Discussions about transit often end up about funding. To help make these discussions productive, I was pleased to co-author a paper through the Transportation Association of Canada titled Importance of Transportation Funding: Framing the Issues.
Working on this with David Kriger, Nick Lovett, Yonghai Xiao, Vahid Ayan, Andrew Devlin, Tamim Raad, and Haytham Sadeq was delightful.
Here’s the abstract:
Transportation funding is becoming an important topic of discussion at all levels of Transportation Association of Canada (TAC) councils and committees, reflecting discussions that are taking place throughout the Canadian transportation community.
Prior to general release, plantae is moving web hosts. This seems like a good time to point out that all of plantae’s code is hosted at Google Code. The project has great potential and deserves consistent attention. Unfortunately, I can’t continue to develop the code. So, if you have an interest in collaborative software, particularly in the scientific context, I encourage you to take a look.
Some technical issues coupled with my road-trip-without-a-laptop conspired to keep Plantae from working correctly. I’ve repaired the damage and isolated Plantae from such problems in the future. My apologies for the downtime.
Hermaphroditism is prevalent in plants but may allow interference between male function (pollen removal and dispersal) and female function (pollen receipt and seed production) within a flower. Temporal or spatial segregation of gender within a hermaphroditic flower may evolve to reduce this interference and enhance male and female reproductive success. We tested this hypothesis using Chamerion angustifolium (Onagraceae), in which pollen removal (male) and pollen deposition (female) were measured directly on hermaphroditic and experimentally produced unisexual flowers.
This book of about 600 pages is written to provide practitioners of pollination biology with a broadly based source of methodologies as well as the basic conceptual background to aid in understanding. Thus, the book reflects the expertise of the assembled a team of internationally acclaimed scientists. Pollination biology enjoys over 200 years of scientific tradition. In recent years, the interdisciplinarity of pollination biology has become a model for integrating physics, chemistry, and biology into natural history, evolutionary and applied ecology.
Protandry, a form of temporal separation of gender within hermaphroditic flowers, may reduce the magnitude of pollen lost to selfing (pollen discounting) and also serve to enhance pollen export and outcross siring success. Because pollen discounting is strongest when selfing occurs between flowers on the same plant, the advantage of protandry may be greatest in plants with large floral displays. We tested this hypothesis with enclosed, artificial populations of Chamerion angustifolium (Onagraceae) by experimentally manipulating protandry (producing uniformly adichogamous or mixed protandrous and adichogamous populations) and inflorescence size (two-, six-, or 10-flowered inflorescences) and measuring pollinator visitation, seed set, female outcrossing rate, and outcross siring success.
In self-compatible plants, small populations may experience reduced outcrossing owing to decreased pollinator visitation and mate availability. We examined the relation between outcrossing and population size in eastern Ontario populations of Aquilegia canadensis. Experimental pollinations showed that the species is highly self-compatible, and can achieve full seed-set in the absence of pollinators via automatic self-pollination. We estimated levels of outcrossing (t) and parental inbreeding coefficients (F) from allozyme variation in naturally pollinated seed families for 10 populations ranging in size from 32 to 750 reproductive individuals.
Historically, dichogamy (the temporal separation of gender in flowering plants) has been interpreted as a mechanism for avoiding inbreeding. However, a comparative survey found that many dichogamous species are self-incompatible (SI), suggesting dichogamy evolved for other reasons, particularly reducing interference between male and female function. Here we re-examined the association between dichogamy and SI in a phylogenetic framework, and tested the hypothesis that dichogamy evolved to reduce interference between male and female function.
Clonal growth in plants can increase pollen and ovule production per genet. However, paternal and maternal reproductive success may not increase because within-clone pollination (geitonogamy) can reduce pollen export to adjacent clones (pollen discounting) and pollen import to the central ramets (pollen limitation). We investigated the relationship between clone size and mating success using clones of Malus x domestica at four orchards (blocks of 1–5 rows of trees). For each block, we measured maternal function as fruit and seed set in all rows and paternal function as siring rate in the first row of the adjacent block.
Protandry (when male function precedes female) can enhance fitness by reducing selfing and increasing pollen export and outcrossed siring success. However, responses to selection on protandry may be constrained by genetic variation and correlations among floral traits. We examined these potential constraints in protandrous Chamerion angustifolium (Onagraceae) by estimating genetic variation in male-phase duration and associated floral traits using a paternal half-sib design and selection experiment. Narrow-sense heritability of male-phase duration was estimated as 0.
Mating by outcrossing plants depends on the frequency and quality of interaction between pollen vectors and individual flowers. However, the historical focus of pollination biology on individual flowers (floricentrism) cannot produce a complete understanding of the role of pollination in plant mating, because mating is an aggregate process, which depends on the reproductive outcomes of all of a plant’s flowers. Simultaneous display of multiple flowers in an inflorescence increases a plant’s attractiveness to pollinators, which should generally enhance mating opportunities.
Pollen and ovules experience diverse fates during pollination, pollen-tube growth, fertilization, and seed development, which govern the male and female potential of flowering plants. This chapter identifies these fates and many of their interactions, and considers their theoretical implications for the evolution of pollen export and the production of selfed and outcrossed seeds. This analysis clarifies the importance of pollen quantity and quality for seed production, including the opportunity for poor pollen quality to cause misidentification of pollen limitation.
Sean Rice’s Evolutionary Theory is an excellent journey through the mathematical foundations of evolutionary biology. The book covers a wide array of theory, including single locus models, drift, Price’s Theorem, game theory, and multilevel selection. Despite the often intense content, the book is written with a great, economical style that is easy to read. More importantly, the consistent presentation of such a broad collection of theory highlights the unifying principles of evolution.
In collaboration with Jana and Steve Vamosi, I have started a new project called Plantae. The goal of this project is to create a community website for the collection of evolutionary and ecological data for plant species. An early prototype of the project is available and we welcome feedback on all aspects of the project.
Although the current implementation is rather rough. I hope to make some rapid progress on the design and function of the site in the new year.
Mating by outcrossing plants depends on the frequency and quality of interaction between pollen vectors and individual flowers. However, the historical focus of pollination biology on individual flowers (floricentrism) cannot produce a complete understanding of the role of pollination in plant mating, because mating is an aggregate process, which depends on the reproductive outcomes of all of a plant’s flowers. Simultaneous display of multiple flowers in an inflorescence increases a plant’s attractiveness to pollinators, which should generally enhance mating opportunities.
Clonality is very common in flowering plants, but its consequences for sexual reproduction have rarely been explored. While clonal growth can increase the number of flowers a plant produces it may also limit reproductive success through pollen discounting (reduction in pollen exported to adjacent clones) and pollen limitation (failure of outside pollen to reach the centre of a clone). Using clones of domestic apple (Malus x domestica) that ranged from 1 to 5 orchard rows wide, we found that the patterns of siring success were consistent with the presence of pollen discounting, but we failed to detect evidence for pollen limitation.
Dichogamy, the temporal separation of gender within a flower, is widespread throughout the angiosperms, occurring in over 250 families. There are two forms of dichogamy: protandry, in which male function precedes female function, and protogyny, the converse. Dichogamy has traditionally been interpreted as a mechanism to avoid inbreeding. However, recent evidence indicates that this inbreeding-avoidance hypothesis cannot completely explain the evolution of dichogamy. An alternate hypothesis is that dichogamy acts to reduce interference between gender functions.
The outcrossing rate is a fundamental attribute of plant populations that determines population genetic structure, individual plant fitness, and ultimately speciation rates. The outcrossing rate can be influenced by population size through reductions in both mate availability and pollinator service. We investigated the effect of population size on the outcrossing rate in 10 populations of Aquilegia canadensis in Southern Ontario, Canada.
Across a range of sizes from 32 to 750 reproductive individuals, we found that small populations (n 90, blue line).
These data measured the genetic architecture of male-phase duration in Chamerion angustifolium. There are three files in the archive used to estimate genetic variances & covariances with VCE. Format:
protandryHeritabilityData.dat: Contains the measured data for male- & female-phase duration, flower size, & display size protandryHeritabilityPedigree.ped: Contains the pedigree information for the selection experiment protandryHeritabilityVCE: Is the VCE file that configures the analysis Citation:
Routley, M.B. & B.C. Husband. 2004. Responses to selection on male-phase duration in Chamerion angustifolium.
Yet another useful site from Google: Google Scholar. The site provides an interface for searching the scientific literature with typical Google ease. Some preliminary tests suggest that it is quite effective at finding relevant literature.
I’ve written a script that imports a JSTOR citation page into BibDesk. To use the script, I suggest adding it to your script menu. Then, with the JSTOR citation page as the active web page in Safari, run the script and the citation will be added to the active BibDesk file. I use the first author’s last name and last two digits of the year as a cite key (e.g. Darwin59), you may want to change this to suit your style.
Plants are sessile and, consequently, many species rely on pollinators for mating opportunities. However, pollinators do not necessarily visit every individual in a population with equal frequency. Plant attributes, such as floral display and reward provisioning, can influence the frequency of pollinator visitation. Furthermore, aspects of population density and structure may also influence visitation patterns. One effect of this unequal distribution of pollinator activity is that pollinators create networks of connections between plants in which a few plant receive many visits and many plants receive few visits.
There’s a powerful approach to modelling called dynamic state variable programming, covered in Dynamic State Variable Models In Ecology by Clark & Mangel. I’ll post more about the approach sometime, but for now I wanted to make an example from the book available. The first chapter of the book includes a guide through the creation of a patch foraging model. A fully implemented version is available in True BASIC, but I’ve decided to use R for all of my modelling and analyses.
Until recently, I was able to use journal abbreviations in all of my manuscripts. Consequently, my .bib file contains only abbreviations in the journal field. Now I need to produce some bibliographies with full journal names. With a .bib file you can use macros to handle changing abbreviated names to full names. However, BibDesk cannot use macros. Instead I wrote a perl script that searches through a .bib file and creates a new file with journal abbreviations changed to full names.
I have been investigating issues of ovule and seed development recently. One question that has come up is: How much variation is there in seed size? I had analysed some seed set data for some earlier work with some image analysis software. Consequently I have a large data set of seed area and perimeter for Chamerion angustifolium. A rough look at the data is:
The data set is available as seedSizeData.
The Ecological Detective by Ray Hilborn and Marc Mangel is an excellent source for learning how to analyse ecological data with sophistication. Traditionally, ecological data is analysed from the binary perspective of hypothesis testing. The goal of such testing is to either accept or reject a null hypothesis. Although it is well entrenched in ecological training and publication, this hypothesis testing has repeatedly been attacked by statisticians and many ecologists.
In some recent research (http://public.me.com/mroutley/SIandDichogamy.pdf) I had to make inferences about families based on character states of the species within the family. One approach is to use a simple majority rule. For example, if more than half of the species possess character state x rather than y, then the family can be described as x. However, this approach seemed rather liberal, which led to a 2/3 majority criterion: if more than 2/3 of the species are x, the family is x; If less than 1/3 is x the family is y; otherwise the family is ambiguous.
I have been working through my references and papers trying to regain some control over the literature. Being reintroduced to the tedium of reference management, it seems like there must be a better way to catalogue and organize this important component of research. Ideally, with the Internet and some good citation support from publishers, I would never have to type a citation – just automagically download whatever I need. Obviously this is not currently available.