The Diversity of the Indo-Pacific Network (DIPnet) was funded as an NSF Research Coordination Network with four major goals. Below, we summarize how we accomplished each of these goals over the five-year span of the RCN grant.

Objective 1) Create a collaborative website and open access database that will serve genetic data and accompanying metadata from the Indo-Pacific.

Objective 2) Compile all existing genetic data from the region which is not publicly available and accession those data into that open access database.

One of DIPnet's primary goals was to make genetic data collected over the past 20 years available in electronic form to researchers throughout the world (http://diversityindopacific.net). DIPnet makes a wealth of genetic data (over 36,000 mitochondrial DNA sequences from over 200 species) available for the first time to those in developing countries who may not have funding to sample outside their borders. The public database - the Genomics Observatories Metadatabase  or GEOME (https://geome-db.org) works with the National Center for Biotechnology Information (NCBI) to store the genetic data. Users complete GEOME metadata templates that capture the "what, where and when" of their biological samples for upload to GEOME. GEOME validates the metadata, ensuring standards compliance, provides a portal for direct upload of their genomic data to NCBI Sequence Read Archive (SRA), while also sharing the metadata as occurrences to the Global Biogeographic Information Facility (GBIF). DIPnet also developed a data usage agreement for GEOME that addresses the global Convention on Biological Diversity, and collaborated on the development of an R package that allows metadata searches in GEOME to be converted into batch downloads from the NCBI SRA to facilitate free and open exchange of existing data.

GEOME's value to the biodiversity community will soon be recognized in an editorial in Molecular Ecology Resources which recommends uptake of GEOME by all who use molecular data to study aspects of biodiversity.

Objective 3) Hold annual workshops to promote capacity development and collaboration among Indo-Pacific researchers.

DIPnet held 4 international training workshops: Indonesia (2015; 36 participants), the Philippines (2016; 40 participants), South Africa (2017; 41 participants) and Fiji (2018; 21 participants) to train researchers from developing countries in essential informatics and data analysis for modern biodiversity science. Each workshop was tailored to the needs of the host country and institution. Workshops in Indonesia and the Philippines partnered with Data Carpentry to give students skills at the command line and with various analytical pipelines, South Africa focused on seascape genomics, and the workshop in Fiji focused on skills to accession 144,446 species occurrence records to GBIF. A final workshop planned for Hawaiʻi in 2020 was converted to an online virtual training workshop due to COVID-19. We solicited applications from students who had lost income or were unable to perform research due to the pandemic, and selected 14 to participate in this training opportunity focused on data curation, biodiversity data standards, and developing their professional networks. Students worked in small groups to learn metadata standards and review the literature to accession retrospective SRA projects into GEOME by which they not only expanded the database, but also learned and tested the system. This effort added over 250 new SRA projects to GEOME's open data archive.

DIPnet has also been a springboard to fund similar collaborative initiatives. Most prominently, the Ira Moana (Genes of the Sea) network in New Zealand provides a prototype for a national-level network. Through workshops (co-taught by DIPnet members) Ira Moana built a network of over 85 GEOME users in New Zealand, accessioning 6,480 records to GEOME. In addition, a seascape genomics symposium (40 participants) was funded as an adjunct to the 2016 Western Society of Naturalists meeting in Monterey. The DIPnet Fiji workshop was co-funded by the GBIF Biodiversity Information for Development program.

Objective 4) Collaboratively address fundamental research topics about marine biodiversity.

DIPnet has worked to leverage existing datasets to better understand the processes that shape Indo-Pacific biodiversity.  Toward these goals, the DIPnet consortium has published three papers (with another in the works) that leverage the huge volume of genetic data synthesized by this effort:

A. Understanding patterns of marine biodiversity across multiple levels of organization

Matias and Riginos (2018) used genetic data from nine species to test hypotheses about the species-level gradient of biodiversity in the Indo-Pacific. Liggins et al. (in prep) have found a correlation between species level biodiversity and genetic diversity.

B. Indo-Pacific Seascapes: Delineating conservation units with molecular data

Crandall, Toonen and Selkoe (2019) used simulations and coalescent metapopulation models for 41 marine species to show that larval dispersal is limited between Hawaiian islands even when traditional F-statistics are not significant.

C. Community Phylogeography: Shared ecological and evolutionary processes

Crandall et al. (2019) used genetic data from 56 coral reef species to test biogeographic hypotheses about barriers to gene flow in the Indo-Pacific.

Last Modified: 09/29/2020
Modified by: Robert J Toonen