Any Reproduction Even in Pa T Congress on Evolutionary B Gy 2018

Emergent patterns of genetic diversity across the Indo-Pacific Ocean

Libby Liggins, Eric D. Crandall, Cynthia Riginos, Michelle Gaither, Eric A. Treml, Chris E. Bird, Sean R. Connolly, Loic Thibaut, Elizabeth Sbrocco, Maria Beger, Peter F. Cowman, Rob J. Toonen,

the Diversity of the Indo-Pacific2018 © II Joint network Congress on Evolutionary (DIPnet Biology 2018.) All rights reserved - Any reproduction even in part is prohibited. 2018 © 48th European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

Species–genetic diversity correlations

Drivers of genetic diversity

Opportunities for Pacific nations

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. Libby Liggins 2018 | Massey University © |48th New Zealand European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

Species–genetic diversity correlations

Drivers of genetic diversity

Opportunities for Pacific nations

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited.

Data Source: IUCN RedList2018 ©of II Joint Threatened Congress on Evolutionary Species, Biology 2018.http All ://rightswww.iucnredlist.org reserved - Any reproduction even in part is prohibited. Libby Liggins 2018 | Massey University © |48th New Zealand European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . Patterns of genetic diversity Important for understanding the processes that generate and maintain biodiversity, such as: Dispersal – routes and rates of colonisation and gene flow Selection – strength and geography Speciation – modes and geography

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . Multispecies patterns of genetic diversity Important for understanding the processes that generate and maintain biodiversity, such as: Dispersal – routes and rates of colonisation and gene flow Selection – strength and geography Speciation – modes and geography

Research progress has been impeded by: The expanse of the Indo-Pacific Ocean 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. The level of biodiversity The availability of metadata

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . Multispecies patterns of genetic diversity ImportantLatitude, for longitude,understanding date, the processestime, sex, weight, microhabitat, that generate and maintaincolour biodiversity, morph etc. such as: V

Dispersal – routes"data and [information] rates of colonisation that provides information and gene flow about other dataV " Selection – strength and geography genetic Speciation – modes and geography

Pope et al. 2015. Not the time or the place: the missing spatio-temporal link in publicly available data. Molecular Ecology 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. Libby GrattonLiggins 2018 |et Massey al. 2016. University © |48th New Zealand European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . Diversity of the Indo-Pacific Network Purpose promote collaboration among researchers regardless of their institutional location make genetic data and metadata available and searchable to the community in a raw, georeferenced form

National Evolutionary Synthesis Center (NESCent) Catalysis Meeting The molecular ecology and evolution of the Indo-Pacific: A collaborative research network ED Crandall and C Riginos, 2012

NESCent Working Group Advancing genetic diversity research in the Indian and Pacific Oceans 2018 © II Joint Congress on CEvolutionary Riginos, Biology 2018.ED All Crandall, rights reserved - Any and reproduction RJ Toonen even in part is prohibited., 2013 - 2015

National Science Foundation – Research Coordination Network Diversity of the Indo-Pacific Network (DIPnet): A collaborative research network and database for advancing marine biodiversity research 2015 - 2020

Collaboration • 60+ members who follow community guidelines • 36,000+ mtDNA sequences from 230+ species and 1,500+ sites • 21 articles published in a special issue of the Bulletin of Marine Science, 2014 • Website, diversityindopacific.net • Collaborative GitHUB repository

60+ network members, 37+ institutions, 19+ countries

Metadata • FIMS, Biocode Field Information Management System • MIxS, metadata for genetic data from the Genomic Standards Consortium • Contributed metadata to Genomics Observatory Metadatabase

Genomics Observatory Metadatabase

• Data upload tools for all sequence data and metadata • Interactive queryable database 2018• © II RJoint package Congress on Evolutionary released Biology 2018. All rights reserved - Any reproduction even in part is prohibited.

Deck et al. 2017. The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples. PLoS Biology 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. Libby Liggins 2018 | Massey University © |48th New Zealand European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

Species–genetic diversity correlations

Drivers of genetic diversity

Opportunities for Pacific nations

The processes responsible for generating species diversity, would also be expected to have bearing on patterns of genetic diversity — Antonovics 1976, Vellend 2005

Corroborated by: Theory of Island Biogeography, Wright’s2018 © II Joint Congress Island on Evolutionary model, Biology Metabolic 2018. All rights reserved theory - Any reproduction even in part is prohibited. Libby Liggins 2018 | Massey University © |48th New Zealand European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

Habitat area +

Age/stability +

Energy +

Isolation -

2018 © II Joint Congresse.g. onLarge Evolutionary areas Biology 2018. of All rights shallow reserved - Any reefreproduction habitat even in part is prohibited.within the Coral Triangle are expected to support large population sizes, and therefore high levels of genetic diversity — Vellend 2003, Bellwood et al. 2005

Data preparation Sequences binned into ecoregions - MEOW, Spalding et al. 2007 Minimum dataset requirements: > 6 sequences per ecoregion, > 3 ecoregions For each species, the species*locus dataset with broadest geographic range, or the most common locus within DIPnet was retained = 90 species, including 58 fishes 78 sp*locus datasets DIPnet database 1 sp*locus dataset

Genetic diversity measures π, nucleotide diversity per site H, haplotype richness: a corrected estimate based on sampling coverage

Visualization Genetic diversity was normalised within each species dataset Mean genetic diversity per Ecoregion was calculated

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . Genetic diversity across the Indo-Pacific patterns 78 sp*locus datasets 1 sp*locus dataset

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . Species-genetic diversity correlation methods Species richness IUCN Red List of Threatened Species data www.iucnredlist.org

Cone snails - all species in genus Conus, ~632 species Lobsters, ~246 species Corals - all warm water reef-building species, ~840 species Mangroves, ~75 species Marine mammals, ~111 species Seagrasses, ~69 species Sea Cucumbers - all commercial species, ~368 species Marine fishes, ~1847 species Seasnakes, ~61 species

Marine fishes

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . Species-genetic diversity correlation methods Species richness All species richness, and marine fishes species richness

Genetic diversity H, coverage corrected haplotype richness

Meta-regression Regression of genetic diversity over species richness, for each species A meta-analysis of the slopes among species was used to obtain an overall effect size 2018 © II Joint Congressand onassociated Evolutionary Biology 2018. standard All rights reserved -error Any reproduction even in part is prohibited.

metafor, R package Viechtbauer 2010. Journal of Statistical Software 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. Libby Liggins 2018 | Massey University © |48th New Zealand European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

** *

Species richness Haplotype richness

~1 extra haplotype per fish species, for every 100 fishes

** *

Species richness Haplotype richness

* P < 0.05 ** < 0.01 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. Libby Liggins 2018 | Massey University © |48th New Zealand European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

~1 extra haplotype per fish species, for every 100 fishes

** *

Species richness Genetic diversity Regionalisation ECO ECO 500km2 PROVINCE

Species–genetic diversity correlations

Drivers of genetic diversity

Opportunities for Pacific nations

Habitat area +

Age/stability +

Energy +

Habitat area Coral reef area km2 Shallow benthic area km2, < 45m Deep benthic area km2, < 120m

Bathymetry data from maps.ngdc.noaa.gov/; coral reef data from data.unep-wcmc.org/datasets/1 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. Libby Liggins 2018 | Massey University © |48th New Zealand European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

Habitat area Coral reef area km2 Shallow benthic area km2, < 45m Deep benthic area km2, < 120m

Age/stability Stability mean, proportion of 100km radius that is between 50-250m deep Proxy for habitat suitability through the Pleistocene based on sea level models of Voris 2000. For explanation see Riginos et al. 2016. Current Zoology

Habitat area Coral reef area km2 Shallow benthic area km2, < 45m Deep benthic area km2, < 120m

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. Energy Sea surface temperature, mean, Sbrocco and Barber 2013. Ecology Chlorophyll a, mean annual (mean of monthly means) Tyberghein et al. 2012. Global Ecology and Biogeography

Genetic diversity for 58 fish species H, coverage corrected haplotype richness

Coral reef habitat area Habitat stability, mean ~ Shallow habitat area Sea surface temperature, mean

Deep habitat area Chlorophyll a, mean

Genetic diversity for 58 fish species H, coverage corrected haplotype richness

Habitat area Stability/age Energy

* P < 0.05 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. Libby Liggins 2018 | Massey University © |48th New Zealand European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

Genetic diversity for 58 fish species H, coverage corrected haplotype richness

Shallow habitat area *

Habitat area Stability/age Energy

Species – genetic diversity correlation

Genetic diversity and shallow benthic area

Consider multiple predictors in the same meta-regression model

Investigate patterns and processes according to species groups: taxonomic, ecology, life history, demographic history etc.

Consider multiple predictors in the same meta-regression model

Investigate patterns and processes according to species groups: taxonomic, ecology, life history, demographic history etc.

Other work The molecular biogeography of the Indo-Pacific: testing hypotheses with multispecies genetic patterns Crandall et al. in review 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited.

Looking into regions of turnover and nestedness in genetic diversity e.g. Liggins et al. 2015 Ecography

Species–genetic diversity correlations

Drivers of genetic diversity

Opportunities for Pacific nations

78 sp*locus datasets DIPnet database 1 sp*locus dataset

Liggins and Arranz-Martinez (2018) Genetic diversity and connectivity of Beveridge Reef's marine biodiversity in an Indo-Pacific wide context. Report for The Department of Agriculture, Forestry and Fisheries of Niue. 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. Libby Liggins 2018 | Massey University © |48th New Zealand European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

78 sp*locus datasets DIPnet database 1 sp*locus dataset

Sampling point 10+sequences 10 sequences

2 sequences

% private haplotypes

Niue

Niue 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. 2018 © 48th European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

78 sp*locus datasets DIPnet database 1 sp*locus dataset

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . NZ partners DIPnet partners Massey University University of Hawaii at Manoa Auckland Museum University of Queensland Victoria University – Peter Ritchie California State University, Monterey Bay University of Otago – Hamish Spencer University of Melbourne University of Auckland – Shane Lavery University of Central Florida + you? Australian National University University of Leeds 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction evenJames in part is prohibited. Cook University There will be… University of California, Berkeley • Datathon days • Early career workshop: coding, analysis of data using R, using GitHub for collaboration, and spatial conservation planning

Amanda Ackiss - Old Dominion University, USA; Nikos Andreakis - Australian Institute of Marine Science, Australia; Kim Andrews - Durham University, UK; Paul Barber - UC Los Angeles, USA; Moises Bernal - California Academy of Science, USA; Michael Berumen - King Abdullah University of Science and Technology, Saudi Arabia; Chris Bird - Texas A&M University, USA; Philippe Borsa - Centre Institut de Recherche pour le Développment de Nouméa, France; Brian Bowen - University of Hawaii, USA; Matthew Cheung - Biomatters Ltd., New Zealand; Sean Connolly - James Cook University, Australia; Joshua Copus - University of Hawaii, USA; Peter Cowman - Yale University, USA; Eric Crandall - UC Santa Cruz/NOAA, USA; Toby Daly-Engel - University of West Florida, USA; Michael Dawson - UC Merced, USA; Dileepa de Croos - Wayamba University of Sri Lanka, Sri Lanka; Timery DeBoer - Northeastern University , USA; John Deck - UC Berkeley, USA; Pindaro Diaz Jaimes - University Nacional Autonoma de Mexico, Mexico; Joseph DiBattista - King Abdullah University of Science and Technology, Saudi Arabia; Jeff Eble - University of West Florida, USA; Cecile Fauvelot - Centre Institut de Recherche pour le Développment de Nouméa, France; Iria Femandez - University of Ryukyus, Japan; Michelle Gaither - Durham University, USA; Xavier Gonzalez - Texas A&M University , USA; Rachel Gotanco - University of the Philippines, Philippines; Michael Hickerson - City College of New York, USA; Eric Hoffman - University of Central Florida, USA; John Horn - University of Algarve, Portugal; Matt Iacchei - University of Hawaii, USA; Steve Karl - University of Hawaii, USA; Marc Kochzius - Vrije University, Belgium; Harilaos Lessios - Smithsonian Tropical Research Institute, USA; William Ludt - Louisiana State University, USA; Hawis Madduppa - Bogor Agriculture University, Indonesia; Chris Meyer - Smithsonian National Museum of Natural History, USA; Monica Mlwale - South African Institute for Aquatic Biodiversity, South Africa; Snaebjorn Paisson - University of Iceland, Iceland; John Pandolfi - University of Queensland, Australia; Cynthia Riginos - University of Queensland, Australia; Pablo Saenz-Agudelo - King Abdullah University of Science and Technology, Saudi Arabia; Elizabeth Sbrocco - National Evolutionary Synthesis Center, USA; Kim Selkoe - NCEAS, USA; Liu Shang-Yin - UC Los Angeles, USA; Rob Toonen - University of Hawaii, USA; Eric Treml - University of Melbourne, Australia; Sophie von der Heyden - Stellenbosch University, South Africa; Robin Waples - National Oceanic and Atmospheric Administration, USA; Gert Worheide - Ludwig Maximilians Universität München, Germany; 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. Nina Yasuda - University of Miyazaki, Japan + you?

βSNE nestedness component

βSIM turnover component

βratio

Nestedness, βSNE Turnover, βSIM

βratio= βSNE/βSOR

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . MARINEFISHES ALL_RICHNESS shallow_km2 chla_mean deep_km2 sst_mean stability_MEAN habitat_reef_km2 MARINEFISHES ALL_RICHNESS 0.98 shallow_km2 0.32 0.33 chla_mean 0.32 0.36 0.51 deep_km2 0.29 0.28 0.93 0.47 sst_mean 0.59 0.65 0.18 0.19 0.11 stability_MEAN 0.44 0.45 0.83 0.65 0.85 0.14 habitat_reef_km2 -0.16 -0.15 0.02 -0.06 -0.06 -0.35 -0.07

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. 2018 © 48th European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .