Biology Commons^™

Polypores And Genus Concepts In Phanerochaetaceae (Polyporales, Basidiomycota), Otto Miettinen, Viacheslav Spirin, Josef Vlasák, Bernard Rivoire, Soili Stenroos, David S. Hibbett

Biology

We explored whether DNA-phylogeny-based and morphology-based genus concepts can be reconciled in the basidiomycete family Phanerochaetaceae. Our results show that macromorphology of fruiting bodies and hymenophore construction do not reflect monophyletic groups. However, by integrating micromor-phology and re-defining genera, harmonization of DNA phylogeny and morphological genus concepts is possible in most cases. In the case of one genus (Phlebiopsis), our genetic markers could not resolve genus limits satisfactorily and a clear morphological definition could not be identified. We combine extended species sampling, microscopic studies of fruiting bodies and phylogenetic analyses of ITS, nLSU and rpb1 to revise genus concepts. Three …

Photography-Based Taxonomy Is Inadequate, Unnecessary, And Potentially Harmful For Biological Sciences, Luis M. P. Ceríaco, Eliécer E. Gutiérrez, Alain Dubois, Rafael O. De Sá, Et Al.

Biology Faculty Publications

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per …

Phylogenetics And Diversification Of Whirligig Beetles (Coleoptera, Gyrinidae), Grey Thomas Gustafson

Biology ETDs

Whirligig beetles are a family of aquatic beetles with an estimated 1,000 species distributed globally. Phylogenetic analysis incorporating molecular data has only recently been conducted on the family and many genera have never received modern taxonomic revision. The first chapter of the dissertation provides a taxonomic revision of the Southeast Asian whirligig beetle genus Porrorhynchus, finding the genus to contain 5 species, and no support for the numerous proposed subspecies. For the second chapter a phylogenetic analysis utilizing the most novel phylogenetic reconstructions methods incorporating the new Fossilized Birth-Death macroevolutionary model implemented in the program MrBayes 3.2.6 was conducted on …

Comparing Apples And Oranges?: Next Generation Sequencing And Its Impact On Microbiome Analysis, Roy D. Sleator, Aisling O'Driscoll, Et. Al.

Department of Biological Sciences Publications

Rapid advancements in sequencing technologies along with falling costs present widespread opportunities for microbiome studies across a vast and diverse array of environments. These impressive technological developments have been accompanied by a considerable growth in the number of methodological variables, including sampling, storage, DNA extraction, primer pairs, sequencing technology, chemistry version, read length, insert size, and analysis pipelines, amongst others. This increase in variability threatens to compromise both the reproducibility and the comparability of studies conducted. Here we perform the first reported study comparing both amplicon and shotgun sequencing for the three leading next-generation sequencing technologies. These were applied to …

Two New Species Of Geosesarma De Man, 1892 (Crustacea: Brachyura: Sesarmidae) From Palawan, The Philippines, Hendrik Freitag, Marivene Manuel-Santos, Peter K.L Ng

Biology Faculty Publications

Two new and relatively large species of semi-terrestrial sesarmid crabs of the genus Geosesarma De Man, 1892, are described from Palawan Island, Philippines. They are distinguishable from congeners by the characteristic structure of their carapace, chelipeds, ambulatory legs and male first gonopods. Aspects of their ecology are briefly discussed

Taxonomy Of Usa East Coast Fishing Communities In Terms Of Social Vulnerability And Resilience, Richard Pollnac, Tarsila Seara, Lisa Colburn, Michael Jepson

Biology and Environmental Science Faculty Publications

Increased concern with the impacts that changing coastal environments can have on coastal fishing communities led to a recent effort by NOAA Fisheries social scientists to develop a set of indicators of social vulnerability and resilience for the U.S. Southeast and Northeast coastal communities. A goal of the NOAA Fisheries social vulnerability and resilience indicator program is to support time and cost effective use of readily available data in furtherance of both social impact assessments of proposed changes to fishery management regulations and climate change adaptation planning. The use of the indicators to predict the response to change in coastal …

Synthesis Of Phylogeny And Taxonomy Into A Comprehensive Tree Of Life, Cody E. Hinchliff, Stephen A. Smith, James F. Allman, J. Gordon Burleigh, Ruchi Chaudhary, Lyndon M. Coghill, Keith A. Crandall, Jiabin Deng, Bryan T. Drew, Romina Gazis, Karl Gude, David S. Hibbett, Laura A. Katz, H. Dail Laughinghouse Iv, Emily Jane Mctavish, Peter E. Midford, Christopher L. Owen, Richard H. Ree, Jonathan A. Rees, Douglas E. Soltis, Tiffani Williams, Karen A. Cranston

Biological Sciences: Faculty Publications

Reconstructing the phylogenetic relationships that unite all line- ages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips— the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. …

Systematics And Biogeography Of Orthaea Kloztsch (Ericaceae: Vaccinieae), Nelson Salinas

Dissertations, Theses, and Capstone Projects

In the first chapter a study of the distribution patterns of the neotropical Vaccinieae (Ericaceae) is presented. Five areas of endemism were recovered: Central America, northern Chocó, southern Chocó, eastern Ecuador, and Yungas. Divergence times estimations indicate that the Andean clade of Vaccinieae migrated to South America during the Late Oligocene or Early Miocene (28.9-17.84 MA), and most of the subsequent diversification took place during the Tertiary. The Yungas was the first Andean area to be colonized, and several dispersals towards the north expanded their distribution range. Both areas of endemism and dispersal events were influenced by geological processes, such …

A New Species Of Sphaerowithius (Pseudoscorpiones, Withiidae) From Namibia, Mark S. Harvey, V. Menhert

Research outputs 2014 to 2021

A new species of Sphaerowithius Mahnert, 1988, S. ansieae sp. n., is described from specimens collected in caves in northern Namibia. The specimens show some slight modifications to an obligate cavernicolous existence including small eyes and long, slender pedipalps.

A Morphological Phylogenetic Analysis And Taxonomic Revision Of The Millipede Family Atopetholidae (Chamberlin) (Diplopoda: Spirobolida) With Descriptions Of New Species And The Conservation Status Of Comanchelus Chihuanus (Chamberlin 1947) (Diplopoda: Spirobolida: Atopetholidae), A Species Of Concern, Michael F. Medrano

Biology ETDs

The taxa of family Atopetholidae Chamberlin 1918 occurring in the southwestern US and Mexico, including Baja California, are revised with new records and species from collections that have never been evaluated. Five new genera, Aculeulus, Bajabolus, Choixulus, Pinnaulus and Tamaulus and twenty new species, Aculeulus monicae, Arinolus anahiae, Arinolus sequoiaensis, Arinolus shelleyi, Atopetholus lowreyi, Atopetholus milleri, Atopetholus westi, Bajabolus bernadinoensis, Bajabolus lapazensis, Choixulus valdezi, Eurelus alisonae, Eurelus isaiasi, Eurelus marisae, Pinnaulus fieldsi, Tamaulus brantleyae, Tamaulus justini, Tamaulus maribelleae, Tamaulus miae, Tamaulus wardae and Watichelus sheari are described using morphological data and 18 synonyms are proposed for a total fauna of …

Systematics Of The Neotropical Genus Leptodactylus Fitzinger, 1826 (Anura: Leptodactylidae): Phylogeny, The Relevance Of Non-Molecular Evidence, And Species Accounts, Rafael O. De Sá, Taran Grant, Arley Camargo, W. R. Heyer, María Laura Ponssa, Edward Stanley

Biology Faculty Publications

A phylogeny of the species-rich clade of the Neotropical frog genus Leptodactylus sensu stricto is presented on the basis of a total evidence analysis of molecular (mitochondrial and nuclear markers) and non-molecular (adult and larval morphological and behavioral characters) sampled from > 80% of the 75 currently recognized species. Our results support the monophyly of Leptodactylus sensu stricto, with Hydrolaetare placed as its sister group. The reciprocal monophyly of Hydrolaetare and Leptodactylus sensu stricto does not require that we consider Hydrolaetare as either a subgenus or synonym of Leptodactylus sensu lato. We recognize Leptodactylus sensu stricto, Hydrolaetare, Adenomera, and Lithodytes …

Phylogenetic Revision Of The Genus Arenivaga (Rehn) (Blattodea: Corydiidae), With Descriptions Of New Species, A Key To The Males, And An Investigation Of Its Ecological Niche, Heidi Hopkins

Biology ETDs

The cockroach genus Arenivaga is revised. Forty-eight Arenivaga species are recognized with nine previously known species and 39 described as new including the following: A. pagana sp. n., A. grandiscanyonensis sp. n., A. haringtoni sp. n., A. hopkinsorum sp. n., A. umbratilis sp. n., A. tenax sp. n., A. impensa sp. n., A. trypheros sp. n., A. darwini sp. n., A. nalepae sp. n., A. sequoia sp. n., A. mckittrickae sp. n., A. gaiophanes sp. n., A. belli sp. n., A. estelleae sp. n., A. delicata sp. n., A. mortisvallisensis sp. n., A. milleri sp. n., A. pratchetti sp. n., …

Taxonomy, Diversity, And Distribution Patterns Of Portunid Crab Megalopae In The Northern Gulf Of Mexico During Fall Of 2003, Carley Rain Knight

Master's Theses

The field of zooplankton biology contributes to more accurate stock assessments as well as to a greater understanding of the marine food web. However, adequate information for the invertebrate component of zooplankton is lacking compared to the ichthyoplankton component. In this thesis, identification of Portunidae (Crustacea: Decapoda) megalopae collected during the fall of 2003 from a NOAA SEAMAP cruise revealed 7 species and 11 morphs with 90% of the total density comprised of Callinectes sapidus, Achelous gibbesii, Callinectes similis, Achelous spinicarpus, and Achelous sp.I. Keys and detailed descriptions are provided along with photographs and morphological drawings for each morph to …

Phylogeny, Taxonomy And Morphological Evolution In Conostegia (Melastomataceae: Miconieae), Ricardo Kriebel

Dissertations, Theses, and Capstone Projects

The genus Conostegia comprises 77 species of shrubs and trees ranging from Central America to northern South America and the Caribbean. They are ecologically important as they provide pollen for native bees and fruits for birds. One of the main questions of this study is if the genus Conostegia is actually monophyletic. I address this question for the first time by gathering genetic data from four chloroplast regions and two nuclear ribosomal regions of DNA. Phylogenetic analyses of these data revealed that Conostegia is not monophyletic and that a group of species in the genera Clidemia and Miconia fall within …

Revision Of Anacaena Thomson, 1859 Xi. Republic Of The Philippines (Coleoptera: Hydrophilidae), Hendrik Freitag

Biology Faculty Publications

The species of Anacaena THOMSON, 1859 (Coleoptera: Hydrophilidae) of the Republic of the Philippines are revised. Fifteen new species are described: Anacaena albay sp.n., A. amplocomata sp.n., A. apo sp.n., A. balabag sp.n., A. cordillera sp.n., A. davao sp.n., A. destructa sp.n., A. emergens sp.n., A. hemisphaerica sp.n., A. levistriata sp.n., A. philippina sp.n., A. princesa sp.n., A. quezona sp.n., A. sulcata sp.n., and A. zamboangana. All species are endemic to the Philippines, twelve are aquatic, the habitat of three species is unknown. All Philippine species are morphologically similar to other species of the eastern Oriental Region and probably do …

A Revision Of The Octocoral Genus Ovabunda Alderslade, 2001 (Anthozoa, Octocorallia, Xeniidae), Catherine S. Mcfadden, Yehuda Benayahu, Anna Halász, Dafna Aharonovich, Robert Toonen

All HMC Faculty Publications and Research

The family Xeniidae (Octocorallia) constitutes an abundant benthic component on many Indo-West Pacific coral reefs and is ecologically important in the Red Sea. The genus Ovabunda Alderslade, 2001 was recently established to accommodate previous Xenia species with sclerites comprised of a mass of minute corpuscle-shaped microscleres. The aim of the present study was to examine type material of Xenia species in order to verify their generic affiliation. We present here a comprehensive account of the genus Ovabunda, using scanning electron microscopy to depict sclerite microstructure. We assign three Xenia species to the genus: O. ainex comb. n., O. …

A New Species Of Ovabunda (Octocorallia, Xeniidae) From The Andaman Sea, Thailand With Notes On The Biogeography Of This Genus, Catherine S. Mcfadden, Michael P. Janes, Thanongsak Chanmethakul

All HMC Faculty Publications and Research

A survey of xeniid octocorals was carried out in the waters off Southwestern Thailand in September, 2007. Microscopic investigation of the colonies revealed that three specimens belonged to the genus Ovabunda. Gross morphological examination is presented here accompanied by scanning electron micrographs of the sclerites. Molecular phylogenetic analysis showed identical genotypes at mtMutS, COI, and 28S rDNA for all three specimens and supports their generic assignment. Colony size and shape, sclerite size, and pinnule arrangement differ from nominal species of Ovabunda and thus a new species, O. andamanensis is introduced here. This work also presents a new …

The Tadpole Of Leptodactylus Caatingae Heyer & Juncá, 2003 (Anura: Leptodactylidae): External Morphology, Internal Anatomy, And Natural History, Felipe De Madeiros Magalhães, Adrian Antonio Garda, Ralita Ferreira Amado, Rafael O. De Sá

Biology Faculty Publications

We describe and illustrate the external morphology, oral disc, chondrocranium, and internal oral anatomy of Leptodactylus caatingae larvae. We analyze the internal oral anatomy using scanning electron microscopy of a larva in Gosner, stage 38 and chondrocranial anatomy is reported for Gosner stage 34. The tadpole at Gosner stage 38 has a globular body shape with low tail fins and a ventral oral disc bordered by two rows of marginal papillae on most of the disc, except for the anterior labium and a medial portion of the posterior labium where papillae are simple; a wide rostral gap is present, labial …

Taxonomy Of Animal Hair Using A Scanning Electron Microscope, Britten D. Sessions, Dr. Wilford M. Hess

Journal of Undergraduate Research

Using a scanning electron microscope (SEM), selected mammalian species were studied to determine hair cuticular patterns. Although other studies have been conducted on mammalian hair, there exists no classification or taxonomy of Western U.S. mammals using an SEM.

Correctly Assigning Dna Barcodes To Organisms, James B. Finlay, Dr. Keith A. Crandall

Journal of Undergraduate Research

Harvard biologist Edward O. Wilson suggested that what makes humans unique is our innate need for closeness to other forms of life. This “biophilia” has been evident since recorded history and was brought to the forefront of science with Darwin’s famous writings about the origin of species. Since that time there has been a major thrust to categorize all life into groups and subgroups in a field known as taxonomy. There are an estimated 10-15 million extant species (Hammond, 1992) on the earth. Taxonomists have classified roughly 1.6 million of these organisms (Wilson, 1992), indicating that much work needs to …

Biogeography And Evolution Of Neotropical Small Mammals, With Emphasis On Hystricognath Spiny Rats Of The Genus Proechimys (Family Echimyidae), Rafael Do Nascimento Leite

Theses and Dissertations

The Neotropical region is the most biologically diverse region on the planet. The region encompasses a variety of ecosystems and has long been the target of researchers interested in patterns of species diversity and distribution. More recently, molecular data have been incorporated into methods for reconstructing the historical relationships among geographical areas and their biotas. Molecular phylogenetics has provided insights into diversification patterns and the influence of Late Cenozoic events on the evolutionary history of the region. Nevertheless, considering the vast extent and complexity of the region, more studies are needed to fully appreciate the patterns of biogeography and the …

Fossil Trachemys (Testudines: Emydidae) From The Late Hemphillian Of Eastern Tennessee And Its Implications For The Evolution Of The Emydidae, Steven E. Jasinski

Electronic Theses and Dissertations

Trachemys (Testudines: Emydidae) represents one of the most well-known turtles today. The evolution of Trachemys, while being heavily documented with various fossil representatives, is not well understood. Numerous fossils from the Gray Fossil Site in northeastern Tennessee are helping to elucidate the taxon’s evolution. The fossil Trachemys at the Gray Fossil Site represent a new species. A review of previously named Trachemys taxa reveals that a huge majority of them are not valid or have been previously misinterpreted. A phylogenetic analysis preformed on modern emydids and supposed fossil representatives of those genera also shows the evolution of a portion …

Systematics Of Longhorned Beetles (Insecta: Coleoptera: Cerambycidae), Eugenio Hernán Nearns

Biology ETDs

The longhorned wood boring beetles (Insecta: Coleoptera: Cerambycidae) are a diverse and economically important group of insects. With an estimated 4,000 genera and more than 35,000 described species, the Cerambycidae comprise one of the largest beetle families. Cerambycid beetles are found on all continents except Antarctica, from sea level to montane sites as high as 4000 m. Cerambycids are among the most serious wood boring pest species globally, affecting many agricultural crops, ornamental trees, and lumber products, causing millions of dollars in damage each year. Despite their economic importance and biological diversity, relatively little is known of cerambycid beetle ecology, …

Diversification And Coexistence In The Madagascar Olive (Noronhia, Oleaceae), Cynthia Hong-Wa

Dissertations

The long-isolated island of Madagascar provides a suitable setting for studying species diversification, with most groups of organisms there both radiating and showing a high level of endemism. Noronhia is one of these groups and represents the most successful radiation of the olive family (Oleaceae) in Madagascar, with ca. 80 species. In this study, using plastid and nuclear DNA sequences obtained from a comprehensive sampling both within Noronhia and the family, I show that Noronhia, together with Indian Ocean species of Chionanthus, form a monophyletic clade sister to African Chionanthus. The diversification of Noronhia followed a likely Cenozoic dispersal from …

Trichoptera Of Mindoro, The Philippines I. New Species And Records From The Baroc River Catchment, Roxas, Oriental Mindoro (Insecta, Trichoptera), Hendrik Freitag, Wolfram Mey

Biology Faculty Publications

The study of a collection of caddisflies from Mindoro yielded a total of 34 species. Eight species proved to be unknown taxa and are described in the present article as: Rhyacophila crenophysetis spec. nov., Agapetus parallelaria spec. nov., Stactobia roxasi spec. nov., Paduniella vicentis spec. nov., Paduniella prodita spec. nov., Psychomyia taugadensis spec. nov., Tinodes hypoplectis spec. nov., and Ecnomus biundularia spec. nov. A list of all collected species is provided.

Ancyronyx Erichson, 1847 (Coleoptera, Elmidae) From Mindoro, Philippines, With Description Of The Larvae And Two New Species Using Dna Sequences For The Assignment Of The Developmental Stages, Hendrik Freitag

Biology Faculty Publications

Ancyronyx buhid sp. n. and Ancyronyx tamaraw sp. n. are described based on adults and larvae, matched using their cox1 or cob DNA sequence data. Additional records of Ancyronyx schillhammeri Jäch, 1994 and Ancyronyx minerva Freitag & Jäch, 2007 from Mindoro are listed. The previously unknown larva of Ancyronyx schillhammeri is also described here, aided by cox1 data. The new species and larval stages are described in detail and illustrated by SEM and stacked microscopic images. Keys to the adult and larval Ancyronyx species of Mindoro and an updated checklist of Philippine Ancyronyx species are provided. The usefulness as bioindicators, …

Hydraena (Hydraenopsis) Ateneo, New Species (Coleoptera, Hydraenidae) And Other Aquatic Polyphaga From A Small Habitat Patch In A Highly Urbanized Landscape Of Metro Manila, Philippines, Hendrik Freitag

Biology Faculty Publications

Seven species of Hydraenidae, Hydrophilidae and Elmidae are recorded from temporary freshwater habitats at the Ateneo de Manila University Campus in the metropolitan area of Manila, Philippines. They were identified as Enochrus (Lumetus) fragiloides d’Orchymont, Helochares (Hydrobaticus) lepidus d’Orchymont, Helochares (Helochares) pallens (MacLeay), Hydraena (Hydraenopsis) scabra d’Orchymont, Hydraena (Hydraenopsis) palawanensis Freitag & Jäch (new record for Luzon Island), Stenelmis sp. A further hydraenid species was unknown to science and is newly described: Hydraena (Hydraenopsis) ateneo Freitag, sp. n. Aedeagus, gonocoxite, spermatheca, and female tergite X are illustrated by …

Sinularia Leptoclados (Ehrenberg, 1834) (Cnidaria: Octocorallia) Re-Examined, Catherine S. Mcfadden, Leen P. Van Ofwegen, Yehuda Benayahu

All HMC Faculty Publications and Research

Sinularia leptoclados (Ehrenberg, 1834) is re-described. Sinularia leptoclados var. gonatodes Kolonko, 1926 is synonymized with S. maxima Verseveldt, 1977. Two new species of Sinularia with digitiform lobules, leptoclados-type surface clubs and unbranched interior spindles, are described. An updated maximum likelihood tree of Sinularia species with leptoclados-type clubs (clade 5C) based on two mitochondrial genes (mtMutS, COI) and a nuclear gene (28S rDNA) is presented.

Molecular Phylogenetic Evidence Supports A New Family Of Octocorals And A New Genus Of Alcyoniidae (Octocorallia: Alcyonacea), Catherine S. Mcfadden, Leen P. Van Ofwegen

All HMC Faculty Publications and Research

Molecular phylogenetic evidence indicates that the octocoral family Alcyoniidae is highly polyphyletic, with genera distributed across Octocorallia in more than 10 separate clades. Most alcyoniid taxa belong to the large and poorly resolved Holaxonia–Alcyoniina clade of octocorals, but members of at least four genera of Alcyoniidae fall outside of that group. As a first step towards revision of the family, we describe a new genus, Parasphaerasclera gen. n., and family, Parasphaerascleridae fam. n., of Alcyonacea to accommodate species of Eleutherobia Pütter, 1900 and Alcyonium Linnaeus, 1758 that have digitiform to digitate or lobate growth forms, completely lack sclerites …

Pushing Taxonomy To Extiction?, Alessandro Minelli, Annemarie Ohler, Erna Aescht, Aaron Bauer, Lucio Bonato, Roger Bour, Marcelo Rodrigues De Carvalho, Rafael O. De Sá, Et Al.

Biology Faculty Publications

Can we describe all species on Earth before they disappear? We argue that this is possible only by endowing taxonomy with professional manpower and appropriate material resources as required by big science.

Contrary to Costello et al.’s (CMS) (1) statements, taxonomy is not an easy discipline accessible to all through a smartphone. It requires exhaustive training and long familiarity with field, specimens and literature (2).

CMS’s argument is framed in terms of species numbers, but different, non-overlapping species concepts apply to bacteria, brambles and birds (3,4,5): “the species” as common unit of biodiversity does not exist (6).

Even ignoring this …