UNDERSTANDING GENOTYPE AND PHENOTYPE

 

Name:    UNDERSTANDING GENOTYPE AND PHENOTYPE

Activity:                Students will get a bag of shells from two beaches, sort them, identify them and look at variations.

Level:                    3

Developer:         Alberto Mimo                                                                                                   

Site:                       Classroom or Laboratory with access to a computer and excel.

Subjects:             Genetics, statistical analyses.

 

Introduction

Darwin and Russell in the 1800’s were interested in understanding how new species came about. They concluded that somehow random changes in their phenotype were best adapted to an environment or situation and those organisms that did not fit would die out, or lived at a disadvantage because they were not well fitted to the new condition. This is in essence the idea of evolution based on natural selection due to the survival of the best-fitted animal or plant. At the same time, a man named Jean-Baptiste Lamarck theorized that animals evolved by the force of adapting themselves to a new environment and changing their phenotype. Long-neck giraffes get longer necks by trying to reach the leaves on the taller trees. In this lesson, we explore the idea of phenotypic plasticity based on environmental conditions or contact with other species

A living organism’s DNA contains the information that will be transferred to its progeny. Some information is not shown physically or physiologically, but it is all there in their genome. Some of the information is displayed in every organism either in its shape or form or in its physiology. (Read about Gregor Mender,  1822-1884) One is called the organism’s genotype and the other is the organism's phenotype.

Organisms within a species are not always exactly alike, there is a variation within each species that refers back to the exact genome they have. In people, some kids have blue eyes and some dark brown, but this variability has to be all accounted for unless there has been a mutation. Mutation could lead to new species, but that is only when that mutation shows to provide that organism with an advantage. See Darwin and Russel's theory of Evolution.

Variability within one species could have been led by small changes in the habitat, other species' competition, or a predator/ prey relationship. (Anurag A. Agrawal in his paper “Phenotypic Plasticity in the Interactions and Evolution of Species”) Published by the Journal of Ecology in 2001 shows how these changes can be derived from competition, mutualism, predation risk, and parasitism/herbivore or food quality.

Thomas J. DeWitt, Andrew Sih, and David Sloan Wilson in their paper “Cost and limits of phenotypic plasticity” Trends in Ecology & Evolution, 1998, discuss the idea that variations on an organism's phenotype have limits and cost. Some of this cost includes Maintenance and Production of the Phenotypic Change, Information Acquisition Cost, Development Instability, and Genetic Cost, but at the same time, there is a benefit of survival.

Some of the terminologies associated with phenotypic plasticity are: (Phenotypic Plasticity and the origin of diversity. Mary Jane West-Eberhand, Annu. Rev. Ecol. Sust. 1989 20:249-78).

• Alternative phenotypes: Two or more forms of behavior, physiological response, or structure maintained in the same life stage in a single population and not simultaneously expressed in the individual.
• Conditional (or condition – sensitivity): The alternative adopted by a particular individual or at a particular time depends on environmental conditions.
• Allelic-Switch: The alternative adopted by a particular individual depends on the allele(s) present at one or more genetic switch loci.
• Combine switch: The alternative adopted depends on a combination of allelic and environmental factors.
• Polyphenism: The existence of environmental-cued alternative phenotypes in a population.
• Polymorphism: The existence of morphological district alternatives in a population (usually: “allelic-switch alternatives”.

 

Hypothesis

Slipper Shells live at the bottom of the Long Island Sound.  They form a tight community of shells at the bottom of the seawater and are constantly subject to being swept away by the current caused by the incoming and outgoing tides. In areas with narrow channels the effort by the shells to stay in place is greater and in more level areas where the current is less strong the effort of the shells is also less.  The speed of the water at different locations within the Sound changes depending on the site, for example, areas located at the entrance of the sound called the race have stronger currents.

The hypothesis here is that at locations where the speed of the water current is high; shells will transform their shape to be more flat reducing the friction with the water. Shells that live in more tranquil areas will be shaped more bumped or higher in the top. So we have two possible different phenotype shapes on these shells. The idea here is to take measurements and see if we can find differences within collection sites. Have C. fornicata shells a phenotypic plasticity?

Read Phenotypic Plasticity and the Origen Of Diversity. Mary Jane West-Eberhard. Annu. Rev. Ecol . Syst. 1989. 20:249-78

Natural History and Anatomy of the Slipper Shell (Crepidula fornicata L.)

Slipper Shells live out in the bottom of the Long Island Sound. They are found in amazing quantities and compete for habitat with oysters and other organisms. These mollusks stack one on top of the other forming a thick layer. During reproduction, they form clusters where the ones at the bottom are females and the ones on top are males. The eggs are found in sacks that are fertilized in the water and released. These organisms are hermaphroditic, so they change sex as they grow. Starting as males and growing into a female, they live for about 7 to 10 years. You can count the number of growth rings. When they die they are carried away by the tide and the water current. They have very few predators so they are a nightmare to the oyster industry.

A cluster of Slipper Shells from the bottom of the LIS (Long Island Sound) mixed with mud from the site. These shells were collected using a drudge from a science vessel. (Next 3 pictures)

                  

 

Mud and shells covers the see floor

 

Some are on top of other; the lower one is a female

See diagram for their anatomy.

 

Anatomy of the slipper shell

Slipper shells do not move much, they crawl at the beginning but once they find the perfect spot they attach permanently. Their typical food is plankton and other particulate organic matter. Their growth rate is between 0.04 to 1.11 mm/day.

Their abundance can be up to 4,770 individuals per m2. They prefer a substrate made up of small boulders, and muddy gravel and they live at the sublittoral fringe where they are sheltered. Their preference is a salinity of 18 to 40 milligrams per centiliter and a water flow of 1 to 3 knots.

Sites for your Collection

You can collect anywhere there are slipper shells but I have included three sites that are located somewhere south of the state, Coastal Center at Milford Pont, a north site at Hammonassett Beach State Park in Madison, and one additional site at the Race of the Long Island Sound at Watch Hill Cove in Rhode Island. It would be best to do this research on-site without taking the shells to school. These slipper shells form the natural habitat of the area.

 

Sites for your Collection

You can collect anywhere there are slipper shells but I have included three sites that are located somewhere south of the state, Coastal Center at Milford Pont, a north site at Hammonassett Beach State Park in Madison and one additional site at the race of the Long Island Sound at Watch Hill Cove in Rhode Island. It would be best to do this research on site without taking the shells to school. These slipper shells form the natural habitat of the area.

Site One

Costal Center at Milford Point

 

Site two

Hammonasset Beach State Park Meigs point

 

 

Site three

Watch Hill Cove, in Rhode Island

Where do the dead shells come from in your collection?

Where do the dead shells come from in your collection?

Before you start your collection you will need to acquire a Scientific Collecting Permit for marine organisms from the CT Department of Energy and Environmental Protection. You can get the forms at their website (https://portal.ct.gov/DEEP). If you intend to take all the measurements at the beach you do not need to get a permit. The scientific collecting permit will cost you $25 and you have to fill out the correct forms.

The shells that you will collect are found on the beach. These are dead shells that were living in the water near your location that for some reason died and washed into the beach by the tides or storms. They are the perfect habitat for Piping Plovers

You need to collect the shells when it is low tide because we also want you to collect a cluster of live shells deposited in the intertidal area by the tide. There should be between 3 and 7 shells that you will use to learn more about the anatomy of the slipper shells. The other slipper shells you are collecting are just shells without the actual animal on them. Just walk close to the water's edge and look for a cluster. There will be several, take only one and throw the others into the water.

Place the cluster into a jar with 70 % alcohol and label it.

 

 

Place the cluster into a jar with 70 % alcohol and label it.

Species: Crepidula fornicata L.

Date:

Location:

Your school name:

Inventorying the beach

Based on the current literature, there are 3 different slipper shells in the Northeast; Crepidula convexa, convexa which is brown with striped or dots of reddish brown, up to 1.3 cm. long, and is less common than other slipper shells; attaches to shells and rock and other hard objects.  There is the Crepidula plana, also known as eastern white slipper shell, pearly white up to 3.3 cm. long often found attached to the underside of horseshoe crab shells and inside large snail shells occupied by hermit crabs. And finally, there is Crepidula fornicata.

Shells accumulated on the beach

Shells accumulated on the beach

Close up of shells

 

Shells clearly left by the tide

Variety of shells on the beach

 

In addition to collecting the slipper shells, we also need to complete an inventory of other organisms found in the same area. A sandy beach about 15 ft. from the high tide line and about 75 feet in linear length parallel to the beach. Remember that many small invertebrates live buried in the sand. Bring a small shovel.

To do this just get several small buckets or plastic bags, one per every two students, and collect just one good specimen, in good shape of every species you see. Sit by the side of the beach and identify the organisms. Make a list. Then take a picture and let them go.

Use the following list to write the length and height of two sets of shells of 45 individuals. Count the rings of 10 shells and each ring is one year. Write the information on the size of this list.

 

To do this just get a number of small buckets or plastic bags, one per every two students and collect just one good specimen, in good shape of every species you see. Sit by the side of the beach and identify the organisms. Make a list. Then take a picture and let them go.

 

Shell number	Age

 

Length and Height measured in mm.

 

Length	Height

 

Measuring each shell

Measure each shell in millimeters using calipers.

 

Length: Largest length of the shell.

 

 

 

 

 

 

 

Height: Place the calipers touching both sides of the shell and the top of the shell.

 

Doing the analyses

Doing the analyses

To show you what kinds of things you can do, here is an example:

1. I went to West Haven to a small beach and collected shells then I went to Hammonnaset State Park and did the same thing, counted them, measured them, and calculated the ratio of height to length. These are the measurements of the shells.

2.        

	Shells A West Haven
Lenth mm	Height mm	Ratio
3788	890	0.23
2556	965	0.38
2757	1052	0.38
2646	1080	0.41
2563	1084	0.42
2418	1110	0.46
2754	1119	0.41
3028	1157	0.38
2927	1179	0.40
3075	1186	0.39
3108	1192	0.38
2927	1200	0.41
2941	1211	0.41
2896	1226	0.42
3004	1228	0.41
2668	1247	0.47
3213	1249	0.39
2786	1257	0.45
2750	1259	0.46
3001	1275	0.42
2952	1278	0.43
2796	1280	0.46
2436	1280	0.53
3307	1297	0.39
2807	1298	0.46
3031	1306	0.43
3398	1307	0.38
3022	1319	0.44
2809	1327	0.47
2774	1336	0.48
2806	1337	0.48
3089	1355	0.44
2908	1368	0.47
3010	1390	0.46
3170	1398	0.44
3100	1420	0.46
3288	1447	0.44
3395	1450	0.43
3231	1490	0.46
3439	1500	0.44
3715	1527	0.41
3425	1532	0.45
3300	1554	0.47
3164	1778	0.56
3625	1791	0.49

 

 

	Shells B Hammonasset
Length mm	Height mm	Ration
2266	616	0.27
2673	682	0.26
2556	952	0.37
2591	958	0.37
2521	982	0.39
2660	990	0.37
3289	991	0.30
3226	1010	0.31
2860	1057	0.37
2585	1084	0.42
2770	1103	0.40
2693	1108	0.41
3153	1110	0.35
2802	1117	0.40
3170	1141	0.36
2985	1143	0.38
2714	1151	0.42
2634	1156	0.44
2890	1169	0.40
2814	1177	0.42
2984	1202	0.40
3226	1208	0.37
2693	1211	0.45
2855	1211	0.42
2971	1245	0.42
2916	1272	0.44
3036	1287	0.42
2953	1288	0.44
3112	1290	0.41
2971	1296	0.44
3288	1306	0.40
2986	1307	0.44
2952	1327	0.45
3296	1328	0.40
3202	1345	0.42
3446	1353	0.39
3033	1363	0.45
3482	1374	0.39
3161	1388	0.44
3353	1397	0.42
3171	1453	0.46
3249	1476	0.45
2984	1512	0.51
3454	1569	0.45
2600	1651	0.64

 

3.       Next I organized them according to the height, from smaller to larger. This is how you do this is in excel:

4.       Go to data

5.       Select sort:

Click OK:

And you are done; all the numbers are lined and sorted by height from lower to largest

6.       Now you can make a line graph showing the progression of height on all these shells.

 

As you can see there are not too many shells that are flat in either sample. If we take the next sample we get:

No flat shells either

Using statistics to compare numbers

We will compare the height of the shells. If the two sets of shells are similar in height then there is not much difference between the two populations. If the shells height is significantly different then there is a difference between the two populations. To do this we will use the t- test in statistics. The t -test is simple to use and we will use the null hypothesis to learn from the results.  The null hypothesis says that if our t value (we will calculate that using excel) is higher than the t Critical Value a .05 percent difference then we do reject the null hypothesis and determine that the two sets of heights are different and come from the different populations, but if the t value is lower  than .0 5 percent then we do not reject the null hypothesis and determine that the two sets are from the same population the same and are comparable.

To do this is in excel do the following:

1.       Line up the two samples of a blank sheet; use the height of the shells

A	B
890	616
965	982
1052	952
1080	1084
1084	958
1110	1651
1119	1156
1157	990
1179	682
1186	1108
1192	1211
1200	1151
1211	1103
1226	1117
1228	1177
1247	1211
1249	1057
1257	1169
1259	1272
1275	1327
1278	1288
1280	1245
1280	1296
1297	1202
1298	1512
1306	1143
1307	1307
1319	1363
1327	1287
1336	1290
1337	1110
1355	1388
1368	1141
1390	1453
1398	1345
1420	1208
1447	1010
1450	1476
1490	1306
1500	991
1527	1328
1532	1397
1554	1353
1778	1569
1791	1374

2.       To use excel  go to data, look at the far right hand corner and choose data analyses.

3.       This will come up

4.       Choose t-Test paired, hit OK

5.       Fill the data for the two shell heights and it will automatically do all the calculations.

6.       Press OK to the next pop-up

 

7.       These are the results for the t-test

Mean	1300.689	1207.911
Variance	32003.49	41482.49
Observations	45	45
Pearson Correlation	0.568208
Hypothesized Mean Difference	0
df	44
t Stat	3.474853
P(T<=t) one-tail	0.00058
t Critical one-tail	1.68023
P(T<=t) two-tail	0.001161
t Critical two-tail	2.015368

 

The t value is 3.47 and the critical value is 2.01 Therefore the t value is larger than the critical value and we reject the null hypothesis and conclude that there is a difference between the two sets of numbers of shells heights. Maybe there is some Lamarckism on the development of the shells. Their Phenotype may be malleable.

Part two of analyses

 

We took two measurements from each shell: The length and the height. Using these two numbers we calculated a ration, by dividing the height by the length. This is a number between 0 and 1. If the height was the same as the length then the answer would be 1.0.  Any height smaller that length is a decimal point number. The lower the height the larger the answer up to 1.0.

Let’s compare the list of ratios and see what we get for a t-test value.

Shells A   Shells B

A	B
0.23	0.27
0.38	0.26
0.38	0.37
0.41	0.37
0.42	0.39
0.46	0.37
0.41	0.3
0.38	0.31
0.4	0.37
0.39	0.42
0.38	0.4
0.41	0.41
0.41	0.35
0.42	0.4
0.41	0.36
0.47	0.38
0.39	0.42
0.45	0.44
0.46	0.4
0.42	0.42
0.43	0.4
0.46	0.37
0.53	0.45
0.39	0.42
0.46	0.42
0.43	0.44
0.38	0.42
0.44	0.44
0.47	0.41
0.48	0.44
0.48	0.4
0.44	0.44
0.47	0.45
0.46	0.4
0.44	0.42
0.46	0.39
0.44	0.45
0.43	0.39
0.46	0.44
0.44	0.42
0.41	0.46
0.45	0.45
0.47	0.51
0.56	0.45
0.49	0.64

 

Results for the t- Test

t-Test: Paired Two Sample for Means
	Variable 1	Variable 2
Mean	0.432222	0.407333
Variance	0.002504	0.003643
Observations	45	45
Pearson Correlation	0.570153
Hypothesized Mean Difference	0
df	44
t Stat	3.21146
P(T<=t) one-tail	0.001235
t Critical one-tail	1.68023
P(T<=t) two-tail	0.00247
t Critical two-tail	2.015368

 

 

T=Value =3.21
Crit -t = 2.01
T value is > Critical  -t
Reject the Null Hypothesis

 

By using the t-test on both calculations we get the same results. The shells from site A are not the same as from site B therefore each individual slipper shell grows at different rates.  In cases such as these we should continue the research by setting up an experiment that includes a control group. Additional information could help to answer some questions such a where the shells come from and what is the water current at that site.