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


Koala Bellows Deciphered

The pitch of male koalas' mating calls is about 20 times lower than it should be, given the Australian marsupial's relatively small size. Now, researchers reporting in the journal Current Biology have discovered their secret: koalas have a specialized sound-producing organ that has never before been seen in any other land-dwelling mammal. The key feature of this newly described organ is its location outside the voice box, what scientists call the larynx (Figure 1).

Koala_anatomy

Figure 1. The velar vocal folds (dark red) of male koalas are located at the intersection between the oral and nasal portions of the pharynx just opposite to the laryngeal entrance. Oral tract in light blue, nasal tract in yellow, soft palate in light red, laryngeal vocal folds in green, and arytenoid cartilage in blue. (From Charlton et al., 2013).

"We have discovered that koalas possess an extra pair of vocal folds that are located outside the larynx, where the oral and nasal cavities connect," says Benjamin Charlton of the University of Sussex. "We also demonstrated that koalas use these additional vocal folds to produce their extremely low-pitched mating calls."

The koala's bellow calls are a continuous series of sounds produced on inhalation and exhalation, similar to a donkey's braying, Charlton explains. On inhalation, koala bellows sound a bit like snoring. As the animals exhale, the sound is more reminiscent of belching. And, as Charlton says, "they are actually quite loud."

They are also incredibly low-pitched, more typical of an animal the size of an elephant. Size is related to pitch in that the dimensions of the laryngeal vocal folds normally constrain the lowest frequency that an animal can generate. As a result, smaller species will typically give calls with higher frequencies than larger ones.

Koalas have bypassed that constraint by putting those vocal folds in a new location. Charlton describes the folds as two long, fleshy lips in the soft palette, just above the larynx at the junction between the oral and nasal cavities. They may not look all that different from the laryngeal vocal folds of other mammals, but their location is highly unusual.

"To our knowledge, the only other example of a specialized sound-producing organ in mammals that is independent of the larynx are the phonic lips that toothed whales use to generate echolocation clicks," Charlton says.

The combination of morphological, video, and acoustic data in the new study represents the first evidence in a terrestrial mammal of an organ other than the larynx that is dedicated to sound production. Charlton says that he and his colleagues will now look more closely at other mammals to find out whether this vocal adaptation is truly unique to koalas.

Source: Modified from materials provided by Cell Press.

Reference

Charleton, B.D., Frey, R., McKinnon, A.J., Fritsch, G., and D. Reby. 2013. Koalas use a novel vocal organ to produce unusually low-pitched mating calls. Current Biology, 23:R1035-R1036.
http://dx.doi.org/10.1016/j.cub.2013.10.069

Read More...

Hyena Scent Posts Use Symbiotic Microbe Messengers

Twitter limits human communication to a mere 140 characters. Animals’ scent posts may be equally as short, relatively speaking, yet they convey an encyclopedia of information about the animals that left them.

In the current issue of the
Proceedings of the National Academy of Sciences, a Michigan State University researcher shows that the detailed scent posts of hyenas (Figure 1) are, in part, products of symbiotic bacteria, microbes that have a mutually beneficial relationship with their hosts.

“When hyenas leave paste deposits on grass, the sour-smelling signals relay reams of information for other animals to read,” said Kevin Theis, the paper’s lead author and MSU postdoctoral researcher. “Hyenas can leave a quick, detailed message and go. It’s like a bulletin board of who’s around and how they’re doing.”

hyena-scent-communication_lg
Figure 1. A spotted hyena scent marking. (courtesy of Michigan State University)

Interestingly, it is the bacteria in pastes – more diverse than scientists had imagined – that appear to be doing the yeoman’s job of sending these messages.

“Scent posts are bulletin boards, pastes are business cards, and bacteria are the ink, shaped into letters and words that provide information about the paster to the boards’ visitors,” Theis said. “Without the ink, there is potentially just a board of blank uninformative cards.”

Theis, who co-authored the study with
Kay Holekamp, MSU zoologist, studied multiple groups of male and female spotted hyenas and striped hyenas in Kenya.

By using molecular surveys, they were afforded unprecedented views of the diversity of microbes inhabiting mammals’ scent glands. The researchers were able to show that the diversity of odor-producing bacteria in spotted hyena scent glands is much greater than historical studies of mammals had suggested (Figure 2).


scentpost
Figure 2. Variation in the bacterial communities and volatile fatty acid (VFA) profiles of the pastes of immigrant male, lactating female, and pregnant female spotted hyenas in the Talek clan. (A and C) A plot showing variation in the structure of paste bacterial communities among Talek clan members. (B) A heat map of the mean abundances of the prominent bacteria in the pastes of Talek hyenas. (D) A heat map of the mean percent abundances of VFAs in the pastes of Talek hyenas. From Theis et al. 2013)

The diversity, however, still consistently varies between hyena species, and with sex and reproductive state among spotted hyenas, Theis added. Importantly, the variation in scent gland bacterial communities was strongly correlated with variation in the glands’ odor profiles, suggesting that bacteria were responsible for the variation in scent.

For the current paper, Theis’ team was the first to combine microbial surveys and complementary odor data from wild animals. The studies’ findings leave Theis anxious to return to the field.

“Now I just need to get back into the field to test new predictions generated by this study,” Theis said. “The next phase of this research will be to manipulate the bacterial communities in hyenas’ scent glands to test if their odors change in predictable ways.”


Source: Modified from materials provided by Michigan State University.

Reference

Theis KR, Venkataraman A, Dycus JA, Koonter KD, Schmitt-Matzen EN, Wagner AP, Holekamp KE, & Schmidt TM (2013). Symbiotic bacteria appear to mediate hyena social odors. Proceedings of the National Academy of Sciences of the United States of America PMID: 24218592


New Mammalogy Textbook Coming in January

The new edition of Mammalogy by Vaughan, Ryan, and Czaplewski will be available in January 2014.

The sixth edition of Mammalogy represents a significant revision because, although the basic framework of the book remains intact, all of the chapters have been extensively revised and
updated with new information. We have completely revised and updated our discussion of the fossil history of mammals, placed related topics in boxed inserts in each chapter, and included two new chapters: “Mammalian Domestication” and “Mammalian Disease and Zoonoses.” We have also added many new photographs and drawings to illustrate key points made in the text, while retaining the original anatomical drawings by senior author Terry Vaughan.

1284032094

An Instructor’s Media CD, compatible with Windows® and Macintosh® operating systems, is available to instructors using Mammalogy, Sixth Edition. The media CD includes the following traditional ancillaries:

• The PowerPoint® Image Bank provides the illustrations, photographs, and tables to which Jones and
Bartlett holds the copyright or has permission to reproduce digitally) inserted into PowerPoint slides.
The images can be easily incorporated into existing lecture slides.

• The PowerPoint Lecture Outline Slides presentation package provides lecture outline notes for each chapter of Mammalogy. Instructors with the
Microsoft PowerPoint software can customize the outlines, art, and order of presentation. Also available to instructors are a downloadable set of Discussion Questions. These questions, presented in Microsoft Word documents by each chapter, provide starting points for classroom discussion or homework and come with suggested answers.

Contact Jones & Bartlett Publishers at:
http://www.jblearning.com/catalog/9781284032093/
for more information.


Ecology Determines Rabies Infection in Bats

A new approach to rabies virus epidemiology in bats shows that the risk of infection is higher in large and multispecies colonies. The research, published on the journal PLOS ONE, was led by Jordi Serra-Cobo, professor from the Department of Animal Biology at the UB and the Biodiversity Research Institute (IRBio).

Bats are a large group of mammals that appeared in our planet around 65 million years ago (Figure 1). They have colonized many natural habitats —except the poles—, and act as primary predators of vast numbers of insects in ecosystems. They are also the mammals which present the widest variety of virus infection (rabies, SARS, Ebola, etc.). Moreover, they are able to neutralize virus and survive infections. “Chiropters, a quite ancient animal group, are major reservoirs for diverse infectious viral diseases”, highlights Serra-Cobo. They have co-lived with virus for a long time and their immunological responses are more effective. According to Serra-Cobo, “this fact opens new research lines on the organisms’ immunological response and strategies to fight against infectious diseases”.

Ratpenat0
Figure 1. A vespertilionid bat from Spain, one of the more than 1,150 bat species.

It is the first time that a research analyses ecological factors that might affect the infection dynamics of the rabies virus in bat colonies. Between 2001 and 2011, 2,393 blood samples were collected from 20 bats species and 25 localities in Catalonia, Aragon and Balearic Islands. The research is centered on the detection of
European bat Lyssavirus 1 (EBL1), one of the twelve different groups of the genus Lyssavirus related to rabies, an emergent zoonosis that affects mammals all over the world.

Jordi Serra-Cobo explains that “EBLV-1 seroprevalence is strongly affected by colony size and species richness. Previous studies have analyzed other aspects such as the seasonal variability. Ecological factors play a relevant role in seroprevalence variability, but they were to date unknown” (Figure 2).

journal.pone.0064467.g002
Figure 2. Variation in the percentages of seropositive bats as a function of species richness and colony size. (from Serra-Cobo et al. 2013)


All bat species do not response in the same way to viral infections. This research proves that immunological response to rabies virus varies among species. “Order Chiroptera has been widely diversified along its evolutionary history —affirms Serra Cobo— and their responses to ultrasound orientation mechanisms, immunological defense, etc. vary with different lineages”.

There are more than 1,150 bat species all over the world and new specimens are described every year. However, the loss of natural habitats due to human activity and climate change poses a major threat to bats. “It is a process of environmental degradation which favors the formation of larger bat colonies, which have a higher probability of EBLV-1 infection”, remarks Serra Cobo.
 
Spain has been free of rabies in terrestrial mammals since 1977. Nevertheless, in some countries it continues to be a problem of public Health. To know risk factors involved in viral disease transmission is essential to improve preventive policies. The new article published on
PLOS ONE will provide new tools to know more about viral infections epidemiology and natural resources management.

Source: Modified from materials provide by The Universitat de Barcelona.


Reference

Jordi Serra-Cobo,, Marc López-Roig,, Magdalena Seguí,, Luisa Pilar Sánchez,, Jacint Nadal,, Miquel Borrás,, Rachel Lavenir,, & Hervé Bourhy (2013). Ecological Factors Associated with European Bat Lyssavirus Seroprevalence in Spanish Bats PLOS ONE DOI: 10.1371/journal.pone.0064467.t003