Showing posts with label taxonomy. Show all posts
Showing posts with label taxonomy. Show all posts

Thursday, February 4, 2016

The Primate Family Tree: A classroom activity in evolution, adaptable for all ages

Feel free to email me to request the document (with all this text and all these figures) which is easier to work with. holly_dunsworth@uri.edu

In this activity, students will…
Observe and describe the similarities and differences between primates and other familiar mammals, and also the similarities and differences among primates.
Classify primate species into groups (superfamily and above). 
Transform Linnaean classification into evolutionary theory by merely changing the question from How do primates look similar and different from one another? to Why do primates look similar and different from one another?
Build a primate “family” tree by turning Linnaean classification into phylogeny (or evolutionary tree-thinking) to describe how common ancestry and change over time explain both similarities and differences among primates.

How old are the students? 
5-105* 
*Prior to about age 8, teachers will need to riff quite creatively off track from this (for one, because reading the Primate Taxonomy Table may be very difficult for younger students), but I include those earlier ages because I believe that teachers of those age groups can find a way to use this lesson if they’d like to. It's possible that just knowing how to read is enough to do a stripped down version of this activity, which includes children even younger than 5. I have used this activity successfully with students aged 8-25. For upper-level anthropology courses I've used it as an ice-breaker to kick off the semester (with students who have a background in evolutionary thinking already).

How long will it take? 
30 minutes minimum (much more depending on detail you wish to cover)

What materials?
Color pictures of a diverse array of primates - approximately 3-5 times as many pictures as students. Too many is better than too few. Rip them out of old textbooks and laminate for durability. Print them off the Internet (arkive.org is one of the best sources) and laminate for durability. Make sure to have at least two different pictures of the same species for many of the species you include. Label most of them with the common names under “examples” on the chart for Part 2 (e.g. “baboon”). But a fraction may be only labeled with geographic region, scientific name, or nothing at all.  Explanation is in the instructions below. Specific sources of primate photos for printing are listed in Appendix A.
Pencil – 1 per student
Note cards -  1 per student (for them to draw a self-portrait or a symbol to represent themselves)
Poster paper, or large sheets of paper – 6, one for each superfamily on the Primate Taxonomy Table (below)
Tacky gum, reusable tape, or some other ingenious sticky tool that can both hold primate pictures to the posters and also be removed and moved to different posters when students change their minds. 
Handout for students (see options below; must at minimum include Part 2: Primate Taxonomy Table)

Teacher Instructions

Part 1. (3 MINUTES minimum) DISCUSS CLASSIFICATION
Using the resources under Part 1 of the materials below, hold a discussion about classification. Don’t talk about relatedness or common ancestry! And especially don’t talk about evolution! (Next, in Part 2, the taxonomic terminology they will use, like “family,” will encourage them to think evolutionarily, hopefully, and this will come into play later in the activity.)  They will already be familiar with how like is grouped with like—I often use sock and underwear drawer analogy, grocery store organization works too. Stick to primates if you’d like, but if you go broader, make sure to end your discussion with primates, including humans. Make sure to explain how (Linnaean) taxonomy/classification works. That is, simply/broadly (or complicated/specifically if you’d like) describe the methods—the use of comparative anatomy and homology and also the binomial species name for the smallest, most exclusive group within ever-more inclusive groups going up to the Kingdom level.

Part 2. (10 MINUTES minimum) CLASSIFY THE PRIMATES INTO SUPERFAMILIES
Hang a poster for each superfamily along the wall in no particular order, lay out a pile of the photos in no particular order. Students get up out of their chairs, and using the Primate Taxonomy Table (below) they stick each primate picture to a poster labeled with the superfamily to which they think it belongs. They are able to do this without any knowledge of primates because you have labeled most of the pictures with “baboon”, for example. They can go to the table on the handout and see that baboons belong in the superfamily “cercopithecoidea” and stick the photo to that poster. Unlabeled baboons should look similar to labeled ones and they should also be sticking those to the cercopithecoidea poster if they are carefully observing and are engaged in the activity. Make sure they stick their own “human” cards to a poster too.  Hopefully they will respectfully work together and move others’ around if they think they have a better case for a different classification of a particular primate.  

Primate Taxonomy Table (handout).
Email me for a file you can work with more easily (holly_dunsworth@uri.edu)

Part 3. (5 MINUTES minimum) STUDENTS SHARE THEIR REASONING FOR THEIR CLASSIFICATION
Lead the students through a tour of the features that unite the primates into each of the superfamilies. First ask them to describe the similarities among all the primate superfamilies (a quick review of Part 1). Then ask them to describe the differences they can see between the superfamilies: what makes hominoids separate from cercopithecoids, etc?  It’s not imperative, but I recommend starting with the primates that share the most with humans (hominoidea) then going to the cercopithecoidea, and so on. This may appear to be difficult because they may observe overall (super) family resemblance but not be able to describe any more detail than that, which is fine! Using the resources under Part 3 below, you can provide details of the differences between the superfamilies, both that are visible in the pictures and that are not. 

Part 4. (2 MINUTES minimum) CHANGE THE QUESTION FROM HOW DO PRIMATES VARY? TO WHY DO PRIMATES VARY? 
Challenge students to explain the patterns of similarities that make all these creatures primates and that, for example, unite the hominoids, the cercopithecoids, etc..., while also explaining the differences that make each species unique and each superfamily unique.  Hopefully, with very little help from you, they will arrive at the idea that relatedness explains it. Family history, on a larger scale than our own families, but the same kind of thing. Common ancestry and change over time since common ancestors. Evolution plain and simple.  

Part 5. (10 MINUTES minimum) BUILD A PRIMATE TREE and DISCUSS ITS MEANING. 
There are many ways to do this and showing more than one way would be great, but one way is to put the known phylogenetic structure, the branches of the tree for the superfamilies (see resources below) on the wall or board and have them deduce where the superfamilies go and stick the posters to those branches. Another way, for older students, is to have them figure out the relatedness of superfamilies first, starting with humans and hominoids and hypothesizing which are more and more distantly related based on increasing differences. Another is to merely show them how to walk through the table for Part 2, and change it into a hypothesis for phylogenetic/evolutionary history, with lineages diverging where each level of taxonomy divides things further into more exclusive groups. So show them how to draw time and descent lines around that evolution-free taxonomy (classification table for Part 2) that they already have and they’ll arrive at.. dun-dun-DUN evolution! I prefer to draw the students’ hypothesized tree like a big oak tree (with a streps/haplorhine split in the trunk deep down near the bottom) on the wall, and to stick the posters at the ends of the branches. But it’s obviously up to teachers and whether they have a big wall to draw on! I cover my wall in paper first so that I can draw the big tree. 


Teacher Resources and Optional Handout Materials
Teachers: Pick and choose what you’d like to include in your handout, depending on what you will cover with your particular students (depending on age, time, goals, etc…). Be careful not to share any handouts too soon and spoil the opportunity for students to think first, if that’s what you have time for and are going for. 

Part 1
  • Where do humans fit in the classification of life on Earth? (link)
  • How do we make these categories? We ask, ‘What’s similar” of the anatomy, when comparing different species.  That is we look to homologous structures.  A great example is the tetrapod forelimb. (link)

  • What makes a primate a primate? (link)

Part 2
Lemuroidea
Nose: wet (hence the name strepsirrhine)
Geographic region: Madagascar
Tail present: yes
Activity: Some nocturnal, some diurnal
Teeth: Many more than we have, some shaped like comb for grooming fur
Body size: Small but variable from the smallest primate alive (<< 1 lb.) to ones as big as big pet cats (20 lbs.)

Lorisoidea
Nose: wet (hence the name strepsirrhine)
Geographic region: Sub-Saharan Africa and Southeast Asia
Tail present: yes and no
Activity: nocturnal
Teeth: Many more than we have
Body size: small

Tarsioidea
Nose: dry (hence the name haplorhine) 
Geographic region: Southeast Asia
Tail present: yes
Activity: nocturnal
Teeth: Many more than we have
Body size: small

Ceboidea
Nose: dry (hence the name haplorhine) 
Nostrils: flat and facing out to the side (hence the name platyrrhine)
Geographic region: Central and South America
Tail present: yes (and some are even prehensile!)
Activity: Most diurnal, some nocturnal
Teeth: four more than humans (one extra premolar/bicuspid in each quadrant of mouth compared to us)
Body size: Variable, with some small (like pygmy marmosets) but the largest, the spider monkey, is 25 lbs.

Cercopithecoidea
Nose: dry (hence the name haplorhine) 
Nostrils: facing down (hence the name catarrhine)
Geographic region: Asia, Southeast Asia, and Africa (all sub-Saharan except the Barbary macaque of Morocco and Gibraltar)
Tail present: yes (but 2-3 species are no or have very small stubs)
Activity: diurnal
Teeth: same number as humans
Body size: Many, including most macaques and baboons, weigh more than any ceboids. Some mandrills weigh over 100 lbs.!

Hominoidea
Nose: dry (hence the name haplorhine) 
Nostrils: facing down (hence the name catarrhine)
Geographic region: Southeast Asia (gibbons, siamangs, orangutans); Sub-Saharan Africa (gorillas, chimpanzees, bonobos); Worldwide (humans)
Tail present:  no
Activity: diurnal
Teeth: same number as humans
Body size: Although gibbons and siamangs are the smallest of the group, this group is the largest in body size and weight of all primate superfamilies and includes gorillas, the largest of all primates which can weigh 400 lbs.!


Part 4

Evolution and phylogenetic thinking is just family history writ large.

Part 5. The Primate Family Tree

Here is an example (one hypothesis, if you will) of a primate phylogeny or phylogenetic tree or evolutionary tree. 



Here's guidance on how to turn Part 2’s table into a phylogeny with students.


Then here it is, stripped down and rotated...



Appendix A.
Sources for primate pictures

Lemuroidea

Lorisoidea

Tarsioidea

Ceboidea

Cercopithecoidea

Hominoidea
Humans: students draw a personal sign, symbol, or self-portrait

Tuesday, August 7, 2012

Ooops! The human genome does not exist! Part V. Why are we so comfortable with type representations?

On reference sequences and various loose ends
We started this series to explore some conceptual complexities and subtleties associated with the universally known, but perhaps less universally understood notion of 'the' human genome.  What seemed like a hard-won and very straightforward entity for human genetics turns out to be a lot less straightforward--even if it's exceedingly useful in many ways.

A type specimen in taxonomy can be a single individual.  If 'the' human genome sequence  in a future iteration is a diploid sequence from one person, it will be similar, as we noted in a previous part of this series.
Helixanthera schizocalyx type specimen
Kew Gardens
We have described the many ways in which such a sequence actually doesn't or never did exist.  In part this is because there will always be errors in the data.  But let's overlook all of that, and agree that the human genome as we know it is a representative or reference sequence--at least until we can get a single representation that digests all known variation in human genomes.  We suggested some ways that might be done, using what are known as gene 'logos' (visually reflecting the underlying data: the relative frequencies of each nucleotide at each position in the genome).

It is important to be aware that even as a reference, what it is a reference of is unclear.  In prior posts of this series we discussed some of the issues.  One general idea is that it's the sequence of the DNA from, at least, a 'normal' person.  But as we noted that is misleading.  The donor--when or if 'the' reference is from one person--is not in any way a particularly superior, nor even a particularly average, person.

A subtle point that seems very widely misperceived is that there is no 'normal' person.  Nobody is at the exact average value for glucose levels, stature, blood pressure, and so on.  Nobody has the 'average' DNA sequence (whatever that means).  No person has ever died at the exact life expectancy in his or her population!  An average, a 'norm', is a digest of variation. It is a Platonic concept.

If 37% of individuals in our species have an A, and 63% have a T at a given position in the genome, no person can be average.  The closest s/he can get is 50% A, 50% T since we each (if we're 'normal'!) have two copies of the genome, so a single person's allele frequencies can only be 0/1 or 50-50.  So it's hopeless even to think of a digest such as 'average' in this context.  The nucleotide frequencies at any give site will change, anyway, as samples increase (but we'll not know by how much, since people are leaving and entering the gene pool at every moment).  And, as a reminder, there is the further problem that the genome instances in each cell of an individual differ: 'the' genome sequence obtained from that individual alone is a reference, not a true description of his/her genomic contents.

So we are not really using a reference sequence to establish an ideal.  Yet, unless to make a point of something like political correctness, we would not use a person with, say, Tay Sachs, or who was congenitally blind, nor an indigenous Australian or an Inuit, as our reference.  This shows in yet another way that terms like 'reference' or 'representative' are potentially quite misleading, or even political.

And yet, an arbitrary reference is very useful!  Why is that?

'The' wildebeest; 'the' mongongo nut': Deep aspects of the mind?
Mongongo nuts
Whatever we eat, or whatever wants to eat us, we must recognize and digest its presence from sensory information--and sometimes we'd better do it fast or we'll be somebody's fast food!  We recognize our prey, and our predators, our dinner and our diners, by analyzing our sensory input and fitting it into categories.

However this works neurally, our ancestors knew what a wildebeest is, or a mongongo nut, even if no two of them are identical.  We have always created mental Platonic ideals and within rather broad limits we instantly fit sensory input into these categories and act on the result.

We use language--terms like 'the chicken' or 'the human genome', but the biological process involved in understanding the concept doesn't depend on language, and it certainly isn't anything particularly human!  Lions recognize wildebeests, bees recognize flowers, and ants recognize enemies.  The wiring process that leads to the ability quickly to characterize is long built-in to neural systems, however they work.

Using type specimens, including whatever we determine to use to represent genomes, is thus a manifestation of a deep mental characteristic.  Where we have trouble is at the edges of our categories, in the range of objects that we include, and this is true not just of taxonomy, or genomics, but in all of life.

Even when it comes to disease and gene mapping!
It is thus no surprise that in human genetics we  hunger for 'the' diabetes gene, or a gene 'for' diabetes--and have a definition of 'diabetes'.  That is an underlying reason for the fervor for enumerative approach to genome mapping of traits.  Categorization can be useful, since categories of disease allow us to develop protocols consisting of categories of treatments, tests, and identification.  For deep as well as pragmatic reasons, we are not easily accepting of complexity: we like to throw the word around perhaps, if it sounds fashionable and insightful, but in fact we do our damndest to reduce quantitative complexity to qualitative simplicity.  We simply can't stop wildebeesting.

Evolutionary typology, too
 We've stressed the central relevance of evolutionary population thinking that should be an omnipresent counterweight to typological thinking.  But we even do the very same Platonic thing in evolutionary biology, no matter how deeply we understand its quantitative nature.  We want there to be 'the' adaptive reason for a trait that we are interested in.  The adaptive 'fitness' of a trait is viewed in effect as an inherent, cosmically existant reality of which each individual's reproductive success is an imperfect reflection.  Indeed, often we do the same thing in defining 'the' trait in the first place: we want 'the' selective explanation for 'bipedalism', for example, as if that were a single thing and evolved as such.

Material Platonism
Categorical thinking is very hard to avoid, and population thinking devilishly hard to ingrain.  A new paper in PLoS One that a colleague, Charlie Sing at the University of Michigan, pointed out to us, looks at the current data from the '1000 Genomes' project, the effort to provide a large number of whole genome sequences, raises--or rather, demonstrates--problems that will be faced by the desire (or dream) of predicting disease from individual genomes.  The structure observed among known variants is used to identify causal variation by various mapping or association tests, as we've commented on many times (e.g., GWAS studies).  But while some variants identified in what might be called disease-specific 'reference' data will have strong effects, this reference even though based on many rather than one sequence, will not include many other relevant variants. 

How we should deal with rare variants is currently a hot topic in many labs, but whether one should be thinking in terms of such single-cause prediction is--or, rather, should be--at best an open question.  No composite of variation will be a perfect genome referent for the moving target that is a species.

Since the real world is at least as quantitative as it is qualitative, categorical type-specimen thinking may sometimes be helpful but also can lead to wasteful effort or even to harmful results.  Even war between 'us' and 'them' is an instance.  It's hard to be careful about how and when to use 'types' even as referents.  In a sense, the macro world has duality the way the micro world does in physics, where particles come in types, and 'the' electron is sometimes a particle, sometimes a wave....something, and yet not something.

Typological thinking is very deeply engrained.  For example, in what is almost laughably misleading yet ineradicably pervasive, almost every geneticist refers to 'mutations' when they mean 'alleles': mutation is a change due to a DNA 'mistake' between one cell and another, as between parent and offspring.  Every element of every sequence on earth today was, at one point, a 'mutation'.  'Allele' properly refers not to a change but to variant states present at any given time.  But we exceptionalize variants in this way by calling them mutations if, for example, they lead to a disease or trait under study.  This arises, conceptually, only because we think there is a 'normal'--a type--from which the variant is a 'mutant' (a world often with denigratory connotations). Yet we know that's at best inaccurate.

Worse, almost everyone in biology unstoppably refers to the 'wild type'--the wild type--when comparing to some variant ('mutant').  This has become ridiculously entrenched, because for reasons we've been discussing, there is no single type.  Even in  mouse research it is absolutely routine to refer to a strain, say C57BL/6 mouse as the 'wild type' relative to an experimental manipulation such as inducing a transgenic 'mutation' into one of those mice.  But there is absolutely nothing 'wild' about a C57BL/6 mouse--it is a laboratory produced inbred strain that couldn't last the proverbial 5 minutes out in the 'wild'.  It, like all inbred strains, have been very un-naturally produced.

So 'wild type' is a persistent, historically derived but obsolete term, a perversion even of the original type-specimen concept.  In daily practice, of course, this is jargon and geneticists know what someone is talking about when contrasting a wild type with a mutant.  But the habit reflects psychologically deep patterns of thinking that are far from what the real world is like, and we have tried to suggest, can be misleading, sometimes when it's important not to mislead.

A simple idea like 'the' human genome intuitively seems to exist, and yet on close inspection doesn't exist.  In a sense, one can say that humans are built for material Platonism.  The ideal, the abstract entity, is a figment of our individual imaginations, but our power of imagination was built by evolution.  Using ideals, based on material objects, comes natural to us.  We depend on it.

Plato's Allegory of the Cave by Jan Saenredam
according to Cornelis van Haarlem, 1604, Albertina, Vienna.
In a deep sense, Plato had things exactly backward.  He used the image of people in a cave, who were only able to see imperfect shadows of the real 'ideal' objects projected by firelight on the cave wall.  But that's backwards.  Ideals do exist, but not 'out there' in some Platonic immaterial realm unobservable by us.  They exist in our heads, and are material in that sense and because we each build ours from real-world observations.  It is thus the ideal that is imperfect relative to reality, not the other way round as Plato had it.  If there is anything mysterious about this, it is that we were designed by evolution to do things that way rather than to be better quantitative thinkers.

In the end, 'the' human genome sequence is imaginable, but doesn't exist, no matter how we might contrive to produce something less arbitrary than the essentially fabricated referent we now use.  The challenge is to understand the limits, as well as the strengths, of categories.

Thursday, January 27, 2011

"and I want no other fame": The tale of the butterfly novelist--Vladimir Nabokov

Lolita may be a story for adults only, but Vladimir Nabokov told another story that can be enjoyed by all.  It appears to be an amateur's triumph, based on a correct guess that was before its time.  No definitive data could have been assembled to tell the tale while Nabokov was alive.  But thanks to the very regular, clocklike way that DNA accumulates variation among descendants over time, the guess seems to have been confirmed with current methods.

Polyommatous blue, by Lilly M.,
Wikimedia Commons
The immediate story is told by Carl Zimmer in the NY Times, but is based on a paper just published in the Proceedings of the Royal Society.  If Lolita was about a man in pursuit of a (too-)young person he obsessively adores, the story of the Polyommatous blue butterflies is one of a man chasing a group of old species that he obsessively adores.

It has long been widely known that Nabokov was a persistent, knowledgeable, dedicated if technically amateur butterfly enthusiast.   It was also long known that he did extensive work on the structures and relationships of the species that came years ago to be known as 'Nabokov blues'.  You can read about this, with maps and illustrations, in a fine book by Kurt Johnson and Steve Coates, Nabokov's Blues: The Scientific Odyssey of a Literary Genius, Zoland Books, 1999.  Johnson is a lepidopterist, expert in these butterflies.

They write "Where South American temperate life-forms had come from became a compelling question from the earliest stages of the continent's exploration." Much of their book, which is a readable, popularized narrative, tells of the efforts by Nabokov and others then and since, to understand the taxonomy--species relationships--among the South American blues and their relatives elsewhere. 

The traits of species available to Nabokov and others did not neatly correlate with their locations in the Andes or down into warmer environments.  That meant that some nearby species seemed too different to have had an evolutionarily recent common ancestor.  And, if they did not, and for the group as a whole, where were their origins then?

This issue had arisen out of the work of many naturalists going back at least to the early 1800s.  From an evolutionary point of view a couple of explanations were plausible.  One is polyphenism: species can have very different morphology or behavior depending on the individuals' local environment or genotypes.  And there is mimicry: distantly related species can come to resemble each other by natural selection. But that will only affect the mimicked trait, leaving the species' other traits less similar.  But in any case how did these butterflies get into the Americas?  There were various suggestions.  One possibility that Nabokov entertained was that the species had expanded into the Americas from Asia, by way of the Bering land bridge--that is, into South America from the north, what is now the Arctic.  The North American ancestral species may then have died out, leaving only their South American descendants.

The story in the Times, like news stories tend to do, makes this seem as if Nabokov got this 'blues' story out of the blue, so to speak, and was insistent on this view.  Indeed, Vila et al. in the Proceedings of the Royal Society paper, do the same:
The radiation of Polyommatus blues in the New World was first appreciated by the famous writer Vladimir Nabokov when he was working as curator in the Museum of Comparative Zoology at Harvard in the early 1940s.
And:
Our results show that Nabokov’s inferences based on morphological characters (primarily of the male genitalia) were uncannily correct in delineating not only species relationships but also the historical ordering of these five key events in the evolution of New World blues.

But even brilliant discoveries occur in a context, and people rarely take immovable positions when the evidence is ambiguous. Johnson and Coates go to great lengths to describe the long history of South American biogeography--the distribution of species over space and how it gets that way.  Ideas of species rafting across vast oceans had been suggested, and when continental drift was discovered, land connections between South America and Asia and Africa provided a possible explanation.  But climate change and a northern connection was another possibility.

There's no taking away from Nabokov that he was diligent and insightful, but others were thinking similar kinds of things, about the biogeography of many different species besides butterflies.  As he said in our title quote, he wanted to be known for this work, and properly so.  But at least Johnson and Coates present the history as one of many widely discussed possibilities by many different investigators--including the Northern origin of South American species generally.  Nabakov appears to have weighed different possibilities, and his preferred hunch, given the set of specimens and knowledge available to him, appears to have been right. 

The new paper uses extensive DNA sequence to resolve these tales in detail, data that of course was unavailable in the past.  The authors draw species-relationship trees based on the degree of sequence identity.  The times of splitting among the species were estimated by the number of DNA sequence differences that had arisen.  Many of the branches were  deep--large numbers of sequence variants, suggesting ancient splits, relative to other nearby species in South America.  Since the nearest relations in these instances were in Asia, the American species must more than once--in different expansion waves--have come from Asia.

Paleoclimatology and continental drift, and known climate tolerance patterns in the butterflies made it possible for the butterflies, over many generations, to expand here from Asia and survive in the warmer climes that existed episodically over an estimated period of 10 million years.  DNA analysis can even work when there has been selection for polyphenism or mimicry.  That's because such selection would distort relationships only at the genes involved in those particular traits, but genomewide variation will accumulate in a pattern that corresponds to the species' histories.  Indeed, DNA evidence could provide evidence for it, by showing that though some species looked similar, they really were not very close relatives overall (genomewide).

Here is an application of genetics that is entirely appropriate, that makes it possible to draw convincing inferences, when morphological or behavioral analysis may not.  A tree of descendant genomes accumulates variation probabilistically, so little can be said from observation of just a few nucleotides.  But these erratic patterns even out when thousands of nucleotides are compared, as these authors did.

Even so, let's keep in mind that genetic analysis is not exactly a scientific miracle.  If genes cause traits, then traits will diverge over evolutionary time in ways that generally reflect underlying genetic divergence.  That is why, in effect, Nabokov was indirectly using genomewide genetics to draw his conclusions--he just couldn't see the genes directly.  This is in essence how Darwin did what he did, too, without a good understanding of what inheritance really was.  But what we now have is explicit genetics to replace Nabokov's inferences from aggregate, implicit genetics. And this can get around problems of phenotypes that don't fit the history.

DNA is more specific and in the sense of time estimation much more rigorously useful than morphology and behavior.  As in forensic applications of genetics, that match sequences to their owners as in crime investigations, analysis that relies on the clear properties of genomes can tell stories that are as powerful as the compelling novels that Vladimir Nabokov wrote.  And he is justly famed for both!