john hawks weblog

paleoanthropology, genetics and evolution

taxonomy

  • Taxonomy through art

    Sun, 2011-10-23 11:50 -- John Hawks

    Within paleoanthropology, we often witness taxonomic clashes. Species that were named on the basis of a single fossil are later discarded. Now with genomics, we can see that the fossil "species" we named for Late Pleistocene humans in fact extensively interbred with each other. I have found it interesting over the last year to talk with artist reconstructors about the way they incorporate this information into their works.

    I was pointed to an essay by James Prosek, a biological artist best known for his books illustrating fish (James Prosek's Amazon page). As he matured as an artist, he discovered that the lines in nature are sometimes blurry, and science sometimes changes much more than nature. The essay was originally printed in the March 2008 issue of Orion ("The failure of names").

    As I painted trout through my late teens, major shifts in trout taxonomy were taking place. Through genetic analysis, which was fairly new in the early ’90s, it was discovered that rainbow trout (from the Pacific coast) and brown trout (introduced from Europe) were not as closely related as once thought. The genes showed that the rainbow trout was more closely related to Pacific salmon, fishes that die when they spawn, of the genus Oncorhynchus. The brown trout was more closely related to the Atlantic salmon, and remained in the genus Salmo. The native trout of my home state, Connecticut, the brook trout, was actually a whole separate genus, Salvelinus, more closely related to the Arctic char than to the rainbow or brown trout. Technically, it was no longer correct even to call the book I was working on Trout. I found myself wanting to ignore the namers because they were getting in the way of my own personal vision.

    The essay recounts how Prosek surpassed this clash with taxonomy. He travelled extensively during the research for his second book, Trout of the World, and explored the variability within (and continuities among) taxonomic groups. His artistic process led him to experiment with visual forms that could communicate both the natural variation and science's

    After drawing curvilinear lines, first emanating from the points on the body of a seahorse, I realized the lines were helpful as visual aids to point out particular parts of a creature that I wanted to bring attention to. The lines activated the space around the animal in a satisfactory way, erasing the need for the name to be written beneath. In this way, the lines became a very personal visual taxonomy, replacing the lingual one.

    (via Karen James)

    Tags: 
    art in science
    species concepts
    taxonomy

  • Primate classification and phylogeny

    Wed, 2011-10-12 13:07 -- John Hawks

    Our relationship to other kinds of primates is in part reflected by the pattern of similarities and differences we share with them. This pattern of similarities and differences is also used to classify different primate species into groups. There are six major branches of primates, classified as superfamilies. These include:

    Lemuroidea
    including the lemurs of Madagascar
    Lorisoidea
    including lorises and galagos
    Tarsioidea
    with the tarsiers
    Ceboidea
    or New World monkeys
    Cercopithecoidea
    or Old World monkeys
    Hominoidea
    including apes and humans

    The last three of these, hominoids, cercopithecoids and ceboids, share a common ancestor that lived sometime before 55 million years ago. These three superfamilies form a single branch, or clade, on the primate evolutionary tree.

    Scientists have often grouped these superfamilies into two major categories, called grades, which express the broad adaptations shared by different groups. Grades are not necessarily evolutionary lineages, but are meant to express the ways that different lineages share common sets of adaptations. One of these grades, the prosimians, includes lemurs, lorises, galagos, and tarsiers. Prosimians share a basic set of adaptations with other primates, including binocular vision, a slower rate of reproduction than many mammal groups, nails on the toes and fingers instead of claws, and other adaptations to life in the trees.

    Other primates include the monkeys, apes, and humans, who are grouped as anthropoids. Unlike the prosimians, the anthropoids form a single evolutionary lineage, or clade, because monkeys, apes, and humans are more closely related to each other than to any other living group. The evolutionary relationship of the anthropoids leads them to share many derived features, including

    Classification and phylogeny of living primate superfamilies

    Lemuroidea

    The lemurs are living and fossil primates of Madagascar. Lemurs share several derived features with lorises, including a set of closely-spaced and projecting lower incisors and canines, called a tooth comb, and a claw rather than a nail on the second toe. Both these features are used for grooming, and are so specialized relative to other primates, that lemurs and lorises may be classified as sister groups in a single clade, called the Strepsirrhini, a relationship supported by the close genetic relationship of the two superfamilies. Lemurs and lorises also share general features that were most likely present in the earliest primates, including a single postorbital bar instead of a bony enclosure for the eye orbits, and an external nose membrane connected to the upper lip.

    Today, the lemurs include five distinct families, all limited to Madagascar. These range in size from the mouse lemurs, which are the smallest living primates at only 60 grams, to the indri, approaching 10 kg. The most divergent living lemuroid is the aye-aye, a nocturnal creature with long bony clawed fingers and perpetually growing incisors, both supporting an adaptation to finding and eating grubs inside of wooden branches. The other lemuroids show a broad range of dietary and locomotor adaptations. Some species, like the sifaka, primarily leap using long hindlimbs and cling to vertical branches. Others are arboreal quadrupeds, or spend substantial time on the ground.

    In the recent past, a greater diversity of lemurs existed on Madagascar than remain today. Large extinct lemurs such as Megaladapis reached over a hundred kilograms at their largest, exceeding the size of female gorillas. Some large extinct lemurs appear to have had a sloth-like adaptation for below-branch suspension and feeding, and most of the larger forms primarily ate leaves. These lemur species existed within the past fifteen hundred years, and were likely driven to extinction by humans, who reached the island within that time period. The discovery of lemur skeletal remains in association with human archaeological sites confirms this extinction hypothesis.

    Lorisoidea

    The living lorisoids include galagos and lorises. Galagos, or bushbabies, are small prosimians weighing for the most part a fraction of a kilogram. Nocturnal creatures with large eyes and ears, and long tails, galagos are found across West Africa and into the central and southern portions of the continent. Galagos eat mainly fruits, insects, and gums, and some species are mostly quadrupedal, while others are adapted to leaping and a vertical posture. Lorises share a similar diet and a nocturnal activity pattern with the galagos, but differ in their relatively slow and deliberate style of foraging. Several species of lorises are distributed across Africa, South Asia, and Southeast Asia.

    Tarsioidea

    Tarsiers are small primates from the islands of Southeast Asia: Java, Borneo, Sulawesi, and the Philippines. Averaging slightly greater than 100 grams, tarsiers have several distinctive skeletal adaptations, including very long legs and ankles, immense eyes, and large hands and feet. These features support the adaptation of tarsiers of clinging to vertical branches and leaping between them, as well as their nocturnal activity pattern. Tarsiers eat insects, lizards, and other small vertebrates.

    The tarsiers share several features with anthropoid primates that may indicate a close phylogenetic relationship between the two. Unlike other prosimians, tarsiers lack a moist external nose, and they have a wide postorbital plate instead of a narrow bar. These and several more subtle cranial features link tarsiers with monkeys and apes. Many paleontologists believe that anthropoids may have originated from an Eocene group, called the omomyids. This group shares many features with living tarsiers and which may represent the common ancestor of both groups of living primates. If true, then the tarsiers are the closest primate relatives to the anthropoids, and the two groups form a clade called the Haplorrhini.

    Ceboidea

    Ceboidea includes the American, or New World, monkeys. Much of the earliest record of primate evolution, dating to greater than 40 million years ago during the Paleocene and Eocene, is from North America. These lineages apparently became extinct in North America by Oligocene times, and the New World monkeys that appear in the Oligocene of South America derive from an early Old World anthropoid lineage. The earliest anthropoid primates now known are from East Asia, which may have been the original source location for the anthropoids. Present-day New World monkeys possess three upper and lower premolars on each side, like most prosimians and the earliest anthropoids. This primitive dental formula distinguishes the New World monkeys from both the Old World monkeys and apes, which have only two premolars rather than three. Because of their round, forward-facing nostrils, the New World monkeys are called Platyrrhini, or flat-nosed, in contrast to the more narrow noses of the cercopithecoids and hominoids, which together are called Catarrhini, or downward-nosed. These differences imply that the platyrrhines existed as a lineage apart from catarrhines at least as early as 35 million years ago, when the first fossil catarrhines lived.

    South America was an island continent until around 5 million years ago, when the connection to North America arose. The first fossil New World monkeys date to the Late Oligocene, some 30 million years ago, meaning that these primates reached South America by an ocean crossing, probably an accidental journey on rafting vegetation from Africa. Once they reached South America, these monkeys underwent an impressive diversification. There are five living subfamilies of New World monkeys, with a total of sixteen genera. These vary from the relatively tiny callitrichines, including the marmosets and tamarins, to the relatively large atelines, including spider monkeys and howler monkeys, but most species range from one to five kilograms in mass. Several New World monkeys, including spider monkeys, howlers, and capuchin monkeys, have prehensile tails.

    Cercopithecoidea

    The cercopithecoids, or Old World monkeys, include two major groups. The cercopithecines, including macaques, baboons, guenons, and mangabeys, have a broad diet based on fruits, leaves, seeds, nuts, and insects. The colobines, including African colobus monkeys and Asian langurs and proboscis monkeys, tend to specialize to a greater degree on leaves in their diets. Old World monkey species have a diversity of anatomical adaptations to support these general patterns. The dietary diversity of cercopithecines is supported by broader incisors and low-crowned molars, typical of fruit eaters, and pouch-like cheeks for stashing food. Colobines have high-crowned molars for shearing leaves, and a large specialized gut for digesting leafy matter.

    A key adaptation shared by all living cercopithecoids is the distinctive shape of their molars. These teeth have cusps aligned into two high ridges extending across the tooth from side to side, a pattern called bilophodont. The ridges on the top and the bottom teeth interlock in opposing sawtooth patterns, creating a strong shearing action, ideal for reducing leaves and other fibrous plant matter, such as fruit rinds. This dental pattern is first found in fossil monkeys from the Early to Middle Miocene of East Africa. The living varieties of cercopithecoids arose later and underwent a major adaptive radiation during the Pliocene. Today the cercopithecoids include some of the most successful varieties of primates because of their geographic extent, the number of their species, and their dense populations.

    Hominoidea

    The hominoids include the living apes and humans, and their fossil relatives. The living great apes belong to four species, including orangutans, gorillas, chimpanzees, and bonobos. The gibbons and siamangs are in the hylobatid family, and include several different species sometimes called lesser apes. Humans and their extinct relatives are the hominins.

    Tags: 
    primates
    taxonomy
    phylogeny

  • A problem of fuzzy mammoths

    Sat, 2011-06-04 03:56 -- John Hawks

    Paleogenomics is changing the way we study evolution. In a number of cases, it now allows us to study extinct organisms with the same methods as we study living ones. A study last year in PLoS Biology[1] used genetic evidence from living elephants, extinct mammoths and mastodons, to reconstruct the times that these species diverged.

    Woolly and Columbian mammoths

    Mammoths are back in the news this week because of a paper by Jacob Enk and colleagues [2]. I think this paper represents a very nice collaboration of paleontologists (Dan Fisher, Ross MacPhee) and paleogeneticists (led by Hendrik Poinar's lab). It's refreshing to read a paper that describes not only the way that the DNA was sampled but also the age and morphological attributes of the sampled mammoths. For example:

    This 60+ year old bull is exceptionally well preserved, and exhibits the classic character suite of his species, including low molar lamellar frequency (Figure S1 in Additional file 3), broadly divergent tusk alveoli, a markedly downturned mandibular symphysis, and tremendous body size. We used tusk fragments for the shotgun sequencing, and both tusk and bone samples for PCR and Sanger sequencing.

    Every genetics paper should have descriptions like that. Very nicely done.

    As an anthropologist, I pay a lot of attention to studies of elephants, because they are another long-lived social mammal, in some ways closer to us in population structure and dynamics than most primates. As in the case of hominins, some taxonomists have argued that we should recognize lots of fossil elephants, others question that distinctiveness. And just as we are discovering for hominins, the elephants are showing evidence for population mixture among groups once considered to be different species.

    Enk and colleagues sampled the mtDNA from two Columbian mammoths and one woolly mammoth from North America. The Columbian mammoth is seen by pretty much everybody as a separate species (Mammuthus columbi) from woolly mammoths (Mammuthus primigenius), and paleontologists have thought that they diverged 1-2 million years ago. Woolly mammoths were Holarctic animals, with a range that extended from Europe to North America, while Columbian mammoths were limited to the Americas south of the U.S.-Canada border, roughly. Already other researchers have recovered dozens of woolly mammoth sequences, and their phylogenetic relations are well characterized (as shown in the paper). What Enk and colleagues show is that the two Columbian mammoths both have mtDNA sequences that belong to a single, relatively young clade that is present in woolly mammoths in Alaska and Yukon.

    The simplest explanation is that the Columbian and woolly mammoths of North America were exchanging genes.

    The authors also suggest the possibility of incomplete lineage sorting (ILS) -- the retention of a single ancestral clade in two isolated species. This seems unlikely given the topology of the clade within woolly mammoths, but the authors omitted the crucial test: the date of the most recent common ancestor of the mtDNA within the clade. If it's truly younger than a million years, we might easily rule out ILS.

    Forest and savanna elephants

    A lot more information about the variation within living elephantids has appeared within the past year. Looking at them compared to the fossil species, it's pretty clear that taxonomists haven't done well matching taxonomic levels in these groups. Here is a quote from the paper by Rohland and colleagues, who considered the genetic relationships of forest and savanna elephants in Africa.

    We also find that savanna and forest elephants, which some have argued are the same species, are as or more divergent in the nuclear genome as mammoths and Asian elephants, which are considered to be distinct genera, thus resolving a long-standing debate about the appropriate taxonomic classification of the African elephants.

    Forest and savanna elephants may deserve a species rank, but we might equally say that the mammoth-Asian elephant divergence doesn't merit the genus rank it has historically been given. As reconstructed in the paper, the forest-savanna elephant and Asian elephant-mammoth divergences both fall within ranges from 2.5 to 5.5 million years. Some widely-recognized mammalian genera (e.g., Homo) are younger, but most mammalian divergences in this range of times are recognized below the genus rank. Should mammoths be put into Elephas? That would probably be a better recognition of the adaptive radiation of Eurasian elephants.

    One way to consider the question is by examining the pattern of speciation. With a large number of sampled loci, a far more detailed consideration of speciation can be achieved. This brings us back to a more careful examination of ILS.

    We find a higher rate of inferred [Incomplete Lineage Sorting (ILS)] in forest and savanna elephants than in Asian elephants and mammoths: (FE+SE)/(AL+ML) = 3.1 (P = 4×10−8 for exceeding unity; Table 2), indicating that there are more lineages where savanna and forest elephants are unrelated back to the African-Eurasian speciation than is the case for Asian elephants and mammoths (Table 2). This could reflect a history in which the savanna-forest population divergence time TFS is older than the Asian-mammoth divergence time TAM, a larger population size ancestral to the African than to the Eurasian elephants, or a long period of gene flow between two incipient taxa. (We use upper case “T” to indicate population divergence time and lower case “t” to indicate average genetic divergence time (t≥T)).

    "A long period of gene flow" would reflect a very gradual speciation event, which might argue that the two resultant species should be classified in the same genus. Or...it might suggest that the ecological differentiation actually commenced much earlier in time than the modal estimate, with later hybridization. Mammoths and Asian elephants, by contrast, seem to have a cleaner separation even though the genetic relationships are almost equally close.

    We're not quite able to test these alternatives, yet, because only a single individual has been sampled from most of these species. Testing for gene flow really will require larger samples of individuals. In particular, the longer geographic distance between Asian and mammoth samples compared to forest-savanna samples may mean that population structure is hiding within this comparison. I just find it remarkable that genetics has arrived at a point where the pattern of speciation of extinct species is within reach.

    The paper uses the extinct mammoth and mastodon comparisons as a frame for discussing the diversity and distinctiveness of African forest elephants. This is in a way unfortunate, because the mammoth-centric questions are probably more interesting to most readers. There's still a lot of productive biology to do there. But the status of forest elephants is a useful hook to hang a paper upon. Whether forest elephants should be given the status of a species has been a hot topic in proboscidean evolutionary biology during the past 10 years. Debruyne [3] gave a good historical review of the issues:

    Indeed, when discovered by Matschie in 1900, [forest elephants] were described as either a potential species, or a regional race of Cameroon (Matschie, 1900). Matschie advocated the usefulness of hydrographical basins in order to subdivide African elephants into distinct units. He thus contributed to the profusion of new taxa to be defined by the turn of the 20th century, so that the taxonomy of the African elephant quickly became extravagant, the most meagre morphological evidence being used to acknowledge a new form (Lyddeker, 1907). Up to 22 forms of Loxodonta were described that were finally assigned either to the savannah or the forest elephant—see Laursen and Bekoff (1978) for a review. Morphologists have addressed this question for decades according to their personal taxonomic perspectives. Some have considered that, although displaying a smaller size, smaller round ears—responsible for their designation as “cyclotis”—more toenail structures on both feet, thin down-pointing tusks and a flatter back and forehead, forest elephants belong to the same species—i.e., Loxodonta africana—as savannah elephants with whom they assumed were reproductively compatible (Backhaus, 1958; Carroll, 1988; Cousins, 1996). Many cases of intermediate morphology have supported this view, which had become prevalent (Laursen and Bekoff, 1978). Conversely, the “splitter” attitude led other authors to put forest elephants apart on the basis of the same anatomical distinctiveness (Frade, 1931; Frade, 1933; Allen, 1936; Petter, 1958). More doubtful morphological characters—extent of hair-covering, color of the skin, carriage of head—have been put forward to support this division.

    The problem became complicated upon recovery of genetic information. Most early phylogeography has been done using mtDNA. The deepest mtDNA clade in the African elephants defines two haplogroups, both of which are shared by the forest and savanna populations. Based on large samples of mtDNA alone, the two populations have been recently exchanging genes.

    Early analyses of nuclear microsatellites indicated the opposite pattern, with relatively little allele sharing between the two elephant varieties. I became interested in the question after a paper by Régis Debruyne (a coauthor on the current paper by Enk and colleagues as well). Debruyne emphasized the great gaps in our sampling of geographic variation in African savanna elephants. Providing some additional data, he showed a very deep mtDNA clade in many forest elephants that was also in many savanna elephants. He argued that the widespread evidence of gene flow refutes the hypothesis of different biological species of elephants.

    Rohland and colleagues also addressed the discordance between mtDNA and nuclear genetic variation.

    Our study also infers a strikingly deep population divergence time between forest and savanna elephant, supporting morphological and genetic studies that have classified forest and savanna elephants as distinct species [13],[16]–. The finding of deep nuclear divergence is important in light of findings from mtDNA, which indicate that the F-haplogroup is shared between some forest and savanna elephants, implying a common maternal ancestor within the last half million years [21]. The incongruent patterns between the nuclear genome and mtDNA (“cytonuclear dissociation”) have been hypothesized to be related to the matrilocal behavior of elephantids, whereby males disperse from core social groups (“herds”) but females do not [13],[38]. If forest elephant female herds experienced repeated waves of migration from dominant savanna bulls, displacing more and more of the nuclear gene pool in each wave, this could explain why today there are some savanna herds that have mtDNA that is characteristic of forest elephants but little or no trace of forest DNA in the nuclear genome [13],[14],[39],[40].

    The scenario may fit with the facts. It was proposed first by Roca and colleagues [4], who proposed it as a "genomic record of ancient habitat changes", which had brought the forest and savanna populations into contact across shifting hybrid zones. They reiterated the hypothesis in a later paper [5] supported with larger samples.

    Further progress will require larger samples and better models. I was interested in Debruyn's account of the geographic holes in genetic sampling across the African range of forest elephants. A highly-resolved test of recent gene flow demands finding and sampling potential contact zones between two populations. Some hypotheses can be tested surprisingly strongly using only a single individual from each population. But the power of such tests depends on the pattern of inbreeding in the past. We can imagine that the ancestry of a single individual stretches through the genealogical network of a species like a cone, widening into the past. Recent events are poorly tested by single individuals.

    If geographic structure is strong enough, distant populations will approximate different species in their recent genealogical connections. So the single individuals in the more recent study by Rohland and colleagues [1] carry a lot of weight.

    There are many parallels here between hominin population dynamics and the elephants. Also, as I pointed out in 2006, the elephant situation helps to clarify how we should consider genetic samples from living great apes.

    The past year has seen a real reversal in the race between data and analysis. For a long time, sequencing has been a bottleneck in serious analysis of population history. The genealogical connections among individuals ramify by double in every generation, so that the inheritance of a single gene reflects one possibility among countless trillions. If we can only afford to sequence a single gene, we are limited to a single sample of the genealogical links among individuals. Whole genomes give enormous samples of the genealogical history among samples. But they create their own challenges of analysis.

    References

    1. Rohland N, Reich D, Mallick S, Meyer M, Green RE, Georgiadis NJ, Roca AL, and Hofreiter M. 2010. Genomic DNA Sequences from Mastodon and Woolly Mammoth Reveal Deep Speciation of Forest and Savanna Elephants. PLoS Biol [Internet] 8:e1000564+. Available from: http://dx.doi.org/10.1371/journal.pbio.1000564
    2. Enk J, Devault A, Debruyne R, King C, Treangen T, O'Rourke D, Salzberg S, Fisher D, MacPhee R, Poinar H, et al. 2011. Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths. Genome Biology [Internet] 12:R51+. Available from: http://dx.doi.org/10.1186/gb-2011-12-5-r51
    3. Debruyne R. 2005. A case study of apparent conflict between molecular phylogenies: the interrelationships of African elephants. Cladistics [Internet] 21:31–50. Available from: http://dx.doi.org/10.1111/j.1096-0031.2004.00044.x
    4. Roca AL, Georgiadis N, and O'Brien SJ. 2004. Cytonuclear genomic dissociation in African elephant species. Nature Genetics [Internet] 37:96–100. Available from: http://dx.doi.org/10.1038/ng1485
    5. Roca A, Georgiadis N, and Obrien S. 2007. Cyto-nuclear genomic dissociation and the African elephant species question. Quaternary International [Internet] 169-170:4–16. Available from: http://dx.doi.org/10.1016/j.quaint.2006.08.008
    Tags: 
    hybridization
    genomics
    taxonomy
    mammoths
    population structure
    introgression
    ancient DNA
    non-primate
    extinction
    elephants
    Synopsis: 
    Mammoth paleogenomics and African elephant population structure pose similar problems of sampling.

  • "The monkeys shall do bugger all."

    Tue, 2011-04-19 21:32 -- John Hawks

    Martin Robbins goes ape:

    Other writers are preoccupied with trivia like the NHS reforms or education funding, but a great crime against pedantry is in progress and it's time for someone to draw a line. Like many of today's problems, this one is epitomized by a Daily Mail headline:

    "Fans go bananas for new Planet Of The Apes trailer which takes humanised monkey effects to a whole new level."

    Really? Really? Only actually, as 'humanised monkeys' go they look a bit rubbish to me, because they don't really look like monkeys at all, they look more like apes, what with the film being 'Planet of the Apes' and all.

    He's got a whole lot of similar examples. There are no end of British papers making stupid comments about monkeys.

    Still, if we're going to be pedantic, I've got to disagree with Robbins' placement of Brian Blessed in the apes:

    Humans are members of the ape family, distinguished by weediness, lack of hair, technological development and widespread ironic denial of their ape heritage.

    Humans are not apes.

    I'm not in denial about our ape heritage, and I know some people will argue with me. The most recent common ancestor of living apes is also a human ancestor. "Ape" as applied to chimpanzees, bonobos, gorillas, orangutans and siamangs, is not a monophyletic group. You have to include humans to make biological sense out of the apes.

    But by that argument, apes are monkeys. Because the living monkeys -- New World and Old -- do not have a common ancestor that living apes and humans do not also have.

    Ah. The perils of pedantry.

    I resolve this problem by recognizing that neither "ape" nor "monkey" is a taxonomic term. We have good terms for the monophyletic groups -- "hominoids" are apes + humans, "anthropoids" are apes + humans + monkeys. We can recognize that apes are not monkeys (because they aren't), and we can recognize in the same way that humans are not apes (because we aren't).

    Tags: 
    humor
    taxonomy
    science writing

  • Is the Biological Species Concept a "minority view"?

    Mon, 2011-02-07 17:25 -- John Hawks

    Last week, Science ran a couple of items by Ann Gibbons that give further perspective on the discoveries last year that Neandertals and Denisovans both contributed to the ancestry of recent human populations. The sidebar piece, titled, "The species problem," raises the taxonomic question:

    Our ancestors had sex with at least two kinds of archaic humans at two different times and places—and those liaisons produced surviving children, according to the latest ancient DNA research (see main text, p. 392). But were the participants in these prehistoric encounters members of separate species? Doesn't a species, by definition, breed only with others of that species?

    I get the most awesome quote in the short article, because I get to defend the Biological Species Concept!

    Gibbons describes this as a "minority view among paleoanthropologists." I can't disagree: Get a dozen paleoanthropologists in a room, and I bet only 1 or 2 will seriously propose that we could apply BSC to hominins.

    This would be sort of understandable, if we were limited to the evidence of 15 years ago, with no genetics. It just wasn't really possible to test the hypothesis of interbreeding among populations, not at the scale at which we can today. There was always skeletal evidence that suggested Neandertals had contributed to later populations, as many of us pointed out repeatedly. But it was hard to quantify the phenomenon, and without quantification, it was possible for people to argue that interbreeding had been "evolutionarily insignificant".

    Paleoanthropologists have instead held species concepts that did not use interbreeding as a primary criterion. Many adopted Cracraft's Phylogenetic Species Concept, or Wiley's treatment of Simpson's Evolutionary Species Concept. Both of these define species in terms of morphological characters visible to the systematist, although they differ with respect to the pattern that justifies recognizing a species.

    Much of this is just ridiculous now. Genetic evidence shows a substantial amount of interbreeding between these Pleistocene groups. Lots of living humans trace more than a couple of percent of their genomes from some ancient non-African population; some may derive more than 8 percent of their ancestry from such populations. That's not rare hybridization. With this kind of evidence, we can apply the BSC.

    One hangup: maybe we can't prove that our Neandertal ancestors contributed genes in proportion to their population numbers. Maybe a large fraction of their genes had a fitness disadvantage in the later population. But this is a hypothesis, not a fact. Any estimate of the fitness of Neandertals in mating with their non-Neandertal contemporaries has to take account of the demographic growth of later populations, including selection on new gene variants. We know for a fact that some Neandertal genes are today very common -- for example, one 100-kilobase region occurs at a frequency of 28 percent outside of Africa. Any assignment to a species is a hypothesis, provisional on finding new facts to refute it. For the moment the facts point to them being the same species as us.

    What do we do with a population like the Neandertals, or the Denisovans? Each was more genetically distant from the average living human than members of living populations are from each other. Each evolved during a long period of isolation or strongly restricted gene flow from each other and from sub-Saharan Africans. Still, the level of genetic difference among these populations was comparable or less than that separating populations of great apes that historically have been recognized as subspecies. So that's what I would call them. Subspecies of Homo sapiens.

    As a postscript, I think that whoever came up with the idea of "Denisovans" as a population name has done us a tremendous favor. The great benefit of the name, "Neandertals", is that we could talk about them without trotting out a taxonomic name. Now we have something similar in eastern Eurasia.

    Also Jerry Coyne, coauthor of Speciation, discusses the issue.

    Tags: 
    Neandertal DNA
    Denisova
    Neandertals
    taxonomy
    species concepts
    species
    Synopsis: 
    After Neandertal genes are found in us, I find myself defending the obvious idea that they're Homo sapiens.

  • Mailbag: Chinese subspecies and Denisovans

    Tue, 2010-12-28 23:42 -- John Hawks

    Re: Denisova:

    Thank you for the very rapid FAQ on this fascinating new article! As you say,
    the findings should not be unexpected. Even the contribution from archaics to
    present-day Melanesians was foretold by the New Mexico group. Maybe this will
    put some sanity into those recurring "Modern humans are from China not Africa"
    stories. Pleistocene Homo sapiens in Asia just gets no respect! This seems to
    show a population of “Chinese Neanderthals” replacing H. erectus and later being
    replaced by OOA, but neither is quite 100%.

    Just thinking… If present-day populations, Neanderthals, and “Denisovans” make a
    near-trichotomy of SUBSPECIES, perhaps Homo sapiens mapaensis Kurth 1965 or Homo
    sapiens daliensis Wu Xinzhi 1981 will be found to have priority…

    Yes, I suspect those names may be available, depending on the timing of these population divergences. The Chinese record has several shoes left to drop.

    Tags: 
    Middle Pleistocene
    paleogenomics
    taxonomy
    China
    Denisova

  • The failures of dinosaur splitters

    Mon, 2010-09-27 10:57 -- John Hawks

    A-HA! We all lecture in our classes about the perils of naming too many species, but now the facts have been statistically proven! Well, at least for dinosaurs:

    Top dinosaur hunters are worst at naming

    The more fossil species you describe, the less likely the names are to stick.

    ...

    "I would have expected that more prolific, experienced authors might be better at recognizing genuinely new species, yet they were less successful than authors who name only a few dinosaurs," says [paleontologist Michael] Benton. "It is hard, and maybe impossible, to construct a case that experience in naming dinosaurs makes one better at the job."

    OK, dinosaurs are a much bigger sample than hominins. But our rate of discard is actually much higher -- we must still be using only 10 or 20 percent of the names that have been proposed, and probably half the ones we're using now will bite the dust. By contrast, more than half the dinosaur names are still accepted.

    It's the failure of the "prolific" taxonomists that deserves to be cited again and again. Oh, they got it right 41% of the time, and a lot of the sunken names date to before 1950, but the phenomenon has not abated with names of the last 50 years. Prolific namers seem to have a lower threshold for erecting a new taxon, and they get it wrong more than half the time.

    Tags: 
    metascience
    dinosaurs
    taxonomy

  • An ape by any other name

    Mon, 2010-08-30 11:40 -- John Hawks

    As usual, I was looking for something else -- this time in the writing of Henry Fairfield Osborn -- and came across an interesting paper that he delivered as a lecture in 1927 [1]. He was addressing general evidence for human evolution, in particular as reflected in the anatomy of anthropoid apes. In the course of this, he rose to the defense of his own theory of human origins, which involved the evolution of our lineage from a Central Asian ancestor that had isolated from the other apes for many millions of years:

    About three years ago I was a firm believer in the anthropoid ape theory of ancestry. I listened to a series of most able papers given by a number of investigators--Doctors Tilney, Morton, McGregor, all members of the Galton society--and felt then that their investigations of the anthropoid ape theory was quite established. A year later, however, I went into the central desert of Asia, in Mongolia; there I came under the influence of a new environment, a desert or semi-arid environment, and it flashed across my mind that this must have been the primitive home of man, that anthropoid apes could not have existed here. From that time to this the idea has been growing upon me, and last April, at the bicentenary meeting of the American Philosophical Society, I stated that I personally had abandoned the anthropoid ape theory and I advanced the opinion that man has a long line of Dawn Man ancestors and that the other theory rests upon a large amount of evidence which proves the kinship of anthropoid apes to man but does not prove the ancestry of man through an anthropoid ape type (Osborn 1927:221, emphasis in original).

    Many people today make a point of saying that humans did not descend from apes, but that we share an ancestor with apes.

    If we confine ourselves to living apes, that is of course true. Our common ancestors with chimpanzees and bonobos (the chumans) were not identical to either of these species, and may have been very different from both. That was one of the key issues raised in the interpretation of Ardipithecus. Lovejoy and colleagues [2] made the case that Ardipithecus is a better representative of many of the traits of our last common ancestor with chimpanzees. Chimpanzees have changed substantially since that ancestor lived, in some ways paralleling the evolution of gorillas and orangutans. If this interpretation is correct, then looking to living apes as models for our ancestors will mislead us on many aspects of their biology -- a point made at length by Lovejoy with Ken Sayers in a 2008 paper [3].

    Still, we shouldn't misunderstand this line of argument. Saying that stem hominines were anatomically distinct from chimpanzees doesn't really change the plain English meaning of the word "ape." If we seek a high degree of phylogenetic precision, we shouldn't use the word "ape" anyway -- it's not a taxonomic term. But to introduce the concept of evolution, it's equally misleading to avoid plain language. We shouldn't shroud Miocene hominoids in mystery, as if phylogenetic branching could magically transform them into new organisms. They evolved. Where once there were only apes, now there are some different apes. And us.

    Osborn's hypothesis marks the dark side of ape denial: If humans didn't evolve from apes, they may instead have evolved independently from some non-ape ancestor instead:

    There is all the difference in the world between kinship and ancestry. When we come down to what we all believe in -- to an anthropoid stem stock, a group from which both the anthropoid apes and man were derived -- we get a neutral form which cannot be defined as either an anthropoid ape or man, but with that type, which has the potentiality of the human stock on the one hand and of the anthropoid ape stock on the other, we come to a parting of our ways, somewhere back in Oligocene time, millions of years ago (Osborn 1927:221, emphasis in original).

    Were the chumans a "neutral form", definable neither as ape nor human?

    In the 1920's, this was a serious scientific question. Living apes seemed to belong to a single family, humans to another. If orangutans and gibbons could be lumped with the chimpanzees and gorillas, then an independent lineage of apes might indeed go back to the Oligocene.

    This idea stood against Darwin's view, and that of most of Osborn's contemporaries (Osborn mentions William Gregory and Arthur Keith explicitly). But it was more or less aligned with Alfred Russel Wallace's view of human evolution, which had been contemporary with Darwin's. Wallace had an independent line of human ancestry going back as far as the Eocene.

    Today a heavy weight of genetic and fossil evidence supports a human-gorilla-chimpanzee clade. The ancestor of that clade, whether taxonomy calls it a hominid, hominine or something else, was in ordinary parlance an ape. In many characteristics it was "neutral" -- not assignable to either human or chimpanzee clades. Neither humans nor chimpanzees yet existed. But apes of many flavors did exist. Our ancestors were among them.

    Here's Osborn's ending paragraph:

    Science works by trial hypotheses. I have one hypothesis, my opponents another. To my mind there is a very strong evidence of the prolonged independent ancestry of man, an ancestry not of anthropoid ape type, but of a neutral, common type. I agree to many arboreal traces in human descent, but I dissent as to the geologic length of arboreal life which my opponents claim resulted in resemblance between apes and man; I dissent as to our ancestry from a type which had specialized as far in arboreal life as the anthropoid ape. My theoretic ancestor belongs to a pro-ape stage, which I call the Dawn Man line. But we are all keeping our minds open; only in that way can we get at the truth (ibid., 230).

    References

    1. Osborn HF. 1928. The influence of habit in the evolution of man and the great apes. Bulletin of the New York Academy of Medicine [Internet] 4:216–230. Available from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2393861/
    2. Lovejoy OC, Suwa G, Simpson SW, Matternes JH, and White TD. 2009. The Great Divides: \\emph{Ardipithecus ramidus} Reveals the Postcrania of Our Last Common Ancestors with {African} Apes. Science [Internet] 326:100–106. Available from: http://dx.doi.org/10.1126/science.1175833
    3. Sayers K, and Lovejoy OC. 2008. The Chimpanzee Has No Clothes: A Critical Examination of \\emph{Pan troglodytes} in Models of Human Evolution. Current Anthropology [Internet] 49:87–114. Available from: http://dx.doi.org/10.1086/523675
    Tags: 
    history of anthropology
    metascience
    history of paleontology
    taxonomy

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