A peek: Natural selection reduced diversity on human Y chromosomes

In science we often get together with other scientists and present preliminary results before the publication of the manuscript.  I think that attending meetings is an excellent opportunity to learn what other people are working on, share the research that I am currently engaged in, and both give and receive feedback about the analysis and interpretations.

In this case, I presented a poster at the scientific meeting I attended, the 2013 annual meeting of the Society for Molecular Biology and Evolution, about work that was recently accepted for publication (expected to be published in January). I'm working on an accessible research blog post about this work. In the meantime, here is the description from the poster this summer, and the pdf version of the poster (you can also download the preprint version here):

Description

The human Y chromosome exhibits surprisingly low levels of genetic diversity. This could result from neutral processes if the effective population size of males is reduced relative to females due to a higher variance in the number of offspring from males than from females. Alternatively, selection acting on new mutations, and affecting linked neutral sites, could reduce variability on the Y chromosome. Here, using genome-wide analyses of X, Y, autosomal and mitochondrial DNA, in combination with extensive population genetic simulations, we show that low observed Y chromosome variability is not consistent with a purely neutral model. Instead, we show that models of purifying selection are consistent with observed Y diversity. Further, the number of sites estimated to be under purifying selection greatly exceeds the number of Y-linked coding sites, suggesting the importance of the highly repetitive ampliconic regions. Because the functional significance of the ampliconic regions is poorly understood, our findings should motivate future research in this area.

Wilson Sayres, Melissa; E. Lohmueller, Kirk; Nielsen, Rasmus (2013): Natural selection reduced diversity on human Y chromosomes. figshare. 
http://dx.doi.org/10.6084/m9.figshare.806296

The platypus is not a hybrid. But, these are still fun.

Speaking of hybrids, I was reminded that after my post about the platypus (check it out here), I received a lot of funny depictions of the platypus as a hybrid. Before I share, however, let's get one thing straight:

The platypus is not a hybrid.
The platypus is not a hybrid.

The platypus is not a hybrid.

Okay, now that we've gotten that out of the way, let's have some fun. Every time you see one, you can be the one to explain that the platypus belongs to a unique lineage of mammals that, while awesome, is not a beaver-duck hybrid (or maybe that's just what I'll do). Please share more in the comments.

From Tracy Heath, via the blog "Something that I like":

Venn diagrams were never so awesome.

From Clement Chow via cheezeburger.com:

Via cheezeburger. com

From a comment, via cheezeburger.com:

Via cheezeburger.com

From Clement Chow, artwork by styrofoamdiablo:

"Beaver+Duck-Eggo: Platypus" by styrofoamdiablo

From Clement Chow, from shirtwoot:

"Mystery of the Platypus Solved" from shirtwoot

From Jacob A. Tennessen (at OSU), the Platypus Trophy, which is awarded to either the Oregon Ducks, or the Oregon State Beavers, after their annual football game.

Platypus Trophy

Yes, you share a common ancestor with pigs, but it was a long, long time ago.

I was recently invited to comment on an Anthropology Network discussion on LinkedIn, where someone asked, "I'm wondering what this community's thoughts are about the theory that humans are a hybrid?" and linked to the blog post by Eugene McCarthy supposing that humans resulted from a hybridization event between chimpanzees and pigs. Because it is a private network, I'd like to repost, with some expansions, what I added to that discussion. But, let's just start off by clearing the air: 

Chimpanzees did not mate with pigs and produce humans.

Chimpanzee, by Ikiwaner (Own work), via Wikimedia Commons

Adorable piggy, by A R, via Wikimedia Commons

I am not a little piggy!

I was surprised that a group of anthropologists would even consider this a reasonable topic for discussion, but perhaps this speaks to the need for more cross-discipline communication. 

I find it distressing that the chimp-pig hybrid article dismisses the abundance of genetic evidence that provides no support for such a hypothesis of human ancestry. There are several scientific and logical flaws with the supposition that humans resulted from what must have been multiple matings between chimpanzees and humans. Also, please see an alternative discussion of this hypothesis by PZ Myers here, then another summary and discussion by ARTIOFAB here. 

1. Humans are genetically very similar to chimpanzees, and genetically distant from pigs
There are no regions of our genome where the genomic content more closely resembles a pig than a chimpanzee. If such a hybridization had occurred, we would, like we do with the Neandertal and Denisovan genomes, find regions where segments of modern humans are more closely related to pigs than any other species, but we do not. 

I really don't understand how anyone can look through images of pigs and think that we resemble pigs more than we do chimpanzees or bonobos:

Pan paniscus (bonobo) By Pierre Fidenci (http://calphotos.berkeley.edu), via Wikimedia Commons

2. Body hair has been lost independently in many mammalian lineages.
Yes, hairlessness over most of our bodies evolved in humans, but it did so independently in the human lineage. Similarly hairlessness independently (we call it convergent evolution) evolved in naked mole rats, manatees, and cetaceans (dolphins and whales). Rodents are actually more closely related, evolutionarily, to humans than pigs, but we don't see a naked mole rat - chimp hybrid theory because it is obviously ridiculous to the general public. The chimp-pig hypothesis is even more improbable. And, furthermore, many pigs have not lost hair on their bodies or faces.

Bearded Pig, by Art G. from Willow Grove, PA, via Wikimedia Commons

3. Chromosomal and genetic differences between chimpanzees and pigs preclude fertile hybrids.
The chromosomal differences between chimpanzees (48) and pigs (38) would preclude any chimp-pig zygote from developing, or even replicating properly. The author greatly over-exaggerates claims about the fertility of hybrids of sheep-goat hybrids (most are stillborn), and also misuses the term geep (which refers to a chimera of sheep/goat cells). The author also ignores the close evolutionary relationship of sheep and goats, where the chromosomes (and the breaks/fusions) can readily be mapped, where most of the gene content is still conserved among chromosomal regions. Such an identity of the order and orientation of gene content does not exist between chimpanzees and pigs, but is possible between the very closely related human and chimpanzee (all chromosomes are one-to-one, except for human chromosome 2, which is a fusion of two ancestral chromosomes that remained unfused in chimpanzee). 

Mapping of human and chimpanzee chromosomes, by JWSchmidt, from Wikimedia Commons

4. Fossil evidence can account for all of humans ancestry to the human-chimp common ancestor.
At what point in time would this have occurred? Certainly not the present. We have fossil evidence of modern humans, ancient humans, ancient hominids, ancient apes, ancient monkeys, and so on. Science can account for the progression of humans from our shared ancestor with chimpanzees, and even further back. At no point in history do the fossils of ancient humans in any way resemble the fossils of ancient pigs. 

5. Modern species share common ancestors, they did not beget each other.  
Modern humans did not evolve from modern chimpanzees any more than modern chimpanzees evolved from modern humans (that is, not at all). Fossil evidence suggests that the chimp-human common ancestor looked a lot more like a modern chimpanzee than it did a modern human, suggesting many more physical changes along the human lineage, but the modern chimpanzee has also experienced changes since our most recent common ancestor together, approximately 6 million years ago. Both humans and chimpanzees share a common ancestor with pigs about 90 million years ago.

6. Domesticated pigs and chimpanzees do not live in the same locations. 
Pigs (with reduced body hair) were domesticated in East Asia and in Europe. Chimpanzees live in central Africa. They live on different continents. They did not ever have the opportunity to get busy. Wild boars can be found in northern Africa, but this is still quite far from where chimpanzees live, and if they do overlap in range, it is only a very recent occurrence.

Wild Boar, by Volker.G (Own work), via Wikimedia Commons

7. Why hasn't an experiment been done? 
You could attempt each of the possible combinations (chimp sperm with pig eggs, and pig sperm with chimp eggs) and test the viability. It it works, we can have this discussion. If not, this guy needs to stop spouting nonsense that detracts from the real science being done.

By David.Monniaux, via Wikimedia Commons

Pumpkins

Little Bear picked out a pie pumpkin at the store last week. She helped me clean out the guts, and wash the seeds. The first thing we made with it was toasted pumpkin seeds:

Delicious toasted seeds. 

Then, I peeled the pumpkin and we boiled it.

Boiled fresh pumpkin.

And puréed it.

Pureed fresh pumpkin - so bright!

I made a pie crust using whole wheat flour and vegetable shortening.

Whole wheat crust.

And looked up a recipe for eggless pumpkin pie (because we were out of eggs at home). I found this one, but used half the sugar.

Ready to bake eggless pie.

It took nearly twice (yes, twice) as long to bake, which makes me high suspect our oven (will have to buy an oven thermometer soon). I don't think it is because of the reduced sugar, but that might have contributed.

But, it turned out to be pretty tasty. I prefer the consistency of pumpkin pie with eggs (more custard-like), but this was a wonderful eggless/vegan option.

Thoughts on scientific publishing, from someone without tenure, or a Nobel prize.

There has been a lot of heated discussion about recent Nobel prize winner, Randy Schekman's article, "How journals like Nature, Cell and Science are damaging science".  In it he argues that these types of journals preferentially publish science that is sensational over science that is important.

Of course they do.
Of course Nature, Cell, and Science choose to publish articles that they think are both scientifically accurate and going to be read by a lot of people. NCS have a brand to promote, and an audience to cater to that expects exciting articles of broad interest. I like to read or skim through articles that aren't in my own field in Science. They have no reason not to publish the articles that will bring in the most readership, and every incentive to seek out the "hottest" research topics.

I have no problem with a journal choosing to publish only a certain kind of research (chemistry, physics, biology, evolution, and so on), or choosing to publish articles that they think will bring in the most readership. It only becomes a problem when the quality of the science is overlooked in favor of the sensationalism. Publishing inaccurate science should not be tolerated.

The real problem.

Schekman argues that part of the problem with "high impact" journals that choose to prioritize flashy results over real scientific advances is that hiring, tenure, and promotion committees view publication in these journals as a measure of the scientific merit of a paper. I don't see this as a problem with the flashy journals, but in the people who assume publication in such a journal should be equated with scientific excellence.

As a postdoc on the job market, I am acutely aware of this, and worried about it. You'll note from my publications that I don't have a single NCS paper. I'm pretty sure that not having those NCS papers has/will hurt my prospects this year. I hope that some schools will still recognize my ability to do good science, to conceptualize projects and bring them to completion, and to successfully mentor students, and will offer me a position despite the lack of NCS-publications. Perhaps foolishly, I do believe there are departments that value science more than the journal where it was published. And, with the development of more detailed, and manuscript-specific, metrics, including downloads, citations, shares, page views, and saves, I think it will be easier in the future to dispense with using journal IF as a measure of scientific merit.

Don't get me wrong, I'm not naive. I know I'm not going to be considered at some institutions because I don't have publications in the NCS journals. While "luxury" journals are valued at "luxury" institutions, it is also important to remember that "luxury" institutions (as pointed out over at Telliamed Revisited) can also be used inappropriately to infer quality of a person and their research. Case and point: I was told on an interview, "It would be really great for our department to hire someone from Berkeley, like you." Ugh. Nothing to make you feel frustrated with the system like thinking you may have been recruited solely because you came from University A instead of University B.

So where does that leave us?
Tenured, well-known, professors have been chiming in on the issue, but will that affect how I proceed with my scientific trajectory. I am confident that any position I advocate cannot be attacked on the basis of, "I've already made it." I can assure you, in this tumultuous academic job environment, I have not "made it". At this stage in my career these are the four things regarding scientific publishing that are important to me:

1. Scientific papers, results, and datasets should be publicly accessible.
2. Classifying research by field is useful.
3. There is value in peer review (pre and/or post).

4. Reviews should be public.


1. Scientific papers, results and datasets should be publicly accessible
For me, the most important aspect of publishing my work is that it should be publicly accessible and reproducible. Nearly all journals now offer an option to pay (sometimes a prohibitive amount) to allow papers to be freely available, and many are requiring data to be submitted with publication. Assuming I have all the funding in the world (ha!), where will I submit?


2. Classifying research by field is useful.

Well, I'll submit wherever I think the audience for my paper will be the best. I tend to find new publications through google scholar and pubMed searches, but on occasion, I'll scan through the recently published articles in journals with a focus that is near my discipline. So, as an early-career scientist, I will publish in journals that are in my field, or through venues where my work can be classified (tagged, labeled) in broad categories, so people who weren't already looking for my specific paper might find it.

3. There is value in peer review (pre and/or post)
I have found peer-reviewed comments to be immensely valuable for my accepted manuscripts. Sometimes this delayed publication for months, and I didn't always agree with the reviewer comments, but that doesn't mean the process itself was worthless. I don't think that the current system is the best, but I also don't think it is terrible. One of the challenges with the peer review process is the huge lag time between submitting a manuscript and it finally being published. Most journals don't have a good way around this. One option would be to go with a system like F1000 or PeerJ, where manuscripts can be archived and immediately available upon submission.


4. Reviews should be public.

For journals with pre-publication peer review, I wish that all papers were published with the pre-publication reviewer comments. I think it would be immensely valuable to see what other scientists thought of the work before it was published. For all work, I think it will be beneficial to have a single location where post-publication comments can be collected, reviewed, and published. This would likely need to be monitored in some way to prevent it from turning into a free-for-all by trolls. 

So, will I publish in Nature, Cell or Science? 
I don't know.

But, I can tell you that I know better than to judge the value of a paper, or a scientist, by the journals they're published in, and that is where we have to start. 

Why sequence the manatee genome?

By Gaylen Rathburn, via Wikimedia Commons

I was excited to learn today that there is genome sequence for the West Indian manatee (Trichechus manatus)!! A friend wondered why I was so excited, asking, "Is it evolutionarily interesting?"

Well, first off, I've always been fascinated with manatees: they are so defenseless, and yet grow so large that they are rarely predated on. They are, however, especially susceptible to human-made water vessels. I am excited for their genome because I've always loved them. But, they are also pretty evolutionarily awesome.

1. Manatees are more closely related to elephants than they are to dolphins or whales.
The manatee and the bottlenosed dolphin are approximately 100 million years diverged from each other. The manatee is classified under the Afrotheria, which also includes elephants, hyraxes, and aardvarks, while the dolphin is classified as Laurasiatheria, which also includes the red panda, hippos, horses, rhinoceros, and bears. You can click on the links above for more detailed lists of the species included in each group.

Although about 100 million years separate manatees from dolphins, the manatee and elephant are only separated by about 61 million years. Unlike dolphins, but like elephants, manatees have toenails:

By Fritz Geller-Grimm, via Wikimedia Commons

2. Manatees convergently (independently) evolved the ability to live under water
Unlike other mammals that live primarily in the water (whales and dolphins), the manatee (and dugong) does not breath air through a blowhole on top of its head. Instead, manatees breath through their nostrils. How cool is that?

By Rusty Clark from Merrit Island FL via Wikimedia Commons

Additionally, manatees independently evolved flippers and wide tails.

Manatees also convergently lost most of their hair (although this isn't unique to water-dwelling mammals as many terrestrial mammals lost most of their hair too, including pigs, naked mole rats, and humans). I wonder whether similar genes are involved (disrupted?) to result in the loss of hair across these mammals?

3. Manatees have a much lower metabolic rate than expected for their body mass.
Manatees are fairly sedentary, and have a low metabolic rate (0.36 times the predicted rate for placental mammals). Dolphins have a much higher metabolic rate, but a similar expected lifespan as manatees (approximately 50-60 years, to my understanding). So, it will be fascinating to investigate how genomes differ between fspecies with similar generation times, but very different metabolic rates.

Running.

In October I completed my longest race: 13.1 miles. Scott and my dad raced also, and Little Bear came along for the ride (a good friend watched her while we ran).

All ready to go before the race.

I did pretty well for the first half. In fact, I must have been doing a pretty good pace for me (as you'll see at the end). Most of the time I was trading places, forward and back with these two (If you haven't heard of you it, you can read more about The Blerch):

The people in front of me most of the race. 

Then, after the half-way mark I felt a strong *pop* in my left knee, and a lot of pain. I couldn't run without extreme shooting pain in my knee, but I could walk. I could even walk quickly. So I did. I speed walked the rest of the race. Luckily there were people like this to keep us motivated:

Motivation.

I finished with a 13 minute per mile pace. At the end of the race I got some ice for my knee

Finished!

It took a few days before I could use stairs without pain. Three weeks after the half-marathon I ran a 10k race, but had quite a bit of discomfort. Then we ran a family 5k for polio research, with some pain in my knee for the last mile. Over the last several weeks I haven't run much, because of travel, so I was hoping everything would be healed.

Today we accomplished half of our family Thanksgiving traditions; we ran our annual family Turkey Trot, a 5k. Everything felt good (except for being a little out of practice), until the last couple blocks. So, I'm not completely healed yet, but on my way.

Platypus, platypus, platypus, platypus!

Platypuses at Berkeley's Museum of Vertebrate Zoology

The platypus is currently tied for my favorite mammal (along with hedgehogs and manatees). Platypuses have a lot of unique characteristics, but one of the features I find most fascinating is their sex chromosomes. Before a post about their chromosomes, there's a few things we need to clear up.

1. The platypus is not a "cross" between a duck and a beaver.
Because of its unique features, there is a lot of confusion about the platypus. The platypus is not some strange hybrid. A duck and a beaver cannot produce an offspring together. The population of platypuses evolved, like all other living organisms.

Upon closer inspection, looking at the picture above, the platypus bill looks very little like a duck bill at all. The platypus bill is wide and flat, and appears to be more leathery than the hard duck bill.

By DickDaniels (http://carolinabirds.org/) (Own work) via Wikimedia Commons

And, even though popular cartoons continue to draw its tail as if it were beaver-like, the platypus tail is relatively short, and is covered with soft brown fur, not at all like a beaver's large hairless tail:

The beaver has a large, flat, hairless tail. By Steve, Washington, DC via Wikimedia Commons

2. The platypus is not the ancestor of modern mammals, it is a modern mammal. 
Although it lays eggs, and doesn't have breasts or nipples, the platypus is still classified as a mammal. Platypuses are part of the group of egg-laying mammals called "monotremes." These are not "proto-mammals." Nor are they "primitive". Monotreme mammals have been evolving for the same amount of time as all other mammals. As humans we share a common ancestor with platypuses, approximately 220 million years ago. That doesn't mean that it isn't useful to understand more about the platypus, but interpretations should be careful not to assume the platypus has maintained the ancestral state of all mammalian traits.

3. The platypus is not the only egg-laying mammal. 
In addition to the platypus, there is another group of monotreme mammals that lay eggs: Echidnas. Echidnas and platypuses diverged from one another about 64 million years ago. While they share some characteristics that are unique to monotreme mammals (relative to other mammals), such as egg-laying and oozing milk out of mammary pores instead of having nipples, the two groups of species have accumulated many differences. Perhaps one of the most notable is that there are at least four species of echidna, and only one species of platypus.

Other cool echidna features include their body covering which includes a mixture of course hair and dense, pointy, spines.

Echidnas at Berkeley's Museum of Vertebrate Zoology

Echidnas also have long durable nails that they use for digging in the sand and dirt.

Check out those nails.

4. Platypuses are about the size of a house cat
I don't know why, but when I was growing up, I always imagined that platypuses would be fairly large critters - not unlike a recently discovered branch in the platypus tree that went extinct 5-15 million years ago. Turns out, modern platypuses are actually about the size of a house cat. You can see the pictures below  with my hand next to them.

Not so giant platypus.

If you want to see a live platypus (which I really, Really, REALLY do!!), check out this video of some people hand feeding a platypus.

Cheeseballs.

Me and Little Bear (2.5) enjoying a beautiful day together.

All the (super) cool kids are doing it

One of the super-fun properties of water is that, under certain conditions, and without many impurities, you can cool it slightly beyond its freezing point (called "super cooling"), then perturb the system, and instantly freeze the water.

What you need for this experiment:

1. Filtered water (some tap water will work, but bottled waters generally work well).

2. Salt and ice water mixture (ice made from tap water is fine) in a 3/4 ratio of salt/ice water

3. Large bowl/container

Instructions:

1. Mix the salt and ice water so that it is dense with ice, and will support your bottles of water.

2. Open lids on filtered water (Opening lids after the bottles are super-cooled could lead to instant freezing. You can leave the lid on loosely, or just take it off.).

3. Sit bottles of water in the salt and ice water mixture for approximately 40 minutes. You may need to check on them slightly before. It is good to have a "tester" bottle of water that you can check to see if the water is super-cooled.

4. After water is super-cooled, pour onto a substrate (ice works well). This will perturb the system and lead to instant freezing of the super-cooled water.

You can find alternative instructions here. 

Observe:

Science is awesome.

Keeping busy

Scientists do lots of things! Here's a little bit about what I've been up to lately:

The Nielsen lab had our second annual retreat. At this meeting we all gave short "chalk talks" about current research we're working on, discussing challenges how to collaborate.

Sept 26: Nielsen lab retreat at Bodega Marine Laboratory 

On Saturday October 5, 2013 Berkeley hosted the Bay Area Population Genomics meeting (it was my turn to organize it this time around). The tweets from the conference are Storified here, and photos are on Flickr.

Oct 5: Introducing Keynote Speaker, Hideki Innan at BAPG IX

The very next day we drove down to San Jose, joined by my dad, where the adults completed the San Jose Rock & Roll Half-Marathon (a first for all three of us!)

Oct 6: Preparing for the San Jose Rock & Roll Half-marathon

The daycare that Little Bear attends was closed for Columbus Indigenous People's Day, so we took the opportunity for a family visit to the Oakland Zoo.

Oct 14: Oakland Zoo

Last week I had my annual eye exam (I actually did better than last year, likely because we're all sleeping better), and got a lot of science done. I finalized revisions and resubmitted my manuscript on human Y diversity, finished peer-reviewing a manuscript, finalized most of my job applications, and met with my current research students to form plans for wrapping up projects by the end of the semester. We also took a family trip to a park down the street after work/daycare.

Oct 16: Playground time. The similarity between their smiles is striking here.

Oh, and on Friday we had a field trip instead of lab meeting; we toured the Museum of Vertebrate Zoology, guided by Jim Patton (more pictures here).

Oct 18: I got to feel platypus fur!!!!

Last weekend we ran some more. I ran 10K (6.2 miles) in the Berkeley 510 race starting at Golden Gate Fields, while Scott completed 8 miles (!!) around town afterwards.

Oct 19: Berkeley 510 10K race

This week is turning out to be another busy one. Today I accepted an invitation to review another manuscript, and attended a session with a panel discussion about the academic job process. Tonight I was very flattered to accept an invitation to attend the "Scholar's Dinner" hosted by an undergraduate student researching with me, Michelle Senar, and her sorority. I had a wonderful time talking with the students about science, life, and future plans.

Oct 21: Scientists before dinner

Tomorrow I give my "finishing talk" for the Miller Institute (am I really in my third year already?!), then need to pack and enjoy the afternoon with my family before getting on a plane to fly to Boston for the annual meeting of the American Society of Human Genetics, where I'll be tweeting (@mwilsonsayres; #ASHG2013).

At the conference I am co-moderating a session on Wednesday:

Wednesday, October 232:00 PM–4:15 PMConcurrent Platform (abstract-driven) Session A (10-18)
SESSION 10 – Which Comes First: The Sequence or the Biology?Hall B2, Level 0 (Lower Level), Convention Center

Moderators:	Maja Bucan, Univ. of Pennsylvania
	Melissa Wilson Sayres, Univ. of California, Berkeley

I will be presenting a poster on Friday. I've uploaded it to FigShare, and it already has over 200 views, which I'm pretty sure is more than the number of people who will stop by and see it on Friday (though I'm not counting that out yet).


Then, catching a flight back to California.

Whew!!

What makes a mammal?

Cross-posted at PandasThumb.

I saw a tweet wondering about what makes an animal a mammal:

@realscientists If a tiger shark's eggs hatch inside it and are born live (I saw a pic recently) is it a mammal or a fish? :-)
— Fiona Howie (@MummyFiFi) September 29, 2013

So, I thought I'd go through a few of the common ideas about shared physical features of mammals.

What makes a mammal? 
Is it giving live birth? Or having hair/fur? What about feeding their babies milk?

Well, kind of (I'll tell you at the end what really does). First, let's go through these three:

Live birth.
Not all mammals give live birth. Monotreme mammals including the echidna:

Short-beaked echidna. Photo by Fir0002/Flagstaffotos

and platypus:

Swiming Platypus. Photo by Peter Scheunis

don't give birth to live young; They lay eggs.

Okay, so not all mammals give birth to live young.

Hair.
What about having hair/fur. All mammals have hair/fur, right?

Well, I suppose technically baby dolphins have whiskers, but you wouldn't know it from the adults.

By U.S. Navy photo by Photographer's Mate 1st Class Brien Aho. [Public domain], via Wikimedia Commons

Pangolins, with their armor-like plates, actually have a little bit of fur on their underside (although it'd be hard to tell):

By Valerius Tygart (Own work) [CC-BY-SA-3.0 or GFDL]

And naked mole rats technically aren't completely naked, they also have whiskers (but they are mostly naked):

By Ltshears - Trisha M Shears [Public domain], via Wikimedia Commons

So, we'll give hair a maybe. Mammals do have hair, but there are several cases where one might mistake a mammal for not having hair.

Milk.
Do all mammals feed their babies milk?

By Trish Steel [CC-BY-SA-2.0], via Wikimedia Commons

First, the snarky answer - No. Male mammals generally do not make milk (although they could).

By User:Ltshears, edited by User:julielangford [Public domain]

Second, more serious answer - Yes. I don't know of any species of mammal that nourishes their offspring with anything other than milk. To learn more about mammals, lactation, and milk, check out the blog "Mammals Suck (... Milk)" by Dr. Hinde.

Breastfeeding. By honey-bee [CC-BY-2.0]

Actually, what makes a mammal is more than just whether they give live birth (because not all do), and have hair, and lactate. And doing each of these things does not necessarily mean the animal should be classified as a mammal. (Note: Although it gives live birth, a tiger shark is not a mammal, it is a shark; sharks are a kind of fish.)

So, what does make a mammal?

Shared evolutionary history
Mammals are a group of species related by their evolutionary history. The picture below is a phylogenetic tree showing the evolutionary relationship between many different species.

CT Amemiya et al. Nature 496, 311-316 (2013) doi:10.1038/nature12027

All mammals share a common ancestral population.

Modified from: CT Amemiya et al. Nature 496, 311-316 (2013) doi:10.1038/nature12027

The classification of "Mammals" was made based of shared physical and anatomical characteristics. But, underlying those, is a shared evolutionary history.

We do make sub-divisions within that larger grouping of mammals. For example, the egg-laying mammals, platypus and echidna are called "Proto-theria", while all other mammals are called "Therians". There are many other sub-classifications, but they are all still part of the broader group of mammals.

There are also larger groupings. For example, on the picture above you can see all the species highlighted in pink are called Tetrapods. These are all descended from a common ancestral population of tetrapods that are generally four-limbed vertebrates.


Although their physical characteristics may change, all species that descended from the common ancestral mammal population will all be mammals.

So, how do you tell what a mammal is? 
Well, the broad rules of thumbs still apply. If you are a Naturalist, roaming through some uncharted region, and you happen across an animal you've never seen, you can start with some of the general physical characteristics (e.g., is it warm-blooded? does it have fur?). But, now you can also take a look at it's DNA as another line of evidence.

You can collect and sequence a sample of DNA from hair, or blood, or a toenail, or even from scat (aka poop), then compare the sequences you find with sequences that are already available to learn more about the creature you sampled. You can build a tree (like the one above) based on the similarity between the sequences. The relationship between the sequences for any one region or gene may not reflect the broader species tree, but it will give you an idea of where your species fits. And, the more DNA sequence you analyze, the better your resolution will be come (although it sometimes happens that biology is just messy).

Mammals
"Mammals" is the term we use to describe the group of species that generally share a defined set of characteristics (warm blooded, lactating, give live birth, have fur/hair), AND share an evolutionarily recent (300ish million years ago) common ancestral population.