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Thursday, May 16, 2013
Friday, December 14, 2012
Friday, November 16, 2012
Rinse, lather, rep()
In some of our assays we sort flies by size, and record the number of individuals found in each sieve. When the data is entered, it might look like this (ht Conor Delar)
But how can we actually compare (in R), for instance, the weight of mated and unmated females from the sample? We could do contingency tables to see if the frequency of counts in the two groups, but what if we wanted to compare the mean "girth" of these two groups? You could tediously enter the size of each individual (e.g. for unmated females, 1420,1420,1420,1356,1313,1313 etc...), but there must be a better way
Here, I will show how we can use the rep() function
Where I will specifiy in the first parameter what values I want repeated, and then for the second how many times I want it repeated.
> deLHM2 Assay2 Size.um. Male.Unmated. Female.Unmated. Male.Mated. Female.Mated. 1 LHm (L2) 1420 1 3 1 3 2 LHm (L2) 1365 4 1 2 3 3 LHm (L2) 1313 1 2 1 3 4 LHm (L2) 1262 2 4 0 1 5 LHm (L2) 1214 6 2 3 0 6 LHm (L2) 1167 3 8 3 3 7 LHm (L2) 1122 7 21 0 3 8 LHm (L2) 1079 4 10 3 0 9 LHm (L2) 1038 2 7 0 2 10 LHm (L2) 998 4 8 0 011 LHm (L2) 948 3 6 0 0
But how can we actually compare (in R), for instance, the weight of mated and unmated females from the sample? We could do contingency tables to see if the frequency of counts in the two groups, but what if we wanted to compare the mean "girth" of these two groups? You could tediously enter the size of each individual (e.g. for unmated females, 1420,1420,1420,1356,1313,1313 etc...), but there must be a better way
Here, I will show how we can use the rep() function
Where I will specifiy in the first parameter what values I want repeated, and then for the second how many times I want it repeated.
> deLHmFU <-rep(c(deLHM2$Size.um.),c(deLHM2$Female.Unmated.)) > deLHmFM <-rep(c(deLHM2$Size.um.),c(deLHM2$Female.Mated.)) > deLHmFU [1] 1420 1420 1420 1365 1313 1313 1262 1262 1262 1262 1214 1214 1167 1167 1167 1167 1167 [18] 1167 1167 1167 1122 1122 1122 1122 1122 1122 1122 1122 1122 1122 1122 1122 1122 1122 [35] 1122 1122 1122 1122 1122 1122 1122 1079 1079 1079 1079 1079 1079 1079 1079 1079 1079 [52] 1038 1038 1038 1038 1038 1038 1038 998 998 998 998 998 998 998 998 948 948 [69] 948 948 948 948 > deLHmFM [1] 1420 1420 1420 1365 1365 1365 1313 1313 1313 1262 1167 1167 1167 1122 1122 1122 1038 [18] 1038 >
Now I could proceed with the correct analyses (in this case due to non-normality of distributions, a Mann-Whitney test and a Cliff's delta) to compare the two groups.
Tuesday, October 23, 2012
Male genotype influences female reproductive investment in Drosophila melanogaster
Pischedda,
A., Stewart, A.D., Little, M.K. & Rice, W. 2011. Male genotype influences
female reproductive investment in Drosophila
melanogaster. Proc Biol Sci 278:2165-72.
This
study is the first form of direct evidence that males vary genetically in their
influences on female fecundity, egg sizes and overall female investment in reproduction.
Female Drosophila melanogasters were
mated with males from 10 different ‘worldwide lines’ (to account for genetic
variation) for 2 hours. After this time, females were placed into individual
oviposition vials for 22 hours, followed by transfer into a new oviposition
vial for another 22 hours. After that, all of the females who mated with males
from the same worldwide line were put into the same egg laying chamber and
allowed 4 hours to oviposition. Eggs from the chamber were then photographed
and measured. Results found that a male’s population of origin did not affect
egg size, but did affect females' fecundity in the first 22 hours after mating.
The genotype of the males within a population did however account for some of
the variation seen in egg size. This study is very useful to me, as it relates
directly to the question at the forefront of my research. It does not however
address the mechanisms causing the variations seen, such as female cryptic
choice or manipulations by males, so leaves room for further investigation and
analysis.
Females increase egg deposition in favour of large males...
Evans,
J.P., Box, T.M., Brooshooft, P., Tatler, J.R. & Fitzpatrick, J.L. 2010. Females
increase egg deposition in favour of large males in the rainbowfish, Melanotaenia australis. Behavioural
Ecology 21:465-469.
Through
this study, the researchers address how sexual selection favours flexibility in
maternal investment, using rainbowfish as a model species. Females were
individually placed into large tanks, with both a small and a large male that
were confined to containers within the tank. First, they observed the amount of
time the female spent within one body length of the containers containing the
males. After four days, either the large or the small male was released into
the tank with the female, and they were allowed 4 more days to interact. The
eggs produced by the female during this time were collected, counted and
photographed. Results showed that during the initial 4 days, females spent 70%
of their time within one body length of the large male, and they produced two
times as many eggs when they mated with the large male (large males are phenotypically
preferred). The variation in maternal investment defined within this study is
important for understanding the effect of a mate’s phenotype on maternal
investment, but it fails to address the effect of a mate’s genetic identity.
While I continue researching for my thesis project,
I’m realizing more and more not to disregard ‘old’ articles just because they
are, well, ‘old’. 3 articles by Partridge and colleagues from the 1980s have
proven to be of great use to me in understanding costs associated with mating,
and how choice influences all individuals in the equation (i.e. males, females
and subsequent offspring.) The following are annotations for these articles:
Fowler, K. & Partridge, L. 1989. A cost of
mating in female fruit flies. Nature 228:760-761.
This article looks at the costs a female endures
when mating with a male in the model organism Drosophila melanogaster. This is done through mating experiments
where virgin females were subjected to either a group of males who all were
capable of mating (high-mating) or a group of males where only one of the males
was actually capable of mating (low-mating). Males in the low-mating scenario
still displayed courting behaviours towards females, but had genitalia removed
so they could not actually mate. Results showed that the females who were
exposed to high-mating scenarios had significantly lower life spans then those
exposed to low-mating. Although this may be a consequence of injury, parasites,
or effects of sperm, it still is related to the actual process of mating. These
results therefore have profound effects on the future reproduction success of
these females. These conclusions are beneficial for me to understand in order
to predict then why a female may alter her investment in the subsequent
offspring, depending on the costs she has endured through mating.
In this experiment, larval survival rates are used
as a measure of D. melanogasters’ offspring
fitness. Males and females are exposed to treatments in which they have the
ability to choose mates (cages with many individuals), or where they are unable
to choose their mate (randomly selected female exposed to single randomly
selected male). Results show higher
fitness in subsequent offspring (i.e. more offspring when exposed to competing
larvae) of parents who did have choice in who they mated with, compared to
those who did not. The author discusses possibilities of the genetics of these
individuals influencing choice, and how if there are differences in paternal
and maternal genes, it can lead to fitter offspring because of heterozygosity.
This information is relevant to my research, because it is important to
understand the how the identity of the parents can have a significant affect on
their offsprings’ fitness, especially since the flies in my experiment are
exposed to a no-choice treatment.
Partridge, L. & Farquhar, M. 1981. Sexual
activity reduces lifespan of male fruit flies. Nature 294:580-581.
Partridge and Farquhar study how mating affects the fruit flies’ lifespan by exposing males (Drosophila melanogaster) to different
numbers of receptive females and comparing their longevity with control groups.
Males in experimental groups were exposed to 1-8 virgin females a day, while
males in the control groups were exposed to females who had already been
inseminated and therefore would not remate, or with no females at all. Males
exposed to the highest number of receptive females (i.e. 8 virgins per day) were
shown to have the lowest longevity compared to males who were exposed to fewer
receptive females (slightly higher longevity), and control groups (greatest
longevity). Understanding the costs associated with mating can help us to
understand differences in parental investment of their offspring.
Although these articles are not exactly directly
related to my research, the basis of mate choice and affect on all of the
individuals involved is very useful background knowledge to have. It allows me to
better understand costs of mating behaviours, and hypothesize therefore why
differences in parental investment based on the identity of mates may have
adaptive benefits.
Friday, October 5, 2012
Long Lab Group Photo October 2012
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