Platypus gene map offers clues to mammal evolution

January 19, 2021

The genome of one of the strangest mammals offers clues about the rest of us. (Unsplash/Meg Jerrard)

Scientists found evolutionary explanations for some of platypuses’ strangest features, such as laying eggs, sweating milk and having 10 sex chromosomes, by creating the most complete genomes of the unusual mammal and the closely related echidna.

Platypuses and echidna are indigenous to Australia, with some echidnas also hailing from the nearby island of New Guinea. The semiaquatic platypus is well known for its distinctive duck-like bill and beaver-like tail; the land-based echidnas more closely resemble a cross between anteaters and porcupines.

What began as a relatively modest investigation into echidnas turned into a four-country, 42-author project published in Nature that involved some of the world’s leading experts on platypuses and echidnas. The genomes they mapped have been an important foundation for present and future research into the egg-laying mammals.

The platypus genome was first sequenced in 2008, but the chromosome locations of only 25% of its genes were mapped, limiting its utility as a resource. Using new genome-reading technology named PacBio, the authors of the recent paper mapped 98% of the platypus genome as well as the first-ever echidna genome. The platypus genome is also the first from a male, providing the first look at the species’ five Y chromosomes.

The genomes of both animals can also provide special insight into the genetic history of humans and other mammals, according to Frank Grutzner, a senior author of the study and a professor at the University of Adelaide in Australia.

“It's really important for understanding mammalian evolution in general because they occupy such a key position in the evolutionary tree,” said Grutzner, who has studied the genetics of platypuses for 15 years.

Monotremes — a category of egg-laying mammals currently represented only by platypuses and echidnas — evolutionarily diverged from the other mammals 187 million years ago, according to the new research. Platypuses and echidnas split at their last common ancestor about 57 million years ago.

But monotremes’ egg-laying can be traced back before their split from other mammals. Platypuses and echidnas have the same gene for an egg protein as birds and reptiles — implying that a common ancestor of all other mammals also once had the egg-protein gene before losing it in the last 187 million years.

But while birds and reptiles have three copies of the gene, the monotremes only have one because they also raise young by lactating milk, according to the researchers. Female platypuses and echidnas secrete milk through pores on their abdomen, unlike the breastfeeding of other mammals, but they share many of the same milk genes and create a comparable fluid.

It was also uncovered that platypus’ unusual sex chromosomes are more similar to those of chickens than those of humans. Male platypuses have five X and Y chromosomes each for a total of 10, a stark difference from the two sex chromosomes found in most other mammals. A comparison with chicken sex chromosomes revealed that all 10 chromosomes may have once formed a single chromosomal ring before breaking into pieces at some point during evolution. A closed chain of chromosomes has been observed in plants but never in animals.

Grutzner, who codiscovered platypuses’ 10 sex chromosomes back in 2004, described his experience of researching them as a “roller coaster.” Long before discussion of a sex-chromosome chain, he had found a comparable chicken gene in a platypus sex chromosome — “One of the most exciting days in my scientific career,” he said — and later learned that genes are arranged in platypus chromosomes much differently than in humans. The latter discovery implied that the X and Y chromosome structures in all other mammals developed relatively recently, after the monotremes split off.

“One of the main contributions the monotremes have done for understanding mammalian evolution is to completely change our understanding of the sex chromosome evolution and all the mechanisms involved in sex-chromosome regulation,” Grutzner said.

Grutzner and his co-authors also analyzed how platypuses and echidnas evolved in relation to their diets, which respectively consist of aquatic invertebrates and insects. The toothless monotremes no longer have at least half of the genes related to tooth development despite their common ancestor having teeth, signaling them as a recent evolutionary loss.

Both animals have also lost many genes related to smell and bitter tasting, which may have been trade-offs for other senses used in hunting — such as being able to sense electricity, an ability not found in any other mammal.

Many of the study’s co-authors simultaneously published papers in GigaScience and Genome Research that constructed and examined new genomes of the emu and pekin duck. Compared alongside chicken genomes, they revealed a wide variety in the evolution of birds’ ZW sex chromosomes (in contrast to mammals’ XY sex chromosomes). In particular, the emu demonstrated a much slower rate of evolution in its W chromosomes, possibly because males and female emus look similar and pressures from sexual selection for sex chromosomes to change have therefore been low.

Better understanding of platypuses and echidnas may also aid conservation efforts. Three of the four echidna species are considered “vulnerable” or “critically endangered,” and a recent assessment recommends upgrading the platypus’ endangered status from “threatened” to the more serious status of “vulnerable.” Learning more about their specialized diets and interactions with their environment could help protect their populations and take better care of them in captivity, Grutzner said.

The team has been making their platypus and echidna genomes publicly available for other researchers who are interested in the monotremes and their evolutionary past.

“We've been dishing out the new genomes to everybody we know, getting as many people as possible to work on it,” Grutzner said. “There’s going to be endless insights coming out of that in coming years, so it’s really more a starting point.”

The article, “Platypus and echidna genomes reveal mammalian biology and evolution,” was published Jan. 6 in NatureThe authors of the study were Yang Zhou, Qiye Li, Jian Wang and Beijing Genomics Institute - Shenzhen; Zhenzhen Song, Huanming Yang and Guojie Zhang, Beijing Genomics Institute - Shenzhen and University of Chinese Academy of Sciences; Linda Shearwin-Whyatt, David Stevens, Filip Pajpach, Natasha Bradley, Tasman Daish, Tahlia Perry and Frank Grutzner, The University of Adelaide; Jing Li and Zexian Zhu, Zhejiang University; Qi Zhou, Zhejiang University and University of Vienna; Takashi Hayakawa, Hokkaido University; Jane Fenelon and Marilyn Renfree, The University of Melbourne; Emma Peel, Yuanyuan Cheng and Katherine Belov, The University of Sydney; Hikoyu Suzuki, Digzyme; Masato Nikaido, Tokyo Institute of Technology; Joana Damas and Harris Lewin, University of California, Davis; Yuncong Geng, Johns Hopkins University; Arang Rhie and Adam Phillippy, National Institutes of Health; Ying Sims, Jonathan Wood and Kerstin Howe, Wellcome Sanger Institute; Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo and Erich Jarvis, The Rockefeller University; Stephen Johnston, The University of Queensland; Oliver Ryder, San Diego Zoo Global; Henrik Kaessmann, Heidelberg University; Peter Donnelly, University of Oxford; Jonas Korlach, Pacific Biosciences; and Jennifer Graves, Australian National University, University of Canberra and La Trobe University. The lead authors were Yang Zhou, Linda Shearwin-Whyatt and Jing Li.

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