Population estimators or progeny tests: what is the best method to assess null allele frequencies at SSR loci?

Nuclear SSRs are notorious for having relatively high frequencies of null alleles, i.e. alleles that fail to amplify and are thus recessive and undetected in heterozygotes. In this paper, we compare two kinds of approaches for estimating null allele frequencies at seven nuclear microsatellite markers in three French Fagus sylvatica populations: (1) maximum likelihood methods that compare observed and expected homozygote frequencies in the population under the assumption of Hardy-Weinberg equilibrium and (2) direct null allele frequency estimates from progeny where parent genotypes are known. We show that null allele frequencies are high in F. sylvatica (7.0% on average with the population method, 5.1% with the progeny method), and that estimates are consistent between the two approaches, especially when the number of sampled maternal half-sib progeny arrays is large. With null allele frequencies ranging between 5% and 8% on average across loci, population genetic parameters such as genetic differentiation (F ST) may be mostly unbiased. However, using markers with such average prevalence of null alleles (up to 15% for some loci) can be seriously misleading in fine scale population studies and parentage analysi

Decomposition theorems for involutive solutions to the Yang-Baxter equation

Motivated by the proof of Rump of a conjecture of Gateva-Ivanova on the decomposability of square-free solutions to the Yang-Baxter equation, we present several other decomposability theorems based on the cycle structure of a certain permutation associated with the solution.Comment: 10 page

Involutive Yang-Baxter: cabling, decomposability, Dehornoy class

We develop new machinery for producing decomposability tests for involutive solutions to the Yang-Baxter equation. It is based on the seminal decomposability theorem of Rump, and on "cabling" operations on solutions and their effect on the diagonal map. Our machinery yields an elementary proof of a recent decomposability theorem of Camp-More and Sastriques, as well as original decomposability results. It also provides a conceptual interpretation (using the braces language) of the Dehornoy class, a combinatorial invariant naturally appearing in the Garside-theoretic approach to involutive solutions.Comment: 13 pages. Theorem E adde

Global to local genetic diversity indicators of evolutionary potential in tree species within and outside forests

There is a general trend of biodiversity loss at global, regional, national and local levels. To monitor this trend, international policy processes have created a wealth of indicators over the last two decades. However, genetic diversity indicators are regrettably absent from comprehensive bio-monitoring schemes. Here, we provide a review and an assessment of the different attempts made to provide such indicators for tree genetic diversity from the global level down to the level of the management unit. So far, no generally accepted indicators have been provided as international standards, nor tested for their possible use in practice. We suggest that indicators for monitoring genetic diversity and dynamics should be based on ecological and demographic surrogates of adaptive diversity as well as genetic markers capable of identifying genetic erosion and gene flow. A comparison of past and present genecological distributions (patterns of genetic variation of key adaptive traits in the ecological space) of selected species is a realistic way of assessing the trend of intra-specific variation, and thus provides a state indicator of tree genetic diversity also able to reflect possible pressures threatening genetic diversity. Revealing benefits of genetic diversity related to ecosystem services is complex, but current trends in plantation performance offer the possibility of an indicator of benefit. Response indicators are generally much easier to define, because recognition and even quantification of, e.g., research, education, breeding, conservation, and regulation actions and programs are relatively straightforward. Only state indicators can reveal genetic patterns and processes, which are fundamental for maintaining genetic diversity. Indirect indicators of pressure, benefit, or response should therefore not be used independently of state indicators. A coherent set of indicators covering diversity–productivity–knowledge–management based on the genecological approach is proposed for application on appropriate groups of tree species in the wild and in cultivation worldwide. These indicators realistically reflect the state, trends and potentials of the world’s tree genetic resources to support sustainable growth. The state of the genetic diversity will be based on trends in population distributions and diversity patterns for selected species. The productivity of the genetic resource of trees in current use will reflect the possible potential of mobilizing the resource further. Trends in knowledge will underpin the potential capacity for development of the resource and current management of the genetic resource itself will reveal how well we are actually doing and where improvements are required

O impacto do homem na estrutura de uma espécie: Portugal, um paradigma

A bacia do Mediterrâneo é caracterizada pelo tradicional desaparecimento da floresta devido à acção do Homem e o impacto humano tem tido influência na alteração da diversidade genética. O pinheiro bravo ocorre em populações fragmentadas na região oeste da bacia do Mediterrâneo e a sua área de distribuição tem sido alterada nos últimos séculos devido a intensa florestação, em particular no SW de França e no Noroeste da Península Ibérica e, também, devido ao comportamento invasivo desta espécie em áreas perturbadas do ponto de vista ecológico. Nesta apresentação pretendemos sintetizar e discutir o resultado de estudos que utilizaram técnicas moleculares para revelar a diversidade do pinheiro bravo e, também, o impacto humano na sua estrutura genética; que é demonstrado paradigmaticamente em Portugal. Os parâmetros genéticos estimados com base em microsatélites do cloroplasto (cpSSR) revelaram que a diversidade genética é muito elevada ao nível da distribuição da espécie. Observou-se uma clara e significativa diferenciação entre grupos de populações de diferente origem geográfica (Portugal, França, Itália, Espanha e Marrocos). Pelo contrário, o grau de divergência dentro dos países é geralmente muito baixo ou próximo de zero, o que indica uma variação homogénea dentro dos grupos. A presença de diferenciação entre grupos de populações de diferentes áreas reflecte a existência de diferentes refúgios durante o Quaternário. Em França, o padrão haplotípico sugere uma mistura de material proveniente de diferentes origens. Só foram encontrados 3 mitótipos, usando marcadores mitocondriais, marcador de herança maternal, o que proporciona uma imagem clara de áreas colonizadas a partir dos diferentes refúgios; nem uma só população possui uma composição mista. Uma análise filogenética feita com base em isoenzimas mostrou que a estrutura geográfica do pinheiro bravo na Península Ibérica (PI) é muito elevada. As populações de Noroeste formam um grupo e as de Sudeste outro. Observou-se níveis elevados de diversidade nas populações de Este e Sul e uma redução importante da variabilidade em populações da região Noroeste da PI. No entanto, pode ter existido em Portugal um refúgio, pois o pinheiro bravo pode ter sobrevivido durante a última glaciação em zonas abrigadas e de baixa altitude junto ao Oceano Atlântico, o que parece também ser evidente devido a descobertas de pólen e carvão fóssil. A distribuição da variação genética do pinheiro bravo em Portugal, observada através de cpSSR indica que a diferenciação entre populações é baixa e que a diversidade existe principalmente dentro das populações. Não se observa nenhum padrão geográfico, mas as evidências existentes de uma forte influência antrópica antropogénica associada a um fluxo genético extensivo poderiam explicar esse resultado

Pharmacokinetics of plasma infusion in congenital thrombotic thrombocytopenic purpura.

BACKGROUND: Congenital thrombotic thrombocytopenic purpura (TTP) is defined by persistent severe deficiency of ADAMTS-13 in the absence of anti-ADAMTS-13 inhibitory antibodies, confirmed by mutational analysis. Replacement of the missing protease prevents disease relapse, primarily using plasma infusion (PI). OBJECTIVES, PATIENTS AND METHODS: There is scant evidence regarding optimal dose and frequency of treatment, tending to be empirically guided. We present a pharmacokinetic analysis of ADAMTS-13 in 6 patients with congenital TTP on established regimes following PI. RESULTS: We found a median clearance of 25.41ml/h and half-life of 130 hours, ranging between 82.6 and 189.5 hours (3.4 to 7.9 days respectively). All patients reached baseline ADAMTS-13 level within 7-10 days post plasma. Median ADAMTS-13 activity peak post PI was 24.05IU/dL. Variation was related to elimination rate, in turn affected by weight and metabolism, but not to von Willebrand factor antigen or activity levels. Using the pharmacokinetic parameters, we simulated individualised protocols based on PI dose or frequency to target hypothetical optimal plasma levels of ADAMTS-13 of 10 and 50IU/dL respectively. Results suggest a target trough ADAMTS-13 of 10IU/dL is feasible but 50IU/dL would not be achievable taking into account volume required. CONCLUSIONS: Further work is needed to compare treatment of congenital TTP with PI versus recombinant ADAMTS-13. PI may provide longer duration of ADAMTS-13 effect, but is limited by plasma volume required, whereas recombinant therapy can provide a higher ADAMTS-13 peak. We propose that investigation of interindividual clearance of ADAMTS-13 is necessary to optimise treatment, to enable rationale for dose and frequency of prophylaxis