scholarly journals Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives

2019 ◽  
Author(s):  
CA Hamilton ◽  
RA St Laurent ◽  
K Dexter ◽  
IJ Kitching ◽  
JW Breinholt ◽  
...  
Keyword(s):  
Natural History ◽  
Biological Data ◽  
Evolutionary Patterns ◽  
Natural History Collections ◽  
Preservation Method ◽  
Modified Dna ◽  
Wide Range ◽  
Anchored Hybrid Enrichment ◽  
Taxonomic Studies ◽  
Probe Set

AbstractBackgroundThe silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying some of the most spectacular forms and ecological traits among insects, relatively little attention has been given to understanding their evolution and the drivers of their diversity.ResultsTo begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, producing a well-supported phylogeny. The tree was overall consistent with prior morphological and molecular studies, although some taxa (e.g.,ArotrosSchaus) were misplaced in the Bombycidae and here formally transferred to Apatelodidae. We identified important evolutionary patterns (e.g., morphology, biogeography, and differences in speciation and extinction), and our analysis of diversification rates highlights the stark increases that exist within the Sphingidae (hawkmoths) and Saturniidae (wild silkmoths).ConclusionsWe postulate that these rate shifts are due to the well-documented bat-moth “arms race” and differences in selective pressures from insectivorous bats. The study establishes a backbone for future evolutionary, comparative, and taxonomic studies, and presents a modified DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections, succeeding in samples up to 30 years old. Our research highlights the flexibility of AHE to generate genomic data from a wide range of museum specimens, both age and preservation method, and will allow researchers to tap into the wealth of biological data residing in natural history collections around the globe.

scholarly journals Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
C. A. Hamilton ◽  
R. A. St Laurent ◽  
K. Dexter ◽  
I. J. Kitching ◽  
J. W. Breinholt ◽  
...  
Keyword(s):  
Natural History ◽  
Biological Data ◽  
Ecological Traits ◽  
Evolutionary Patterns ◽  
Natural History Collections ◽  
Preservation Method ◽  
Wide Range ◽  
Anchored Hybrid Enrichment ◽  
Taxonomic Studies ◽  
Probe Set

Abstract Background Silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying spectacular forms and diverse ecological traits, relatively little attention has been given to understanding their evolution and drivers of their diversity. To begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, with a newly developed DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections. Results The well-supported tree was overall consistent with prior morphological and molecular studies, although some taxa were misplaced. The bombycid Arotros Schaus was formally transferred to Apatelodidae. We identified important evolutionary patterns (e.g., morphology, biogeography, and differences in speciation and extinction), and our analysis of diversification rates highlights the stark increases that exist within the Sphingidae (hawkmoths) and Saturniidae (wild silkmoths). Conclusions Our study establishes a backbone for future evolutionary, comparative, and taxonomic studies of Bombycoidea. We postulate that the rate shifts identified are due to the well-documented bat-moth “arms race”. Our research highlights the flexibility of AHE to generate genomic data from a wide range of museum specimens, both age and preservation method, and will allow researchers to tap into the wealth of biological data residing in natural history collections around the globe.

scholarly journals Uncertain Geo-Uncertainty: Ecological research and public biodiversity data repositories

2019 ◽  
Vol 3 ◽  
Author(s):  
Arnald Marcer ◽  
Elspeth Haston ◽  
Quentin Groom ◽  
F. Xavier Picó ◽  
Agustí Escobar ◽  
...  
Keyword(s):  
Natural History ◽  
Spatial Information ◽  
Species Distribution Modelling ◽  
Location Information ◽  
Ecological Research ◽  
Biodiversity Data ◽  
Data Repositories ◽  
Ecological Requirements ◽  
Natural History Collections ◽  
Wide Range

Natural history collections represent a vast and superb wealth of information gathered and curated across centuries by institutions such as natural history museums and botanical gardens around the world. The relatively recent advent and maturation of accessible computer technology has allowed the initiation of major digitization projects aimed at making the contents of these collections publicly available for education and research purposes. The final destinations of these newly digitized data are public biodiversity data repositories, of which, GBIF is the main one. These respositories are gateways where researchers can access and retrieve the data for use in a wide range of analyses. This unprecedented volume of information on biodiversity represents an extraordinary asset for research in ecology and evolution. A particularly important part of the digitized data for any given specimen is its collection location, as it indirectly gives information on the species’ habitat and thus, its ecological requirements. Many specimens in natural history collections come from a time where the collecting event, which includes the location information, was hand-written on physical tags attached to the specimen. This location information was given as a description of a place, e.g. a site name, and could be a rather precise or vague description. In order to convert this description of locality into a digitized research-grade georeferenced record, the research community has come up with a set of guidelines and recommendations; the most prominent one the point-radius method devised by Wieczorek et al. in 2004. However, and despite the public availability of this know-how, the end result is that the data available at the end of the pipeline, e.g. GBIF, often lacks georeferencing information with enough quality to be used for research purposes. Occurrence records from natural history collection datasets held at GBIF, often lack spatial coordinates and, if present, in most cases their precision and uncertainty fields are blank. The final consequence of this lack of complete georeferencing information is that the affected records are rendered useless for many kinds of research. For example, the flourishing field of species distribution modelling absolutely depends on accurate spatial information in order to be able to retrieve information on the environmental conditions in which the species live. The availability of global environmental and remote sensing datasets together with the sophisticated geospatial tools at the disposal of the researcher become powerless if no quality geoinformation is available. In this study, we perform a preliminary analysis on the status and availability of geoferencing information in datasets originated from specimens in natural history collections held at GBIF, discuss how the quality of this spatial info may affect ecological research, and conclude with some recommendations on how to better describe the georeferencing process within public digital biodiversity repositories.

scholarly journals Towards Linked Open Molecular Data: Recommendations for researchers, collections, infrastructures and publishers

2019 ◽  
Vol 3 ◽  
Author(s):  
Gabriele Droege ◽  
Ilene Karsch-Mizrachi ◽  
Katharine Barker ◽  
Jonathan Coddington ◽  
Ole Seberg
Keyword(s):  
Natural History ◽  
Dna Sequencing ◽  
Biological Material ◽  
Sequence Data ◽  
Open Data ◽  
Molecular Data ◽  
Biological Data ◽  
Global Biodiversity Information Facility ◽  
Natural History Collections ◽  
Long Run

The variety of molecular methods used to analyze biosamples is continuously increasing, as is the need for the standardized deposition, documentation and citation of both the samples as well as the methods applied to them. Global initiatives such as the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org), Barcode of Life Data System (BOLD, http://www.boldsystems.org), the Global Biodiversity Information Facility (GBIF, http://www.gbif.org) and the Global Genome Biodiversity Network (GGBN, http://www.ggbn.org), in addition to many others, have been working towards standardized access to biological data for many years. Collectively, these biodiversity data management platforms provide a considerable and indispensable infrastructure to the research community. However, cross-linking the massive amounts of protein and DNA sequence data submitted to these databases every year with standardized records of the underlying biological material remains challenging. Best practices for standardized data submissions and data citations are urgently needed. In the long run, two goals should be achieved above all else: all sequence data should be linked to natural history collections, and biological material that was used for molecular research, especially DNA sequencing, should be deposited and, thus, made accessible in public, well curated collections. all sequence data should be linked to natural history collections, and biological material that was used for molecular research, especially DNA sequencing, should be deposited and, thus, made accessible in public, well curated collections. Here we will provide recommendations both for researchers and collections how to cite underlying biological material at INSDC and in publications in a standardized way towards Linked Open Data. We will also address how the global infrastructures and publishers can improve their interoperability.

scholarly journals The Importance of Storing and Delivering Geochemical Data for Earth Science Collections

2019 ◽  
Vol 3 ◽  
Author(s):  
Giles Miller ◽  
Kerstin Lehnert
Keyword(s):  
Natural History ◽  
Hydrothermal Vents ◽  
Earth Science ◽  
Volcanic Eruptions ◽  
Geochemical Data ◽  
Mass Extinctions ◽  
Museum Collections ◽  
Natural History Collections ◽  
Wide Range ◽  
Biodiversity Changes

The composition and state of the earth’s lithosphere through time has had profound effect on past and present biodiversity and will continue to do so into the future. Environments ranging from deep sea hydrothermal vents to active continental volcanic centres provide a wide range of ecosystems that have shaped the planet we know. Catastrophic events relating to movements of the lithosphere and events deep in the mantle have also caused major biodiversity changes such as mass extinctions. Our museum collections contain rock and fossil specimens collected from many of these environments and suites of samples specifically collected in order to better understand the evolution of our planet. Requests to carry out geochemical investigations on these samples are common and a large amount of data is generated as a result. Currently there are no natural history collections management systems tailored towards recording and delivering these datasets and the result is that the data is recorded in various distributed systems and cannot be easily assessed and used. It is important for these analyses on our museum collections to be delivered in a standard way so that the importance and relevance of these collections can be demonstrated and large datasets generated to answer big questions regarding the geological evolution of our planet. Examples of these questions include “how and when will volcanic eruptions will occur?” and “what has been the role of volcanism during mass extinction?”. Other geochemical studies such as oxygen isotope studies have been carried out on museum collections in order to investigate past oceanic environments and the effects of changes in climate on our oceans. Geochemical data aggregators such as EarthChem have made great strides in working towards international data standards and providing portals for delivering this type of data. As we progress towards one European Collection (DiSSCo) it is vital that we recognise the importance of these natural history collections related geochemical datasets and include delivering them on the general roadmap.

Joseph Sidebotham: vicissitudes of a Victorian collector

2015 ◽  
Vol 42 (2) ◽  
pp. 197-210 ◽  
Author(s):  
Laurence M. Cook
Keyword(s):  
Natural History ◽  
Species Limits ◽  
Clear Cut ◽  
Natural History Collections ◽  
As Species ◽  
Scientific World

Joseph Sidebotham (1824–1885) was a Manchester cotton baron whose natural history collections are now in the Manchester Museum. In addition to collecting he suggested a method for identifying and classifying Lepidoptera and investigated variation within species as well as species limits. With three close collaborators, he is credited with discovering many species new to Britain in both Lepidoptera and Coleoptera. A suspicion of fraud attaches to these claims. The evidence is not clear-cut in the Lepidoptera, but a possible reason is suggested why Sidebotham, as an amateur in the increasingly professional scientific world, might have engaged in deceit.

The Banksian natural history collections of the Endeavour voyage and their relevance to modern taxonomy

1981 ◽  
Vol 1981 (1) ◽  
pp. 61-70
Author(s):  
H. B. Carter ◽  
Judith A. Diment ◽  
C. J. Humphries ◽  
Alwyne Wheeler
Keyword(s):  
Natural History ◽  
Natural History Collections

Correspondence between Adolphe Brongniart and Robert Schomburgk: trading natural history collections for honours

2002 ◽  
Vol 29 (3) ◽  
pp. 333-336
Author(s):  
PIOTR DASZKIEWICZ ◽  
MICHEL JEGU
Keyword(s):  
Nineteenth Century ◽  
Natural History ◽  
Dominican Republic ◽  
Southeast Asia ◽  
Herbarium Specimens ◽  
British Guiana ◽  
Natural History Collections ◽  
History Of ◽  
Source Of Information ◽  
German Naturalist

ABSTRACT: This paper discusses some correspondence between Robert Schomburgk (1804–1865) and Adolphe Brongniart (1801–1876). Four letters survive, containing information about the history of Schomburgk's collection of fishes and plants from British Guiana, and his herbarium specimens from Dominican Republic and southeast Asia. A study of these letters has enabled us to confirm that Schomburgk supplied the collection of fishes from Guiana now in the Laboratoire d'Ichtyologie, Muséum National d'Histoire Naturelle, Paris. The letters of the German naturalist are an interesting source of information concerning the practice of sale and exchange of natural history collections in the nineteenth century in return for honours.

Fault Tolerant Reliable Protocol (FTRP) Performance Evaluation in Wireless Sensor Networks: An Extensitive Study

2019 ◽  
pp. 1-36
Keyword(s):  
Wireless Sensor Networks ◽  
Fault Tolerance ◽  
Sensor Networks ◽  
Fault Tolerant ◽  
Cluster Head ◽  
Biological Data ◽  
Wireless Sensor ◽  
Delivery Ratio ◽  
Good Performer ◽  
Wide Range

Fault Tolerant Reliable Protocol (FTRP) is proposed as a novel routing protocol designed for Wireless Sensor Networks (WSNs). FTRP offers fault tolerance reliability for packet exchange and support for dynamic network changes. The key concept used is the use of node logical clustering. The protocol delegates the routing ownership to the cluster heads where fault tolerance functionality is implemented. FTRP utilizes cluster head nodes along with cluster head groups to store packets in transient. In addition, FTRP utilizes broadcast, which reduces the message overhead as compared to classical flooding mechanisms. FTRP manipulates Time to Live values for the various routing messages to control message broadcast. FTRP utilizes jitter in messages transmission to reduce the effect of synchronized node states, which in turn reduces collisions. FTRP performance has been extensively through simulations against Ad-hoc On-demand Distance Vector (AODV) and Optimized Link State (OLSR) routing protocols. Packet Delivery Ratio (PDR), Aggregate Throughput and End-to-End delay (E-2-E) had been used as performance metrics. In terms of PDR and aggregate throughput, it is found that FTRP is an excellent performer in all mobility scenarios whether the network is sparse or dense. In stationary scenarios, FTRP performed well in sparse network; however, in dense network FTRP’s performance had degraded yet in an acceptable range. This degradation is attributed to synchronized nodes states. Reliably delivering a message comes to a cost, as in terms of E-2-E. results show that FTRP is considered a good performer in all mobility scenarios where the network is sparse. In sparse stationary scenario, FTRP is considered good performer, however in dense stationary scenarios FTRP’s E-2-E is not acceptable. There are times when receiving a network message is more important than other costs such as energy or delay. That makes FTRP suitable for wide range of WSNs applications, such as military applications by monitoring soldiers’ biological data and supplies while in battlefield and battle damage assessment. FTRP can also be used in health applications in addition to wide range of geo-fencing, environmental monitoring, resource monitoring, production lines monitoring, agriculture and animals tracking. FTRP should be avoided in dense stationary deployments such as, but not limited to, scenarios where high application response is critical and life endangering such as biohazards detection or within intensive care units.

Sign in / Sign up

Export Citation Format

Share Document