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Research paper thumbnail of Data Paper. Data Paper

File List Ascii text, comma delimited. No compression schemes were used. Empty fields are denoted... more File List Ascii text, comma delimited. No compression schemes were used. Empty fields are denoted by -99999. M_pyrifera_net_primary_production_and_growth.txt M_pyrifera_standing_crop_plant_density_and_loss_rates.txt Census_of_fronds_on_marked_plants.txt Description Marine macroalgae are believed to be among the most productive autotrophs in the world. However, relatively little information exists about spatial and temporal variation in net primary production (NPP) by these organisms. The data presented here are being collected to investigate patterns and causes of variation in NPP by the giant kelp, <i>Macrocystis pyrifera,</i> which is believed to be one of the fastest growing autotrophs on earth. The standing crop and loss rates of <i>M. pyrifera</i> are measured monthly in permanent plots at three sites in the Santa Barbara Channel, USA. Collection of these data began in June 2002 and is ongoing. Seasonal estimates of NPP and growth rate are made by combining the field data with a model of kelp dynamics. The purpose of this Data Paper is to make available a time series of <i>M. pyrifera</i> NPP, growth, and standing crop that is appropriate for examining seasonal and interannual patterns across multiple sites. Data on plant density in each plot and censuses of fronds on tagged plants at each site are also made available here. NPP, mass-specific growth rate, and standing crop are presented in four different metrics (wet mass, dry mass, carbon mass, and nitrogen mass) to facilitate comparisons with previous studies of <i>M. pyrifera</i> and with NPP measured in other ecosystems. Analyses of these data reveal seasonal cycles in growth and standing crop as well as substantial differences in <i>M. pyrifera </i>NPP among sites and years. <i>Key words</i>: <i>giant kelp; growth rate;</i> Macrocystis pyrifera<i>; marine algae; net primary production; standing crop</i>.

Research paper thumbnail of Genetic Diversity and Spatial Genetic Structure of an Epiphytic Bromeliad in Costa Rican Montane Secondary Forest Patches

Biotropica, Jun 10, 2014

Corsica and Sardinia represent major hotspots of plant diversity in the Mediterranean area and ar... more Corsica and Sardinia represent major hotspots of plant diversity in the Mediterranean area and are priority regions for conservation due to their high number of endemic plant species. However, information supporting human decision-making on the conservation of these species is still scarce, especially at the genetic level. In this work, the first assessment is reported of the species-wide spatial genetic structure and diversity of Ferula arrigonii Bocchieri, a Corso-Sardinian endemic located in a few coastal sites and on small islands. Nine populations covering the entire natural range of the species were investigated by means of AFLP (amplified fragment length polymorphism) markers. Results indicate that this species is characterised by high levels of genetic polymorphism (92% polymorphic fragments) and of genetic diversity (H w = 0.317) and by relatively low differentiation among populations (F st = 0.057). PCoA, Bayesian analysis and neighbour-joining clustering were also employed to investigate the genetic structure of this species. Three genetically distinct groups were detected, although with considerable overlap between populations.

Research paper thumbnail of Is opbrengen van maaisel effectief

Research paper thumbnail of Ecoducts and genetic exchange among ground beetles

Research paper thumbnail of Natuurbruggen en genenuitwisseling van loopkevers

Research paper thumbnail of MOESM4 of BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology

Additional file 4. Scientific studies using the BioVeL platform.

Research paper thumbnail of MOESM2 of BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology

Additional file 2: Table S1. Service groups and capabilities for processing and analysis in biodi... more Additional file 2: Table S1. Service groups and capabilities for processing and analysis in biodiversity science.

Research paper thumbnail of Maculinea alcon microsatellite data

The file Maculinea alcon microsatellite data includes the data from 12 microsatellites for 398 un... more The file Maculinea alcon microsatellite data includes the data from 12 microsatellites for 398 unique genotypes of Maculinea alcon from in total 14 sampling locations located in Belgium and The Netherlands. The data matrix also include the spatial coordinates of each sampled population, given in the two last columns

Research paper thumbnail of AFLP data

The file AFLP data.txt includes the binary matrix of AFLP band presence (1) – absence (0) for 451... more The file AFLP data.txt includes the binary matrix of AFLP band presence (1) – absence (0) for 451 AFLP-markers and 422 individuals of Liparis loeselii sampled in 38 populations. The matrix also include the spatial coordinates of each sampled population, given in the two last columns. The markers are numbered M1 to M451. The description of each marker (size in base pairs, primer combination) is given in the file readme.txt

Research paper thumbnail of Data from: High levels of effective long-distance dispersal may blur ecotypic divergence in a rare terrestrial orchid

Background: Gene flow and adaptive divergence are key aspects of metapopulation dynamics and ecol... more Background: Gene flow and adaptive divergence are key aspects of metapopulation dynamics and ecological speciation. Long-distance dispersal is hard to detect and few studies estimate dispersal in combination with adaptive divergence. The aim of this study was to investigate effective long-distance dispersal and adaptive divergence in the fen orchid (Liparis loeselii (L.) Rich.). We used amplified fragment length polymorphism (AFLP)-based assignment tests to quantify effective long-distance dispersal at two different regions in Northwest Europe. In addition, genomic divergence between fen orchid populations occupying two distinguishable habitats, wet dune slacks and alkaline fens, was investigated by a genome scan approach at different spatial scales (continental, landscape and regional) and based on 451 AFLP loci. Results: We expected that different habitats would contribute to strong divergence and restricted gene flow resulting in isolation-by-adaptation. Instead, we found remarkably high levels of effective long-distance seed dispersal and low levels of adaptive divergence. At least 15% of the assigned individuals likely originated from among-population dispersal events with dispersal distances up to 220 km. Six (1.3%) ‘outlier’ loci, potentially reflecting local adaptation to habitat-type, were identified with high statistical support. Of these, only one (0.22%) was a replicated outlier in multiple independent dune-fen population comparisons and thus possibly reflecting truly parallel divergence. Signals of adaptation in response to habitat type were most evident at the scale of individual populations. Conclusions: The findings of this study suggest that the homogenizing effect of effective long-distance seed dispersal may overwhelm divergent selection associated to habitat type in fen orchids in Northwest Europe

Research paper thumbnail of Meer soorten op de hei: red het heischraal grasland

Research paper thumbnail of forests and associated vascular epiphytes in a subtropical island of East Asia 1

Aim This study aims to assess the impact of climate change on forests and vascular epiphytes, usi... more Aim This study aims to assess the impact of climate change on forests and vascular epiphytes, using species distribution models (SDMs). Location Island of Taiwan, subtropical East Asia. Methods A hierarchical modelling approach incorporating forest migration velocity and forest type–epiphyte interactions with classical SDMs was used to model the responses of eight forest types and 237 vascular epiphytes for the year 2100 under two climate change scenarios. Forest distributions were modelled and modified by dominant tree species’ dispersal limitations and hypothesized persistence under unfavourable climate conditions (20 years for broad-leaved trees and 50 years for conifers). The modelled forest projections together with 16 environmental variables were used as predictors in models of epiphyte distributions. A null method was applied to validate the significance of epiphyte SDMs, and potential vulnerable species were identified by calculating range turnover rates. Results For the yea...

Research paper thumbnail of BioVeL Deliverable Report D2.1: State-of-the-art & trends review on biospheric carbon sequestration, ecosystem functioning and valuation, and invasive species management

This is the final version of deliverable D2.1. The first draft was prepared, improved and updated... more This is the final version of deliverable D2.1. The first draft was prepared, improved and updated during July and August of 2012. Further comments and feedbacks were included by 28 th of August.

Research paper thumbnail of Pleistocene sea-level changes as a predictor for insular species richness?

Trabajo presentado en el el congreso Island Biology 2014 celebrado en Hawai del 7 al 11 de julio ... more Trabajo presentado en el el congreso Island Biology 2014 celebrado en Hawai del 7 al 11 de julio de 2014.

Research paper thumbnail of DemographicDemographic consequences of inbreeding andand outbreeding in Arnic a montana : aa field experiment

Genetical reinforcement of small populations by adding seeds or individuals from other population... more Genetical reinforcement of small populations by adding seeds or individuals from other populationss may be an important management tool to prevent threatened plant species from extinction. However,, a negative consequence of mixing gene pools might be the reduction of plant fitness as coadaptedd gene complexes are disrupted. In the declining, self-incompatible perennial Arnica montana (Asteraceae),, we analysed the demographic consequences of inbreeding and outbreeding in five populationss of varying size. We analysed seed production and fruit weight following the pollination treatments.. From 1997 to 2000, plant growth, survival and flowering were monitored on plants introducedd as seeds and as four-week old seedlings in a field experiment. Reducedd seed set after selfing was due to self-incompatibility. There was significant heterosis for seed sett after inter-population crosses, probably due to low mate availability, in one of the small populations. Significantt but low inbreeding depression was observed for growth rates of plants introduced as seedlings.. We found significant heterosis for flowering probability of plants introduced as seeds, but for plantss introduced as seedlings, heterosis for seedling size and flowering probability was only marginally significant.. Although no outbreeding depression was observed in the F|, it may still be expressed in the forthcomingg generations as recombination of genes start to break up the coadapted gene complexes associatedd with local fitness. It is not clear to what degree the observed heterosis may outweigh this outbreedingg depression. Nevertheless, considering the rapid decline of A. montana in The Netherlands, geneticall reinforcement of the numerous small populations may be more important than the possible negativee consequences of outbreeding depression.

Research paper thumbnail of Gene flow and effective population sizes of the Alcon blue butterfly Maculinea alcon in a highly fragmented, anthropogenic landscape: Flash presentation

Research paper thumbnail of Ontwikkeling van zoet-zoutgradienten met en zonder dynamisch kustbeheer : een onderzoek naar de mogelijkheden voor meer natuurlijke ontwikkelingen in het kustgebied

Disclaimer/Complaints regulations If you believe that digital publication of certain material inf... more Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: http://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible.

Research paper thumbnail of A new geodiversity index to support biodiversity research in alpine areas

Research paper thumbnail of Outbreeding depression and breeding system evolution in small, remnant populations of Primula vulgaris: consequences for genetic rescue

Conservation Genetics, 2017

Many species suffer from anthropogenic habitat fragmentation. The resulting small and isolated po... more Many species suffer from anthropogenic habitat fragmentation. The resulting small and isolated populations are more prone to extinction due to, amongst others, genetic erosion, inbreeding depression and Allee-effects. Genetic rescue can help mitigate such problems, but might result in outbreeding depression. We evaluated offspring fitness after selfing and outcrossing within and among three very small and isolated remnant populations of the heterostylous plant Primula vulgaris. We used greenhouse-grown offspring from these populations to test several fitness components. One population was fixed for the pin-morph, and was outcrossed with another population in the field to obtain seeds. Genetic diversity of parent and offspring populations was studied using microsatellites. Morph and population-specific heterosis, inbreeding and outbreeding depression were observed for fruit and seed set, seed weight and cumulative fitness. Highest fitness was observed in the field-outcrossed F1-population, which also showed outbreeding depression following subsequent between-population (back) crossing. Despite outbreeding depression, fitness was still relatively high. Inbreeding coefficients indicated that the offspring were more inbred than their parent populations. Offspring heterozygosity and inbreeding coefficients correlated with observed fitness. One population is evolving homostyly, showing a thrum morph with an elongated style and high autonomous fruit and seed set. This has important implications for conservation strategies such as genetic rescue, as the mating system will be altered by the introduction of homostyles.

Research paper thumbnail of Biología de la conservación de endemismos vagetales de los parques nacionales canarios

[ES] El presente proyecto se centra en aplicar técnicas de biología molecular, demográficas y de ... more [ES] El presente proyecto se centra en aplicar técnicas de biología molecular, demográficas y de biología reproductiva en cuatro endemismos canarios amenazados que se encuentran total o parcialmente localizados en los parques nacionales de Canarias: Silene ...

Research paper thumbnail of Data Paper. Data Paper

File List Ascii text, comma delimited. No compression schemes were used. Empty fields are denoted... more File List Ascii text, comma delimited. No compression schemes were used. Empty fields are denoted by -99999. M_pyrifera_net_primary_production_and_growth.txt M_pyrifera_standing_crop_plant_density_and_loss_rates.txt Census_of_fronds_on_marked_plants.txt Description Marine macroalgae are believed to be among the most productive autotrophs in the world. However, relatively little information exists about spatial and temporal variation in net primary production (NPP) by these organisms. The data presented here are being collected to investigate patterns and causes of variation in NPP by the giant kelp, <i>Macrocystis pyrifera,</i> which is believed to be one of the fastest growing autotrophs on earth. The standing crop and loss rates of <i>M. pyrifera</i> are measured monthly in permanent plots at three sites in the Santa Barbara Channel, USA. Collection of these data began in June 2002 and is ongoing. Seasonal estimates of NPP and growth rate are made by combining the field data with a model of kelp dynamics. The purpose of this Data Paper is to make available a time series of <i>M. pyrifera</i> NPP, growth, and standing crop that is appropriate for examining seasonal and interannual patterns across multiple sites. Data on plant density in each plot and censuses of fronds on tagged plants at each site are also made available here. NPP, mass-specific growth rate, and standing crop are presented in four different metrics (wet mass, dry mass, carbon mass, and nitrogen mass) to facilitate comparisons with previous studies of <i>M. pyrifera</i> and with NPP measured in other ecosystems. Analyses of these data reveal seasonal cycles in growth and standing crop as well as substantial differences in <i>M. pyrifera </i>NPP among sites and years. <i>Key words</i>: <i>giant kelp; growth rate;</i> Macrocystis pyrifera<i>; marine algae; net primary production; standing crop</i>.

Research paper thumbnail of Genetic Diversity and Spatial Genetic Structure of an Epiphytic Bromeliad in Costa Rican Montane Secondary Forest Patches

Biotropica, Jun 10, 2014

Corsica and Sardinia represent major hotspots of plant diversity in the Mediterranean area and ar... more Corsica and Sardinia represent major hotspots of plant diversity in the Mediterranean area and are priority regions for conservation due to their high number of endemic plant species. However, information supporting human decision-making on the conservation of these species is still scarce, especially at the genetic level. In this work, the first assessment is reported of the species-wide spatial genetic structure and diversity of Ferula arrigonii Bocchieri, a Corso-Sardinian endemic located in a few coastal sites and on small islands. Nine populations covering the entire natural range of the species were investigated by means of AFLP (amplified fragment length polymorphism) markers. Results indicate that this species is characterised by high levels of genetic polymorphism (92% polymorphic fragments) and of genetic diversity (H w = 0.317) and by relatively low differentiation among populations (F st = 0.057). PCoA, Bayesian analysis and neighbour-joining clustering were also employed to investigate the genetic structure of this species. Three genetically distinct groups were detected, although with considerable overlap between populations.

Research paper thumbnail of Is opbrengen van maaisel effectief

Research paper thumbnail of Ecoducts and genetic exchange among ground beetles

Research paper thumbnail of Natuurbruggen en genenuitwisseling van loopkevers

Research paper thumbnail of MOESM4 of BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology

Additional file 4. Scientific studies using the BioVeL platform.

Research paper thumbnail of MOESM2 of BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology

Additional file 2: Table S1. Service groups and capabilities for processing and analysis in biodi... more Additional file 2: Table S1. Service groups and capabilities for processing and analysis in biodiversity science.

Research paper thumbnail of Maculinea alcon microsatellite data

The file Maculinea alcon microsatellite data includes the data from 12 microsatellites for 398 un... more The file Maculinea alcon microsatellite data includes the data from 12 microsatellites for 398 unique genotypes of Maculinea alcon from in total 14 sampling locations located in Belgium and The Netherlands. The data matrix also include the spatial coordinates of each sampled population, given in the two last columns

Research paper thumbnail of AFLP data

The file AFLP data.txt includes the binary matrix of AFLP band presence (1) – absence (0) for 451... more The file AFLP data.txt includes the binary matrix of AFLP band presence (1) – absence (0) for 451 AFLP-markers and 422 individuals of Liparis loeselii sampled in 38 populations. The matrix also include the spatial coordinates of each sampled population, given in the two last columns. The markers are numbered M1 to M451. The description of each marker (size in base pairs, primer combination) is given in the file readme.txt

Research paper thumbnail of Data from: High levels of effective long-distance dispersal may blur ecotypic divergence in a rare terrestrial orchid

Background: Gene flow and adaptive divergence are key aspects of metapopulation dynamics and ecol... more Background: Gene flow and adaptive divergence are key aspects of metapopulation dynamics and ecological speciation. Long-distance dispersal is hard to detect and few studies estimate dispersal in combination with adaptive divergence. The aim of this study was to investigate effective long-distance dispersal and adaptive divergence in the fen orchid (Liparis loeselii (L.) Rich.). We used amplified fragment length polymorphism (AFLP)-based assignment tests to quantify effective long-distance dispersal at two different regions in Northwest Europe. In addition, genomic divergence between fen orchid populations occupying two distinguishable habitats, wet dune slacks and alkaline fens, was investigated by a genome scan approach at different spatial scales (continental, landscape and regional) and based on 451 AFLP loci. Results: We expected that different habitats would contribute to strong divergence and restricted gene flow resulting in isolation-by-adaptation. Instead, we found remarkably high levels of effective long-distance seed dispersal and low levels of adaptive divergence. At least 15% of the assigned individuals likely originated from among-population dispersal events with dispersal distances up to 220 km. Six (1.3%) ‘outlier’ loci, potentially reflecting local adaptation to habitat-type, were identified with high statistical support. Of these, only one (0.22%) was a replicated outlier in multiple independent dune-fen population comparisons and thus possibly reflecting truly parallel divergence. Signals of adaptation in response to habitat type were most evident at the scale of individual populations. Conclusions: The findings of this study suggest that the homogenizing effect of effective long-distance seed dispersal may overwhelm divergent selection associated to habitat type in fen orchids in Northwest Europe

Research paper thumbnail of Meer soorten op de hei: red het heischraal grasland

Research paper thumbnail of forests and associated vascular epiphytes in a subtropical island of East Asia 1

Aim This study aims to assess the impact of climate change on forests and vascular epiphytes, usi... more Aim This study aims to assess the impact of climate change on forests and vascular epiphytes, using species distribution models (SDMs). Location Island of Taiwan, subtropical East Asia. Methods A hierarchical modelling approach incorporating forest migration velocity and forest type–epiphyte interactions with classical SDMs was used to model the responses of eight forest types and 237 vascular epiphytes for the year 2100 under two climate change scenarios. Forest distributions were modelled and modified by dominant tree species’ dispersal limitations and hypothesized persistence under unfavourable climate conditions (20 years for broad-leaved trees and 50 years for conifers). The modelled forest projections together with 16 environmental variables were used as predictors in models of epiphyte distributions. A null method was applied to validate the significance of epiphyte SDMs, and potential vulnerable species were identified by calculating range turnover rates. Results For the yea...

Research paper thumbnail of BioVeL Deliverable Report D2.1: State-of-the-art & trends review on biospheric carbon sequestration, ecosystem functioning and valuation, and invasive species management

This is the final version of deliverable D2.1. The first draft was prepared, improved and updated... more This is the final version of deliverable D2.1. The first draft was prepared, improved and updated during July and August of 2012. Further comments and feedbacks were included by 28 th of August.

Research paper thumbnail of Pleistocene sea-level changes as a predictor for insular species richness?

Trabajo presentado en el el congreso Island Biology 2014 celebrado en Hawai del 7 al 11 de julio ... more Trabajo presentado en el el congreso Island Biology 2014 celebrado en Hawai del 7 al 11 de julio de 2014.

Research paper thumbnail of DemographicDemographic consequences of inbreeding andand outbreeding in Arnic a montana : aa field experiment

Genetical reinforcement of small populations by adding seeds or individuals from other population... more Genetical reinforcement of small populations by adding seeds or individuals from other populationss may be an important management tool to prevent threatened plant species from extinction. However,, a negative consequence of mixing gene pools might be the reduction of plant fitness as coadaptedd gene complexes are disrupted. In the declining, self-incompatible perennial Arnica montana (Asteraceae),, we analysed the demographic consequences of inbreeding and outbreeding in five populationss of varying size. We analysed seed production and fruit weight following the pollination treatments.. From 1997 to 2000, plant growth, survival and flowering were monitored on plants introducedd as seeds and as four-week old seedlings in a field experiment. Reducedd seed set after selfing was due to self-incompatibility. There was significant heterosis for seed sett after inter-population crosses, probably due to low mate availability, in one of the small populations. Significantt but low inbreeding depression was observed for growth rates of plants introduced as seedlings.. We found significant heterosis for flowering probability of plants introduced as seeds, but for plantss introduced as seedlings, heterosis for seedling size and flowering probability was only marginally significant.. Although no outbreeding depression was observed in the F|, it may still be expressed in the forthcomingg generations as recombination of genes start to break up the coadapted gene complexes associatedd with local fitness. It is not clear to what degree the observed heterosis may outweigh this outbreedingg depression. Nevertheless, considering the rapid decline of A. montana in The Netherlands, geneticall reinforcement of the numerous small populations may be more important than the possible negativee consequences of outbreeding depression.

Research paper thumbnail of Gene flow and effective population sizes of the Alcon blue butterfly Maculinea alcon in a highly fragmented, anthropogenic landscape: Flash presentation

Research paper thumbnail of Ontwikkeling van zoet-zoutgradienten met en zonder dynamisch kustbeheer : een onderzoek naar de mogelijkheden voor meer natuurlijke ontwikkelingen in het kustgebied

Disclaimer/Complaints regulations If you believe that digital publication of certain material inf... more Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: http://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible.

Research paper thumbnail of A new geodiversity index to support biodiversity research in alpine areas

Research paper thumbnail of Outbreeding depression and breeding system evolution in small, remnant populations of Primula vulgaris: consequences for genetic rescue

Conservation Genetics, 2017

Many species suffer from anthropogenic habitat fragmentation. The resulting small and isolated po... more Many species suffer from anthropogenic habitat fragmentation. The resulting small and isolated populations are more prone to extinction due to, amongst others, genetic erosion, inbreeding depression and Allee-effects. Genetic rescue can help mitigate such problems, but might result in outbreeding depression. We evaluated offspring fitness after selfing and outcrossing within and among three very small and isolated remnant populations of the heterostylous plant Primula vulgaris. We used greenhouse-grown offspring from these populations to test several fitness components. One population was fixed for the pin-morph, and was outcrossed with another population in the field to obtain seeds. Genetic diversity of parent and offspring populations was studied using microsatellites. Morph and population-specific heterosis, inbreeding and outbreeding depression were observed for fruit and seed set, seed weight and cumulative fitness. Highest fitness was observed in the field-outcrossed F1-population, which also showed outbreeding depression following subsequent between-population (back) crossing. Despite outbreeding depression, fitness was still relatively high. Inbreeding coefficients indicated that the offspring were more inbred than their parent populations. Offspring heterozygosity and inbreeding coefficients correlated with observed fitness. One population is evolving homostyly, showing a thrum morph with an elongated style and high autonomous fruit and seed set. This has important implications for conservation strategies such as genetic rescue, as the mating system will be altered by the introduction of homostyles.

Research paper thumbnail of Biología de la conservación de endemismos vagetales de los parques nacionales canarios

[ES] El presente proyecto se centra en aplicar técnicas de biología molecular, demográficas y de ... more [ES] El presente proyecto se centra en aplicar técnicas de biología molecular, demográficas y de biología reproductiva en cuatro endemismos canarios amenazados que se encuentran total o parcialmente localizados en los parques nacionales de Canarias: Silene ...