Animals caring for their young, such as a lioness carrying her cub by their scruff or a matriarchal elephant herd nursing young calves, are the kinds of behavior that many would pay good money to watch on a safari. OUPblog - Academic insights for the ...
Animals caring for their young, such as a lioness carrying her cub by their scruff or a matriarchal elephant herd nursing young calves, are the kinds of behavior that many would pay good money to watch on a safari. However, fish, especially father fish, caring for their young has received limited popular attention, except maybe for the clownfish father-son duo featured in Finding Nemo. Findings published in the recent article “Parental care drives the evolution of male reproductive accessory glands across ray-finned fishes” in the journal Evolution by a group of scientists in Canada shed new light on the evolution of fish paternal care. Lucas Eckert (McGill University), along with his co-advisors Ben Bolker and Sigal Balshine (both at McMaster University) and their co-authors Jessica Miller and John Fitzpatrick, show that, among ray-finned fish, species in which fathers look after young evolved reproductive accessory organs six times faster than those without male care.
Ray-finned fish, bony fish with webbed fins supported by thin, long rays of bone, represent the vast majority of known fish species. Some of these species have reproductive accessory organs, which are parts analogous to prostate glands in humans. These organs are not directly involved in producing gametes, but they optimize reproductive potential through functions such as sperm storage and nourishment. They also produce fluids that increase the ability of sperm to move and fertilize eggs. Research on how these glands evolved has focused mostly on mammals and insects, with little known about their evolution in fish.
“Accessory reproductive glands are a bit of a ‘mystery organ’ when it comes to fish”, says Dr. Sigal Balshine, fish behavioral ecologist and co-principal investigator of this study. “Some fish have them while some don’t have them at all. We know of their existence only in a very few species out of nearly 30,000 fish species in the world. Even when they are present, accessory reproductive glands show bizarre diversity which has always made me think that there must be interesting evolutionary drivers shaping them. There was a lot we didn’t know regarding how or when they evolved, which is why we started collecting data on them”.
In certain groups of animals, sperms of multiple males compete to fertilize the eggs of a single female, a scenario known as sperm competition. Accessory glands produce secretions that enhance sperm performance, and scientists have long believed that they evolved as a weapon to aid in this post-copulatory war in organisms such as rodents and insects. Most fish biologists assumed fish reproductive accessory glands followed the same evolutionary trend. However, in their study, Eckert and colleagues shift the focus away from sperm competition towards parental care. These authors reconstruct the evolutionary history of reproductive accessory organs, testing whether parental care and/or mate competition among males contributed to their evolution.
“There was evidence that these organs were super important in the species that have them, in securing reproductive success and fitness through a variety of functions. In that context, when some species have them and some don’t, the most obvious question was what were the drivers that selected for their evolution in the first place.” says Lucas Eckert, PhD student and lead author of the study, and one of the many students who have been collecting these data since 2017.
The team approaches this question using a quantitative synthesis of phylogenetic, morphological, and behavioral trait data of ray-finned fish collected from published databases. A plethora of published research data is available on reproductive traits of fishes, owing to their remarkable diversity in reproductive organs and behaviors. However, previous studies mostly only describe these traits, without formally testing any hypotheses regarding their evolution. In this study, the authors compile reproductive trait data for over 600 fish species from research conducted over many decades, to quantify the influence that sperm competition and parental care have had in shaping the accessory glands.
In this study, we have been able to put existing data and methods together in ways that they have not been connected before”, says Dr. Ben Bolker, mathematical biologist and co-principal investigator of the study. “This study has been able to find ways to ask the question and find, how much sperm competition and parental care contribute to the evolution of accessory reproductive organs of ray-finned fish, rather than ask what exactly caused accessory glands to evolve, because in biology everything does everything”.
Left: Upside-down round goby (Neogobius melanostomus) male guarding his eggs. Photo by Sina Zarini. Right: Simplified phylogeny highlighting the main ray-finned fish groups in which accessory glands are present (red branches). Illustration by Lucas Eckert.
The special benefits accessory glands provide male fish for improving their reproductive success explains why they evolved faster in species with paternal care. Unlike in many other animal groups where mothers take care of their young, when it comes to fish, that duty was most commonly delegated to fathers by evolution: they had the resources to maximize the survival of fertilized eggs, such as territory, security and nutrition. Accessory glands produce secretions that protect fertilized eggs against microbial infections and increase sperm adhesiveness and the viable period of sperm after release. These secretions allow these stay-at-home fish dads to multi-task in keeping their sperm viable for newly spawning females even while taking care of their young and defending their nests.
Though the evolution of accessory glands is traditionally thought to be driven by sperm competition, this study uncovers a new angle on drivers of fish accessory gland evolution by considering parental care behaviors. The authors hope that these results will encourage researchers to take a closer look at these mysterious glands and consider their potential importance in the species that possess them.
Featured image: Goby eggs by Olivier Dugornay, via Wikimedia Commons (CC BY 4.0).
I often tell my students that biology has become a data-driven field. Certainly, there’s a general sense that methods related to biological sequences (that is methods in genomics and bioinformatics) have become very widespread. But what does that really mean?
To put a little flesh on those bones, I decided to look in detail at all the biology-related articles in a single issue of the journal Nature (issue 8069, the one that was current when I started). I’m focusing here on articles, representing novel peer reviewed research. By my count, 16 of the 26 papers in this issue are related to biology in one way or another. (Those 16 also include neuroscience and bio-engineering related papers).
For each of these articles I went through the methods looking for genomics and bioinformatics related approaches. I sorted what I found into a few categories. Here’s a short summary:
Four of the papers (25%) used high throughput DNA sequencing.
Four were doing phylogenetic reconstruction. (Two of these were doing both phylogenetic reconstruction and sequencing).
Four were doing RNA seq, that is high throughput sequencing of RNA to study gene expression.
Five used computational methods of sequence analysis (e.g. alignment or its derivatives).
My “other high throughput methods” category also contained five papers.
Considering all high throughput sequence-related methods together, I found that 10/16 papers fell into at least one of these categories. That is, just over 60% of biology papers in this issue were using one or another such method. Which is to say, these methods really are very common in modern research.
The papers in issue 8069 used these methods to study a huge diversity of questions. One paper used sequencing based approaches to better characterize variation in the pea plant studied by Gregor Mendel, using this to get insights into the basis of several of his traits (which had not previously been known). Another looked at deep phylogenetic relationships among eukaryotes. Still another compared patterns of methylation during development between eutherian and marsupial mammals. I could go on, but the message is that genomics and bioinformatics are used to answer many different kinds of questions.
The take-away is that these are foundational methods for modern biology. As such they should be basic training for any student interested in continuing with research in the biological sciences. This is not only so students can conduct research on their own, but also so they can understand papers they read in a deeper and more sophisticated way.
In our recent second edition of the book Concepts in Bioinformatics and Genomics, we try to balance biology, mathematics and programming, as well as build knowledge from the ground up. Topics range from RNA-Seq and genome-wide association studies to alignment and phylogenetic reconstruction. Our hope is that this approach will help students understand the research they encounter on a deeper level and prepare them to potentially participate in that enterprise.
Many criminal investigations, including “cold cases,” do not have a suspect but do have DNA evidence. In these cases, a genetic profile can be obtained from the forensic specimens at the crime scene and electronically compared to profiles listed in criminal DNA databases. If the genetic profile of a forensic specimen matches the profile of someone in the database, depending on other kinds of evidence, that individual may become the prime suspect in what was heretofore a suspect-less crime.
Searching DNA databases to identify potential suspects has become a critical part of criminal investigations ever since the FBI reported its first “cold hit” in July 1999, linking six sexual assault cases in Washington, D.C., with three sexual assault cases in Jacksonville, Florida. The match of the genetic profiles from the evidence samples with an individual in the national criminal database ultimately led to the identification and conviction of Leon Dundas.
How the statistical significance of a match obtained with a database search is presented to the jury should, in my view, be straightforward but, given the adversarial nature of our criminal justice system, remains contentious. One view is that if the profiles of the evidence and a suspect who had been identified by the database search match, then the estimated population frequency of that particular genetic profile (equivalent to the Random Match Probability in a non-database search case) is still the relevant statistic to be presented to the jury. The Random Match Probability (RMP) is an estimate of the probability that a randomly chosen individual in a given population would also match the evidence profile. The RMP is estimated as the population frequency of the specific genetic profile, which is calculated by multiplying the probabilities of a match at each individual genetic marker (the “Product Rule”).
An alternative view, often invoked by the defense, is that the size of the database should be multiplied by the RMP. For example, if the RMP is 1/100 million and the database that was searched is 1 million, this perspective argues that the number 1/100 is the one that should be presented to the jury. This calculation, however, represents the probability of getting a “hit” (match) with the database and not the probability of a coincidental match between the evidence and suspect (1/100 million), the more relevant metric for interpreting the probative significance of a DNA match. Although these arguments may seem arcane, the estimates that result from these different statistical metrics could be the difference between conviction and acquittal.
There are many different kinds of DNA databases. Ethnically defined population databases are used to calculate genotype frequencies and, thus, to estimate RMPs but are not useful for searching. The first DNA searches were of databases of convicted felons. In some jurisdictions, databases of arrestees have also been established and searched. These searches have recently been expanded to include “partial matches,” potentially implicating relatives of the individuals in the database. This strategy, known as “familial searching,” has been very effective but contentious, with discussions typically focused on the “trade-offs” between civil liberties and law enforcement. In some jurisdictions, the “trade-off” has been between two different controversial criminal database programs. In Maryland, for example, an arrestee database (albeit one specifying arraignment) was allowed but familial searching was outlawed. Familial searching has been critiqued as turning relatives of people in the database into “suspects.” A more accurate description is that these partial matches revealed by familial searching identify “persons of interest” and that they provide potential leads for investigation.
Recently, searching for partial matches in the investigation of suspect-less crimes has expanded from criminal databases to genealogy databases, as applied in the Golden State Killer case in 2018. These databases consist of genetic profiles from people seeking information about their ancestry or trying to find relatives. Genetic genealogy involves constructing a large family tree going back several generations based on the individuals identified in the database search and on genealogical records. Identifying several different individuals in the database whose profile shares a region of DNA with the evidence profile allows a family tree to be constructed. The shorter the shared region between two individuals or between the evidence and someone in the database, the more distant the relationship. This is because genetic recombination, the shuffling of DNA regions that occurs in each generation, reduces the length of shared DNA segments over time. So, in the construction of a family tree, the length of the shared region indicates how far back in time you have to go to locate the common ancestor. Tracing the descendants in this family tree who were in the area when the crime was committed identifies a set of potential suspects.
The DNA technologies used in investigative genetic genealogy (IGG) are different from those typically used in analyzing the evidence samples or the criminal database samples, which are based on around 25 short tandem repeat markers (STRs). The genotyping technology used to generate profiles in genealogy databases is based on analyzing thousands of single nucleotide polymorphisms (SNPs). With the recent implementation of Next Generation Sequencing technology to sequence the whole genome, even more informative searching for shared DNA regions can be accomplished. (Next Generation Sequencing of the whole genome is so powerful that it can now distinguish identical (monozygotic) twins!)
Investigative genetic genealogy (IGG) has completely upended the trade-offs and guidelines proposed for familial searching as well as many of the arguments. Many of the rationales justifying familial searching of criminal databases, such as the recidivism rate, and the presumed relinquishing by convicts of certain rights do not apply to genealogical databases. Also, the concerns about racial disparities in criminal databases don’t apply to these non-criminal databases either. In general, it’s very hard to draw lines in the sand when the sands are shifting so rapidly and the technology is evolving so quickly. And it is particularly difficult when dramatic successes in identifying the perpetrators of truly heinous unsolved crimes are lauded in the media, making celebrities of the forensic scientists who carried out the complex genealogical analyses that finally led to the arrest of the Golden State Killer and, shortly thereafter, to many others.
It’s still possible and desirable to set some guidelines for IGG, a complex and expensive procedure. It should be restricted to serious crimes. The profiles in the database should be restricted to those individuals who have consented to have their personal genomic data searched for law enforcement purposes. With the appropriate guidelines, the promise of DNA database searching to solve suspect-less crimes can truly transform our criminal justice system.
Claude Monet once said, “I perhaps owe having become a painter to flowers.” Perhaps he should have given bees equal credit for his occupation. Without them, the dialectical coevolutionary dance with flowers that has lasted 125 million years would not have produced the colorful landscapes he so cherished. For Darwin, it was an abominable mystery; for Monet, an endless inspiration.
Bees, like Monet, paint the landscape. Their tool kit, however, is not one of canvas, paint pigments, and brushes, but consists of special body parts and behavior. Their bodies, covered with branched hairs, trap pollen when they rub against floral anthers and transfer it to the stigma—pollination. Their visual spectrum is tuned to the color spectrum of flowers, not an adaptation of the bees to flowers but an adaptation of flowers to attract the pollinators. Insects evolved their color sensitivities long before flowering plants exploited them.
Monet’s ‘Le jardin de l’artiste à Giverny,’ 1900. Public Domain via Wikimedia Commons.
The behavioral toolkit of honey bees is expansive. Bees learn the diurnal nectar delivery rhythms of the flowers; they also learn their colors, shapes, odors, and where they are located. Honey bees are central-place foragers, meaning they have a stationary nest from which they explore their surroundings. They can travel more than 300 km2 in search of rewarding patches of flowers. To do this, they have a navigational tool kit. First, they need to know how far they have flown: an odometer. This they accomplish by measuring the optical flow that traverses the nearly 14,000 individual facets that make up their compound eyes, similar to us driving through a city and noting how much city flows by in our periphery. They calculate how far they have flown and the angle of their trajectory relative to the sun, requiring a knowledge of the sun’s location and a compass. Then they integrate the individual paths they took and determine a straight-line direction and distance from the nest. Equipped with this information, they return to the nest and tell their sisters the location of the bonanza they discovered.
Bee dance diagram. Emmanuel Boutet, CC BY-SA 2.5 via Wikimedia Commons.
Communication among honey bees is not done with airborne sounds, as they have no organs for detecting them. Information is conveyed through a dance performed by returning foragers on the vertical surface of a comb in a dark nest. New recruits gather on the comb dance floor, attend the dances, and learn the direction and distance to the patch of flowers. How they perceive the information in the dance is not known, but to us as observers, we can decipher the direction by the orientation of the dance, and the distance by timing one part of it. Because the dance is done on a vertical comb inside a dark cavity, perhaps a hollow tree or a box hive provided by a beekeeper, the forager has two challenges. First, she must perform a bit of analytical geometry and translate the angle of the food source relative to the location of the sun from a horizontal to a vertical plane, then she must represent the direction of the sun at the top of comb. This is a constant like north at the top of our topographical maps.
Walker canyon wildflowers. Mike’s Birds, CC BY-SA 2.0 via Wikimedia Commons.
Equipped with this information, recruits fly out of the nest in the direction of the resource for the distance indicated by the dance and seek the flowers. The flowers lure them in with attractive colors, shapes, odors, and sweet nectar that the bees imbibe and in the process transfer pollen onto the stigma, fertilizing the ova. The seeds develop, drop to the ground and wait until the following spring when the plants emerge and paint the fresh landscape with a kaleidoscope of colors that rivals Claude Monet.
2024’s UN climate summit in Azerbaijan is a key moment for world leaders to express their convictions and plans to address the escalating stakes of the climate crisis. This month we sat down with Genevieve Guenther—author of The Language of Climate Politics, and founder of End Climate—to discuss the current state of climate activism and how propaganda from the fossil fuel industry has shaped the discourse.
Sarah Butcher: How did you first get involved in climate change activism?
Genevieve Guenther: I got really concerned about climate change after I had a child and started to worry about what kind of world he would inherit after I died. So I utilized my training as a scholar to master the field of climate communication, while learning about climate science and economics, in the hopes of using my expertise in the political effects of language to help move our climate politics forward. Eventually I began working on The Language of Climate Politics, and while I was writing it I also founded the group End Climate Silence to help push the news media to cover climate change with the urgency it deserves.
SB: How did you come to recognize that the language people–and more importantly the media—use was having an impact on efforts to actually create change?
GG: As recently as 2018, public-opinion surveys showed that even many Democrats felt some doubt that climate change was real. I could see that this doubt tracked very neatly onto the rise of the disinformation that there was a lot of scientific “uncertainty” around the issue. (Scientists were projecting a range of possible outcomes from rising carbon emissions, but they were definitely not saying that climate change was fake.) I realized that voters had heard about this supposed uncertainty because, at the time, news outlets were platforming so-called “climate skeptics” to provide what they called “a balance of opinion” about climate change. Later I discovered that most Americans learn everything they know about climate change from the news media. So it became apparent to me that how journalists talk about climate change had, and still has, a great deal of influence over America’s climate politics!
SB: Do you have any examples of fossil-fuel propaganda that you share with people to illustrate the scope of the problem?
Guenther presented her book The Language of Climate Politics at the book’s launch event at The UN bookshop. Image courtesy of Genevieve Guenther, used with permission.
GG: Fossil-fuel propaganda is a huge phenomenon! There are many lies about climate change and clean energy floating around. You may have heard that developing off-shore wind turbines is killing whales (it isn’t), or that fossil fuels are the most reliable form of energy (they aren’t), or that focusing on your personal carbon footprint is the most important thing you can do to fight climate change (it definitely isn’t). But the propaganda I investigate in my book is the complex of lies, myths, and incorrect assumptions that create the false and dangerous belief that we can keep using coal, oil, and gas but still deal with climate change anyway. We cannot! So I expose the scientists, economists, lobbyists, and journalists who propagate this false belief, illuminating the bankruptcy of their ideas and giving readers clear, actionable messages to counter mis- and disinformation in their own conversations about climate change. Focus-group polling shows that these messages increase concerned Democrats’ and Republicans’ support for phasing out fossil fuels by up to ten points.
SB: What are the biggest misconceptions you see around fossil-fuel propaganda?
GG: That it spreads only among the uneducated or the right wing. My book shows how some scientists, economists, journalists, and even climate advocates sometimes inadvertently echo the core fossil-fuel propaganda and thereby normalize it, shaping mainstream views about climate change.
SB: What sets your book on the climate change crisis apart?
GG: I think my book is personal and accessible, but also has a real scope. I try to sort out the whole kaleidoscope of climate disinformation, so we can see and counter it clearly. The book discusses what the science says will happen to the US and the UK if we don’t phase out fossil fuels; how past economic models have low-balled climate damages and what the new economic models project for the future; the promise and challenges of climate technologies; the recent history of US and international climate politics; advice for coping with climate change emotionally and helping to build a more powerful climate movement; and more! The climate journalist Amy Westervelt said in her endorsement that the book “takes the whole overwhelming universe of fossil-fuel propaganda and distills it,” providing “one of the best explanations I’ve read of how the heck the climate crisis has gone unchecked for so long.” And Kieran Setiya, who’s not even a climate person, but a Professor of Philosophy at MIT, said: “if you want to understand the climate crisis and you only have time to read one book, this should be it.” I’m pretty proud of that, honestly.
SB: What was the most surprising thing you discovered working on this book?
GG: That China has enacted a whole-of-government, whole-of-society climate policy, called the “1 + N” policy, to achieve net-zero emissions by 2060. That was a huge surprise! I hadn’t known that China had passed comprehensive climate legislation. I don’t think many people in the West know this either. But I describe the provisions of China’s climate policies in Chapter 4, so hopefully now more people will understand the depth of China’s commitment to decarbonization.
SB: Is there anything in the current debate that gives you hope about our climate future?
GG: I try not to deal in hope. Hope keeps my focus on things I cannot control. Instead, I try to embrace what I think of as intellectual humility—I don’t know what’s going to happen politically, because no one does—and I try to accept what I take to be my duty. That is, I feel like, being alive with relative privilege at this historical moment, I have a responsibility to help resolve the climate crisis, so that at the end of the day I can say I did my best. I mean, that’s all that can be asked of us, right?
SB: What do you hope readers take away from your book?
GG: I hope they feel equipped to resist the dominant forms of climate disinformation in public discourse and feel empowered to talk about the climate crisis in ways that will focus the conversation on phasing out fossil fuels. And I hope they feel fortified and inspired to do that work!
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