Cracking the code: Genome sequencing reveals why songbirds are larger in colder climates

Scientists have unlocked the genetic basis underlying the remarkable variation in body size observed in song sparrows, one of North America's most familiar and beloved songbirds. This discovery also provides insights into this species' capacity to adapt to the challenges of climate change.

The study, published today in Nature Communications, used genomic sequencing to successfully pinpoint eight genetic variants, or DNA mutations, largely responsible for the nearly threefold difference in body size observed across the song sparrow range from Mexico to Alaska. For instance, song sparrows that live year-round in the Aleutian Islands can be up to three times larger than their counterparts in the coastal marshes of California.

Katherine Carbeck, the study's first author and a PhD candidate in the faculty of forestry, University of British Columbia, explains that body size varies predictably in many species that inhabit vastly different climatic conditions, aligning with "Bergmann's rule" which states that organisms in cooler climates tend to be larger as an adaptation to regulate body temperature.

"The existence of 'locally adapted' populations implies that natural selection has shaped the genetic makeup of song sparrow populations across their range, enabling individuals to survive and reproduce in drastically different climatic conditions," said Carbeck. "However, the genetic mechanisms underlying Bergmann's rule have remained elusive until now."

Whole-genome sequencing cracks the code

Carbeck and colleagues from the Cornell Lab of Ornithology, University of Alaska and Ouachita Baptist University used the power of whole-genome sequencing to decode the entire song sparrow genome and unlock its secrets.

They combed through genetic samples from the two largest song sparrow subspecies that live year-round in the Aleutian Islands, as well as two smaller subspecies: one that breeds in Alaska but migrates to warmer sites in winter, and one that lives year-round on the B.C. coast, where the Pacific Ocean maintains comparatively mild winter weather.

Their comparison of the larger and smaller-bodied subspecies revealed several candidate genes associated with body mass. By characterizing these candidates, they identified eight specific genetic variants closely linked to body mass -- aligning with Bergmann's rule.

Genetic diversity helps life adapt to climate change

The researchers suggest that revealing a genetic basis for Bergmann's rule helps us to understand how evolution, natural selection and climate have interacted throughout a species' history.

"Our results highlight the potential role habitat conservation plays in enabling the continued exchange of genes between populations -- which is important in the face of ongoing change," said Carbeck.

Dr. Jen Walsh, a study co-author and research associate at the Cornell Lab of Ornithology, added: "From a genomic perspective, identifying a small number of candidate genes with an apparently large impact on variation in body size is really interesting. The magnificent range of phenotypic diversity seen in song sparrows suggest they offer exciting opportunities to identify genes underlying a host of well-known and generally accepted eco-geographic rules."

Dr. Peter Arcese, a co-author and a professor in UBC's department of forest and conservation sciences, said the findings suggest a resilient future for these birds.

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Plague trackers: Researchers cover thousands of years in a quest to understand the elusive origins of the Black Death

Seeking to better understand more about the origins and movement of bubonic plague, in ancient and contemporary times, researchers at McMaster University, University of Sydney and the University of Melbourne, have completed a painstaking granular examination of hundreds of modern and ancient genome sequences, creating the largest analysis of its kind.

Despite massive advances in DNA technology and analysis, the origin, evolution and dissemination of the plague remain notoriously difficult to pinpoint.

The plague is responsible for the two largest and most deadly pandemics in human history. However, the ebb and flow of these, why some die out and others persist for years has confounded scientists.

In a paper published today in the journal Communications Biology, McMaster researchers use comprehensive data and analysis to chart what they can about the highly complex history of Y. pestis, the bacterium that causes plague.

The research features an analysis of more than 600 genome sequences from around the globe, spanning the plague's first emergence in humans 5,000 years ago, the plague of Justinian, the medieval Black Death and the current (or third) Pandemic, which began in the early 20th century.

"The plague was the largest pandemic and biggest mortality event in human history. When it emerged and from what host may shed light on where it came from, why it continually erupted over hundreds of years and died out in some locales but persisted in others. And ultimately, why it killed so many people," explains evolutionary geneticist Hendrik Poinar, director of McMaster's Ancient DNA Centre.

Poinar is a principal investigator with the Michael G. DeGroote Institute for Infectious Disease Research and McMaster's Global Nexus for Pandemics & Biological Threats.

The team studied genomes from strains with a worldwide distribution and of different ages and determined that Y. pestis has an unstable molecular clock. This makes it particularly difficult to measure the rate at which mutations accumulate in its genome over time, which are then used to calculate dates of emergence.

Because Y. pestis evolves at a very slow pace, it is almost impossible to determine exactly where it originated.

Humans and rodents have carried the pathogen around the globe through travel and trade, allowing it to spread faster than its genome evolved. Genomic sequences found in Russia, Spain, England, Italy and Turkey, despite being separated by years are all identical, for example, creating enormous challenges to determining the route of transmission.

To address the problem, researchers developed a new method for distinguishing specific populations of Y. pestis, enabling them to identify and date five populations throughout history, including the most famous ancient pandemic lineages which they now estimate had emerged decades or even centuries before the pandemic was historically documented in Europe.

"You can't think of the plague as just a single bacterium," explains Poinar. "Context is hugely important, which is shown by our data and analysis."

To properly reconstruct pandemics of our past, present, and future, historical, ecological, environmental, social and cultural contexts are equally significant.

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Endangered Devils Hole pupfish is one of the most inbred animals known

As its name implies, the Devil's Hole pupfish lives in a truly hellish environment.

Confined to a single deep limestone cave in Nevada's Mojave Desert, 263 of them live in water that hovers around 93 degrees Fahrenheit year-round, with food resources so scarce that they are always on the edge of starvation, and with oxygen levels so low that most other fish would die immediately. The pupfish, Cyprinodon diabolis, live in the smallest habitat of any known vertebrate.

New research now documents the extreme effect that these harsh and isolated conditions have had on this fish's genetic diversity.

In a paper published this week in the journal Proceedings of the Royal Society B, University of California, Berkeley, biologists report the first complete genome sequences of eight pupfish species from the American Southwest -- 30 individuals in all, including eight Devils Hole pupfish. Astoundingly, the Devils Hole pupfish is so inbred that 58% of the genomes of these eight individuals are identical, on average.

"High levels of inbreeding are associated with a higher risk of extinction, and the inbreeding in the Devils Hole pupfish is equal to or more severe than levels reported so far in other isolated natural populations, such as the Isle Royale wolves in Michigan, mountain gorillas in Africa and Indian tigers," said lead researcher Christopher Martin, UC Berkeley associate professor of integrative biology and curator of ichthyology in the campus's Museum of Vertebrate Zoology. "Although we were not able to directly measure fitness, the increased inbreeding in these pupfish likely results in a substantial reduction in fitness."

Other pupfish species are also inbred, the researchers found, but only between 10% and 30% of their genomes are identical.

Graduate student David Tian, lead author of the study, said that the level of inbreeding in the Devils Hole pupfish is equivalent to what would happen if four to five generations of siblings mated with one another. This tends to burn in or fix, rather than weed out, harmful mutations, potentially dooming a population to extinction by mutational meltdown. The Devils Hole pupfish species is currently doing well in the wild and in captive or "refuge" populations, but such low genetic diversity could spell trouble as the climate changes and human impacts become greater.

In the face of these potential threats, the new genome sequences will help scientists and conservationists assess the health of native pupfish populations and potentially intervene in refuge populations to increase the genetic diversity of these species -- the Devils Hole pupfish, in particular.

"With this new genomic data, there's a lot of potential to look not just at genetic diversity and how these species are related to each other phylogenetically, but also look at inbreeding and mutation load to get an idea of what their current status is, how evolutionary history may have influenced their current genetic variation, and think about where the population is going and what we should do, if anything, to preserve these species," Tian said.

Population decline and rescue

Pupfish species are scattered around the globe and tend to like isolated lakes and springs, often with extreme conditions that most fish would find unsurvivable. About 30 species inhabit warm, salty desert springs and streams in California and Nevada. Martin has studied various pupfish populations, including several on San Salvador Island in the Bahamas, to understand the genetics behind their adaptation to extreme conditions and unusual ecological niches.

The Devils Hole pupfish, however, is unique in its small range and perilous existence, Martin said, making its fluctuating population in the wild worrisome to conservationists.

"Part of the question about these declines is whether they may be due to the genetic health of the population," Martin said. "Maybe the declines are because there are harmful mutations that have become fixed because the population is so small."

The small population is partly a result of human incursions into their habitat, Martin noted. Local ranchers and developers pumped groundwater in the region in the 1960s and '70s that drastically reduced the water level in Devils Hole, leading to a drop in population levels. A 1976 Supreme Court ruling that allowed the federal government to limit groundwater pumping saved Devils Hole and the resident population, while captive breeding at a nearby 100,000-gallon pool in the Ash Meadows National Wildlife Refuge rescued the species. Nevertheless, a decline in the 1990s led the wild population to its nadir in 2013: 35 individuals. The wild population has since recovered, while the refuge population has ballooned to about 400, twice the wild population.

Humans are not totally to blame for the lack of genetic diversity in the Devils Hole pupfish, however. The UC Berkeley researchers also sequenced the genome of a pupfish collected in 1980 and held at the University of Michigan. It showed inbreeding and a lack of genetic diversity similar to that found in individuals collected recently, most of which died a natural death. This implies that the pupfish has likely seen population bottlenecks frequently over hundreds, if not thousands, of years.

One result of this, Martin and Tian found, is that 15 genes have disappeared entirely from the Devils Hole pupfish genome. Five of them seem to be involved in adaptation to living in low-oxygen or hypoxic environments.

"These deletions are a paradox, because this is a habitat where you're most exposed to hypoxia," Martin said. "It could have something to do with the stability of the habitat over time. But it looks to us like the hypoxia pathway is broken. Once you break one gene, it doesn't really matter if you break additional genes in that regulatory pathway. Our future work is to actually look at what these deletions do. Do they increase tolerance of hypoxia? Do they decrease tolerance of hypoxia? I think those two scenarios are equally plausible at this time."

Selective breeding within a captive population of Devils Hole pupfish could help increase the diversity and perhaps save the species from eventual extinction, he said. And to restore genes already lost, CRISPR genome editing could add them back.

The fact that the genome of the fish collected in 1980 was about as inbred as today's fish is "maybe good news," Martin said, "in that the population has historically been highly inbred with very low genetic diversity, suggesting that the recent decline in the '90s, with population bottlenecks to only 35 fish in 2013 and 38 fish in 2007, doesn't seem to have had much of an effect."

Tian is currently analyzing about 150 complete genome sequences of nine species of American pupfish to get a more complete picture of the deleterious mutations and gene deletions in the various Southwestern populations. He sees the study as an example of what conservation genomics can do for endangered and possibly inbred populations around the world.

"We're on a really cool cusp when it comes to using genomic data and applying it to conservation, especially at a time where it's a problem that is likely only going to get worse with climate change and increased habitat fragmentation and just anthropogenic changes," he said.

Tian is leery of genetic interventions, however, since little is known about how genes influence the physical and behavioral characteristics of a species and how this relates to fitness and adaptation to a specific environment. Conservation should still be a priority.

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