01 Dec 2017 During the past few years, anthropologists have been questioning the long-held idea that human birth is uniquely risky for mothers and infants because of the narrow size of the human pelvis. This week, Josie Glausiusz has an article for Undark that reviews the topic:. The assumption that “women are compromised bipedally in order to give birth,” is widely accepted says anthropologist Holly Dunsworth of the University of Rhode Island. But Dunsworth sees flaws in this premise. Women already have a range of dimensions in their birth canal, she thought, and they are all walking just fine. Indeed, research on human skeletons by anthropologist Helen Kurki of the University of Victoria in Canada has shown that the size and shape of the human birth canal varies very widely, even more so than the size and shape of their arms. May 12, 2015. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec pretium, tortor vitae porttitor suscipit, sapien purus aliquet risus, eu finibus arcu ante nec risus. Mauris porta a massa sed consectetur. Fusce porta, quam sit amet tincidunt facilisis, ipsum enim semper nunc, ut sodales ipsum lectus eget dolor. Fun Fear Factor games, challenges, activities and ideas for invitations. Amazing Race pitstop mat. Amazing Race Party Ideas for Pit stops, challenges. One possible explanation is a factor that the model does not include: the introgression into the Denisovan genome by a “hyperarchaic” ghost population. Spreading such a misconception is much like the strategy of “fear, uncertainty, and doubt” that was once deployed by software companies in their battle for market. Thank you FloraCraft® for sponsoring today's fun craft challenge! So, have you seen some of the amazing FloraCraft® Foam Head projects floating around out there. A list of television series broadcast and produced in Norway. Explore Susanne Iversen's board 'Trivsel' on Pinterest. Now before you start shouting the dangers of the use of food in games, I'd like to say that I've played many games of this sort (under supervision) and everythi. The article provides a fair summary of the conversation about birth and human evolution happening now in the field. It focuses on Dunsworth’s ideas about metabolic limits on gestation, and Jonathan Wells’ hypothesis that most complications with birth seen today are results of postagricultural changes to human nutrition and subsistence patterns. The topic of the obstetrical dilemma illuminates many ways that people become confused about what evolution means to us in our lives. Human babies are born relatively helpless compared to other primate babies, and they are born with a smaller proportion of their adult brain mass, leaving more of their brain growth for the first year of life. But human babies are not born early compared to other primates. Adult body mass predicts gestation length in primates pretty well and human babies are born about when we would expect for a primate with human body mass. People make a huge deal out of the difficulty of human childbirth. Traditional people around the world recognize that human childbirth is difficult compared to many other animals. In the Christian tradition, the difficulty of human childbirth is even recognized in the bible, with Genesis 3:16 saying, “I will greatly multiply Your pain in childbirth, In pain you will bring forth children.” Still, although childbirth can be very difficult for both mother and child, the extent of this difficulty varies greatly among women and among births by the same mother. Pain is hard to compare across species, as non-human primates cannot report what they are experiencing during uterine contractions. The dimensions of the pelvic inlet and the average newborn head are much easier to compare objectively. Compared to great apes like chimpanzees and gorillas, human infants have larger heads, and the maternal pelvic inlet is much smaller. But many other species of smaller primates also have relatively large infant heads compared to the maternal pelvic inlet: Infant head dimensions at birth (black outline) compared to average maternal pelvic inlet dimensions (open outline) in various primate species and humans. This figure is from Rosenberg and Trevathan (1995), using data from Adolph Schultz. What makes humans different from macaques, as Rosenberg and Trevathan pointed out, is not only the small size of the maternal pelvic inlet relative to infant head size, but also that its long axis is side-to-side instead of front-to-back. This means that most infants must rotate as they pass through the birth canal, while the smaller primates are typically born with the back of infant heads facing toward the back of the mother. Still, the large heads of small primates show that there’s nothing inherently paradoxical about the human “obstetrical dilemma”. Trade-offs shape the timing of life history events. In both small-scale human societies and in primates, mortality at the time of birth is slight compared to infant mortality during the first year of life. Babies could be born earlier and smaller, but both have substantial costs that balance the occasional mortality from cephalopelvic disproportion. References Rosenberg, K., & Trevathan, W. Bipedalism and human birth: The obstetrical dilemma revisited. Evolutionary Anthropology: Issues, News, and Reviews, 4(5), 161-168. 30 Nov 2017 A nice article by Anna Goldfield in Sapiens today profiles the work of zooarchaeologist Grace Veach, who is examining the remains of rodents in Liang Bua Cave, on the island of Flores. This site is otherwise well-known as the discovery locality of Homo floresiensis. By looking at the markings and textures, such as gouges or scrapes, on the surfaces of the rat bones, Veatch can tell whether the animal was butchered or whether it passed through the digestive tract of one of the local birds of prey. Most of the small- and medium-sized rats from Liang Bua seem to have been consumed by birds. However, Veatch was surprised to find some unexpected cut marks on one small specimen from the material associated with H. This introduced the possibility that the “hobbit” diet included all sizes of rat. The article makes note of a paradox in archaeological thinking. Archaeologists often interpret small mammal remains as evidence for advanced behavioral solutions like nets and snares, at least when they find such remains in sites where they think modern humans were active. But when the find small mammal remains in Neandertal or archaic human sites, they have often dismissed or ignored them. That is changing, at least with respect to Neandertals, as a newer generation of archaeologists has revisited the importance of small mammals and birds in Neandertal foraging strategies. Human foragers today rely upon a wide array of animal But we are only starting to learn about the foraging behavior of the Flores hominins. I’ll be looking forward to seeing more of this research. This is a nice piece in ChronicleVitae by Terry McGlynn:. Regardless, in every field, scholars run academic blogs that reflect the professional discourse, and sometimes those blogs will drive the broader conversation. Even if you don’t read academic blogs, they may be driving the conversation in your discipline. It typically takes several months for traditional peer-reviewed journals to publish research and then publish rebuttals and responses. In blogs, the same kind of academic conversation can take place over the course of days, or even hours. I find that the blogging environment has changed enormously since Facebook became ubiquitous. People are discussing blogs and blog posts in their own networks with other professionals. Those conversations often happen in places separate from the blog posts themselves, and not followed by the blog author. I think that’s generally healthy, because it enables people to talk (really, write) through issues with people they know and trust. But these decentralized conversations within the discipline have a big downside. What seems like “common knowledge” actually may only be shared among a small group of people, and they reinforce each other’s voices like an echo chamber. I’ve spent less time blogging during the last couple of years, because my fieldwork and research commitments have taken a lot of my energy. But I can say that blog posts—whether here or —are having a greater readership and impact than ever before. 01 Nov 2017 This is a nice write-up by Laura Geggel of a current exchange of comments in Nature about dinosaur phylogeny:. The upshot is that last spring, Matthew Baron and colleagues (2017) claimed that the traditional groupings of dinosaurs were all wrong. For more than a hundred years, paleontologists have grouped theropods together with sauropods, as “saurischians”, based on pelvic morphology. Suggested that the theropods are instead relatives of the ornithischians—including duckbills and ceratopsians. These branches are within the deepest part of the dinosaur phylogeny, and many of the fossil groups in the dataset lived much later and have many derived traits that would have been absent in their common ancestors. This makes it harder test their relationships than one might expect. The problem is analogous to determining relationships among the very deepest nodes of the mammal phylogeny—for example, do we group together primates, bats, and rodents into a higher level taxon, and are insectivores really a single group? Paleontologists have radically revised some ideas about early mammal diversification in the wake of genetic comparisons of living species, because these relationships just are not well reflected by morphological traits. For dinosaurs, there are no genetic comparisons, and we shouldn’t be very surprised that morphology might not be a straightforward indication of the deepest relationships. But the new exchange of comments, initiated by Max Langer and colleagues, shows that the dinosaur phylogeny is not going to be overturned easily. In their assessment, Baron and coworkers scored some characters incorrectly. They suggest that the correct data still support the traditional hypothesis that connects the theropods and sauropods. I don’t have any deep insight about dinosaur phylogeny. But I am interested in the case because it reflects a singular problem with phylogenetic analyses that we are also seeing expressed in the study of hominin relationships. Many empirical sciences are going through a “replication crisis”, as statisticians are showing that studies are systematically underpowered and results driven by false positives and p-hacking. We can’t precisely compare phylogenetic methods to the kind of statistical analyses underlie many hypothesis tests in other branches of science. But something very similar is true in phylogenetics. Scientists working on fossil relationships are working with sparse data matrices, many key taxa are very poorly represented, with samples that often include only a single individual, and many interesting questions involve deep nodes. The advent of genetics in the phylogenetics of mammals, birds, and many other groups has shown just how badly morphological data represent deep relationships. The adoption of Bayesian methods has helped a bit, in that the Bayes factor provides at least a way of saying that the data don’t clearly distinguish hypotheses from each other. I think that today many scientists working on hominin relationships have a fairly healthy attitude, that we just do not know how some key species should be arranged in a phylogeny. Certainly we face that problem with species like Homo naledi and Australopithecus sediba. These species are exceptionally well represented across the skeleton by fossils, but their placement cannot be determined with any confidence except in very broad terms. For dinosaurs, I expect that this phylogenetic problem will continue for quite a while, as the current exchange shows that the phylogenetic methods are very sensitive to small changes in the datasets. References Baron, M. G., Norman, D. B., & Barrett, P. A new hypothesis of dinosaur relationships and early dinosaur evolution. Nature, 543(7646), 501-506. Untangling the dinosaur family tree. Nature 551, E1–E3. 29 Oct 2017 Via Jay Shendure, who: Original advertisement that brought in the donors for Human Genome Project (Buffalo News, 3/23/1997), h/t Pieter de Jong, who placed the ad People who worked with HGP data in the early days will remember how the entire genome appeared to be designed by committee. Genetic samples from around thirty people were ultimately included, so different parts actually reflected the genetic heritage of entirely different individuals. These were chosen to be “representative” of the genetics of the U.S., meaning that some parts of the draft genome were African in ancestry, most were European, and a few were Asian. But the identities of the individuals were anonymous, and the first draft of the genome was being completed at a time when the diversity of most parts of the genome was unknown (by definition, since they hadn’t ever been sequenced in anybody!). Given the incredible expense of the project, I think this was an appropriate (if unavoidable) decision, but it did make some kinds of population genetic analysis very difficult to carry out. In genetics, how variation was first identified–the “ascertainment” of a variant–exerts a statistical bias on results. To understand the significance of variations, first it is necessary to know the direction of this bias. Many of us did a lot of complicated modeling to try to work around this aspect of the Human Genome Project draft. The decision had a legacy that lived on for the first few generations of microarrays, because the single nucleotide polymorphisms (SNPs) that these microarrays tested were found in human samples that were initially very small, many of them HGP samples. When applying a microarray to individuals from a population, it is very important to know whether the SNPs were ascertained within the same population or a different population–a microarray will always miss rare variation in a sample, but it will miss much more common variation in a sample from a different population than the ascertainment sample. Over time, microarray SNPs began to be ascertained on broader samples of populations, and resequencing–especially the 1000 Genomes Project–began to address the problems of representation that were insoluble in the HGP. But it’s interesting to see this historical ad that put into motion a long-lasting statistical problem. 28 Oct 2017 Paige Madison pointed me today to her post from 2015 recounting the discovery of the LB1 skeleton, from Liang Bua, Flores:. Better known as the type specimen of the species, Homo floresiensis, the first description of the fossil was published on this day in 2004. Cast of LB1 skeleton, at Belgian Academy of Sciences. Photo: Ghedoghedo (CC-BY-SA 4.0, ) Recent, unconsolidated sediments like those in the Liang Bua cave are among the most challenging situations to excavate skeletal remains, and the story of this discovery emphasizes those challenges. Madison also discusses the way that chance was involved in the discovery. All in all, fascinating context. 19 Oct 2017 Are you curious about open science, but don’t really know what it means? The September issue of The SAA Archaeological Record includes an article that reviews “open science” approaches in archaeology:. This article was the brainchild of Ben Marwick, who has helped to organize the new Open Science Interest Group within the Society for American Archaeology. I’m proud to be able to support and participate in this group, and to have joined with 48 other professionals in this paper. I work at all levels within my scientific research to advance the principles that the article describes. The paper begins with a short discussion of what “open science” actually means. Often described as “open science,” these new norms include data stewardship instead of data ownership, transparency in the analysis process instead of secrecy, and public involvement instead of exclusion. I approve strongly of this definition. Open science is nothing radically new, it reflects a recognition that responsible scientific approaches lie at one end of an axis, where the opposite end is really an antiscientific attitude of exclusion. The new paper refers to open access (in publication), open data, and open methods. All these tend to increase transparency and replicability in the production of knowledge. I would add a couple of aspects that the article doesn’t discuss in detail. Archaeological sites are not merely data sources, they are physical places. Allowing colleagues and the public to see the sites and inspect work at sites is part of providing confidence and transparency in archaeologists as stewards of heritage. That access can be provided today with technology, as many projects (including our Rising Star project) are doing. Or access to sites can be provided in cooperation with national heritage authorities through responsible tourism and site visits. Scientific projects are complex social undertakings that involve power and funding, and open collaboration may be just as important as open methods and open data in providing transparency of scientific processes. Some people have the misconception that open approaches are less rigorous compared to approaches that involve long gestation of ideas in relative secrecy. Unfortunately, this misconception is still actively promoted by a few irresponsible scientists. Spreading such a misconception is much like the strategy of “fear, uncertainty, and doubt” that was once deployed by software companies in their battle for market share against open source software projects. In my experience, open approaches are more rigorous than secretive ones. Open approaches rely strongly upon establishing transparent methods that emphasize replicability. When researchers follow through on a commitment to provide the data that underlie their analyses, they provide the means for independent researchers to check their results and conclusions. It’s a basic principle of scientific credibility: Conclusions that cannot be checked should not be believed. I know that academic articles about how to do academic work are not always exciting, but these articles are necessary to build the scholarly background for changing practices, especially in building support for responsible practices among institutions and grant agencies. I applaud the Society for American Archaeology for supporting this initiative. There is no such thing as inertia—some people and institutions actively maintain processes that exclude colleagues and the public. Let’s subject those practices to examination and let institutions justify them if they are necessary. Meanwhile we must make the real costs of closed systems explicit, not hide them. More: I’ve long been an advocate for open data practices, which I describe in my white paper. 18 Oct 2017 Nature Genetics has a remarkable editorial in the current issue that makes a point of criticizing citation practices by authors in “articles we have recently published”:. Neutral citation, for example, “this field exists (refs. 1–20),” may on the face of it seem to be a fair practice, giving evenhanded and minimal citation credit to a range of preexisting works as background to the current report. But it can also be malpractice, artificially inflating the metrics of irrelevant or trivially related works by including them in lists of relevant publications. Those are tough words. The editors’ recommendation is to add more background that gives necessary context for cited works: Best citation practice is to summarize the claim made in the cited work without distorting whether it was of cause, correlation or conjecture, much as you would for your own findings (Nat. 47, 305, 2015). The relevant reasons for citing pertinent publications should also be introduced early in the article rather than discussed as late afterthoughts. This best practice will often entail making statements that are strongly supported by prior publications in the background introducing your findings. We believe this is key to writing research papers with impact that can benefit from peer review, as it encourages explanation of the knowledge gap that motivates the research as well as clear explanation of the conceptual advances made by the main findings of the new research. I’m strongly in favor of this approach. But take a look at the that lists the requirements for papers submitted to Nature Genetics: Letters The text is limited to 1500 words, excluding the introductory paragraph, online Methods, references and figure legends. Articles An Article is a substantial novel research study, with a complex story often involving several techniques or approaches. The main text (excluding abstract, online Methods, references and figure legends) is 2,000-4,000 words. In a letter with only 30 references, giving appropriate context for each reference would take up 500 words – a third of the paper. For an article of 2000 words with 100 references, it would likewise take up 2/3 to half of the paper. I agree that adding better context for citations would make better scientific papers. Adding more citations would in many cases improve papers. This is especially true in areas of science that lie on the boundaries of disciplines, where many readers will need more context to understand where citations fit together. But word limits and limits on citation number prevent authors from adding such context! If Nature Genetics wants well-written and well-referenced papers, it is going to have to change its editorial practices to enable authors to spend the necessary words. I especially like citation formats that enable authors to add context in the reference section—listing a short synopsis or reason why each citation is valuable. Books have that kind of facility in endnotes, so it’s a fairly widespread practice in scholarship. More scientific journals should enable greater context in references. 05 Oct 2017 In September, the team was underground in the Rising Star cave system, working at new excavations in the Lesedi Chamber and Dinaledi Chamber. I posted updates on the excavation goals and the progress at the end of the month on Medium, and I thought it would be helpful to provide links to those articles here. A look at some photos of the live National Geographic Classroom events in the Rising Star cave system In the first week, I reviewed the hypotheses that we set out to test:. Key among them is the formation of the fossil assemblage within the Dinaledi Chamber. Many people have been curious whether some other entrance to this chamber may have existed in the past. So far, geological work in the chamber has found no other passage that might have allowed hominins or their bodies to get in. There’s a lot of evidence that the chamber must have been very inaccessible when the remains of H. Naledi arrived — especially the clear difference in sediment composition between Dinaledi and other nearby chambers, and the lack of evidence for any other medium or large animal remains. It appears that the hominin remains must have entered the chamber in the same way we do today, down this Chute. But nearly all of the hominin remains so far come from a tiny area of excavation, only 0.8 square meters, at the far end of the chamber more than 10 meters from the Chute. Later, near the end of the excavation work, I reviewed some of the discoveries the team made:. Perhaps the most interesting is a feature just beneath the base of the Chute: This mass of bone has emerged just at the base of the Chute, the narrow entry channel into which the team enters the chamber. After weeks of careful excavation, the team can now see part of an articulated hand, ribs and a possible shoulder, even some teeth in what appears to be proper anatomical order. This may be the partial skeleton of a single hominin individual. We do not know how much additional bone may yet remain just beneath the surface. It will be some time before we know fully the results of the September excavation. We will need to consolidate the feature at the base of the Chute and extract it to the laboratory for further preparation. We will also need to get chemical and biological results back from samples taken inside both chambers. We have a lot of work ahead of us, and we’ll update as we can. 29 Aug 2017 Science reports on a new initiative to provide 3D scan data on thousands of vertebrates:. Then last year David Blackburn, a herpetologist at the Florida Museum of Natural History in Gainesville, saw Summers's #scanAllFish hashtag on Twitter and light-heartedly countered that he would 'scan all frogs.' Blackburn had just chatted with museum curators about starting a new digitization effort, so he also called Summers. They decided to up the ante and seek money to 'scan it all.' Now they have $2.5 million in National Science Foundation funding in hand, and on 1 September they will launch their project: oVert, for 'Open Exploration of Vertebrate Diversity in 3D.' Many scientists simply know it as the 'scan-all-vertebrates' project. The project, “oVert”, will deposit scans of museum specimens onto the site, so that people can download and use them. This is a tremendous win for open access science, and for the value of the MorphoSource repository. Can you imagine the projects that will be fueled by this dataset? It will become an essential morphological research tool–probably setting a new standard. And it will enable massive educational projects. This is such an effective expenditure of money, and I wish that other NSF-funded projects would follow this model! 03 Aug 2017 For some people who follow human evolution news, recognizing “species” is really just about whether you’re a lumper or a splitter. Many people assume that the names of species are about ego, not evidence. But nature presents us with real challenges, which still cause different scientists to approach the past with different assumptions. Let me give some examples. Just today, I got notification of a new paper by Walter Neves and colleagues, in which they suggest that Australopithecus sediba and Homo naledi are actually South African representatives of Homo habilis. Some people might scoff at this—after all, the Dinaledi fossils are only 236,000–335,000 years old, while the latest-known H. Habilis is around 1.6 million. But a young date for some fossils doesn’t bar them from from membership in a species with much older fossil representatives. Identity is tested with morphological evidence, not geological age. Now, I disagree with the idea that H. Naledi is the same species as H. Habilis—Neves and colleagues have come to this taxonomic conclusion by neglecting all the morphological evidence showing H. Naledi is different from H. But it’s not so easy to reject the idea that these species might be close relatives. As we pointed out earlier this year, H. Naledi might even conceivably be a descendant of H. Habilis or Au. On the other hand, Mana Dembo and colleagues showed last year that H. Naledi seems to be closer to modern and archaic H. Sapiens than to H. Erectus (and much closer than H. These are stark differences of interpretation, from similar parts of the skeleton. [see my article: “The plot to kill Homo habilis ”] At the other extreme, this week Jeffrey Schwartz is set to present results of his own examination of the Dinaledi Chamber sample. According to his abstract, all the teeth belong to one species, but some of the skulls represent another—two species in this assemblage, not just one. I haven’t seen the details of this analysis, but I’m pretty sure I disagree with this one, too. I admit that it would be fatuous to say that ego plays no role in paleoanthropology. Scientists express provocative opinions that will draw attention from the press. Still, the trouble with taxonomy isn’t just about new fossil discoveries like H. Naledi or Au. We have seen similarly broad and vociferous diversity of opinions in the last few years about H. Deyiremeda, Au. Anamensis, H. Floresiensis, Denisovans, Neanderthals, H. Heidelbergensis, Kenyanthropus platyops, and others. These are species new and old, and the same issues keep arising again and again. Many people would say that taxonomic debates just reflect basic philosophy about variation—again, lumping versus splitting. But that’s really only one of the dimensions: • How much variation should a species include? Broadly, all of us recognize that some species are polytypic (as humans are today), but small and fragmentary samples make it very hard to distinguish polytypy from distinct species. There are living polytypic species that include very extensive variation, and living sister species that barely differ from each other, making model selection difficult. • What kind of data provide evidence of similarity or difference? Some researchers rely mainly on phenetic similarity measures, using geometric morphometrics, principal components or canonical variates approaches. Others examine discrete (or threshold) traits, counting shared derived traits as evidence of similarity and ignoring shared primitive traits. This group was once dominated by cladists, but in recent years Bayesian approaches have become more and more common. • What temporal or geological information is sufficient to justify pooling fossil specimens into a single sample? Some scientists are willing to assume that fossils from the same 500,000-year period belong to a single population, even if they preserve different parts of the skeleton or minimally overlap. Others draw trees that separate every specimen into its own “operational taxonomic unit”. The concept of a paleodeme is based on lumping specimens by date and geography, an approach that has come more and more into question as the fossil record increases. Anthropologists may get a bad rap from other biologists for arguing about taxonomy so much, but in reality many areas of taxonomy are undergoing seismic shifts following more widespread application of genetics and phylogeographic analyses. For example, bovid systematists have been arguing for the last few years about whether to double the number of species they recognize—a debate about living species with abundant morphological samples and genetic data. Meanwhile, living and fossil elephants are on the verge of a complete revision of relationships, based on ancient DNA and the appreciation of deep diversity between forest and savanna African populations. Similar examples are unfolding across mammalian systematics. Neandertal and Denisovan DNA has shown us that hominins also exchanged genes by introgression, occasionally but recurrently despite hundreds of thousands of years on their own trajectories. Genetic evidence of African “ghost lineages” means other long-lasting Pleistocene populations once existed. Naledi might potentially be one such lineage. I have no idea what the closest relative of H. Naledi will prove to be. Whether it reproduced with human populations or not, it shows that many cherished human features may not have been uniquely derived evolutionary developments. I can’t help but feel that we are standing at a special moment in the history of paleoanthropology. New data give us the opportunity to make progress on old areas of disagreement about species and phylogeny. We have to start by taking what we now know about the later Pleistocene, and seriously appling these lessons to earlier periods of human evolution. Our assumptions about the past really are changing. Whatever we choose to call species won’t change their nature. But our assumptions determine the way we frame our future studies, including our attempts to find more fossil evidence. That makes it important to communicate clearly about what these ancient species mean, both with each other and with the public. 01 Aug 2017 Two Dutch biomedical researchers discuss how they are trying to move their institution away from mere quantity of research and citations, and toward real clinical impact:. They begin their essay with a scenario that reminds me of human evolution research: A Ph.D. Student wants to submit his research to a journal that requires sharing the raw data for each paper with readers. His supervisors, however, hope to extract more articles from the dataset before making it public. The researcher is forced to postpone the publication of his findings, withholding potentially valuable knowledge from peers and clinicians and keeping useful data from other researchers. I agree with much of what they say in this essay. But I think their opening scenario doesn’t really express a trade-off they are trying to illustrate between an artificial measure of “impact” and real impact. What we keep finding in human evolution research is that sharing the data leads to higher impact. Papers are published faster, they are cited more widely, and they lead to career advancement for the authors. It is true that some scientists try to keep datasets private so that other researchers cannot replicate their work. But that is counterproductive to their own research, not only to the field. Researchers who are publishing slowly, not distributing data in a way that can be inspected and used, are not achieving publications, citations, or “impact” even in the artificial, publication-oriented sense. Using open approaches is not just the way to advance science and its impact on the public, it is also the way to advance careers. There is no trade-off here, not that I’ve experienced at least. 15 Jun 2017 Earlier this month in eLife, Matthias Meyer and colleagues published a cool paper:. The straight-tusked elephants lived in Europe and western Eurasia as far east as India during the Pleistocene. Most people are familiar with other extinct elephant relatives, such as mammoths or mastodons. The straight-tusked elephants were not mammoths, and they are assumed to be much more like living elephants because they seem to have entered more northerly parts of Europe mainly during interglacial times. Paleontologists have noted that the straight-tusked elephants share some morphological features with Asian elephants, as mammoths do also. For some paleontologists, these similarities are so compelling that they have classified Palaeoloxodon as part of the Asian elephant genus, Elephas. Ancient DNA evidence is breaking open the study of how the extinct relatives of living elephants moved, interacted, and evolved. First mitochondrial, and more recently nuclear gene sequences have revealed different populations that lasted more than a million years, yet hybridized and mixed where they met. During the last ten years, it has become clear that populations of elephants in the central African forest have a long history as an evolving lineage distinct from savanna elephants across most of Africa. Forest and savanna elephants have increasingly been recognized as two species, Loxodonta cyclotis in the forest, and L. Africana across the rest of Africa. No fossils have been attributed to L. Cyclotis, and the L. Africana fossil record is quite sparse up until 20,000 years ago. Before that time, Africa itself was rich in elephants attributed to Palaeoloxodon, especially P. Recki, which many sources identify as Elephas recki. Recki has been identified from fossils as early as 4 million years ago, and as late as 300,000 years ago. Other African species of Palaeoloxodon (again, often classified as Elephas) have been interpreted as part of a single P. Recki lineage, including the earlier P. Ekorensis and the later P. Iolensis survived until around 30,000 years ago. With so many species identified as Elephas or closely related to Elephas, and with mammoths sharing so many features with living Asian elephants, the basic idea has been the Asian elephant branch of the elephant phylogeny was once global, with mammoths spread across the northern tier of Eurasia and across the Americas, extinct P. Antiquus in western Eurasia, extinct P. Namascus further east in Asia, and extinct P. Recki in Africa. Paleontologists have speculated that P. Namascus may itself be the immediate ancestor of living Asian elephants, Elephas maximus. Living African elephants, Loxodonta, were the odd elephants out. Meyer and colleagues obtained mitochondrial genomes from four individuals of P. Antiquus, three of them from Neumark-Nord, Germany, and one from Weimar-Ehringsdorf, Germany. They find that the Neumark-Nord elephants probably date to the last interglacial, around 120,000 years ago, while the Weimar-Ehringsdorf elephant dates to the previous interglacial, around 230,000 years ago. This is a pretty small section of the overall geographic range covered by P. Antiquus: Figure 1 from Meyer et al. 2017, original caption: ' Palaeoloxodon antiquus, geographic range based on fossil finds (after Pushkina, 2007). White dots indicate the locations of Weimar-Ehringsdorf and Neumark-Nord.' What they found was that P. Antiquus mitochondrial genomes are not related to Elephas at all; they’re related to forest elephants: Surprisingly, P. Antiquus did not cluster with E. Maximus, as hypothesized from morphological analyses. Instead, it fell within the mito-genetic diversity of extant L. Cyclotis, with very high statistical support (Figure 2). The four straight-tusked elephants did not cluster together within this mitochondrial clade, but formed two separate lineages that share a common ancestor with an extant L. Cyclotis lineage 0.7–1.6 Ma (NN) and 1.5–3.0 Ma (WE) ago, respectively. That’s not a small difference. Living Asian and African elephants came from a common ancestral population more than 6 million years ago, during the Late Miocene. They are about as different from each other genetically as humans and chimpanzees. The fossil story was just wrong–and it’s as big a difference as misidentifying a Neanderthal as a fossil chimpanzee. Elephant mtDNA and nuclear DNA phylogeny from Meyer et al. The Neumark-Nord (NN) and Weimar-Ehringsdorf (WE) straight-tusked elephants are indicated. The mtDNA tree has a time scale (bottom) but the nuclear DNA tree has no time scale associated with it. All four of the P. Antiquus mitochondrial lineages are on the same branch as living forest elephants, and in fact some forest elephants have mtDNA genomes that are closer to P. Antiquus than to some other forest elephants. In other words, the mitochondrial genomes of P. Antiquus fall within the variation of L. Within this variation, the mitochondrial lineage of the earlier Weimar-Ehringsdorf elephant is part of a different clade than the three Neumark-Nord elephants, so the P. Antiquus mitochondrial genomes are not a monophyletic group. Now, we might well expect the story with the nuclear genome would be different for elephants. We know that the story for Neandertals is different considering the mitochondrial and nuclear genomes: the Sima de los Huesos nuclear genome groups clearly with later Neandertals even though the mtDNA of later Neandertals is more similar to that of living humans. There is another reason why elephant nuclear and mtDNA genomes might be discordant. In humans, mtDNA is markedly less diverse than most parts of the nuclear genome, and mtDNA types occur across wide geographic areas. Elephants are the opposite. Their mitochondrial DNA exhibits substantially greater variation among populations than the average for the nuclear genome, because female elephants very rarely transfer between groups. Most gene flow in elephants is male-mediated, and male elephants sometimes disperse over very long distances. These contrasting patterns of nuclear and mitochondrial diversity in elephants are consistent enough to provide a way to “triangulate” the region that ivory samples originated (Ishida et al. Meyer and colleagues cannot assess yet whether the Weimar-Ehringsdorf elephant would yield a divergent nuclear genome, because they didn’t get nuclear evidence from it. But two of the Neumark-Nord P. Antiquus specimens yielded nuclear genome data and they are a close sister group compared to all the forest elephants. That is, the African forest elephants were much broader in their mtDNA phylogeny, and tighter together in their nuclear genome, just as one would expect from the mass of evidence about them. Antiquus tooth. Photo credit: Khruner,. So, that’s an interesting data point about elephant evolution. A widespread extinct species of elephant, which on morphological grounds was interpreted as an Asian elephant relative, is actually related to forest elephants within Africa. Forest elephants today are a relative island species in central Africa, surrounded by savanna elephants. So from today’s standpoint, forest elephants look like a geographic and phylogenetic relict of a much more diverse lineage that once existed. We already know that today’s situation did not exist earlier in the Pleistocene. In the past, many parts of Africa were inhabited not by today’s savanna elephants but instead by other extinct species, for much of the Early and Middle Pleistocene, P. Savanna elephants are found in the fossil record as early as 500,000 years ago, but they are a relatively rare component of the elephant diversity in comparison to the extinct Palaeoloxodon species. Of course, without ancient DNA evidence, it’s not certain that these other extinct Palaeoloxodon species are closely related to the forest elephants and P. Furthermore, the nuclear genome evidence presented by Meyer and colleagues does not establish whether the P. Antiquus population may have exchanged genes with Asian elephants, thereby accounting for some of its anatomical resemblance to them. Hybridization has already been found to be widespread among the varieties of mammoths, and it continues to occur between savanna and forest elephants despite what appears to be a multi-million year separation. We might expect the same of other extinct elephant species. When Eleftheria Palkopoulou presented on some of these data at a conference in 2016, she did talk about hybridization. Ewen Callaway reported on that conference presentation at the time:. Palkopoulou and her colleagues also revealed the genomes of other animals, including four woolly mammoths ( Mammuthus primigenius) and, for the first time, the whole-genome sequences of a Columbian mammoth ( Mammuthus columbi) from North America and two North American mastodons ( Mammut americanum). The researchers found evidence that many of the different elephant and mammoth species had interbred. Straight-tusked elephants mated with both Asian elephants and woolly mammoths. And African savannah and forest elephants, who are known to interbreed today — hybrids of the two species live in some parts of the Democratic Republic of Congo and elsewhere — also seem to have interbred in the distant past. Palkopoulou hopes to work out when these interbreeding episodes happened. None of these scientific results concerning interbreeding and hybridization are in the new paper by Meyer and colleagues. So I expect we will see much more from these new genome sequences.
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February 2018
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