A photo of a reddish wolf, Dhole or Cuon alpinus

Weekend Reads | Coyotes and Gray Wolves and Dogs, Oh My!

by Kevin Schofield

Do you remember the “tree of life” that we all studied in high school biology classes, the one that documented how the species on Earth today descended from common ancestors? For hundreds of years, species ancestry was pieced together the hard way: by comparing the phenotypes of organisms. A phenotype is the set of observable characteristics of a species, everything from basic size, shape, and color to specific body parts, such as fingers, toes, wings, and eyes. Understanding that evolution is a long series of small adjustments, rather than large leaps, biologists looked for physical resemblances to make judgments about how closely related two species are.

And then, in the middle of the 20th century, DNA was discovered. Scientists suddenly had a far more accurate tool for determining where a species should be placed on the tree of life: its genotype, or genetic composition. Not only can they measure how much DNA two species have in common, but they can also trace specific genetic mutations back to common ancestors, and in some cases, precisely determine how long ago they diverged genetically. However, until recently, genetic sequencing was prohibitively expensive. In 2001, it cost $100 million to sequence an entire human genome; by 2011, it had dropped to about $10,000, and today, it costs less than $1,000. The cost of genetic sequencing continues to drop, especially for applications that don’t require the entire genome. That has removed the last practical barrier to collecting and mining genetic data, and has opened up the floodgates for widespread collection and sharing of databases of genetic samples from a vast number of species.

Biologists are now discovering that they made a lot of mistakes when phenotypes were the only tool they had, and they are busy rewriting the tree of life using genetic data as their guide. Take, for example, orangutans: Up until 1996, it was believed that there was only one species of orangutan native to the islands of Borneo and Sumatra. Then, in 1996, scientists discovered that there are two genetically distinct species, one on each island. Five years ago, they discovered a third species of orangutan in a remote corner of Sumatra.

Likewise, the number of species and subspecies of giraffes is still being revised. The latest thinking is that there are four species of giraffe and seven subspecies, but that is still controversial and is likely to change in the years to come.

And that brings us to this weekend’s read: a research paper from 2011 looking at the genetic makeup of wolves, coyotes, and domesticated dogs in North America. A long-standing topic of discussion among biologists and conservationists has been how much interbreeding has occurred between these three species, given that their phenotype is so similar (i.e., they are hard to tell apart just by looking at them) and their geographical ranges overlap. A group of researchers wanted to get a more definitive answer to the question by collecting hundreds of DNA samples from coyotes, wolves, and dogs and comparing them.

It turns out that a vast portion of the DNA of all living organisms is identical, so researchers focus on the small locations in our genetic makeup where there are differences, which are called “single nucleotide polymorphisms,” or SNPs (pronounced “snips”). In this particular research study, about 48,000 SNPs were identified and compared. And they found some very interesting stuff.

“Figure 3. Principal component analysis of all wolf-like canids for the 48K SNP data set (IRNP, Isle Royale National Park).” Copyright Cold Spring Harbor Laboratory Press; used with permission.

First, the top-line finding: For the most part, coyotes, wolves, and domestic dogs haven’t interbred; they stick to their own kind. Where there is interbreeding, it occurs in places where the population has crashed and so few individuals remain that interbreeding is essentially the only option. Further, the crossover DNA seems to remain in the smaller population; it doesn’t get reintegrated back into the larger population of “purebred” dogs, wolves, and coyotes. In western North America, there is little to no interbreeding, but in the Great Lakes region and in the southeastern United States, the remaining wolves and coyotes show a substantial amount of interbreeding in their genotypes. For example, the Great Lakes wolf is 15% coyote, the Algonquin wolf is 40% coyote, and the red wolf turns out to be 75% coyote — one more example of DNA evidence leading to a big change in the tree of life. The researchers also found three subspecies of coyotes that had substantial amounts of dog DNA in their genotype.

“Figure 4. structure clustering analysis of domestic and wild canids for the 44K SNP pruned data set (see Supplemental Table S2). Separate analyses of North American (n = 68) and Eurasian (n = 74) wolves further resolves biologically informative clusters (K = 7; the top layer in plot). The three captive Mexican wolf colonies (Studbook, S; Ghost Ranch, G; and Aragon, A) are shown. See discussion in the Supplemental Material for an explanation of how K values were chosen for presentation. Coyote abbreviations: Midwest/Southern, MID; Northeastern, NE; and Western, WEST. North American abbreviations: Algonquin, Alg; Isle Royale NP, IRNP; Minnesota, MN; Ontario, Ont; Wisconsin, WI; Alaska/Canada, AK/Ca; British Columbia, BC; Mexico, Mex; Northern Canada, NCa; Northern Quebec, NQue; and Yellowstone, YNP. Eurasian abbreviations: Belarus, Be; Bulgaria, Bu; Croatia, Cr; Greece, Gr; India, In; Iran, Ir; Israel, Is; Italy, It; Lithuania, Li; Middle East, ME; Oman, Om; Poland, Po; Russia, Ru; Saudi Arabia, SA; Slovakia, Sl; Southwest Asia, SWA; Spain, Sp; Sweden, Sw; Turkey, Tu; and Ukraine, Uk.” Copyright Cold Spring Harbor Laboratory Press; used with permission.
“Figure 6. Ancestry analysis of 38 canine autosomes. Plots show ancestry blocks and their assignments for representative individuals of canid populations with average size of blocks, percent ancestry, and number of generations since most recent admixture (t) indicated. Two-ancestor (coyote, A; gray wolf, B) analyses are presented for a Great Lakes wolf from Minnesota (C ), a captive red wolf (D), and an Algonquin wolf (E ). Three-ancestor analyses (coyote, A; gray wolf, B; dog, F ) are presented for a Northeastern coyote from Vermont (G), a Southern coyote from Louisiana (H), and a Midwestern coyote from Ohio (I). Individual results are given in Supplemental Tables S5 and S6.” Copyright Cold Spring Harbor Laboratory Press; used with permission.

The paper also has some interesting discussion of the timing of interbreeding for these species. Their best guess is that the interbreeding of gray wolves and coyotes began between 250 and 300 years ago, as gray wolf populations plummeted in the southern and midwestern United States. However, and not surprisingly, the mixing of domesticated dog DNA with some species of coyotes happened much more recently, approximately 30 to 100 years ago.

The ability to data-mine genetic material is opening up huge new fields of learning and discovery. It’s also changed the way we track diseases: The same technology allows us to quickly identify new variants of the coronavirus that causes COVID-19, to track those variants as they spread around the world, to design targeted mRNA vaccines, and to know when those vaccines need to be updated because they no longer match the dominant variants in circulation.

That said, we have barely scratched the surface in our understanding of genetics. We can’t “read” DNA the way we read a book: We can identify the basic building blocks and compare them to know when something has changed, but we don’t know how they fit together into larger concepts, and we don’t know what it means when something changes. We’re still far away from being able to write new genetic code that has any useful semantics; to the extent that “genetic therapies” exist today, for the most part, they simply overwrite mutations back to what we think should be “normal.” Researchers are learning in bits and pieces by making small tweaks to the genotype and observing what changed in the phenotype, i.e., rewriting a SNP and seeing what difference that makes in the organism’s size, shape, and biological functions. But reverse-engineering complex organisms this way is slow and frustrating. For better or worse, being able to “program” biology is still well beyond our capabilities for anything beyond the most rudimentary applications.

Nevertheless, we are still learning a great deal from even the simple stuff we can do today, and it’s constantly updating our understanding of how evolution works.

A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids

Kevin Schofield is a freelance writer and publishes Seattle Paper Trail. Previously he worked for Microsoft, published Seattle City Council Insight, co-hosted the “Seattle News, Views and Brews” podcast, and raised two daughters as a single dad. He serves on the Board of Directors of Woodland Park Zoo, where he also volunteers.

📸 Featured image by Mikhail Gnatkovskiy/Shutterstock.com.

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