Marine fish diversification along the water column gradient: a tale of many threads

Decades of investigation about the evolutionary mechanisms responsible for the astonishing diversity of fishes have suggested habitat transitions along the water column as a prominent ecological divergence axis affecting morphological and lineage diversification. This process is pervasive across all major freshwater and marine fish clades, and evidence supporting its importance comes from a broad spatiotemporal spectrum. On a narrow scale, recent parallel invasions of freshwater lakes by marine three-spined stickleback populations have repeatedly triggered the evolution of two divergent types: a deep-body form living in association with the bottom (benthic) and a slender-body form found in the water column (pelagic). On the other end of the spectrum, evidence from the fossil record suggests that a significant component of the diversification of spiny-rayed fishes (acanthomorphs) has resulted from the colonization of the ecological space previously occupied by pelagic species that became extinct during the Cretaceous-Paleogene (K–Pg) mass extinction. Nevertheless, despite important progress made on this front, further investigation of the processes associated with benthic-pelagic transitions in a robust phylogenetic framework is necessary for bridging evidence from both ends of the evolutionary continuum. The overarching goal of my dissertation was to produce comprehensive phylogenomic trees and to use an array of phylogenetic comparative methods (PCMs) to investigate the drivers and the effects of the adoption of habitat regimes in two evolutionarily intriguing and economically important ray-finned fish groups: the family Lutjanidae (ca. 130 species), including snappers and fusiliers; and the series Carangaria (ca. 1090 species), including flatfishes, jacks, marlins, barracudas, remoras, and allies. Additionally, my dissertation provides new evidence supporting the (recently challenged) single evolutionary origin of flatfishes, and used phylogenetically-informed genotype-to-phenotype (PhyloG2P) approaches to identify the molecular mechanisms underlying their asymmetrical development--a key adaptation linked to transitions from pelagic to benthic habitats. In the first chapter of my dissertation, I applied an integrative approach to quantify the scope and strength of convergent evolution in pelagic lutjanids. As part of a large collaborative effort, I collected genome-wide DNA sequence data for approximately 80% of the total number of species in the group and aggregated data layers for body shape, habitat occupancy, geographic distribution, and paleontological information. The results show that multiple independent colonizations of the water column by ancestrally benthic lutjanid lineages are persistently associated with the convergent evolution of slender bodies and furcate caudal fins. Lineage diversification and transition dynamics vary asymmetrically between habitats, with benthic lineages diversifying faster and colonizing midwater habitats more often than the reverse. These findings demonstrate that convergent phenotypes are ubiquitous among pelagic lutjanids, likely resulting from the strong locomotion constraints imposed by the viscosity of water and drag flow. For my second chapter, I assessed how transitions along the water column triggered by ecological opportunity in the wake of the Cretaceous-Paleogene (K-Pg) mass extinction shaped diversification dynamics in Carangaria. The results suggest that a remarkable proportion of Carangaria’s morphological variation originated in tandem with a marked incidence of habitat shifts along the benthic-pelagic axis during the Paleocene. Likewise, lineage diversification analyses show that species accumulation rates vary as a function of time, with peaks reached early in the clade’s history. These results indicate that all major lineages and body plans in Carangaria originated in an early burst of evolution shortly after the K-Pg mass extinction, allowing the occupation of newly released ecological niches along the water column gradient. In my third chapter, I explored the evolutionary origins of the flatfish asymmetric body plan—an extreme evolutionary innovation responsible for the successful colonization and diversification in benthic habitats by carangarian lineages. I analyzed three independent genome-scale phylogenetic datasets, showing that lineage-specific variation in base composition (i.e., base compositional non-stationarity) of exonic markers deeply affects the ability of commonly-used phylogenetic models to resolve flatfishes as monophyletic. This problem can be alleviated, however, by using models that accommodate lineage-specific variation in base composition. The implementation of such models provides decisive support for the single-origin hypothesis of the asymmetric body plan. I also applied models of codon substitution using complete genomes to investigate the molecular bases of the complex phenotypic modifications in flatfishes. The findings corroborate that the flatfish cranial asymmetry results from a complex interaction between thyroid hormones (THs) and other important developmental pathways (e.g., WNT, BMP, RA). In summary, my analyses demonstrate that ecological divergence along the benthic-pelagic axis greatly impacts rates of morphological and lineage diversification in different clades. Transitions are ubiquitous in time and space but are largely affected by periods of enhanced ecological opportunities, such as the wake of mass extinction events. This process is correlated with the recurrent evolution of convergent body plans but also with some of the most extreme morphological and physiological innovations among vertebrates, such as the internal body temperature regulation (endothermy) in marlins, billfishes, and swordfishes that allows the exploitation of a broad thermal niche, and the flatfish asymmetric body-plan responsible for their successful colonization of the sea bottom. These new insights represent an important step towards understanding the dynamics of animal biodiversity origination in the aquatic realm, ultimately providing a reference to compare against other groups of organisms diversifying along habitat gradients

MARCADA DIFERENCIAÇÃO CARIOTÍPICA ENTRE AS “MANJUBAS” Atherinella blackburni E A. brasiliensis (ATHERINIFORMES).

Atheriniformes is represented by only three species in the Brazilian coast. Species and populations identifications in some small fishes, useful in biological conservation are restricted, due markedly to the absence of conspicuous morphological features. Generally small coastal fish are included at common sense in an indistinct polyphyletic group that depending on the geographic region may receive several popular designations. Among these often are included the Brazilians atheriniforms, whose cytogenetic data are still very limited. Aiming to identify the mechanisms of karyotypic diversification in this group, were analyzed cytogenetically Atherinella blackburni and A. brasiliensis by Giemsa staining, Ag-NOR, C-banding and base-specific fluorochrome CMA3/DAPI. Both species have 2n=48 chromosomes, but distinct karyotypes. So, Atherinella blackburni has 38m (metacentric) + 6sm (submetacentric) + 4a (acrocentric) (NF=92), while A. brasiliensis 4m +14 sm +18 st +12 a (NF=84). Ag-NORs sites (regions CG+) were present in the terminal portions of the short arms of pair 1 (m) in A. blackburni and pair 3 (sm) in A. brasiliensis. The high heterochromatin content in both species is distributed in centromeric and pericentromeric regions, occupying much of the short arms in the most two-armed chromosomes. Much of the heterochromatin of chromosomes of A. blackburni is GC-rich. The striking structural chromosomal diversity between the species was apparently mediated by pericentric inversions and differential heterochromatinization process.Keywords: fish names; fish cytogenetics; heterochromatinization; taxonomic cytomarker.Atheriniformes é representada por apenas três espécies na costa brasileira. A identificação de espécies e populações em alguns grupos de peixes de pequeno porte, útil na conservação biológica é restrita e decorrente em grande parte da ausência de características morfológicas conspícuas. Em geral peixes costeiros de pequeno porte são incluídos pelo senso comum em indistinto grupo polifilético que dependendo da região geográfica pode receber várias denominações populares. Entre estes muitas vezes são incluídos os atheriniformes brasileiros, cujos dados citogenéticos são ainda muito restritos. Visando contribuir para a identificação dos mecanismos de diversificação cariotípica na Ordem, foram analisadas citogeneticamente as espécies do gênero Atherinella, A. blackburni e A. brasiliensis através de coloração com Giemsa, Ag-RONs, bandamento C e fluorocromos base-específicos CMA3/DAPI. Ambas as espécies apresentam 2n=48 cromossomos, mas fórmulas cariotípicas distintas. Atherinella blackburni, possui um cariótipo formado por 38m (metacêntricos) + 6sm (submetacêntricos) + 4a (acrocêntricos) (NF=92; i.e. número de braços cromossômicos), enquanto que o cariótipo de A. brasiliensis é formado por 4m+14sm+18st+12a (NF=84). Sítios Ag-RONs (regiões GC+) estavam presentes no 1o par (m) em posição telomérica, em A. blackburni e na porção terminal do braço curto do 3o par (sm), em A. brasiliensis. O elevado conteúdo heterocromático, em ambas as espécies, está distribuído em regiões centroméricas e pericentroméricas, ocupando grande parte dos braços curtos na maioria dos cromossomos bibraquiais. Grande parte das heterocromatinas dos cromossomos de A. blackburni é rica em bases GC. A marcante diversificação cromossômica estrutural, entre as espécies aparentemente foi mediada por processos de inversões pericêntricas e heterocromatinização diferenciais.Palavras-chave:nomes de peixes, citogenética de peixes, heterocromatinização, citomarcadores taxonômicos

A preliminary inventory of the catfishes of the lower Rio Nhamundá, Brazil (Ostariophysi, Siluriformes)

The Rio Nhamundá is a poorly-known clearwater river draining the southern Guiana Shield of Brazil. In this study we report the findings of a preliminary ichthyological survey, focusing on catfishes (Siluriformes). We identify a total of 36 species (31 genera, seven families) from the Nhamundá, including 11 species already recorded from the river. Overall, our survey results show that even rapid surveys can provide important information on Amazon fish biodiversity, suggesting potential new species, providing range extensions for nominal species, and additionally highlighting taxa in need of taxonomic revision and genetic study. As well as the traditional forms of data collected on biodiversity surveys (i.e. preserved specimen vouchers), our study also provides "new" types of data in the form of DNA barcodes and images of fishes exhibiting colouration in life, information that will be invaluable in future work addressing difficult groups. O Rio Nhamundá é um rio de água clara, pouco conhecido, que drena parte do Escudo das Guianas em território brasileiro. Nesse estudo, nós reportamos os resultados de um levantamento ictiofaunístico preliminar dessa área, tendo como foco os bagres (Siluriformes). Nós identificamos um total de 36 espécies (31 gêneros, sete famílias) provenientes de nossa coleta, e adicionamos 11 espécies já conhecidas para o rio. De maneira geral, os resultados de nossa pesquisa mostram que mesmo levantamentos rápidos podem gerar informações importantes sobre a biodiversidade de peixes amazônicos, sugerindo potenciais espécies novas, ampliando a área de distribuição de espécies, além de apontar a necessidade de revisões taxonômicas e estudos genéticos para alguns taxa. Para além das formas tradicionais de dados coletados em pesquisas de biodiversidade (i.e. espécimes preservados), nosso estudo fornece "novas" formas de dados, como DNA barcodes e imagens com o padrão de coloração dos espécimes vivos, informações essas que serão de valor inestimável para futuros estudos que abordem grupos taxonômicos difíceis. © Collins R et al

Evolutionary determinism and convergence associated with water-column transitions in marine fishes

Repeatable, convergent outcomes are prima facie evidence for determinism in evolutionary processes. Among fishes, well-known examples include microevolutionary habitat transitions into the water column, where freshwater populations (e.g., sticklebacks, cichlids, and whitefishes) recurrently diverge toward slender-bodied pelagic forms and deep-bodied benthic forms. However, the consequences of such processes at deeper macroevolutionary scales in the marine environment are less clear. We applied a phylogenomics-based integrative, comparative approach to test hypotheses about the scope and strength of convergence in a marine fish clade with a worldwide distribution (snappers and fusiliers, family Lutjanidae) featuring multiple water-column transitions over the past 45 million years. We collected genome-wide exon data for 110 (∼80%) species in the group and aggregated data layers for body shape, habitat occupancy, geographic distribution, and paleontological and geological information. We also implemented approaches using genomic subsets to account for phylogenetic uncertainty in comparative analyses. Our results show independent incursions into the water column by ancestral benthic lineages in all major oceanic basins. These evolutionary transitions are persistently associated with convergent phenotypes, where deep-bodied benthic forms with truncate caudal fins repeatedly evolve into slender midwater species with furcate caudal fins. Lineage diversification and transition dynamics vary asymmetrically between habitats, with benthic lineages diversifying faster and colonizing midwater habitats more often than the reverse. Convergent ecological and functional phenotypes along the benthic–pelagic axis are pervasive among different lineages and across vastly different evolutionary scales, achieving predictable high-fitness solutions for similar environmental challenges, ultimately demonstrating strong determinism in fish body-shape evolution. This is a postprint of the published article.This research was supported by NSF grants DEB-1932759 and DEB-1929248 to R.B.-R., DEB-1457426 and DEB-1541554 to G.O., DEB-1541552 to C.C.B., and DEB-2015404 to D.A. M.R.-S. was supported by a postdoctoral fellowship from Colciencias (Grant 848-2019). Financial support was provided from the Office of the Vice President for Research and Partnerships and the Office of the Provost, University of Oklahoma.Ye

Post-Cretaceous bursts of evolution along the benthic-pelagic axis in marine fishes

Ecological opportunity arising in the aftermath of mass extinction events is thought to be a powerful driver of evolutionary radiations. Here, we assessed how the wake of the Cretaceous–Palaeogene (K-Pg) mass extinction shaped diversification dynamics in a clade of mostly marine fishes (Carangaria), which comprises a disparate array of benthic and pelagic dwellers including some of the most astonishing fish forms (e.g. flatfishes, billfishes, remoras, archerfishes). Analyses of lineage diversification show time-heterogeneous rates of lineage diversification in carangarians, with highest rates reached during the Palaeocene. Likewise, a remarkable proportion of Carangaria's morphological variation originated early in the history of the group and in tandem with a marked incidence of habitat shifts. Taken together, these results suggest that all major lineages and body plans in Carangaria originated in an early burst shortly after the K-Pg mass extinction, which ultimately allowed the occupation of newly released niches along the benthic-pelagic habitat axis

Carangaria-MCC

Maximum Clade Credibility (MCC) tree obtained with BEAST

Rabosky1006

1006-taxa imputed tree from Rabosky et al. 2018, which was populated with simulated taxa in place of missing tip

Harrington45

45-taxa tree (from Harrington et al. 2016

MVMORPH

R script to calculate relative fit of alternative models of morphological evolution using MvMORPH

TESS-CoMET

R script to calculate CoMET function in TESS