Early cattle management in NE China

From the paper:

The haplogroup retrieved has so far not been found in modern cattle. However, as mtDNA represents a single genetic locus, it is prone to genetic drift and could easily have been lost by drift even if hybridization between the population to which the Chinese specimen belonged and other domesticated cattle populations has occurred. Further analyses on nuclear DNA will be necessary to show whether this early Chinese cattle management was a short-lived episode or whether it has contributed to the nuclear gene pool of modern cattle.

Nature Communications 4, Article number: 2755 doi:10.1038/ncomms3755

Morphological and genetic evidence for early Holocene cattle management in northeastern China

Hucai Zhang et al.

The domestication of cattle is generally accepted to have taken place in two independent centres: around 10,500 years ago in the Near East, giving rise to modern taurine cattle, and two millennia later in southern Asia, giving rise to zebu cattle. Here we provide firmly dated morphological and genetic evidence for early Holocene management of taurine cattle in northeastern China. We describe conjoining mandibles from this region that show evidence of oral stereotypy, dated to the early Holocene by two independent 14C dates. Using Illumina high-throughput sequencing coupled with DNA hybridization capture, we characterize 15,406 bp of the mitogenome with on average 16.7-fold coverage. Phylogenetic analyses reveal a hitherto unknown mitochondrial haplogroup that falls outside the known taurine diversity. Our data suggest that the first attempts to manage cattle in northern China predate the introduction of domestic cattle that gave rise to the current stock by several thousand years.

Link

European pigs replacing Near Eastern ones in Iron Age Israel

Related:

• The comings and goings of Near Eastern and European domestic pigs (Ottoni et al. 2012)

Scientific Reports 3, Article number: 3035 doi:10.1038/srep03035

Ancient DNA and Population Turnover in Southern Levantine Pigs- Signature of the Sea Peoples Migration?

Meirav Meiri et al.

Near Eastern wild boars possess a characteristic DNA signature. Unexpectedly, wild boars from Israel have the DNA sequences of European wild boars and domestic pigs. To understand how this anomaly evolved, we sequenced DNA from ancient and modern pigs from Israel. Pigs from Late Bronze Age (until ca. 1150 BCE) in Israel shared haplotypes of modern and ancient Near Eastern pigs. European haplotypes became dominant only during the Iron Age (ca. 900 BCE). This raises the possibility that European pigs were brought to the region by the Sea Peoples who migrated to the Levant at that time. Then, a complete genetic turnover took place, most likely because of repeated admixture between local and introduced European domestic pigs that went feral. Severe population bottlenecks likely accelerated this process. Introductions by humans have strongly affected the phylogeography of wild animals, and interpretations of phylogeography based on modern DNA alone should be taken with caution.

Link

mtDNA from (non-frozen) >300 thousand year old cave bear from Sima de los Huesos

PNAS doi: 10.1073/pnas.1314445110

Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments

Jesse Dabney et al.

Abstract

Although an inverse relationship is expected in ancient DNA samples between the number of surviving DNA fragments and their length, ancient DNA sequencing libraries are strikingly deficient in molecules shorter than 40 bp. We find that a loss of short molecules can occur during DNA extraction and present an improved silica-based extraction protocol that enables their efficient retrieval. In combination with single-stranded DNA library preparation, this method enabled us to reconstruct the mitochondrial genome sequence from a Middle Pleistocene cave bear (Ursus deningeri) bone excavated at Sima de los Huesos in the Sierra de Atapuerca, Spain. Phylogenetic reconstructions indicate that the U. deningeri sequence forms an early diverging sister lineage to all Western European Late Pleistocene cave bears. Our results prove that authentic ancient DNA can be preserved for hundreds of thousand years outside of permafrost. Moreover, the techniques presented enable the retrieval of phylogenetically informative sequences from samples in which virtually all DNA is diminished to fragments shorter than 50 bp.

Link

Native Native American dogs

Proc. R. Soc. B doi: 10.1098/rspb.2013.1142

Pre-Columbian origins of Native American dog breeds, with only limited replacement by European dogs, confirmed by mtDNA analysis

Barbara van Asch et al.

Dogs were present in pre-Columbian America, presumably brought by early human migrants from Asia. Studies of free-ranging village/street dogs have indicated almost total replacement of these original dogs by European dogs, but the extent to which Arctic, North and South American breeds are descendants of the original population remains to be assessed. Using a comprehensive phylogeographic analysis, we traced the origin of the mitochondrial DNA lineages for Inuit, Eskimo and Greenland dogs, Alaskan Malamute, Chihuahua, xoloitzcuintli and perro sín pelo del Peru, by comparing to extensive samples of East Asian (n = 984) and European dogs (n = 639), and previously published pre-Columbian sequences. Evidence for a pre-Columbian origin was found for all these breeds, except Alaskan Malamute for which results were ambigous. No European influence was indicated for the Arctic breeds Inuit, Eskimo and Greenland dog, and North/South American breeds had at most 30% European female lineages, suggesting marginal replacement by European dogs. Genetic continuity through time was shown by the sharing of a unique haplotype between the Mexican breed Chihuahua and ancient Mexican samples. We also analysed free-ranging dogs, confirming limited pre-Columbian ancestry overall, but also identifying pockets of remaining populations with high proportion of indigenous ancestry, and we provide the first DNA-based evidence that the Carolina dog, a free-ranging population in the USA, may have an ancient Asian origin.

Link

The history of great apes

Nature (2013) doi:10.1038/nature12228

Great ape genetic diversity and population history

Javier Prado-Martinez et al.

Most great ape genetic variation remains uncharacterized1, 2; however, its study is critical for understanding population history3, 4, 5, 6, recombination7, selection8 and susceptibility to disease9, 10. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria–Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.

Link

700,000-year old horse sequenced

A 700.000 year old horse gets its genome sequenced

It is nothing short of a world record in DNA research that scientists at the Centre for GeoGenetics at the Natural History Museum of Denmark (University of Copenhagen) have hit. They have sequenced the so far oldest genome from a prehistoric creature. They have done so by sequencing and analyzing short pieces of DNA molecules preserved in bone-remnants from a horse that had been kept frozen for the last 700.000 years in the permafrost of Yukon, Canada. By tracking the genomic changes that transformed prehistoric wild horses into domestic breeds, the researchers have revealed the genetic make-up of modern horses with unprecedented details. The spectacular results are now published in the international scientific journal Nature.

... 

First, by comparing the genome in the 700,000 year old horse with the genome of a 43,000 year old horse, six present day horses and the donkey the researchers could estimate how fast mutations accumulate through time and calibrate a genome-wide mutation rate. This revealed that the last common ancestor of all modern equids was living about 4.0-4.5 million years ago. Therefore, the evolutionary radiation underlying the origin of horses, donkeys and zebras reaches back in time twice as long as previously thought. Additionally, this new clock revealed multiple episodes of severe demographic fluctuation in horse history, in phase with major climatic changes such as the Last Glacial Maximum, some 20,000 years ago.

I'll add the paper abstract later.

Nature (2013) doi:10.1038/nature12323

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

Ludovic Orlando et al.

The rich fossil record of equids has made them a model for evolutionary processes1. Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560–780 thousand years before present (kyr BP)2, 3. Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43?kyr BP), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski’s horse (E. f. przewalskii) and a donkey (E. asinus). Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0–4.5?million years before present (Myr BP), twice the conventionally accepted time to the most recent common ancestor of the genus Equus4, 5. We also find that horse population size fluctuated multiple times over the past 2?Myr, particularly during periods of severe climatic changes. We estimate that the Przewalski’s and domestic horse populations diverged 38–72?kyr BP, and find no evidence of recent admixture between the domestic horse breeds and the Przewalski’s horse investigated. This supports the contention that Przewalski’s horses represent the last surviving wild horse population6. We find similar levels of genetic variation among Przewalski’s and domestic populations, indicating that the former are genetically viable and worthy of conservation efforts. We also find evidence for continuous selection on the immune system and olfaction throughout horse evolution. Finally, we identify 29 genomic regions among horse breeds that deviate from neutrality and show low levels of genetic variation compared to the Przewalski’s horse. Such regions could correspond to loci selected early during domestication.

Link

Dog domestication parameters from full genome sequencing

This paper casts doubt on the dominant scenario about the Southeast Asian geographical origin of dogs, while at the same time affirming their monophyletic origin and late pre-Neolithic domestication. The authors also document traits that were under selection during domestication.

It would be interesting to know what kinds of roles early dogs. Presumably early pre-Neolithic dogs functioned more as hunting companions, while those of Neolithic societies also had an increasing role as guards -since there was then property that needed guarding. How do modern dog breeds differ genetically to accommodate these roles, and might we one day figure out the original tasks of "multi-purpose" animals such as dogs?

arXiv:1305.7390 [q-bio.GN]

Genome Sequencing Highlights Genes Under Selection and the Dynamic Early History of Dogs

Adam H. Freedman et al.

To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we analyzed novel high-quality genome sequences of three gray wolves, one from each of three putative centers of dog domestication, two ancient dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. We find dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow, which confounds previous inferences of dog origins. In dogs, the domestication bottleneck was severe involving a 17 to 49-fold reduction in population size, a much stronger bottleneck than estimated previously from less intensive sequencing efforts. A sharp bottleneck in wolves occurred soon after their divergence from dogs, implying that the pool of diversity from which dogs arose was far larger than represented by modern wolf populations. Conditional on mutation rate, we narrow the plausible range for the date of initial dog domestication to an interval from 11 to 16 thousand years ago. This period predates the rise of agriculture, implying that the earliest dogs arose alongside hunter-gathers rather than agriculturists. Regarding the geographic origin of dogs, we find that surprisingly, none of the extant wolf lineages from putative domestication centers are more closely related to dogs, and the sampled wolves instead form a sister monophyletic clade. This result, in combination with our finding of dog-wolf admixture during the process of domestication, suggests a re-evaluation of past hypotheses of dog origin is necessary. Finally, we also detect signatures of selection, including evidence for selection on genes implicated in morphology, metabolism, and neural development. Uniquely, we find support for selective sweeps at regulatory sites suggesting gene regulatory changes played a critical role in dog domestication.

Link

33,000-year old dog from the Altai

From the paper:

In conclusion, our analyses support the hypothesis that the Altai specimen is more closely related to domestic dogs than to extant wolves, but we stress the point that these analyses were limited to a single, maternally inherited locus and more sequence data would be needed to obtain a statistically well supported phylogeny and unambiguously resolve the genetic relationship of the Altai specimen. However, this preliminary analysis affirms the conclusion that the Altai specimen is likely an ancient dog with a shallow divergence from ancient wolves. These results suggest a more ancient history of the dog outside the Middle East or East Asia, previously suggested as centres of dog origin. Additional discoveries of ancient dog-like remains are essential for further narrowing the time and region of origin for the domestic dog [5].

An ancient dog with shallow divergence from ancient wolves is probably what we might expect if dogs had been domesticated by some of the first Upper Paleolithic Eurasians a few thousand years prior to the date of this particular specimen.

PLoS ONE 8(3): e57754. doi:10.1371/journal.pone.0057754

Ancient DNA Analysis Affirms the Canid from Altai as a Primitive Dog

Anna S. Druzhkova et al.

The origin of domestic dogs remains controversial, with genetic data indicating a separation between modern dogs and wolves in the Late Pleistocene. However, only a few dog-like fossils are found prior to the Last Glacial Maximum, and it is widely accepted that the dog domestication predates the beginning of agriculture about 10,000 years ago. In order to evaluate the genetic relationship of one of the oldest dogs, we have isolated ancient DNA from the recently described putative 33,000-year old Pleistocene dog from Altai and analysed 413 nucleotides of the mitochondrial control region. Our analyses reveal that the unique haplotype of the Altai dog is more closely related to modern dogs and prehistoric New World canids than it is to contemporary wolves. Further genetic analyses of ancient canids may reveal a more exact date and centre of domestication.

Link

Our rabbit-hunting ancestors (Fa et al. 2013)

From the paper:

Relative to other mammal groups, rabbit bone abundance was always significantly higher during the Upper Palaeolithic (76%) and Mesolithic (59%) than during the Middle Palaeolithic (Fig. 4). The difference between the average rabbit remains and that of cervids, the second most abundant prey item, were less than 10% during the Mousterian. In contrast, during the Upper Palaeolithic and Mesolithic, the difference between the rabbit and the second-most important prey items was over 60% and 20%, respectively. After the rabbit, large ungulates (caprids, cervids and equids) were relatively important during the Middle and Upper Palaeolithic, while caprids, cervids and suids took that place during the Mesolithic (Fig. 4).

and:

Our evidence indicates that hominin diets may have changed from one dependent on large mammals during the Middle Palaeolithic to diets dominated by smaller species in the Upper Palaeolithic, in particular by the wild rabbit. The explanation for this transition is either that climate change negatively impacted large mammal populations, forcing prehistoric people to incorporate smaller vertebrate species into their diets, or that people themselves negatively impacted large mammal populations, which in turn forced foragers to add smaller species to their diets. 

I am not sure how modern hunter-gatherers hunt rabbits, but I would think that trapping, or some type of slingshot or blowdart would be ideal for this small and fast-moving animal. Did Neandertals simply lack efficient technology to capture rabbit, or is there some other reason why they underutilized the species?

Journal of Human Evolution DOI: 10.1016/j.jhevol.2013.01.002

Rabbits and hominin survival in Iberia 

John E. Fa et al.

High dependence on the hunting and consumption of large mammals by some hominins may have limited their survival once their preferred quarry became scarce or disappeared. Adaptation to smaller residual prey would have been essential after the many large-bodied species decreased in numbers. We focus on the use of a superabundant species, the rabbit, to demonstrate the importance of this taxon in Iberia as fundamental to predators. We show that the use of the rabbit over time has increased, and that there could have been differential consumption by Neanderthals and Anatomically Modern Humans (AMH). Analysis of bone remains from excavations throughout Iberia show that this lagomorph was a crucial part of the diet of AMH but was relatively unutilised during the Mousterian, when Neanderthals were present. We first present changes in mammalian biomass and mean body mass of mammals over 50,000 years, to illustrate the dramatic loss of large mammalian fauna and to show how the rabbit may have contributed a consistently high proportion of the available game biomass throughout that period. Unlike the Italian Peninsula and other parts of Europe, in Iberia the rabbit has provided a food resource of great importance for predators including hominins. We suggest that hunters that could shift focus to rabbits and other smaller residual fauna, once larger-bodied species decreased in numbers, would have been able to persist. From the evidence presented here, we postulate that Neanderthals may have been less capable of prey-shifting and hence use the high-biomass prey resource provided by the rabbit, to the extent AMH did.

Link

Southeast Asian Neolithic dogs

From the paper:

Nevertheless, the close phylogenetic clustering of haplotypes from Thailand, Brunei, Bali, and the Philippines suggests these populations originated from the same source, consistent with a single migration event, whereas the dingoes, NGSDs, and dogs from Taiwan appear sufficiently distinct from these to reflect a distinct migration event (Fig. 2b-c). The clustering of the three Island Southeast Asian populations with Thailand also was more consistent with origination from Mainland Southeast Asia than Taiwan (in agreement with mtDNA findings of Oskarsson et al. 2011).

and:

In light of findings from the present study, it seems clear that both post-Victorian and Neolithic exchanges link eastern and western Eurasian dogs. However, the cause of post-Victorian haplotype sharing between Western breed dogs and Southeast Asian village dogs apparently reflects very recent introduction of Western dogs to the East rather than extraction of Eastern dogs to create Western breeds during the Victorian Era.

and:

Specifically, our aging of this European haplogroup to 5,800 (±SE = 1750) or 8,400 (±SE = 2500) years (depending on the dingo calibration to 3,500 or 5,000 years, respectively) suggests that the connection between pre-Victorian European and Southeast Asian dogs traces only to the Neolithic period and is not of sufficient antiquity to support the hypothesis of a single origin of dogs from Southeast Asia. Thus, although future studies are needed to combine the Y SNPs and STR markers in a geographically broader sampling of dogs than was considered here, our findings support the hypothesis for a massive Neolithic expansion of dogs from Southeast Asia rather than a Paleolithic origin of dogs from this region.

This massive Neolithic expansion of Southeast Asian dogs is testable by looking at early European dogs; these ought not to belong to haplogroup H1. It would also be interesting to speculate about the trade routes and/or population movements that facilitated the spread of dogs from SE Asia to Europe during the Neolithic.

Mol Biol Evol (2013) doi: 10.1093/molbev/mst027

Y chromosome analysis of dingoes and Southeast Asian village dogs suggests a Neolithic continental expansion from Southeast Asia followed by multiple Austronesian dispersals

Benjamin N. Sacks et al.

Dogs originated >14,000 BP, but the location(s) where they first arose is uncertain. The earliest archaeological evidence of ancient dogs was discovered in Europe and the Middle East, some 5–7 millennia before that from Southeast Asia. However, mitochondrial DNA analyses suggest that most modern dogs derive from Southeast Asia, which has fueled the controversial hypothesis that dog domestication originated in this region despite the lack of supporting archaeological evidence. We propose and investigate with Y chromosomes an alternative hypothesis for the proximate origins of dogs from Southeast Asia--a massive Neolithic expansion of dogs from this region that largely replaced more primitive dogs to the west and north. Previous attempts to test matrilineal findings with independent patrilineal markers have lacked the necessary genealogical resolution and mutation rate estimates. Here, we used Y chromosome genotypes, composed of 29 SNPs and 5 STRs, from 338 Australian dingoes, New Guinea singing dogs, and village dogs from Island Southeast Asia, along with modern European breed dogs, to estimate the evolutionary mutation rates of Y chromosome STRs based on calibration to the independently known age of the dingo population. Dingoes exhibited a unique haplogroup characterized by a single distinguishing SNP mutation and 14 STR haplotypes. The age of the European haplogroup was estimated to be only 1.7 times older than that of the dingo population, suggesting an origin during the Neolithic rather than the Paleolithic (as predicted by the Southeast Asian origins hypothesis). We hypothesize that isolation of Neolithic dogs from wolves in Southeast Asia was a key step accelerating their phenotypic transformation, enhancing their value in trade and as cargo, and enabling them to rapidly expand and replace more primitive dogs to the West. Our findings also suggest that dingoes could have arrived in Australia directly from Taiwan, independently of later dispersals of dogs through Thailand to Island Southeast Asia.

Link

Genetic diversity of modern horses

Some very distinctive groupings of modern breeds emerge in this survey of modern horse breed genetic variation, and some of these groups have clear geographical associations.

Horses are very mobile, and can also be traded; much of their existing variation may also be the result of artificial breeding which might have included both selection for particular desirable traits as well as mixing different populations.

Now that there is a fairly clear picture of modern variation, it will be useful to explore how this has emerged over time. It'll be interesting to see how ancient horses fit into the modern picture: will they prove ancestral to those living in the same regions, or is there a process of continuous renewal, with multiple episodes of turnover, as good breeds emerge somewhere across the geographical range of the animal, and quickly replace less advantageous ones?

PLoS ONE 8(1): e54997. doi:10.1371/journal.pone.0054997

Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data

Jessica L. Petersen et al.

Horses were domesticated from the Eurasian steppes 5,000–6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection.

Link

Zoogeographic map of the world

I have written informally about the Sahara-Arabia belt in conjunction with my "two deserts" theory of modern human origins (=pre-100kya in North Africa, post-70kya from Arabia), so it's nice to see that it corresponds to some real zoogeographic entity derived from the distribution of thousands of species. So, perhaps an early evolution of modern humans in that area, followed by their dispersal and admixture with other hominins living in the Palearctic and Afrotropical regions might make sense.

Science DOI: 10.1126/science.1228282

An Update of Wallace's Zoogeographic Regions of the World

Ben G. Holt et al.

Modern attempts to produce biogeographic maps focus on the distribution of species and are typically drawn without phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions of the world.

Link

Admixture matters (for polar bears too!)

In Admixture matters, I argued, inter alia, that "admixture can also deflate divergence, if there is subsequent gene flow between the diverged populations."

Interestingly, polar bears are now providing us with a wonderful example of this process in action. It has been abundantly clear for a while now, that polar bears are an arctic-adapted form of non-polar bears, bow how far back in time can there evolutionary relationship be pushed?

A new open access paper in PNAS answers this question:

We first used a simple isolation model (15), comparing pairs of genomes under the assumption of allopatric speciation. However, for all comparisons, we obtained estimates of very recent split times and very large ancestral effective population sizes (Ne ), consistent with mis-specification of the demographic model and suggesting that the true demographics involved are not simple splits but instead initial splits followed by prolonged periods with structured populations and gene flow. WWe therefore applied an extended model estimating an initial split time followed by a period of gene flow before a complete split (SI Appendix). We estimated an initial split between black bears and their sister lineage 4 to 5 Mya followed by gene flow until 100 to 200 kya (Fig. 3)

There you have it: low split times/high effective sizes are inferred in a tree model ("simple isolation model"), but when one does not take into account gene flow between the diverged populations, split times balloon and effective sizes shrink.

Of course in this case, we actually do have extant brown/black/polar samples to work with. But, leaving zoology and going back to anthropology, we only have on extant species (H. sapiens) within the genus Homo and only two (H. Neandertalensis and "Denisovans") of several archaic hominins that once roamed the planet, in some cases, apparently until very recently. Both the cases we do have indicate differential admixture levels with modern human groups.

I think we need to open ourselves to the possibility that shallow divergence times and higher effective population sizes in some human populations may not be the result of Biblical-level bottlenecks as small tribes of humans "conquered the earth", but of thorough and long-term gene flow between populations within the genus Homo.


PNAS doi: 10.1073/pnas.1210506109

Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

Webb Miller et al.

Polar bears (PBs) are superbly adapted to the extreme Arctic environment and have become emblematic of the threat to biodiversity from global climate change. Their divergence from the lower-latitude brown bear provides a textbook example of rapid evolution of distinct phenotypes. However, limited mitochondrial and nuclear DNA evidence conflicts in the timing of PB origin as well as placement of the species within versus sister to the brown bear lineage. We gathered extensive genomic sequence data from contemporary polar, brown, and American black bear samples, in addition to a 130,000- to 110,000-y old PB, to examine this problem from a genome-wide perspective. Nuclear DNA markers reflect a species tree consistent with expectation, showing polar and brown bears to be sister species. However, for the enigmatic brown bears native to Alaska's Alexander Archipelago, we estimate that not only their mitochondrial genome, but also 5–10% of their nuclear genome, is most closely related to PBs, indicating ancient admixture between the two species. Explicit admixture analyses are consistent with ancient splits among PBs, brown bears and black bears that were later followed by occasional admixture. We also provide paleodemographic estimates that suggest bear evolution has tracked key climate events, and that PB in particular experienced a prolonged and dramatic decline in its effective population size during the last ca. 500,000 years. We demonstrate that brown bears and PBs have had sufficiently independent evolutionary histories over the last 4–5 million years to leave imprints in the PB nuclear genome that likely are associated with ecological adaptation to the Arctic environment.

Link

To survive: be fat or be smart

The bottom line is that it makes sense for an animal to combine the "fat" and "smart" strategies to survive. It makes sense: a very fat but very dumb animal has all the energy reserves it will ever need, but at the expense of locomotion efficiency, avoidance of predators, etc. A very smart but very lean animal has all the brain power needed to survive, but has very little "in the tank" if it finds itself in a bad spot and has to go without food for a long time.

The versatile strategy is best, and humans are the one species that seems to have gone the "brain power" way, without sacrificing completely other traits needed for survival.

Nature (2011) doi:10.1038/nature10629

Energetics and the evolution of human brain size

Ana Navarrete et al.

The human brain stands out among mammals by being unusually large. The expensive-tissue hypothesis1 explains its evolution by proposing a trade-off between the size of the brain and that of the digestive tract, which is smaller than expected for a primate of our body size. Although this hypothesis is widely accepted, empirical support so far has been equivocal. Here we test it in a sample of 100 mammalian species, including 23 primates, by analysing brain size and organ mass data. We found that, controlling for fat-free body mass, brain size is not negatively correlated with the mass of the digestive tract or any other expensive organ, thus refuting the expensive-tissue hypothesis. Nonetheless, consistent with the existence of energy trade-offs with brain size, we find that the size of brains and adipose depots are negatively correlated in mammals, indicating that encephalization and fat storage are compensatory strategies to buffer against starvation. However, these two strategies can be combined if fat storage does not unduly hamper locomotor efficiency. We propose that human encephalization was made possible by a combination of stabilization of energy inputs and a redirection of energy from locomotion, growth and reproduction.

Link

Time-independent evolutionary mtDNA mutation rates in Penguins

The study is reminiscent of another recent paper on Penguins, and strikes another blow against the idea that over long time periods genetic diversity accumulates at a slow rate.

Trends in Genetics, Volume 25, Issue 11, doi:10.1016/j.tig.2009.09.005

High mitogenomic evolutionary rates and time dependency

Sankar Subramanian et al.

Using entire modern and ancient mitochondrial genomes of Adélie penguins (Pygoscelis adeliae) that are up to 44000 years old, we show that the rates of evolution of the mitochondrial genome are two to six times greater than those estimated from phylogenetic comparisons. Although the rate of evolution at constrained sites, including nonsynonymous positions and RNAs, varies more than twofold with time (between shallow and deep nodes), the rate of evolution at synonymous sites remains the same. The time-independent neutral evolutionary rates reported here would be useful for the study of recent evolutionary events.

Link

Time-dependent evolutionary mutation rate? Adélie Penguins say no

I have been a vocal critic of the applicability of the evolutionary mutation rate for human Y-chromosomes. Now, a new ancient mtDNA study on Antarctic penguins shows that the evolutionary and germline mutation rates over a period of 37,000 years are not significantly different.

This is an important discovery, since the mutation rate is a basic component of the molecular clock method. A molecular clock infers the amount of time necessary to accumulate the observed present-day variation if this variation accumulates according to a particular rate.

A "slow" evolutionary rate, allegedly supported by fossils in some species, or motivated by the presence of bottlenecks in humans, leads to an overestimation of ages.

From the paper:

Therefore, in order to compare molecular rates accurately over different time periods and within a single species, the following are required: extant natural populations from which large numbers of pedigree samples can be collected, along with large numbers of ancient samples of the same species from an undisturbed environment. Adélie penguins meet these requirements and therefore represent an ideal model for resolving disparate views about the time dependency of molecular rates. Using this species, it is possible to estimate both mutation and evolutionary rates for the same region of the genome precisely.

PLoS Genetics doi: 10.1371/journal.pgen.1000209

Mutation and Evolutionary Rates in Adélie Penguins from the Antarctic

Craig D. Millar et al.

Abstract

Precise estimations of molecular rates are fundamental to our understanding of the processes of evolution. In principle, mutation and evolutionary rates for neutral regions of the same species are expected to be equal. However, a number of recent studies have shown that mutation rates estimated from pedigree material are much faster than evolutionary rates measured over longer time periods. To resolve this apparent contradiction, we have examined the hypervariable region (HVR I) of the mitochondrial genome using families of Adélie penguins (Pygoscelis adeliae) from the Antarctic. We sequenced 344 bps of the HVR I from penguins comprising 508 families with 915 chicks, together with both their parents. All of the 62 germline heteroplasmies that we detected in mothers were also detected in their offspring, consistent with maternal inheritance. These data give an estimated mutation rate (μ) of 0.55 mutations/site/Myrs (HPD 95% confidence interval of 0.29–0.88 mutations/site/Myrs) after accounting for the persistence of these heteroplasmies and the sensitivity of current detection methods. In comparison, the rate of evolution (k) of the same HVR I region, determined using DNA sequences from 162 known age sub-fossil bones spanning a 37,000-year period, was 0.86 substitutions/site/Myrs (HPD 95% confidence interval of 0.53 and 1.17). Importantly, the latter rate is not statistically different from our estimate of the mutation rate. These results are in contrast to the view that molecular rates are time dependent.

Link