Potential Datasets For Projects

We want practice with real-world data sets that are the appropriate to build our skills. I strongly believe the best data sets are one you care about / are invested in. But not all of you have those. Here are some data sets for you if you don’t have any data sets that you’re invested in.

These examples are all stolen from Whitlock and Schluter (2020) .

Zika and head size

Zika virus can be spread by mosquitos, sexual contact or from mom to fetus. In 2015 there was an outbreak in Brazil that spread to other countries in the Americas. Small head size (microcephaly) associated with abnormal brain development was frequently reported in newborn babies of infected mothers. Here are data for head measurements of fetuses in pregnant women infected with Zika, taken from ultrasounds between 33 and 36 weeks. A head size between 80 and 94 mm is considered normal for uninfected mothers at this age.

Data link: https://raw.githubusercontent.com/ybrandvain/datasets/master/zika.csv
Read the study.

FIGURE 7.9: Microcephaly image from New England Journal of Medicine. Their legend: Infants with Moderate or Severe Microcephaly Associated with Maternal Zika Virus Infection, as Compared with a Typical Newborn.

Salmon size

After approximately three years as baby salmon become mature and are ready for the ocean. Hendry et al, measured the mass and length of female salmon who have been in the ocean for two or three years. The data are here.

data link: https://whitlockschluter3e.zoology.ubc.ca/Data/chapter02/chap02f2_5SalmonBodySize.csv
Read the paper.

Life at high altitude

Living at high altitude represents some physiological challenges of living with a limited oxygen supply. Human populations in the Andes, Ethiopia, and Tibet have faced these challenges, and adapted. One potential mechanism of this adaptation is to raise the hemoglobin content of blood to get more oxygen. Beall et al measured the hemoglobin content of people from these three populations as well as a control of males living at sea level in America.

data: https://whitlockschluter3e.zoology.ubc.ca/Data/chapter02/chap02e3bHumanHemoglobinElevation.csv, Read the paper.

FIGURE 7.10: A mountain in Tibet from the New York Times

Hearing color

Some people experience one of their senses through another. For example, you might hear the name “Bob” and see grey. Saenz and Koch were interested to see how this type of perception impacted the ability to complete complex multi-sensory tasks. So they compared people with and without this unique type of sensory perception (known as synesthetes) to a group of people without such abilities, on a test involving rhythmic temporal patterns similar to Morse code.
data: https://whitlockschluter3e.zoology.ubc.ca/Data/chapter02/chap02q10Synesthetes.csv
Read the paper.

FIGURE 7.11: Synestheses mix modes of perceptions

Eat less, live longer?

For some reason, restricting food intake often increases lifespan. To see if this was the case, Mattison et al fed 17 rhesus monkeys (7 females, 10 males) a reduced diet with 30% of the normal nutrition, and 17 other rhesus monkeys (8 females, 9 males) a normal nutritious diet.

data: https://whitlockschluter3e.zoology.ubc.ca/Data/chapter02/chap02q35FoodReductionLifespan.csv
Read the paper.

A gene for monogamy?

The gene for the vasopressin receptor V1a is expressed at higher levels in the forebrain of monogamous than promiscuous vole species. To see if expression of this gene influenced monogamy, Lim et al experimentally enhanced V1a expression in the forebrain of 11 males of the meadow vole - a solitary promiscuous species, and compared the percentage of time these and control males spent huddling with a female placed with him (ass a measure of monogamy). data: https://whitlockschluter3e.zoology.ubc.ca/Data/chapter03/chap03q15VasopressinVoles.csv
Read the paper.

FIGURE 7.12: Image of cuddling voles from Newsweek

Running with a lighter load

Male spiders in the genus Tidarren are tiny and weigh about 1 percent as much as females. Just before sexual maturity, males voluntarily amputate one of their two organs just before sexual maturity. Could this maybe allow them to move faster?

data: https://whitlockschluter3e.zoology.ubc.ca/Data/chapter03/chap03e2SpiderAmputation.csv
Read the paper.

FIGURE 7.13: Image of Tidarren from Ramos et al. Their legend A male T. sisyphoides before (A) and after (B) removing a pedipalp. Note the pedipalps overlap in the two-pedipalp condition (A), whereas the one pedipalp is carried in a central position after pedipalp removal (B). (The scale bars represent 1 mm.)

Protected fish

The marine threespine stickleback is a small coastal fish named for its defensive armor. It has three sharp spines on its back, two pelvic spines under its belly and a series of lateral bony plates down its side. The armor seems to reduce mortality from predatory fish and diving birds. In lakes and stream (as compared to the ocean) there are fewer predators, and fish have reduced armor. Researchers hypothesized this difference may mediated by a gene called ectodysin. They crossed marine (M) and freshwater (m) fish to make F1 Mm heterozygotes and crossed these to one another two make individuals who have 0 (mm), 1 (Mm), or 2 (MM) copies of the marine allele at the ectodysin locus.

data: https://whitlockschluter3e.zoology.ubc.ca/Data/chapter03/chap03e3SticklebackPlates.csv
Read the paper.

FIGURE 7.14: Image of benthic and marine sticklebacks

Clarkia pollen movement

How far pollen is carried within a plant population determines which plants are able to mate with each other and therefore has important impacts on the genetic structure of these populations. This dataset features fluorescent-labeled pollen counts on stigmas collected at known distances from a specific labeled pollen donor in a field experiment. Stigmas were collected for three days in each of nine different populations. The dataset also includes the density of flowers within 0.5 m of the plant each stigma was collected from. This is Brooke’s dataset, so you can slack her if you have any questions!

data: https://raw.githubusercontent.com/ybrandvain/datasets/master/clarkia_pollen.csv

FIGURE 7.15: Image of quantum dot pollen labelling

References

Whitlock, Michael C, and Dolph Schluter. 2020. The Analysis of Biological Data. Third Edition.