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Population genomics and phenotypic differentiation between pairs of sister species of clownfishes, Joris Bertrand [et al.]

Population genomics and phenotypic differentiation between pairs of sister species of clownfishes, Joris Bertrand [et al.]

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Quantifying the emergent geography of

dispersal barriers and environmental

gradients: biogeographic implications across

the Indo-Pacific.

Eric Treml


∗† 1

, Libby Liggins 2 , Cynthia Riginos


University of Melbourne – Melbourne, VIC, Australia


Massey University – Auckland, New Zealand


The University of Queensland – Brisbane, Australia

Dispersal limitations and environmental gradients are known to restrict larval exchange and

species’ ranges and contribute to broad-scale biogeographic and phylogeographic patterns. However, the relative roles of biophysical processes and environmental variables in forming biogeographic patterns varies across the seascapes. In this study, we map the geographic structure of

multivariate environmental gradients and intersect these with the location and strength of multispecies dispersal barriers across the Indo-Pacific Ocean. Specifically, we ask three questions:

(1) What is the spatial structure and range in environmental gradients across this seascape? (2)

What is the geographic configuration and biophysical drivers of multispecies dispersal barriers?

(3) What spatial sampling strategy would maximise the likelihood of testing the influence of

dispersal and environmental factors on bio/phylogeographic patterns? Here, we analyse eight

commonly used seascape parameters (e.g., sea surface temperature, salinity, depth, and net

primary productivity) with other key seascape factors, such as a thermal stress metric and a

proxy for Pleistocene habitat stability, to quantify the spatial structure of environmental gradients across the seascape. A biophysical dispersal model was used to quantify and map the

emergent patterns of multi-species population connectivity and predict the strength of concordant dispersal barriers arising from seascape features. Although individual taxa varied in their

predicted fine-scale population connectivity, there was broad-scale consistency in the location of

dispersal barriers. Across all trait combinations, reproductive output (fecundity and density of

reproductive adults), reproductive strategy (spawning phenology) and the length of the larval

dispersal phase determined the strength of barriers at the seascape scale. Combining these dispersal barriers and corridors with the hotspots of change in environmental gradients allows us

to develop spatially-explicit sampling strategies to explore genetic-environmental associations

while considering species’ dispersal potential (such as when search for loci under selection in

population genomic investigations). This targeted strategy maximises the likelihood of finding

key associations while allowing one to sample at appropriate distances to minimise autocorrelation among sample sites and accommodate the dispersal scales of interest. This spatially-explicit

approach may contribute to the development of a more holistic understanding of the regions’



Corresponding author: etreml@unimelb.edu.au


Response of reef fish functional groups to

local stressors in American Samoa

Alice Lawrence


∗ 1

American Samoa Department of Marine and Wildlife Resources – PO Box 3730, Pago Pago, 96799.,

American Samoa

American Samoa has a long history of quantitative coral reef surveys, dating back to 1917,

with more regular surveys initiated after the 1979 Acanthaster plancii outbreak. Past studies to

assess the correlations between human activities and coral reef health proved difficult, possibly

due to the masking effect of this disturbances, in addition to hurricane and bleaching events.

A watershed-based coral reef monitoring program instigated by the local EPA office in 2015 was

the foundation for collaboration between local resources agencies to increase the understanding

of the linkages between water quality and coral reef health. This study focusses on initial investigations into the linkages between reef fish communities, benthic habitat composition, and

key local environmental predictor variables. Statistical analysis of the EPA 2013 dataset using

forward step-wise regression modeling highlighted wave energy, fishing access, and disturbed

land as the strongest contributing variables predicting ecosystem condition.

Thirty reef slope sites were surveyed over a three-week period in November 2016 around Tutuila

Island, providing a novel opportunity to analyse the largest number of sites surveyed over a short

time period for over 10 years. The survey was designed to improve statistical confidence, sites

were selected based on a human population density gradient, and all sites were located at the

same distance from major stream mouths. Reef fish species from non-cryptic families were included in the analysis, with the exception of Pomacentridae analysed in a complementary study.

Fish health metrics were derived by univariate and multivariate analysis approaches, and regression models run using R Studio. Environmental predictors were derived using GIS data layers

to develop proxies for natural environmental factors and human stressors, and standardised for

building regression models. Initial results were imported into an ArcGIS geodatabase which assisted with visualising trends, including interesting relationships between trophic feeding groups

and fishing access. Monthly water quality data sampled at each site over a one-year period will

be integrated into the modeling process by end of 2017. Future work will investigate temporal

changes and in-depth ecological studies to further understand the drivers and predictors of reef

fish communities in the territory.



Revisiting the ”Center Hypotheses” of the

Indo-West Pacific: Idiosyncratic genetic

diversity of nine reef species offers weak

support for a center of biodiversity.

Ambrocio Melvin Matias


∗† 1,2

, Cynthia Riginos


University of Queensland (UQ) – School of Biological Sciences The University of Queensland St Lucia,

QLD 4072, Australia


University of the Philippines Diliman (UPD) – Institute of Biology, University of the Philippines

Diliman, Quezon City 1101, Philippines

Several hypotheses seek to explain the distribution of marine species diversity in the IndoWest Pacific (IWP), particularly the extreme high species diversity at its center – the Coral

Triangle (CT). Among these hypotheses, the various ”centers hypotheses” have sustained ongoing interest among biogeographers and phylogeographers. Delineating the causes of IWP

biodiversity, however, remains an unresolved question. Though the underlying processes behind

these hypotheses are not mutually exclusive, they offer explicit predictions regarding patterns

of biodiversity in the IWP, which we test using intraspecific genetic diversity. Here, we use

existing mitochondrial DNA data of nine reef species and augment them with new samples from

the Philippines to cover key regions of the IWP. Using these data, we first examine patterns of

genetic diversity across the IWP to test if genetic diversity peaks in the CT. We then investigate

the historical demography of these species to evaluate the possible correlation of genetic diversity

with likely Pleistocene refugia. Finally, we estimate gene flow between regions – CT vs Indian

Ocean (IO) and CT vs Pacific Ocean (PO) – to assess concordance with predicted patterns of

connectivity. Contrary to our expectation, we do not find evidence for higher genetic diversity

in the CT relative to the IO and PO. Moreover, we find highly variable patterns of genetic

diversity when species are evaluated individually. Although there is no significant correlation

between genetic diversity and likely refugia, genetic patterns suggest that some populations

have experienced expansions, which is typical after bottlenecks. The regions with signals of

expansion, however, are also inconsistent across species. Gene flow estimates indicated very

limited exchange between regions, lending poor support for the different hypotheses tested. In

summary, patterns of genetic diversity across nine reef species are not concordant with no single

hypothesis regarding biogeographic origins of marine biodiversity supported for events in the

recent past.


Corresponding author: ambrocio.matias@uq.net.au


The biogeography of tropical reef fishes:

endemism and provinciality through time

Peter Cowman



∗ 1

, Valeriano Parravicini 2 , Michel Kulbicki 3 , Sergio

Floeter 4

ARC Centre of Excellence for Coral Reef Studies (CoralCoE) – ARC Centre of Excellence for Coral

Reef StudiesJames Cook University TownsvilleQueensland 4811 Australia, Australia


CRIOBE – Universit´e de Perpignan – Perpignan, France


Laboratoire dExcellence

CORAIL (LabEX CORAIL) – Institut de Recherche pour le D´eveloppement

– Labex Corail58, avenue Paul Alduy66860 Perpignan CEDEXT´el. : 04 30 19 23 32Email :

contact@labex-corail.fr, France


Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina (UFSC) –

Florianopolis, Brazil

The largest marine biodiversity hotspot straddles the Indian and Pacific Oceans, driven by

taxa associated with tropical coral reefs. Centred on the Indo-Australian Archipelago (IAA),

this biodiversity hotspot forms the ‘bullseye’ of a steep gradient in species richness from this

centre to the periphery of the vast Indo-Pacific region. Complex patterns of endemism, wideranging species and assemblage differences have obscured our understanding of the genesis of

this biodiversity pattern and its maintenance across two-thirds of the world’s oceans. But timecalibrated molecular phylogenies coupled with ancestral biogeographic estimates have provided

a valuable framework in which to examine the origins of coral reef fish biodiversity across the

tropics. Herein, we examine phylogenetic and biogeographic data for coral reef fishes to highlight

temporal patterns of marine endemism and tropical provinciality. The ages and distribution of

endemic lineages have often been used to identify areas of species creation and demise in the

marine tropics and discriminate among multiple hypotheses regarding the origins of biodiversity

in the IAA. Despite a general under-sampling of endemic fishes in phylogenetic studies, the

majority of locations today contain a mixture of potential paleo- and neo-endemic fishes, pointing

to multiple historical processes involved in the origin and maintenance of the IAA biodiversity

hotspot. Increased precision and sampling of geographic ranges for reef fishes has permitted

the division of discrete realms, regions and provinces across the tropics. Yet, such metrics are

only beginning to integrate phylogenetic relatedness and ancestral biogeography. Phylogenetic

dissimilarity clustering of extant assemblages identifies a large Indo-West Pacific cluster, but

also clusters distant Pacific island together based on peripherally isolated, but phylogenetically

close lineages. Through time, clustering of estimated ranges reveals the dynamic nature of reef

assemblages with provincial changes reflecting large scale tectonic rearrangement of the tropical




The reefish Atlas

Fran¸cois Guilhaumon ∗ 1 , Louis Nerriere 2 , Fabien Leprieur 2 , Valeriano

Parravicini 3 , Michel Kulbicki 4 , Robert Myers 5



MARine Biodiversity Exploitation and Conservation (UMR MARBEC) – Institut de Recherche pour

le D´eveloppement : UMRD 248, Institutf ranc¸aisdeRecherchepourl ExploitationdelaM er :

U M R9190, U niversit´

edeM ontpellier : U M R9190, CentreN ationaldelaRechercheScientif ique :

U M R9190 − −U niversit´

edeM ontpellier, P laceEug`

eneBataillon, M ontpellier, F rance

MARine Biodiversity Exploitation and Conservation (UMR MARBEC) – Institut de Recherche pour

le D´eveloppement : UMRD 248, Institutf ranc¸aisdeRecherchepourl ExploitationdelaM er :

U M R9190, U niversit´

edeM ontpellier : U M R9190, CentreN ationaldelaRechercheScientif ique :

U M R9190 − −M ontpellier, F rance


Centre de recherches insulaires et observatoire de l’environnement (CRIOBE) – Universit´e de

Perpignan Via Domitia, Ecole Pratique des Hautes Etudes, Centre National de la Recherche

Scientifique : USR3278 – BP 1013 Papetoiai 98729 PAPETOAI, France


Ecologie marine tropicale des oc´eans Pacifique et Indien (ENTROPIE [Perpignan]) – Institut de

Recherche pour le D´eveloppement – 52, avenue Paul Alduy, 68860 Perpignan Cedex 9, France


Sea Clicks – 9273 Silent Oak Cir West Palm Beach, FL 33411, United States

The reefish Atlas is an open, collaborative and reproducible initiative to gather, curate and

diffuse openly taxonomic and biogeographic information about Indo-Pacific coral reef fishes.

Based on more than 650 reviewed checklists, the reefish Atlas website propose scientists, and

more generally people interested in coral reef fishes, to browse, download and comment on

the presence/absence patterns of more than 2000 Indo-Pacific coral reef fishes (belonging for

now to 18 families, but more are to be incorporated) in more than 150 marine bio-regions.

Implemented in a transparent and reproducible manner, the reefish Atlas is open from the

beginning and welcome expert discussions about the biogeographical patterns presented. On top

of biogeographical patterns and pictures contributed by the reefish Atlas authors, the website is

a hub gathering life history traits, threat status and taxonomic information available from other

global data bases such as fishbase, the WoRMS or the IUCN red list. We believe the review

and diffusion of hundreds of checklists is timely and will provide community acknowledged

information to be used in scientific research and outreach.



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Population genomics and phenotypic differentiation between pairs of sister species of clownfishes, Joris Bertrand [et al.]

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