Genetic considerations in ecosystem restoration using native tree species

Rehabilitation and restoration of forest ecosystems are in growing demand to tackle climate change, biodiversity loss and desertification—major environmental problems of our time. Interest in restoration of ecosystems is increasingly translated into strong political commitment to large-scale tree planting projects. Along with this new impetus and the enormous scale of planned projects come both opportunities and risks: opportunities to significantly increase the use of native species, and risks of failure associated with the use of inadequate or mismatched reproductive material, which though it may provide forest cover in the short term, will not likely establish a self-sustaining ecosystem. The value of using native tree species in ecosystem restoration is receiving growing recognition both among restoration practitioners and policy makers. However, insufficient attention has been given to genetic variation within and among native tree species, their life histories and the consequences of their interactions with each other and with their environment. Also restoration practitioners have often neglected to build in safeguards against the anticipated effects of anthropogenic climate change. Measurement of restoration success has tended to be assessments of hectares covered or seedling survival in a short timeframe, neither of which is an indicator of ecosystem establishment in the long term. In this article, we review current practices in ecosystem restoration using native tree species, with a particular focus on genetic considerations. Our discussion is organised across three themes: (i) species selection and the sourcing of forest reproductive material; (ii) increasing resilience by fostering natural selection, ecological connectivity and species associations; and (iii) measuring the success of restoration activities. We present a number of practical recommendations for researchers, policymakers and restoration practitioners to increase the potential for successful interventions. We recommend the development and adoption of decision-support tools for: (i) collecting and propagating germplasm in a way that ensures a broad genetic base of restored tree populations, including planning the sourcing of propagation material of desired species well before the intended planting time; (ii) matching species and provenances to restoration sites based on current and future site conditions, predicted or known patterns of variation in adaptive traits and availability of seed sources; and (iii) landscape-level planning in restoration projects

Is local best? Examining the evidence for local adaptation in trees and its scale

Background: Although the importance of using local provenance planting stock for woodland production, habitat conservation and restoration remains contentious, the concept is easy to understand, attractive and easy to ‘sell’. With limited information about the extent and scale of adaptive variation in native trees, discussion about suitable seed sources often emphasises “local” in a very narrow sense or within political boundaries, rather than being based on sound evidence of the scale over which adaptation occurs. Concerns exist over the actual scale (magnitude and spatial scale) of adaptation in trees and the relative dangers of incorrect seed source or restricted seed collection, leading to the establishment of trees with restricted genetic diversity and limited adaptive potential. Tree provenance and progeny field trials in many parts of the world have shown the existence of genotype by environment interaction in many tree species, but have not necessarily looked at whether this is expressed as a home site advantage (i.e. whether provenance performance is unstable across sites, and there is better performance of a local seed source). Methods/design: This review will examine the evidence for local adaptation and its scale in a number of native tree species from different trial sites across the globe (e.g. tropical, Mediterranean, temperate). These trials have been measured and in some cases results published in a range of formats. The data have, however, usually been presented in the form of which provenances grow best at which sites. The review will examine existing data (published and unpublished) in the context of the scale of local adaptation, with the results being presented in two formats: (a) relating survival, performance of provenances (classified by seed zone/provenance region of origin) to seed zone/provenance region of the planting site; (b) plotting survival, performance provenances against the distance (Euclidean/ecological) between the provenance and the trial site.EEA BarilocheFil: Boshier, David. University of Oxford. Department of Plant Sciences; Reino UnidoFil: Broadhurst, Linda. CSIRO National Research Collections Australia (NRCA). Centre for Australian National Biodiversity Research (CANBR); AustraliaFil: Cornelius, Jonathan. International Center for Research in Agroforestry. World Agroforestry Centre; PerúFil: Gallo, Leonardo Ariel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche; ArgentinaFil: Koskela, Jarkko. FAO; ItaliaFil: Loo, Judy. Bioversity International; ItaliaFil: Petrokofsky, Gillian. University of Oxford. Department of Zoology; Reino UnidosFil: St Clair, Bradley. US Forest Service. Pacific Northwest Research Station; Estados Unido

Is local best? Examining the evidence for local adaptation in trees and its scale

Background: Although the importance of using local provenance planting stock for woodland production, habitat conservation and restoration remains contentious, the concept is easy to understand, attractive and easy to ‘sell’. With limited information about the extent and scale of adaptive variation in native trees, discussion about suitable seed sources often emphasises “local” in a very narrow sense or within political boundaries, rather than being based on sound evidence of the scale over which adaptation occurs. Concerns exist over the actual scale (magnitude and spatial scale) of adaptation in trees and the relative dangers of incorrect seed source or restricted seed collection, leading to the establishment of trees with restricted genetic diversity and limited adaptive potential. Tree provenance and progeny field trials in many parts of the world have shown the existence of genotype by environment interaction in many tree species, but have not necessarily looked at whether this is expressed as a home site advantage (i.e. whether provenance performance is unstable across sites, and there is better performance of a local seed source). Methods/design: This review will examine the evidence for local adaptation and its scale in a number of native tree species from different trial sites across the globe (e.g. tropical, Mediterranean, temperate). These trials have been measured and in some cases results published in a range of formats. The data have, however, usually been presented in the form of which provenances grow best at which sites. The review will examine existing data (published and unpublished) in the context of the scale of local adaptation, with the results being presented in two formats: (a) relating survival, performance of provenances (classified by seed zone/provenance region of origin) to seed zone/provenance region of the planting site; (b) plotting survival, performance provenances against the distance (Euclidean/ecological) between the provenance and the trial site.EEA BarilocheFil: Boshier, David. University of Oxford. Department of Plant Sciences; Reino UnidoFil: Broadhurst, Linda. CSIRO National Research Collections Australia (NRCA). Centre for Australian National Biodiversity Research (CANBR); AustraliaFil: Cornelius, Jonathan. International Center for Research in Agroforestry. World Agroforestry Centre; PerúFil: Gallo, Leonardo Ariel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche; ArgentinaFil: Koskela, Jarkko. FAO; ItaliaFil: Loo, Judy. Bioversity International; ItaliaFil: Petrokofsky, Gillian. University of Oxford. Department of Zoology; Reino UnidosFil: St Clair, Bradley. US Forest Service. Pacific Northwest Research Station; Estados Unido

Aquaporins in the wild: natural genetic diversity and selective pressure in the PIP gene family in five Neotropical tree species

<p>Abstract</p> <p>Background</p> <p>Tropical trees undergo severe stress through seasonal drought and flooding, and the ability of these species to respond may be a major factor in their survival in tropical ecosystems, particularly in relation to global climate change. Aquaporins are involved in the regulation of water flow and have been shown to be involved in drought response; they may therefore play a major adaptive role in these species. We describe genetic diversity in the PIP sub-family of the widespread gene family of Aquaporins in five Neotropical tree species covering four botanical families.</p> <p>Results</p> <p>PIP Aquaporin subfamily genes were isolated, and their DNA sequence polymorphisms characterised in natural populations. Sequence data were analysed with statistical tests of standard neutral equilibrium and demographic scenarios simulated to compare with the observed results. Chloroplast SSRs were also used to test demographic transitions. Most gene fragments are highly polymorphic and display signatures of balancing selection or bottlenecks; chloroplast SSR markers have significant statistics that do not conform to expectations for population bottlenecks. Although not incompatible with a purely demographic scenario, the combination of all tests tends to favour a selective interpretation of extant gene diversity.</p> <p>Conclusions</p> <p>Tropical tree PIP genes may generally undergo balancing selection, which may maintain high levels of genetic diversity at these loci. Genetic variation at PIP genes may represent a response to variable environmental conditions.</p

Range-wide differential adaptation and genomic vulnerability in critically endangered Asian rosewoods

In the billion-dollar global illegal wildlife trade, rosewoods have been the world’s most trafficked wild product since 2005. Dalbergia cochinchinensis and D. oliveri are the most sought-after rosewoods in the Greater Mekong Subregion. They are exposed to significant genetic risks and the lack of knowledge on their adaptability limits the effectiveness of conservation efforts. Here we present genome assemblies and range-wide genomic scans of adaptive variation, together with predictions of genomic vulnerability to climate change. Adaptive genomic variation was differentially associated with temperature and precipitation-related variables between the species, although their natural ranges overlap. The findings are consistent with differences in pioneering ability and in drought tolerance. We predict their genomic offsets will increase over time and with increasing carbon emission pathway but at a faster pace in D. cochinchinensis than in D. oliveri. These results and the distinct gene-environment association in the eastern coastal edge suggest species-specific conservation actions: germplasm representation across the range in D. cochinchinensis and focused on vulnerability hotspots in D. oliveri. We translated our genomic models into a seed source matching application, seedeR, to rapidly inform restoration efforts. Our ecological genomic research uncovering contrasting selection forces acting in sympatric rosewoods is of relevance to conserving tropical trees globally and combating risks from climate change

ESTIMATIVAS DE PARÂMETROS GENÉTICOS PARA CRESCIMENTO EM PROGÊNIES DE DUAS PROCEDÊNCIAS DE Roupala montana var. brasiliensis (PROTEACEAE)

Roupala montana var. brasiliensis (carvalho-brasileiro) é uma espécie de potencial madeireiro que foi extensivamente explorada e com pouca informação sobre suas populações naturais. Dessa forma, a presente pesquisa teve como objetivo estimar parâmetros genéticos quantitativos na fase de viveiro, a partir de um teste de procedências e progênies. O delineamento utilizado foi o de blocos casualizados, com três blocos e um número variável de plantas por parcela, num total de 201 mudas para sete tratamentos (progênies). Os caracteres valiados aos 60, 120 e 180 dias foram o diâmetro do colo (DC) e altura (ALT). As herdabilidades no sentido restrito foram consideradas medianas a altas para DC e altas para altura, enquanto a herdabilidade média foi alta para ambas as variáveis. O coeficiente de variação ambiental resultou alto para todas as avaliações, embora o coeficiente de variação genética indique a existência de alta variabilidade genética. Os resultados indicam existência de variabilidade genética nas progênies avaliadas. O teste de progênies foi implantado no Campus Irati da Unicentro

Priorities, challenges and opportunities for supplying tree genetic resources

Special issue on Landscape restoratio

Expiratory flow rate, breath hold and anatomic dead space influence electronic nose ability to detect lung cancer

BACKGROUND: Electronic noses are composites of nanosensor arrays. Numerous studies showed their potential to detect lung cancer from breath samples by analysing exhaled volatile compound pattern ("breathprint"). Expiratory flow rate, breath hold and inclusion of anatomic dead space may influence the exhaled levels of some volatile compounds; however it has not been fully addressed how these factors affect electronic nose data. Therefore, the aim of the study was to investigate these effects. METHODS: 37 healthy subjects (44 +/- 14 years) and 27 patients with lung cancer (60 +/- 10 years) participated in the study. After deep inhalation through a volatile organic compound filter, subjects exhaled at two different flow rates (50 ml/sec and 75 ml/sec) into Teflon-coated bags. The effect of breath hold was analysed after 10 seconds of deep inhalation. We also studied the effect of anatomic dead space by excluding this fraction and comparing alveolar air to mixed (alveolar + anatomic dead space) air samples. Exhaled air samples were processed with Cyranose 320 electronic nose. RESULTS: Expiratory flow rate, breath hold and the inclusion of anatomic dead space significantly altered "breathprints" in healthy individuals (p 0.05). These factors also influenced the discrimination ability of the electronic nose to detect lung cancer significantly. CONCLUSIONS: We have shown that expiratory flow, breath hold and dead space influence exhaled volatile compound pattern assessed with electronic nose. These findings suggest critical methodological recommendations to standardise sample collections for electronic nose measurements

Immune Imprinting Drives Human Norovirus Potential for Global Spread

Understanding the complex interactions between virus and host that drive new strain evolution is key to predicting the emergence potential of variants and informing vaccine development. Under our hypothesis, future dominant human norovirus GII.4 variants with critical antigenic properties that allow them to spread are currently circulating undetected, having diverged years earlier. Through large-scale sequencing of GII.4 surveillance samples, we identified two variants with extensive divergence within domains that mediate neutralizing antibody binding. Subsequent serological characterization of these strains using temporally resolved adult and child sera suggests that neither candidate could spread globally in adults with multiple GII.4 exposures, yet young children with minimal GII.4 exposure appear susceptible. Antigenic cartography of surveillance and outbreak sera indicates that continued population exposure to GII.4 Sydney 2012 and antigenically related variants over a 6-year period resulted in a broadening of immunity to heterogeneous GII.4 variants, including those identified here. We show that the strongest antibody responses in adults exposed to GII.4 Sydney 2012 are directed to previously circulating GII.4 viruses. Our data suggest that the broadening of antibody responses compromises establishment of strong GII.4 Sydney 2012 immunity, thereby allowing the continued persistence of GII.4 Sydney 2012 and modulating the cycle of norovirus GII.4 variant replacement. Our results indicate a cycle of norovirus GII.4 variant replacement dependent upon population immunity. Young children are susceptible to divergent variants; therefore, emergence of these strains worldwide is driven proximally by changes in adult serological immunity and distally by viral evolution that confers fitness in the context of immunity. IMPORTANCE In our model, preepidemic human norovirus variants harbor genetic diversification that translates into novel antigenic features without compromising viral fitness. Through surveillance, we identified two viruses fitting this profile, forming long branches on a phylogenetic tree. Neither evades current adult immunity, yet young children are likely susceptible. By comparing serological responses, we demonstrate that population immunity varies by age/exposure, impacting predicted susceptibility to variants. Repeat exposure to antigenically similar variants broadens antibody responses, providing immunological coverage of diverse variants but compromising response to the infecting variant, allowing continued circulation. These data indicate norovirus GII.4 variant replacement is driven distally by virus evolution and proximally by immunity in adults