62 Works

Data from: Sequential adaptive introgression of the mitochondrial genome in Drosophila yakuba and D. santomea

Ana Llopart, Danielle Herrig, Evgeny Brud & Zachary Stecklein
Interspecific hybridization provides the unique opportunity for species to tap into genetic variation present in a closely related species and potentially take advantage of beneficial alleles. It has become increasingly clear that when hybridization occurs, mitochondrial DNA (mtDNA) often crosses species boundaries, raising the possibility that it could serve as a recurrent target of natural selection and source of species’ adaptations. Here we report the sequences of 46 complete mitochondrial genomes of Drosophila yakuba and...

Data from: Validation of serum neurofilaments as prognostic & potential pharmacodynamic biomarkers for ALS

Michael Benatar, Lanyu Zhang, Lily Wang, Volkan Granit, Jeffrey Statland, Richard Barohn, Andrea Swenson, John Ravitz, Carlayne Jackson, Ted Burns, Jaya Trivedi, Erik Pioro, James Caress, Jonathan Katz, Jacob McCauley, Rosa Rademakers, Andrea Malaspina, Lyle Ostrow & Joanne Wuu
Objective. Identify preferred neurofilament assays, and clinically validate serum NfL and pNfH as prognostic and potential pharmacodynamic biomarkers relevant to ALS therapy development. Methods. Prospective, multi-center, longitudinal observational study of patients with ALS (n=229), primary lateral sclerosis (PLS, n=20) and progressive muscular atrophy (PMA, n=11). Biological specimens were collected, processed and stored according to strict standard operating procedures (SOPs) 1. Neurofilament assays were performed in a blinded manner by independent contract research organizations (CROs). Results....

Data from: Male phenotypes in a female framework: evidence for degeneration in sperm produced by male snails from asexual lineages

Joseph Jalinsky, John Logsdon & Maurine Neiman
How changes in selective regimes affect trait evolution is an important open biological question. We take advantage of naturally occurring and repeated transitions from sexual to asexual reproduction in a New Zealand freshwater snail species, Potamopyrgus antipodarum, to address how evolution in an asexual content— including the potential for relaxed selection on male-specific traits— influences sperm morphology. The occasional production of male offspring by the otherwise all-female asexual P. antipodarum lineages affords a unique and...

Data from: Sex in the wild: how and why field-based studies contribute to solving the problem of sex

Maurine Neiman, Patrick Gerardus Meirmans, Tanja Schwander & Stephanie Meirmans
Why and how sexual reproduction is maintained in natural populations, the so-called “queen of problems”, is a key unanswered question in evolutionary biology. Recent efforts to solve the problem of sex have often emphasized results generated from laboratory settings. Here, we use a survey of representative “sex in the wild” literature to review and synthesize the outcomes of empirical studies focused on natural populations. Especially notable results included relatively strong support for mechanisms involving niche...

Data from: De novo transcriptome characterization of a sterilizing trematode parasite (Microphallus sp.) from two species of New Zealand snails

Laura Bankers & Maurine Neiman
Snail-borne trematodes represent a large, diverse, and evolutionarily, ecologically, and medically important group of parasites, often imposing strong selection on their hosts and causing host morbidity and mortality. Even so, there are very few genomic and transcriptomic resources available for this important animal group. We help to fill this gap by providing transcriptome resources from trematode metacercariae infecting two congeneric snail species, Potamopyrgus antipodarum and P. estuarinus. This genus of New Zealand snails has gained...

Data from: The quantitative genetics of incipient speciation: heritability and genetic correlations of skeletal traits in populations of diverging Favia fragum ecomorphs.

David B Carlon, Ann F Budd, Catherine Lippé & Rose L Andrew
Recent speciation events provide potential opportunities to understand the microevolution of reproductive isolation. We used a marker-based approach and a common garden to estimate the additive genetic variation in skeletal traits in a system of two ecomorphs within the coral species Favia fragum: a Tall ecomorph that is a seagrass specialist, and a Short ecomorph that is most abundant on coral reefs. Considering both ecomorphs, we found significant narrow-sense heritability (h²) in a suite of...

Data from: Wide variation in ploidy level and genome size in a New Zealand freshwater snail with coexisting sexual and asexual lineages

Maurine Neiman, Dorota Paczesniak, Deanna M Soper, Austin T Baldwin & Gery Hehman
Natural animal populations are rarely screened for ploidy-level variation at a scale that allows detection of potentially important aberrations of common ploidy patterns. This type of screening can be especially important for the many mixed sexual/asexual systems where sexuals are presumed to be dioecious diploids and asexuals are assumed to be triploid and all-female. For example, elevation of ploidy level above triploidy can be a source of genetic variation and raises the possibility of gene...

Data from: Divergence before the host shift? Prezygotic reproductive isolation among three varieties of a specialist fly on a single host plant

Alaine C. Hippee, Maren E. Elnes, Jarod S. Armenta, Marty A. Condon & Andrew A. Forbes
1. Although divergence via host-plant shifting is a common theme in the speciation of some phytophagous insects, it is not clear whether host shifts are typically initiators of speciation or if they instead contribute to divergence events already in progress. While host shifts appear to be generally associated with speciation events for flies in the genus Strauzia, three sympatric varieties of the sunflower fly [Strauzia longipennis (Wiedemann)] co-occur on the same host plant in the...

Data from: Genome-wide association studies in dogs and humans identify ADAMTS20 as a risk variant for cleft lip and palate

Zena T. Wolf, Harrison A. Brand, John R. Shaffer, Elizabeth J. Leslie, Boaz Arzi, Cali E. Willet, Timothy C. Cox, Toby McHenry, Nicole Narayan, Eleanor Feingold, Xioajing Wang, Saundra Sliskovic, Nili Karmi, Noa Safra, Carla Sanchez, Frederic W. B. Deleyiannis, Jeffrey C. Murray, Claire M. Wade, Mary L. Marazita & Danika L. Bannasch
Cleft lip with or without cleft palate (CL/P) is the most commonly occurring craniofacial birth defect. We provide insight into the genetic etiology of this birth defect by performing genome-wide association studies in two species: dogs and humans. In the dog, a genome-wide association study of 7 CL/P cases and 112 controls from the Nova Scotia Duck Tolling Retriever (NSDTR) breed identified a significantly associated region on canine chromosome 27 (unadjusted p=1.1 x 10-13; adjusted...

Data from: Are there age-related differences in the ability to learn configural responses?

Rachel Clark, Michael Freedberg, Eliot Hazeltine & Michelle W. Voss
Age is often associated with a decline in cognitive abilities that are important for maintaining functional independence, such as learning new skills. Many forms of motor learning appear to be relatively well preserved with age, while learning tasks that involve associative binding tend to be negatively affected. The current study aimed to determine whether age differences exist on a configural response learning task, which includes aspects of motor learning and associative binding. Young (M =...

Tree species of wet tropical forests differ in their tissue biochemistry and effects on soil carbon dynamics

Ann Russell, Rachel Marek & Daniel Olk
Given the hypothesized effects on soil organic matter (SOM) of polyphenols in plant tissues, differences among tree species in their biochemical composition could influence the turnover and accrual of SOM in various ways. The extent to which the biochemical composition of leaf and fine-root tissues differ among tropical tree species, and the effects on soil dynamics, are largely undocumented, however. We used cupric oxide analyses of plant tissues and soil in long-term, replicated, mono-dominant 15-yr-old...

Data from: Male offspring production by asexual Potamopyrgus antipodarum, a New Zealand snail

Maurine Neiman, Katelyn Larkin, Andrew R. Thompson & Peter Wilton
As only females contribute directly to population growth, sexual females investing equally in sons and daughters experience a two-fold cost relative to asexuals producing only daughters. Typically, researchers have focused on benefits of sex that can counter this ‘cost of males’ and thus explain its predominance. Here, we instead ask whether asexuals might also pay a cost of males by quantifying the rate of son production in 45 experimental populations (‘lineages’) founded by obligately asexual...

Data from: What’s in an outgroup? The impact of outgroup choice on the phylogenetic position of Thalattosuchia (Crocodylomorpha) and the origin of Crocodyliformes

Eric W. Wilberg
Outgroup sampling is a central issue in phylogenetic analysis. However, good justification is rarely given for outgroup selection in published analyses. Recent advances in our understanding of archosaur phylogeny suggest that many previous studies of crocodylomorph and crocodyliform relationships have rooted trees on outgroup taxa that are only very distantly related to the ingroup (e.g., Gracilisuchus stipanicicorum), or might actually belong within the ingroup. Thalattosuchia, a group of Mesozoic marine crocodylomorphs, has a controversial phylogenetic...

Data from: Corollary discharge in precerebellar nuclei of sleeping infant rats

Didhiti Mukherjee, Greta Sokoloff & Mark S. Blumberg
In week-old rats, somatosensory input arises predominantly from external stimuli or from sensory feedback (reafference) associated with myoclonic twitches during active sleep. A previous study suggested that the brainstem motor structures that produce twitches also send motor copies (or corollary discharge, CD) to the cerebellum. We tested this possibility by recording from two precerebellar nuclei—the inferior olive (IO) and lateral reticular nucleus (LRN). In most IO and LRN neurons, twitch-related activity peaked sharply around twitch...

Data from: Characterization of transcriptomes from sexual and asexual lineages of a New Zealand snail (Potamopyrgus antipodarum)

Peter R. Wilton, Daniel B. Sloan, John M. Logsdon, Harshavardhan Doddapaneni, Maurine Neiman &
Understanding the evolution and maintenance of sexual reproduction is one of the central challenges of evolutionary biology, yet we know very little about how sex influences molecular evolution. The New Zealand freshwater snail Potamopyrgus antipodarum is ideally suited to address this knowledge gap because obligately sexual individuals often coexist with multiple independently derived obligately asexual lineages. This unusual situation allows direct comparisons both between sexual and asexual P. antipodarum and across populations that differ in...

Data from: Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history

Jeffrey L. Peters, Trina E. Robert, Kevin Winker, Kevin G. McCracken & Trina E. Roberts
Inferring aspects of the population histories of species using coalescent analyses of non-coding nuclear DNA has grown in popularity. These inferences, such as divergence, gene flow, and changes in population size, assume that genetic data reflect simple population histories and neutral evolutionary processes. However, violating model assumptions can result in a poor fit between empirical data and the models. We sampled 22 nuclear intron sequences from at least 19 different chromosomes (a genomic transect) to...

Data from: Meek mothers with powerful daughters: effects of novel host environments and small trait differences on parasitoid competition

Gabriela Hamerlinck, Nathan P. Lemoine, Glen R. Hood, Karen C. Abbott & Andrew A. Forbes
Outcomes of competition may depend both on subtle differences in traits relevant to fitness and on how those traits are expressed in the context of the environment. Environmental effects on traits impacting population dynamics are often overlooked in studies of parasitic wasp (parasitoid) competition. Lineages of the parasitoid Diachasma alloeum (Hymenoptera: Braconidae) differ in relative ovipositor length (a trait affecting the proportion of hosts available for parasitism). Since the size of natal hosts affects the...

Data from: Tales from the crypt: a parasitoid manipulates the behaviour of its parasite host

Kelly L. Weinersmith, Sean M. Liu, Andrew A. Forbes & Scott P. Egan
There are many examples of apparent manipulation of host phenotype by parasites, yet few examples of hypermanipulation—where a phenotype-manipulating parasite is itself manipulated by a parasite. Moreover, few studies confirm manipulation is occurring by quantifying whether the host's changed phenotype increases parasite fitness. Here we describe a novel case of hypermanipulation, in which the crypt gall wasp Bassettia pallida (a phenotypic manipulator of its tree host) is manipulated by the parasitoid crypt-keeper wasp Euderus set,...

Character data for taxa added to phylogenetic analyses in \"A new crocodylid from the middle Miocene of Kenya and the timing of crocodylian faunal change in the late Cenozoic of Africa\"

Christopher Brochu
Brochuchus is a small crocodylid originally based on specimens from the early Miocene of Rusinga Island, Lake Victoria, Kenya. Here, we report occurrences of Brochuchus from several early and middle Miocene sites. Some are from the Lake Victoria region, and others are in the Lake Turkana Basin. Specimens from the middle Miocene Maboko locality form the basis of a new species, Brochuchus parvidens, which has comparatively smaller maxillary alveoli. Because of the smaller alveoli, the...

Data from: Parasite resistance predicts fitness better than fecundity in a natural population of the freshwater snail Potamopyrgus antipodarum

Dorota Paczesniak, Kirsten Klappert, Kirstin Kopp, Maurine Neiman, Katri Seppälä, Curtis M. Lively & Jukka Jokela
The cost of males should give asexual females an advantage when in competition with sexual females. In addition, high-fecundity asexual genotypes should have an advantage over low-fecundity clones, leading to reduction in clonal diversity over time. To evaluate fitness components in a natural population, we measured the annual reproductive rate of individual sexual and asexual female Potamopyrgus antipodarum, a New Zealand freshwater snail, in field enclosures that excluded competitors and predators. We used allozyme genotyping...

Abnormal Development of Cerebellar-Striatal Circuitry in Huntington’s Disease: Supplemental Figures

Jordan Schultz, Alexander Tereshchenko, Joel Bruss, Vincent Magnotta, Eric Epping & Peg Nopoulos
Objective: To test the hypothesis that the trajectory of functional connections over time of the striatum and the cerebellum differs between pre-symptomatic patients with the HD gene expansion (GE) and patients with a family history of HD but without the gene-expansion (GNE), we evaluated function MRI data from the Kids-HD study. Methods: We utilized resting-state, functional MRI data from participants in the Kids-HD study between 6 to 18 years old. Participants were divided into the...

Data from: The neuropathic diabetic foot ulcer microbiome is associated with clinical factors.

Sue E. Gardner, Stephen L. Hillis, Kris Heilmann, Julia A. Segre & Elizabeth A. Grice
Nonhealing diabetic foot ulcers (DFUs) are a common and costly complication of diabetes. Microbial burden, or "bioburden," is believed to underlie delayed healing, although little is known of those clinical factors that may influence microbial load, diversity, and/or pathogenicity. We profiled the microbiomes of neuropathic nonischemic DFUs without clinical evidence of infection in 52 individuals using high-throughput sequencing of the bacterial 16S ribosomal RNA gene. Comparatively, wound cultures, the standard diagnostic in the clinic, vastly...

Data from: Sequential divergence and the multiplicative origin of community diversity

Glen R. Hood, Andrew A. Forbes, Thomas H. Q. Powell, Scott P. Egan, Gabriela Hamerlinck, James J. Smith & Jeffrey L. Feder
Understanding how new life forms originate is a central question in biology. Population divergence is usually studied with respect to how single lineages diverge into daughter taxa. However, populations may not always differentiate in isolation; divergence of one taxon could create new niche opportunities in higher trophic levels, leading to the sequential origin of many new taxa. Here, we show that this may be occurring for three species of parasitoid wasps attacking Rhagoletis fruit flies....

Data from: Genetic variation for mitochondrial function in the New Zealand freshwater snail Potamopyrgus antipodarum

Joel Sharbrough, Jennifer L. Cruise, Megan Beetch, Nicole M. Enright & Maurine Neiman
The proteins responsible for mitochondrial function are encoded by two different genomes with distinct inheritance regimes, rendering rigorous inference of genotype–phenotype connections intractable for all but a few model systems. Asexual organisms provide a powerful means to address these challenges because offspring produced without recombination inherit both nuclear and mitochondrial genomes from a single parent. As such, these offspring inherit mitonuclear genotypes that are identical to the mitonuclear genotypes of their parents and siblings and...

Data from: Phylogenomic analyses of Crassiclitellata support major Northern and Southern Hemisphere clades and a Pangaean origin for earthworms

Frank Anderson, Bronwyn Waller Williams, Kevin H. Horn, Christer Erséus, Kenneth M. Halanych, Scott R. Santos & Samuel W. James
Background: Earthworms (Crassiclitellata) are a diverse group of annelids of substantial ecological and economic importance. Earthworms are primarily terrestrial infaunal animals, and as such are probably rather poor natural dispersers. Therefore, the near global distribution of earthworms reflects an old and likely complex evolutionary history. Despite a long-standing interest in Crassiclitellata, relationships among and within major clades remain unresolved. Methods: In this study, we evaluate crassiclitellate phylogenetic relationships using 38 new transcriptomes in combination with...

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