The Scope of Published Population Genetic Data for Indo-Pacific Marine Fauna and Future Research Opportunities in the Region

Marine biodiversity reaches its pinnacle in the tropical Indo-Pacific region, with high levels of both species richness and endemism, especially in coral reef habitats. While this pattern of biodiversity has been known to biogeographers for centuries, causal mechanisms remain enigmatic. Over the past 20 yrs, genetic markers have been employed by many researchers as a tool to elucidate patterns of biodiversity above and below the species level, as well as to make inferences about the underlying processes of diversification, demographic history, and dispersal. In a quantitative, comparative framework, these data can be synthesized to address questions about this bewildering diversity by treating species as “replicates.” However, the sheer size of the Indo-Pacific region means that the geographic and genetic scope of many species’ data sets are not complementary. Here, we describe data sets from 116 Indo-Pacific species (108 studies). With a mind to future synthetic investigations, we consider the strengths and omissions of currently published population genetic data for marine fauna of the Indo-Pacific region, as well as the geographic and taxonomic scope of the data, and suggest some ways forward for data collection and collation

A novel widespread cryptic species and phylogeographic patterns within several giant clam species (Cardiidae: Tridacna) from the Indo-Pacific Ocean

Giant clams (genus Tridacna) are iconic coral reef animals of the Indian and Pacific Oceans, easily recognizable by their massive shells and vibrantly colored mantle tissue. Most Tridacna species are listed by CITES and the IUCN Redlist, as their populations have been extensively harvested and depleted in many regions. Here, we survey Tridacna crocea and Tridacna maxima from the eastern Indian and western Pacific Oceans for mitochondrial (COI and 16S) and nuclear (ITS) sequence variation and consolidate these data with previous published results using phylogenetic analyses. We find deep intraspecific differentiation within both T. crocea and T. maxima. In T. crocea we describe a previously undocumented phylogeographic division to the east of Cenderawasih Bay (northwest New Guinea), whereas for T. maxima the previously described, distinctive lineage of Cenderawasih Bay can be seen to also typify western Pacific populations. Furthermore, we find an undescribed, monophyletic group that is evolutionarily distinct from named Tridacna species at both mitochondrial and nuclear loci. This cryptic taxon is geographically widespread with a range extent that minimally includes much of the central Indo-Pacific region. Our results reinforce the emerging paradigm that cryptic species are common among marine invertebrates, even for conspicuous and culturally significant taxa. Additionally, our results add to identified locations of genetic differentiation across the central Indo-Pacific and highlight how phylogeographic patterns may differ even between closely related and co-distributed species

An Indo-Pacifc coral spawning database

The discovery of multi-species synchronous spawning of scleractinian corals on the Great Barrier Reef in the 1980s stimulated an extraordinary effort to document spawning times in other parts of the globe. Unfortunately, most of these data remain unpublished which limits our understanding of regional and global reproductive patterns. The Coral Spawning Database (CSD) collates much of these disparate data into a single place. The CSD includes 6178 observations (3085 of which were unpublished) of the time or day of spawning for over 300 scleractinian species in 61 genera from 101 sites in the Indo-Pacific. The goal of the CSD is to provide open access to coral spawning data to accelerate our understanding of coral reproductive biology and to provide a baseline against which to evaluate any future changes in reproductive phenology

ME_opinionRdata_tidy

This is an excel csv file that contains summary information concerning the public data archiving of genetic, geographic and temporal information for articles published in Molecular Ecology from 2009 to 201

Data from: Not the time or the place: the missing spatio-temporal link in publicly available genetic data

Genetic data are being generated at unprecedented rates. Policies of many journals, institutions and funding bodies aim to ensure that these data are publicly archived so that published results are reproducible. Additionally, publicly archived data can be ‘repurposed’ to address new questions in the future. In 2011, along with other leading journals in ecology and evolution, Molecular Ecology implemented mandatory public data archiving (the Joint Data Archiving Policy). To evaluate the effect of this policy, we assessed the genetic, spatial and temporal data archived for 419 data sets from 289 articles in Molecular Ecology from 2009 to 2013. We then determined whether archived data could be used to reproduce analyses as presented in the manuscript. We found that the journal's mandatory archiving policy has had a substantial positive impact, increasing genetic data archiving from 49 (pre-2011) to 98% (2011–present). However, 31% of publicly archived genetic data sets could not be recreated based on information supplied in either the manuscript or public archives, with incomplete data or inconsistent codes linking genetic data and metadata as the primary reasons. While the majority of articles did provide some geographic information, 40% did not provide this information as geographic coordinates. Furthermore, a large proportion of articles did not contain any information regarding date of sampling (40%). Although the inclusion of spatio-temporal data does require an increase in effort, we argue that the enduring value of publicly accessible genetic data to the molecular ecology field is greatly compromised when such metadata are not archived alongside genetic data

All results ME15-008_final R script

This R script can be run to generate all results presented in our publication, and includes notes to clarify how these calculations were performed

Data from: Not the time or the place: the missing spatio-temporal link in publicly available genetic data

Genetic data are being generated at unprecedented rates. Policies of many journals, institutions and funding bodies aim to ensure that these data are publicly archived so that published results are reproducible. Additionally, publicly archived data can be “repurposed” to address new questions in the future. In 2011, along with other leading journals in ecology and evolution, Molecular Ecology implemented mandatory public data archiving (the Joint Data Archiving Policy). To evaluate the effect of this policy we assessed the genetic, spatial and temporal data archived for 419 datasets from 289 articles in Molecular Ecology from 2009 to 2013. We then determined whether archived data could be used to reproduce analyses as presented in the manuscript. We found that the journal's mandatory archiving policy has had a substantial positive impact, increasing genetic data archiving from 49 (pre-2011) to 98% (2011-present). However, 31% of publicly archived genetic datasets could not be recreated based on information supplied in either the manuscript or public archives, with incomplete data or inconsistent codes linking genetic data and metadata as the primary reasons. While the majority of articles did provide some geographic information, 40% did not provide this information as geographic coordinates. Furthermore, a large proportion of articles did not contain any information regarding date of sampling (40%). Although the inclusion of spatio-temporal data does require an increase in effort, we argue that the enduring value of publicly accessible genetic data to the molecular ecology field is greatly compromised when such metadata are not archived alongside genetic data

All results ME15-008_final R script

This R script can be run to generate all results presented in our publication, and includes notes to clarify how these calculations were performed

RDat

This data file can be used alongside our R script to generate the results produced in our article. This is identical to page two of our final data excel file. The readme file associated with the excel file should be used to understand the categories here

The role of habitat creation in coral reef conservation: a case study from Aceh, Indonesia

Abstract We describe the successful creation of new reef habitat on Pulau Weh, Indonesia. Coral cover on artificial reef modules increased from a mean of 24±SE 2.4% 1 year after the initial attachment of Acropora spp. coral fragments to 64±SE 4.8% after 3 years. The artificial reef modules were also rapidly colonized by coral recruits. Recruit densities were 53±SE 3.2 m on modules that had been submerged for only 1 year, nearly twice as high as recruit densities on natural reef substratum (31±2.8 m ). Consequently, the original Acropora assemblage had increased to include at least 23 coral taxa, including 10 additional Acropora species. The artificial reefs also supported at least 29 reef fish species, from 11 families. Unfortunately, this initial success in habitat creation was abruptly halted by a rapid rise in sea temperature in May 2010 that killed almost all corals on the artificial reefs and on nearby natural reefs. Notwithstanding the general view that reef rehabilitation is yet to deliver ecological and conservation benefits at meaningful scales, other benefits of this project included raising the awareness of reef conservation in the local community, promotion of tourism on Pulau Weh and job creation. We conclude, therefore, that habitat creation has a legitimate role as part of an integrated marine conservation strategy