Sedgwick Reserve, where I study pollen and seed dispersal in Quercus agrifolia and Q. lobata.

Intron length distributions within the 5'UTR, coding sequence, and 3'UTR of Arabidopsis thaliana genes.

Flower of Delonix regia

Pollen from Delonix regia stained to estimate viability; viable grains are dark blue, nonviable grain is pale blue.

Sork Lab main page

Douglas G. Scofield, Ph.D.

I no longer maintain this webpage. My site is now found at http://sites.google.com/site/douglasgscofield. You will be redirected there in 10 seconds.

Research Associate,

dgscofield@ucla.edu
douglasgscofield@gmail.com (preferred)

+1 (310) 794-1431 (office)
+1 (786) 514-9141 (mobile)
+1 (310) 206-0484 (fax)

Another version of this webpage can be found at http://sites.google.com/site/douglasgscofield.

Research Associate, University of California, Los Angeles, 2009-present
Postdoctoral Fellow, University of California, Los Angeles, 2007-2009
Postdoctoral Fellow, Indiana University, 2004-2007
Ph.D., Biology, University of Miami, Coral Gables, Florida, 2004
B.S., Botany, Florida Atlantic University, Boca Raton, Florida, 1997 (summa cum laude)
B.S., Computer Science, Michigan State University, East Lansing, Michigan, 1988

Click here for my curriculum vitae (PDF format).

I am a broadly trained plant evolutionary biologist working at the interface of theory and empirical biology. My research covers three main areas united by the application of mathematics and modeling to evolutionary biology:

• Consequences of somatic mutation in plants
• Evolution of gene and genome structure and transcript processing
• Pollen and seed dispersal in plant populations

I originally trained as a computer scientist with a minor in mathematics, and worked as a software engineer for several years in south Florida. The increased pace of botanical life and death at the edge of the tropics, in comparison to that of the temperate flora in my native Michigan, awoke the sleeping biologist within me. I returned to school, and was naturally drawn toward research in which I could apply my quantitative and programming skills. Because of my path toward research biology I also have a strong interest in natural history, especially with respect to plants and birds, and in teaching people the wonders of our natural world.

Consequences of somatic mutation in plants

Unlike nearly all animals, plants violate Weismann's doctrine for the separation of germline and soma. In animals, the germline - the cell lineage giving rise to gametes - is segregated early in development from the cell lineages which give rise to the soma, that is the rest of the body. These germline cells remain relatively isolated from the body for the remainder of the animal's life. Any mutations that occur outside of the germline cannot be inherited through gametes.

In plants, which have meristematic growth, this is not at all the case. When plants create gametophytes in the form of pollen grains and ovules, the gametes contained within are the descendents of meristematic cell lineages that have ultimately given rise not only to the gametophytes but also all of the airborne tissues of the plant. Thus gametes may be produced from cell lineages that are comparatively active and may have undergone dozens to hundreds to hundreds of thousands of potentially imperfect mitoses which may give rise to errors during DNA replication or genomic damage during interphase. If these somatic mutations persist within the cell ineage, they may be inherited through gametes.

Sources of de novo mutation load due to somatic mutation in a growing plant
Flower locations are indicated in red, and the slope of the line is equal to the somatic mutation rate Um.

I use a combination of fieldwork, labwork, theoretical modelling and meta-analysis to develop a general model explaining stature-based differences in evolutionary constraints on plant mating systems. The Φ model of plant evolution assumes that the per-generation mutation rate has two primary components. The first component is the rate of mutations occurring during meiosis (U_e), including errors during DNA replication, insertions/deletions due to unequal crossing-over, etc. The second component is the rate of mutations occurring during each mitotic division within a cell lineage (U_m). The total contribution of mitotic mutations is a positive function of Φ, the number of mitoses that occur in a plant's lifetime from zygote to gamete production. The association between the Greek letter Φ and mitosis is reflected in its resemblance to a dividing cell.

Some general predictions of the Φ model include: (1) correlations between Φ and any plant traits that depend upon mutation rate; (2) the importance of somatic mutation increases with plant size (and hence Φ); and (3) selection arising from somatic mutation strengthens with plant size.

With respect to mating systems evolution, the Φ model predicts that while small-statured (`low-Φ') plants such as herbs are free to have a mating system that includes selfing, large-statured (`high-Φ') plants such as trees have a per-generation mutation rate that is too high to allow for selfed progeny to reach reproductive maturity under nearly all natural conditions. This occurs because inbreeding depression, the reduced fitness of selfed vs. outcrossed progeny, is maintained at a higher level and is more resistent to being decreased via selection when the mutation rate is higher, as it is expected to be in large-statured plants. For further details, see Scofield and Schultz (2006).

Population genetic data supporting the Φ model of plant evolution
Data are adult inbreeding coefficient (F) vs. progeny selfing rate (S) measured in the same population of a variety of species of (a) small-statured, `low-Φ plants, and (b) large-statured, `high-Φ' plants. All data from published studies. Lines represent model fits as determined by several genetic models for the evolution of inbreeding depression. Figure from Scofield and Schultz (2006).

Because Φ is a critical component of the model, I've developed methods for estimating Φ itself. I started by estimating Φ in the tropical legume Delonix regia using mature medial pith cells in twigs. For further details see Scofield (2006).

Distribution of medial pith cell sizes (Φ per meter) in Delonix regia

Based on predictions of the Φ model, I developed two techniques for estimating somatic mutation parameters in large-statured plants: the autogamy depression test (first proposed by Klekowski in his 1988 book), which relies upon fitness differences between selfed progeny created from gametes belonging to different cell lineages within the same tree; and the flower position test, which relies upon fitness differences occurring at different flower positions within the same cell lineage. From these fitness differences, and the variance in fitness differences among experimental trees and branches, the rate and selection and dominance coefficients of somatic mutations may be estimated. For further details, see Schultz and Scofield (2009).

Estimating somatic mutation parameters via the autogamy depression test...
Autogamous (within-flower) selfed progeny are created via pollination of a flower with its own pollen, while geitonogamous (between-flower) selfed progeny are created via pollination of a flower with pollen from a different flower borne on a different primary branch. If somatic mutation is non-negligible, then fitness of progeny resulting from autogamy (WA) will be lower than fitness of progeny resulting from geitonogamy (WG) with the fitness difference increasing with the number of cell divisions separating the cell lineages involved in geitonogamous pollination (Φi). This is expected because a higher number of de novo somatic mutations are shared by the ovules and pollen grains from the same flower than ovules and pollen grains from different branches within the same tree.
... and the flower position test
Autogamous progeny are created within flowers at two positions within the same cell lineage. These positions have an ancestor-descendant relationship that is either indirect (left) or direct (right). If the effects of somatic mutation are not negligible, then the difference in fitness between flowers at basal (Wai) and apical (Waj) positions within the same cell lineage is expected to be a function of the number of cell divisions (Δ) separating the basal and apical positions. This fitness difference is expected because flowers at more apical positions within a cell lineage have had a greater opportunity to accumulate somatic mutations than have flowers at more basal positions.

Evolution of gene and genome structure and transcript processing

My first post-doctoral position was the study of gene and genome evolution with Michael Lynch at Indiana University. My research projects included the first thorough examination of the natural history and evolution of introns within untranslated regions of genes (UTRs), for which I received a NSF Postdoctoral Research Fellowship in Biological Informatics (DBI-0434671). The 5' and 3' UTRs which bracket the protein-coding sequence (CDS) are fundamental to the structure of every eukaryotic gene. However, the natural history and evolutionary dynamics of introns in UTRs have been largely unexplored. I work expand our knowledge of UTR introns through several interrelated goals: (1) summaries of basic natural history information for UTR introns; (2) development and testing of hypotheses concerning intron evolution within UTRs; (3) the estimation of UTR-specific rates of intron gain and loss in separate evolutionary lineages, and development of new analytic techniques to estimate lineage-specific rates of character evolution; (4) the determination of patterns and constraints on sequence evolution within UTR introns; and (5) the creation of a publicly-available database of UTR intron information. To address these research goals, I used a combination of bioinformatics techniques, theoretical modelling and extensive computer simulation.

Figure: Median intron size throughout the 5' UTR and CDS of four model organisms. I proposed an evolutionary model that explains the increased size of introns in the 5' UTR and the sharp drop in intron size at the 5' UTR-CDS boundary via differing strengths of selection against intron splice site shifts within the 5' UTR and CDS, arising from sequence constraints and the presence of potentially deleterious premature start codons (uAUGs) upstream of the true Start codon. Figure from Hong, Scofield and Lynch (2006). 23:2392-2404).

Pollen and seed dispersal in plant populations

Pollen and seeds represent the only opportunities plants have to move their genes in the landscape. In this research area, I focus on both analytic and empirical approaches to studying pollen and seed dispersal in plant populations. I work with two oak species, Quercus agrifolia and Q. lobata. In oaks, pollen is wind-dispersed while seeds are dispersed by a variety of animals. My dispersal projects include:

1. Comparative forabing behavior of acorn woodpeckers on Quercus lobata. In collaboration with undergraduate Brian Alfaro, I compared the foraging behavior of acorn woodpeckers on Q. lobata between bird groups at two California oak savanna-woodland sites. We compared seed source diversity within and between granaries at both sites as compared our indirect genetic results to those obtained from direct observations the same year at one site. We also found that acorn woodpeckers preferentially locate territories containing a preferred density of Q. lobata trees which somewhat higher than the overall density of Q. lobata at one site and somewhat lower than the density at the other site.
2. The consequences of individual variation in dispersal patterns. Individuals which disperse pollen and/or seeds within populations may vary not only in their fecundity but their dispersal ability – the relative densities of pollen/seeds at varying distances away from the source. Via simulation studies, I have established the extent to which individual variation in dispersal biases estimates of dispersal kernels and predicted frequency of long-distance dispersal events. I developed an analytic approach using mixed-effects models which I showed reduces bias in both kernel estimates and predictions of long-distance dispersal.
3. Together with graduate student Pam Thompson, I am synthesizing datasets representing the foraging behavior of acorn woodpeckers across multiple years and multiple oak species. We are asking how consistently acorn woodpeckers forage from the same trees and same spatial extent between years and between Quercus species; how acorn woodpecker foraging patterns respond to year-to-year variation in acorn availability; and the extent to which acorn woodpeckers forage optimally from Quercus when filling their central-place granary given acorn availability and already-established energetic and nutritive content of acorns from each species.