I am a Biologist with a Ph.D. in Ecology and Biodiversity (2013) with great passion for animals and plants, and 22 years of vast experience in: botany, taxonomy, ethnobotany, demography, conservation and advising students. I have a strong modelling and organisational skills gained in research.
Background: Making forecasts about biodiversity and giving support to policy relies increasingly ... more Background: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as " Web services ") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust " in silico " science. However, use of this approach in biodiversity science and ecology has thus far been quite limited. Results: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on‑line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorpo‑ rating R programs. Deploying these tools into an easy‑to‑use and accessible 'virtual laboratory' , free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool devel‑ opers to try out the services and contribute to the activity.
The Taverna workflow tool suite (http://www.taverna.
org.uk) is designed to combine distributed W... more The Taverna workflow tool suite (http://www.taverna. org.uk) is designed to combine distributed Web Services and/or local tools into complex analysis pipelines. These pipelines can be executed on local desktop machines or through larger infrastructure (such as supercomputers, Grids or cloud environments), using the Taverna Server. In bioinformatics, Taverna workflows are typically used in the areas of high-throughput omics analyses (for example, proteomics or transcriptomics), or for evidence gathering methods involving text mining or data mining. Through Taverna, scientists have access to several thousand different tools and resources that are freely available from a large range of life science institutions. Once constructed, the workflows are reusable, executable bioinformatics protocols that can be shared, reused and repurposed. A repository of public workflows is available at http://www. myexperiment.org. This article provides an update to the Taverna tool suite, highlighting new features and developments in the workbench and the Taverna Server.
Background: Making forecasts about biodiversity and giving support to policy relies increasingly ... more Background: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as " Web services ") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust " in silico " science. However, use of this approach in biodiversity science and ecology has thus far been quite limited. Results: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on‑line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorpo‑ rating R programs. Deploying these tools into an easy‑to‑use and accessible 'virtual laboratory' , free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool devel‑ opers to try out the services and contribute to the activity.
Summary
Secondary hemiepiphytes have one of the most bizarre life histories among vascular plants... more Summary Secondary hemiepiphytes have one of the most bizarre life histories among vascular plants. They germinate on the forest floor, climb onto a host tree, gradually grow up and start producing seeds if the host tree is taller than the minimum height required for reproductive onset. Because most of the host trees in the forest are too small to allow reproduction, most seedlings of secondary hemiepiphytes of the genus Heteropsis climb onto unsuitable hosts. This problem may be remediated by moving from unsuitable to suitable hosts by vegetative propagation, providing a second chance to contribute to recruitment. Still, such a strategy comes at a demographic risk of increased mortality and may thus contribute little to population growth.
Here we ask what are the relative contributions of Heteropsis individuals on suitable vs. unsuitable hosts to their population growth rates (λ). We studied the demography of three species of the genus Heteropsis in the Colombian Amazon, distinguishing sub-populations on suitable and unsuitable hosts. We constructed multi-state matrix population models and performed elasticity and loop analyses.
For all three Heteropsis species, λ ≥ 1, indicating that studied populations are viable. Vital rates and loop elasticities showed that individuals on suitable hosts contributed 85–98% and 80–96% respectively. Consequently, individuals that climb directly to suitable hosts predominantly drive the population dynamics of the three studied Heteropsis species and second chances (vegetative reproduction) do not matter for demographic viability.
Our results are evidence of a strong source-sink dynamic for the studied species, whereby individuals on unsuitable hosts act as sink subpopulations and individuals on suitable hosts as source subpopulations. The population growth rates of the examined Heteropsis species were strongly limited by recruitment of individuals on suitable hosts and the high proportion of seedlings climbing onto unsuitable hosts, which are demographic ‘lost cases’.
Synthesis: Our study illustrates a strong environmental filtering and multiple bottlenecks in the life cycle of secondary hemiepiphytes. Our findings contribute with an understudied plant life-history strategy to the extensive repertoire of better-known ecological plant strategies such as tree-gap dynamics, clonal reproduction and permanent seedbanks.
Secondary hemiepiphytes rely on other plants (hosts) to grow vertically. After germinating on the... more Secondary hemiepiphytes rely on other plants (hosts) to grow vertically. After germinating on the forest floor, their seedlings search a host to ascend. We recorded information on survival, growth, reproduction and vegetative propagation of three Heteropsis species, to evaluate what drives their vital rates. We measured 700 individuals of each study species between 2007 and 2009 in the southern Colombian Amazon. A gradual increase in stem length, leaf size, number of roots and plagiotropic branches was found with increasing height of Heteropsis individuals on their hosts. Survival of leafless non-climbing seedlings was very low (28% annually); increasing substantially (84–94%) once the seedling had ascended a host. The three Heteropsis species presented slow height growth rates (c. 2–8 cm y−1) with large variation, while a substantial percentage of the stems (31–62%) did not grow or dried out. Vegetative propagation in Heteropsis may act as a dispersion-propagation strategy to find a suitable host and reach the canopy again after falling. The slow growth rates suggest that Heteropsis individuals that have reached the canopy are rather old. Once plants have reached the tree crowns, their longevity is largely determined by the survival of the host tree.
As climbing plants lack the capacity to hold themselves upright, they need to encounter a suitabl... more As climbing plants lack the capacity to hold themselves upright, they need to encounter a suitable host. Vines, lianas, and secondary hemiepiphytes need, therefore, an effective searching strategy. Various hypotheses have been put forward on searching strategies, including ‘skototropism’—growth toward darkness—and random searching. We studied host searching strategies of three secondary hemiepiphyte species belonging to the genus Heteropsis. We recorded information on the diameter distribution of host and evaluated whether these hosts were ‘suitable’, i.e., sufficiently tall for Heteropsis individuals to reach reproductive size. The diameter distribution of host trees bearing Heteropsis seedlings was similar to that of the trees in our study plots. Also, we found that 72–81 percent of the Heteropsis seedlings were present on unsuitable hosts (seedlings, saplings, herbs). These results suggest that Heteropsis seedlings search hosts in a random manner and not by skototropism. We found quite a distinct pattern for adult Heteropsis individuals, which predominantly occur on host trees bigger than 10 cm dbh. Host diameter distribution for Heteropsis adults differed significantly from that of the entire tree community. This difference suggests that Heteropsis individuals may change hosts if they are initially present on nonsuitable hosts. We observed that Heteropsis seedlings and juveniles on unsuitable hosts often produced vegetative shoots that searched for another host. In many cases, such shoots did not find a suitable host. For Heteropsis, our results suggest that host tree searching is a long-term trial and error process that is governed by a random searching strategy.Abstract in Spanish is available in the online version of this article.
This PhD study aimed to improve our understanding of the life history, population dynamics and ho... more This PhD study aimed to improve our understanding of the life history, population dynamics and host searching strategy of three sympatric Heteropsis species (secondary hemiepiphytes) in the Colombian Amazon. The objectives of the present study were: 1.To provide insight into how three sympatric Heteropsis species search for a host. 2. To describe and explain patterns of survival, growth, retrogression, vegetative and sexual reproduction of the three Heteropsis species and the implications of the host suitability for these vital rates. 3. To provide insights into the main drivers of population growth of the three Heteropsis species, with particular focus on the contribution of subpopulations on suitable and non-suitable hosts to population growth and the importance of vegetative reproduction to population growth. 4. To estimate the age at which Heteropsis species become reproductive and at which their roots can be harvested. Outltline Of This Thesis This thesis addresses the demography and the relative importance of host suitability of three species of Heteropsis used for the manufacture of indigenous basketry and handicrafts across the Amazon. Chapter 2 describes the host-searching strategies of the three Heteropsis species, using information on the size distribution of hosts with climbing Heteropsis individuals and the suitability of those hosts. We analyze this for seedlings of the three Heteropsis species as well as for vegetatively produced ramets. Chapter 3 discusses the results of a study on survival, growth, reproduction and vegetative propagation of the three Heteropsis species and the implications of host suitability for these vital rates. With these data we quantify and evaluate the effect of plant height, plant size and host suitability on these vital rates. The importance and consequences of vegetative propagation are further discussed. Chapter 4 analyses the demography of three Heteropsis species, using multi-state population models. In this chapter I separated dynamics of Heteropsis on suitable vs. non-suitable hosts in order to determine the relative contribution of plants on non-suitable hosts for population growth. I also quantified the importance of vital rates, particularly focusing on the importance of the forms of vegetative reproduction that allow Heteropsis plants to change hosts and survive after host mortality.
Background: Making forecasts about biodiversity and giving support to policy relies increasingly ... more Background: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as " Web services ") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust " in silico " science. However, use of this approach in biodiversity science and ecology has thus far been quite limited. Results: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on‑line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorpo‑ rating R programs. Deploying these tools into an easy‑to‑use and accessible 'virtual laboratory' , free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool devel‑ opers to try out the services and contribute to the activity.
The Taverna workflow tool suite (http://www.taverna.
org.uk) is designed to combine distributed W... more The Taverna workflow tool suite (http://www.taverna. org.uk) is designed to combine distributed Web Services and/or local tools into complex analysis pipelines. These pipelines can be executed on local desktop machines or through larger infrastructure (such as supercomputers, Grids or cloud environments), using the Taverna Server. In bioinformatics, Taverna workflows are typically used in the areas of high-throughput omics analyses (for example, proteomics or transcriptomics), or for evidence gathering methods involving text mining or data mining. Through Taverna, scientists have access to several thousand different tools and resources that are freely available from a large range of life science institutions. Once constructed, the workflows are reusable, executable bioinformatics protocols that can be shared, reused and repurposed. A repository of public workflows is available at http://www. myexperiment.org. This article provides an update to the Taverna tool suite, highlighting new features and developments in the workbench and the Taverna Server.
Background: Making forecasts about biodiversity and giving support to policy relies increasingly ... more Background: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as " Web services ") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust " in silico " science. However, use of this approach in biodiversity science and ecology has thus far been quite limited. Results: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on‑line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorpo‑ rating R programs. Deploying these tools into an easy‑to‑use and accessible 'virtual laboratory' , free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool devel‑ opers to try out the services and contribute to the activity.
Summary
Secondary hemiepiphytes have one of the most bizarre life histories among vascular plants... more Summary Secondary hemiepiphytes have one of the most bizarre life histories among vascular plants. They germinate on the forest floor, climb onto a host tree, gradually grow up and start producing seeds if the host tree is taller than the minimum height required for reproductive onset. Because most of the host trees in the forest are too small to allow reproduction, most seedlings of secondary hemiepiphytes of the genus Heteropsis climb onto unsuitable hosts. This problem may be remediated by moving from unsuitable to suitable hosts by vegetative propagation, providing a second chance to contribute to recruitment. Still, such a strategy comes at a demographic risk of increased mortality and may thus contribute little to population growth.
Here we ask what are the relative contributions of Heteropsis individuals on suitable vs. unsuitable hosts to their population growth rates (λ). We studied the demography of three species of the genus Heteropsis in the Colombian Amazon, distinguishing sub-populations on suitable and unsuitable hosts. We constructed multi-state matrix population models and performed elasticity and loop analyses.
For all three Heteropsis species, λ ≥ 1, indicating that studied populations are viable. Vital rates and loop elasticities showed that individuals on suitable hosts contributed 85–98% and 80–96% respectively. Consequently, individuals that climb directly to suitable hosts predominantly drive the population dynamics of the three studied Heteropsis species and second chances (vegetative reproduction) do not matter for demographic viability.
Our results are evidence of a strong source-sink dynamic for the studied species, whereby individuals on unsuitable hosts act as sink subpopulations and individuals on suitable hosts as source subpopulations. The population growth rates of the examined Heteropsis species were strongly limited by recruitment of individuals on suitable hosts and the high proportion of seedlings climbing onto unsuitable hosts, which are demographic ‘lost cases’.
Synthesis: Our study illustrates a strong environmental filtering and multiple bottlenecks in the life cycle of secondary hemiepiphytes. Our findings contribute with an understudied plant life-history strategy to the extensive repertoire of better-known ecological plant strategies such as tree-gap dynamics, clonal reproduction and permanent seedbanks.
Secondary hemiepiphytes rely on other plants (hosts) to grow vertically. After germinating on the... more Secondary hemiepiphytes rely on other plants (hosts) to grow vertically. After germinating on the forest floor, their seedlings search a host to ascend. We recorded information on survival, growth, reproduction and vegetative propagation of three Heteropsis species, to evaluate what drives their vital rates. We measured 700 individuals of each study species between 2007 and 2009 in the southern Colombian Amazon. A gradual increase in stem length, leaf size, number of roots and plagiotropic branches was found with increasing height of Heteropsis individuals on their hosts. Survival of leafless non-climbing seedlings was very low (28% annually); increasing substantially (84–94%) once the seedling had ascended a host. The three Heteropsis species presented slow height growth rates (c. 2–8 cm y−1) with large variation, while a substantial percentage of the stems (31–62%) did not grow or dried out. Vegetative propagation in Heteropsis may act as a dispersion-propagation strategy to find a suitable host and reach the canopy again after falling. The slow growth rates suggest that Heteropsis individuals that have reached the canopy are rather old. Once plants have reached the tree crowns, their longevity is largely determined by the survival of the host tree.
As climbing plants lack the capacity to hold themselves upright, they need to encounter a suitabl... more As climbing plants lack the capacity to hold themselves upright, they need to encounter a suitable host. Vines, lianas, and secondary hemiepiphytes need, therefore, an effective searching strategy. Various hypotheses have been put forward on searching strategies, including ‘skototropism’—growth toward darkness—and random searching. We studied host searching strategies of three secondary hemiepiphyte species belonging to the genus Heteropsis. We recorded information on the diameter distribution of host and evaluated whether these hosts were ‘suitable’, i.e., sufficiently tall for Heteropsis individuals to reach reproductive size. The diameter distribution of host trees bearing Heteropsis seedlings was similar to that of the trees in our study plots. Also, we found that 72–81 percent of the Heteropsis seedlings were present on unsuitable hosts (seedlings, saplings, herbs). These results suggest that Heteropsis seedlings search hosts in a random manner and not by skototropism. We found quite a distinct pattern for adult Heteropsis individuals, which predominantly occur on host trees bigger than 10 cm dbh. Host diameter distribution for Heteropsis adults differed significantly from that of the entire tree community. This difference suggests that Heteropsis individuals may change hosts if they are initially present on nonsuitable hosts. We observed that Heteropsis seedlings and juveniles on unsuitable hosts often produced vegetative shoots that searched for another host. In many cases, such shoots did not find a suitable host. For Heteropsis, our results suggest that host tree searching is a long-term trial and error process that is governed by a random searching strategy.Abstract in Spanish is available in the online version of this article.
This PhD study aimed to improve our understanding of the life history, population dynamics and ho... more This PhD study aimed to improve our understanding of the life history, population dynamics and host searching strategy of three sympatric Heteropsis species (secondary hemiepiphytes) in the Colombian Amazon. The objectives of the present study were: 1.To provide insight into how three sympatric Heteropsis species search for a host. 2. To describe and explain patterns of survival, growth, retrogression, vegetative and sexual reproduction of the three Heteropsis species and the implications of the host suitability for these vital rates. 3. To provide insights into the main drivers of population growth of the three Heteropsis species, with particular focus on the contribution of subpopulations on suitable and non-suitable hosts to population growth and the importance of vegetative reproduction to population growth. 4. To estimate the age at which Heteropsis species become reproductive and at which their roots can be harvested. Outltline Of This Thesis This thesis addresses the demography and the relative importance of host suitability of three species of Heteropsis used for the manufacture of indigenous basketry and handicrafts across the Amazon. Chapter 2 describes the host-searching strategies of the three Heteropsis species, using information on the size distribution of hosts with climbing Heteropsis individuals and the suitability of those hosts. We analyze this for seedlings of the three Heteropsis species as well as for vegetatively produced ramets. Chapter 3 discusses the results of a study on survival, growth, reproduction and vegetative propagation of the three Heteropsis species and the implications of host suitability for these vital rates. With these data we quantify and evaluate the effect of plant height, plant size and host suitability on these vital rates. The importance and consequences of vegetative propagation are further discussed. Chapter 4 analyses the demography of three Heteropsis species, using multi-state population models. In this chapter I separated dynamics of Heteropsis on suitable vs. non-suitable hosts in order to determine the relative contribution of plants on non-suitable hosts for population growth. I also quantified the importance of vital rates, particularly focusing on the importance of the forms of vegetative reproduction that allow Heteropsis plants to change hosts and survive after host mortality.
Uploads
org.uk) is designed to combine distributed Web
Services and/or local tools into complex analysis
pipelines. These pipelines can be executed on local
desktop machines or through larger infrastructure
(such as supercomputers, Grids or cloud environments),
using the Taverna Server. In bioinformatics,
Taverna workflows are typically used in the areas of
high-throughput omics analyses (for example, proteomics
or transcriptomics), or for evidence gathering
methods involving text mining or data mining.
Through Taverna, scientists have access to several
thousand different tools and resources that are freely
available from a large range of life science institutions.
Once constructed, the workflows are
reusable, executable bioinformatics protocols that
can be shared, reused and repurposed. A repository
of public workflows is available at http://www.
myexperiment.org. This article provides an update
to the Taverna tool suite, highlighting new features
and developments in the workbench and the Taverna
Server.
Secondary hemiepiphytes have one of the most bizarre life histories among vascular plants. They germinate on the forest floor, climb onto a host tree, gradually grow up and start producing seeds if the host tree is taller than the minimum height required for reproductive onset. Because most of the host trees in the forest are too small to allow reproduction, most seedlings of secondary hemiepiphytes of the genus Heteropsis climb onto unsuitable hosts. This problem may be remediated by moving from unsuitable to suitable hosts by vegetative propagation, providing a second chance to contribute to recruitment. Still, such a strategy comes at a demographic risk of increased mortality and may thus contribute little to population growth.
Here we ask what are the relative contributions of Heteropsis individuals on suitable vs. unsuitable hosts to their population growth rates (λ). We studied the demography of three species of the genus Heteropsis in the Colombian Amazon, distinguishing sub-populations on suitable and unsuitable hosts. We constructed multi-state matrix population models and performed elasticity and loop analyses.
For all three Heteropsis species, λ ≥ 1, indicating that studied populations are viable. Vital rates and loop elasticities showed that individuals on suitable hosts contributed 85–98% and 80–96% respectively. Consequently, individuals that climb directly to suitable hosts predominantly drive the population dynamics of the three studied Heteropsis species and second chances (vegetative reproduction) do not matter for demographic viability.
Our results are evidence of a strong source-sink dynamic for the studied species, whereby individuals on unsuitable hosts act as sink subpopulations and individuals on suitable hosts as source subpopulations. The population growth rates of the examined Heteropsis species were strongly limited by recruitment of individuals on suitable hosts and the high proportion of seedlings climbing onto unsuitable hosts, which are demographic ‘lost cases’.
Synthesis: Our study illustrates a strong environmental filtering and multiple bottlenecks in the life cycle of secondary hemiepiphytes. Our findings contribute with an understudied plant life-history strategy to the extensive repertoire of better-known ecological plant strategies such as tree-gap dynamics, clonal reproduction and permanent seedbanks.
1.To provide insight into how three sympatric Heteropsis species search for a host.
2. To describe and explain patterns of survival, growth, retrogression, vegetative and sexual reproduction of the three Heteropsis species and the implications of the host suitability for these vital rates.
3. To provide insights into the main drivers of population growth of the three Heteropsis species, with particular focus on the contribution of subpopulations on suitable and non-suitable hosts to population growth and the importance of vegetative reproduction to population growth.
4. To estimate the age at which Heteropsis species become reproductive and at which their roots can be harvested.
Outltline Of This Thesis
This thesis addresses the demography and the relative importance of host suitability of three species of Heteropsis used for the manufacture of indigenous basketry and handicrafts across the Amazon.
Chapter 2 describes the host-searching strategies of the three Heteropsis species, using information on the size distribution of hosts with climbing Heteropsis individuals and the suitability of those hosts. We analyze this for seedlings of the three Heteropsis species as well as for vegetatively produced ramets.
Chapter 3 discusses the results of a study on survival, growth, reproduction and vegetative propagation of the three Heteropsis species and the implications of host suitability for these vital rates. With these data we quantify and evaluate the effect of plant height, plant size and host suitability on these vital rates. The importance and consequences of vegetative propagation are further discussed.
Chapter 4 analyses the demography of three Heteropsis species, using multi-state population models. In this chapter I separated dynamics of Heteropsis on suitable vs. non-suitable hosts in order to determine the relative contribution of plants on non-suitable hosts for population growth. I also quantified the importance of vital rates, particularly focusing on the importance of the forms of vegetative reproduction that allow Heteropsis plants to change hosts and survive after host mortality.
org.uk) is designed to combine distributed Web
Services and/or local tools into complex analysis
pipelines. These pipelines can be executed on local
desktop machines or through larger infrastructure
(such as supercomputers, Grids or cloud environments),
using the Taverna Server. In bioinformatics,
Taverna workflows are typically used in the areas of
high-throughput omics analyses (for example, proteomics
or transcriptomics), or for evidence gathering
methods involving text mining or data mining.
Through Taverna, scientists have access to several
thousand different tools and resources that are freely
available from a large range of life science institutions.
Once constructed, the workflows are
reusable, executable bioinformatics protocols that
can be shared, reused and repurposed. A repository
of public workflows is available at http://www.
myexperiment.org. This article provides an update
to the Taverna tool suite, highlighting new features
and developments in the workbench and the Taverna
Server.
Secondary hemiepiphytes have one of the most bizarre life histories among vascular plants. They germinate on the forest floor, climb onto a host tree, gradually grow up and start producing seeds if the host tree is taller than the minimum height required for reproductive onset. Because most of the host trees in the forest are too small to allow reproduction, most seedlings of secondary hemiepiphytes of the genus Heteropsis climb onto unsuitable hosts. This problem may be remediated by moving from unsuitable to suitable hosts by vegetative propagation, providing a second chance to contribute to recruitment. Still, such a strategy comes at a demographic risk of increased mortality and may thus contribute little to population growth.
Here we ask what are the relative contributions of Heteropsis individuals on suitable vs. unsuitable hosts to their population growth rates (λ). We studied the demography of three species of the genus Heteropsis in the Colombian Amazon, distinguishing sub-populations on suitable and unsuitable hosts. We constructed multi-state matrix population models and performed elasticity and loop analyses.
For all three Heteropsis species, λ ≥ 1, indicating that studied populations are viable. Vital rates and loop elasticities showed that individuals on suitable hosts contributed 85–98% and 80–96% respectively. Consequently, individuals that climb directly to suitable hosts predominantly drive the population dynamics of the three studied Heteropsis species and second chances (vegetative reproduction) do not matter for demographic viability.
Our results are evidence of a strong source-sink dynamic for the studied species, whereby individuals on unsuitable hosts act as sink subpopulations and individuals on suitable hosts as source subpopulations. The population growth rates of the examined Heteropsis species were strongly limited by recruitment of individuals on suitable hosts and the high proportion of seedlings climbing onto unsuitable hosts, which are demographic ‘lost cases’.
Synthesis: Our study illustrates a strong environmental filtering and multiple bottlenecks in the life cycle of secondary hemiepiphytes. Our findings contribute with an understudied plant life-history strategy to the extensive repertoire of better-known ecological plant strategies such as tree-gap dynamics, clonal reproduction and permanent seedbanks.
1.To provide insight into how three sympatric Heteropsis species search for a host.
2. To describe and explain patterns of survival, growth, retrogression, vegetative and sexual reproduction of the three Heteropsis species and the implications of the host suitability for these vital rates.
3. To provide insights into the main drivers of population growth of the three Heteropsis species, with particular focus on the contribution of subpopulations on suitable and non-suitable hosts to population growth and the importance of vegetative reproduction to population growth.
4. To estimate the age at which Heteropsis species become reproductive and at which their roots can be harvested.
Outltline Of This Thesis
This thesis addresses the demography and the relative importance of host suitability of three species of Heteropsis used for the manufacture of indigenous basketry and handicrafts across the Amazon.
Chapter 2 describes the host-searching strategies of the three Heteropsis species, using information on the size distribution of hosts with climbing Heteropsis individuals and the suitability of those hosts. We analyze this for seedlings of the three Heteropsis species as well as for vegetatively produced ramets.
Chapter 3 discusses the results of a study on survival, growth, reproduction and vegetative propagation of the three Heteropsis species and the implications of host suitability for these vital rates. With these data we quantify and evaluate the effect of plant height, plant size and host suitability on these vital rates. The importance and consequences of vegetative propagation are further discussed.
Chapter 4 analyses the demography of three Heteropsis species, using multi-state population models. In this chapter I separated dynamics of Heteropsis on suitable vs. non-suitable hosts in order to determine the relative contribution of plants on non-suitable hosts for population growth. I also quantified the importance of vital rates, particularly focusing on the importance of the forms of vegetative reproduction that allow Heteropsis plants to change hosts and survive after host mortality.