Saturday, March 03, 2007
Scientists say Climate Change caused Neanderthal extinction in Iberia
Recent studies carried out in Gorham's cave*, on Gibraltar, proved to be definitive for this work.
The research work has been published in Quaternary Science Reviews journal.
Climate - and not modern humans - was the cause of the Neanderthal extinction in the Iberian Peninsula (Cave Art). Such is the conclusion of the University of Granada research group RNM 179 - Mineralogy and Geochemistry of sedimentary and metamorphic environments, headed by professor Miguel Ortega Huertas and whose members Francisco Jose Jimenez Espejo, Francisca Martínez Ruiz and David Gallego Torres work jointly at the department of Mineralogy and Petrology of the University of Granada (Universidad de Granada) and the Andalusian Regional Institute of Earth Sciences (CSIC-UGR).
Together with other scientists from the Gibraltar Museum, Stanford University and the Japan Marine Science and Technology Center (JAMSTEC), the Spanish scientists published in the scientific journal Quaternary Science Reviews an innovative work representing a considerable step forward in the knowledge of human ancestral history.
During the last Ice Age, the Iberian Peninsula was a refuge for Neanderthals, who had survived in local pockets during previous Ice Ages, bouncing back to Europe when weather conditions improved.
The study is based upon climate reconstructions elaborated from marine records and using the experience of Spanish and international research groups on Western Mediterranean paleoceanography. The conclusions point out that Neanderthal populations did suffer fluctuations related to climate changes before the first Homo Sapiens arrived in the Iberian Peninsula. Cold, arid and highly variable climate was the least favourable weather for Neanderthals and 24,000 years ago they had to face the worst weather conditions in the last 250,000 years.
The most important about these data is that they differ from the current scientific paradigm which makes Homo Sapiens responsible for the Neanderthal extinction. This work is a contribution to a new scientific current - leaded by Dr. Clive Finlayson, from the Gibraltar Museum - according to which Neanderthal isolation and, possibly, extinction were due to environmental factors.
These studies on climate variability are part of the work of the group RNM 179, funded by the excellence project RNM 0432 of the Andalusian Regional Government's Department for Innovation, Science and Business and by the MARCAL project of the Spanish Ministry of Education and Science, both linked to the Andalusian Environment Centre (CEAMA - Centro Andaluz de Medio Ambiente).
Source (adapted): University of Granada PR "Spanish scientists point at climate changes as the cause of the Neanderthal extinction in the Iberian Peninsula" February 25 2007 [alt. Neandertal, Neandertals]
 Based on the paper:
Climate forcing and Neanderthal extinction in Southern Iberia: insights from a multiproxy marine record
Francisco J. Jimenez-Espejo, Francisca Martínez-Ruiz, Clive Finlayson, Adina Paytan, Tatsuhiko Sakamoto, Miguel Ortega-Huertas, Geraldine Finlayson, Koichi Iijima, David Gallego-Torres and Darren Fa
Quaternary Science Reviews (Article in Press)
Paleoclimate records from the western Mediterranean have been used to further understand the role of climatic changes in the replacement of archaic human populations inhabiting South Iberia. Marine sediments from the Balearic basin (ODP Site 975) was analysed at high resolution to obtain both geochemical and mineralogical data. These data were compared with climate records from nearby areas. Baexcces was used to characterize marine productivity and then related to climatic variability. Since variations in productivity were the consequence of climatic oscillations, climate/productivity events have been established. Sedimentary regime, primary marine productivity and oxygen conditions at the time of population replacement were reconstructed by means of a multiproxy approach. Climatic/oceanographic variations correlate well with Homo spatial and occupational patterns in Southern Iberia. It was found that low ventilation (U/Th), high river supply (Mg/Al), low aridity (Zr/Al) and low values of Baexcess coefficient of variation, may be linked with Neanderthal hospitable conditions. We attempt to support recent findings which claim that Neanderthals populations continued to inhabit southern Iberia between 30 and approx 28 ky cal BP and that this persistence was due to the specific characteristics of South Iberian climatic refugia. Comparisons of our data with other marine and continental records appear to indicate that conditions in South Iberia were highly inhospitable approx 24 ky cal BP. Thus, it is proposed that the final disappearance of Neanderthals in this region could be linked with these extreme conditions.
[Spain, Anthropology, Archaeology]
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Friday, March 02, 2007
Study: Why Do Birds Migrate?
Why do some birds fly thousands of miles back and forth between breeding and non-breeding areas every year whereas others never travel at all?
One textbook explanation suggests either eating fruit or living in non-forested environments were the precursors needed to evolve migratory behavior.
Not so, report a pair of ecologists from The University of Arizona in Tucson. The pressure to migrate comes from seasonal food scarcity.
Royal Flycatcher (Copyright 2004 Alice Boyle)
"It's not just whether you eat insects, fruit, nectar or candy bars or where you eat them -- it matters how reliable that food source is from day-to-day," said W. Alice Boyle. "For example, some really long-distance migrants like arctic terns are not fruit-eaters."
Boyle, an adjunct lecturer in UA's department of ecology and evolutionary biology and co-author Courtney J. Conway, a UA assistant professor of natural resources and a research scientist with the U.S. Geological Survey, reported their findings in the March 2007 issue of American Naturalist .
To figure out the underlying pressures that drive some birds to leave home for the season, the team wanted to examine a related set of species and compare their size, food type, habitat, migratory behavior and whether they fed in flocks.
Boyle and Conway focused on 379 species of New World flycatchers from the suborder Tyranni. One of the largest groups of New World birds, the Tyranni includes kingbirds, flycatchers, phoebes and such southern Arizona birdwatchers' delights as vermillion flycatchers and rose-throated becards. Tropical members include manakins and cotingas.
First the scientists had to construct the first "supertree" for New World flycatchers.
"No one has ever compiled all those birds together into one megafamily tree," Boyle said, adding that "supertree" is a technical term among evolutionary biologists.
Yellow-bellied Flycatcher (Copyright 2004 Alice Boyle)
Having the tree let the researchers compare a variety of traits across the many species of Tyranni by using a computer analysis called phylogenetic independent contrasts.
The technique allowed the scientists to sort out whether a bird was migratory because that's what species on their side of the family tree always did or whether the bird's travel habits had some ecological correlates.
Food scarcity was the number one issue that predicted a species' migratory behavior, the team found. Boyle said, "Food availability is the underlying process, not diet and habitat."
One strategy for dealing seasonal changes in food availability is migration. The team also found that species that forage in flocks are less likely to migrate.
"If you are faced with food scarcity, you have two options," Boyle said. "You can either forage with other birds or you can migrate."
When birds band together to search for food, the group is more likely to find a new patch of food than is one lone individual, she said. "Flocking can be an alternative way to deal with food shortages."
A universal assumption about bird migration has been that short-distance migration is an evolutionary stepping stone to long-distance migration. The team's work contradicts that idea by showing that short-distance migrants are inherently different from their globe-trotting cousins.
The National Science Foundation and the Natural Sciences and Engineering Research Council of Canada funded the work.
 Based on the paper:
Why Migrate? A Test of the Evolutionary Precursor Hypothesis
W. Alice Boyle and Courtney J. Conway
Am. Nat. 2007. Vol. 169, pp. 344-359.
The question of why birds migrate is still poorly understood despite decades of debate. Previous studies have suggested that use of edge habitats and a frugivorous diet are precursors to the evolution of migration in Neotropical birds. However, these studies did not explore other ecological correlates of migration and did not control for phylogeny at the species level. We tested the evolutionary precursor hypothesis by examining the extent to which habitat and diet are associated with migratory behavior, using a species-level comparative analysis of the Tyranni. We used both migratory distance and sedentary versus migratory behavior as response variables. We also examined the influences of foraging group size, membership in mixed-species flocks, elevational range, and body mass on migratory behavior. Raw species analyses corroborated some results from studies that put forth the evolutionary precursor hypothesis, but phylogenetically independent contrast analyses highlighted an important interaction between habitat and diet and their roles as precursors to migration. Foraging group size was consistently associated with migratory behavior in both raw species and independent contrast analyses. Our results lead to a resource variability hypothesis that refines the evolutionary precursor hypothesis and reconciles the results of several studies examining precursors to migration in birds.
A 2006 related paper:
Phylogenetic tests of hypotheses for the evolution of avian migration: a case study using the Motacillidae
The Auk April 2006 123:455-466
The evolution of avian migration continues to be an intriguing research subject, even though relationships between migration and factors such as seasonality clearly exist. The question remains whether these relationships are evident within phylogenies containing both sedentary and migratory taxa. We explore the evolution of migration in the family Motacillidae by evaluating existing hypotheses for the evolution of migration in a comparative, phylogenetic framework at the interspecific level. Many hypotheses to explain the evolution of avian migration - such as the "evolutionary precursor" hypothesis (Levey and Stiles 1992, Chesser and Levey 1998) and the "stepping-stone" hypothesis (Cox 1968, 1985) - are based on New World migratory systems. The central components of these hypotheses should apply across biogeographic realms (i.e. the Old World), given that seasonality and habitat regimes are similar in the New and Old worlds. Using a molecular phylogeny containing most species in the Motacillidae, we investigated the potential interactions of seasonality and ecology with migratory and sedentary behavior. Our results suggest that habitat and migration are not correlated in the manner predicted by the evolutionary precursor hypothesis, but they also suggest the importance of increasing seasonality in explaining the patterns of the evolution of migration, an expected but previously unexamined evolutionary relationship. While understanding the limitations of applying generalizations to a complex evolutionary system such as migration, we have delineated here a broad methodology for testing hypotheses about the evolution of migration within a phylogenetic context.
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Thursday, March 01, 2007
Genes and Genius: Confirmation of association between Gene and Intelligence
A team of scientists, led by psychiatric geneticists at Washington University School of Medicine in St. Louis, has gathered the most extensive evidence to date that a gene that activates signaling pathways in the brain influences one kind of intelligence. They have confirmed a link between the gene, CHRM2, and performance IQ, which involves a person's ability to organize things logically.
"This is not a gene for intelligence," says Danielle M. Dick, Ph.D., assistant professor of psychiatry and lead author on the study. "It's a gene that's involved in some kinds of brain processing, and specific alterations in the gene appear to influence IQ. But this single gene isn't going to be the difference between whether a person is a genius or has below-average intelligence."
Dick's team comprehensively studied the DNA along the gene and found that several variations within the CHRM2 gene could be correlated with slight differences in performance IQ scores, which measure a person's visual-motor coordination, logical and sequential reasoning, spatial perception and abstract problem solving skills. When people had more than one positive variation in the gene, the improvements in performance IQ were cumulative. The study's findings are available online in Behavioral Genetics and will appear in an upcoming print issue of that journal .
IQ tests also measure verbal skills and typically include many subtests. For this study, subjects took five verbal subtests and four performance subtests, but the genetic variations influenced only performance IQ scores.
"One way to measure performance IQ may be to ask people to order pictures correctly to tell a story," Dick explains. "A simple example might be pictures of a child holding a vase, the vase broken to bits on the floor and the child crying. The person taking the test would have to put those pictures into an order that tells the story of how the child dropped the vase and broke it and then cried."
The researchers studied DNA gathered as part of the Collaborative Study on the Genetics of Alcoholism (COGA). In this multi-center study, people who have been treated for alcohol dependence and members of their families provide DNA samples to researchers, who isolated DNA regions related to alcohol abuse and dependence, as well as a variety of other outcomes.
Some of the participants in the study also took the Wechsler Adult Intelligence Scale-Revised, a traditional IQ test. In all, members of 200 families, including more than 2,150 individuals, took the Wechsler test, and those results were matched to differences in individuals' DNA.
By comparing individual differences embedded in DNA, the team zeroed in on CHRM2, the neuronal receptor gene on chromosome 7. The CHRM2 gene activates a multitude of signaling pathways in the brain involved in learning, memory and other higher brain functions. The research team doesn't yet understand how the gene exerts its effects on intelligence.
Intelligence was one of the first traits that attracted the attention of people interested in the interplay of genes and environmental influences. Early studies of adopted children, for example, showed that when children grow up away from their biological parents, their IQs are more closely correlated to biological parents, with whom they share genes, than adoptive parents, with whom they share an environment.
But in spite of the association between genes and intelligence, it has been difficult to find specific variations that influence intelligence. The genes identified in the past were those that had profoundly negative effects on intelligence - genes that cause mental retardation, for example. Those that contribute to less dramatic differences have been much harder to isolate.
Dick's team is not the first to notice a link between intelligence and the CHRM2 gene. In 2003, a group in Minnesota looked at a single marker in the gene and noted that the variation was related to an increase in IQ. A more recent Dutch study looked at three regions of DNA along the gene and also noticed influences on intelligence. In this new study, however, researchers tested multiple genetic markers throughout the gene.
"If we look at a single marker, a DNA variation might influence IQ scores between two and four points, depending on which variant a person carries," Dick explains. "We did that all up and down the gene and found that the variations had cumulative effects, so that if one person had all of the 'good' variations and another all of the 'bad' variations, the difference in IQ might be 15 to 20 points. Unfortunately, the numbers of people at those extremes were so small that the finding isn't statistically significant, but the point is we saw fairly substantial differences in our sample when we combined information across multiple regions of the gene."
Dick says the next step is to look at the gene and its numerous variants to learn what is going on biologically that might affect cognitive performance. Presently, she says it's too early to predict how small changes in the gene might be influencing communication in the brain to affect intelligence, and she says it's nearly certain CHRM2 is not the only gene involved.
"Perhaps as many as 100 genes or more could influence intelligence," she says. "I think all of the genes involved probably have small, cumulative effects on increasing or decreasing I.Q., and I expect overall intelligence is a function of the accumulation of all of these genetic variants, not to mention environmental influences ranging from socio-economic status to the value that's placed on learning when children are growing up."
Source: Washington University in St Louis School of Medicine PR "Genes and genius: Researchers confirm association between gene and intelligence" February 27 2007
 Association of CHRM2 with IQ: Converging Evidence for a Gene Influencing Intelligence
Danielle M. Dick et al.
ISSN 0001-8244 (Print) 1573-3297 (Online)
The cholinergic neurotransmitter system is thought to be involved in many aspects of memory, attention, and higher cognition. In the Collaborative Study on the Genetics of Alcoholism (COGA) sample, we have previously reported linkage and association to the cholinergic muscarinic 2 receptor gene (CHRM2) on chromosome 7 with evoked EEG oscillations (Jones et al. 2004), providing evidence that this gene may be involved in human brain dynamics and cognition. In addition, a small number of genetic markers were genotyped in CHRM2 in the Minnesota Twin and Family Study (Comings et al. 2003) and a Dutch family study (Gosso et al. 2006, in press) and both research groups found evidence that this gene may be involved in intelligence. In the COGA sample, we have extensively genotyped SNPs (single nucleotide polymorphisms) within and flanking the CHRM2 gene. We find evidence of association with multiple SNPs across CHRM2 and Performance IQ, as measured by the Wechsler Adult Intelligence Scale-Revised (WAIS-R). These results remain significant after taking into account alcohol dependence and depression diagnoses in the sample.
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Wednesday, February 28, 2007
Study: Early Europeans unable to stomach milk
The first direct evidence that early Europeans were unable to digest milk has been found by scientists at UCL (University College London) and Mainz University.
In a study, published in the journal PNAS  (Proceedings of the National Academy of Sciences), the team shows that the gene that controls our ability to digest milk was missing from Neolithic skeletons dating to between 5840 and 5000 BC. However, through exposure to milk, lactose tolerance evolved extremely rapidly, in evolutionary terms (see lactose intolerance). Today, it is present in over ninety per cent of the population of northern Europe and is also found in some African and Middle Eastern populations but is missing from the majority of the adult population globally.
Dr Mark Thomas, UCL Biology, said: "The ability to drink milk is the most advantageous trait that's evolved in Europeans in the recent past. Without the enzyme lactase, drinking milk in adulthood causes bloating and diarrhoea. Although the benefits of milk tolerance are not fully understood yet, they probably include: the continuous supply of milk compared to the boom and bust of seasonal crops; its nourishing qualities; and the fact that it's uncontaminated by parasites, unlike stream water, making it a safer drink. All in all, the ability to drink milk gave some early Europeans a big survival advantage."
The team carried out DNA tests on Neolithic skeletons from some of the earliest organised farming communities in Europe. Their aim was to find out whether these early Europeans from various sites in central, northeast and southeast Europe, carried a version of the lactase gene that controls our ability to produce the essential enzyme lactase into adulthood. The team found that it was absent from their ancient bone DNA. This led the researchers to conclude that the consumption and tolerance of milk would have been very rare or absent at the time.
Scientists have known for decades that at some point in the past all humans were lactose intolerant. What was not known was just how recently lactose tolerance evolved.
Dr Thomas said: "To go from lactose tolerance being rare or absent seven to eight thousand years ago to the commonality we see today in central and northern Europeans just cannot be explained by anything except strong natural selection. Our study confirms that the variant of the lactase gene appeared very recently in evolutionary terms and that it became common because it gave its carriers a massive survival advantage. Scientists have inferred this already through analysis of genes in today's population but we've confirmed it by going back and looking at ancient DNA."
This study challenges the theory that certain groups of Europeans were lactose tolerant and that this inborn ability led the community to pursue dairy farming. Instead, they actually evolved their tolerance of milk within the last 8000 years due to exposure to milk.
Dr Thomas said: "There were two theories out there: one that lactose tolerance led to dairy farming and another that exposure to milk led to the evolution of lactose tolerance. This is a simple chicken or egg question but one that is very important to archaeologists, anthropologists and evolutionary biologists. We found that the lactose tolerance variant of the lactase gene only became common after dairy farming, which started around 9 thousand years ago in Europe.
"This is just one part of the picture researchers are gathering about lactose tolerance and the origins of Europeans. Next on the list is why there is such disparity in lactose tolerance between populations. It's striking, for example, that today around eighty per cent of southern Europeans cannot tolerate lactose even though the first dairy farmers in Europe probably lived in those areas. Through computer simulations and DNA testing we are beginning to get glimpses of the bigger early European picture."
Source: University College London PR February 27 2007
 Based on the PNAS paper:
Absence of the lactase-persistence-associated allele in early Neolithic Europeans
J. Burger, M. Kirchner, B. Bramanti, W. Haak, and M. G. Thomas
Published online before print February 28, 2007
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0607187104
Lactase persistence (LP), the dominant Mendelian trait conferring the ability to digest the milk sugar lactose in adults, has risen to high frequency in central and northern Europeans in the last 20,000 years. This trait is likely to have conferred a selective advantage in individuals who consume appreciable amounts of unfermented milk. Some have argued for the "culture-historical hypothesis," whereby LP alleles were rare until the advent of dairying early in the Neolithic but then rose rapidly in frequency under natural selection. Others favor the "reverse cause hypothesis," whereby dairying was adopted in populations with preadaptive high LP allele frequencies. Analysis based on the conservation of lactase gene haplotypes indicates a recent origin and high selection coefficients for LP, although it has not been possible to say whether early Neolithic European populations were lactase persistent at appreciable frequencies. We developed a stepwise strategy for obtaining reliable nuclear ancient DNA from ancient skeletons, based on (i) the selection of skeletons from archaeological sites that showed excellent biomolecular preservation, (ii) obtaining highly reproducible human mitochondrial DNA sequences, and (iii) reliable short tandem repeat (STR) genotypes from the same specimens. By applying this experimental strategy, we have obtained high-confidence LP-associated genotypes from eight Neolithic and one Mesolithic human remains, using a range of strict criteria for ancient DNA work. We did not observe the allele most commonly associated with LP in Europeans, thus providing evidence for the culture-historical hypothesis, and indicating that LP was rare in early European farmers.
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Sunday, February 25, 2007
Study reduces Chimpanzee-Human split to 4 million years ago
Anthropology and Primatology - Excerpts from the February 23, 2007 PLoS Genetics paper "Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model" (Adapted) by Asger Hobolth, Ole F. Christensen, Thomas Mailund, and Mikkel H. Schierup:
[Related news story from Scientific American - "Humans, chimps split 4 million years ago: study": A new study, certain to be controversial, maintains that chimpanzees and humans split from a common ancestor just 4 million years ago - a much shorter time than current estimates of 5 million to 7 million years ago.]
Primate evolution is a central topic in biology and much information can be obtained from DNA sequence data. A key parameter is the time "when we became human," i.e., the time in the past when descendents of the human-chimp ancestor split into human and chimpanzee. Other important parameters are the time in the past when descendents of the human-chimp-gorilla ancestor split into descendents of the human-chimp ancestor and the gorilla ancestor, and population sizes of the human-chimp and human-chimp-gorilla ancestors. To estimate speciation times and ancestral population sizes we have developed a new methodology that explicitly utilizes the spatial information in contiguous genome alignments. Furthermore, we have applied this methodology to four long autosomal human-chimp-gorilla-orangutan alignments and estimated a very recent speciation time of human and chimp (around 4 million years) and ancestral population sizes much larger than the present-day human effective population size. We also analyzed X-chromosome sequence data and found that the X chromosome has experienced a different history from that of autosomes, possibly because of selection.
Citation: Hobolth A, Christensen OF, Mailund T, Schierup MH (2007) Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model. PLoS Genet 3(2): e7 doi:10.1371/journal.pgen.0030007
The genealogical relationship of human, chimpanzee, and gorilla varies along the genome. We develop a hidden Markov model (HMM) that incorporates this variation and relate the model parameters to population genetics quantities such as speciation times and ancestral population sizes. Our HMM is an analytically tractable approximation to the coalescent process with recombination, and in simulations we see no apparent bias in the HMM estimates. We apply the HMM to four autosomal contiguous human-chimp-gorilla-orangutan alignments comprising a total of 1.9 million base pairs. We find a very recent speciation time of human-chimp (4.1 plus/minus 0.4 million years), and fairly large ancestral effective population sizes (65,000 plus/minus 30,000 for the human-chimp ancestor and 45,000 plus/minus 10,000 for the human-chimp-gorilla ancestor). Furthermore, around 50% of the human genome coalesces with chimpanzee after speciation with gorilla. We also consider 250,000 base pairs of X-chromosome alignments and find an effective population size much smaller than 75% of the autosomal effective population sizes. Finally, we find that the rate of transitions between different genealogies correlates well with the region-wide present-day human recombination rate, but does not correlate with the fine-scale recombination rates and recombination hot spots, suggesting that the latter are evolutionarily transient.
The recent evolutionary history of the human species can be investigated by comparative approaches using the genomes of the great apes: chimpanzee, gorilla, and orangutan. Nucleotide differences, accumulated by fixation of mutations, carry a wealth of information on important issues such as speciation times, properties of ancestral species (e.g., population sizes), and how speciation occurred. Genes or genomic fragments with unusual patterns of nucleotide differences and divergence may have been under strong natural selection during recent evolution of the human species. Sequence analyses can also aid interpretations of the incomplete primate fossil records and aid assignment of dated fossils to evolutionary lineages. For instance, it is still debated whether the Millennium man, Orrorin tugenensis, which has been dated to 6 million years (Myr) ago, and Sahelanthropus tchadensis, which has been dated to 6-7 Myr ago, belong to the human lineage or the human-chimp (HC) lineage.
Comparative analyses of multiple alignments of small fragments of human, chimpanzee, gorilla, and orangutan sequence have revealed that the human genome is more similar to the gorilla genome than to the chimpanzee genome for a considerable fraction of single genes. Such a conflict between species and gene genealogy is expected if the time span between speciation events is small measured in the number of 2N generations, where N is the effective population of the ancestral species (see Figure 1). In that case, N can be estimated from the proportion of divergent genealogies if one assumes that speciation is an instantaneous event. Indeed, this has been done in several studies that find a HC ancestral effective population size NHC of 2-10 times the human present-day effective population size NH = 10,000. Recently, Patterson et al. studied a very large number of small human-chimp-gorilla-orangutan-macaque alignments. They found, in agreement with O'hUigin et al., that a large proportion of sites supporting alternative genealogies are caused by hypermutability and that the fraction of the genome with alternative genealogies therefore has been overestimated in previous studies. After using a statistical correction for substitution rate heterogeneity, Patterson et al. found that the variance in coalescence times is too large to be accounted for by instant speciation and a large ancestral effective population size, and that the speciation process therefore must have been complex. Particularly, the X chromosome shows a deviant pattern, which also led them to conclude that HC gene flow ceased and final speciation occurred as recently as 4 Myr ago. This date is generally believed to be the most recent time compatible with the fossil record, if the Millennium man and Sahelanthropus are not on the human lineage.
Whole genome sequences of gorilla and orangutan will soon supplement the already available whole genome sequences of human and chimpanzee. These four genomes are so closely related that alignments of large contiguous parts of the genomes can be constructed. Analysis of such large fragments is challenging because different parts of the alignment will have different evolutionary histories (and thus different genealogies, see Figure 1) because of recombination. Ideally, one would like to infer the genealogical changes directly from the data and then analyze each type of genealogy separately. A natural approach to this challenge is to move along the alignment, and simultaneously compute the probabilities of different relationships and speciation times. While recombination has been considered in previous likelihood models, the spatial information along the alignment has largely been ignored.
In this paper we describe a hidden Markov model (HMM) that allows the presence of different genealogies along large multiple alignments. The hidden states are different possible genealogies (labeled HC1, HC2, HG, and CG in Figures 1 and 2). Parameters of the HMM include population genetics parameters such as the HC and human-chimp-gorilla (HCG) ancestral effective population sizes, NHC and NHCG, and speciation times tau1 and tau2 (see Figure 1). We therefore name our approach a coalescent HMM (coal-HMM). The statistical framework of HMMs yields parameter estimates with associated standard errors, and posterior probabilities of hidden states. We show by simulation studies that the coal-HMM recovers parameters from the coalescence with recombination process, and we apply the coal-HMM to five long contiguous human-chimp-gorilla-orangutan (HCGO) alignments obtained from the NIH Intramural Sequencing Center comparative sequencing program (Targets 1, 106, 121, and 122 on four different autosomes and Target 46 on the X chromosome). We consistently find very recent estimates of HC speciation times and a large variance in the time to common ancestry along the genome. Similar to Patterson et al., we find that the X chromosome has a smaller effective population size than expected. The mapping of genealogical states further allows us to correlate transitions in genealogies with properties of the genome, and here we focus on fine-scale and region-wide recombination rate estimates.
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