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The evolution of teleost otolith morphology and its applications in paleoichthyology, Werner Schwarzhans [et al.]

The evolution of teleost otolith morphology and its applications in paleoichthyology, Werner Schwarzhans [et al.]

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The features of the Neogene stage of the

North Pacific ichthyofauna development as

inferred from two fossil fish complexes from

Sakhalin, Russia

Mikhail Nazarkin


∗ 1

Zoological Institute Russian Academy of Sciences (ZIN RAS) – 199034, Universitetskaya Emb., 1,

Sankt-Petersburg, Russia, Russia

The two contemporary complexes of fossil fishes came from the Middle-Late Miocene deposits

of the Sakhalin Isl., Russia. The fish community from Agnevo Formation consists from the 27

species of 15 families of shallow-water fishes, with predominance of cottoids, stichaeoids and

pleuronectids. The complex from Kurasi Formation contains the fossils of 32 species of 23

fish families and comprises mainly mesopelagic dwellers, such as myctophids, argentiniforms,

stomiiforms and aulopiforms.

Both complexes comprise mainly the representatives of the recent fish families, whereas the

extinct families are rare and, probably, are the remnants of the pre-Miocene ichthyofauna. The

structure of these fish complexes brightly differs at the level of the genera. Whereas extinct

genera make only 6 % of the deep-sea fishes of Kurasi F., this index for the shallow-water

community of Agnevo F. is about 50 %. The higher degree of differences between extinct and

recent species of the same genera among the shallow-water, than among the deep-sea fishes

can be postulated at the species level. Extinct deep-water fishes usually differ from the recent

congeners by the modal values of the counts, some body proportions, and the shape of separate

bones. The revealed differences are usually plesiomorphic. Therefore the Miocene forms can be

treated as closest to hypothetical ancestors of the recent species. The Miocene shallow-water

dwellers are usually characterized by more reliable characters such as the hiatus in counts,

configuration of the lateral lines or skin ossicles structure.

Since the Middle Miocene, the Sakhalin region underwent considerable changes resulted from

the development of the JapanSea rift, shifts in coastline configurations, transgressive cycles and

temperature fluctuations. Obviously, evolutionary responses of deep- and shallow-water fish

faunas to changing environment were not identical: the coastal communities were affected much

more than the deep-water ones, as indicated by the degree of changes in their structure to the

present time. Thus, the rates of evolution of coastal fishes since the Middle-Late Miocene were

significantly higher, than those of deep-water dwellers.



A2/ Genes to Genomes: Forging

ahead in the study of marine



A high-quality Genome of the Clownfish

Amphiprion Percula

Robert Lehmann ∗ 1 , Damien Lightfoot 1 , Celia Schunter 1 , Rita

Bartossek 1 , David Miller 2 , Michael Berumen 1,3 , Philip Munday† 2 ,

Timothy Ravasi‡ 1


KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental

Sciences and Engineering (KAUST) – Thuwal, Kingdom of Saudi Arabia, Saudi Arabia


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

Reef StudiesJames Cook University TownsvilleQueensland 4811 Australia, Australia


Red Sea Research Center, King Abdullah University of Science and Technology (RSRC) – Thuwal,

Kingdom of Saudi Arabia, Saudi Arabia

The iconic clownfish is a model organism for studying ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, marine mutualisms,

habitat selection and the impact of climate change. The clownfish was also the first species for

which it was demonstrated that the response to ecologically important olfactory cues is impaired

by ocean acidification. Here we present the first ever sequenced genome of a clownfish species.

The de novo genome of Amphiprion percula, an endemic species from the Australian’s Great

Barrier Reef, was sequenced using the Pacific Biosciences SMRT sequencing technology. We

sequenced the genomic DNA from the brain of a wild-caught clownfish to a coverage of 124X.

The final and presented genome was selected from several tentative assemblies based on both

measures of quality and contiguity. It features a contig’s N50 of 1.86 Mbp spanning 0.9 Gbp total sequence length and contains 30594 predicted genes covering 97% of the expected orthologs.

By phasing the genome using the Phase Genomics Hi-C technique we were able to arrange 1,073

contigs into 24 chromosome scale scaffolds spanning 98% (0.89 Gbp) of the initial assembly,

resulting in a final genome with an N50 of 38 Mbp across 365 scaffolds. This represents the

highest-quality and most complete genome of a tropical reef fish presently available.The availability of a high quality clownfish genome makes this species an emerging model system for

evolutionary, ecology and climate change studies. In my talk, I will also present how, by means

of comparative genomics, we were able to identify genomic elements responsible for the observed

clownfish’s plastic response to ocean acidification.


Corresponding author: philip.munday@jcu.edu.au

Corresponding author: timothy.ravasi@kaust.edu.sa


Addressing intractable groups in the Fish

Tree of Life using genome-wide Gene

Genealogy Interrogation

Ricardo Betancur


∗ 1

, Lily Hughes 2 , Dahiana Arcila 2 , Guillermo Orti


University of Puerto Rico - Rio Piedras – P.O. Box 23360, San Juan, PR 00931-3360, Puerto Rico


George Washington University – 2023 G St NW, Washington, DC, 20052, United States

Much progress has been achieved in disentangling evolutionary relationships among species

in the Tree of Life, but some taxonomic groups remain difficult to resolve despite increasing

availability of genome-scale data sets. Recently, we introduced a new practical approach, named

Gene Genealogy Interrogation (GGI), that uses constrained tree searches in combination with

topology tests to account for gene tree estimation error and its downstream effects in coalescent analyses. We initially showed its efficacy in resolving controversial relationships within the

largest freshwater fish radiation (Otophysi) based on newly generated DNA sequences for 1,051

exons from 225 species. Here, we address other difficult nodes in the Fish Tree of Life based

on a large-scale phylogenomic dataset consisting of 1,105 exons, which was assembled via in

silico mining of 305 genome- and transcriptome-enabled fish species. In addition to revisiting

Otophysi with the new dataset, other difficult nodes addressed include the base of teleosts, protacanthopterygians, base of acanthomorphs, sister group of percomorphs, and atherinomorphs.

Our GGI results show that, while phylogenetic resolution for major protacanthopterygian and

acanthomorph lineages remains contentious, the majority genes favor a single tree topology in

all other cases. GGI provides a powerful approach to identify incompatible signals in large data

sets and to discern between estimation error and actual biological conflict explaining gene tree




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The evolution of teleost otolith morphology and its applications in paleoichthyology, Werner Schwarzhans [et al.]

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