What the Fish? Episode 15: Exploring Collection-Based Research

Episode 15: Exploring Collection-Based Research

In our last episode, we discussed the role of collection data for scientific investigation. In this episode, we explore the value of the research on museum specimens and artifacts themselves, focusing on the use of specimen examination and evolutionary hypotheses to better explain the natural world. To help us discuss this topic, we are pleased to be joined by Dr. Peter Makovicky, The Field Museum's own Curator of Dinosaurs and Chair of the Department of Geology. Phylogenies (a hypothesis of how life is related evolutionarily) are crucial for predicting the distribution of incompletely studied organismal characteristics ranging from the presence of venom in fishes, to feathers on dinosaurs, or how the anatomy of eyes change in the deep sea as a result of selective pressures. In other words, knowledge of the evolutionary relationships of life allows for effective predictions about the unstudied characteristics of species. Museum collections are a critical component of this work, from the initial collection of samples used to infer our hypotheses of how life is related (e.g., whole specimens, tissues used to extract DNA for genetic work) to our ability of accessing this material again to test and explore evolutionary hypotheses.

An example of the biological questions we can explore in this manner is tracing the evolution of venomous fishes. By looking at venomous fishes from an evolutionary perspective, we generated a much more accurate picture of fish venom evolution than was previously suggested using a strictly observational approach. To explore venom evolution, we began by taking a major stab at the fish tree of life by analyzing all suborders and known venomous groups of spiny-rayed (Acanthomorpha) fishes for the first time. Using the resulting family tree of fishes as a framework, we mapped the species that were known to be venomous on to this DNA-based tree. This provided an initial estimate of how many times venom evolved and allowed us to predict which fish species beyond the "knowns" should be venomous or could possibly be venomous. To test these predictions, we explored the museum collections and dissected scores of specimens to look at the detailed anatomy of fish venom glands and clarify how many times venom evolved on the fish tree of life. By working our way down the fish tree of life by comparing ever more distantly related fishes from the known venomous fishes, we could pinpoint the number of times venom evolved, the exact groups of fishes that are venomous, and revise the identity of venomous fishes. This type of research is occurring world wide based on the collections at The Field Museum, and similar institutions that house, maintain, and allow access to museum specimens for scientific research. This example is just one of the many stories surrounding research done at The Field Museum with collection-based research.

What the Fish? Episode 14: The Value and Role of Collection Data

Field Museum Collection Data

In previous What the Fish? podcasts, we have covered topics ranging from what makes a fish a fish to aquatic bioluminescence and sensory systems.  We have augmented these fishy topics with discussions surrounding the role scientists play in developing content for museum exhibits and the excitement, hardships, and discoveries made during fieldwork.  Herein, we present the first part of our What the Fish? collections-based research episodes exploring the value and role of Museum collections and their associated data in scientific investigation. To help us discuss the topic of the analysis of collections data, we are joined by Hannah Owens who is a doctoral candidate at The University of Kansas. Hannah combines museum collections data, fisheries data, and ecological data to explore the role of climate change in the evolutionary history and the biogeography of fishes. Hannah's research combines ecological niche, macroevolution, and climate data to explore the "fish stick" fishes or cods, hakes, and relatives from the order Gadiformes.  

What are collection data, and why are they useful?

When ichthyologists conduct their fieldwork, they collect much more than the specimens themselves.  Fish biologists minimally collect geographic (e.g., latitude and longitude) and temporal (date and time) data, but they frequently collect habitat information, depth, salinity, temperature, visibility, and a wealth of other ecological data that are databased along with the specimen identification and information in databases such as those at The Field Museum.  Individually, these records are valuable for ichthyologists interested in the distribution or biogeography of particular species, but when taken in aggregate (e.g., through pooled resources such as GBIF) these data can be explored in "meta-analysis" that can inform countless ecological and evolutionary studies. For example, predictive modeling of organismal distributions has brought these data together to better predict the expansion of introduced species, to predict the potential presence of animals or plants in unexplored regions, and to test for the impacts of climate change. These predictions and analyses are only going to become more critical as species continue to be introduced, species distributions continue to shrink toward extinction, fieldwork becomes more difficult, or large-scale climate change becomes increasingly studied. These collection data, based on well-curated specimens, are the only verifiable data that can be brought to bear on these questions. Distributional data that lack preserved specimens (vouchers) can always be questioned at a later date because the species identifications cannot be reassessed. This same value in being able to reassess species identifications based on whole-specimen vouchers is equally important for genetic or DNA-based research where the discovery of cryptic species (morphologically similar species representing  diagnosable and genetically different forms) is a frequent occurrence.  In cases where there are no voucher specimens to examine, researchers are required to return to the field to corroborate their molecular hypotheses.  These are just a few of the cases where specimens and their associated data have contributions well beyond ecology and evolutionary biology.  Listen to the podcast to learn additional examples! 

What the Fish? Episode 13: Exploring Fish Evolution on the Tree of Life

Piecing Together the Mysteries of the Fish Tree of Life

One of the primary reasons that we here at What the Fish? are fascinated with the evolutionary history of life on Earth is that it provides a context and scientific hypothesis from which we can further study the wonderful biodiversity of fishes. For example, if we have a working scientific hypothesis of how different species of clownfishes are related to one another, we can address questions surronding the number of times clownfishes have formed symbiotic relationships with anemones. But how do we build these evolutionary trees of fishes, such as the one seen below? Well there are various different kinds of scientific data that can be used to infer evolutionary relationships through time (e.g. variation in the sequence of DNA/genes, anatomical features, behavioral traits) that scientists around the world collect in order to support these hypotheses. Shared anatomical characteristics, such as the position of a spiny-rayed dorsal fin, may be indicative of common evolutionary ancestry, and scientists use this evidence to produce hypotheses regarding the evolution of life on Earth.

What the Fish? Episode 11: Feeding Frenzy

You Are What You Eat

Among fishes, the different types of food and the ways in which they are consumed are as incredibly varied as the fishes themselves. Some fishes are vegetarians, including the Piranha relative the Pacu, while others are ferocious carnivores, such as the African Tiger Fish. Fishes often have very specilized dentition and feeding structures depending on their source of food. For example, fishes that crush hard crustacean shells may have large boulder-like teeth. Filter feeding fishes, such as the Whale Shark seen below, have evolved fine filamentous structures to help sift through plankton. Overall, fishes eat almost anything you might find in an aquatic environment, and they do so efficiently!

What the Fish? Episode 6: Tales from the Field

2.5 million specimens don't collect themselves!

The Field Museum's Division of Fishes houses approximately 2.5 million specimens of fish, including whole specimens in alcohol, skeletal specimens, tissue samples, and cleared and stained material. That is a lot of fishes! But the fishes did not just arrive overnight; scientists and researchers have been adding to the collection at The Field Museum since 1894. 

Museum collections serve as records of the natural world, as well as critical resources for scientists wanting to study the biodiversity of the planet. The fishes collection has grown through continued fieldwork by ichthyologists that use a vast array of tools and strategies for sampling living and extinct fishes from around the world. Tune into our podcast this week with a special paleoichthyological guest, Sarah Gibson of the University of Kansas. Listen to us as we discuss the many different ways we collect fishes in the field.

What The Fish? Episode 5: Shark Week 2012

The allure of sharks

Sharks, and cartilaginous fishes in general, have long mesmerized scientists and the public alike. They are fascinating creatures!  Fossil remains indicate that sharks have been evolving on this planet for well over 400 million years. They have been described in popular culture as "perfect killing machines," and it is hard to argue with their abilities to hunt and secure prey of all shapes and sizes. Be it the incredible filter-feeding of the immense Whale and Basking sharks or the pure power and incredible bite of the Great White Shark, few organisms in nature portray an aura of such efficiency. Sharks are among the earliest known jawed-vertebrate lineages, and since their initial evolution, they have wasted no time in putting those jaws to work. After 400 million years they still remain some of the oceans most incredible predators with no signs of slowing down. 

Sharks are venomous and bioluminescent?

However, there are more to sharks then just teeth! A number of lineages have independently evolved venom, including the horn sharks and angel sharks. The horn sharks release venom out of spines that stick out from each of their dorsal fins, making them an unattractive meal for even larger predatory fishes. The spines of the dorsal fins in some squaliform (or dogfish sharks) are also known to be venomous, including species within the lanternsharks. Sharks have also independently evolved bioluminescence, the ability to generate and emit light, as they have invaded the deep sea. These include predominantly deep-sea taxa, such as the lanternsharks and the bizarre Cookie Cutter Shark that sucks on to prey and rips off hunks of flesh before speeding away. These deep-sea sharks all use bioluminescence to hide from potential prey items, to avoid being eaten themselves, and for communication.

What the Fish? Episode 4: Sneaker Males Are my Anemone

To milt or not to milt?

For most fishes, reproduction involves eggs and milting, which is like crop-dusting with sex cells (aka gametes). The vast majority of fishes are oviparous, which means they lay eggs that are fertilized and develop outside the mother's body. In these situations, males typically milt, which is the release and spreading of their gametes, onto the eggs that have been deposited in the environment. In ovoviviparous fishes, the eggs develop inside the body of the mother, and male gametes have to be passed into the females’ body through specialized structures, such as claspers (modified pelvic fins) in sharks or gonopodiums (modified anal fins) in guppies. Live birth (viviparity) has also evolved in a number of lineages of fishes, including sharks, guppies, and rockfishes. In viviparous fishes, the young develop within the mothers’ body.

Male, female, or both?

While most fishes have separate sexes, a number of lineages are simultaneous or sex-switching hermaphrodites. Some fishes, such as clownfishes, can change their sex once during their lifetimes either from female to male, or male to female depending on environmental and/or behavior scenarios. A small number of fish species are simultaneous hermaphrodites capable of producing both male and female gametes at the same time (e.g., lancetfish, some species of moray eels as seen above). Scientific studies have identified that at least some of these species (e.g., the mangrove killifish Kryptolebias marmoratus) are capable of self-fertilization!

What the Fish? Episode 3: You Light Up my Life

How does a fish make light?

Bioluminescence, the production and emission of light from a living creature, is widespread among different groups of marine fishes (e.g., anglerfishes, flashlight fishes, dragonfishes). Most organisms produce light through a chemical reaction between luciferin (a small molecule) and oxygen. The enzyme luciferase speeds up this reaction, resulting in the production of light. But unlike the incandescent lightbulbs in your home, this light gives off almost no heat. Some fish species have the ability to produce the chemical compounds necessary for bioluminescence themselves (such as lanternfishes), while others rely on symbiotic bacteria to create and generate light (including the beloved anglerfish in our logo).

Why would a fish want to make light?

The majority of bioluminescent fishes are found in the deep sea. Below 1,000 meters there is no visible sunlight in the ocean. As a result, many organisms that live below this depth have evolved bioluminescent structures, and fishes use this light in a variety of ways. Some fishes use light for camouflage, specifically counterillumination.  This is where the fish emits light around its belly to match any light coming from overhead, making it invisible to predators looking upwards for shadows in the water column. Others use light to attract and catch prey, such as the beckoning luminescent lure of the anglerfish. Fishes will even use light for communication in order to recognize each other in the darkness of the deep or to communicate with potential breeding partners.

What the Fish? Episode 2: Smells Like Freshwater Eels

Fishes have the five major human senses

Fishes use the same five major senses that all humans have: hearing, sight, smell, taste, and touch.  But for fishes, all of these senses differ somewhat from our normal day-to-day experience. 

Quite simply, living in a liquid environment is a very different thing than living in a gas (air) environment.  Think about the difference between smell and taste.  At some level tasting is like smelling wet things.  How different are these senses when you are already wet or underwater?  From an evolutionary or anatomical perspective, they do have fundamental, different origins and innervations, but because of their aquatic lifestyle these senses have more overlap in fishes when compared to humans.  Given this similarity, one of the most striking differences is that fishes actually cover various parts of their bodies (ranging from their skin to specialized barbels, whiskers, or fin rays) with taste buds rather than just focusing on the tongue like we do.  The whiskers of a catfish, like the one shown here, allow these fishes to taste the mud that they are digging around in.  Would you want to drag your tongue around in the mud?  We wouldn’t either.

Did you say seven senses?

Humans actually have more than five senses.  For example, we have sensors for balance, temperature, and pain, but the five main senses dominate our daily lives and take up more relative sensory area in our brains. Fishes have two other major senses that are not found among the senses we experience: electroreception and mechanoreception (or distance touch).  Electroreception is less common among fishes, but it is comparatively easy to grasp. This electro-sensitive system is much like a beach comber searching a sandy beach for valuable metals.  Fishes use this system for a variety of reasons, but many fishes use this sense for hunting or gathering.  A hammerhead shark or paddlefish will move the enlarged regions of their heads to search for small electrical signals in the water coming from animals respiring or moving.  Specifically, fishes respiring underwater produce a small ionic charge that will stimulate electroreceptors, which allows a predator to find a sand dab or sea robin buried under the sand.

Mechanoreception is the sensory system that allows fishes to school, fishes to measure the surrounding current to hold their position in a moving stream, and fishes in the dark (e.g., deep-sea or caves) to find cave walls or rocky outcroppings. This is carried out by particular hair cells that are housed in a series of tubed scales along the side of a fish, found on the surface “pit organs” that cover the skin of some fishes, and distributed within bony canals in the head of a fish.  These specialized hair cells or neuromasts are stimulated (bent/displaced) by the change in motion of water over the structures.  This bending of the hairs in particular directions tells the fish that their schooling partners are changing direction or that a shark is quickly approaching, hence its common name of distance touch.  If you are like us, you wish that you had these other wonderful vertebrate senses; but alas, they only work when you live underwater…