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

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

Bosnian pine (Pinus heldreichii syn. Pinus leucodermis)

Technical guidelines are targeted to practical forest managers and provide summarized information on the biology and ecology of tree species, distribution ranges, importance and use, genetic knowledge, threats to genetic diversity and recommendations for long-term genetic conservation. For the full list of Technical guidelines produced, please visit http://www.euforgen.org/publications/technical_guidelines.htm

Causes and consequences of large clonal assemblies in a poplar hybrid zone.

Asexual reproduction is a common and fundamental mode of reproduction in plants. Although persistence in adverse conditions underlies most known cases of clonal dominance, proximal genetic drivers remain unclear, in particular for populations dominated by a few large clones. In this paper, we studied a clonal population of the riparian tree Populus alba in the Douro river basin (northwestern Iberian Peninsula) where it hybridizes with P. tremula, a species that grows in highly contrasted ecological conditions. We used 73 nuclear microsatellites to test whether genomic background (species ancestry) is a relevant cause of clonal success, and to assess the evolutionary consequences of clonal dominance by a few genets. Additional Genotyping-by-Sequencing (GBS) data were produced to estimate the age of the largest clones. We found that a few ancient (over a few thousand years old) and widespread genets dominate the population, both in terms of clone size and number of sexual offspring produced. Interestingly, large clones possessed two genomic regions introgressed from P. tremula, which may have favored their spread under stressful environmental conditions. At the population level, the spread of large genets was accompanied by an overall ancient (>0.1 Myr) but soft decline of effective population size. Despite this decrease, and the high clonality and dominance of sexual reproduction by large clones, the Douro hybrid zone still displays considerable genetic diversity and low inbreeding. This suggests that, even in extreme cases as in the Douro, asexual and sexual dominance of a few large, geographically-extended individuals does not threaten population survival. This article is protected by copyright. All rights reserved

Mediterranean firs (Abies spp)

Technical guidelines are targeted to practical forest managers and provide summarized information on the biology and ecology of tree species, distribution ranges, importance and use, genetic knowledge, threats to genetic diversity and recommendations for long-term genetic conservation. For the full list of Technical guidelines produced, please visit http://www.euforgen.org/publications/technical_guidelines.htm

The role of forest genetic resources in responding to biotic and abiotic factors in the context of anthropogenic climate change

The current distribution of forest genetic resources on Earth is the result of a combination of natural processes and human actions. Over time, tree populations have become adapted to their habitats including the local ecological disturbances they face. As the planet enters a phase of human-induced climate change of unprecedented speed and magnitude, however, previously locally-adapted populations are rendered less suitable for new conditions, and ‘natural’ biotic and abiotic disturbances are taken outside their historic distribution, frequency and intensity ranges. Tree populations rely on phenotypic plasticity to survive in extant locations, on genetic adaptation to modify their local phenotypic optimum or on migration to new suitable environmental conditions. The rate of required change, however, may outpace the ability to respond, and tree species and populations may become locally extinct after specific, but as yet unknown and unquantified, tipping points are reached. Here, we review the importance of forest genetic resources as a source of evolutionary potential for adaptation to changes in climate and other ecological factors. We particularly consider climate-related responses in the context of linkages to disturbances such as pests, diseases and fire, and associated feedback loops. The importance of management strategies to conserve evolutionary potential is emphasised and recommendations for policy-makers are provided