Friday, June 26, 2015

92 Letters Out Of 1.2 Billion

Just 82 DNA letters, out of a total of about 1.2 billion
, separate the carrion and hooded-crow genomes.

The traditional way to define two related organisms as distinct species is by their inability to mate. The Swedish naturalist Carl Linnaeus, who wandered the halls of Uppsala University more than 250 years ago, employed this definition when he created the classification system we still use today. But scientists have been arguing over what makes a species for more than a century.

Charles Darwin himself declined to define the concept in his landmark book “On the Origin of Species.” “Darwin, when he proved that species evolved, also proved there was no such thing as species,” said James Mallet, an evolutionary biologist at Harvard University. If organisms are constantly evolving, then drawing a precise dividing line between two different species will necessarily be difficult.

Indeed, evolutionary biologists tend to take a more pragmatic approach to defining species, one that depends on their avenue of study. A distinction could be based on morphological or genetic differences, for example. “When we start speaking of species, it’s in the eye of the beholder,” Wolf said.

The more interesting and important question, biologists say, is what drives two populations to diverge, a process known as speciation. That question has heated up over the last five years with the rapid advance of genomic technology. Until recently, the study of speciation has focused on ecology and behavior out in the field, as well as mating experiments, but scientists now find themselves able to analyze the genomes of a menagerie of wild creatures, including closely related ones. “Just a few years ago, it wasn’t possible to sequence the genome of wild organisms,” Wolf said. “Now we can, and that’s fantastic.”

The results — from studies of crows, butterflies, mosquitoes, fish and other organisms — suggest that the concept of species is even more muddled than we thought, and that genetic changes don’t always align with more visible ones, such as appearance. “In some cases, species have big morphological and behavioral changes with only a few genetic changes, and in other cases, there is lots of genetic change with few visible results,” said Matthew Hahn, a biologist at Indiana University.

By any standard of analysis, dogs and wolves are as speciated as polar bears and grizzly bears, hooded crows and carrion crows, barred owls and spotted owls, Asian elephants and African elephants, leopards and mountain lions.

As Adam H. Freedman, et. al, note in their paper, Genome Sequencing Highlights the Dynamic Early History of Dog in PLOS:

To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we generated high-quality genome sequences from three gray wolves, one from each of the three putative centers of dog domestication, two basal dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. Analysis of these sequences supports a demographic model in which dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow. In dogs, the domestication bottleneck involved at least a 16-fold reduction in population size, a much more severe bottleneck than estimated previously. A sharp bottleneck in wolves occurred soon after their divergence from dogs, implying that the pool of diversity from which dogs arose was substantially larger than represented by modern wolf populations. We narrow the plausible range for the date of initial dog domestication to an interval spanning 11–16 thousand years ago, predating the rise of agriculture. In light of this finding, we expand upon previous work regarding the increase in copy number of the amylase gene (AMY2B) in dogs, which is believed to have aided digestion of starch in agricultural refuse. We find standing variation for amylase copy number variation in wolves and little or no copy number increase in the Dingo and Husky lineages. In conjunction with the estimated timing of dog origins, these results provide additional support to archaeological finds, suggesting 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 is more closely related to dogs, and, instead, the sampled wolves form a sister monophyletic clade. This result, in combination with dog-wolf admixture during the process of domestication, suggests that a re-evaluation of past hypotheses regarding dog origins is necessary.


jeffrey thurston said...

Aahh- this IS fun! Like two antique men o'war lining up for the cannonade! I assure you I read this post at least 3 times carefully and I've read the Freedman et al. Jan. 2014 article at least 5 times. And again- I'm less convinced than ever that wolves and dogs aren't the same species. The first article or reprint you post with its yellowed highlights can be used to support either argument- it just says that speciation is a vague unknowable hard-to-pin-down process. Remember that for most of time since modern science was born in the 16th and 17th centuries dogs and wolves were non-controversially supposed to be separate species. it is only since the late 1990's early 2000s that wolves and dogs became ths same species because their DNA is basically the same. This has become the new norm- and if I'm a scientist trying to gwet a paper published I'm not going to say- "yeah- ho hum- dogs are wolves just as the DNA says." No-- I'm going to say "They're very differnt and diverged long ago!" Hah! 11- to 15,000 years is a light speed blink evolutionarily! You say "By any standard dogs and wolves are as speciated as...etc. polar bears and grizzlies, ...elepahnts...leopards and mountain lions..." Really- you really think that? Almost by NO standard are any of those pairs as close as dogs and wolves- all very different in appearance and all divergent for millions of years. As false as the chimp-human scenario. I think really what we are talking about is differences of SUB-species. I don't deny that wolves and dogs seem different- and maybe we're just having a toMAYto-toMAHto argument. To me it is obvious that what vexes the canine biologists about the origin of dogs is how radically and completely man himself has changed the animal- those genetic bottleneck the Freedman people found seems to hint at the radicalness of the domestication event and the awakening of Homo Sapiens as a factor in the whole earth landscape...

jeffrey thurston said...

BTW- I had to write this quickly at work- sorry about the spelling-