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At least 19 recordsLinked to original sources

bioRxiv2016

A logic approach to modeling nomenclatural change

We utilize an Answer Set Programming (ASP) approach to show that the principles of nomenclature are tractable in computational logic. To this end we design a hypothetical, 20 nomenclatural taxon use case with starting conditions that embody several overarching principles of the International Code of Zoological Nomenclature; including Binomial Nomenclature, Priority, Coordination, Homonymy, Typification, and the structural requirement of Gender Agreement. The use case ending conditions are triggered by the reinterpretation of the diagnostic features of one of 12 type specimens anchoring the corresponding species-level names. Permutations of this child-to-parent reassignment action lead to 36 alternative scenarios, where each scenario requires 1-14 logically contingent nomenclatural emendations. We show that an ASP transition system approach can correctly infer the Code-mandated changes for each scenario, and visually output the ending conditions. The results provide a foundation for further developing logic-based nomenclatural change optimization and compliance verification services, which could be applied in globally coordinated nomenclatural registries. More generally, logic explorations of nomenclatural and taxonomic change scenarios provide a novel means of assessing design biases inherent in the principles of nomenclature, and thus may inform the design of future, big data-compatible identifier systems for systematic products that recognize and mitigate these constraints.

Evolutionary Biology↗

bioRxiv2016

Are foundation species effects different than those of dominant species? A case study of ant assemblages in northeastern North American forests

Foundation species uniquely control associated biodiversity through non-trophic effects, whereas dominant species are locally abundant but are replaceable in ecological systems. Long-term data on ant assemblages at the Harvard Forest Hemlock Removal Experiment (HF-HeRE) and the Black Rock Future of Oak Forests Experiment (BRF-FOFE) provide insights into how ant assemblages change and reassemble following the loss of a foundation species (Tsuga canadensis) or a dominant genus (Quercus). At HF-HeRE, removal of T. canadensis trees resulted in taxonomic and functional shifts in ant assemblages relative to control stands. In contrast, ant assemblages at BRF-FOFE varied little regardless of whether oaks or non-oaks were removed from the canopy. Non-trophic effects of foundation species were stronger than indirect trophic effects on taxonomic and functional diversity of ant assemblages. In contrast, non-trophic effects of dominant species were weaker than indirect trophic effects on ant taxonomic diversity and some measures of ant functional diversity.\n\nStatement of authorshipA.M. Ellison and S. Record conceived the study. A.M. Ellison, T. 17 McCabe, and S. Record collected field data. T. McCabe and S. Record did the taxonomic diversity analyses. B. Baiser and S. Record did the functional diversity analyses. All authors contributed to drafts of the manuscript.\n\nData accessibilityAll data (i.e., ant and trait) and R code are available from the Harvard Forest Data Archive (http://harvardforest.fas.harvard.edu/data-archive), datasets HF-118 (HF-HeRE) and HF-097 (BRF-FOFE). Nomenclature follows Bolton (2016); voucher specimens are stored at the Harvard Forest and at the Museum of Comparative Zoology.

Ecology↗

bioRxiv2017

Chromosome Number of the Monarch Butterfly, Danaus plexippus (Linnaeus 1758) and the Danainae

The monarch butterfly, Danaus plexippus (Linnaeus 1758) is a charismatic butterfly known for its multi-generational migration in Eastern North America, and is emerging as an important system in the study of evolutionary genetics. Assigning genes or genetic elements to chromosomes is an important step when considering how genomes evolved. The monarch butterfly has a reported haploid chromosome number of 30. The specimens that this count is based on are from Madras, India where D. plexippus does not occur. As a consequence the reported haplotype for the D. plexippus is incorrect. A literature review revealed that the specimens this count was based on were most likely Danaus genutia (Cramer 1779), which Linnaeus and others conflated with D. plexippus. In a 1954 Opinion (#282) the International Code of Zoological Nomenclature decided that the name D. genutia refers to specimens originating from the Orient and D. plexippus to those from North America. To clarify the haplotype number of D. plexippus from North America I conducted chromosome squashes of male 5th instar larvae. All specimens examined had a haploid chromosome count of n = 28. Following these new data, I then reconstructed the evolution of haplotypes throughout the Danainae subfamily to provide a testable hypothesis on the evolution of chromosome number for this group.

evolutionary biology↗

bioRxiv2017

Enterovirus-A76 of South-East Asian ancestry in a Captive Chimpanzee (Pan troglodytes) in Jos, Nigeria

We recently detected EV-A119 and EV-B111 (previously shown to co-circulate between nonhuman primates (NHPs) and humans) in Nigerian children diagnosed with acute flaccid paralysis (AFP). This study was designed to investigate and catalogue EVs present in captive NHPs in Nigeria.\n\nTwenty-seven fecal samples collected from captive NHPs in a Wild Life Park and Zoological garden at Jos, Nigeria in April 2016 were analyzed in this study. Samples were resuspended in a phosphate buffered saline (PBS)/chloroform mixture, and the clarified supernatant was subjected to RNA extraction, cDNA synthesis, a Panenterovirus 5I-UTR assay, and three different enterovirus VP1 snPCR assays. All amplicons from the snPCR assays were sequenced, and enteroviruses identified using the enterovirus genotyping tool and phylogenetic analysis.\n\nEight (29.63%) (two each from Chimpanzees, Patas Monkey, Mona Monkey and Baboon) of the 27 samples were positive for the 5I-UTR assay. One (3.70%) of the 27 samples was positive for the enterovirus VP1 snPCR assays in addition to its positivity by 5I-UTR assay. The same sample happens to be one of the two samples from Chimpanzees that tested positive for the 5I-UTR assay, and it was subsequently identified as EV-A76 of South-East Asia ancestry.\n\nThis study documents the first recorded attempt to detect and identify enteroviruses in NHPs in Nigeria. It also reports the first detection and identification of EV-A76 in Nigeria and particularly in a NHP. It is of utmost importance that the enterovirus VP1 assays be improved to enable detection of EVs that have been detected in NHPs but yet to be described in humans.

microbiology↗

bioRxiv2013

Filling up the tree: considering the self-organization of avian roosting behavior

In this paper, models for understanding bird roosting will be considered for purposes of developing better Artificial Life models of complex behavior. Roosting involves multiple flocks of birds picking a single tree limb to rest on for the night, and can be considered an iterative, time-dependent process that unfolds over a 45-minute interval roughly corresponding to twilight. Two models will be used to better understand the main components of this behavior. The constrained dynamics model, which represents continuous random absorption on a one-dimensional lattice, will be used to characterize the dynamics of crowding in the tree structure over time. A second approach involves the relationships between complex networks and roosting behaviors, in particular the evolution of structured networks via rules of incorporation and interaction. Finally, the percolation model will be proposed as a way to bridge behaviors explained by the constrained dynamics and complex network models.

Zoology↗

bioRxiv2013

Morphometrics of a wild Asian elephant exhibiting disproportionate dwarfism

Dwarfism is a condition characterized by shorter stature, at times accompanied by differential skeletal growth pro-portions relative to the species-typical physical conformation. Causes vary and well-documented in humans as well as certain mammalian species in captive or laboratory conditions, but rarely observed in the wild. Here we report on a single case of apparent dwarfism in a free-ranging adult male Asian elephant (Elephas maximus) in Sri Lanka, comparing physical dimensions to those of other males in the same population, males in other populations, and records in previous literature. The subject was found to have a shoulder height of approximately 195cm, is shorter than the average height of typical mature males, with a body length of 218cm. This ratio of body length to height deviates from what is typically observed, which is approximately 1:1. In absolute height the subject was similar to the attributes of a captive elephant documented in 1955 in Sri Lanka, also said to be a dwarf, however the two specimens differed in the relative proportions of height vs. body length. The subject also exhibits a slight elongation of the skull. We discuss how this phenotype compares to cases of dwarfism in other non-human animals.

Zoology↗

bioRxiv2014

Immune stimulation reduces sleep and memory ability in Drosophila melanogaster

Psychoneuroimmunology studies the increasing number of connections between neurobiology and immunology. We establish Drosophila melanogaster as a tractable model in this field by demonstrating the effects of the immune response on two fundamental behaviours: sleep and memory ability.\n\nWe used the Geneswitch system to upregulate peptidoglycan receptor protein (PGRP) expression, thereby stimulating the immune system in the absence of infection. Geneswitch was activated by feeding the steroid RU486, to the flies. Importantly, by stimulating the immune system of adult flies in the absence of infection we have avoided the added complications of developmental and disease effects that have confounded other studies. We used an aversive classical conditioning paradigm to quantify memory and measures of activity to infer sleep.\n\nImmune stimulated flies exhibited reduced levels of sleep, which could not be explained by a generalised increase in waking activity. The effects on sleep were more pronounced for day compared to night sleep. Immune stimulated flies also showed a reduction in memory abilities.\n\nThese are important results as they establish Drosophila as a model for immune-neural interactions and provide a possible role for sleep in the interplay between the immune response and memory.

Zoology↗

bioRxiv2014

Mitochondrial DNA variation and structure among North American populations of Megaselia scalaris

The scuttle fly Megaselia scalaris is a pest species whose larvae consume living or dead plant or animal tissue, and parasitize humans. Although known to exist on most continents, often transported passively with humans, the connectivity between populations has not been investigated. We use mitochondrial cytochrome B sequences to investigate structure among North American isolates of this species. Despite small sample sizes, we detected statistically significant structure among populations. This finding suggests that local measures may be effective in controlling this pest species.

Zoology↗

bioRxiv2014

The mandibular gland in Nasonia vitripennis (Hymenoptera: Pteromalidae)

The mandibular gland of Nasonia vitripennis (Hymenoptera: Pteromalidae) is visualized for the first time, using Confocal Laser Scanning Microscopy and dissection. The gland was previously hypothesized to exist, based on observations of the wasps courtship behaviors, but its presence had never been confirmed.

Zoology↗

bioRxiv2014

The impact of radio-tags on Ruby-throated Hummingbirds (Archilochus colubris)

Radio telemetry has advanced the field of wildlife biology, especially with the miniaturization of radio-tags. However, the major limitation faced with radio-tagging birds is the size of the animal to which a radio-tag can be attached. We tested how miniature radio-tags affected flight performance and behavior of Ruby-throated Hummingbirds (Archilochus colubris), possibly the smallest bird species to be fitted with radio-tags. Using eyelash adhesive, we fitted hatch year individuals (n=20 males and 15 females) with faux radio-tags of three sizes varying in mass and antenna length (220mg-12.7cm, 240mg-12.7cm, and 220mg-6.35cm), then filmed the birds in a field aviary to quantify activity budgets. We also estimated flight range using flight simulation models. When the three radio-tag packages were pooled for analysis, the presence of a radio-tag significantly decreased both flight time (-8%) and modeled flight range (-23%) when compared to control birds. However, a multiple comparison analysis between the different packages revealed that there was a significant difference in flight time when the larger radio-tag package (240mg) was attached and no significant difference in flight time when the lighter radio-tag packages (220mg) were attached. Our results are similar to other studies which analyzed the flight time or flight range of birds wearing radio-tags. Therefore, currently available light weight radio-tags ([≤]220mg) may be a new option to aid in the study of hummingbird biology. Future study should focus upon the additional drag created by the radio-tag and the effects of the lightest radio-tag packages on free ranging birds. These studies would provide additional information to determine the feasibility on the use of radio-tags to study hummingbird biology.

Zoology↗

bioRxiv2014

Myoinhibitory peptide regulates feeding in the marine annelid Platynereis

During larval settlement and metamorphosis, marine invertebrates undergo changes in habitat, morphology, behavior and physiology. This change between life-cycle stages is often associated with a change in diet or a transition between a non-feeding and a feeding form. How larvae regulate changes in feeding during this life cycle transition is not well understood. Neuropeptides are known to regulate several aspects of feeding, such as food search, ingestion and digestion. The marine annelid Platynereis dumerilii has a complex life cycle with a pelagic non-feeding larval stage and a benthic feeding postlarval stage, linked by the process of settlement. The conserved neuropeptide myoinhibitory peptide (MIP) is a key regulator of larval settlement behavior in Platynereis. Whether MIP also regulates the initiation of feeding, another aspect of the pelagic-to-benthic transition in Platynereis, is currently unknown. Here, we explore the contribution of MIP to feeding in settled Platynereis postlarvae. We find that MIP is expressed in the gut of developing larvae in sensory neurons that densely innervate the foregut and hindgut. Activating MIP signaling by synthetic neuropeptide addition causes increased gut peristalsis and more frequent pharynx extensions leading to increased food intake. Conversely, morpholino-mediated knockdown of MIP expression inhibits feeding. In the long-term, treatment of Platynereis postlarvae with synthetic MIP increases growth rate and results in earlier cephalic metamorphosis. Our results show that MIP activates ingestion and digestion in Platynereis postlarvae. MIP is expressed in sensory-neurosecretory cells of the digestive system indicating that following larval settlement, feeding is initiated by a direct sensory mechanism. This is similar to the mechanism by which MIP induces larval settlement. The pleiotropic roles of MIP may thus have evolved by redeploying the same signaling mechanism in different aspects of a life cycle transition.

Zoology↗

bioRxiv2014

The Histology of Nanomia bijuga (Hydrozoa: Siphonophora)

The siphonophore Nanomia bijuga is a pelagic hydrozoan (Cnidaria) with complex morphological organization. Each siphonophore is made up of many asexually produced, genetically identical zooids that are functionally specialized and morphologically distinct. These zooids predominantly arise by budding in two growth zones, and are arranged in precise patterns. This study describes the cellular anatomy of several zooid types as well as of the stem and gas-filled float, called the pneumatophore. The distribution of cellular morphologies across zooid types enhances our understanding of zooid function. The unique absorptive cells in the palpon, for example, indicate specialized intracellular digestive processing in this zooid type. Furthermore, there are multiple areas of both endodermal and ectodermal epithelial complexity. Though cnidarians are usually thought of as mono-epithelial, we characterize at least two cellular populations in this species which are not connected to a basement membrane. This work provides a greater understanding of epithelial diversity within the cnidarians, and will be a foundation for future studies on Nanomia bijuga, including functional assays and gene expression analyses.

Zoology↗

bioRxiv2014

Recognition and identification of species in the Bombus lucorum-complex - A review and outlook

The recognition of cryptic species represents one of the major challenges in current taxonomy and affects our understanding of global diversity. In practice, the process from discovery to acceptance in the scientific community can take an extensive length of time. A prime example is the traditionally difficult taxonomy of the cryptic bumblebee species belonging to the Bombus lucorum-complex. The status of the three European species in the group - Bombus lucorum and the closely related Bombus cryptarum and Bombus magnus - has recently become widely accepted, primarily due to investigations of nucleotide sequences and marking pheromones. In contrast, doubts prevail concerning the validity of species identification based on morphology. As a consequence, our knowledge of the species is muddled in a mire of unreliable and confusing literature data from a large number of authors over the centuries. To clarify this issue, this paper provides a recapitulation of the historical literature and highlights the milestones in the process of species recognition. Further, the possibility of a morphologically based species identification is discussed in the context of new molecular data. Finally, this review outlines the current challenges and provides directions for future issues.

Zoology↗

bioRxiv2015

Acute and chronic gregarisation are associated with distinct DNA methylation fingerprints in desert locusts

Desert locusts (Schistocerca gregaria) show a dramatic form of socially induced phenotypic plasticity known as phase polyphenism. In the absence of conspecifics, locusts occur in a shy and cryptic solitarious phase. Crowding with conspecifics drives a behavioural transformation towards gregariousness that occurs within hours and is followed by changes in physiology, colouration and morphology, resulting in the full gregarious phase syndrome. We analysed methylation-sensitive amplified fragment length polymorphisms (MS-AFLP) to compare the effect of acute and chronic crowding on DNA methylation in the central nervous system. We find that crowd-reared and solitary-reared locusts show markedly different neural MS-AFLP fingerprints. However, crowding for a day resulted in neural MS-AFLP fingerprints that were clearly distinct from both crowd-reared and uncrowded solitary-reared locusts. Our results indicate that changes in DNA methylation associated with behavioural gregarisation proceed through intermediate states that are not simply partial realisations of the endpoint states.

Zoology↗

bioRxiv2015

The Moose of Isle Royale: An Unnatural Condition?

The now iconic moose of Isle Royale National Park arrived on the island sometime between 1910 and 1915 (Hickie, 1936; Murie, 1934). Prior to that period there is no evidence of moose in either naturalist reports or in the archaeological history of the island (Murie, 1934; Scarpino, 2011). Early naturalists-while observing the moose during their first 20 years on the island--noted both their dramatic expansion, and equally dramatic population crash in the 1930s, see Figure 1. Around 1950, and just as the moose were rebounding, wolves crossed a frozen Lake Superior and began what is now one of our most emblematic predator/prey systems (Peterson, 1995). Recently, the wolves on Isle Royale appear headed for local extinction (Mlot, 2015). Calls to repopulate the island have renewed the vigorous debate surrounding what is and what is not wild about Isle Royale (Scarpino, 2011; Cronon, 1996; Nelson & Callicott, 2008; Cronon, 2003; Peterson, 1999).\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC=\"FIGDIR/small/019984_fig1.gif\" ALT=\"Figure 1\">\nView larger version (12K):\norg.highwire.dtl.DTLVardef@1fd3c26org.highwire.dtl.DTLVardef@77f332org.highwire.dtl.DTLVardef@ff6d66org.highwire.dtl.DTLVardef@1675891_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO The early population dynamics of moose on Isle Royale. Estimates of moose population size were taken from early naturalist reports of Isle Royale (see map for the islands location). The points indicate the average trend and the shaded region represents the reported discrepancy. The lower bound of the shaded region represents the actual value reported in the literature and were used for model fitting.\n\nC_FIG

Zoology↗

bioRxiv2015

Phylogenetic relationships of the Helmeted Woodpecker (Dryocopus galeatus): A case of interspecific mimicry?

Examples of phenotypic convergence in plumage coloration have been reported in a wide diversity of avian taxonomic groups, yet the underlying evolutionary mechanisms driving this phenomenon have received little scientific inquiry. Herein, we document a striking new case of plumage convergence in the Helmeted Woodpecker (Dryocopus galeatus) and explore the possibility of visual mimicry among Atlantic Forest woodpeckers. Our multi-locus phylogenetic analyses unequivocally place D. galeatus within Celeus, indicating the former has subsequently converged in appearance upon the distantly related and syntopic Dryocopus lineatus, to which it bears a remarkable resemblance in plumage coloration and pattern. Although details of the Helmeted Woodpeckers ecology and natural history are only now beginning to emerge, its smaller size and submissive behavior are consistent with predictions derived from evolutionary game theory models and the interspecific social dominance mimicry hypothesis (ISDM). Moreover, estimates of avian visual acuity suggest that size-related mimetic deception is plausible at distances ecologically relevant to Celeus and Dryocopus foraging behavior. In light of our results, we recommend taxonomic transfer of D. galeatus to Celeus and emphasize the need for detailed behavioral studies that examine the social costs and benefits of plumage convergence to explicitly test for ISDM and other forms of mimicry in these Atlantic Forest woodpecker communities. Future field studies examining potential cases of competitive mimicry should also take into account the mimics acoustic behavior, particularly in the presence of putative model species and other heterospecific competitors, as any discontinuity between morphological and behavioral mimicry would likely preclude the possibility of deception.

Zoology↗

bioRxiv2015

The rediscovery of Strix butleri (Hume, 1878) in Oman and Iran, with molecular resolution of the identity of Strix omanensis Robb, van den Berg and Constantine, 2013

BackgroundMost species of owls (Strigidae) represent cryptic species and their taxonomic study is in flux. In recent years, two new species of owls of the genus Strix have been described from the Arabian peninsula by different research teams. It has been suggested that one of these species, S. omanensis, is not a valid species but taxonomic comparisons have been hampered by the lack of specimens of S. omanensis, and the poor state of the holotype of S. butleri.\n\nMethodsHere we use new DNA sequence data to clarify the taxonomy and nomenclature of the S. butleri complex. We also report the capture of a single S. butleri in Mashhad, Iran.\n\nResultsA cytochrome b sequence of S. omanensis was found to be identical to that of the holotype of S. butleri, indicating that the name S. omanensis is best regarded as a junior synonym of S. butleri. The identity of the S. butleri captured in Mashhad, Iran, was confirmed using DNA sequence data. This represents a major (1,400 km) range extension of this species.\n\nConclusionsThe population discovered in Oman in 2013 and originally named S. omanensis actually represents the rediscovery of S. butleri, which was known from a single specimen and had not been recorded since 1878. The range of S. butleri extends into northeast Iran. Our study augments the body of evidence for the recognition of S. butleri and S. hadorami as separate species and highlights the importance of using multiple evidence to study cryptic owl species.

Zoology↗

bioRxiv2015

Distribution and abundance of the West Indian manatee (Trichechus manatus) in the Panama Canal

The West Indian manatee (Trichechus manatus) is threatened throughout its distribution, and is categorized as vulnerable by IUCN (Lefebvre 2001, IUCN 2007). The number of mature individuals is currently estimated at less than 10,000 and is expected to decline at a rate of at least 10% over the next 20 years as a result of both habitat loss and anthropogenic factors (Deutsch et al. 2008). While the West Indian manatee is the most widespread of all existing sirenians, some populations are estimated at fewer than 10 individuals (Deutsch et al. 2008, Quintana-Rizzo and Reynolds 2010). In addition, in most Central American countries reliable information on manatee distribution and conservation status is missing and there is need to assess these remnant populations to guide future management strategies.

Zoology↗