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Thursday, January 27, 2011

A species by any other name...would leave us with the same problem

ResearchBlogging.org
This is a great big week for anthropology coverage. The sequencing of the orangutan (Pongo species) genome made the cover of Nature. It's grant-writing-dissertation-formulating-prelim-studying time for me so I haven't had a chance to read this one yet. Science has a couple paleoanthropology-related stories, including two by Ann Gibbons. The first is about recent research on ancient DNA, and how this informs the debate about 'modern human' origins. But there's also a short blurb on what the eff "species" means.

This is a great effing question! The textbook species definition is that proffered by Ernst Mayr: populations of actually or potentially interbreeding individuals, capable of producing viable (and fertile) offspring. Cool, so a dog and a cat are different species because if they mated (ew) no ungodly animal would come from this monstrous union. Expensive high-tech multivariate Scientific reconstruction simulations show the abomination would probably look like this:

But there are many "good" plant and animal species that do mate and reproduce successfully ('hybridize'). Very often these hybrids are sterile, but then very often they're not. This has led researchers to come up with scores of other ways to define species (Holliday (2003) has a great discussion on the matter).

Worse, there's no way to measure, genetically or morphologically, just how different things should be before they can be called different species. The late Morris Goodman and others (Wildman et al. 2003) argued that humans and chimpanzees are so genetically similar that chimps, now in the genus Pan, should be moved to our genus Homo to denote how similar we are. But any other, non-genetic comparison would put our chimp cousins in a very different group from us. Moreover, the effects of hybridization seem, to me at least, to be fairly unpredictable, at least superficially. That is, the outcome of hybridization is highly contingent on what animals are hybridizing, and on these lineages' own evolutionary histories (this is the intractable problem that made me abandon doing hybrid work for my dissertation. Some day though...).

A major issue relates to what I blogged about yesterday: both 'species' and 'hybrid' are terms we've found ourselves with, but they have no inherent meaning in themselves, other than whatever we give them. So it's funny to read this from Gibbons' story:
In the real world, [Jean-Jacques Hublin] says, Mayr's concept doesn't hold up: "There are about 330 closely related species of mammals that interbreed, and at least a third of them can produce fertile hybrids."
But is it Mayr's species concept that's flawed, or was it misguided to have put these hybridizers into different species in the first place? Should we delineate species based on our a priori conception about whether two things are different, or should a definition of 'species' determine what we call them? Or does it even matter?

To this end, Gibbons's other story describes the morphologically-unremarkable Denisova fossils as belonging to "a new type of human." Well, now what the eff does that mean? We're back to "The Species Problem" (the title of Gibbons's article), but with a new term. And pretend for a moment that the Denisovan fossils didn't yield DNA: the pinky and tooth probably would not have made headlines. Pretend they did have diagnostic cranial remains - would we have recognized them as being so distinct as their genes indicate?

For that matter, I wonder how many arguably 'modern' human fossils would still retain the modern moniker if we could analyze their genes...

References
Gibbons, A. (2011). The Species Problem Science, 331 (6016), 394-394 DOI: 10.1126/science.331.6016.394

Gibbons, A. (2011). A New View Of the Birth of Homo sapiens Science, 331 (6016), 392-394 DOI: 10.1126/science.331.6016.392

Holliday, T. (2003). Species Concepts, Reticulation, and Human Evolution Current Anthropology, 44 (5), 653-673 DOI: 10.1086/377663

Wildman, D. (2003). Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: Enlarging genus Homo Proceedings of the National Academy of Sciences, 100 (12), 7181-7188 DOI: 10.1073/pnas.1232172100

Wednesday, January 26, 2011

Statistics: Friend or Foe?

ResearchBlogging.org
In this week's Science, Greg Miller describes recent uproar about a study that claims to have scientific support for the existence of extrasensory perception (ESP). Of course, ESP being in the realm of the paranormal, it ought to be somewhat outside the purview of Big Science.

But who cares about ESP?! What comes under scrutiny is statistics, the mathematical theory underlying hypothesis testing. And inference. The brief story is worth a read, as it cites statisticians on what these statistical tests actually tell us, as well as the ups and downs of Bayesian stats.

An important thing to keep in mind is that no matter how mathematical, statistics is nevertheless like everything else in science - a human endeavor. No matter how creative and insightful humans can be, there's always a limit to our ability to decipher the world around us. I'm certainly not decrying statistics, but it's important to keep in mind that these aren't just handed down to us from on high. We human beings play a critical (and often subjective) hand in how we apply statistics to address our research questions.

Along these lines, just last night I was reading about body mass variation in the Gombe chimpanzees (Pusey et al. 2005), and the authors provide a very insightful quote from statistician George Box:
All models are wrong; some models are useful.
As I added to this on Facebook, "... some models can be hott."

References
Miller G (2011). Statistics. ESP paper rekindles discussion about statistics. Science (New York, N.Y.), 331 (6015), 272-3 PMID: 21252321

Pusey, A., Oehlert, G., Williams, J., & Goodall, J. (2005). Influence of Ecological and Social Factors on Body Mass of Wild Chimpanzees International Journal of Primatology, 26 (1), 3-31 DOI: 10.1007/s10764-005-0721-2

Thursday, January 20, 2011

Dobzhanksy on Posh Hybrids

Long-time readers may recall that one thing I wish I did active research on is hybridization: the crossing of divergent species or lineages, the developmental abnormalities arising from hybridization, and the potential role of hybridization in human evolution. One such developmental abnormality is "heterosis," a.k.a. 'hybrid vigor.' In general, heterosis refers to any trait in hybrids that is larger than the average of the two parents' (or the parents' species) values for that trait. The phenomenon was recognized in plant domestication as far back as the 19th century - crosses between different plant (namely corn) strains produced hybrid strains with much greater yield than their parent species.

Implicit in the term is that heterosis, or larger size, is a more adaptive condition than found in the parents. Here's what the late, brilliant Theodosius Dobzhansky (1950: on hybrids: 557) had to say on the matter.
The advisability of applying the term "heterosis" to cases in which heterozygotes are larger in body size, or show "increases" in any "traits," but no evidence of higher adaptive value compared to the corresponding homozygotes, is open to question. Perhaps the word "luxuriance" would be a better designation for such cases, the word "heterosis" or "euheterosis" to be used for adaptive superiority of heterozygotes to homozygotes. . . . it is clear that the mechanisms underlying euheterosis and luxuriance are quite different.
I wonder if these luxuriant (not heterotic) hybrids also love diamonds, yoga and kopi luwak coffee?
Reference
DOBZHANSKY T (1950). Genetics of natural populations. XIX. Origin of heterosis through natural selection in populations of Drosophila pseudoobscura. Genetics, 35 (3), 288-302 PMID: 15414931
ResearchBlogging.org

Tuesday, January 18, 2011

Speciation and reticulation

ResearchBlogging.org Hey, "all you lovers out there," which is how Marvin Berry introduced "Earth Angel" at the Enchantment Under the Sea dance back in good-olde 1955. And by "lovers" I mean "geneticists."

Poring over the recent Neandertal nuclear genome paper (Green et al. 2010) for seminars, we're struck by two contradictory ideas. On the one hand, the authors demonstrate pretty convincingly that Neandertals and the more 'anatomically modern' humans of Europe and Asia interbred. This doesn't come from genetic comparisons of Neandertal and contemporaneous human fossils, but of Neandertals with living humans traipsing modern soil. But on the other hand, the authors estimate the time of the divergence of Neandertal and living human populations.

Herein lies the rub:
"Population divergence [is] defined as the point in time when two populations last exchanged genes." (Green et al. 2010: 717)
Which they estimate, based on genome sequence divergence and some other assumptions, to be anywhere from ~270,000 - 440,000 years ago. But then this:
"[The Out-of-Africa] model for modern human origins suggests that all present-day humans trace all their ancestry back to a small African population that expanded and replaced [Neandertals] without admixture. Our analysis of the Neandertal genome may not be compatible with this view because Neanertals are on average closer to individuals in Eurasia..." (Green et al. 2010: 721)
Though they say "may not" they probably should've just said "isn't." Either way, they estimate an ancient date at which the groups in question "last exchanged genes," but also demonstrate that these populations last exchanged genes much more recently.

So what is "population divergence," then? As a wise man asked, "what does divergence mean when there is reticulation?" (I'm assuming he would prefer to go nameless) Reticulation referring not to pythons or chipmunks, but to mating between individuals in different populations. Is "divergence" not so much the last time genes were exchanged, but rather the time when the genomes began to become different?

Now that I bring it up, wouldn't it also be neat to see a fight between the reticulated python and northern reticulated chipmunk?

Reference
Green, R., Krause, J., Briggs, A., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M., Hansen, N., Durand, E., Malaspinas, A., Jensen, J., Marques-Bonet, T., Alkan, C., Prufer, K., Meyer, M., Burbano, H., Good, J., Schultz, R., Aximu-Petri, A., Butthof, A., Hober, B., Hoffner, B., Siegemund, M., Weihmann, A., Nusbaum, C., Lander, E., Russ, C., Novod, N., Affourtit, J., Egholm, M., Verna, C., Rudan, P., Brajkovic, D., Kucan, Z., Gusic, I., Doronichev, V., Golovanova, L., Lalueza-Fox, C., de la Rasilla, M., Fortea, J., Rosas, A., Schmitz, R., Johnson, P., Eichler, E., Falush, D., Birney, E., Mullikin, J., Slatkin, M., Nielsen, R., Kelso, J., Lachmann, M., Reich, D., & Paabo, S. (2010). A Draft Sequence of the Neandertal Genome Science, 328 (5979), 710-722 DOI: 10.1126/science.1188021

Friday, January 7, 2011

Human Tears Are Not Sexy


Let's have a mature, adult conversation for a moment. I understand that there are lots of things in the world that turn people on in a sensual sort of way. People get aroused by the strangest things, stuff that when you hear about it you think you're being lied to. But women's teardrops are not such a fetish, at least not among the men in a recent study.

Shani Gelstein and colleagues report in the journal Science that human tears not only fail to arouse male test subjects, but the smell of tears actually decreases arousal. The researchers had men sniff two womens' "negative-emotion-related" tears, which were induced by having the women watch sad movies all alone :(

Apparently, most men will think a woman in a picture is less hott (see Tanya Harding, right), when he has just smelled the human female tears that soak the cloth taped to his lip. Having now considered it, I suppose having tears taped under my nose would probably not be an expeditious way to arouse me, either. I shudder at the thought of the man who finds a vial of tears the choice aphrodisiac.

What's more, when the male test subjects smelled plain, unadultered saline solution (as a control) they were less likely to think, "Buzz, your girlfriend - wuff!' but were more amenable think damngrrrl. Testosterone levels also declined after tear treatment, as did sex-related brain activity. Which I figure is synonymous with death for a man. Apparently human female tears send a chemical signal that males receive and it keeps their minds from contemplating ribald grabassery.

So why do humans cry when we get sad? Are tears mere spandrels in the sense of Gould and Lewontin (1979), or do they really serve some adaptive purpose for us? I figured it was so other people could more easily detect if we were upset and thereby take advantage of our weakness. But Gelstein and her crew of tear harvesters make a pretty compelling case for some kind of chemical signal. After all, the men never saw pictures of women crying - the women just stared off plain-faced - what differed was males' olfactory exposure to the salty milk of female sadness.

Another question they raise is an interesting one - do all tears make people find others sexually unappetizing? Would women react the same way to man-tears, how would children react to their grandparents' tears? Or what about our tears from crying because of the 'e pluribus anus' flag on Community? Is sexual de-arousal even the selected purpose of tears in the first place?

Needless to say, I'm concerned about our tears. But I'm not gonna cry about it, because it might make others think I'm not sexy. Which would be outrageous.

ResearchBlogging.org
References
Gelstein S, Yeshurun Y, Rozenkrantz L, Shushan S, Frumin I, Roth Y, & Sobel N (2011). Human Tears Contain a Chemosignal. Science (New York, N.Y.) PMID: 21212322

Gould, S., & Lewontin, R. (1979). The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme Proceedings of the Royal Society B: Biological Sciences, 205 (1161), 581-598 DOI: 10.1098/rspb.1979.0086

Saturday, January 1, 2011

01/01/2011: Looking forward and backward, so fast you may barf

2010 was a big year for anthropology and lawn-chair-anthropologists. There was laughter and crying, and maybe also some yelling. And smiling. Let's take a look back at some of the big events of the past year.
  1. Ancient DNA. What a great year for ancient human DNA! In April, Krause and colleagues (2010) announced the sequencing of mitochondrial DNA from a ~50,000 year old girl from Denisova in Siberia. This sequence was twice as divergent from humans as Neandertal mtDNA, which really shocked a lot of people. Then just a week or so ago Reich and colleagues (2010) announced nuclear DNA from the site. The big news was that these ancient humans contributed genes to modern day Melanesians, but not other modern humans sampled. In May, Green and the Pääbo lab announced a draft sequence of the Neandertal nuclear genome. Like with the Denisova story, Neandertal mtDNA is fairly distinct from that of modern humans, and the nuclear genome revealed contribution to some modern humans but not to others. Basically, ancient DNA came out supporting the multiregional model of modern human origins.
  2. Malapa hominids. Lee Berger and researchers announced a new fossil site, Malapa, in South Africa. This site yielded 2 partial skeletons (and others forthcoming), including a very well-preserved skull of a subadult. Superficially the thing looked to me like Australopithecus africanus, though the authors argue that it shows some features derived toward the condition of early Homo. But at an estimated 1.9-1.7 million years old, it's a little too young to have anything to do with the origin of Homo - not to mention its small 400 cubic centimeter cranial capacity. I really don't know what to do with Malapa yet.
  3. Woranso-Mille Australopithecus afarensis. This site dates to around 3.6 million years ago, so it's roughly contemporaneous with Laetoli afarensis, or intermediate in age between Laetoli and later afarensis sites like Maka and Hadar. Haile-Selassie and colleagues described a partial skeleton from the site. This male includes part of the pelvis, which didn't get much coverage. But it has a 1st rib, scapula and clavicle, indicating a fairly human-like (rather than ape-like) torso shape. So even for how well we know A. afarensis, we're always learning more about our ancestor.
  4. Saadanius hijazensis and catarrhines. I didn't blog about this one at the time as I was getting ready to hit the field. But this was exciting because Iyad Zalmout and friends here at UM discovered and analyzed it. Saadanius was found in ~29 million year old deposits in Saudi Arabia, right around the estimated time of origins of apes. The fossil looks like an Aegyptopithecus to my untrained eye, but apparently may be similar to the last common ancestor of apes and old world monkeys.
  5. Field work. I had my first (of hopefully more!) field season at Dmanisi in Georgia. Paleoanthropology would be nothing without fossils, so an important aspect of the job I'd like to do more of is increasing the fossil record. Dmanisi is an amazing place for this, being among the oldest human sites outside Africa, and the interesting 'intermediacy' of the Dmanisi hominids between early Homo and more classic H. erectus. We found some great stuff last year, and I anticipate the site will produce more great fossils in the future. Who knows, maybe more fossiliferous deposits will be found in nearby regions?
So it was a helluva year, 2010. What excitement will 2011 bring? Here are some things I'd like to, or expect to, see this year:
  1. More ancient DNA - the surprise that many researchers got from Denisova and Neandertal ancient DNA clearly warrants more work on other ancient DNA. What does that of other fossil humans look like? Will the picture of human origins become further complicated (that is, different from paradigmatic out-of-Africa replacement)? In this regard we need to analyze DNA from more late Pleistocene fossils regarded as 'anatomically modern.'
  2. a) More about Malapa. I want to say I heard somewhere that there were more hominids than just the 2 presented in the Science paper. These additional specimens will provide further evidence, including what variation within the site was like, and how it fits with other South African specimens. From the appearance of things, these fossils may be late-persisting A. africanus, somehow contemporaneous (roughly sympatric?) with A. robustus and possibly early Homo. Perhaps more work on the geology and taphonomy of Malapa will show it to be older, contemporaneous with the nearby site of Sterkfontein known for abundant A. africanus fossils? Probably not.
    b) More hominid sites and fossils in South Africa. One thing that was neat about Malapa was that it was from slightly outside the rest of the South African 'cradle' sites like Sterkfontein, Kromdraai, Drimolen, and Swartkrans. When I was in the area in 2008 I went with some researchers on survey of the Sterkfontein valley, new sites are definitely being sought. Perhaps 2011 will see the discovery of more Malapa-like sites?
  3. Human fossils from East Asia. Maybe even ancient DNA recovery from the region. East Asia has long been thought to be a potential 'center' of human origins. Earlier in the year, fossils coming from Zhirendong suggest some of the earliest evidence of chin, arguably a 'modern human' feature. Recent fossil and genetic discoveries ought to usher a renewed vigor in examining human evolution in Asia.
That's all I feel like doing for now. Happy New Year, all!
ResearchBlogging.org

References
Berger, L., de Ruiter, D., Churchill, S., Schmid, P., Carlson, K., Dirks, P., & Kibii, J. (2010). Australopithecus sediba: A New Species of Homo-Like Australopith from South Africa Science, 328 (5975), 195-204 DOI: 10.1126/science.1184944

Cann, R., Stoneking, M., & Wilson, A. (1987). Mitochondrial DNA and human evolution Nature, 325 (6099), 31-36 DOI: 10.1038/325031a0

Green, R., Krause, J., Briggs, A., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M., Hansen, N., Durand, E., Malaspinas, A., Jensen, J., Marques-Bonet, T., Alkan, C., Prufer, K., Meyer, M., Burbano, H., Good, J., Schultz, R., Aximu-Petri, A., Butthof, A., Hober, B., Hoffner, B., Siegemund, M., Weihmann, A., Nusbaum, C., Lander, E., Russ, C., Novod, N., Affourtit, J., Egholm, M., Verna, C., Rudan, P., Brajkovic, D., Kucan, Z., Gusic, I., Doronichev, V., Golovanova, L., Lalueza-Fox, C., de la Rasilla, M., Fortea, J., Rosas, A., Schmitz, R., Johnson, P., Eichler, E., Falush, D., Birney, E., Mullikin, J., Slatkin, M., Nielsen, R., Kelso, J., Lachmann, M., Reich, D., & Paabo, S. (2010). A Draft Sequence of the Neandertal Genome Science, 328 (5979), 710-722 DOI: 10.1126/science.1188021

Haile-Selassie, Y., Latimer, B., Alene, M., Deino, A., Gibert, L., Melillo, S., Saylor, B., Scott, G., & Lovejoy, C. (2010). An early Australopithecus afarensis postcranium from Woranso-Mille, Ethiopia Proceedings of the National Academy of Sciences, 107 (27), 12121-12126 DOI: 10.1073/pnas.1004527107

Krause, J., Fu, Q., Good, J., Viola, B., Shunkov, M., Derevianko, A., & Pääbo, S. (2010). The complete mitochondrial DNA genome of an unknown hominin from southern Siberia Nature, 464 (7290), 894-897 DOI: 10.1038/nature08976

Liu W, Jin CZ, Zhang YQ, Cai YJ, Xing S, Wu XJ, Cheng H, Edwards RL, Pan WS, Qin DG, An ZS, Trinkaus E, & Wu XZ (2010). Human remains from Zhirendong, South China, and modern human emergence in East Asia. Proceedings of the National Academy of Sciences of the United States of America, 107 (45), 19201-6 PMID: 20974952

Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin JJ, Kelso J, Slatkin M, & Pääbo S (2010). Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature, 468 (7327), 1053-60 PMID: 21179161

Zalmout IS, Sanders WJ, Maclatchy LM, Gunnell GF, Al-Mufarreh YA, Ali MA, Nasser AA, Al-Masari AM, Al-Sobhi SA, Nadhra AO, Matari AH, Wilson JA, & Gingerich PD (2010). New Oligocene primate from Saudi Arabia and the divergence of apes and Old World monkeys. Nature, 466 (7304), 360-4 PMID: 20631798