Digital Commons Network^™

Identifying Plant Functional Traits To Assist Ecological Intervention In A Drying Landscape, Ana Luiza Muler

Theses: Doctorates and Masters

Mediterranean-type ecosystems (MTEs) are among the most vulnerable to land use and climate change and many attempts are in place to restore these ecosystems. Therefore, it is necessary to assess differences in plants’ ability to withstand water-stress, including biotic interactions. Such knowledge helps us understand community assembly, which is crucial for ecological intervention. This study involved: (1) reviewing the literature on traits that can differentiate functional types; (2) adapting the methodology to measure leaf water potential at turgor loss point (πtlp) for small-leaved species; (3) using these traits to quickly identify water-use strategies of adult …

Permanent Slides For Morphological Studies Of Small Crustaceans: Serban's Method And Its Variation Applied On Bathynellacea (Malacostraca), Giulia Perina, Ana I. Camacho

Research outputs 2014 to 2021

Morphological studies of small invertebrates often involve the preparation of slides to observe minute body parts under a compound microscope. Preparation should facilitate observation, through traditional optical microscopy, of small surface structures on different planes, like pores, spines and setae. Various methods and techniques, using different mounting media that specialists have adopted to observe and preserve small crustaceans, have their advantages and disadvantages.Within the order Bathynellacea, specimens in the family Bathynellidae are particularly challenging due to their small size (0.5 to 2.25 mm body length) and very delicate exoskeleton, which tends to be completely digested when using common clearing mounting …

Asal Usul Formasi Savana: Tinjauan Dari Nusa Tenggara Timur Dan Hasil Penelitian Di Baluran Jawa Timur [Origin Of Savanna Formation: Literature Review From East Nusa Tenggara And Research Results From Baluran East Java Indonesia], Sutomo

Research outputs 2014 to 2021

Savannas are ecosystems mostly confined to tropical and subtropical regions that are characterized by a continuous cover of C₄ grasses that have different characteristics based on seasonality and where woody plants are also an important feature, but with sparse cover and no closed canopy. This is common formation in the driest part of Indonesia such as East Nusa Tenggara, however savana can also be found in Java Island: Baluran Savanna in East Java. There has been considerable amount of debat among scientists, botanists in Indonesia regarding the origin of Indonesian savanna. Using literature study and also field observation at …

Small Unmanned Aerial Vehicles (Micro-Uavs, Drones) In Plant Ecology, Mitchell B. Cruzan, Ben G. Weinstein, Monica R. Grasty, Brendan F. Kohrn, Elizabeth C. Hendrickson, Tina M. Arredondo, Pamela G. Thompson

Biology Faculty Publications and Presentations

Premise of the study: Low-elevation surveys with small aerial drones (micro–unmanned aerial vehicles [UAVs]) may be used for a wide variety of applications in plant ecology, including mapping vegetation over small- to medium-sized regions. We provide an overview of methods and procedures for conducting surveys and illustrate some of these applications.

Methods: Aerial images were obtained by flying a small drone along transects over the area of interest. Images were used to create a composite image (orthomosaic) and a digital surface model (DSM). Vegetation classification was conducted manually and using an automated routine. Coverage of an individual species …

Evaluating Brandt’S Cormorant (Phalacrocorax Penicillatus) Reproductive Success: Effects Of Parental Care Behaviors And Estimating Individual Chick Survival, Shannon Murphy

Cal Poly Humboldt theses and projects

Variation in reproductive success is widely measured in seabird biology in an effort to indicate changes in the marine environment, or understand basic questions about ecology or conservation of seabirds. When variation in seabird reproductive success is suggested to indicate changes in the marine environment without identifying the proximate causes of such variation, inference is limited to association, and the proximate causes themselves could prove more effective as indicators. My study informs this problem by examining and quantifying proximate causes of variation in reproductive success, at the level of nests and individual chicks.

I used video of Brandt’s Cormorant ( …

Genetic Structure And Connectivity Of The Endangered Giant Kangaroo Rat (Dipodomys Ingens) In A Heterogeneous Environment, Nathan Alexander

Cal Poly Humboldt theses and projects

Movement ecology and dispersal are important aspects of species’ life histories that can inform conservation and management. Dispersal is often cryptic and difficult to detect, but recent advances genetic technology and applications have provided new approaches to identifying and describing dispersal patterns. Giant kangaroo rats (Dipodomys ingens) are an endangered heteromyid that appear to persist in small subpopulations in a heterogeneous environment of their northern range, the Ciervo-Panoche Natural Area, California. Previous work suggested high levels of genetic diversity between populations with genetic distances not being correlated to geographic distances. Here, I identified landscape population structure through clustering …

Early Seral Mixed-Conifer Forest Structure And Composition Following A Wildfire Reburn In The Sierra Nevada, Erin Alvey

Cal Poly Humboldt theses and projects

Before the era of modern fire suppression, California’s northern Sierra Nevada mixed-conifer and yellow pine forests were self-regulating; recurring short-interval, low-mixed severity wildfires maintained forest structure and composition, which in turn exerted bottom-up controls on subsequent wildfires. As a result of fire suppression, and coupled with the effects of climate warming and other anthropogenic disturbances, the fundamental structure of mixed-conifer and yellow pine forests has shifted. Wildfires may now be increasing in size, severity, and frequency across western North America. However, little is known about the post-fire impacts of repeat wildfire on a forest after a long era of suppression. …

Juvenile Survival And Adult Return As A Function Of Freshwater Rearing Life History For Coho Salmon In The Klamath River Basin, Molly Gorman

Cal Poly Humboldt theses and projects

The Scott and Shasta rivers, Klamath River tributaries, experience spatial disparity in habitat quality in spring and summer as a result of historical and current land-use. Juvenile Coho Salmon (Oncorhynchus kisutch) born in the upper tributary reaches often rear in natal streams before migrating to sea. However, those born in the lower reaches often encounter unsuitable habitat and emigrate during their first spring to seek non-natal rearing habitats. It is assumed that these early outmigrants are population losses. This study evaluated first-summer survival, and contribution to the adult population, of non-natal rearing juveniles in the Klamath River Basin. …

Effects Of Stream Degradation On Ecosystem Function Are Mediated By Local Microbial And Macroinvertebrate Leaf Litter Processing, Carla Rothenbuecher

Murray State Theses and Dissertations

Riparian areas are fundamental to aquatic ecosystems by regulating temperature and light regimes, and providing allochthonous subsidies critical to the survival of aquatic and terrestrial species. On a global scale, increased rates of anthropogenic disturbance from agricultural activities and urbanization have caused the degradation of aquatic habitats. As a result, billions of dollars have been spent on stream restoration projects to protect aquatic resources; however, fundamental ecosystem processes like litter decomposition are rarely addressed. We conducted a litterbag experiment in a degraded high desert stream proposed for large-scale restoration to test the effects of reach location, canopy cover, and temperature …

Predicting The Impact Of Future Climate On Ecologically Important Macroalgae, Charlie Phelps

Theses: Doctorates and Masters

Macroalgae play an important role in coastal reef systems and are often referred to as ecosystem engineers. They serve as primary producers, supporting a diverse range of organisms, and are a sink for atmospheric CO2. Water acidification and ocean warming caused by anthropogenic activities are affecting many marine flora and fauna, potentially impacting the physical and chemical performance of macroalgae and the consumption rates of associated herbivores. Many studies have focused on ocean acidification or ocean warming individually but there is an overall lack of research investigating the combined effects and the ensuing repercussions on consumer-prey relationships.

Three species of …

Why Fish Do Not Feel Pain, Brian Key

Animal Sentience

Only humans can report feeling pain. In contrast, pain in animals is typically inferred on the basis of nonverbal behaviour. Unfortunately, these behavioural data can be problematic when the reliability and validity of the behavioural tests are questionable. The thesis proposed here is based on the bioengineering principle that structure determines function. Basic functional homologies can be mapped to structural homologies across a broad spectrum of vertebrate species. For example, olfaction depends on olfactory glomeruli in the olfactory bulbs of the forebrain, visual orientation responses depend on the laminated optic tectum in the midbrain, and locomotion depends on pattern generators …

Why Human Pain Can’T Tell Us Whether Fish Feel Pain, Victoria A. Braithwaite, Paula Droege

Animal Sentience

In his target article, Key (2016) reviews the neuroanatomy of human pain and uses what is known about human pain to argue that fish cannot experience pain. We provide three reasons why the conclusions reached by Key are unsupported. They consider (i) why it is not sufficient to conclude that only human neural structures can process conscious pain, (ii) why an understanding of pain in humans and non-human animals needs to be based within a framework of consciousness, and (iii) evidence already exists that fish treated with noxious stimuli lose the ability to perform normal behaviours: This was a behavioral …

Comparative Evolutionary Approach To Pain Perception In Fishes, Culum Brown

Animal Sentience

Arguments against the fact that fish feel pain repeatedly appear even in the face of growing evidence that they do. The standards used to judge pain perception keep moving as the hurdles are repeatedly cleared by novel research findings. There is undoubtedly a vested commercial interest in proving that fish do not feel pain, so the topic has a half-life well past its due date. Key (2016) reiterates previous perspectives on this topic characterised by a black-or-white view that is based on the proposed role of the human cortex in pain perception. I argue that this is incongruent with our …

Could Fish Feel Pain? A Wider Perspective, Yew-Kwang Ng

Animal Sentience

Key’s (2016) target article provides some strong arguments but also makes some logical mistakes. The arguments are not sufficient to support a definite conclusion that fish cannot feel pain. A multi-faceted perspective taking into account brain structure, chemical secretion in brain, animal behavior, and evolutionary biology may be useful and appears, at least in some aspects, to suggest the opposite conclusion from that of the target article.

Should Fish Feel Pain? A Plant Perspective, František Baluška

Animal Sentience

Key (2016) claims fish that fish do not feel pain because they lack the necessary neuronal architecture: their responses to noxious stimuli, according to Key, are executed automatically without any feelings. However, as pointed out by many of his commentators, this conclusion is not convincing. Plants might provide some clues. Plants are not usually thought to be very active behaviorally, but the evidence suggests otherwise. Moreover, in stressful situations, plants produce numerous chemicals that have painkilling and anesthetic properties. Finally, plants, when treated with anesthetics, cannot execute active behaviors such as touch-induced leaf movements or rapid trap closures after localizing …

Fish Lack The Brains And The Psychology For Pain, Stuart W.G. Derbyshire

Animal Sentience

Debate about the possibility of fish pain focuses largely on the fish’s lack of the cortex considered necessary for generating pain. That view is appealing because it avoids relatively abstract debate about the nature of pain experience and subjectivity. Unfortunately, however, that debate cannot be entirely avoided. Subcortical circuits in the fish might support an immediate, raw, “pain” experience. The necessity of the cortex only becomes obvious when considering pain as an explicitly felt subjective experience. Attributing pain to fish only seems absurd when pain is considered as a state of explicit knowing.

Brain Processes For “Good” And “Bad” Feelings: How Far Back In Evolution?, Jaak Panksepp

Animal Sentience

The question of whether fish can experience pain or any other feelings can only be resolved by neurobiologically targeted experiments. This commentary summarizes why this is essential for resolving scientific debates about consciousness in other animals, and offers specific experiments that need to be done: (i) those that evaluate the rewarding and punishing effects of specific brain regions and systems (for instance, with deep-brain stimulation); (ii) those that evaluate the capacity of animals to regulate their affective states; and (iii) those that have direct implications for human affective feelings, with specific predictions — for instance, the development of new treatments …

Why Babies Do Not Feel Pain, Or: How Structure-Derived Functional Interpretations Can Go Wrong, Helmut Segner

Animal Sentience

The response to pain involves a non-conscious, reflexive action and a conscious perception. According to Key (2016), consciousness — and thus pain perception — depends on a neuronal correlate that has a “unique neural architecture” as realized in the human cortex. On the basis of the “bioengineering principle that structure determines function,” Key (2016) concludes that animal species such as fish, which lack the requisite cortex-like neuroanatomical structure, are unable to feel pain. This commentary argues that the relationship between brain structure and brain function is less straightforward than suggested in Key’s target article.

Anthropomorphic Denial Of Fish Pain, Lynne U. Sneddon, Matthew C. Leach

Animal Sentience

Key (2016) affirms that we do not know how the fish brain processes pain but denies — because fish lack a human-like cortex — that fish can feel pain. He affirms that birds, like fish, have a singly-laminated cortex and that the structure of the bird brain is quite different from that of the human brain, yet he does not deny that birds can feel pain. In this commentary we describe how Key cites studies that substantiate mammalian pain but discounts the same kind of data as evidence of fish pain. We suggest that Key's interpretations are illogical, do not …

Fish Pain: An Inconvenient Truth, Culum Brown

Animal Sentience

Whether fish feel pain is a hot political topic. The consequences of our denial are huge given the billions of fish that are slaughtered annually for human consumption. The economic costs of changing our commercial fishery harvest practices are also likely to be great. Key outlines a structure-function analogy of pain in humans, tries to force that template on the rest of the vertebrate kingdom, and fails. His target article has so far elicited 34 commentaries from scientific experts from a broad range of disciplines; only three of these support his position. The broad consensus from the scientific community is …

Fish Pain: A Painful Topic, Carl Safina

Animal Sentience

If fish cannot feel pain, why do stingrays have purely defensive tail spines that deliver venom? Stingrays’ ancestral predators are fish. And why do many fishes possess defensive fin spines, some also with venom that produces pain in humans? These things did not evolve just in case sentient humans would evolve millions of years later and then invent scuba. If fish react purely unconsciously to “noxious” stimuli, why aren’t sharp jabbing spines enough? Why also stinging venom?

How Welfare Biology And Commonsense May Help To Reduce Animal Suffering, Yew-Kwang Ng

Animal Sentience

Welfare biology is the study of the welfare of living things. Welfare is net happiness (enjoyment minus suffering). Since this necessarily involves feelings, Dawkins (2014) has suggested that animal welfare science may face a paradox, because feelings are very difficult to study. The following paper provides an explanation for how welfare biology could help to reduce this paradox by answering some difficult questions regarding animal welfare. Simple means based on commonsense could reduce animal suffering enormously at low or even negative costs to humans. Ways to increase the influence of animal welfare advocates are also discussed, focusing initially on farmed …

Death In The Family, Maria Botero

Animal Sentience

Barbara King presents grief as the result of the capacity of human and non-human animals for social and affectionate bonds. This is a novel approach that provides a context for interpreting behavioral evidence of grief. The book also offers thought-provoking insights into the relationship between emotion and the expression of emotion. The most surprising element of King’s approach is that, throughout the book, her account of non-human animal grief forces us to reassess the way we treat them.

Modulation Of Behavior In Communicating Emotion, Martin Gardiner

Animal Sentience

King discusses many examples where two animals, as they bond, behave in ways we interpret as expressing love for one another. If one of the bonded animals then dies, signs of loving are replaced by signs we interpret as expressing grief by the animal who remains. I propose a pathway for emotional communication between an animal and an observer that can have a central role in these and other observations by King and in our overall ability to interpret observed behavior in relation to emotion. This pathway provides evidence of emotion in an observed animal by communicating evidence of emotion’s …

Considering Animals’ Feelings: Précis Of Sentience And Animal Welfare (Broom 2014), Donald M. Broom

Animal Sentience

The concept of sentience concerns the capacity to have feelings. There is evidence for sophisticated cognitive concepts and for both positive and negative feelings in a wide range of nonhuman animals. All vertebrates, including fish, as well as some molluscs and decapod crustaceans have pain systems. Most people today consider that their moral obligations extend to many animal species. Moral decisions about abortion, euthanasia, and the various ways we protect animals should take into account the research findings about sentience. In addition, all animal life should be respected and studies of the welfare of even the simplest invertebrate animals should …

Animal Sentience: The Other-Minds Problem, Stevan Harnad

Animal Sentience

The only feelings we can feel are our own. When it comes to the feelings of others, we can only infer them, based on their behavior — unless they tell us. This is the “other-minds problem.” Within our own species, thanks to language, this problem arises only for states in which people cannot speak (infancy, aphasia, sleep, anaesthesia, coma). Our species also has a uniquely powerful empathic or “mind-reading” capacity: We can (sometimes) perceive from the behavior of others when they are in states like our own. Our inferences have also been systematized and operationalized in biobehavioral science …

The Interrelationships Of Placental Mammals And The Limits Of Phylogenetic Inference, James E. Tarver, Mario Dos Reis, Siavash Mirarab, Raymond J. J. Moran, Sean Parker, Joseph E. O'Reilly, Benjamin L. King, Mary J. O'Connell, Robert J. Asher, Tandy Warnow, Kevin J. Peterson, Philip C.J. Donoghue, Davide Pisani

Dartmouth Scholarship

Placental mammals comprise three principal clades: Afrotheria (e.g., elephants and tenrecs), Xenarthra (e.g., armadillos and sloths), and Boreoeutheria (all other placental mammals), the relationships among which are the subject of controversy and a touchstone for debate on the limits of phylogenetic inference. Previous analyses have found support for all three hypotheses, leading some to conclude that this phylogenetic problem might be impossible to resolve due to the compounded effects of incomplete lineage sorting (ILS) and a rapid radiation. Here we show, using a genome scale nucleotide data set, microRNAs, and the reanalysis of the three largest previously published amino acid …

Vestigial Serrula In Scorpion Genera Paravaejovis, , Smeringurus And Vejovoidus (Scorpiones: Vaejovidae), Victor Fet, Michael E. Soleglad, Michael S. Brewer, David P. A. Neff, Michael L. Norton

Euscorpius

The presence of vestigial serrula on the ventral edge of the cheliceral movable finger is established for vaejovid genera Paravaejovis, Paruroctonus, Smeringurus, and Vejovoidus. Detailed descriptions and SEM images illustrating the various manifestations of this interesting cheliceral structure are provided for many species of these four genera. A brief systematic overview of this structure as it exists in Recent scorpions is also presented.

Serrula In Retrospect: A Historical Look At Scorpion Literature (Scorpiones: Orthosterni), Matthew R. Graham, Victor Fet

Euscorpius

Serrula, a small comb-like structure on the ventral aspect of cheliceral movable finger in scorpions, has often been overlooked or ignored. Scorpion genera that are currently known to possess serrula belong to six families: Chactidae, Euscorpiidae, Iuridae, Pseudochactidae, Superstitioniidae, and Vaejovidae. All relevant literature on scorpion serrula is reviewed, and serrula of representative scorpion taxa is illustrated by SEM images. We suggest that the inconsistency in reporting serrula is based on several factors (or combination thereof): (a) serrula tines can quite often be broken off partially or completely, especially in adults; (b) serrula can be vestigial and hardly visible under …

On The Poorly Known Genus Mesotityus González-Sponga, 1981 (Scorpiones: Buthidae), Luis F. De Armas, Fernando J. M. Rojas-Runjaic

Euscorpius

Examination of new available material (18 females and six males) of the rare Venezuelan scorpion Mesotityus vondangeli González-Sponga, 1981 (Buthidae) demonstrated that there are consistent taxonomic characters to consider it as a genus different from Tityus C. L. Koch, 1836 sensu stricto. Nevertheless, it shares important characters with species of the Tityus clathratus group (=subgenus Archaeotityus Lourenço, 2006). An emended diagnosis of Mesotityus is given, as well as data on natural history, meristic and morphometric variation.