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  1. Article ; Online: The reduced genome of a heritable symbiont from an ectoparasitic feather feeding louse

    Leila Alickovic / Kevin P. Johnson / Bret M. Boyd

    BMC Ecology and Evolution, Vol 21, Iss 1, Pp 1-

    2021  Volume 11

    Abstract: Abstract Background Feather feeding lice are abundant and diverse ectoparasites that complete their entire life cycle on an avian host. The principal or sole source of nutrition for these lice is feathers. Feathers appear to lack four amino acids that ... ...

    Abstract Abstract Background Feather feeding lice are abundant and diverse ectoparasites that complete their entire life cycle on an avian host. The principal or sole source of nutrition for these lice is feathers. Feathers appear to lack four amino acids that the lice would require to complete development and reproduce. Several insect groups have acquired heritable and intracellular bacteria that can synthesize metabolites absent in an insect’s diet, allowing insects to feed exclusively on nutrient-poor resources. Multiple species of feather feeding lice have been shown to harbor heritable and intracellular bacteria. We expected that these bacteria augment the louse’s diet with amino acids and facilitated the evolution of these diverse and specialized parasites. Heritable symbionts of insects often have small genomes that contain a minimal set of genes needed to maintain essential cell functions and synthesize metabolites absent in the host insect’s diet. Therefore, we expected the genome of a bacterial endosymbiont in feather lice would be small, but encode pathways for biosynthesis of amino acids. Results We sequenced the genome of a bacterial symbiont from a feather feeding louse (Columbicola wolffhuegeli) that parasitizes the Pied Imperial Pigeon (Ducula bicolor) and used its genome to predict metabolism of amino acids based on the presence or absence of genes. We found that this bacterial symbiont has a small genome, similar to the genomes of heritable symbionts described in other insect groups. However, we failed to identify many of the genes that we expected would support metabolism of amino acids in the symbiont genome. We also evaluated other gene pathways and features of the highly reduced genome of this symbiotic bacterium. Conclusions Based on the data collected in this study, it does not appear that this bacterial symbiont can synthesize amino acids needed to complement the diet of a feather feeding louse. Our results raise additional questions about the biology of feather chewing lice and the roles of ...
    Keywords Phthiraptera ; Endosymbiont ; Keratin ; Genome reduction ; Metabolic complementation ; Ecology ; QH540-549.5 ; Evolution ; QH359-425
    Subject code 572
    Language English
    Publishing date 2021-06-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Global shifts in species richness have shaped carpet shark evolution

    Bret M. Boyd / Jason C. Seitz

    BMC Ecology and Evolution, Vol 21, Iss 1, Pp 1-

    2021  Volume 10

    Abstract: Abstract Background The evolutionary processes that shape patterns of species richness in marine ecosystems are complex and may differ between organismal groups. There has been considerable interest in understanding the evolutionary processes that led to ...

    Abstract Abstract Background The evolutionary processes that shape patterns of species richness in marine ecosystems are complex and may differ between organismal groups. There has been considerable interest in understanding the evolutionary processes that led to marine species richness being concentrated in specific geographical locations. In this study we focus on the evolutionary history of a group of small-to-medium sized sharks known as carpet sharks. While a few carpet shark species are widespread, the majority of carpet shark species richness is contained within a biodiversity hotspot at the boundary of the Indian and Pacific oceans. We address the significance of this biodiversity hotspot in carpet shark evolution and speciation by leveraging a rich fossil record and molecular phylogenetics to examine the prehistoric distribution of carpet sharks. Results We find that carpet sharks species richness was greatest in shallow seas connected to the Atlantic Ocean during the Late Cretaceous, but that there was a subsequent loss of biodiversity in Atlantic waters. Fossil evidence from sites in close geographic proximity to the current center of carpet shark diversity are generally restricted to younger geologic strata. Conclusions From this data we conclude that (1) center of carpet shark biodiversity has shifted during the last 100 million years, (2) carpet sharks have repeatedly dispersed to nascent habitat (including to their current center of diversity), and (3) the current center of carpet shark biodiversity conserves lineages that have been extirpated from this prehistoric range and is a source of new carpet shark species. Our findings provide insights into the roles of marine biodiversity hotspots for higher-tropic level predators and the methods applied here can be used for additional studies of shark evolution.
    Keywords Orectolobiformes ; Biodiversity hotspot ; Dispersal ; Phylogenetics ; Fossil ; Ecology ; QH540-549.5 ; Evolution ; QH359-425
    Subject code 333
    Language English
    Publishing date 2021-10-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Both living bacteria and eukaryotes in the mosquito gut promote growth of larvae.

    Luca Valzania / Vincent G Martinson / Ruby E Harrison / Bret M Boyd / Kerri L Coon / Mark R Brown / Michael R Strand

    PLoS Neglected Tropical Diseases, Vol 12, Iss 7, p e

    2018  Volume 0006638

    Abstract: We recently reported that larval stage Aedes aegypti and several other species of mosquitoes grow when living bacteria are present in the gut but do not grow when living bacteria are absent. We further reported that living bacteria induce a hypoxia ... ...

    Abstract We recently reported that larval stage Aedes aegypti and several other species of mosquitoes grow when living bacteria are present in the gut but do not grow when living bacteria are absent. We further reported that living bacteria induce a hypoxia signal in the gut, which activates hypoxia-induced transcription factors and other processes larvae require for growth. In this study we assessed whether other types of organisms induce mosquito larvae to grow and asked if the density of non-living microbes or diet larvae are fed obviate the requirement for living organisms prior results indicated are required for growth. Using culture conditions identical to our own prior studies, we determined that inoculation density of living Escherichia coli positively affected growth rates of Ae. aegypti larvae, whereas non-living E. coli had no effect on growth across the same range of inoculation densities. A living yeast, alga, and insect cell line induced axenic Ae. aegypti first instars to grow, and stimulated similar levels of midgut hypoxia, HIF-α stabilization, and neutral lipid accumulation in the fat body as E. coli. However, the same organisms had no effect on larval growth if heat-killed. In addition, no axenic larvae molted when fed two other diets, when fed diets supplemented with heat-killed microbes or lysed and heat-killed microbes. Experiments conducted with An. gambiae yielded similar findings. Taken together, our results indicate that organisms from different prokaryotic and eukaryotic groups induce mosquito larvae to grow, whereas no conditions were identified that stimulated larvae to grow in the absence of living organisms.
    Keywords Arctic medicine. Tropical medicine ; RC955-962 ; Public aspects of medicine ; RA1-1270
    Subject code 590
    Language English
    Publishing date 2018-07-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article: Cophylogenetic patterns are uncorrelated between two lineages of parasites on the same hosts

    Sweet, Andrew D / Bret M. Boyd / Kevin P. Johnson

    Biological journal of the Linnean Society. 2016 Aug., v. 118, no. 4

    2016  

    Abstract: Free‐living organisms are often host to multiple lineages of closely related parasites. Different lineages of obligate parasites living on the same hosts might potentially be expected to display similar cophylogenetic patterns. However, there are also ... ...

    Abstract Free‐living organisms are often host to multiple lineages of closely related parasites. Different lineages of obligate parasites living on the same hosts might potentially be expected to display similar cophylogenetic patterns. However, there are also reasons why these lineages might have different evolutionary histories (e.g. host switching, host geography). In the present study, we use mitochondrial and nuclear DNA sequence data to evaluate the cophylogenetic patterns between doves and their wing and body lice. Previous studies have found that the wing and body lice of doves have different levels of congruence between their phylogenetic histories. However, these studies are limited in scope, either taxonomically or geographically. We used both new and existing data to generate a worldwide and taxonomically diverse data set for doves and two independent groups of lice: wing and body lice. Using event and topology‐based methods, we found that cophylogenetic patterns were not correlated between wing and body lice, even though both groups showed evidence of cospeciation with their hosts. These results indicate that external factors vary in their impact on different groups of parasites and also that broad sampling is critical for identifying patterns in cophylogenetic analyses.
    Keywords data collection ; DNA ; doves ; geography ; hosts ; lice ; mitochondria ; nuclear genome ; nucleotide sequences ; Pediculus humanus ; phylogeny
    Language English
    Dates of publication 2016-08
    Size p. 813-828.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 1461865-5
    ISSN 1095-8312 ; 0024-4066
    ISSN (online) 1095-8312
    ISSN 0024-4066
    DOI 10.1111/bij.12771
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets

    Therese A. Catanach / Andrew D. Sweet / Nam-phuong D. Nguyen / Rhiannon M. Peery / Andrew H. Debevec / Andrea K. Thomer / Amanda C. Owings / Bret M. Boyd / Aron D. Katz / Felipe N. Soto-Adames / Julie M. Allen

    PeerJ, Vol 7, p e

    an example with hepatitis B virus

    2019  Volume 6142

    Abstract: Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be ... ...

    Abstract Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. Traditionally, alignments are produced with automated algorithms and then checked and/or corrected “by eye” prior to phylogenetic inference. However, this manual curation is inefficient at the data scales required of modern phylogenetics and results in alignments that are not reproducible. Recently, methods have been developed for fully automating alignments of large data sets, but it is unclear if these methods produce alignments that result in compatible phylogenies when compared to more traditional alignment approaches that combined automated and manual methods. Here we use approximately 33,000 publicly available sequences from the hepatitis B virus (HBV), a globally distributed and rapidly evolving virus, to compare different alignment approaches. Using one data set comprised exclusively of whole genomes and a second that also included sequence fragments, we compared three MSA methods: (1) a purely automated approach using traditional software, (2) an automated approach including by eye manual editing, and (3) more recent fully automated approaches. To understand how these methods affect phylogenetic results, we compared resulting tree topologies based on these different alignment methods using multiple metrics. We further determined if the monophyly of existing HBV genotypes was supported in phylogenies estimated from each alignment type and under different statistical support thresholds. Traditional and fully automated alignments produced similar HBV phylogenies. Although there was variability between branch support thresholds, allowing lower support thresholds tended to result in more differences among trees. Therefore, ...
    Keywords Genome ; Automated alignment ; Manual alignment ; Virus ; s-region ; HBV ; Medicine ; R ; Biology (General) ; QH301-705.5
    Subject code 004
    Language English
    Publishing date 2019-01-01T00:00:00Z
    Publisher PeerJ Inc.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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