Explosive diversification of marine fishes at the Cretaceous–Palaeogene boundary

Abstract

The Cretaceous-Palaeogene (K-Pg) mass extinction is linked to the rapid emergence of ecologically divergent higher taxa (for example, families and orders) across terrestrial vertebrates, but its impact on the diversification of marine vertebrates is less clear. Spiny-rayed fishes (Acanthomorpha) provide an ideal system for exploring the effects of the K-Pg on fish diversification, yet despite decades of morphological and molecular phylogenetic efforts, resolution of both early diverging lineages and enormously diverse subclades remains problematic. Recent multilocus studies have provided the first resolved phylogenetic backbone for acanthomorphs and suggested novel relationships among major lineages. However, these new relationships and associated timescales have not been interrogated using phylogenomic approaches. Here, we use targeted enrichment of >1,000 ultraconserved elements in conjunction with a divergence time analysis to resolve relationships among 120 major acanthomorph lineages and provide a new timescale for acanthomorph radiation. Our results include a well-supported topology that strongly resolves relationships along the acanthomorph backbone and the recovery of several new relationships within six major percomorph subclades. Divergence time analyses also reveal that crown ages for five of these subclades, and for the bulk of the species diversity in the sixth, coincide with the K-Pg boundary, with divergences between anatomically and ecologically distinctive suprafamilial clades concentrated in the first 10 million years of the Cenozoic.

An integrated pathway for building regional phylogenies for ecological studies

“…Our trees include 71% of the New Zealand species, over 89% of families and 98% of orders. Overall, the phylogenetic relationships and the time‐line retrieved were in close general agreement with accepted relationships for fishes within the tree of life (Alfaro et al, ; Betancur‐R, Broughton et al, ; Betancur‐R et al, , ; Hughes et al, ; Matschiner et al, ; Near et al, , ; for more detailed comparisons of time lines from these studies, see Supporting Information Appendix S7). Our new phylogenies dramatically improve our ability to rigorously incorporate phylogenetic relationships into regional studies of ecological biodiversity for New Zealand's marine fish fauna.…”

Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes*

“…; Alfaro et al. ). Fortunately, this is not the case for the apparent incongruence in otophysan relationships or characiform monophyly.…”

“…Therefore, the ability to "dissect" a subset of well supported clades around the node of interest that meet the monophyly criterion may become another critical limitation of the GGI approach. For example, this seems to be the case with the difficulty of resolving controversial branching patterns proposed by different studies at the base of the neoteleost and acanthopterygian fish radiations (Near et al 2012;Betancur-R. et al 2013;Grande et al 2013;Davesne et al 2016;Nelson et al 2016;Alfaro et al 2018). Fortunately, this is not the case for the apparent incongruence in otophysan relationships or characiform monophyly.…”

Morphology and evolution of bioluminescent organs in the glowbellies (Percomorpha: Acropomatidae) with comments on the taxonomy and phylogeny of Acropomatiformes

“…The molecular terminals analyzed in this study and GenBank accession numbers corresponding to the gene fragments sequenced are listed in Supporting Information Table 1. For these analyses, the 94 novel DNA sequences were combined with 436 previously published DNA sequences from the following sources: (Alfaro et al, ; Betancur‐R, Broughton et al, ; Betancur‐R, Li, Munroe, Ballesteros, & Ortí, ; Bossu, Beaulieu, Ceas, & Near, ; Cawthorn, Steinman, & Witthuhn, ; Chang et al, ; Chen, Ruiz‐Carus, & Ortí, ; Davis et al, ; Dunlap et al, ; Durand et al, ; Holcroft & Wiley, ; Kenchington, Baillie, Kenchington, & Bentzen, ; Kimmerling et al, ; Li et al, ; Li, Ortí, & Zhao, ; Near et al, , , , ; Near & Keck, ; Rabosky et al, ; Sanciangco et al, ; Satoh, ; Satoh, Miya, Mabuchi, & Nishida, ; Smith et al, ; Smith, Smith, & Wheeler, ; Smith & Craig, ;Smith & Wheeler, , ; Sparks & Smith, ; Thacker et al, ; Tsunashima et al, ; Wainwright et al, ; Yagishita et al, ; Yamanoue et al, ; and 21 unpublished studies). The matrix was 70.4% complete at the amplicon level.…”