Efforts to diversify an inbred population must take into account the genetic backgrounds of the founders.

The nocturnal flightless parrot known as the kākāpō was once abundant throughout New Zealand. But after the introduction of mammalian predators, the species all but disappeared. Today, every living kākāpō is descended from a tiny handful of island survivors and a single male from the mainland. The entire population of 201 birds is closely watched over by conservationists on a few predator-free island refuges, where they hope the hefty green parrots will continue to breed.

But because their numbers dropped into the double digits, the kākāpō face a genetic bottleneck. Inbreeding can increase rates of genetic disease and contribute to poor health among the population. Geneticists studying the remaining kākāpō have quantified the amount of inbreeding among the birds as one way to understand the health of the species. Their results, reported in a new paper in G3: Genes|Genomes|Genetics, suggest that inbreeding isn’t necessarily hurting chicks’ chances of survival and that introducing additional genetic diversity may not always have the intended effect.

Saved from extinction

“Kākāpō have a really interesting natural history,” says Yasmin Foster, a graduate student at the University of Otago and the study’s lead author. “They were functionally extinct, but then a small population was found on an island in the south of New Zealand.”

“Functionally extinct” in this case meant no more females could be found on the New Zealand mainland; only a few males remained. In 1977, about 50 kākāpō were discovered living on Stewart Island, a large island about 19 miles south of the mainland. Predators such as feral cats roamed Stewart Island, however, so in 1982 conservationists began relocating the birds to several smaller, mammal-free outlying islands.

By then, only one male kākāpō remained on the mainland, and he was taken to a predator-free island refuge along with the Stewart Island population. The Stewart Island kākāpō had diverged from the mainland population around 10,000 years ago, giving the two groups time to develop distinct genetic profiles. Introducing the mainland bird was meant to help boost genetic diversity among a new generation of chicks.

Now, the population has grown to 201 individuals. To help inform conservation strategies, Foster and her colleagues set out to document the amount of inbreeding in the colony. Creating a large, multigenerational pedigree of the wild kākāpō wouldn’t work for a founder population of this type, so the researchers turned to DNA sequence analysis. Thanks to the availability of a high-quality kākāpō reference genome, the team could genotype the birds using genome-wide mapping of single nucleotide polymorphisms (SNPs).

Comparing measures of inbreeding

“We had this unique founding population with 50 Stewart Island birds and one mainland male,” says Foster. “From the inbreeding metrics I looked at, we found that they’re both inbred, but in different ways.” She says the study raises an interesting point about how combining two inbred populations in an attempt to increase genetic diversity can actually introduce more deleterious alleles.

Comparing multiple inbreeding metrics helped Foster get a robust view of the birds’ genome, and also to evaluate the accuracy of each one. “Some people just use one or another, but what I found was that some of them give a different story,” she says.

She started by calculating the coefficient of inbreeding, or F_H, which is the probability of an individual inheriting two copies of the same allele from the same ancestor on both sides. She compared this with a newer method of measurement, called “runs of homozygosity” or F_ROH, which looks for long sections of the genome where both copies are the same.

A third method, using pairwise analysis to construct a genomic-relatedness matrix, turned out to be the weakest of the metrics, Foster says. “Other people have found that when you have a small group of individuals that are a lot different to the larger group, they skew the outcome maybe a bit too much,” she says. “Their genetic information is more rare, and the way the maths compute this inbreeding metric, it gives more power to those rare alleles.”

‘Hybrid vigor’ – or not

In addition, they compared levels of inbreeding with survival in chicks. When the mainland male was added to the Stewart Island population, the expectation was that he would infuse genetic diversity into a new generation of chicks, boosting their health. But that turned out not to be the case: decreased inbreeding did not correspond to improved survival, partly because the less-inbred chicks had unexpectedly high levels of mortality.

“That was probably down to the mainland individuals also being reduced to a small population for a long period of time,” says Foster. The mainland male apparently brought in quite a few detrimental mutations that had been lost from the island population over the years.

The inbreeding study and others like it could help guide conservation strategies moving forward. Kākāpō have a lek mating system, which means that the males all congregate and compete to entice the females. The most popular male will produce the most offspring, and this can tighten the genetic bottleneck even more.

“One male kākāpō had fathered 22 chicks, which is really significant when there’s only 200 left,” says Foster. “Obviously his genetic material spread across the population. He was so successful, we had to translocate him to another island to give some of the other males a chance.”

CITATION

Genomic signatures of inbreeding in a critically endangered parrot, the kākāpō

Yasmin Foster, Ludovic Dutoit, Stefanie Grosser, Nicolas Dussex, Brodie J. Foster, Ken G. Dodds, Rudiger Brauning, Tracey Van Stijn, Fiona Robertson, John C. McEwan, Jeanne M. E. Jacobs, and Bruce C. Robertson

G3 Genes|Genomes|Genetics 2021; jkab307

https://doi.org/10.1093/g3journal/jkab307

Discovery of thiabendazole target explains vascular disrupting action.

Even after hundreds of millions of years of evolution, some yeast genes persist mostly intact in humans and other vertebrates. Despite the huge differences between yeast and humans, these genes perform the same molecular function in both organisms but have been adapted over time into new contexts. Learning about these evolutionarily enduring genes can provide important insight into complex systems in large organisms.

About a decade ago, researchers led by molecular biologist Edward Marcotte and John Wallingford of the University of Texas at Austin discovered that a medication used to treat fungal infections and ringworm could also stop new blood vessel formation in vertebrates. The drug, called thiabendazole (TBZ), would even cause recently formed blood vessels to break apart and dissolve. Although TBZ had been in clinical use for decades, nobody knew exactly how the drug worked at the molecular level.

Now, in a new paper in GENETICS, Marcotte and colleagues have identified the molecular target of TBZ’s blood vessel-disrupting action. It’s called beta-tubulin 8, or TUBB8, a structural protein that helps provide the cell’s skeletal system. The discovery explains why TBZ kills fungi but not vertebrates.

Studying human genes in yeast

The story began with the realization that certain interacting networks of genes needed for survival in single-celled organisms like yeast had survived billions of years of evolution and remained active in vertebrates, including humans. 

“They’re inherited intact as a system,” Marcotte explains. As new organisms emerged through evolutionary processes, they developed different body plans and ecological niches. During these changes, many gene networks continued working together, but were recruited to different systems in different organisms. 

“In yeast, they get wired up to do one thing, and ultimately in the vertebrate lineage they get wired up to do something else,” Marcotte says. “That’s the kind of process we’re talking about.”

Studying these networks revealed that a set of genes that keep the yeast cell wall intact also help blood vessels grow properly in vertebrates. This led to the discovery that TBZ could stop blood vessel formation.

“That discovery got us really intrigued about the extent that human and yeast genes were still doing the same thing,” says Marcotte. “Questions like that made us wonder how much yeast and human genes were still equivalent.”

To study the questions, the researchers created strains of yeast in which they substituted the original yeast gene with its human counterpart. In cases where the human gene adequately sufficed for the lost yeast gene, the “humanized” strain of yeast became a valuable research tool. They successfully created several hundred of these strains.

“What’s great about yeast is that we can study human genes in a simplified context,” says Riddhiman Garge, the paper’s co-first author, who is now a postdoctoral fellow at the University of Washington and performed the work collaboratively with researcher Hye Ji Cha.

Tracing the tubulin family tree

TBZ, they knew, killed yeast by disrupting a structural protein called beta-tubulin. While yeast have one beta-tubulin gene, humans have accumulated nine versions of the gene, and two of them can substitute for the yeast gene. 

“We used molecular modeling to build models of the yeast beta-tubulin and the various beta-tubulins in humans,” Marcotte says. Using these computer models, they simulated interactions between TBZ and each tubulin.

“Out of the nine beta-tubulins, only one looked like it would actually be responsive to the drug,” says Marcotte. 

Over the course of evolution, the one beta-tubulin ancestral gene had been copied and changed until humans had 9 beta-tubulins. Eight of them contain naturally occurring mutations that confer resistance to TBZ. The one that doesn’t, TUBB8, is expressed in blood vessels.

“Thiabendazole doesn’t kill humans, like it does fungus and nematodes, because most human cells have resistant forms of tubulin,” Marcotte says. “It’s known to have a very good safety profile over the decades of use. This result explains why that’s the case, but also explains why it turns out to be active in just a particular tissue in human.”

Potentially, TBZ could be used to treat diseases in which abnormal blood vessel growth is a problem, such as hemangiomas, which are bright red rubbery lumps on the skin made up of excess blood vessels that grow in a cluster. Cancers also tend to spur new blood vessel formation to feed the energy needs of a fast-growing tumor.

Libraries of yeast strains containing human genes can also be used to identify other genetic interactions, or screen for other drugs that have tissue-specific functions in humans.

“I truly believe this is just scratching the surface,” says Garge. “I would love to see more of the community leverage such systems-wide comparisons to gain insights into human health.”

CITATION

Discovery of new vascular disrupting agents based on evolutionarily conserved drug action, pesticide resistance mutations, and humanized yeast

Riddhiman K Garge,  Hye Ji Cha,  Chanjae Lee,  Jimmy D Gollihar,  Aashiq H Kachroo, John B Wallingford,  Edward M Marcotte

GENETICS 2021, iyab101, https://doi.org/10.1093/genetics/iyab101

A new genome assembly for Antarctic fur seals sheds light on their historic comeback after 19^th century hunting.

In the late 19^th century, the Antarctic fur seal was thought to be effectively extinct. After over a century of overexploitation driven by demand for the seal’s prized pelt, populations at known breeding grounds seemed to have disappeared, making further hunting impossible—and suggesting that the species may even have died out altogether. But in the 1930s, a small breeding population was discovered on South Georgia, a remote island in the southern Atlantic Ocean with no indigenous human inhabitants. Today, the Antarctic fur seal has made a comeback, with a population thought to number as many as two or three million—but a new G3 report by Humble et al. suggests this picture of the seal’s dramatic rebound is incomplete.

As a well-studied species that has undergone a remarkable recovery, the Antarctic fur seal (Arctocephalus gazella) holds great interest for conservation biologists and others seeking to understand the genomic impacts of population changes. In the report, a multinational team of authors describe an improved A. gazella genome assembly and a collection of 677,607 single nucleotide polymorphisms (SNPs), both useful tools for deeper dives into the genetics of the species. Their data also contain clues about how the Antarctic fur seal may have repopulated much of its former range.

Humble et al. found that linkage disequilibrium in A. gazella is on par with that of other vertebrates—a result that may seem strange given that such a severe population bottleneck should increase linkage disequilibrium. However, a separate analysis recently hinted that the population may not have dropped as low as once thought and could have included hundreds of individuals at its minimum. The Antarctic fur seal population also recovered within just a few generations, reducing the amount of time inbreeding and genetic drift would have had to impact linkage disequilibrium.

Although the species has a large, free-ranging population, the researchers found that some individuals were more inbred than others. This may be due in part to the fact that both males and females of the species return to the same breeding grounds each year with great precision—in one study, females were found to return to within one body length of the places they were born. Further, the species is highly polygynous, with one male often siring offspring with over a dozen females in a given season.

Information about fur seal population structure gave the team evidence that A. gazella may have persisted at a small number of the breeding grounds and thus was not limited to South Georgia, where it was first spotted after hunting ceased. Further investigation of how the seal recovered from being critically endangered, including the role of these final holdouts, could provide valuable information to guide conservation of other species facing extinction. And while A. gazella now numbers in the millions, any such insight may one day be important for its preservation, too: climate change and an increase in tourism has begun to put pressure on many Antarctic species, including the resilient fur seal.

CITATION:

RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding
Emily Humble, Kanchon K. Dasmahapatra, Alvaro Martinez-Barrio, Inês Gregório, Jaume Forcada, Ann-Christin Polikeit, Simon D. Goldsworthy, Michael E. Goebel, Jörn Kalinowski, Jochen B. W. Wolf, Joseph I. Hoffman
G3: Genes, Genomes, Genetics 2018 8: 2709-2722; https://doi.org/10.1534/g3.118.200171
http://www.g3journal.org/content/8/8/2709

Watch presentations from the conference, including talks from Katie Peichel and Jonathan Pritchard.

Now that the dust has settled from the whirlwind of the first ever standalone GSA Population, Evolutionary, and Quantitative Genetics Conference (PEQG18), we’re delighted to be able to share the audio and synched slides from the Keynote and Crow Award sessions.

We’re gratified too that attendees got so much of value from the conference. Many have approached GSA staff and the conference organizers with rave reviews of their experience, and, despite the usual growing pains of a new conference, the results from the attendee survey have also been overwhelmingly positive.

We’re excited to incorporate some of the lessons we’ve learned into planning the next PEQG. It will be held April 22–26, 2020 in the metro Washington, DC, area at The Allied Genetics Conference (TAGC20). PEQG will join the C. elegans, Drosophila, mouse, Xenopus, yeast, and zebrafish research communities for a mix of community-specific and cross-community sessions.

Stay tuned for more announcements on the upcoming conference and for several more PEQG18 blog reports in the coming weeks. Enjoy the talks below!

PEQG18 Keynotes

Jonathan Pritchard Stanford University/HHMI

Omnigenic Architecture of Human Complex Traits

Catherine Peichel University of Bern

Genetics of Adaptation in Sticklebacks

Trudy Mackay North Carolina State University

Context-Dependent Effects of Alleles Affecting Genetic Variation of Quantitative Traits COMING SOON

Finalists for the 2018 Crow Award for Early Career Researchers

Amy Goldberg UC Berkeley

A mechanistic model of assortative mating in a hybrid population

Emily Josephs UC Davis

Detecting polygenic adaptation in maize

Jeremy Berg Columbia University 

Population genetic models for highly polygenic disease

Katherine Xue University of Washington 

Evolutionary dynamics of influenza across spatiotemporal scales

Alison Feder Stanford University 

Intra-patient evolutionary dynamics of HIV drug resistance evolution in time and space

Emily Moore North Carolina State University 

Genetic variation at a conserved non-coding element contributes to microhabitat-associated behavioral differentiation in Malawi African cichlid fishes

Videos

Jonathan Pritchard 

[youtube https://youtu.be/H18k55ruCOY&w=500&rel=0]

Catherine Peichel

[youtube https://youtu.be/QRCcLixjUtc&w=500&rel=0]

Amy Goldberg 

[youtube https://youtu.be/kccUNkF7SgY&w=500&rel=0]

Emily Josephs 

[youtube https://youtu.be/CxQOrK9h6D4&w=500&rel=0]

Jeremy Berg

[youtube https://youtu.be/HqA1H24LPZc&w=500&rel=0]

Katherine Xue

[youtube https://youtu.be/fTdaAwqdt0k&w=500&rel=0]

Alison Feder

[youtube https://youtu.be/ntM0448h2lA&w=500&rel=0]

Emily Moore

[youtube https://youtu.be/aX4_HS0K1kA&w=500&rel=0]

It’s surprisingly common for babies to be born missing one or both kidneys; an estimated one in one thousand babies are born with a single kidney. Called renal agenesis, this condition is fatal if both kidneys are missing, and having just one can also lead to serious health problems like hypertension and early renal failure. In the September issue of GENETICS, Brophy et al. show for the first time that renal agenesis in humans can be caused by disruptions in the retinoic acid receptor pathway. They used whole exome sequencing in two affected families to identify a causal mutation and applied innovative CRISPR mutagenesis in mice to confirm their findings.

Two unrelated families from Iowa and Denmark each had multiple cases of renal agenesis. For both families, the researchers identified potentially causal mutations by comparing the whole exome sequences of several affected and unaffected family members. The gene GREB1L carried harmful mutations in both families: a missense SNV in one and a deletion interrupting a splice site in the other. Further sequencing confirmed that all affected individuals carried the mutated gene copies.

GREB1L is a cofactor for retinoic acid receptors that until now has never been implicated in mammalian kidney development—let alone renal agenesis. To confirm its effect, the researchers obtained a zebrafish mutant for the corresponding gene. Fish homozygous for the mutation showed abnormal early kidney development and died before reaching maturity. Knockdown treatment that decreased GREB1L expression in genetically normal fish had similar results, suggesting that GREB1L was indeed the gene causing the kidney developmental problems.

The final confirmation came from CRISPR-mediated mutations which were generated in F0 mice, eliminating the need for performing genetic crosses. Brophy et al. replicated the GREB1L mutation found in the Iowa family and generated mice with a variety of kidney development phenotypes spanning the range observed in the family. This suggests that there is developmental flexibility in how much GREB1L expression is needed to make one or two healthy kidneys. Furthermore, the use of CRISPR to generate mice that mirrored human phenotypes demonstrate how this technology can be used to quickly model idiosyncratic human mutations to better understand the causes of conditions like renal agenesis.

CITATION:

A Gene Implicated in Activation of Retinoic Acid Receptor Targets Is a Novel Renal Agenesis Gene in Humans

Patrick D. Brophy, Maria Rasmussen, Mrutyunjaya Parida, Greg Bonde, Benjamin W. Darbro, Xiaojing Hong, Jason C. Clarke, Kevin A. Peterson, James Denegre, Michael Schneider, Caroline R. Sussman, Lone Sunde, Dorte L. Lildballe, Jens Michael Hertz, Robert A. Cornell, Stephen A. Murray and J. Robert Manak

GENETICS September 1, 2017 207: 1 215-228; https://doi.org/10.1534/genetics.117.1125

http://www.genetics.org/content/207/1/215

Malinois dogs are working animals known for being used by the Secret Service to guard the White House. These dogs, a subtype of the Belgian Shepherd breed, are robust, with an average life expectancy of 10-12 years. But some puppies are afflicted by a genetic condition called spongy degeneration with cerebellar ataxia (SDCA). A puppy diagnosed with SDCA quickly loses all coordination and needs to be put down. In the August issue of G3, Mauri et al. report the genetic cause of one type of SDCA, a finding that will allow breeders to eliminate the problem from their lines.

The group previously showed that there is more than one type of SDCA in Belgian Shepherds. They identified causal mutations in one gene, KCNJ10, but that gene didn’t account for all cases of SDCA. In their current study, they examined the genomes of several other affected puppies and found mutations in a gene called ATP1B2. Since this was a different gene than identified previously, they propose to call the new form of the disorder affecting these puppies SDCA2.

ATP1B2 encodes a subunit of the enzyme Na⁺/K⁺-ATPase, a protein complex essential for maintaining ion gradients across the cell membrane. In guinea pigs, inhibiting the enzyme causes seizures and makes the brain take on a spongy appearance, similar to that found in dogs with SDCA. Mice without their version of ATP1B2 also have spongy brains and rapidly progressing motor disturbances. Although no ATP1B2 variants have been found in humans, mutations in genes encoding the other subunits of Na⁺/K⁺-ATPase cause neurological problems, such as certain types of migraines and a fast-onset form of Parkinsonism.

The function of ATP1B2 is also similar to that of the gene that causes SDCA1. Both are involved in maintaining potassium homeostasis—especially in the cerebellum—further substantiating the conclusion that mutations in ATP1B2 are the cause of SDCA2. The evidence presented by Mauri et al. will enable development of genetic tests for both types of SDCA. Now that they’ve found that mutations in ATP1B2 cause SDCA2 in dogs, checking people with family histories of cerebellar disorders without known causes for problems with ATP1B2 might provide insight into previously inexplicable conditions.

CITATION:    

Mauri, N.; Kleiter, M.; Dietschi, E.; Leschnik, M.; Högler, S.; Wiedmer, M.; Dietrich, J.; Henke, D.; Steffen, F.; Schuller, S.; Gurtner, C.; Stokar-Regenscheit, N.; O’Toole, D.; Bilzer, T.; Herden, C.; Oevermann, A.; Jagannathan, B.; Leeb, T.

A SINE Insertion in ATP1B2 in Belgian Shepherd Dogs Affected by Spongy Degeneration with Cerebellar Ataxia (SDCA2).
G3, 7(8), 2729-2737.
DOI: 10.1534/g3.117.043018
http://www.g3journal.org/content/7/8/2729