Ecology and Evolutionary Biology Commons^™

Embryonic Origin And Genetic Basis Of Cave Associated Phenotypes In The Isopod Crustacean Asellus Aquaticus., Hafasa Mojaddidi, Franco E Fernandez, Priscilla A Erickson, Meredith E. Protas

Meredith Protas

Characteristics common to animals living in subterranean environments include the reduction or absence of eyes, lessened pigmentation and enhanced sensory systems. How these characteristics have evolved is poorly understood for the majority of cave dwelling species. In order to understand the evolution of these changes, this study uses an invertebrate model system, the freshwater isopod crustacean, Asellus aquaticus, to examine whether adult differences between cave and surface dwelling individuals first appear during embryonic development. We hypothesized that antennal elaboration, as well as eye reduction and pigment loss, would be apparent during embryonic development. We found that differences in pigmentation, eye …

Policing A Negotiated World: A Partial Test Of Klinger’S Ecological Theory Of Policing, Christopher Salvatore, Travis A. Taniguchi

Christopher Salvatore

The primary goal of the current study is to examine a portion of Klinger’s theory. Specifically, we test the influence of organizational and environmental contextual factors, guided by Klinger’s theory, on one measure of officer vigor. To date, few studies have taken this approach to examine Klinger’s theory. The study builds on prior research that has tested aspects of Klinger’s theory and adds new analytic strategies that prior studies have not used. The results of this study have implications for both theory and practice, and they add to the growing literature examining the influence of ecological and organization factors on …

Selaginella Moellendorffii Telomeres: Conserved And Unique Features In An Ancient Land Plant Lineage, Eugene V. Shakirov, Dorothy E. Shippen

Yevgeniy (Eugene) Shakirov

Telomeres, the essential terminal regions of linear eukaryotic chromosomes, consist of G-rich DNA repeats bound by a plethora of associated proteins. While the general pathways of telomere maintenance are evolutionarily conserved, individual telomere complex components show remarkable variation between eukaryotic lineages and even within closely related species. The recent genome sequencing of the lycophyte Selaginella moellendorffii and the availability of an ever-increasing number of flowering plant genomes provides a unique opportunity to evaluate the molecular and functional evolution of telomere components from the early evolving non-seed plants to the more developmentally advanced angiosperms. Here we analyzed telomere sequence in S. …

Drought Responsive Gene Expression Regulatory Divergence Between Upland And Lowland Ecotypes Of A Perennial C4 Grass, John T. Lovell, Scott Schwartz, David B. Lowry, Eugene V. Shakirov, Jason E. Bonnette, Xiaoyu Weng, Mei Wang, Jenifer Johnson, Avinash Sreedasyam, Christopher Plott, Jerry Jenkins, Jeremy Schmutz, Thomas E. Juenger

Yevgeniy (Eugene) Shakirov

Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C₄ grass, Panicum hallii, in natural field conditions. Overall, we find that cis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit drought-responsive G×E. …

The Genomic Landscape Of Molecular Responses To Natural Drought Stress In Panicum Hallii., John T. Lovell, Jerry Jenkins, David B. Lowry, Sujan Mamidi, Avinash Sreedasyam, Xiaoyu Weng, Kerrie Barry, Jason Bonnette, Brandon Campitelli, Chris Daum, Sean P. Gordon, Billie A. Gould, Albina Khasanova, Anna Lipzen, Alice Macqueen, Juan Diego Palacio-Mejía, Christopher Plott, Eugene V. Shakirov, Shengqiang Shu, Yuko Yoshinaga, Matt Zane, Dave Kudrna, Jason D. Talag, Daniel Rokhsar, Jane Grimwood, Jeremy Schmutz, Thomas E. Juenger

Yevgeniy (Eugene) Shakirov

Environmental stress is a major driver of ecological community dynamics and agricultural productivity. This is especially true for soil water availability, because drought is the greatest abiotic inhibitor of worldwide crop yields. Here, we test the genetic basis of drought responses in the genetic model for C4 perennial grasses, Panicum hallii, through population genomics, field-scale gene-expression (eQTL) analysis, and comparison of two complete genomes. While gene expression networks are dominated by local cis-regulatory elements, we observe three genomic hotspots of unlinked trans-regulatory loci. These regulatory hubs are four times more drought responsive than the genome-wide average. Additionally, cis- and trans-regulatory …

The Economic Impacts Of Blackbird (Icteridae) Damage To Sunflower In The Usa, Karina Ernst, Julie Elser, George Linz, Hans Kandel, Jason Holderieath, Samantha Degroot, Steven Shwiff, Stephanie Shwiff

Jason Holderieath

BACKGROUND: Blackbird (Icteridae) damage to ripening sunflower (Helianthus annuus L.) has been a persistent economic issue in the USA for the last five decades. To quantify losses, we surveyed blackbird damage from 2001 to 2013 (excluding 2004) to physiologically mature sunflower in eight states: North Dakota, South Dakota, Texas, Nebraska, Minnesota, Colorado, Kansas, and Vermont.

RESULTS:We pooled data gathered during the most recent 5 years (2009 to 2013) of the survey and found losses averaged $US2.5 million and $US11.3 million for confectionery and oilseed hybrids, respectively. Three states, North Dakota, South Dakota, and Nebraska, had sufficient acreage and bird damage …

Hpi Reactivity Does Not Reflect Changes In Personality Among Trout Introduced To Bold Or Shy Social Groups, Jack S. Thomson, Phillip C. Watts, Tom G. Pottinger, Lynne U. Sneddon

Lynne Sneddon, PhD

Physiological stress responses often correlate with personalities (e.g., boldness). However, this relationship can become decoupled, although the mechanisms underlying changes in this relationship are poorly understood. Here we quantify (1) how an individual’s boldness (response to novel objects) in rainbow trout, Oncorhynchus mykiss, changes in response to interactions with a population of either bold or shy conspecifics and we (2) measured associated post-stress cortisol levels. Initially-bold trout became shyer regardless of group composition, whereas shy trout remained shy demonstrating that bold individuals are more plastic. Stress-induced plasma cortisol reflected the original personality of fish but not the personality induced …

Fish Sentience Denial: Muddying The Waters, Lynne U. Sneddon, Javier Lopez-Luna, David C.C. Wolfenden, Matthew C. Leach, Ana M. Valentim, Peter J. Steenbergen, Nabila Bardine, Amanda D. Currie, Donald M. Broom, Culum Brown

Lynne Sneddon, PhD

Recent empirical studies have reported evidence that many aquatic species, including fish, cephalopods and crustaceans, have the capacity for nociception and pain, and that their welfare should be taken into consideration. Some sceptics, rejecting the precautionary principle, have denied that any study demonstrates pain or other aspects of sentience in fish. This target article discusses some of the scientific shortcomings of these critiques through a detailed analysis of a study exploring nociception and analgesia in larval zebrafish.

Ample Evidence For Fish Sentience And Pain, Lynne U. Sneddon, David C.C. Wolfenden, Matthew C. Leach, Ana M. Valentim, Peter J. Steenbergen, Nabila Bardine, Donald M. Broom, Culum Brown

Lynne Sneddon, PhD

The majority of commentaries are supportive of our position on the scepticism that muddies the waters surrounding fish pain and sentience. There is substantial empirical evidence for pain in fish. Animals’ experience of pain cannot be compared to artificial intelligence (AI) because AI can only mimic responses to nociceptive input on the basis of human observations and programming. Accepting that fish are sentient would not be detrimental to the industries reliant on fish. A more proactive discussion between scientists and stakeholders is needed to improve fish welfare for the benefit of all.

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

Lynne Sneddon, PhD

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 …

Social Assemblages And Mating Relationships In Prairie Dogs: A Dna Fingerprint Analysis, Steven E. Travis, Con Slobodchikoff, Paul Kefan

Con Slobodchikoff, PhD

Mating system characterizations have been hindered by difficulties in accurately assigning parentage to offspring. We investigated the relationship between social assemblages and mating relationships in a territorial harem polygynous mammal, the Gunnison's prairie dog, using a combination of behavioral and molecular analyses. We demonstrate multiple paternity and an extraordinarily high incidence of extraterritorial fertilizations (i.e., 61% of all progeny), in combination with the existence of female kin groups. On this basis, we conclude that social assemblages alone provide a poor description of the Gunnison's prairie dog mating system, and suggest several potential reasons for the maintenance of territoriality in this …

Habitat Structure And Alarm Call Dialects In Gunnison's Prairie Dog (Cynomys Gunnisoni), Bianca S. Perla, C. N. Slobodchikoff

Con Slobodchikoff, PhD

We examined the relationship between habitat structure and alarm call characteristics in six colonies of Gunnison’s prairie dogs (Cynomys gunnisoni) near Flagstaff, Arizona, before and after a mid-summer vegetation change. We found significant differences in alarm call characteristics between colonies, confirming the existence of alarm call dialects. Differences in frequency components but not temporal components of calls were associated with differences in habitat structure. Playback experiments revealed that differences in alarm call structure affected acoustic transmission of calls through the local habitat. Thus, we identify habitat structure as one factor that may contribute to alarm call differences between colonies of …

Resources And The Evolution Of Social Behavior, Con Slobodchikoff

Con Slobodchikoff, PhD

No abstract provided.

Raising Consciousness About Chicken Consciousness, Bernard Rollin

Bernard Rollin, PhD

The topics explored by Marino are definitive, and should work well to lay to rest forever the widespread belief that chickens have no personality, are unintelligent, or in any other way lack a mental life.

Far More To Sheep Than Meets The Casual Eye, Bernard Rollin

Bernard Rollin, PhD

Marino & Merskin’s survey of the cognitive and social capacities of sheep is an eye-opener about the individuality and emotionality of this most maligned of all farm animals. My own eyes had already been opened by an adopted orphaned lamb, so much more like a dog as a companion animal than the mindless robot I had been conditioned to expect. I am morally certain that Marino & Merskin’s survey will have a similar effect on readers open to changing their minds.

Raising The Moral Consciousness Of Science, Bernard Rollin

Bernard Rollin, PhD

Precaution on behalf of sentient animals should not be tempered by the questionable principle of the amorality of science.

Unity Of Consciousness In Animals, Bernard E. Rollin

Bernard Rollin, PhD

Both Descartes the rationalist and Hume the empiricist, polar opposites philosophically, denied the unity and continuity of animal mind. Kant pointed out that the presence of retrievable memories entails unity of consciousness. Rowlands now argues that animals too have unity of consciousness.

Human Superiority?, Bernard Rollin

Bernard Rollin, PhD

Like Charles Darwin and George Romanes, I am quite willing to use anecdotal information as a source of knowledge about animal behavior. There are many more people observing nonhuman animals than there are people conducting controlled experiments, and we can thereby learn that behaviors we think are unique to humans are shared by other animals. From a strictly biological point of view, it makes no sense to speak of “human superiority.” One species of animal can be superior to another only in terms of survival and niche occupation. As moral concern for animals increases across the world, claims of human …

Thinking About Thinking Chickens, Lori Marino

Lori Marino, PhD

This response focuses on three major conceptual threads that run through the peer commentary on my target article: (1) how the use of chickens influences our views of them, (2) whether education is effective, and (3) what components of chicken psychology are most relevant to understanding who chickens are.

“I Am Not An Animal”, Lori Marino

Lori Marino, PhD

The answer to Chapman & Huffman’s question — “Why do we want to think humans are different?” — lies in the work of Ernest Becker and the social psychology literature known as Terror Management Theory, according to which our deep anxiety about animality and death can drive our need to feel superior to the other animals.

Deepening Our Understanding Of Sheep, Lori Marino, Debra Merskin

Lori Marino, PhD

Our Response is centered on five major themes: (1) our presentation of human mythologies about sheep; (2) the relevance of cognitive complexity (“intelligence”) as a dimension underlying the way people perceive and treat sheep; (3) whether our review is too anthropocentric or anthropomorphic; (4) animal welfare versus animal rights (abolitionism); and (5) whether knowledge and education are enough to change human attitudes and behavior.

Octopus Minds Must Lead To Octopus Ethics, Barbara J. King, Lori Marino

Lori Marino, PhD

Mather argues convincingly for the existence of minds in octopuses based largely on laboratory experiments. Many of these experiments are highly invasive and involve mutilation and death. Moreover, octopuses are now being hailed as a “new model” for biological research and are being enthusiastically bred in captivity, both for research and for food. We argue that the compelling evidence for mind in octopuses must be accompanied by intense scrutiny of the ethics that shape how we treat them and that the intrinsic value of their individual lives must be recognized.

The Inconvenient Truth About Thinking Chickens, Lori Marino

Lori Marino, PhD

Original Abstract: Domestic chickens are members of an order, Aves, which has been the focus of a revolution in our understanding of neuroanatomical, cognitive, and social complexity. Some birds are now known to be on a par with many mammals in their intelligence, emotional sophistication, and social interaction. Yet views of chickens have largely remained unrevised in light of this new evidence. In this paper, I examine the data on cognition, emotions, personality, and sociality in chickens, exploring such areas as self-awareness, cognitive bias, social learning and self-control, and comparing their abilities with other birds and other vertebrates, particularly …

Intelligence, Complexity, And Individuality In Sheep, Lori Marino, Debra Merskin

Lori Marino, PhD

Domestic sheep (Ovis aries) are among the earliest animals domesticated for human use. They are consumed worldwide as mutton, hogget, and lamb, kept as wool and milk producers, and used extensively in scientific research. The popular stereotype is that sheep are docile, passive, unintelligent, and timid, but a review of the research on their behavior, affect, cognition, and personality reveals that they are complex, individualistic, and social.

Debunking Human Prejudice And Blindness, Peter J. Li

Peter J. Li, PhD

Human prejudice and blindness to animal suffering are shocking. Despite their differences in culture, politics, and religious beliefs, humans have one thing in common. They see nonhuman animals as inferior and have since time immemorial assumed a dominant position in an asymmetrical human-animal relationship. When it comes to human-animal relations, there is no “clash of civilizations.” Human prejudice and blindness are predicated on “common sense assumptions” about the natural world and nonhuman animals in particular. Marino & Merskin’s review is part of the growing effort to debunk the assumptions that have shaped human actions so as to end the injustice …

The Precautionary Principle: A Cautionary Note, Robert C. Jones

Robert C. Jones, PhD

The precautionary principle regarding animal sentience is often used in decision-making about human actions that may cause harm to nonhuman animals. Birch (2017) develops an account of the precautionary principle requiring two pragmatic rules for its implementation. I support Birch's proposal but offer a cautionary note about relying on precautionary principles if one's ultimate goal is to emancipate animals from human domination.

Fish Sentience Denial: Muddy Moral Water, Robert C. Jones

Robert C. Jones, PhD

Sneddon et al. (2018) authoritatively summarize the compelling and overwhelming evidence for fish sentience, while methodically dismantling one rather emblematic research paper (Diggles et al. 2017) intended to discount solid evidence of fish sentience (Lopez-Luna et al. 2017a, 2017b, 2017c, & 2017d). I explore the larger practical moral contexts within which these debates take place and argue that denials of animal sentience are really moral canards.

Animal Pain And The Social Role Of Science, Leslie Irvine

Leslie Irvine, PhD

Assuming that all animals are sentient would mean ending their use in most scientific research. This does not necessarily imply an unscientific or anti-scientific stance. Examining the social role of science reveals its considerable investment in preserving the status quo, including the continued use of animal subjects. From this perspective, the use of animal subjects is a custom that science could move beyond, rather than a methodological requirement that it must defend.

Wildlife Conservation, Zoos And Animal Protection: A Strategic Analysis, Andrew N. Rowan

Andrew N. Rowan, DPhil

The publication consists of the proceedings of a workshop, sponsored by the Gilman Foundation, and held in April of 1994 at the White Oak Conservation Center in Florida. About thirty participants were invited from zoos, animal protection groups and academic institutions to discuss concepts such as wild, captive and tame; animal well-being in the wild and in zoos; and protecting individuals versus conserving populations. In order to maximize the time engaged in discussion, several individuals were identified to prepare target articles which were distributed to all participants before the meeting. These articles form the main chapters in this book. Other …

Outdoor Cats: An Animal Welfare And Protection Perspective, John Hadidian, Inga Gibson, Susan Hagood, Nancy Peterson, Bernard Unti, Betsy Mcfarland, Katie Lisnik, Heather Bialy, Inga Fricke, Kathleen Schatzmann, Jennifer Fearing, Pam Runquist, Andrew N. Rowan (Ed.)

Andrew N. Rowan, DPhil

First raised as a serious conservation issue more than 100 years ago, the impact of free-roaming cats on wildlife has been a subject of debate, controversy, and conflict since then. Cats have been tied directly to the extinction of sensitive species in island environments and implicated as major threats to certain wildlife populations elsewhere. Yet the study of free-roaming cats and the problems attributed to them lags behind the standards of research typical with more traditional vertebrate “pest” species. Alternative management approaches, ranging from traditional practices such as removal and depopulation to emerging concepts such as Trap- Neuter-Return (TNR), have …