem repeats. Southern blot analysis was used to document the frequency of crickets heteroplasmic for two or more different-sized mtDNAs. In New England populations of G. firmus and a close relative Gryllus pennsylvanicus approximately 60% of the former and 45% of the latter were heteroplasmic. From densitometry of autoradiographs the frequencies of mtDNA size classes were determined for the population samples and are shown to very different in the two species. However, in populations where hybridization between the two species has occurred, the frequencies of size classes and cytoplasmic genotypes in each species' distinct mtDNA lineage were shifted in a manner suggesting nuclear-cytoplasmic interactions. The data were applied to reported diversity indices and hierarchical statistics. The hierarchical statistics indicated that the greatest proportion of variation for mtDNA size was due to variation among individuals in their cytoplasmic genotypes (heteroplasmic or homoplasmic state). The diversity indices were used to estimate a per-generation mutation rate for size variants of 10(-4). The data are discussed in light of the relationship between genetic drift and mutation in maintaining variation for mtDNA size.

Animals↗
PubMed1997

The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations.

Levels of neutral genetic diversity in populations subdivided into two demes were studied by multilocus stochastic simulations. The model includes deleterious mutations at loci throughout the genome, causing 'background selection', as well as a single locus at which a polymorphism is maintained, either by frequency-dependent selection or by local selective differences. These balanced polymorphisms induce long coalescence times at linked neutral loci, so that sequence diversity at these loci is enhanced at statistical equilibrium. We study how equilibrium neutral diversity levels are affected by the degree of population subdivision, the presence or absence of background selection, and the level of inbreeding of the population. The simulation results are compared with approximate analytical formulae, assuming the infinite sites neutral model. We discuss how balancing selection can be distinguished from local selection, by determining whether peaks of diversity in the region of the polymorphic locus are seen within or between demes. The width of such diversity peaks is shown to depend on the total species population size, rather than local deme sizes. We show that, with population subdivision, local selection enhances between-deme diversity even at neutral sites distant from the polymorphic locus, producing higher FST values than with no selection; very high values can be generated at sites close to a selected locus. Background selection also increases FST, mainly because of decreased diversity within populations, which implies that its effects may be distinguishable from those of local selection. Both effects are stronger in selfing than outcrossing populations. Linkage disequilibrium between neutral sites is generated by both balancing and local selection, especially in selfing populations, because of linkage disequilibrium between the neutral sites and the selectively maintained alleles. We discuss how these theoretical results can be related to data on genetic diversity within and between local populations of a species.

Alleles↗
PubMed1995

Primary repair of colon injuries: a prospective randomized study.

Due to the results of a 6-year experience with civilian penetrating colon injuries at Mount Carmel/Grace Hospital, in Detroit, Michigan, which had favored primary repair of colon injuries, a prospective randomized study was performed. Seventy-one patients with penetrating colon injuries were entered in a prospective randomized study. Forty-three patients were treated with primary repair or resection and anastomosis, and 28 patients were treated with diversion. The average Penetrating Abdominal Trauma Index score was 25.5 for the primary repair and 23.4 for the diversion groups. The majority of injuries as assessed by the Colon Injury Score (CIS) for the primary repair group were grades 2 (58%) and 3 (28%). The diversion group predominantly had grades 2 (64%) and 3 (25%). There was no significant difference between the two groups. There were 8 (19%) patients with colon and noncolon-related complications in the primary repair group, and 10 (36%) patients with colon, noncolon, and colostomy-related complications in the diversion group. In addition, there were 2 (7%) patients with complications following colostomy reversal. Independent risk factors for adverse outcomes were compared and used to calculate the probability for adverse outcomes with respect to the mode of treatment. The probability for adverse outcomes was statistically greater in the diversion group. An analysis was also made within the primary repair group comparing the subgroups of primary repair with, and without, resection of colon. It appears that the primary repair with resection of colon may have fewer complications; however, this conclusion is based on a statistically insufficient sample size. The authors contend that primary repair or resection with anastomosis is the method of choice for treatment of all penetrating colon injuries in the civilian population despite any associated risk factors for adverse outcomes.

Adolescent↗
PubMed2003

User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries.

Directed evolution of proteins depends on the production of molecular diversity by random mutagenesis. While a number of methods have been developed for introducing this diversity, the best ways to sample it are not always clear. Here we used simple statistics to analyse completeness and diversity in randomized libraries generated by oligonucleotide-directed mutagenesis, error-prone polymerase chain reaction (epPCR) and in vitro recombination of highly homologous sequences. For oligonucleotide-directed mutagenesis, we derive equations to estimate how complete a given library is expected to be and also to predict the size of library required to give a fixed probability of being 100% complete. We describe the statistical bases for computer programs which estimate the number of distinct variants represented in epPCR and shuffled libraries, dubbed PEDEL and DRIVeR, respectively. These programs allow the user to calculate (rather than guess) the diversity represented in a given library and also provide empirical guidelines for maximizing this diversity. PEDEL and DRIVeR are available at www.bio.cam.ac.uk/ approximately blackburn/stats.html.

Algorithms↗
PubMed2004

Taxon richness and climate in angiosperms: is there a globally consistent relationship that precludes region effects?

We comment on a recent paper by Francis and Currie that reports a globally consistent relationship between plant family diversity in large geographic grid cells and factors in the physical environment. This relationship was interpreted as demonstrating local ecological determination of diversity, leaving little room for regional and historical effects. We suggest that using family richness to describe patterns of diversity reduces regional effects owing to the lower endemism of plants at the family compared with the species level. Regardless of the taxonomic level of analysis, we further point out that unless regional effects are tested explicitly, statistically significant differences in diversity between regions can be overlooked. Finally, even correlations between diversity and physical conditions of the environment can have primarily historical and evolutionary origins when lineages diversify within ecological zones of origin and spread more slowly to diverse environments. Thus, local ecological determinism should not have primacy over evolutionary-historical explanations for patterns of diversity between or within regions. Ecologists must evaluate patterns in local diversity within historical and geographic, as well as ecological, contexts.

Biodiversity↗
PubMed2006

Estimating relatedness between individuals in general populations with a focus on their use in conservation programs.

Relatedness estimators are widely used in genetic studies, but effects of population structure on performance of estimators, criteria to evaluate estimators, and benefits of using such estimators in conservation programs have to date received little attention. In this article we present new estimators, based on the relationship between coancestry and molecular similarity between individuals, and compare them with existing estimators using Monte Carlo simulation of populations, either panmictic or structured. Estimators were evaluated using statistical criteria and a diversity criterion that minimized relatedness. Results show that ranking of estimators depends on the population structure. An existing estimator based on two-gene and four-gene coefficients of identity performs best in panmictic populations, whereas a new estimator based on coancestry performs best in structured populations. The number of marker alleles and loci did not affect ranking of estimators. Statistical criteria were insufficient to evaluate estimators for their use in conservation programs. The regression coefficient of pedigree relatedness on estimated relatedness (beta2) was substantially lower than unity for all estimators, causing overestimation of the diversity conserved. A simple correction to achieve beta2 = 1 improves both existing and new estimators. Using relatedness estimates with correction considerably increased diversity in structured populations, but did not do so or even decreased diversity in panmictic populations.

Alleles↗
PubMed2006

Low genetic structure in an epiphytic Orchidaceae (Oncidium hookeri) in the Atlantic rainforest of South-eastern Brazil.

BACKGROUND AND AIMS: Oncidium hookeri is a neotropical species of epiphytic Orchidaceae found in the Brazilian Atlantic rainforest at the top of the Mantiqueira Range of mountains. The genetic variation of O. hookeri was studied to assess the distribution of genetic variability within and among six populations localized in Atlantic rainforest remnants. Gene flow among populations and the occurrence of recent bottlenecks were investigated in order to infer the degree of isolation of these populations. METHODS: Thirteen polymorphic loci were used for allozyme electrophoresis. The data were analysed by means of standard statistical approaches, to estimate gene diversity and the genetic structure of the populations. KEY RESULTS: The mean gene diversity and allelic richness were H(e) = 0.099 and A = 1.75, respectively. F-statistics revealed high heterozygote deficiencies in all populations (F(IS) = 0.43-0.82). Several rare alleles were found in all the populations, and three populations presented private alleles. Low genetic differentiation among O. hookeri populations was detected (F(ST) = 0.029); natural selection may be involved in PGM locus differentiation among populations. The genetic differentiation between paired populations was low, bearing no correlation with geographic distance (Mantel test: r = -0.34, P = 0.72). Only two populations showed signs of recent bottlenecks. CONCLUSIONS: The heterozygote deficiency found seems to be caused by pollinator behaviour; the low frequencies of several alleles of different loci can be maintained due to clonal propagation. Despite the stochastic nature of the wind-dispersal of seeds to long distances, this process may promote an effective gene flow among populations, thus avoiding genetic differentiation.

Brazil↗
PubMed2002

Entropy, visual diversity, and preference.

The author reports relationships between subjective impressions of visual diversity or pleasure with statistical entropies of stimuli. The stimuli were 34 rows of houses that varied in color, scale, and shape, or in shape and articulation. Entropies ranged from 0.0 to 5.6 bits. Fifty-seven participants rated the stimuli on scales of pleasant/unpleasant and uniform/diverse. The relationship between rated diversity and entropy was strong and linear. The relationship between rated pleasure and entropy was either linear or asymptotic, but no evidence was found for an inverted U relationship.

Adult↗
PubMedDate not supplied

[The validity of the Willis Law for taxonomy].

Different explanations of Willis' law are discussed. The common view on the observed relationship between species and genus frequencies suggests that Willis' rule is artifact of two independent processes. However, actual data on similarity of the diversity patterns in different taxa contradicts with this of view and show that there are intrinsic laws regulating biological diversity. The analysis of statistical parameters of diagnostic keys reveals that distribution of differential features according to the frequency of their usage appeas to be ranked. Considering taxon size as extensional characteristic and the set of differential features as intensional characteristic one can conclude that nature of disctribution is identical in both cases. Existed data indicates that biological diversity is self-organizated and self-ordered. It allow to reconsider the conception of Natural system which could be considered as fractal with the properties of the whole composed of parts (taxa) similar by their properties to each other and to the whole. The lowest parts, units of Natural system are taxa of generic rank, their characteristics is subjected to the Willis' rule.

Animals↗
PubMed2006

Classification of a diverse set of Tetrahymena pyriformis toxicity chemical compounds from molecular descriptors by statistical learning methods.

Toxicity of various compounds has been measured in many studies by their toxic effects against Tetrahymena pyriformis. Efforts have also been made to use computational quantitative structure-activity relationship (QSAR) and statistical learning methods (SLMs) for predicting Tetrahymena pyriformis toxicity (TPT) at impressive accuracies. Because of the diversity of compounds and toxicity mechanisms, it is desirable to explore additional methods and to examine if these methods are applicable to more diverse sets of compounds. We tested several SLMs (logistic regression, C4.5 decision tree, k-nearest neighbor, probabilistic neural network, support vector machines) for their capability in predicting TPT by using 1129 compounds (841 TPT and 288 non-TPT agents) which are more diverse than those in other studies. A feature selection method was used for improving prediction performance and selecting molecular descriptors responsible for distinguishing TPT and non-TPT agents. The prediction accuracies are 86.9% approximately 94.2% for TPT and 71.2% approximately 87.5% for non-TPT agents based on 5-fold cross-validation studies, which are comparable to some of earlier studies despite the use of more diverse sets of compounds. The selected molecular descriptors are consistent with those used in other studies and experimental findings. These suggest that SLMs are useful for predicting TPT potential of diverse sets of compounds and for characterizing the molecular descriptors associated with TPT.

Animals↗
PubMed2004

Mitochondrial DNA diversity in tribal and caste groups of Maharashtra (India) and its implication on their genetic origins.

Genetic relationships among caste-groups are not uniform across the geographical regions of India. Many anthropologists have speculated on the tribal origin of some caste groups in Maharashtra and other states of India. To test this hypothesis, we used neutral mtDNA markers to study genetic relatedness among tribal and caste groups from Maharashtra. Descriptive statistics such as nucleotide diversity, gene diversity and average mismatches were found to be of the same magnitude. Phylogenetic network analysis exhibited a star-like expansion that may date back to the peopling of Eurasia, approximately 50,000 year ago. The reconstruction of mtDNA haplogroups showed that both the caste and tribal populations share similar branches of the tree. Also, the coalescence age estimation of caste and tribal populations suggests the persistence of maternal lineages with their root in early late Pleistocene. Our mtDNA analyses show some preliminary and significant evidence for the origin of prehistoric tribal and hierarchical caste societies of Maharashtra.

Adult↗
PubMed2002

Assessment of genetic management at three specific-pathogen-free rhesus macaque (Macaca mulatta) colonies.

Genetic management is required to maintain genetic diversity by minimizing inbreeding and genetic subdivision in colonies of animals bred for biomedical research. Polymorphic short tandem repeat (STR) loci are useful for genetic management because they facilitate parentage assignments, genetic characterization of individuals, and estimates of baseline population genetic parameters. Using highly informative STR loci, we estimated gene diversity and F-statistics to determine the level of genetic heterogeneity and genetic structure of three specific-pathogen-free (SPF) rhesus macaque (Macaca mulatta) colonies. Effective population sizes, variance in male reproductive success, and rate of decrease in genetic variability also were estimated for two of the three colonies. We documented the overall success of genetic management in maintaining genetic diversity in captive colonies. We report that even genetically managed SPF colonies, despite maintaining high and stable levels of gene diversity (over 0.75), are prone to genetic subdivision due to different management strategies, founder effects, genetic isolation, and drift. These processes are accelerated by the high variances in male reproductive success and low adult sex ratios that are typical of captive rhesus macaque breeding groups, both of which reduce the effective population sizes of these groups.

Animal Husbandry↗
PubMed2001

Genetic basis for co-adaptive gene complexes in rice (Oryza sativa L.) landraces.

One hundred and twenty-two AFLP markers were mapped using an IR64 x Azucena rice doubled-haploid (DH) population. The distribution of these mapped markers was monitored across a set of 48 diverse landraces of rice. Strong statistical associations were observed between 960 of the 7381 possible pairs of markers across the diverse material. These 960 strongly associated pairs of markers mapped to the same chromosomes in only 111 cases. The remaining 849 pairs were the result of association between markers found on different chromosomes. More than 21% of these genetically unlinked but strongly associated markers are not randomly distributed across the genome but instead occupy blocks of DNA on different rice chromosomes. Amongst associated blocks, there has clearly been maintenance of combinations of marker alleles across very diverse germplasm. Analyses have also revealed that markers are found in association with performance for each of four quantitative traits in both the diverse landrace material and a DH mapping population. It is proposed that the present data provide strong evidence for the co-adaptation of geographically distinct landraces and that this has resulted over time in the maintenance of 'adaptive gene complexes' involving agronomically important quantitative traits.

Adaptation, Biological↗
PubMed1989

[Epidemiologic diversity].

We summarize our results with the adaptation of the so called diversity indexes, often used in the statistical ecology. We refer to the sexual difference of the diversity of death causes, and the specific formation of the diversity of morbidity and mortality by the years of life. We mention the possible explanation of this. It is also a new observation the characteristic change in the concentration of the causes of death measured by diversity indexes. In the second part of the paper we enumerate some possible new branches of research, which should develop the investigations on the epidemiological diversity.

Cause of Death↗
PubMed1997

Theoretical calculation and prediction of Caco-2 cell permeability using MolSurf parametrization and PLS statistics.

PURPOSE: To statistically model the permeability across Caco-2 cell monolayers using theoretically computed molecular descriptors and multivariate statistics. METHODS: Seventeen structurally diverse compounds were investigated. The program MolSurf was used to compute theoretical molecular descriptors related to physico-chemical properties such as lipophilicity, polarity, polarizability and hydrogen bonding. The multivariate Partial Least Squares Projections to Latent Structures (PLS) method was used to delineate the relationship between the permeability across Caco-2 cell monolayers and the theoretically computed molecular descriptors. RESULTS: Excellent statistical models were derived. Properties associated with hydrogen bonding had the largest impact on diffusion through the monolayers and should be kept at a minimum to promote high permeability. High lipophilicity and the presence of surface electrons, i.e. valence electrons, which are not tightly bonded to the molecule, were also found to have a favorable influence to achieve high permeability. CONCLUSIONS: The results indicate that theoretically computed molecular MolSurf descriptors in conjunction with multivariate statistics of PLS type can be used to successfully model permeability across Caco-2 cell monolayers and, thus, differentiate drugs with poor permeability from those with acceptable permeability at an early stage of the preclinical drug discovery process.

Caco-2 Cells↗