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Marine connectivity in time and space: Insights from an intertidal goby, Joshua Thia [et al.]

Marine connectivity in time and space: Insights from an intertidal goby, Joshua Thia [et al.]

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Pathways and perils: Building up genomic

resources in a specialized group of reef fish

Joseph Dibattista

1



∗ 1



Curtin University – Department of Environment and Agriculture, Curtin University, PO Box U1987,

Perth, WA 6845, Australia, Australia



Closely related species can provide valuable insights into evolutionary processes through

their ecology, distribution, and the history recorded in their genomes. Butterflyfish are particularly interesting given that they are dependent on coral reefs for food and shelter, and represent

a model system to study general questions of biogeography, evolution, and population genetics.

From a biogeographic perspective, butterflyfishes are prominent in fish assemblages of one of the

most unique and geologically complex regions of the world’s oceans, the Red Sea and Arabian

Sea. This environment at the western periphery of the Indo-Pacific is characterized by strong

latitudinal gradients in water temperature, salinity, and nutrient load that may act as ecological barriers to larval dispersal and the eventual settlement of marine fauna. The aim of this

presentation is to outline our recent experiences building up genomic resources for ”non-model”

butterflyfish species by sequencing and annotating the genome of the range-restricted blacktail

butterflyfish, which may serve as a starting point for investigations of genes underlying adaptation to the unique Arabian environment. I will further discuss: 1) isolating restriction site

associated DNA (RAD-seq) single nucleotide polymorphism (SNP) markers to quantify connectivity and natural selection in nine butterflyfish species from the Red Sea and Arabian Sea, 2)

how we validated the butterflyfish genome as a scaffold for congeneric RAD-seq data, 3) metabarcoding their gut contents to characterize diet and niche partitioning, and 4) deep sequencing

ultraconserved elements (UCEs) across the Chaetodontidae family to help explain the high levels

of endemism in the region.







Speaker



68



Population genomics of New Zealand

snapper and testing for size-selective fishing

using ancient DNA

Peter Ritchie

1



∗ 1



Victoria University of Wellington – PO Box 600 Wellington 6140 NEW ZEALAND, New Zealand



Chrysophrys auratus (Australasian snapper) is a common sparid species found in the coastal

waters of New Zealand and Australia. It is a valuable commercial species and frequently targeted

by recreational fishers. We have used genetic markers to assess the level of gene flow among sites

around the New Zealand North Island and northern parts of the South Island. The results did

not show a consistent pattern of population genetic structure when compared to the findings

of previous studies. To resolve this uncertainty, we have determined the genome sequence of

C. auratus and are using a Genotyping-by-Sequencing approach to quantify the genome-wide

levels of variation and testing for differentiation. We are also able to use the genome data to

test for loci under selection from environmental pressures, such as size-selective fishing. Bone

measurements from archaeological sites have been used to suggest that the overall size of New

Zealand snapper has reduced since the onset of commercial scale size-selective fishing. We will

use well-preserved DNA that can be retrieved from prehistoric fish bones and compare them to

modern fish using genome sequencing. This approach will enable us to determine whether there

is a genetic pattern associated with size reduction and if it is correlated with the conditions

needed for fishing-induced evolution.







Speaker



69



The Future of Phylogenomics

Prosanta Chakrabarty

1



∗ 1



Louisiana State University Museum of Natural Science (LSU) – Louisiana State University Museum of

Natural Science, United States



The end of systematics will be the day we have a Tree of Life with complete genomic sampling

of every species on Earth, and all the fossil taxa we can fit into it. Well before that day comes we

will be using reduced genomic sampling from target capture to sequence phylogenomic markers

such as ultraconserved elements and exons to study the history of major clades. Although

phylogenomic markers are a great leap forward from Sanger sequencing, we now have more

data than we can handle with few analytical tools for studying coalescence, divergence times,

or evolutionary process. We will present case studies from a number of fish lineages that reveal

how much further we have to go before we can transition into full genome phylogenies.







Speaker



70



The Genomic Observatories Metadatabase

(GeOMe): A new repository for field and

sampling event metadata associated with

genetic samples

Eric D. Crandall ∗ 1 , Michelle Gaither† 2 , Cynthia Riginos 3 , Neil Davies

4

, Robert Toonen 2 , Rodney Ewing 5 , Christopher Bird 6 , Christopher

Meyer 7 , John Deck 8

1



7



California State University Monterey Bay (CSUMB) – Marina, CA, United States

2

Hawaii Institute of Marine Biology (HIMB) – Kaneohe, HI, United States

3

University of Queensland (UQ) – Brisbane, Australia

4

Gump South Pacific Research Station – Moorea, French Polynesia

5

Biocode, LLC – Junction City, OR, United States

6

Texas AM University, Corpus Christi – Texas, United States

National Museum of Natural History, Smithsonian Institution – Washington D.C., United States

8

Berkeley Natural History Museums – Berkeley, CA, United States



Documenting patterns of global biodiversity and understanding how that diversity is generated and maintained are important first steps towards mitigating the effects of anthropogenic

stressors. Genetic data are key to this effort. Whereas public databases have served as vital

repositories for DNA sequences, they do not accession the metadata required for ecological or

evolutionary analyses. This ”metadata gap” means that vital information about sampling events,

such as precise sampling location, date, habitat, and organism life history are rarely reported.

Instead most of this information is left unpublished, greatly diminishing the potential value of

the data. To fill this ”metadata gap” we have developed the Genomic Observatories Metadatabase (GeOMe; http://www.geome-db.org/); an open access repository for geographic and

ecological metadata associated with genetic data. GeOMe provides a user-friendly, web-based

interface that allows data contributors to create a customized, yet standards compliant spreadsheet that captures the temporal and geospatial context of each biosample. These metadata

are then validated and permanently linked to archived genetic data stored in NCBI’s Sequence

Read Archive via unique persistent identifiers. Under the auspices of the Diversity of the Indo

Pacific Network (DIPnet) GeOMe has already assembled over 35,000 individual mitochondrial

sequences from and over 200 coral reef associated species sampled at over 1,500 sites across the

Indo-Pacific making GeOMe the most extensive database of georeferened sequence data.









Speaker

Corresponding author: michellergaither@gmail.com



71



Through a liquid glass to the eye of the

beholder: Visual ecology of coral reef fishes

isolated by the Isthmus of Panama

Michele Pierotti

1



∗ 1



, W Owen Mcmillan 1 , D Ross Robertson



1



Smithsonian Tropical Research Institute (STRI) – Balboa, Ancon, Panama



Coral reef fishes are ideal system for studies examining the effects of ecological selection

on traits involved in sensory divergence and the evolution of animal communication systems.

Here we take advantage of a unique natural experiment, the 3.1 my old uplift of the Isthmus of

Panama, which separated a once single aquatic ecosystem into two isolated and highly different

oceans, the Caribbean and the Tropical East Pacific (TEP). This ’placed’ similar genomes,

those of sister species isolated on either side of the isthmus, into radically different photic

environments: the turbid nutrient-rich waters in the Eastern Pacific or the clear oligotrophic

waters in the Caribbean. We collect underwater spectral data, characterize rods and cones visual

sensitivities physiologically, and employ RNAseq transcriptome sequencing to identify the opsin

complement and relative expression in each geminate pair. This design allows us to test, within a

well-characterized timeframe (3.1 mya), whether the spectral characteristics of these two bodies

of water drove similar selective pressures on visual sensitivities in phylogenetically distant reef

fish families. In addition, by contrasting geminate pairs that differ in peak diel activity, foraging

strategies and position in the water column, we examine the role of these ecological factors in

shaping reef fish visual systems. We discuss our findings in relation to the visual ecology of

related species in the Great Barrier Reef.







Speaker



72



Time-calibrated Phylogenomic

Reconstruction of Batfishes (Lophiiformes:

Ogcocephalidae)

Cerise Chen

1



∗† 1,2



Department of Ecology and Evolutionary Biology [UC Santa Cruz] (EEB) – 1156 High St, Santa

Cruz, CA 95064, United States

2

Department of Ichthyology[California Academy of Sciences] – 55 Music Concourse Drive, San

Francisco, CA, 94118, United States



Batfishes (family Ogcocephalidae), some described as aliens, are a group of bizarre walking

fishes related to the coral reef frogfishes (family Antennariidae), both belong in the anglerfish

order Lophiiformes. The family Ogcocephalidae contains 10 genera and 78 species, of which 7

genera and 55 species are found in the Indo-Pacific Ocean. The family represents one of the

least known lophiiform families, therefore having a solid phylogenetic history available is crucial

to the understanding of the evolutionary history of this group of fish. Even to this date the most

comprehensive molecular phylogeny based on mitochondrial genes and protein-coding nuclear

genes contained less than 20% of all species of Ogcocephalidae. Despite discrepancies between

morphological and molecular phylogeny, both support a monophyletic Ogcocephalidae. The discovery of fossil record of batfishes (Tarkus squirei gen. et sp. nov.) from the late early Eocene

of Monte Bolca may enable the application of coalescent approaches to calibrate divergence estimates for the proposed study. Elucidation of the origin of Ogcocephalidae may also provide an

age estimation as a reference for other lophiiforms and their tree of life, hence I wish to apply

Next-Generation Sequencing tools such as targeted enrichment of ultraconserved nuclear DNA

elements (UCEs) and their flanking regions for time-calibrated phylogenomic reconstruction of

batfishes. Fresh genetic materials of 24 species of Ogcocephalidae and other lophiiforms including members of 4 species of Lophiidae and 2 species of Chaunacidae from Taiwan were obtained,

DNA sampling was also made possible from old museum specimens thus enable archival sampling to be used in revealing the evolution of batfishes and their kin.

This is a presentation of a project proposal.









Speaker

Corresponding author: jchen263@ucsc.edu



73



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