Life Sciences Commons^™

Alfred Russel Wallace Notes 30. Wallace A Theist? Part I., Charles H. Smith

Faculty/Staff Personal Papers

Alfred Russel Wallace (1823−1913) has been portrayed as a ‘theist’ on a large number of occasions from his own time on to the present. In this, the first of a two part work, this assessment is questioned. In part one, the matter of Wallace’s personal philosophy and spiritual orientation is explored, the conclusion being that Wallace was a lifelong agnostic who can hardly be aligned with theism.

Sulfur Assimilation Using Gaseous Carbonyl Sulfideby The Soil Fungus Trichoderma Harzianum, Ryuka Iizuka, Shohei Hattori, Yusuke Kosaka, Yoshihito Masaki, Yusuke Kawano, Iwao Ohtsu, David Hibbett, Yoko Katayama, Makoto Yoshida

Biology

Fungi have the capacity to assimilate a diverse range of both inorganic and organic sulfur compounds. It has been recognized that all sulfur sources taken up by fungi are in soluble forms. In this study, we present evidence that fungi can utilize gaseous carbonyl sulfide(COS) for the assimilation of a sulfur compound. We found that the filamentousfungus Trichoderma harzianum strain THIF08, which has constitutively high COS-degrading activity, was able to grow with COS as the sole sulfur source. Cultivation with 34S-labeled COS revealed that sulfur atom from COS was incorporated into intracellular metabolites such as glutathione and ergothioneine. COS degradation …

Alfred Russel Wallace Notes 27. When Wallace Broke With Darwin., Charles H. Smith

Faculty/Staff Personal Papers

The year 1866 was the first year Alfred Russel Wallace showed definite signs of breaking with Darwin over the limits of natural selection. Attention is drawn to a July 1866 exchange of letters between the two, and how this foreshadowed what followed.

Overcoming Genetic Paucity Of Camelina Sativa: Possibilities For Interspecific Hybridization Conditioned By The Genus Evolution Pathway, Rostyslav Y. Blume, Ruslan Kalendar, Liang Guo, Edgar B. Cahoon, Yaroslav B. Blume

Center for Plant Science Innovation: Faculty and Staff Publications

Camelina or false flax (Camelina sativa) is an emerging oilseed crop and a feedstock for biofuel production. This species is believed to originate from Western Asian and Eastern European regions, where the center of diversity of the Camelina genus is located. Cultivated Camelina species arose via a series of polyploidization events, serving as bottlenecks narrowing genetic diversity of the species. The genetic paucity of C. sativa is foreseen as the most crucial limitation for successful breeding and improvement of this crop. A potential solution to this challenge could be gene introgression from Camelina wild species or from …

Morphological Trait Evolution In Solanum (Solanaceae): Evolutionary Lability Of Key Taxonomic Characters, Rebecca Hilgenhof, Edeline Gagnon, Sandra Knapp, Xavier Aubriot, Eric Tepe, Lynn Bohs, Leandro Giacomin, Yuri Gouvea, Andres Orejuela, Christopher T. Martine, Clara Ines Orozco, Iris E. Peralta, Tina Sarkinen

Faculty Journal Articles

Solanum is one of the world's largest and economically most important plant genera, including 1245 currently accepted species and several major and minor crops (e.g., tomato, potato, brinjal eggplant, scarlet eggplant, Gboma eggplant, lulo, and pepino). Here we provide an overview of the evolution of 25 key morphological traits for the major and minor clades of this giant genus based on stochastic mapping using a well-sampled recently published phylogeny of Solanum. The most evolutionarily labile traits (showing >100 transitions across the genus) relate to plant structure (growth form and sympodial unit structure), herbivore defence (glandular trichomes), pollination (corolla shape …

Bio 013: Writing In The Sciences - Human Origins, Esther Muehlbauer

Open Educational Resources

Bio. 013: Writing in the Sciences - Human Origins is an OER syllabus for a College Writing 2 course that develops student writing for different audiences, following the trajectory of how scientists work: Scientists Writing for themselves (a field journal); Scientists writing for other scientists (a review article); Scientists writing for society (an essay for Natural History Magazine).

Alfred Russel Wallace Notes 25. Wallace And The 'Physical Environment'., Charles H. Smith

Faculty/Staff Personal Papers

Alfred Russel Wallace’s natural selection essay of 1858 has been held to frame a greater role for the physical environment in forcing selection regimes than we find in Darwin’s writings, but here that verdict is challenged by a re-examination of both the essay itself, and period usage of the term ‘physical.’

The Foreign Earth: An Exercise In Speculative Biology, Aidyn Ruf

WWU Honors College Senior Projects

Speculative Biology is the practice of examining hypothetical scenarios about the potential evolution of life. This project explores one such perspective timeline, utilizing scientific illustration, scientific information, and creative writing to estimate what the organisms of Earth might look like 250 million years into the future. Basic parameters were established, examining our current knowledge about geology and the environment to determine how the Earth itself might look. This included examining factors such as tectonic movement, adjusted ocean currents, and planetary heat cycles. Then, I studied mass extinctions and the animals which survived them, creating a baseline of ancestors the future …

Pillars Of Biology: 'The Genetical Evolution Of Social Behaviour, I And Ii'., Geoff Wild

Applied Mathematics Publications

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Corrigendum: Evolution, Ecology, And Zoonotic Transmission Of Betacoronaviruses: A Review, Herbert F. Jelinek, Mira Mousa, Eman Alefishat, Wael Osman, Ian Spence, Dengpan Bu, Samuel F. Feng, Jason Byrd, Paola A. Magni, Shafi Sahibzada, Guan K. Tay, Habiba S. Alsafar

Research outputs 2022 to 2026

In the published article, there was an error in the legend for Figure 1 as published. The figure legend did not indicate that it has been adapted from Plowright et al. (2017). Copyright permission was obtained from Springer Nature to adapt Figure 1 from Plowright et al. (2017). The corrected legend appears below. Figure 1. Zoonotic risk distribution, pathway to spillover, and the multimodal role of the determinants of spillover. The zoonotic risk is demonstrated by the accumulated distribution of reservoir hosts and vectors that play a role in the pathway to spillover. The risk of spillover is determined by …

Natural Selection Of Immune And Metabolic Genes Associated With Health In Two Lowland Bolivian Populations, Amanda J. Lea, Angela Garcia, Jesusa Arevalo, Julien F. Ayroles, Kenneth Buetow, Steve W. Cole, Daniel Eid Rodriguez, Maguin Gutierrez, Heather M. Highland, Paul L. Hooper, Anne Justice, Thomas Kraft, Kari E. North, Jonathan Stieglitz, Hillard Kaplan, Benjamin C. Trumble, Michael Gurven

ESI Publications

A growing body of work has addressed human adaptations to diverse environments using genomic data, but few studies have connected putatively selected alleles to phenotypes, much less among underrepresented populations such as Amerindians. Studies of natural selection and genotype–phenotype relationships in underrepresented populations hold potential to uncover previously undescribed loci underlying evolutionarily and biomedically relevant traits. Here, we worked with the Tsimane and the Moseten, two Amerindian populations inhabiting the Bolivian lowlands. We focused most intensively on the Tsimane, because long-term anthropological work with this group has shown that they have a high burden of both macro and microparasites, as …

The Evolutionary Dynamics Of Infectious Diseases On An Unstable Planet: Insights From Modeling The Stockholm Paradigm, Angie T.C. Souza, Sabrina B.L. Araujo, Walter A. Boeger

MANTER: Journal of Parasite Biodiversity

Emerging infectious diseases (EIDs) are, besides a question of food safety and public health, an ecological and evolutionary issue. The recognition of this condition combined with the accumulation of evidence that pathogens are not specialists in their original hosts evidences the need for understanding how the dynamics of interaction between pathogens and hosts occurs. The Stockholm Paradigm (SP) provides the theoretical fundaments to understand the dynamics of diseases and design proactive measures to avoid the emergence and reemergence of infectious diseases. In this review, we revisit the models that evaluate several aspects of the proposed dynamics of the SP, including …

Keeping 21st Century Paleontology Grounded: Quantitative Genetic Analyses And Ancestral State Reconstruction Re-Emphasize The Essentiality Of Fossils, Tesla A. Monson, Marianne F. Brasil, Michael Mahaney, Christopher A. Schmitt, Catherine E. Taylor, Leslea J. Hlusko

School of Medicine Publications and Presentations

Advances in genetics and developmental biology are revealing the relationship between genotype and dental phenotype (G:P), providing new approaches for how paleontologists assess dental variation in the fossil record. Our aim was to understand how the method of trait definition influences the ability to reconstruct phylogenetic relationships and evolutionary history in the Cercopithecidae, the Linnaean Family of monkeys currently living in Africa and Asia. We compared the two-dimensional assessment of molar size (calculated as the mesiodistal length of the crown multiplied by the buccolingual breadth) to a trait that reflects developmental influences on molar development (the inhibitory cascade, IC) and …

Alfred Russel Wallace Notes 22: Stumbling Blocks To An Understanding Of Wallace's Worldview, Charles H. Smith

Faculty/Staff Personal Papers

The writings of Alfred Russel Wallace (1823−1913) present a challenge to modern readers, both for the large range of subjects he entertained, and his unique point of view. In this short treatment, ten ‘stumbling blocks’ to an appreciation of Wallace’s thought are outlined which, it is suggested, have caused problems of interpretation in the past.

Reconstructing The Ecological Relationships Of Late Cretaceous Antarctic Dinosaurs And How Functional Tooth Morphology Influenced These Relationships, Ian D. Broxson

2022 Symposium

The Sandwich Bluff Formation of the James Ross Basin of Antarctica has recently yielded a group of five late Cretaceous dinosaurs that lived contemporaneously with each other, a first for Antarctica. These five dinosaurs include fragmentary remains of two differently sized elasmarian ornithopods, a possible megaraptor, a hadrosaur, and a nodosaur. In this study we will construct a model of the ecological relationships of late Cretaceous Antarctica. Additionally, we will look at what specific factors allowed this group of four herbivores and a carnivore to coexist in a restricted locality and what niches were filled by each species. Methods to …

White Lies Matter: The Evolution, Persistence, And Impact Of Scientific Racism, Kim Keay

WWU Honors College Senior Projects

A dissection of the origins, history, persistence, and impacts of various threads of scientific racism. This paper traces scientific racism from its roots in evolutionary biology through Social Darwinism and eugenics. By exploring the historical connection between scientific racism and white supremacy, this research aims to reveal some of the ways in which contemporary science, racism, and society at large have been shaped by the past. Tracing these threads will follow scientific racism from its origins to the beginnings of Social Darwinism and eugenics, through American cultivation of eugenics and its connections to Nazi Germany, to ongoing eugenicist policies and …

Phylogenomic Discordance Suggests Polytomies Along The Backbone Of The Large Genus Solanum, Edeline Gagnon, Rebeccca Hilgenhof, Andrés Orejuela, Angela J. Mcdonnell, Gaurav Sablok, Xavier Aubriot, Leandro Giacomin, Yuri Gouvêa, Thamyris Bragionis, João Renato Stehmann, Lynn Bohs, Steven Dodsworth, Christopher T. Martine, Péter Poczai, Sandra Knapp, Tiina Särkinen

Faculty Journal Articles

Premise of the study

Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants.

Methods

A densely sampled species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) …

Why Sequence All Eukaryotes?, Mark Blaxter, John M. Archibald, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Federica Di Palma, Richard Durbin, Scott V. Edwards, Jennifer A.M. Graves, Kevin J. Hackett, Neil Hall, Erich D. Jarvis, Rebecca N. Johnson, Elinor K. Karlsson, W. John Kress, Shigehiro Kuraku, Mara K. N. Lawniczak, Kerstin Lindblad-Toh, Jose V. Lopez, Nancy A. Moran, Gene E. Robinson, Oliver A. Ryder, Beth Shapiro, Pamela S. Soltis, Tandy Warnow, Guojie Zhang, Harris A. Lewin

Biology Faculty Articles

Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes—about 2 million species—should be sequenced to high quality to produce a …

(Non)Parallel Developmental Mechanisms In Vertebrate Appendage Reduction And Loss, Samantha Swank, Thomas Sanger, Yoel E. Stuart

Biology: Faculty Publications and Other Works

Appendages have been reduced or lost hundreds of times during vertebrate evolution. This phenotypic convergence may be underlain by shared or different molecular mechanisms in distantly related vertebrate clades. To investigate, we reviewed the developmental and evolutionary literature of appendage reduction and loss in more than a dozen vertebrate genera from fish to mammals. We found that appendage reduction and loss was nearly always driven by modified gene expression as opposed to changes in coding sequences. Moreover, expression of the same genes was repeatedly modified across vertebrate taxa. However, the specific mechanisms by which expression was modified were rarely shared. …

The Evolution Of Bioluminescence Across The Shrimp Family Sergestidae: A Genomic Skimming And Phylogenetic Approach, Charles G. Golighty Iii

FIU Electronic Theses and Dissertations

The family Sergestidae provide a unique system for studying the evolution of bioluminescence, with species possessing one of three distinct forms of photophores. This study capitalizes on molecular data to construct a genus-level phylogeny of sergestid shrimp. “Genome skimming” was implemented, capturing mitochondrial genomic data across 19 species. Additional individuals were incorporated through Sanger sequencing of four partial gene regions. The -sergestes group of genera was recovered as non-monophyletic, with the -sergia group of genera being recovered as monophyletic. Ancestral state reconstructions of light organ type indicate the organs of Pesta photophore is the ancestral state for the …

Reproductive Aging In Caenorhabditis Elegans: From Molecules To Ecology, Andrea Scharf, Franziska Pohl, Brian M. Egan, Zuzana Kocsisova, Kerry Kornfeld

Biological Sciences Faculty Research & Creative Works

Aging animals display a broad range of progressive degenerative changes, and one of the most fascinating is the decline of female reproductive function. In the model organism Caenorhabditis elegans, hermaphrodites reach a peak of progeny production on day 2 of adulthood and then display a rapid decline; progeny production typically ends by day 8 of adulthood. Since animals typically survive until day 15 of adulthood, there is a substantial post reproductive lifespan. Here we review the molecular and cellular changes that occur during reproductive aging, including reductions in stem cell number and activity, slowing meiotic progression, diminished Notch signaling, and …

Phenotype Bias Determines How Natural Rna Structures Occupy The Morphospace Of All Possible Shapes, Fatme Ghaddar, Dr Kamaludin Dingle, Dr Petr Sulc, Prof Ard A. Louis

Undergraduate Research Symposium

The relative prominence of developmental bias versus natural selection is a long standing controversy in evolutionary biology. Here we demonstrate quantitatively that developmental bias is the primary explanation for the occupation of the morphospace of RNA secondary structure (SS) shapes. By using the RNAshapes method to define coarse-grained SS classes, we can measure the frequencies that non-coding RNA SS shapes appear in nature. Our main findings are firstly that only the most frequent structures appear in nature; the vast majority of possible structures in the morphospace have not yet been explored. Secondly, and perhaps more surprisingly, these frequencies are accurately …

Leaf Form Diversification In An Ornamental Heirloom Tomato Results From Alterations In Two Different Homeobox Genes, Hokuto Nakayama, Steven D. Rowland, Zizhang Cheng, Kristina Zumstein, Julie Kang, Yohei Kondo, Neelima R. Sinha

Faculty Publications

Domesticated plants display diverse phenotypic traits. However, the influence of breeding effort on this phenotypic diversity remains unknown. Here, we demonstrate that a single nucleotide deletion in the homeobox motif of BIPINNATA, a BEL-LIKE HOMEODOMAIN gene, led to a highly complex leaf phenotype in an heirloom tomato (Solanum lycopersicum), Silvery Fir Tree (SiFT), which is used as a landscaping and ornamental plant. A comparative gene network analysis revealed that repression of SOLANIFOLIA, the ortholog of WUSCHEL RELATED HOMEOBOX 1, caused the narrow leaflet phenotype seen in SiFT. Comparative genomics indicated that the bip mutation in SiFT likely arose de novo …

Telomere Roles In Fungal Genome Evolution And Adaptation, Mostafa Rahnama, Baohua Wang, Jane Dostart, Olga Novikova, Daniel Yackzan, Andrew T. Yackzan, Haley Bruss, Maray Baker, Haven Jacob, Xiaofei Zhang, April Lamb, Alex Stewart, Melanie Heist, Joey Hoover, Patrick Calie, Li Chen, Jinze Liu, Mark L. Farman

Plant Pathology Faculty Publications

Telomeres form the ends of linear chromosomes and usually comprise protein complexes that bind to simple repeated sequence motifs that are added to the 3′ ends of DNA by the telomerase reverse transcriptase (TERT). One of the primary functions attributed to telomeres is to solve the “end-replication problem” which, if left unaddressed, would cause gradual, inexorable attrition of sequences from the chromosome ends and, eventually, loss of viability. Telomere-binding proteins also protect the chromosome from 5′ to 3′ exonuclease action, and disguise the chromosome ends from the double-strand break repair machinery whose illegitimate action potentially generates catastrophic chromosome aberrations. Telomeres …

Accepting Evolution Entails Kufr? A Critical Appraisal Of Nuh Ha Mim Keller’S Fatwa, Shoaib Ahmed Malik, Elvira Kulieva, Ayub Ayub

All Works

Muslim scholars who oppose the compatibility of Islam and evolution usually advance three kinds of arguments: scientific, metaphysic, and hermeneutic. This paper will examine the position of Nuh Ha Mim Keller, a prominent Sunni scholar who employ these three lines of arguments and proposes that believing in human evolution entails kufr. In this article we will critically analyze Keller’s understanding of the science of evolution in which he claims that the theory of evolution is not robust. We argue that through the consilience of induction, evolution is the best explanation for the biological origins and diversity. We also argue that …

Insights Into The Molecular Evolution Of Fertilization Mechanism In Land Plants, Vijyesh Sharma, Anthony J. Clark, Tomokazu Kawashima

Plant and Soil Sciences Faculty Publications

Land plants have evolved successive changes during their conquest of the land and innovations in sexual reproduction have played a major role in their terrestrialization. Recent years have seen many revealing dissections of the molecular mechanisms of sexual reproduction and much new genomics data from the land plant lineage, including early diverging land plants, as well as algae. This new knowledge is being integrated to further understand how sexual reproduction in land plants evolved, identifying highly conserved factors and pathways, but also molecular changes that underpinned the emergence of new modes of sexual reproduction. Here, we review recent advances in …

Chloroplast Genomes In Populus (Salicaceae): Comparisons From An Intensively Sampled Genus Reveal Dynamic Patterns Of Evolution, Jiawei Zhou, Shuo Zhang, Jie Wang, Hongmei Shen, Bin Ai, Wei Gao, Cuijun Zhang, Qili Fei, Daojun Yuan, Zhiqiang Wu, Luke R. Tembrock, Sen Li, Cuiha Gu, Xuezhu Liao

Aspen Bibliography

The chloroplast is one of two organelles containing a separate genome that codes for essential and distinct cellular functions such as photosynthesis. Given the importance of chloroplasts in plant metabolism, the genomic architecture and gene content have been strongly conserved through long periods of time and as such are useful molecular tools for evolutionary inferences. At present, complete chloroplast genomes from over 4000 species have been deposited into publicly accessible databases. Despite the large number of complete chloroplast genomes, comprehensive analyses regarding genome architecture and gene content have not been conducted for many lineages with complete species sampling. In this …

The Phoenix, Fernanda Perez-Alvarez

Montserrat Annual Writing Prize

This article uses a mythical creature, the phoenix, to examine and illustrate the biological principles for generation of an adult body plan from a single cell. Using the study of developmental biology, it explores the cellular and molecular biology that underpins the massive complexity of creating an adult body plan. It also explores the similarities and differences between different embryos, and how nature and evolution have shaped the biology of those embryos to create different body plans.

Evidence For The Role Of Cyp51a And Xenobiotic Detoxification In Differential Sensitivity To Azole Fungicides In Boxwood Blight Pathogens, Stefanos Stravoravdis, Robert E. Marra, Nicholas R. Leblanc, Joanne Crouch, Jonathan P. Hulvey

Microbiology Department Faculty Publication Series

Boxwood blight, a fungal disease of ornamental plants (Buxus spp.), is caused by two sister species, Calonectria pseudonaviculata (Cps) and C. henricotiae (Che). Compared to Cps, Che is documented to display reduced sensitivity to fungicides, including the azole class of antifungals, which block synthesis of a key fungal membrane component, ergosterol. A previous study reported an ergosterol biosynthesis gene in Cps, CYP51A, to be a pseudogene, and RNA-Seq data confirm that a functional CYP51A is expressed only in Che. The lack of additional ergosterol biosynthesis genes showing significant differential expression suggests that the functional CYP51A in Che could contribute to …

Epigenetic Memories And The Evolution Of Infectious Diseases, Geoff Wild

Biology Publications

Genes with identical DNA sequence may show differential expression because of epigenetic marks. Where epigenetic marks respond to past conditions, they represent a form of “memory”. Despite their medical relevance, the impact of memories on the evolution of infectious diseases has rarely been considered. Here we explore the evolution of virulence in pathogens that carry memories of the sex of their previous host. We show that this form of memory provides information about the sex of present and future hosts when the sexes differ in their pathogen’s transmission pattern. Memories of past hosts enable the evolution of greater virulence in …