The Origin of Domestic Dogs Just Got More Complicated

Dogs and wolves evolved from a common ancestor between 9,000 and 34,000 years ago, before humans transitioned to agricultural societies, according to an analysis of modern dog and wolf genomes from areas of the world thought to be centers of dog domestication.

The study, published in
PLoS Genetics on January 16, 2014, also shows that dogs are more closely related to each other than wolves, regardless of geographic origin. This suggests that part of the genetic overlap observed between some modern dogs and wolves is the result of interbreeding after dog domestication, not a direct line of descent from one group of wolves.

This reflects a more complicated history than the popular story that early farmers adopted a few docile, friendly wolves that later became our beloved, modern-day companions. Instead, the earliest dogs may have first lived among hunter-gatherer societies and adapted to agricultural life later.

"Dog domestication is more complex than we originally thought," said John Novembre, associate professor in the Department of Human Genetics at the University of Chicago and a senior author on the study. "In this analysis we didn't see clear evidence in favor of a multi-regional model, or a single origin from one of the living wolves that we sampled (Figure 1). It makes the field of dog domestication very intriguing going forward."

wolf
Figure 1. A pack of wolves (Canis lupus).

The team generated the highest quality genome sequences to date from three gray wolves: one each from China, Croatia and Israel, representing three regions where dogs are believed to have originated. They also produced genomes for two dog breeds: a basenji, a breed which originates in central Africa, and a dingo from Australia, both areas that have been historically isolated from modern wolf populations. In addition to the wolves and dogs, they sequenced the genome of a golden jackal to serve as an "outgroup" representing earlier divergence.

Their analysis of the basenji and dingo genomes, plus a previously published boxer genome from Europe, showed that the dog breeds were most closely related to each other. Likewise, the three wolves from each geographic area were more closely related to each other than any of the dogs.

Novembre said this tells a different story than he and his colleagues anticipated. Instead of all three dogs being closely related to one of the wolf lineages, or each dog being related to its closest geographic counterpart (i.e. the basenji and Israeli wolf, or the dingo and Chinese wolf), they seem to have descended from an older, wolf-like ancestor common to both species (Figure 2).

dogs

Figure 2.
Demographic model of domestication. (A) The population tree best supported by genome-wide sequence divergence (B) a regional domestication model, and (C) a single wolf lineage origin model in which dogs diverged most recently from the Israeli wolf lineage. The width of each population branch is proportional to inferred population size. Horizontal gray dashed lines indicate timing of lineage divergences, with associated means in bold, and 95% credible intervals in parentheses. Migration bands are shown in green. (from Freedman et al. 2014)


"One possibility is there may have been other wolf lineages that these dogs diverged from that then went extinct," he said. "So now when you ask which wolves are dogs most closely related to, it's none of these three because these are wolves that diverged in the recent past. It's something more ancient that isn't well represented by today's wolves."
Accounting for gene flow between dogs and wolves after domestication was a crucial step in the analyses. According to Adam Freedman, a postdoctoral fellow at the University of California, Los Angeles (UCLA) and the lead author on the study, gene flow across canid species appears more pervasive than previously thought.

"If you don't explicitly consider such exchanges, these admixture events get confounded with shared ancestry," he said. "We also found evidence for genetic exchange between wolves and jackals. The picture emerging from our analyses is that these exchanges may play an important role in shaping the diversification of canid species."

Domestication apparently occurred with significant bottlenecks in the historical population sizes of both early dogs and wolves. Freedman and his colleagues were able to infer historical sizes of dog and wolf populations by analyzing genome-wide patterns of variation, and show that dogs suffered a 16-fold reduction in population size as they diverged from wolves. Wolves also experienced a sharp drop in population size soon after their divergence from dogs, implying that diversity among both animals' common ancestors was larger than represented by modern wolves.

The researchers also found differences across dog breeds and wolves in the number of amylase (
AMY2B) genes that help digest starch. Recent studies have suggested that this gene was critical to domestication, allowing early dogs living near humans to adapt to an agricultural diet. But the research team surveyed genetic data from 12 additional dog breeds and saw that while most dog breeds had high numbers of amylase genes, those not associated with agrarian societies, like the Siberian husky and dingo, did not. They also saw evidence of this gene family in wolves, meaning that it didn't develop exclusively in dogs after the two species diverged, and may have expanded more recently after domestication.

Novembre said that overall, the study paints a complex picture of early domestication. "We're trying to get every thread of evidence we can to reconstruct the past," he said. "We use genetics to reconstruct the history of population sizes, relationships among populations and the gene flow that occurred. So now we have a much more detailed picture than existed before, and it's a somewhat surprising picture."

Source: Modified from materials provided by The University of Chicago Medical Center.


Reference

Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, Han E, et al. (2014) Genome Sequencing Highlights the Dynamic Early History of Dogs. PLoS Genet 10(1): e1004016. doi:10.1371/journal.pgen.1004016


Orangutans plan and communicate their travel plans

For a long time it was thought that only humans had the ability to anticipate future actions, whereas animals are caught in the here and now. But in recent years, clever experiments with great apes in zoos have shown that they do remember past events and can plan for their future needs. Anthropologists at the University of Zurich have now investigated whether wild apes also have this skill, following them for several years through the dense tropical swamplands of Sumatra.

It turns out that wild male orangutans do plan their travel route up to one day in advance and communicate it to other members of their species (Figure 1). In order to attract females and repel male rivals, they call in the direction in which they are going to travel. Anthropologists at the University of Zurich have found that not only captive, but also wild-living orangutans make use of their planning ability.

Fig2
Figure 1. Travel maps of wild orangutans. Green arrows show “long calls”. (from van Schaik et al. 2013)

Orangutans generally journey through the forest alone, but they also maintain social relationships. Adult males sometimes emit loud ‘long calls’ to attract females and repel rivals. Their cheek pads act as a funnel for amplifying the sound in the same way as a megaphone. Females that only hear a faint call come closer in order not to lose contact. Non-dominant males on the other hand hurry in the opposite direction if they hear the call coming loud and clear in their direction (Figure 1).

Fig1
Figure 2. A Orangutan males give long calls to attract females (or repel rival males). Female A perceives a faint call compared to female B, even if they are at the same distance from the calling male, because the male is facing female B. If the male is moving in the same direction as he is calling, female A should move in the direction of the male whereas B need not. (from van Schaik et al. 2013)

“To optimize the effect of these calls, it thus would make sense for the male to call in the direction of his future whereabouts, if he already knew about them”, explains Carel van Schaik. “We then actually observed that the males traveled for several hours in approximately the same direction as they had called.” In extreme cases, long calls made around nesting time in the evening predicted the travel direction better than random until the evening of the next day. Carel van Schaik and his team conclude that orangutans plan their route up to a day ahead.
In addition, the males often announced changes in travel direction with a new, better-fitting long call. The researchers also found that in the morning, the other orangutans reacted correctly to the long call of the previous evening, even if no new long call was emitted. “Our study makes it clear that wild orangutans do not simply live in the here and now, but can imagine a future and even announce their plans. In this sense, then, they have become a bit more like us”, concludes Carel van Schaik.

Source: Modified from materials provided by The University of Zurich.

Reference:

Carel P. van Schaik,, Laura Damerius,, & Karin Isler (2013). Wild Orangutan Males Plan and Communicate Their Travel Direction One Day in Advance PLOS ONE DOI: 10.1371/journal.pone.0074896


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Christian Haugen
Figure 1. A living dugong from the Indo-Australian region (Dugong dugon). (From Christian Haugen/Flickr)

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dugong2
Figure 2. An illustration by Carl Buell showing the three species in each fossil dugongid assemblage. Multispecies communities are from Florida (top left), India (top right) and Mexico (bottom right) over the past 26 million years. (From Velez-Juarbe et al., 2012)


By evaluating a suite of ecomorphological characters including the size and shape of the upper tusk, the degree of downward deflection of the snout, and overall body size, the researcher constructed a phylogenetic tree of fossil sirenians. The tree revealed that late Oligocene dugongs from Florida differed in body size and tusk size (Figure 3). Likewise the early Miocene dugong assemblage from India consisted of three taxa with different degrees of skull deflection and two body size categories. The early Pliocene dugongs from Mexico differed in body size and tusk shape (cross-sectional shape).

dugong1
Figure 3. Ecomorphological features for the fossil taxa used in this study. A)
Categories of upper incisor size and depth (gray) for late Oligocene species from Florida B) body sizes comparisons among dugongids in this study. C) Fossil dugongids from India showing differences in rostral deflection. D) Cross-sectional outline of incisors of fossil dugongids from Mexico. (From
Velez-Juarbe et al., 2012)

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References

Velez-Juarbe, J., Domning, D., & Pyenson, N. (2012). Iterative Evolution of Sympatric Seacow (Dugongidae, Sirenia) Assemblages during the Past ∼26 Million Years PLoS ONE, 7 (2) DOI: 10.1371/journal.pone.0031294
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