Halichoeres sanchezi n. sp., a new wrasse from the Revillagigedo Archipelago of Mexico, tropical eastern Pacific Ocean (Teleostei: Labridae).

A new labrid fish species, Halichoeres sanchezi n. sp., is described from eight specimens collected in the Revillagigedo Archipelago in the tropical eastern Pacific Ocean, off the coast of Mexico. The new species belongs to the Halichoeres melanotis species complex that is found throughout the region, differing by 2.4% in the mtDNA cytochrome c oxidase I sequence from its nearest relative, H. melanotis from Panama, and 2.9% from Halichoeres salmofasciatus from Cocos Island, off Costa Rica. The complex is distinguished from others in the region by having a black spot on the opercular flap and a prominent black area on the caudal fin of males. The juveniles and initial phase of the new species closely resemble those of H. salmofasciatus and Halichoeres malpelo from Malpelo Island of Colombia, differing in having an oblong black spot with a yellow dorsal margin on the mid-dorsal fin of initial-phase adults as well as on juveniles. In contrast, the terminal-phase male color pattern is distinct from other relatives, being vermilion to orangish brown with dark scale outlines, a white patch on the upper abdomen, and a prominent black band covering the posterior caudal peduncle and base of the caudal fin. The new species adds to the list of endemic fish species for the isolated archipelago and is an interesting case of island endemism in the region. The discovery was made during the joint 2022 collecting expedition to the archipelago, which featured a pioneering collaborative approach to an inventory of an island ichthyofauna, specifically including expert underwater photographers systematically documenting specimens in situ, before hand-collection, and then photographed fresh, tissue-sampled, and subsequently vouchered in museum collections.

A reference genome for Bluegill (Centrarchidae: Lepomis macrochirus).

North American sunfishes (Family Centrarchidae) are among the most popular sportfish throughout the United States and Canada. Despite the popularity of sunfishes, their ecological importance, and their extensive stocking and aquacultural history, few molecular studies have examined the evolutionary relationships and species boundaries among members of this group, many of which are known to hybridize. Here, we describe a chromosome-scale genome assembly representing Bluegill (Lepomis macrochirus), one of the most widespread centrarchid species. By combining long-read, Oxford Nanopore sequencing data with short-insert, whole-genome and HiC sequence reads, we produced an assembly (Lm_LA_1.1) having a total length of 889 Mb including 1,841 scaffolds and having a scaffold N50 of 36 Mb, L50 of 12, N90 of 29 Mb, and L90 of 22. We detected 99% (eukaryota_odb10) and 98% (actinopterygii_odb10) universal single-copy orthologs (BUSCOs), and ab initio gene prediction performed using this new assembly identified a set of 17,233 genes that were supported by external (OrthoDB v10) data. This new assembly provides an important addition to the growing set of assemblies already available for spiny-rayed fishes (Acanthomorpha), and it will serve as a resource for future studies that focus on the complex evolutionary history of centrarchids.

Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous.

Spiny-rayed fishes (Acanthomorpha) dominate modern marine habitats and account for more than a quarter of all living vertebrate species. Previous time-calibrated phylogenies and patterns from the fossil record explain this dominance by correlating the origin of major acanthomorph lineages with the Cretaceous-Palaeogene mass extinction. Here we infer a time-calibrated phylogeny using ultraconserved elements that samples 91.4% of all acanthomorph families and investigate patterns of body shape disparity. Our results show that acanthomorph lineages steadily accumulated throughout the Cenozoic and underwent a significant expansion of among-clade morphological disparity several million years after the end-Cretaceous. These acanthomorph lineages radiated into and diversified within distinct regions of morphospace that characterize iconic lineages, including fast-swimming open-ocean predators, laterally compressed reef fishes, bottom-dwelling flatfishes, seahorses and pufferfishes. The evolutionary success of spiny-rayed fishes is the culmination of multiple species-rich and phenotypically disparate lineages independently diversifying across the globe under a wide range of ecological conditions.

First detection of biofluorescence in a deep-sea anglerfish.

Biofluorescence has been observed in a variety of fishes, but is rare in deep-sea environments where light from the surface cannot reach. Here, we document biofluorescence in an oceanic anglerfish, the Pacific footballfish. Green biofluorescence was observed in small spots on the distal surface of the esca. While the wavelength of bioluminescent light is unknown for this species, it is possible that light produced by this species also results in biofluorescent emission that may create a more complex lure for attracting prey or mates.

Comparing Ultraconserved Elements and Exons for Phylogenomic Analyses of Middle American Cichlids: When Data Agree to Disagree.

Choosing among types of genomic markers to be used in a phylogenomic study can have a major influence on the cost, design, and results of a study. Yet few attempts have been made to compare categories of next-generation sequence markers limiting our ability to compare the suitability of these different genomic fragment types. Here, we explore properties of different genomic markers to find if they vary in the accuracy of component phylogenetic trees and to clarify the causes of conflict obtained from different data sets or inference methods. As a test case, we explore the causes of discordance between phylogenetic hypotheses obtained using a novel data set of ultraconserved elements (UCEs) and a recently published exon data set of the cichlid tribe Heroini. Resolving relationships among heroine cichlids has historically been difficult, and the processes of colonization and diversification in Middle America and the Greater Antilles are not yet well understood. Despite differences in informativeness and levels of gene tree discordance between UCEs and exons, the resulting phylogenomic hypotheses generally agree on most relationships. The independent data sets disagreed in areas with low phylogenetic signal that were overwhelmed by incomplete lineage sorting and nonphylogenetic signals. For UCEs, high levels of incomplete lineage sorting were found to be the major cause of gene tree discordance, whereas, for exons, nonphylogenetic signal is most likely caused by a reduced number of highly informative loci. This paucity of informative loci in exons might be due to heterogeneous substitution rates that are problematic to model (i.e., computationally restrictive) resulting in systematic errors that UCEs (being less informative individually but more uniform) are less prone to. These results generally demonstrate the robustness of phylogenomic methods to accommodate genomic markers with different biological and phylogenetic properties. However, we identify common and unique pitfalls of different categories of genomic fragments when inferring enigmatic phylogenetic relationships.

Natural history collections are critical resources for contemporary and future studies of urban evolution.

Urban environments are among the fastest changing habitats on the planet, and this change has evolutionary implications for the organisms inhabiting them. Herein, we demonstrate that natural history collections are critical resources for urban evolution studies. The specimens housed in these collections provide great potential for diverse types of urban evolution research, and strategic deposition of specimens and other materials from contemporary studies will determine the resources and research questions available to future urban evolutionary biologists. As natural history collections are windows into the past, they provide a crucial historical timescale for urban evolution research. While the importance of museum collections for research is generally appreciated, their utility in the study of urban evolution has not been explicitly evaluated. Here, we: (a) demonstrate that museum collections can greatly enhance urban evolution studies, (b) review patterns of specimen use and deposition in the urban evolution literature, (c) analyze how urban versus rural and native versus nonnative vertebrate species are being deposited in museum collections, and (d) make recommendations to researchers, museum professionals, scientific journal editors, funding agencies, permitting agencies, and professional societies to improve archiving policies. Our analyses of recent urban evolution studies reveal that museum specimens can be used for diverse research questions, but they are used infrequently. Further, although nearly all studies we analyzed generated resources that could be deposited in natural history collections (e.g., collected specimens), a minority (12%) of studies actually did so. Depositing such resources in collections is crucial to allow the scientific community to verify, replicate, and/or re-visit prior research. Therefore, to ensure that adequate museum resources are available for future urban evolutionary biology research, the research community-from practicing biologists to funding agencies and professional societies-must make adjustments that prioritize the collection and deposition of urban specimens.

Cave-adapted evolution in the North American amblyopsid fishes inferred using phylogenomics and geometric morphometrics.

Cave adaptation has evolved repeatedly across the Tree of Life, famously leading to pigmentation and eye degeneration and loss, yet its macroevolutionary implications remain poorly understood. We use the North American amblyopsid fishes, a family spanning a wide degree of cave adaptation, to examine the impact of cave specialization on the modes and tempo of evolution. We reconstruct evolutionary relationships using ultraconserved element loci, estimate the ancestral histories of eye-state, and examine the impact of cave adaptation on body shape evolution. Our phylogenomic analyses provide a well-supported hypothesis for amblyopsid evolutionary relationships. The obligate blind cavefishes form a clade and the cave-facultative eyed spring cavefishes are nested within the obligate cavefishes. Using ancestral state reconstruction, we find support for at least two independent subterranean colonization events within the Amblyopsidae. Eyed and blind fishes have different body shapes, but not different rates of body shape evolution. North American amblyopsids highlight the complex nature of cave-adaptive evolution and the necessity to include multiple lines of evidence to uncover the underlying processes involved in the loss of complex traits.

A taxonomic revision of Cheilodactylidae and Latridae (Centrarchiformes: Cirrhitoidei) using morphological and genomic characters.

Systematic relationships within the Cirrhitoidei, a suborder of five closely related families, have been uncertain for over a century. This is particularly true in reference to the families Cheilodactylidae and Latridae, which have been revised numerous times over the past several decades. Species that have been included in these two families are found in temperate regions around the world, which has led to regionally-focused studies that have only exacerbated taxonomic confusion. Here we examine systematic relationships within the Cheilodactylidae and the Latridae using ultraconserved genomic elements with near complete taxonomic sampling, and place our results in the context of the Cirrhitoidei. Our results agree with previous findings suggesting that Cheilodactylidae is restricted to two South African species, with the type species of the family, Cheilodactylus fasciatus Lacépède, forming a clade with C. pixi Smith that together is more closely related to the Chironemidae than to other species historically associated with the genus. We also strongly resolve the relationships of species within the Latridae. As a result of our analyses we revise the taxonomy of Latridae, name a new genus, and re-elevate Chirodactylus and Morwong.

Boomeranging around Australia: Historical biogeography and population genomics of the anti-equatorial fish Microcanthus strigatus (Teleostei: Microcanthidae).

The geographic distributions of marine fishes have been shaped by ancient vicariance and ongoing dispersal events. Some species exhibit anti-equatorial distributions, inhabiting temperate regions on both sides of the tropics while being absent from equatorial latitudes. The perciform fish Microcanthus strigatus (the stripey) exhibits such a distribution with disjunct populations occurring in East Asia, Hawaii, Western Australia, and the southwest Pacific. Here, we examine the historical biogeography and evolutionary history of M. strigatus, based on more than 80 specimens sampled from the four major populations. We analysed 36 morphological characters, three mitochondrial markers, and two sets of 7,120 and 12,771 single-nucleotide polymorphisms from the nuclear genome. Our results suggest that M. strigatus represents a cryptic species complex comprising at least two genetically distinct populations worthy of species-level recognition, with one population exhibiting strong genetic structuring but with intermittent, historical gene flow. We provide evidence for a southwest Pacific origin for the ancestral Microcanthus and explain how past connectivity between these regions might have given rise to the relationships observed in present-day marine fauna. Our ancestral range reconstructions and molecular-clock analyses support a southwest Pacific centre of origin for Microcanthus, with subsequent colonization of Western Australia through the Bass Strait followed by transequatorial dispersals to the Northern Hemisphere during the Pleistocene. Our results detail an anti-tropical dispersal pattern that is highly unusual and previously undocumented, thereby emphasizing the importance of integrative systematics in the evaluation of widespread species.

Genomic, ecological, and morphological approaches to investigating species limits: A case study in modern taxonomy from Tropical Eastern Pacific surgeonfishes.

A wide variety of species are distinguished by slight color variations. However, molecular analyses have repeatedly demonstrated that coloration does not always correspond to distinct evolutionary histories between closely related groups, suggesting that this trait is labile and can be misleading for species identification. In the present study, we analyze the evolutionary history of sister species of Prionurus surgeonfishes in the Tropical Eastern Pacific (TEP), which are distinguished by the presence or absence of dark spots on their body. We examined the species limits in this system using comparative specimen-based approaches, a mitochondrial gene (COI), more than 800 nuclear loci (Ultraconserved Elements), and abiotic niche comparisons. The results indicate there is a complete overlap of meristic counts and morphometric measurements between the two species. Further, we detected multiple individuals with intermediate spotting patterns suggesting that coloration is not diagnostic. Mitochondrial data recovered a single main haplotype shared between the species and all locations resulting in a complete lack of structure (ΦST = 0). Genomic analyses also suggest low levels of genetic differentiation (F ST = 0.013), and no alternatively fixed SNPs were detected between the two phenotypes. Furthermore, niche comparisons could not reject niche equivalency or similarity between the species. These results suggest that these two phenotypes are conspecific and widely distributed in the TEP. Here, we recognize Prionurus punctatus Gill 1862 as a junior subjective synonym of P. laticlavius (Valenciennes 1846). The underlying causes of phenotypic variation in this species are unknown. However, this system gives insight into general evolutionary dynamics within the TEP.

Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting.

Resolving patterns of ancient and rapid diversifications is one of the most challenging tasks in evolutionary biology. These difficulties arise from confusing phylogenetic signals that are associated with the interplay of incomplete lineage sorting (ILS) and homoplasy. Phylogenomic analyses of hundreds, or even thousands, of loci offer the potential to resolve such contentious relationships. Yet, how much useful phylogenetic information these large data sets contain remains uncertain and often goes untested. Here, we assess the utility of different data filtering approaches to maximize phylogenetic information and minimize noise when reconstructing an ancient radiation of Neotropical electric knifefishes (Order Gymnotiformes) using ultraconserved elements. We found two contrasting hypotheses of gymnotiform evolutionary relationships depending on whether phylogenetic inferences were based on concatenation or coalescent methods. In the first case, all analyses inferred a previously-and commonly-proposed hypothesis, where the family Apteronotidae was found as the sister group to all other gymnotiform families. In contrast, coalescent-based analyses suggested a novel hypothesis where families producing pulse-type (viz., Gymnotidae, Hypopomidae, and Rhamphichthyidae) and wave-type electric signals (viz., Apteronotidae, Sternopygidae) were reciprocally monophyletic. Nodal support for this second hypothesis increased when analyzing loci with the highest phylogenetic information content and further increased when data were pruned using targeted filtering methods that maximized phylogenetic informativeness at the deepest nodes of the Gymnotiformes. Bayesian concordance analyses and topology tests of individual gene genealogies demonstrated that the difficulty of resolving this radiation was likely due to high gene-tree incongruences that resulted from ILS. We show that data filtering reduces gene-tree heterogeneity and increases nodal support and consistency of species trees using coalescent methods; however, we failed to observe the same effect when using concatenation methods. Furthermore, the targeted filtering strategies applied here support the use of "gene data interrogation" rather than "gene genealogy interrogation" approaches in phylogenomic analyses, to extract phylogenetic signal from intractable portions of the Tree of Life.

The first complete mitochondrial genomes of sawtail surgeonfishes (Acanthuridae: Prionurus).

Surgeonfishes of the family Acanthuridae are primarily large-bodied herbivores that provide critical ecosystem services to coral reefs. Five out of the six genera that comprise the family have had mitochondrial genomes sequenced, with the exception of the genus Prionurus. Here, for the first time, we assemble and annotate the mitochondrial genomes of two sawtail surgeonfishes. The circular genomes of P. biafraensis and P. laticlavius are 16,552 bp and 16,531 bp in length, respectively, and contain 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. Gene arrangement and codon usage were similar to reported mitochondrial genomes of other surgeonfish genera, and a phylogenetic analysis of protein-coding genes recovers a topology for Acanthuridae that is consistent with nuclear analyses.

Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes.

Ostariophysi is a superorder of bony fishes including more than 10,300 species in 1100 genera and 70 families. This superorder is traditionally divided into five major groups (orders): Gonorynchiformes (milkfishes and sandfishes), Cypriniformes (carps and minnows), Characiformes (tetras and their allies), Siluriformes (catfishes), and Gymnotiformes (electric knifefishes). Unambiguous resolution of the relationships among these lineages remains elusive, with previous molecular and morphological analyses failing to produce a consensus phylogeny. In this study, we use over 350 ultraconserved element (UCEs) loci comprising 5 million base pairs collected across 35 representative ostariophysan species to compile one of the most data-rich phylogenies of fishes to date. We use these data to infer higher level (interordinal) relationships among ostariophysan fishes, focusing on the monophyly of the Characiformes-one of the most contentiously debated groups in fish systematics. As with most previous molecular studies, we recover a non-monophyletic Characiformes with the two monophyletic suborders, Citharinoidei and Characoidei, more closely related to other ostariophysan clades than to each other. We also explore incongruence between results from different UCE data sets, issues of orthology, and the use of morphological characters in combination with our molecular data. [Conserved sequence; ichthyology; massively parallel sequencing; morphology; next-generation sequencing; UCEs.].

Skipping across the tropics: the evolutionary history of sawtail surgeonfishes (Acanthuridae: Prionurus).

Fishes described as "anti-equatorial" have disjunct distributions, inhabiting temperate habitat patches on both sides of the tropics. Several alternative hypotheses suggest how and when species with disjunct distributions crossed uninhabitable areas, including: ancient vicariant events, competitive exclusion from the tropics, and more recent dispersal during Pliocene and Pleistocene glacial periods. Surgeonfishes in the genus Prionurus can provide novel insight into this pattern as its member species have disjunct distributions inhabiting either temperate latitudes, cold-water upwellings in the tropics, or low diversity tropical reef ecosystems. Here the evolutionary history and historical biogeography of Prionurus is examined using a dataset containing both mitochondrial and nuclear data for all seven extant species. Our results indicate that Prionurus is monophyletic and Miocene in origin. Several relationships remain problematic, including the placement of the Australian P. microlepidotus, and the relationship between P. laticlavius and P. punctatus. Equatorial divergence events between temperate western Pacific habitats occurred at least twice in Prionurus: once in the Miocene and again in the late Pliocene/early Pleistocene. Three species with tropical affinities, P. laticlavius, P. punctatus, and P. biafraensis, form a clade that originated in the Pliocene. These results suggest that a variety of mechanisms may regulate the disjunct distribution of temperate fishes, and provide support for both older and younger equatorial crossing events. They also suggest that interspecific competitive exclusion may be influential in fishes with "anti-equatorial" distributions.

Examining evolutionary relationships and shifts in depth preferences in batfishes (Lophiiformes: Ogcocephalidae).

Batfishes (Ogcocephalidae) are an understudied, group of marine anglerfishes that are dorsoventrally flattened and have an illicium and esca (terminal lure) used to attract prey. The family contains 10 genera and 75 recognized species from nearly all tropical and subtropical seas. Relationships among these taxa, as well as the position of Ogcocephalidae within Lophiiformes, remain poorly understood with previous studies showing conflicting, and poorly resolved results. The timing of divergence and depth of origination in the water column have also not been explored in any detail. In this study a concatenated nuclear (three genes) and mitochondrial (two genes) dataset was constructed across several anglerfish families to elucidate phylogenetic relationships among all ten batfish genera, to clarify the placement of Ogcocephaloidei within Lophiiformes, and to estimate divergence times using fossil calibrations. An ancestral state reconstruction was also conducted to examine the history of shifts in preferred habitat depths within batfishes. Phylogenetic analyses supported monophyly of each sub-order within Lophiiformes and placed Ogcocephaloidei as the sister group to Antennarioidei. Batfish genera were divided into an Eastern Pacific/Western Atlantic clade and an Indo-Pacific clade; Halieutaea was recovered as the sister group to all other batfishes. Based on divergence time estimations and ancestral state reconstructions of preferred depth, Ogcocephalidae is Eocene in age and originated on the lower continental shelf/upper continental slope (disphotic zone).

Living in the past: phylogeography and population histories of Indo-Pacific wrasses (genus Halichoeres) in shallow lagoons versus outer reef slopes.

Sea level fluctuations during glacial cycles affect the distribution of shallow marine biota, exposing the continental shelf on a global scale, and displacing coral reef habitat to steep slopes on oceanic islands. In these circumstances we expect that species inhabiting lagoons should show shallow genetic architecture relative to species inhabiting more stable outer reefs. Here we test this expectation on an ocean-basin scale with four wrasses (genus Halichoeres): H. claudia (N = 194, with ocean-wide distribution) and H. ornatissimus (N = 346, a Hawaiian endemic) inhabit seaward reef slopes, whereas H. trimaculatus (N = 239) and H. margaritaceus (N = 118) inhabit lagoons and shallow habitats throughout the Pacific. Two mitochondrial markers (cytochrome oxidase I and control region) were sequenced to resolve population structure and history of each species. Haplotype and nucleotide diversity were similar among all four species. The outer reef species showed significantly less population structure, consistent with longer pelagic larval durations. Mismatch distributions and significant negative Fu's F values indicate Pleistocene population expansion for all species, and (contrary to expectations) shallower histories in the outer slope species. We conclude that lagoonal wrasses may persist through glacial habitat disruptions, but are restricted to refugia during lower sea level stands. In contrast, outer reef slope species have homogeneous and well-connected populations through their entire ranges regardless of sea level fluctuations. These findings contradict the hypothesis that shallow species are less genetically diverse as a consequence of glacial cycles.