Insect phylogenetics in the digital age
Introduction
Digital tools and resources are revolutionizing insect phylogenetics. Over the past 50 years, as computing power and storage capacity have grown and become affordable, and programming technologies have become more versatile, automation of many of the steps involved in a phylogenetic study has become possible. Tools for managing field sampling data and notes, curating and managing specimens, and compiling and analyzing phenotypic and genomic data continue to be improved and Internet-accessible databases useful for systematics research (e.g., scientific names, specimen occurrence data, DNA sequences, morphology, images) are growing exponentially.
Recent advances and grand challenges in biodiversity informatics overall have been reviewed recently (e.g. [1, 2]). This review deals more specifically with progress on digital resources relevant to insect systematics.
Section snippets
Data and specimen acquisition
Specimens are the raw materials upon which phylogenetic research is based. Thus, specimen acquisition is the crucial first step in any phylogenetic study not based on previously published data. Mass insect sampling methods (e.g., insecticidal fogging of forest canopy) adopted over the past several decades are adding vast quantities of new specimens to the billions already housed in museums, but processing and identification of specimens remains a major bottleneck and practical methods for
Data management and synthesis
Once acquired, phylogenetically relevant data need to be managed and integrated with other kinds of data to facilitate analysis, sharing and long-term preservation. In addition to the morphological or molecular character data used in the phylogenetic analysis, taxonomic nomenclature, specimen-level occurrence data, bibliographic data and images are also integral to systematics research. Although various software is available for managing phylogenetic data, most available systems manage a few
Data analysis
Despite the development of increasingly efficient programs for analyzing phylogenetic datasets using desktop computers, the flood of phylogenetic data resulting from inexpensive genome-sequencing technologies has begun to overwhelm the capacity of desktop computers to conduct phylogenetic analyses in reasonable amounts of time. Efforts have already been made to broaden access to supercomputing resources by the systematics community. These include the web portals Phylogeny.fr [33], T-REX [34],
Data dissemination
The Convention on Biological Diversity [https://www.cbd.int/convention/text/] and the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization [http://www.cbd.int/abs/doc/protocol/nagoya-protocol-en.pdf] established goals for sharing and open access to specimens and data within the global scientific community but these standards have not yet been fully implemented. Initiatives such as the Genomic Observatories initiative and
Concluding remarks
Technological hurdles hindering progress toward development of a comprehensive tree of life are being rapidly overcome but many barriers remain, including the social preference among many systematists for solitary research as opposed to large-scale collaboration [1, 2, 42]. Despite nearly 300 years of effort, insect systematists have, so far, only documented a small fraction (<20%) of extant insect biodiversity, large numbers of documented species are known from only a few museum specimens with
References and recommended reading
Papers of particular interest, published within the period of review, have been highlighted as:
• of special interest
•• of outstanding interest
Acknowledgements
C.H. Dietrich and D.A. Dmitriev were funded, in part, by the U.S. National Science Foundation [grants EF-1115112, DEB-1239788, and DBI-1458285]. Any opinions, findings, and conclusions or recommendations expressed in this article are those of the authors and do not necessarily reflect the views of the National Science Foundation.
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