Life Sciences Commons^™

Acoustic Divergence In The Rut Vocalizations Of Persian And European Fallow Deer, J. B. Stachowicz, E. Vannoni, B. J. Pitcher, Elodie F. Briefer, E. Geffen, A. G. Mcelligott

Alan G. McElligott, PhD

We conducted a study of the male rut vocalizations (groans) of two closely related species, Persian and European fallow deer. Persian fallow deer are endangered, restricted to Iran and Israel, and their rut vocalizations have never been studied. By contrast, European fallow deer are one of the most common deer species in the world, and have been the subject of numerous detailed studies. Persian bucks are approximately 16% larger than European bucks, and this can have important implications for vocalizations. Persian bucks were recorded in Israel, and European bucks were recorded in the UK and Ireland. We measured temporal, fundamental …

Comparison Of Thaumarchaeotal Populations From Four Deep Sea Basins., Stephen Techtmann, Nagissa Mahmoudi, Kendall T Whitt, Maria Fernanda Campa, Julian L Fortney, Dominique C Joyner, Terry C Hazen

Michigan Tech Publications

The nitrogen cycle in the marine environment is strongly affected by ammonia-oxidizing Thaumarchaeota. In some marine settings, Thaumarchaeotes can comprise a large percentage of the prokaryotic population. To better understand the biogeographic patterns of Thaumarchaeotes, we sought to investigate differences in their abundance and phylogenetic diversity between geographically distinct basins. Samples were collected from four marine basins (The Caspian Sea, the Great Australian Bight, and the Central and Eastern Mediterranean). The concentration of bacterial and archaeal 16S rRNA genes and archaeal amoA genes were assessed using qPCR. Minimum entropy decomposition was used to elucidate the fine-scale diversity of Thaumarchaeotes. We …

Phylogenetic Patterns Of Foliar Mineral Nutrient Accumulation Among Gypsophiles And Their Relatives In The Chihuahuan Desert, Clare Muller, Michael J. Moore, Zoe Feder, Helene Tiley, Rebecca E. Drenovsky

2017 Faculty Bibliography

PREMISE OF THE STUDY: Gypsum endemism in plants (gypsophily) is common on gypsum outcrops worldwide, but little is known about the functional ecology of Chihuahuan Desert gypsophiles. We investigated whether leaf chemistry of gypsophile lineages from the northern Chihuahuan Desert are similar to leaves of related nonendemic (gypsovag) species relative to their soil chemistry. We expected widely distributed gypsophiles (hypothesized to be older lineages on gypsum) would have distinct leaf chemistry from narrowly distributed, relatively younger lineages endemic to gypsum and gypsovags, reflecting adaptation to gypsum.

METHODS: We collected leaves from 23 gypsophiles and related nonendemic taxa growing on nongypsum …

Mitochondrial Phylogenomics Of Hemiptera Reveals Adaptive Innovations Driving The Diversification Of True Bugs, Hu Li, John Moeller Leavengood Jr., Eric G. Chapman, Daniel Burkhardt, Fan Song, Pei Jiang, Jinpeng Liu, Xuguo Zhou, Wanzhi Cai

Entomology Faculty Publications

Hemiptera, the largest non-holometabolous order of insects, represents approximately 7% of metazoan diversity. With extraordinary life histories and highly specialized morphological adaptations, hemipterans have exploited diverse habitats and food sources through approximately 300 Myr of evolution. To elucidate the phylogeny and evolutionary history of Hemiptera, we carried out the most comprehensive mitogenomics analysis on the richest taxon sampling to date covering all the suborders and infraorders, including 34 newly sequenced and 94 published mitogenomes. With optimized branch length and sequence heterogeneity, Bayesian analyses using a site-heterogeneous mixture model resolved the higher-level hemipteran phylogeny as (Sternorrhyncha, (Auchenorrhyncha, (Coleorrhyncha, Heteroptera))). Ancestral character …

Classification, Natural History, And Evolution Of The Subfamily Peloniinae Opitz (Coleoptera: Cleroidea: Cleridae). Part Viii. Systematics Of The Checkered Beetle Genus Chariessa Perty, Weston Opitz

Insecta Mundi

The New World genus Chariessa Forster (Coleoptera: Cleroidea: Cleridae) is revised and includes C. catalina Opitz, new species, C. elegans Horn, C. dichroa (LeConte), C. floridana Schaeffer, C. pilosa (Forster), C. texana Wolcott, C. ramicornis Perty, C. vestita (Chevrolat), and C. duponti (Spinola). Enoplium pilosa var. marginata Say is synonymized with Chariessa pilosa Forster. Lectotypes are designated for C. pilosa (Forster), C. ramicornis Perty, and C. vestita (Chevrolat). Available information indicates that Chariessa adult and immature individuals are predatory on lignicolous insects with a particular affinity for cerambycids and buprestids that infest species of oak. It is postulated …

Expanding Metabolic Diversity Of Two Archaeal Phyla: Nanoarchaeota And Korarchaeota, John Forad Kelley

Dissertations and Theses

Culture independent studies have revealed a greater diversity of Archaea than the two kingdoms initially defined by Carl Woese. Culturing species from the newly discovered archaeal lineages, as with the majority of microbes, has been difficult. To overcome the culturing dilemma, metagenomics is being used to reconstruct environmental genomes. Two metagenomic studies are presented in this thesis, with the aim of recovering newly proposed archaeal genomes from the Nanoarchaeota and Korarchaeota.

In the first study, a sediment sample, NZ13, was collected from a terrestrial New Zealand hot spring. Along with the sediment sample, two complex enrichments were sequenced on an …

The Influence Of Phylogeny And Niche Differentiation On The Diets Of Malagasy Primates, Rebekka S. Hughes

Theses and Dissertations

Previous studies have shown that haplorhine diet is affected by phylogeny; however, until now studies in Malagasy strepsirrhines were lacking. The evolution of differences in Malagasy primates’ diets appears to differ from the pattern shown in haplorhines. My results indicate that niche differentiation may be a stronger predictor of diet.

A Linkage Map For The Newt Notophthalmus Viridescens: Insights In Vertebrate Genome And Chromosome Evolution, Melissa C. Keinath, S. Randal Voss, Panagiotis A. Tsonis, Jeramiah J. Smith

Biology Faculty Publications

Genetic linkage maps are fundamental resources that enable diverse genetic and genomic approaches, including quantitative trait locus (QTL) analyses and comparative studies of genome evolution. It is straightforward to build linkage maps for species that are amenable to laboratory culture and genetic crossing designs, and that have relatively small genomes and few chromosomes. It is more difficult to generate linkage maps for species that do not meet these criteria. Here, we introduce a method to rapidly build linkage maps for salamanders, which are known for their enormous genome sizes. As proof of principle, we developed a linkage map with thousands …

Variation In Dna Methylation Is Not Consistently Reflected By Sociality In Hymenoptera, Karl M. Glastad, Samuel V. Arsenault, Kim L. Vertacnik, Scott M. Geib, Sasha Kay, Bryan N. Danforth, Sandra M. Rehan, Catherine R. Linnen, Sarah D. Kocher, Brendan G. Hunt

Biology Faculty Publications

Changes in gene regulation that underlie phenotypic evolution can be encoded directly in the DNA sequence or mediated by chromatin modifications such as DNA methylation. It has been hypothesized that the evolution of eusocial division of labor is associated with enhanced gene regulatory potential, which may include expansions in DNA methylation in the genomes of Hymenoptera (bees, ants, wasps, and sawflies). Recently, this hypothesis garnered support from analyses of a commonly used metric to estimate DNA methylation in silico, CpG content. Here, we test this hypothesis using direct, nucleotide-level measures of DNA methylation across nine species of Hymenoptera. In doing …

Genetic Diversity Among Eight Dendrolimus Species In Eurasia (Lepidoptera: Lasiocampidae) Inferred From Mitochondrial Coi And Coii, And Nuclear Its2 Markers, Alexander Kononov, Kirill Ustyantsev, Baode Wang, Victor C. Mastro, Victor Fet, Alexander Blinov, Yuri Baranchikov

Victor Fet

Background: Moths of genus Dendrolimus (Lepidoptera: Lasiocampidae) are among the major pests of coniferous forests worldwide. Taxonomy and nomenclature of this genus are not entirely established, and there are many species with a controversial taxonomic position. We present a comparative evolutionary analysis of the most economically important Dendrolimus species in Eurasia. Results: Our analysis was based on the nucleotide sequences of COI and COII mitochondrial genes and ITS2 spacer of nuclear ribosomal genes. All known sequences were extracted from GenBank. Additional 112 new sequences were identified for 28 specimens of D. sibiricus, D. pini, and D. superans from five regions …

Phylogeny And Species Boundaries In The “Flying Dragons” Of The Draco Maculatus Species Complex (Family Aamiedae), Randy Klabacka, Dr. Jack W. Sites

Journal of Undergraduate Research

Indo-Burma, comprising most of Mainland Southeast Asia east of India and north of Peninsular Malaysia, is a biodiversity hotspot within Southeast Asia that has been called a contender for the “hottest of hotspots” (Mittermeier, 1999). A remarkable majority of this species diversity remains hidden from human recognition in two areas: (1) undiscovered in natural habitat, and (2) conspicuously masquerading under known taxa. While solutions to the former require continued field work, solutions for the latter require further study of already identified taxa for hidden diversity therein. Indo-Burma is the endemic home to the “spotted flying dragon” (Draco maculatus; …

Systematics, Biogeography, And Species Delimitation Of The Malagasy Psorospermum (Hypericaceae), Heritiana S. Ranarivelo

Dissertations

Psorospermum belongs to the tribe Vismieae (Hypericaceae). Morphologically, Psorospermum is very similar to Harungana, which also belongs to Vismieae along with another genus, Vismia. Interestingly, Harungana occurs in both Madagascar and mainland Africa, as does Psorospermum; Vismia occurs in both Africa and the New World. However, the phylogeny of the tribe and the relationship between the three genera are uncertain. Using freshly collected specimens from my fieldwork as well as extant herbarium specimens, I aimed first, to generate a phylogeny of Psorospermum; second, to investigate its biogeography; and third, to investigate species boundaries within Malagasy Psorospermum …

Evolutionary Enhancement Of Zika Virus Infectivity In Aedes Aegypti Mosquitoes, Yang Liu, Jianying Liu, Senyan Du, Cheng-Feng Qin, Penghua Wang, Pei-Yong Shi, Gong Cheng

NYMC Faculty Publications

Zika virus (ZIKV) remained obscure until the recent explosive outbreaks in French Polynesia (2013-2014) and South America (2015-2016). Phylogenetic studies have shown that ZIKV has evolved into African and Asian lineages. The Asian lineage of ZIKV was responsible for the recent epidemics in the Americas. However, the underlying mechanisms through which ZIKV rapidly and explosively spread from Asia to the Americas are unclear. Non-structural protein 1 (NS1) facilitates flavivirus acquisition by mosquitoes from an infected mammalian host and subsequently enhances viral prevalence in mosquitoes. Here we show that NS1 antigenaemia determines ZIKV infectivity in its mosquito vector Aedes aegypti, which …

Molecular Phylogenetic Studies Of The Genera Of Tribe Polygonateae (Asparagaceae: Nolinoideae): Disporopsis, Heteropolygonatum, And Polygonatum., Aaron Jennings Floden

Doctoral Dissertations

The Polygonateae (Asparagaceae) are a subtribe of the Nolinoideae that is redefined here to include three genera which are investigated here: Disporopsis; Heteropolygonatum, and Polygonatum. This group of genera, characterized by their axillary-flowered habit, are closely related but differ greatly in their morphology, cytology, and diversity. A molecular phylogeny is presented to show their relationships to one another and to closely related outgroups based on data from whole chloroplast genomes with low taxonomic sampling. The results show that the genera of the Polygonateae are each monophyletic, and also show that a fourth genus, Maianthemum, that was …

Exploring The Use Of Free Bioinformatics Modules In An Introductory Biochemistry Course, Charlsey Dodgen, Uzezi Uwerosuo, Chulhee Kang, Cathy Lee

Georgia Journal of Science

Although bioinformatics, the use of computational science to study biology, has become imperative in many areas of the biological sciences and related career paths, introductory biochemistry courses may disregard practical knowledge on bioinformatics. For this reason, we merged a hands-on activity module into an undergraduate biochemistry course in two ways. First, we incorporated bioinformatics modules for building phylogenetic trees by aligning the active sites of 10 chosen related α-amylase enzymes using freely available data. Secondly, we chose three of those 10 α-amylase enzymes to compare the 3D structure of their active sites. This module gives the students an opportunity to …

Assessing And Improving Student Understanding Of Tree-Thinking, Tyler A. Kummer

Theses and Dissertations

Evolution is the unifying theory of biology. The importance of understanding evolution by those who study the origins, diversification and diversity life cannot be overstated. Because of its importance, in addition to a scientific study of evolution, many researchers have spent time studying the acceptance and the teaching of evolution. Phylogenetic Systematics is the field of study developed to understand the evolutionary history of organisms, traits, and genes. Tree-thinking is the term by which we identify concepts related to the evolutionary history of organisms. It is vital that those who undertake a study of biology be able to understand and …

The Family Rhabdoviridae: Mono- And Bipartite Negative-Sense Rna Viruses With Diverse Genome Organization And Common Evolutionary Origins, Ralf G. Dietzgen, Hideki Kondo, Michael M. Goodin, Gael Kurath, Nikos Vasilakis

Plant Pathology Faculty Publications

The family Rhabdoviridae consists of mostly enveloped, bullet-shaped or bacilliform viruses with a negative-sense, single-stranded RNA genome that infect vertebrates, invertebrates or plants. This ecological diversity is reflected by the diversity and complexity of their genomes. Five canonical structural protein genes are conserved in all rhabdoviruses, but may be overprinted, overlapped or interspersed with several novel and diverse accessory genes. This review gives an overview of the characteristics and diversity of rhabdoviruses, their taxonomic classification, replication mechanism, properties of classical rhabdoviruses such as rabies virus and rhabdoviruses with complex genomes, rhabdoviruses infecting aquatic species, and plant rhabdoviruses with both mono- …

Phylogenetic Status And Genetic Diversity Of Corsac Fox(Vulpes Corsac) In Golestan Province, Iran, Jalil Imani Harsini, Hamid Reza Rezaei, Saeid Naderi, Hosein Varasteh Moradi

Turkish Journal of Zoology

The lack of detailed and precise reports about the presence of corsac fox has caused ambiguities about the presence or absence or even extinction status of this species in its distribution range in Iran. Therefore, this is one of the complicated issues in Iran?s wildlife fauna and there has been no clear scientific answer to this question to date. In this study, 7 mitochondrial DNA control region haplotypes were identified in 10 corsac fox samples (4 tissue and 6 scat) taken from Golestan Province in Iran, and haplotype diversity was equal to 0.93. The genetic distance between individuals showed large …

Morphological And Molecular Characterization And Phylogenetic Position Of A Newrecord, Tylenchorhynchus Zeae, And Some Known Species Of Telotylenchidae Siddiqi,1960 And Merliniidae Siddiqi, 1971 From Iran, Somaye Alvani, Esmat Mahdikhani Moghaddam, Hamid Rouhani, Abbas Mohammadi

Turkish Journal of Zoology

In order to identify the plant-parasitic nematodes associated with Berberis vulgaris, Crocus sativus, and Ziziphus zizyphus, 360 soil samples were collected from the rhizosphere of these plants in the South Khorasan Province of Iran during 2012-2014. Among the identified species, Tylenchorhynchus zeae Sethi and Swarup, 1968 of Telotylenchidae Siddiqi, 1960 is a new record from Iran and the isolate is described and illustrated based on morphological, morphometric, and molecular characteristics. The phylogenetic tree inferred from partial sequences of the 28S rRNA (D2D3 segments) grouped the Iranian isolate with other T. zeae sequences, forming a strongly supported clade (Bayesian posterior probability: …

Komarekiella Atlantica Gen. Et Sp. Nov. (Nostocaceae, Cyanobacteria): A New Subaerial Taxon From The Atlantic Rainforest And Kauai, Hawaii, Jeffrey R. Johansen, Guilherme Scotta Hentschke, Nicole Pietrasiak, Janaina Rigonato, Marli F. Fiore, Célia Leite Sant’Anna

2017 Faculty Bibliography

Six strains of Cyanobacteria sampled in the Brazilian Atlantic rainforest and one strain from Kauai, Hawaii, were studied using morphological and molecular approaches, including 16S rRNA gene phylogenies and 16S–23S ITS secondary structures, and are herein described as Komarekilla atlantica gen. et sp. nov.. Morphologically they are similar to Nostoc, Desmonostoc, Halotia, and Mojavia and indistinguishable from Chlorogloeopsis. The parsimony and Bayesian phylogenies of the 16S rDNA show that these strains are close to nostocacean strains, in strongly supported clades and separated from all other genera. The secondary structures of the 16S–23S ITS were very consistent between strains of K. …

An 18s Rdna Perspective On The Classification Of Criconematoidea, Thomas O. Powers, Timothy Harris, Rebecca Higgins, Peter Mullin, Kirsten Powers

Department of Plant Pathology: Faculty Publications

In the nematode family Criconematidae, a taxonomy primarily based on cuticle characters has created classifications that are notoriously volatile. Molecular characters may lead to their stabilization. A phylogenetic tree of Criconematoidea was constructed using 166 new near full-length 18S rDNA sequences and 58 sequences from GenBank. Bayesian and maximum likelihood (ML) analyses produced trees with similar topologies. Major features include a strongly supported clade that includes Criconematidae and Hemicycliophoridae, excluding Paratylenchidae and Tylenchulidae. Another well-supported clade groups Criconema, Ogma, Crossonema, and Hemicriconemoides plus Xenocriconemella, combining nematodes with cuticular scales with those without scales at any life stage. Mesocriconema, Discocriconemella limitanea, …

The Female Urogynecological Microbiome: Determining Niche Specificity, Krystal Thomas-White

Dissertations

Contrary to dogma, urine is not sterile. Recent discoveries show that the female urinary bladder contains a unique microbiome,with differences in healthy and disease states. This female urinary microbiome (FUM) is distinguishable from vulvo-vaginal contamination; yet, only the few centimeters of the urethra separate these two niches. Recent studies show that the most common bladder organisms are Lactobacillus, Gardnerella, Streptococcus, Corynebacterium, and a diverse group of anaerobes, the same genera commonly found in the vagina. Thus, we asked if the bladder and vaginal microbiomes are interconnected.

Previous work suggests a link between these two niches. The vaginal tract of reproductive …

Redescription Of Euscorpius Tauricus (C.L. Koch, 1837), With The Description Of Two New Related Species From Greece (Scorpiones: Euscorpiidae), Gioele Tropea, Victor Fet, Aristeidis Parmakelis, Panayiota Kotsakiozi, Iasmi Stathi

Biological Sciences Faculty Research

Euscorpius tauricus (C. L. Koch, 1837) was previously known only from the Crimea Peninsula, Ukraine. We report an unexpected presence of this species in the Cyclades Islands (Greece) and northwestern Anatolia (Turkey). In addition we designate a neotype for this species. We synonymize Euscorpius carpathicus aegaeus Di Caporiacco, 1950 syn. n., from Antiparos Island and Euscorpius rahsenae Yağmur et Tropea, 2013 syn. n., from Anatolia, with E. tauricus. In addition, we describe two new species related to E. tauricus, from the Cyclades Islands: E. curcici sp. n., from Ios and Sikinos Islands, and E. amorgensis sp. n., from Amorgos Island. …

Phylogenomic Analysis Of Copepoda (Arthropoda, Crustacea) Reveals Unexpected Similarities With Earlier Proposed Morphological Phylogenies, Seong-Il Eyun

Nebraska Center for Biotechnology: Faculty and Staff Publications

Background: Copepods play a critical role in marine ecosystems but have been poorly investigated in phylogenetic studies. Morphological evidence supports the monophyly of copepods, whereas interordinal relationships continue to be debated. In particular, the phylogenetic position of the order Harpacticoida is still ambiguous and inconsistent among studies. Until now, a small number of molecular studies have been done using only a limited number or even partial genes and thus there is so far no consensus at the order-level.

Results: This study attempted to resolve phylogenetic relationships among and within four major copepod orders including Harpacticoida and the phylogenetic position of …

A New Species Of Catenotaenia (Cestoda: Catenotaeniidae) From Pygeretmus Pumilio Kerr, 1792 From The Gobi Of Mongolia, Altangerel Tsogtsaikhan Dursahinhan, Batsaikhan Nyamsuren, Danielle Marie Tufts, Scott Lyell Gardner

Scott L. Gardner Publications

From 1999 through 2012, a total of 541 individual rodents (jerboas of the family Dipodidae) were collected from several habitat types, primarily from the Gobi region of Mongolia, and were examined for helminth and protistan parasites. Of those rodents, 25 were identified as Pygeretmus pumilio Kerr, 1792 (Rodentia: Dipodidae), whereas 516 were other species of jerboa from the provinces of Dornogobi, Dundgobi, Omnogobi, Ovorhangai, Bayanhongor, Gobi Altai, and Hovd. During our field work, we collected several cestodes; some of which represented undescribed species, and these new species occurred in 40% of P. pumilio from four separate collecting localities. We designate …

A New Species Of Micromeria (Lamiaceae) From Köyceğiz (Muğla, Southwest Of Turkey), Hayri̇ Duman, Tuncay Di̇rmenci̇

Turkish Journal of Botany

A new species, Micromeria aybalae H.Duman & Dirmenci (Lamiaceae), Micromeria Benth. sect. Micromeria, is described from Muğla Province in southwestern Turkey. A description, taxonomic note, distribution map, habitat, and nrDNA ITS and cpDNA trnL-F based phylogeny are presented. The differences between the new species and its allies, Micromeria cremnophila Boiss. & Heldr. s.l. and M. hispida Benth., are discussed, and an identification key is provided for the Turkish Micromeria.

Taxonomy Of Poa Jubata And A New Section Of The Genus (Poaceae), Evren Cabi̇, Robert John Soreng, Lynn Gillespie

Turkish Journal of Botany

Poa jubata A.Kern. is an ephemeral, southeastern European species of which little is known. A molecular phylogenetic analysis of Poa L., including all previously identified major lineages, shows this species to be isolated, with a genotype here designated as J (plastid) j (nrDNA). It is assigned to the monotypic P. sect. Jubatae sect. nov. The section is differentiated from other Poa sections in having 5-nerved upper glumes, very narrow palea flanges, an annual habit, and erect solitary culms. Poa jubata occurs along coastal regions of the Balkans and is rather rare. Two new collections were made in 2015 in Thrace, …

Dianthus Ucarii (Caryophyllaceae): A New Species From The Northwest Of Turkey, Ergi̇n Hamzaoğlu, Murat Koç, İlker Büyük

Turkish Journal of Botany

Dianthus ucarii Hamzaoğlu & Koç (Caryophyllaceae) is described as a new species to science based on material collected in Kırklareli Province in northwestern Turkey. The new taxon belongs to sect. Carthusiani (Boiss.) F.N.Williams and it is closely related to Dianthus pinifolius Sm., an Eastern Mediterranean element. A description, illustration, and identification key for the new species are given. In addition, D. ucarii and D. pinifolius are compared in terms of general morphology and molecular phylogeny.