Louis-Marie Bobay was not intending to redefine how we think of “species,” it all came about rather by chance. “I was mostly focusing on gene flow, how recombination happens across bacterial strains,” says the University of Texas at Austin biologist. In the course of developing methods to quantify gene-flow and recombination across bacterial strains, he saw something. “One day I realized when I was resampling a lot of strains because I could actually see that some strains were behaving very differently compared to the other ones,” says Bobay. “They seemed to be isolated from the other ones in terms of gene flow.” He was working with nearly every type bacteria he could find, downloading entire sequence databases. At the start, “I was just using those species which are very well studied,” such as E. coli and Salmonella. “But then the goal was to extend [the method] to every genome that has been sequenced.” The results of his nearly 2-year analysis was recently published in Genome Biology Evolution in a paper titled “Biological species are universal across Life’s domains” (Bobay and Ochman 2017). In it, Bobay and his co-author, Howard Ochman, propose a remarkable new view of bacterial species. They can be lumped, he believes, into communities that regularly swap genes, much as other species, such as plants and animals, are grouped by interbreeding individuals that are reproductively isolated from other groups. Although Bacteria and Archaea reproduce asexually (via cloning), they can transfer and exchange genes though homologous recombination. “Here we show that barriers to homologous gene exchange define biological species in prokaryotes with the same efficacy as in sexual eukaryotes,” write Bobay and Ochman. The suggestion is a remarkable and unifying idea: the way we define “species” in sexually reproducing eukaryotes can be extended to the entire tree of life. Naturally, as with all things in biology, it is not exactly that simple. To start, there is more than one way to think of a species. Competing with the “biological species concept” is the “cladistic species concept,” the “cohesion species concept” and more than a half dozen other “species concepts.” And, of course, bacteria and archaea are not sexually reproducing, so at best the biological species concept can only be applied to them with modifications. “The paper makes bold statements,” says Jesse Shaprio, an evolutionary genomicist at the University of Montreal, “about things that apply across the tree of life, but nothing is universal.” That said, he believes Bobay and Ochman hedge themselves wisely. “I think this is a very useful approach. I think it should be applied with some caution, but I think the authors appreciate that,” says Shapiro, who has floated related ideas, but was not involved in the current work. Bobay’s method for analyzing bacterial genomes is appealing to researchers because it is genome-based, says Shapiro. “It can be applied in high-throughput, standard way, which doesn’t require specialized knowledge of each individual species.” Bobay arrived at his method by resampling strains that are considered one species to see if the traces of gene flow would be different. “So imagine you have 50 genomes of a species,” explains Bobay. “Instead of just analyzing 50 genomes together, I decided to randomly take 40 or 35 and recalculate the recombination rates across these different groups that are randomly chosen.” He found that in a lot of species the amount of gene flow was very consistent in no matter what sample he would take. “And then I realized that in some of the species, whatever I would sample would have a very strong impact on the amount of gene flow and some [others] were at the point where the levels of gene flow was near zero,” says Bobay. “That made me realize that in doing this resampling procedure we could actually try to identify strains that are not recombining [by homologous exchange] with the other ones GBE

Sponges seem relatively simple. They have no specialized tissues or organs. Some have even argued that sponges aren’t animals at all, just colonies of cells that work together to function. That said, for those who study sponges, these delicate, simple animals are remarkable, with much to teach us. As the phylum Porifera is a key candidate to be the sister-group to all other animals (Telford et al. 2016), close study of these organisms’ genes and life cycles can illuminate features of early animal evolution. A recent paper published in Genome Biology Evolution (Fierro-Constaı́n et al. 2017) aims to settle an evolutionary question, one raised in the early part of this decade. After the discovery that genes once thought to be only expressed in forming sex cells were also expressed in other cell types (e.g., multipotent cells) in animals with bilateral symmetry, researchers began proposing the existence of a set of genes—a germline multipotency program (GMP)—that had long been part of the animal family tree and was able to operate in both pluriand multipotent somatic cells and germ cells. In 2013, Jordi Solana elaborated on this (Solana 2013), proposing the hypothesis of primordial stem cells (PriSCs). These cells would appear while the embryo was forming and developing. In most sexually reproducing bilaterians (e.g., animals other than sponges, jellyfish and comb jellies), Solana expected, the PriSCs would give rise to the primordial germ cells and some somatic stem cells. In animals reproducing asexually and/or capable of regeneration, such as flatworms (a bilatrian lineage), these cells might be present at the adult stage keeping a mixed germ/soma potential. But, were these genes inherited from an animal ancestor? The data needed to answer that, says Emmanuelle Renard, wasn’t conclusive. His lab and team at the Station marine d’Endoume in Marseille has considerable expertise in sponge biology (which is no easy feat given that sponges can be extremely challenging to grow in the lab). So, some of his research team, including then PhD student Laura FierroConstaı́n, sought to illuminate the question by examining the expression of this set of genes during the formation of sex cells and other stages of the life cycle in their favorite sponge model Oscarella lobularis. They found that the GMP toolkit is involved in sexual reproduction in sponges, as it is in every animal examined so far. They also find the GMP expressed in other sponge cell types not involved in sexual reproduction. Therefore, write the authors, “not only the well documented—in a plethora of bilaterians—piwi, vasa and nanos genesg have to be abandoned as germline specific markers, but rather a wider GMP set (for which expression data were sparser until now).” “Eleven of these genes are expressed not only in sex cells but also in other cell types,” says Renard. “Therefore, exciting questions are raised. Our results suggest that all cell types—except one—are expected to be multipotent in this species. Crazy isn’t it? The next question can be, why other animals did not keep such capacity—so useful for regenerating a body in case of injury, for example?” Renard and his team are also interested in investigating how environmental cues, like temperature and pollutants, trigger gene expression and the switching between sexual and asexual reproduction. For researchers like Solana, who was not involved in the study, this work is further confirmation that genes classically thought to be only involved in the germline, are quite active in all stages of life for some animals. Multipotent cells like choanocytes (in sponges) and the neoblasts of planarians, which express the GMP program and are able to become all other types of cells, can be thought of as equivalent to embryonic stem cells in humans. “I think this is the broader picture,” says Solana. “We are starting to see that somehow all of this is connected together. This is my opinion only, but I would say they are homologous characters.” Currently, the fields of embryonic stem cell research and early animal evolution are very separate. This division is not supported by the work of Fierro-Constaı́n and colleagues. Instead, the goal, says Solana, is to connect these two fields. “Once we do,” he says, “planarians and sponges could become a model for human embryonic stem cell research.” GBE

For wild, complex innovation one domain of life stands heads, shoulders, tentacles, tree bark and coral reefs above the rest: with full respect bacteria and archaea, many of evolution’s most interesting inventions are a product of eukaryotic life. “The complexity of life on earth can only be understood if we understand eukaryotes,” says Neil Blackstone, a biologist at Northern Illinois University. But there’s a problem. Most biologists believe that the last eukaryotic common ancestor (or LECA) had all of the complex features associated with modern eukaryotes: sex through meiosis and chromosomes held in a nucleus. That makes it very difficult to compare various eukaryotes a route to study how features arrived—as one might with tetrapods or land plants. It’s all there from the start. “So it’s a tough problem to get at, yet it’s crucial if we’re going to understand life,” says Blackstone. “I think right now we’re seeing a lot of foment where people are coming to grips with the issue—realizing that we can’t use methods of comparative biology.” If the field of evolutionary biology could use a new big idea to chew on, discuss and try to prove or try to disprove, they may perhaps have found a candidate in a richly detailed paper (Garg and Martin 2016) recently published in Genome Biology and Evolution by Sriram G. Garg and William F. Martin (Editor-in-Chief of GBE). In it they propose a somewhat radical idea: “We’re proposing that mitosis evolved from meiosis,” says Martin, “which is exactly contrary to what everybody has always assumed.” This happened, they believe, following the acquisition of the bacterial ancestor of mitochondria, as it established itself within the cytosol of its archaeal host. Thinking back to high school biology you may remember, the purpose of mitosis and meiosis are very different, though at first glance the processes can seem very similar. In both, the function is to make new nuclei and ultimately cells. The names for steps in the nuclear cycle (prophase, metaphase, anaphase and telophase) are parallel between the processes (with a few additional steps for meiosis). However, their purpose is very different. Cells go through meiosis to make gametes, recombining genetic material (thereby creating genetic diversity) and halving the number of chromosomes of the mother cell. Mitosis is purely for asexual reproduction. When it goes right, the daughter cells look just like the mother cell. In great detail over more than 30 pages, Garg and Martin detail how they believe a proto-mitochondrial bacterium began living inside an archaeon and there developed meiosis. Only later, the believe, did mitosis start. One of the reasons the authors believe this is sequence of events is Muller’s ratchet: without genetic recombination, bad mutations pile up in an asexually reproducing population, making life difficult and eventually near-impossible. So the lineage giving rise to modern eukaryotes, they reason, had to have some method of recombining DNA. If this was the case, the authors write, “the lineage was necessarily recombining [. . .] leaving neither selective pressure to evolve anything as complicated as meiosis and sex, nor benefit from it once it arose. This line of thought actually renders the origin of meiosis from mitosis altogether unlikely.” A first step in their time line was the evolution of the nucleus: As individual proto-mitochondria died inside their host archaeal cells, the authors propose the mitochondrial genes released their DNA into the cell which then glommed on to the archaean genome. And, through nonhomologous recombination, these genes integrated. But this carried some consequences: the host had to deal with self-splicing introns which can copy themselves and reinsert into the genome. “And that’s what triggers the whole cascade,” says Blackstone, who was not involved in the Garg and Martin paper. “It’s really triggered by evolutionary conflict at the genomic level.” Because the self splicing introns were slow and translation in ribosomes was fast, it was dangerous to let the ribosomes get to the message RNA until the cell splicing introns had sort of finished their work of splicing themselves out. So, a physical barrier evolved to mediate these conflicts: the nucleus, and it became the hallmark of eukaryotes. But, as often happens, the solution to one problem can create new ones. If chromosomes are confined to the nucleus they can no longer attach to the cell membrane. When the

Scientists can now track how cancer spreads, study cells in the retina, or watch HIV infections progress, thanks to the harnessing and development of green fluorescent protein (GFP). It is fair to say GFP has transformed biomedical research. In fact, Martin Chalfie, Osamu Shimomura, and Roger Tsien received the 2008 Nobel Prize in chemistry for their discovery and development of GFP. Despite several decades of use, GFP and fluorescent proteins (FPs) in general are surrounded by a halo of mystery. GFP was found in Aequorea victoria jellyfish, sometimes called the crystal jelly. It is unknown why jellyfish have such proteins, though they are far from alone in carrying them. Several coral species also have them. Better understanding these proteins and how they serve marine species could push science forward in several ways. It could help biotech engineers develop new fluorescent markers, for applications where GFP cannot serve. For example, GFP does not work well in live mammals, as hemoglobin absorbs the visible light the protein emits, often masking its presence. Ecologists also would love to know why reef-building corals carry these proteins, as they look for ways to aid threatened coral reefs. A recent paper in Genome Biology Evolution takes a step toward these goals by analyzing the FPs in two stony coral species: Acropora digitifera and Acropora tenuis (TakahashiKariyazono et al. 2016). In it Yohey Terai, biologist at the Graduate University for Advanced Studies in Japan, and colleagues uncover new diversity for coral FPs, along with an unexpectedly high number of gene copies. The results indicate that FPs play some yet-to-be-determined crucial biological role. “We did not imagine we’d find this. It’s surprising because we still don’t know the function,” says Terai, adding that he hopes their results will lead them towards understanding the proteins’ role in living corals.

For those who love and study insects and arachnids, they can see the underappreciated wonders of the biological realm. In the face of so much diversity, so much remains to be discovered. A recent study in Genome Biology Evolution is a case in point. Researchers sequencing the genome of a mite have found what might seem stranger than fiction: a mite that has retained genes important to sight, despite having no eyes, and has spread genes important for the development of body segments all over its genome, in stark contrast to most organisms, keeps these genes close together in a tidy line. Coauthor Stephen Richards, from the Baylor College of Medicine in Texas, says his “mind is still blown” when he reflects on this finding. “I always thought having the Hox genes all in a row was kind of important for animals, and apparently it's not,” he says. In other arthropods whose genomes have been examined, Hox genes are collinear, with few to no intervening genes. But in their examined mite, Metaseiulus occidentalis, the genes aren't just spaced apart, they're on completely different gene scaffolds. In this mite, researchers also found an unusually high number of intron gains and losses, indicating that the evolutionary background of this arthropod (at least from a genome point of view) has been full of unexpected genetic gymnastics. “It really makes me wonder what’s been happening in this lineage,” says Richards. It'll take the sequencing of other related animals to determine if this mite started out with orderly Hox genes (which is assumed to be the historical arrangement). Or, Richards floats an alternate possibility, perhaps “it is more basal in the mites?”

There are many ways to build a car: from stretch limousines to tiny economy cars, as long as the vehicle drives and is reasonably safe, no one design is inherently right or wrong. Comparing different models is useful, says Mark Field of the School of Life Sciences at the University of Dundee, because it quickly makes clear what the essence of a car is. Early cars tended to be very similar to each other. Now cars are more variable, versatile, and complex than ever. Some use petrol, some diesel, some use electricity, others run on hybrid systems. All something need to pass for a car is four wheels, a means to take in energy, and a propulsion system that is geared so it can speed up and slow down. As a biologist interested in the mechanics of eukaryotic evolution, Field applies the same sort of comparison to living organisms as well. If you look at what’s different between one car and another, it can tell you something about its owner or its purpose, he says. And if you look at how organisms have changed over time, you can learn something about the complexity of evolution.

Chaperone proteins are a guiding force within the cell. Not only do they usher newly minted protein molecules into their correct functional shapes but it seems that in doing this, they also can promote genetic diversity in a somewhat unexpected way.

The basic text of all life is written in a simple alphabet. Adenine, thymine, guanine, and cytosine form the units that allow DNA to write the books of Earth’s elaborately complex lifeforms.Curiously though, despite doing a seemingly equivalent job at conveying information, the prevalence of certain base pairs (G-C or A-T) in the genome is mysteriously variable, across both phyla and environment. Currently, it’s unclear why this should be. That makes nucleotide content a fascinating area ripe study, says Ruth Hershberg, an assistant professor at the Technion-Israel Institute of Technology in Haifa. It’s a highly variable, easy-to-measure trait. One that, she says, “affects every nucleotide in the gene. We really don’t know why it’s so variable, or what determines it, so that makes it interesting.” It might also be important too, she says. Mutations tend to move in a G-C ! A-T direction, meaning G-C rich genomes could potentially have higher mutation rates. Nucleotide content might also affect codon usage and regulatory genes, she says. Hershberg and colleagues, including Erin Reichenberger, Gail Rosen, and Uri Hershberg (her brother) have recently begun to unpick why nucleotide content varies so widely, publishing their findings online April 9 in Genome Biology Evolution (Reichenberger et al. 2015).

Once upon a time the island of Mauritius held no mammals. But as this small island, 2,000 km off the coast of Africa in the Indian Ocean, became an important stop on the trade route between the East and Europe, it was visited frequently by both Dutch and Portuguese sailors. And it was likely one of these sea-faring salty dogs who brought Mauritius its first nonhuman mammal: the “crab-eating” or cynomolgus macaque, likely from Java, originally as pets. “The founding population was probably between 4 and 12 at the most,” says Antoine Blancher, an immunologist at the Toulouse University Hospital in France (CHU de Toulouse). “But they grew very fast and became important invaders. The poor farmers who were trying to cultivate sugar cane were totally desperate because the macaques destroyed all their efforts. The farmers eventually abandoned the island and the macaque population just exploded.” Thus the seeds were planted for an interesting experiment: how would the descendants fare? Would harmful mutations accumulate in the population? Or, might selection win out over genetic drift, keeping the population relatively healthy? A recent whole-genome analysis of a selection of these monkeys, completed by Osada et al. (2015) reveal that these macaques retained a surprising amount of genetic diversity, and have enjoyed fairly good health, during their 400 or so years on Mauritius. As a more practical matter, for medical researchers the cynomolgus macaque is a key animal used to test vaccines, immunosuppressive drugs for organ transplants and other treatments. “For experimental immunologists these animals are very precious,” Blancher says. Genetically they are quite close to humans yet they are still allowed to be used in experiments (in the United States the government recently outlawed the use of chimpanzees in research, following a recommendation by the National Institutes of Health). This particular kind of macaque is especially attractive to researchers, as they are free of the herpes B virus—a potentially fatal disease for humans. To survey the polymorphic diversity within the Mauritian cynomolgus macaques (Macaca fasicularis) the team extracted DNA from blood samples of six wild-caught macaques collected for a different research project. They then sequenced the genomes at the Beijing Genomics Institute in Shenzhen, China. The results were a surprise for the research team. “Despite this severe population bottleneck, the Mauritian macaques were quite diverse—about as polymorphic as the global human population,” Blancher says. And as for the accumulation of deleterious mutations? None were seen—an observation consistent with recent theoretical and experimental work in humans finding that recent demographic changes do not strongly affect the genetic load of a population. Here, it seems the push of selection has balanced the pull of genetic drift. “One force is eliminating these deleterious mutations and the other one is promoting their accumulation and the balance is relatively neutral,” says Blancher. “They do not accumulate dangerous mutation as was assumed before, in the case of most Mauritius animals they are perfectly healthy. This is very good news, I think, for species conservationists.” If the starting population is genetically quite heterogeneous, he says, a healthy population can be maintained starting from just a few individuals. The observed level of polymorphism also makes these monkeys well suited to some areas of research. “Ignoring the degree of polymorphism in your study animals is very dangerous,” Blancher says. “If you validate your work with only a few animals you can be totally puzzled by the response when the treatment is used in humans.” “This is important work,” says Zhenxin Fan, a genetics researcher at Sichuan University in China, who has previously sequenced Tibetan macaques. “The smaller genetic diversity of this population than Malaysian cynomolgus macaques is an advantage in biomedical studies and we need to know their genetic diversity and demographic history.” GBE

Many species, one healthIn the race to save endangered frogs from extinction, disease ecologists are hunting for patterns of infection that could also improve human well-being.

Nestled in the South Pacific archipelago of New Caledonia, the island of Lifou is home to a famous bird. To biologists interested in biodiversity, white-eyes (genus Zosterops) are the masters of spawning diversity. Evolutionary biologists Ernst Mayr and Jared Diamond dubbed the birds the “great speciator.” White-eyes are remarkable for appearing in so many varieties. Their order, the passerines, accounts for half of all the species richness found within birds. Among passerines Zosterops is the most diverse of genera, with about 80 described species found in Africa, Australasia, and the South Pacific islands. The birds excel at colonizing islands. Three sympatric species exist on Lifou, which spans just about 1,200 km2, providing scientists with an ideal study model. “The island is incredible. You arrive and find three endemic species of Zosterops living in the same habitat, which is very unusual,” says Luis Valente, coauthor of a recent study analyzing why white-eyes do so well at speciation. “From an evolutionary biologist’s perspective, it’s a really exciting environment.” Previous work has established that these are rapidly evolving birds, but little has been done to peek at the underlying mechanisms. Valente and colleagues were recently the first to sequence and publish a reference genome of Zosterops. They use it as a model against which they can test hypothesis regarding why white-eyes diversified so abundantly compared with other birds. Their work can be found in the XXXXX issue of Genome Biology Evolution (Cornetti et al. 2015). “The idea is that if we look at these species that have been evolving quite rapidly, we can get perhaps more information about the processes that create biodiversity,” says Valente. Valente and coauthors compared the genomes of the three species endemic to Lifu with each other and then expanded their view to compare the genome of Zoetropes as a whole with the genomes of other bird groups (ones which do not diversify as fast and whose genomes have already been published). “The most interesting thing,” Valente says, “is that all of the results went in the direction that we’d expect.” (Such is not always the case in similar investigations, Valente explains.) The team hypothesized that Zoetropes would have a relatively higher number of substitutions, because the changes in their DNA sequences are very rapid. And so it was. They also found a very high number of gene duplications, implying that there are more new genes being formed in the Zoetropes lineage compared with other birds. They also find many genes under positive selection, indicating that the genome of Zoetropes is quite evolutionarily flexible. “When you think of the theory of how things evolve very rapidly, this is exactly what we find in the genomes of Zoetropes,” says Valente. Valiant cautions the work is preliminary and theoretical, but the idea is, he says, if a species has a genome that is very flexible and changes so that new genes are easily formed or different features of the phenotypes appear (rapidly changing wings, for instance) then this can potentially lead to the formation of new species faster than normal. The work might be preliminary, but it is interesting, says Walter Jetz, an evolutionary biologist who was not involved in the study. He would like to see genomes from other species given the same analytical treatment, but says “the work provides a nice demonstration of the sorts of new insights gained from combining genomic among and within species in an explicit spatial and biogeographic context.” Prior to publishing the results of their analysis, Valente says that they were eager to release the reference genome of silvereyes for others to use. “It’s quite exciting to be able to produce the first genome for Zoestrops,” he says, “because it has been a model system for quite a few years and the genome has been in quite some demand.” Asking questions about how genomic characteristics underpin diversification is primarily a theoretical exercise—one that works at solving a fundamental question in biology. Yet Valente thinks this could also be a useful tool for conservationists intent on preserving biodiversity. Though white-eyes are not endangered the method “could show where the genetic diversity is and which populations are priorities for conservation,” he says. “It’s important information to have, but conservationists generally don’t do it because it is very expensive.” In all likeliness, genomic sequencing will continue to become more accessible in the future, and will help cast light on how biodiversity is generated and maintained. If we understand that, Valente says, “perhaps we can predict what might happen to the equilibrium of species if we disturb habitats. It’s quite a wide fundamental question really.”

Taking care of our children seems like the most natural reflex. For humans and many other animals, so it is. The cuddling, feeding, diaper changing, baseball-throwing-lessons, and pushes to study for college entrance exams comes so automatically, that some might be surprised to reflect that these barely conscious behaviors have genetic underpinnings. Put another way, we do not do them because we want to. We do them because we are made that way. While human social interactions are of near-bewildering complexity (and a long way from being satisfactorily understood) simpler models exist which could lay the foundation for a better understanding of sociality. Consider the curious example of the burying beetle (Nicrophorus vespilloides). This type of carrion beetle bury the carcasses of small animals, such as mice or birds, as food for their larvae. Both males and females will care for young. Now, a group of biologists centered at the University of Georgia has made a start at picking apart the mechanism for this behavior. To start, they have analyzed the genome and methylome of N. vespilloides, presenting their work in a recent issue of Genome Biology and Evolution. To date, honey bees, ants, termites, and other eusocial insects (hailing primarily from Hymenoptera) have been front and center of most studies of sociality in insects. The information collected by Chris Cunningham, Allen Moore and their colleagues (2015) may help change that. “This might be a better model for vertebrate behaviors [than honey bees],” explains Cunningham. While behavioral changes in Hymenopterans tend to be tied to developmental changes, parenting behavior in burying beetles seems to have an on-off switch. “If you took one of the burying beetles and you put a larvae in front of it, it would eat it, which is bad parenting,” says Moore in the understatement of the year. “So something switches in them to make them a parent.” The way to prime the beetles for parenting is simple. “Give the beetles a dead mouse,” Moore continues, “and 48 hours later they’ll parent anything you put in front of them” – even larvae of different species – “they’re not particular.” The beetles lay eggs beside the dead carcass (after hatching the larvae crawl into it). The parents protect the carcass against decay by laying down chemicals to stem fungal and microbial growth. Once hatched, larvae wave their limbs at the adults (presumably to catch their attention) and the beetles feed them by regurgitating food into their mouths. “You really have the insect equivalent of a bird, but parental care lasts for about two or three days, which is about my attention span, so it’s much better than a bird,” says Moore with a laugh. A few days later, put a larvae in front of those same beetles, and they will make a snack out of it. What is changed in this time? Obviously not their genome. Could it perhaps be the methylome? Methylation is a well-known way to make epigenetic changes of the genome that last only as long as they are needed. Prior to the team’s sequencing of N. vespilloides, only one other beetle’s genome had been sequenced and published (Tribolium castaneum) and it seemed to lack methylation. Thus, it had been assumed that methylation was not present in beetles at all. “That’s quite a thing to say because there are over a million beetles and only one had been looked at,” says Cunningham. Still, when the team did find evidence for methylation it was an enjoyable surprise. This was also a key point of intrigue for Rebecca Kilner, a professor of Evolutionary Biology at the University of Cambridge. “DNA methylation might therefore be a common genomic feature of social insects because it facilitates the transition between behavioral castes (or task specialization) which these insects have in common.” Evaluating how the beetles are using methylation is the next clear step says Cunningham. “I’m now trying to see if they use it in the way honeybees do, to regulate gene expression.” But he says the fact that the switch in beetle behavior is not developmentally coupled makes it especially fascinating for him. Moore says his ultimate goal is to find the genes responsible for social interaction. “What makes an organism socially compatible?” he wonders. After all, most organisms in the world do not like being around others. “Put two of them together they either run away or they fight. So, what is it that leads to social tolerance? Or if you put a larvae in front of a beetle, why should it takes care of it instead of eating it?” He even wonders if the genes involved in this are common across all social organisms, beetles, bees, birds, and humans included. By laying out this organism’s genome and methylome, his lab is paving the way for many more investigations. In particular, researchers can start asking how cues generate varied gene expression and how that, in turn, leads to the wide panoply of behaviors that determine how we conduct ourselves, how we approach mates and how we keep our children alive.

For the first time, a complex behavior, mothers caring for their offspring, has been linked to a semimysterious repeating amino acid sequence common to mammals. These repeats, found more often in mammals than other vertebrates, have been seen in the past to affect protein–protein interactions, transcriptional regulation, and phenotypic variation. Japanese biologists Shintaroh Ueda, Den'etsu Sutoo, and colleagues from the University of Tokyo and the University of Tsukuba wanted to know whether these repeats had evolutionary significance. To investigate, the researchers replaced a gene in mice with its ortholog from western clawed frogs. The amphibian version of the transcription factor Pou3f2 is repeat-free, whereas the mammalian version is rich in glycine, glutamine, and proline repeats. They report their findings in a recent issue of Genome Biology Evolution (Makoto et al. 2014). Before starting the experiments, says Ueda, it was hard to guess what changes they would see, but he felt confident something would appear. The effects were dramatic: Carrying nonmammalian Pou3f2 essentially turned female mice into bad mothers. Though giving birth to healthy, normal-sized pups, a dam was less interested in her pups, and less likely to fetch them and bring them to her nest. Most pups born to “knock-in” mothers did not survive to weaning, whereas most pups born to normal mothers did. “This is significant, I think, for reminding us that we shouldn't just be looking at the regions of proteins traditionally considered functional,” says Noel Faux, a research fellow at the Florey Institute for Neuroscience and Mental Health in Melbourne, Australia, who was not involved in the research. “Regions we wouldn't normally consider obviously do have a function here.” Without the repeating homopolymeric amino acids, the mice did not have as much dopamine and serotonin in their brains—past studies have shown that these two neurotransmitters heavily affect how mammalian mothers care for their offspring. Dopamine and serotonin regulate many other complex thoughts and behaviors: Anxiety, fear, mood control, motivation, cognition, reward, movement, regulation of body temperature, and drug abuse. “We hypothesize that the regulation of these functions is not sufficiently strict in nonmammals including amphibians,” write Ueda et al. Although animals such as fish and amphibians behave more or less instinctively, mammals behave in ways that are not necessarily instinctive, they show emotion, bond socially, and nurturing their young. “This study opens a host of interesting questions,” says Faux. “If you give these [knock-in] mice tests for memory, anxiety or depression, how do they perform?” In a more technical vein, he is curious to know how the structure of transcription factor Pou3f2 differs between knock in and normal mice. Although orthologous proteins fold in a similar manner, the repeats presumably, he says, affect structure in some way. Does the length of the repeats affect neurotransmitter levels and behavior, he wonders. Also, in this study, all three repeat-rich regions of the mammalian Pou3f2 gene were swapped for no-repeat amphibian versions. He would like to see experiments removing each of those regions individually, to see which has the strongest effect on behavior. Faux says many of his colleagues will be intrigued by the study. It may, he hopes, bolster support for their research: “The more evidence that these [repeats] do have an impact the more the granting bodies are likely to take it on board. It's sort of a new area and people are still a bit skeptical that these things can have an effect on fairly large behaviors.” Ueda also believes that this field of research is just beginning. There are hundreds of mammalian genes with homopolymeric amino acid repeats, he says, and the majority are evolutionarily conserved in length across mammals and have important roles in transcription, translation, and signaling processes. These knock-in mice, says Ueda, are available as models for researchers to deeply dive into the characteristics that make mammals unique.

As part of the 2013 International Genetically Engineered Machine Foundation synthetic biology competition, students were able to reclaim gold from electronic waste with the help of a synthetically derived bacterium, shown here in an artist’s conception. Image courtesy of Joanna Hoffman (University of Arts in Poznan, Poznan, Poland).

Life is far more dynamic, varied, and exciting than we typically appreciate, genetically at least. Evolutionary biologists Angela Oliverio and Laura Katz believe epigenetics, polyploidy, and extensive genome reshuffling are found—not just in the strange corners of biology where exceptions are found—but across the whole tree of life, stemming as far back as the last universal common ancestor or LUCA. In a new review in Genome Biology Evolution, Oliverio and Katz, both from Smith College, argue for a more expansive and inclusive view of biology and a turn away from what is typically taught in textbooks (Oliverio and Katz 2014). “I like to study the weird, wonderful things in biology, things that didn’t read the textbook and don’t know how they’re supposed to structure their genome,” says Katz, whose lab at Smith studies eukaryotic genome evolution. So widespread are the “nontextbook examples” of reproduction, ploidy number, and epigenetic interactions, in fact, that the authors suggest popular notions of LUCA may need an update. All of life uses DNA to produce RNA to produce proteins, a commonality known as the central dogma of biology. Because the same biochemical machinery is used in the path from DNA to proteins, it is reasonable to assume that LUCA used the same machinery. Also, because dynamic genome features can be found in each of the three main branches of life, perhaps they may have been part of LUCA’s genetic toolbox as well. “The ability to do things like regulate the copied numbers of chromosomes and genome rearrangements while still inheriting full genome complements may have allowed LUCA to inhabit niches in new ways,” Katz says. The authors examine three key ways in which genomes, bacterial ones especially, are unexpectedly dynamic: copied numbers of chromosomes, epigenetics, and variations in life cycle. Though many bacterial species are usually thought of as having just one copy of a chromosome, they typically have many. (Generally this “polyploidy” isn’t like the polyploidy found in plants and animals, however, where distinct chromosomes are inherited from different parents.) For several bacteria, including Escherichia coli, the number of chromosomes varies with growth rate. When Synechocystis is growing exponentially, it has 218 genome copies. It still holds a considerable 58 copies in its linear growth phase. Epulopiscium, not to be outdone, copies its genome tens of thousands of times. The advantage to all this extra copying may be to provide backups in the case of DNA damage or supporting a large cell size by allowing for gene expression to be regulated globally. It could also allow for certain copies to be inherited unchanged while other copies are recombined in novel experimentation. In discussing epigenetics, the authors use an expansive definition coined by Denise Barlow, the woman who discovered the first imprinted gene in 1991: “Epigenetics has always been all the weird and wonderful things that can’t be explained by genetics.” This includes regulated rearrangements in a genome, the incorporation of foreign material, and any heritable changes beyond changes in DNA sequence. For example, the eukaryotic ciliates Katz studies can make millions of chromosome copies. They take genes, scramble them into little pieces, and reform them into functional gene products. Showing a similar genetic juggling ability, some bacteria reshuffle genetic material to generate a diversity of antigens on the cell surface. These novelties help them escape host immune systems. The DNA of Deinococcus radiodurans can be ripped to shreds by radiation, and yet the organism is able to reassemble their genome as if it were no bother. Similar repair systems are found in archaea as well. Among textbooks, bacterial and archaeal reproduction by binary fission is the common story, but one that is grossly oversimplified. Some bacteria reproduce by budding or multiple fissions, requiring coordinated inheritance of genetic material. Some bacterial and archaeal species can produce multiple internal offspring in a kind of “live birth.” Maternal DNA still operates in the “mother cell” and likely helps maintain metabolism while the daughter cells are growing. This life cycle calls for a clear replication and regulation of genome content and the capacity to mark and separate the genome to be inherited by the offspring. Other bacteria reproduce by asymmetrical cell division, where one big cell spins off many smaller cells. If the genomes GBE

Whatever your luck in life, the consequence of old age is unavoidable. Death visits us all. But despite its universality, the timing of this call varies. In developed nations, most people can expect to live to 80 or 85. Only about 1–2% of the population celebrates their 100th birthday. Like many traits of interest, longevity is complex—determined by the interactions of our behavior, environment, and genetic background. Centenarians are not that easy to find, so past studies seeking to link genetic variation to longevity in humans have suffered from small sample sizes. However, a robust, novel approach by researchers at the University of California (UC) Irvine and Cornell University, using fruit flies, may point toward a clearer understanding of genome-wide variations associated with longevity in humans as well. The authors describe their results in Genome Biology and Evolution (Burke et al. 2013). Pools of old chromosomal DNA from the longest surviving 2% of females (analogous to centenarians) was sequenced alongside control DNA from young adult females from the same cohort. The flies were from recombinant lines developed by Anthony Long (a coauthor) and Stuart Macdonald as part of the Drosophila Synthetic Population Resource. By using this experimental mapping population with a defined genetic background, Burke and her team could define regions of the Drosophila genome that differed between “normal” and long-living flies more rigorously than what is possible in human genome-wide association studies. “We found using this approach really narrows down the number of locations genome-wide that are implicated in longevity,” said Molly Burke, a postdoctoral researcher at UC Irvine. “That’s what we felt was a strength of the paper.” Although this current study did not go so far as to pinpoint specific genes, the authors did identify eight regions that seem important. The areas of the genome that most changed between the two groups tended to be toward the ends or the center of the chromosomes—regions that rarely recombine during meiosis. This suggests, says Burke, that deleterious mutations that affect longevity are able to accumulate in these regions of the genome. This observation harmonizes with the mutation accumulation evolutionary theory of aging, based on the idea that unconditionally deleterious alleles can accumulate if their fitness effects strike only in the postreproductive phase of life. “This is a result of general significance, I think,” Burke says, “that could be informative in the search for human longevity genes. Perhaps the centromeres and telomeres are somewhere we need to look more carefully.” Regions of normal recombination that differed significantly between the two populations held genes needed for immune function as well as a gene family (glutathione transferase) involved in oxidative stress response. These findings are perhaps intuitive: a healthy immune system would logically help flies fight pathogenic bacteria and live longer as a result. The glutathione transferase family is part of an enzyme class that scavenges free radicals (reactive oxygen species supposed to damage molecule) created by oxidative stress. “I think it’s a great experiment,” says David Rand, an evolutionary geneticist from Brown University, who studies mitochondrial–nuclear genome interactions within Drosophila. “[The authors found] a logical, empirical approach to studying centenarians. In a way, their major result is a lack of a result.” The authors agree, writing: “While our gene list is ripe for the validation of candidate longevity genes perhaps the list’s most interesting feature is an absence of genes previously described in the literature.” A long list has been compiled in the fruit fly genetics literature, presenting about 300 alleles in approximately 150 genes as being important for aging. Burke and her colleagues essentially found no overlap. “This was surprising,” Burke says. “But the flies that we studied in this experiment are not inbred flies, they’re outbred flies that have been freely mating and recombining for many generations, so they’re genetically diverse and more representative of fruit fly populations in the wild.” Most of the Drosophila aging studies historically have used inbred lab strains to study the effects of mutations in genes. Even though those mutations have an effect on lab strains, they’re unlikely to have large effects in outbred, more natural populations. “This suggests that to find natural variants important for a phenotype like longevity,” says Burke, “we need to do experiments in outbred populations, whatever the species.” Anthony Long is currently studying another complex phenotype in fruit flies—sensitivity to chemotherapy. His current approach works, he says, but is incredibly labor intensive: “It's not pretty, we operate by brute force.” The pooling technique used here, he believes, points the way forward when studying traits that draw on multiple genetic factors. “It suggests some approaches where we could take our lines, combine them, treat the combined population with a chemo drug and then identify the elite individuals that survive that treatment well and then sequence that pool,” he says. “This might be 10 to 50 times more efficient, freeing us up to assay some extremely interesting phenotypes that we can’t right now.” Burke expects the study to be influential in her research as well. “Just because we identified these really interesting genes in silico,” she says, “does not mean that we have proven that mutations in these genes affect longevity.” To find such proof, she is learning to do transgenic experiments in yeast—where one version of a gene can be swapped for another. This may, in time, point the way toward genes affecting human longevity as well. “Given the limitations of working with human studies,” she says, “researching model systems like this is where I think the frontier lies.”

Evolution is the story of shifting genes: New ones arise, old ones pass away, existing ones become more or less widespread in response to the pressures of life. Without the creation of new genes this dance would not be possible. New research suggests that, regarding new gene creation, plants and animals have much more in common than meets the eye. More than a decade ago research groups began to publish papers detailing the evolutionary patterns of new genes in animals, noting that they often seemed to arise in male sex organs. This work developed and became known, eventually, as the “out of testis” hypothesis, where the testis, the male reproductive organ, is the origin for the birth and evolution of new genes (Kaessmann 2010). But now geneticists from the Chinese Academy of Sciences and the University of Toronto have proposed an “out of pollen” hypothesis, showing that in plants too, new genes seem to arise in the male sex cells. Their research was recently published in Genome Biology Evolution (Wu et al. 2014). “This inclusion of the pollen case makes the whole picture bizarre and even more interesting,” says Manyuan Long from the Department of Ecology and Evolution at the University of Chicago. Long did some of the original work which laid the basis for the “out of testis” hypothesis. What is really interesting, he says, is that most plants do not have different sexed organisms, but are hermaphrodites. “Perhaps this can help us derive some theory independent of sex determination in animals, because in Arabidopsis there is no such thing, so we have to think, what are the properties in common between animals and plants? Why do they have similar kinds of phenomenon?” For their study Wu et al. searched the ProteinHistorian database for the ages of genes in Arabidopsis thaliana, a common model organism in plant biology and genetics. They looked for these genes in the microarray expression data of 79 tissue samples from Arabidopsis taken in different stages of development. Wu and his team found that mature pollen expresses more young genes than any other tested tissue (a finding consistent with other studies). Interestingly, perhaps strangely, the team found that new genes are more likely to be expressed in the vegetative nucleus than in the sperm cells in a pollen grain. (Mature pollen is composed of three cells: One vegetative nucleus and two sperm cells.) The sperm cells are the parental cells in a pollen grain, contributing DNA to the next generation. The vegetative nucleus is important for fertilization as it helps grow the pollen tube to transport the male gamete cells. “We expected that vegetative nucleus cells could not be the source of new genes if they do not contribute to the next generation of individuals,” says Wu. “Genes originating in these cells would be dead-ends, the same as if they duplicated in somatic cells of animals. […] It is paradoxical that new genes are more likely generated from the VN that does not contribute DNA directly to the progeny.” For some plant geneticists, however, the phenomenon does not seem quite so strange. “If it helps the pollen grow and fertilize then it’ll be an advantage,” says Jeff Bennetzen, who studies the genome structure and evolution of plants at the University of Georgia. “I don’t find it as paradoxical as they do. Pollen growth and pollen fertilization is under as much selection as anything else.” A lot of genes that are not expressed in other tissues are expressed in the vegetative nucleus, Bennetzen says. Many transposable elements, the origin of many sequences that look like genes tend to be expressed in high levels in the vegetative nucleus as well. “So it’s a good place to think that selection could first work on them,” says Bennetzen, “and if they have an advantage then they persist and eventually become real genes.” Bennetzen would like to see what roles the assumed new genes play in plant development. The study, he says, is “provocative, a good starting point for investigating if theses ‘new genes’ have selectable function.” The authors write that very few of the new genes are involved in the reproductive system, instead they seem to be slanted toward adaptive responses to environmental stimuli. “There is a lot of bizarre phenomenon [in biology] challenging us to do further research,” says Long, delighted to have new questions to ponder. “When I was a grad student people who worked on plants, animals, bacteria rarely talked to each other. Today there are more and more connections identified, it helps us understand life as a total and complete unit, a whole connected one.”