LABORATORY EXERCISE 5. Evolutionary relationships (8%)

Introduction

A main goal of evolutionary biologists is to understand the evolutionary relationships among different organisms, and this can sometimes be accomplished by identifying traits that are shared across species.  There are countless examples of organisms having similar traits. Even organisms that are seemingly very different can have similar traits. For example, wings on birds and insects are similar traits on very different organisms. Traits can be similar for one of two reasons: they can be ancestrally derived (that is, present in a shared ancestor and appear in contemporary organisms due to shared evolutionary history), or due to convergent evolution, where a similar trait evolves in separate lineages due to similar selection pressures favouring that trait. A trait that is ancestrally derived is called a synapomorphyand one that is similar due to convergent evolution is called a homoplasy.Wings on birds and insects are an example of a homoplasy as they are similar due to similar selection pressures and not due to shared evolutionary history; this type of trait does not tell us which species are most closely related. On the other hand, the forelimbsof mammals represent a synapomorphy as the underlying bones in, for example, humans, dogs, and whales, are the same due to evolutionary history, despite the functions of those forelimbs being very different; this type of trait can help us identify evolutionary relationships.

We can infer whether traits are likely to be homoplasies or synapomorphies using phylogenetic trees. We can group organisms based on values of a particular trait (e.g., relative size or presence/absence) and then examine whether groups based on trait values align with what we already know about evolutionary relationships between organisms.

Procedure

The goals of this lab are to 1) reconstruct a phylogenetic tree of several different bird species in order to illustrate their evolutionary relationships to one another based on five different traits, 2) provide a hypothesis (with rationale) about whether each trait is a homoplasy or a synapomorphy, 3) provide a hypothesis (with rationale) of the role that natural selection may have played in the evolution of each trait; 4) search the primary literature* for relevant examples of natural selection.

*Primary literature refers to publications that convey the results of original research, most commonly journal articles.In comparison, secondary literature summarizes the results of research that others have done, for example review articles and textbooks.

Part I.Traits, tables, and ratios

In the Blackboard folder for this lab, you will find a spreadsheet of raw data you will use for this lab. The data are on 14 species of bird. You will use five traits (note, there are more than five in the data file) to try and infer evolutionary relationships between these species. Three of the traits are selected for you (i.e., you have to use them) and are detailed below. You may choose the other two (see options in the data file).

1. Trait 1: Beak shape (columns B to D in spreadsheet).Data in the data file includethe maximum length and the maximum width of the beak of each bird. You will calculate the ratio of beak length to beak width (i.e., divide beak width by beak length) to get an idea of ‘beak shape’. Higher values indicate long, narrow beaks and smaller values indicate shorter, boarder beaks. In table 1 below, record two things: i) the ratio of beak length to beak width (from column D in the data sheet), and ii) the ‘bin’ that you put the value into so that you have discrete traits (e.g., narrow beak vsbroad beak vs intermediate).
2. Trait 2: Wing:tail length (columns E to G in spreadsheet).Data in the data file include wing length and tail length of each bird. You will calculate the ratio of wing length to tail length (i.e., divide tail length by wing length) to get an idea of wing length relative to tail length. Higher values indicate longwings and smaller values indicate short wings. In table 1 below, record two things: i) the ratio of wing length to tail length (from column G in the data sheet), and ii) the ‘bin’ that you put the value into so that you have discrete traits (e.g.,long wings vsshort wings vs intermediate wings).
3. Trait 3: Relative leg length (columns H to J in spreadsheet).Data in the data file includetarsus (leg)length (Figure 1) and body length of each bird. You will calculate the ratio oftarsus length to body length (i.e., divide body length by tarsus length) to get an idea of relative leg length. Higher values indicate long legs and smaller values indicate short legs. In table 1 below, recordtwo things: i) the ratio of tarsus length to body length (from column J in the data sheet), and ii) the ‘bin’ that you put the value into so that you have discrete traits (e.g.,long legs vsshort legs vs intermediatelegs).

The final two traits are your choice. Think about traits that might be evolutionarily important. These could be morphological, behaviour, or life history traits. There are extra traits included in the data set. You can use those or you are welcome to use other traits based on what you know or what you look up about the species. If these traits are described by values (e.g., a range of numbers), as with Traits 1-3,include the raw data (you will have to add a column to ‘Table 1 continued’ and also write in Table 1 the discrete value (the ‘bin’) that you assigned foreach trait similar to what you did for Traits 1, 2, and 3.To use a non-bird example, if you were recording the number of flowers that is typically produced by a single plant in that species, report 5-7 flowers, but also turn it into a discrete value in comparison with the other 13 species (e.g., large vs intermediate vs small number of flowers per plant).

Figure 1:Drawing showing the tarsus (lower leg) of a bird.

Use the data in the Raw data file posted to Blackboard to fill in the table below (table continued on next page, too). An example has been included for you based on the data in the EXAMPLE row in the posted data file. I chose the ‘bin’ level based on the value in the ratio columns (i.e., the yellow columns – columns D, G, and J – in the data file). For example, Trait 1 ratios for all the birds ranged from 0.94 to 9.47. Smaller values mean short, broad peaks and larger values mean long, narrow beaks. The hermit thrush value of 2.41 is in the middle, so I called it an ‘intermediate’ beak. Once you calculate all your ratios, YOU decide how to divvy up the species into bins. Note, that you re-start making bins with every trait (i.e., a bird doesn’t have to be in the same level of bin for each trait)

Table 1: STUDENTS WRITE YOUR OWN CAPTION (/15)

Table 1 continued. Enter the data from the posted data file for whatever two other traits you use. Fill in the names of the traits and the values. These SHOULD be copy-pasted from the provided data. Your TA will need them to grade your work.

Part II.Phylogenetic trees, homoplasies,and synapomorphies

In this section you will generate six phylogenetic trees.Each of the first five trees will be based on one of the five traits that you recorded in Table 1.Use the discrete traits (i.e., the ‘bins’, e.g. small, medium, large, etc) instead of the raw numbers.Construct your trees by grouping together species that have the same trait.Your trees may not all look the same. Use a piece of scrap paper to figure out your trees before copying your final version into the boxes below.

NOTE, you CAN submit hand-drawn trees. You are to take photos/scans of the trees and place them in the appropriate box below. Your trees MUST be legible and upside-right or they will receive a grade of 0.

Once you have made your first 5 trees, make Tree 6 based on the actual taxonomic relationships of the bird species. To do this, look up the Order and Family of each species (you already have the genus and species) and then make a tree grouping species within genera, genera within families, and families within orders.

Then, compare each of your first five trees to Tree 6.Study eachtree carefully to determine whether the groupings based on the trait (Trees 1 to 5) are similar to the groupings based on taxonomy (Tree 6). Identify whether each trait appears to be a homoplasy or a synapomorphy.In each case, explain the basis for your conclusion.

Part III. Natural selection.

Propose a hypothesis for each trait which could explain the evolution of that particular trait, and include some rationale for your hypothesis which explains why you came up with this hypothesis. Your rationale should include a brief discussion of why particular traits were likely selected for, i.e., why they would have increased fitness. For example, if you hypothesized that furbies have different coloured fur depending on which predators are common in a particular area, your rationale could be that furbies that can camouflage from common predators would survive better and leave more offspring (therefore, have higher fitness). For each hypothesis, find a reference from the primary literature which at least partly supports your statement. Include a statement of the relevant finding from the reference and the reference itself. Your example from the literature does NOT have to be about one of the species of birds we have included here.

For example, if you hypothesized that furbies have different coloured fur depending on which predators are common in a particular area (as above), find a reference which demonstrates that fur colour for at least some taxa has evolved in response to predator cues. State this main finding from the paper and include the reference (in the format required for this course).IMPORTANT NOTE: You are to summarize/paraphrase this main finding. You are NOT to include a direct quotation from the paper. These will receive a grade of ZERO. Keep in mind that at least some of your traits are based on a comparison of two morphological features, e.g., beak width vs beak length. This means that your hypothesis could focus on why beaks are relatively long (or short), or why they are relatively wide (or narrow). In other words, your hypothesis does not have to capture every aspect of your measurements, just focus on one aspect of morphology. 

Trait 1 – Beak shape

Trait name:

Part II answers for Trait 1

Tree 1 (/2): Paste tree below. This CAN be a scan/photograph of a hand-drawn tree, but it MUST be legible and right-side-up.

The answers below must be TYPED.

Homoplasy or synapomorphy (/1)?Provide abrief explanation. (/2)

Part III Answers for Trait 1

Hypothesis (one sentence) (/1):

Rationale (two or three sentences) (/2):

Main finding from primary literature that supports at least part of your rationale (one sentence) (/2):

Reference (/2):

Trait 2–Wing length: tail length

Part II answers for Trait 2

Tree 2 (/2): Paste tree below. This CAN be a scan/photograph of a hand-drawn tree, but it MUST be legible and right-side-up.

The answers below must be TYPED.

Homoplasy or synapomorphy (/1)? Provide a brief explanation. (/2)

Part III Answers for Trait 2

Hypothesis (one sentence) (/1):

Rationale (two or three sentences) (/2):

Main finding from primary literature that supports at least part of your rationale (one sentence) (/2):

Reference (/2):

Trait 3 – Relative leg length

Part II answers for Trait 3

Tree 3 (/2): Paste tree below. This CAN be a scan/photograph of a hand-drawn tree, but it MUST be legible and right-side-up.

The answers below must be TYPED.

Homoplasy or synapomorphy (/1)? Provide a brief explanation. (/2)

Part III Answers for Trait 3

Hypothesis (one sentence) (/1):

Rationale (two or three sentences) (/2):

Main finding from primary literature that supports at least part of your rationale (one sentence) (/2):

Reference (/2):

Trait 4 – put name of trait below

Trait name:

Part II answers for Trait 4

Tree 4 (/2): Paste tree below. This CAN be a scan/photograph of a hand-drawn tree, but it MUST be legible and right-side-up.

The answers below must be TYPED.

Homoplasy or synapomorphy (/1)? Provide a brief explanation. (/2)

Part III Answers for Trait 4

Hypothesis (one sentence) (/1):

Rationale (two or three sentences) (/2):

Main finding from primary literature that supports at least part of your rationale (one sentence) (/2):

Reference (/2):

Trait 5 – put name of trait below

Trait name:

Part II answers for Trait 5

Tree 5 (/2): Paste tree below. This CAN be a scan/photograph of a hand-drawn tree, but it MUST be legible and right-side-up.

The answers below must be TYPED.

Homoplasy or synapomorphy (/1)? Provide a brief explanation. (/2)

Part III Answers for Trait 5

Hypothesis (one sentence) (/1):

Rationale (two or three sentences) (/2):

Main finding from primary literature that supports at least part of your rationale (one sentence) (/2):

Reference (/2):

Tree 6 (/5)

Taxonomic tree based on the Order, Family, Genus, species of each of the available birds. Compare this to each of your other five trees in order to complete Part II for each Trait/Tree.

Paste tree below. This CAN be a scan/photograph of a hand-drawn tree, but it MUST be legible and right-side-up.

Lab 5 assignment (8%) – 80 marks. DUE March 27 at 4 PM (accepted up to 72 hours late without penalty) 

You will submit this assignment in CrowdMark. In order to submit to CrowdMark, you will separate the questions onto new pages as detailed below and then save and submit as a pdf.

The assignment for this lab comprises the following:

• Table 1 (on as many pages as needed)
• Traits 1 to 5 – Each tree with the accompanying typed answers (for both Parts II and III) on a separate page. Put each tree and the accompanying typed answers on its own page (so, five pages). You CAN submit photos/scans of hand-drawn trees, but they must be legible and right-side up. The explanations under each tree are TO BE TYPED.
• Tree 6 (on its own page). This CAN be a photo/scan of a hand-drawn tree, but it must be legible and right-side up.

Notes/tips/reminders

1. Scientific names are to be formatted properly EVERY TIME – that means in italics when typed and underlined when hand written AND with proper capitalizing (or not) of genus and species names. See lab 1 again for a reminder if needed.
2. The hypothesis and rationale for each of your five traits needs to be about fitness, not about whether a trait is a homoplasy/synapomorphy. Re-read the paragraphs about Part III on page 5-6 above, paying particular attention to the furbie example.
3. Direct quotations for the ‘finding from the primary literature’ will NOT be accepted. You are to summarize/paraphrase the relevant finding in your own words and then provide the full reference.