Specimen collection is essential for modern science.

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.

Disentangling historical relationships within Poeciliidae (Teleostei: Cyprinodontiformes) using ultraconserved elements.

Poeciliids (Cyprinodontiformes: Poeciliidae), commonly known as livebearers, are popular fishes in the aquarium trade (e.g., guppies, mollies, swordtails) that are widely distributed in the Americas, with 274 valid species in 27 genera. This group has undergone various taxonomic changes recently, spurred by investigations using traditional genetic markers. Here we used over 1,000 ultraconserved loci to infer the relationships within Poeciliidae in the first attempt at understanding their diversification based on genome-scale data. We explore gene tree discordance and investigate potential incongruence between concatenation and coalescent inference methods. Our aim is to examine the influence of incomplete lineage sorting and reticulate evolution on the poeciliids' evolutionary history and how these factors contribute to the observed gene tree discordace. Our concatenated and coalescent phylogenomic inferences recovered four major clades within Poeciliidae. Most supra-generic level relationships we inferred were congruent with previous molecular studies, but we found some disagreements; the Middle American taxa Phallichthys and Poecilia (Mollienesia) were recovered as non-monophyletic, and unlike other recent molecular studies, we recovered Brachyrhaphis as monophyletic. Our study is the first to provide signatures of reticulate evolution in Poeciliidae at the family level; however, continued finer-scale investigations are needed to understand the complex evolutionary history of the family along with a much-needed taxonomic re-evaluation.

Evolutionary relationships of anglerfishes (Lophiiformes) reconstructed using ultraconserved elements.

The macroevolutionary consequences of evolving in the deep-sea remain poorly understood and are compounded by the fact that convergent adaptations for living in this environment makes elucidating phylogenetic relationships difficult. Lophiiform anglerfishes exhibit extreme habitat and predatory specializations, including the use of a fin-spine system as a luring device and unique reproductive strategies where parasitic males attach and fuse to females. Despite their notoriety for these odd characteristics, evolutionary relationships among these fishes remain unclear. We sought to clarify the evolutionary history of Lophiiformes using data from 1000 ultraconserved elements and phylogenomic inference methods with particular interest paid to the Ceratioidei (deep-sea anglerfishes) and Antennarioidei (frogfishes and handfishes). At the suborder level, we recovered similar topologies in separate phylogenomic analyses: The Lophioidei (monkfishes) are the sister group to the rest of the Lophiiformes, Ogcocephaloidei (batfishes) and Antennarioidei (frogfishes) form a sister group, and Chaunacioidei (coffinfishes) and Ceratioidei (deep-sea anglerfishes) form a clade. The relationships we recover within the ceratioids disagree with most previous phylogenetic investigations, which used legacy phylogenetic markers or morphology. We recovered non-monophyletic relationships in the Antennarioidei and proposed three new families based on molecular and morphological evidence: Histiophrynidae, Rhycheridae, and Tathicarpidae. Antennariidae was re-evaluated to include what was known as Antennariinae, but not Histiophryninae. Non-bifurcating signal in splits network analysis indicated reticulations among and within suborders, supporting the complicated history of the Lophiiformes previously found with morphological data. Although we resolve relationships within Antennarioidei, Ceratioidei relationships remain somewhat unclear without better taxonomic sampling.

Bridging the Research Gap between Live Collections in Zoos and Preserved Collections in Natural History Museums.

Zoos and natural history museums are both collections-based institutions with important missions in biodiversity research and education. Animals in zoos are a repository and living record of the world's biodiversity, whereas natural history museums are a permanent historical record of snapshots of biodiversity in time. Surprisingly, despite significant overlap in institutional missions, formal partnerships between these institution types are infrequent. Life history information, pedigrees, and medical records maintained at zoos should be seen as complementary to historical records of morphology, genetics, and distribution kept at museums. Through examining both institution types, we synthesize the benefits and challenges of cross-institutional exchanges and propose actions to increase the dialog between zoos and museums. With a growing recognition of the importance of collections to the advancement of scientific research and discovery, a transformational impact could be made with long-term investments in connecting the institutions that are caretakers of living and preserved animals.

They like to move it (move it): walking kinematics of balitorid loaches of Thailand.

Balitorid loaches are a family of fishes that exhibit morphological adaptations to living in fast flowing water, including an enlarged sacral rib that creates a 'hip'-like skeletal connection between the pelvis and the axial skeleton. The presence of this sacral rib, the robustness of which varies across the family, is hypothesized to facilitate terrestrial locomotion seen in the family. Terrestrial locomotion in balitorids is unlike that of any known fish: the locomotion resembles that of terrestrial tetrapods. Emergence and convergence of terrestrial locomotion from water to land has been studied in fossils; however, studying balitorid walking provides a present-day natural laboratory to examine the convergent evolution of walking movements. We tested the hypothesis that balitorid species with more robust connections between the pelvic and axial skeleton (M3 morphotype) are more effective at walking than species with reduced connectivity (M1 morphotype). We predicted that robust connections would facilitate travel per step and increase mass support during movement. We collected high-speed video of walking in seven balitorid species to analyze kinematic variables. The connection between internal anatomy and locomotion on land are revealed herein with digitized video analysis, µCT scans, and in the context of the phylogenetic history of this family of fishes. Our species sampling covered the extremes of previously identified sacral rib morphotypes, M1 and M3. Although we hypothesized the robustness of the sacral rib to have a strong influence on walking performance, there was not a large reduction in walking ability in the species with the least modified rib (M1). Instead, walking kinematics varied between the two balitorid subfamilies with a generally more 'walk-like' behavior in the Balitorinae and more 'swim-like' behavior in the Homalopteroidinae. The type of terrestrial locomotion displayed in balitorids is unique among living fishes and aids in our understanding of the extent to which a sacral connection facilitates terrestrial walking.

Molecular systematics of the Awaous banana complex (River gobies; Teleostei: Oxudercidae).

Diadromous fishes can exhibit interesting evolutionary and population-level patterns given their use of freshwater and marine environments as part of their life histories. The River goby genus Awaous are prominent members of riverine ichthyofaunas and occur throughout Atlantic and Pacific slopes of the Americas from the southern United States to Ecuador and Brazil. Here we study the widespread and polymorphic Awaous banana complex to assess phylogeographic patterns and test previous hypotheses that all populations of this species in the Americas belong to the same species. Analysis of sequence data based on the mitochondrial cytochrome oxidase I gene shows multiple clades within the Atlantic and Pacific basins, which correspond to previously described species. Additionally, haplotype analysis demonstrates unique and unconnected networks between these species. Within these clades we document biogeographic patterns that are congruent with results of other co-occurring diadromous species, as well as a novel biogeographic pattern for the region. Our results support the recognition of distinct species of Awaous in the Atlantic (A. banana and A. tajasica) and Pacific (A. transandeanus) basins. These results are concordant with previously established morphological characters permitting the separation of these species.

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.

Phylogenomic analysis on the exceptionally diverse fish clade Gobioidei (Actinopterygii: Gobiiformes) and data-filtering based on molecular clocklikeness.

The use of genome-scale data to infer phylogenetic relationships has gained in popularity in recent years due to the progress made in target-gene capture and sequencing techniques. Data filtering, the approach of excluding data inconsistent with the model from analyses, presumably could alleviate problems caused by systematic errors in phylogenetic inference. Different data filtering criteria, such as those based on evolutionary rate and molecular clocklikeness as well as others have been proposed for selecting useful phylogenetic markers, yet few studies have tested these criteria using phylogenomic data. We developed a novel set of single-copy nuclear coding markers to capture thousands of target genes in gobioid fishes, a species-rich lineages of vertebrates, and tested the effects of data-filtering methods based on substitution rate and molecular clocklikeness while attempting to control for the compounding effects of missing data and variation in locus length. We found that molecular clocklikeness was a better predictor than overall substitution rate for phylogenetic usefulness of molecular markers in our study. In addition, when the 100 best ranked loci for our predictors were concatenated and analyzed using maximum likelihood, or combined in a coalescent-based species-tree analysis, the resulting trees showed a well-resolved topology of Gobioidei that mostly agrees with previous studies. However, trees generated from the 100 least clocklike frequently recovered conflicting, and in some cases clearly erroneous topologies with strong support, thus indicating strong systematic biases in those datasets. Collectively these results suggest that data filtering has the potential improve the performance of phylogenetic inference when using both a concatenation approach as well as methods that rely on input from individual gene trees (i.e. coalescent species-tree approaches), which may be preferred in scenarios where incomplete lineage sorting is likely to be an issue.

Coordinated Dispersal and Pre-Isthmian Assembly of the Central American Ichthyofauna.

We document patterns of coordinated dispersal over evolutionary time frames in heroine cichlids and poeciliine live-bearers, the two most species-rich clades of freshwater fishes in the Caribbean basin. Observed dispersal rate (DO) values were estimated from time-calibrated molecular phylogenies in Lagrange+, a modified version of the ML-based parametric biogeographic program Lagrange. DO is measured in units of "wallaces" (wa) as the number of biogeographic range-expansion events per million years. DO estimates were generated on a dynamic paleogeographic landscape of five areas over three time intervals from Upper Cretaceous to Recent. Expected dispersal rate (DE) values were generated from alternative paleogeographic models, with dispersal rates proportional to target area and source-river discharge volume, and inversely proportional to paleogeographic distance. Correlations between DO and DE were used to assess the relative contributions of these three biogeographic parameters. DO estimates imply a persistent dispersal corridor across the Eastern (Antillean) margin of the Caribbean plate, under the influence of prevailing and perennial riverine discharge vectors such as the Proto-Orinoco-Amazon river. Ancestral area estimation places the earliest colonizations of the Greater Antilles and Central America during the Paleocene-Eocene (ca. 58-45 Ma), potentially during the existence of an incomplete Paleogene Arc (∼59 Ma) or Lesser Antilles Arc (∼45 Ma), but predating the GAARlandia land bridge (∼34-33 Ma). Paleogeographic distance is the single best predictor of DO. The Western (Central American) plate margin did not serve as a dispersal corridor until the Late Neogene (12-0 Ma), and contributed relatively little to the formation of modern distributions.

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.].

Biological evidence supports an early and complex emergence of the Isthmus of Panama.

The linking of North and South America by the Isthmus of Panama had major impacts on global climate, oceanic and atmospheric currents, and biodiversity, yet the timing of this critical event remains contentious. The Isthmus is traditionally understood to have fully closed by ca. 3.5 million years ago (Ma), and this date has been used as a benchmark for oceanographic, climatic, and evolutionary research, but recent evidence suggests a more complex geological formation. Here, we analyze both molecular and fossil data to evaluate the tempo of biotic exchange across the Americas in light of geological evidence. We demonstrate significant waves of dispersal of terrestrial organisms at approximately ca. 20 and 6 Ma and corresponding events separating marine organisms in the Atlantic and Pacific oceans at ca. 23 and 7 Ma. The direction of dispersal and their rates were symmetrical until the last ca. 6 Ma, when northern migration of South American lineages increased significantly. Variability among taxa in their timing of dispersal or vicariance across the Isthmus is not explained by the ecological factors tested in these analyses, including biome type, dispersal ability, and elevation preference. Migration was therefore not generally regulated by intrinsic traits but more likely reflects the presence of emergent terrain several millions of years earlier than commonly assumed. These results indicate that the dramatic biotic turnover associated with the Great American Biotic Interchange was a long and complex process that began as early as the Oligocene-Miocene transition.

Swim bladder morphology changes with female reproductive state in the mouth-brooding African cichlid Astatotilapia burtoni.

Mouth brooding is an extreme form of parental care in which the brooding parent carries the developing young in their buccal cavity for the duration of development. Brooding fish need to compensate for the brood weight on the anterior portion of their body. For fishes with a compartmentalized swim bladder, gas distribution between the chambers may aid in regulating buoyancy during brooding. To test this hypothesis, we took radiographs of Astatotilapia burtoni to compare the swim bladder morphology of gravid, mouth-brooding and recovering females. Following spawning, females carry developing fish in their buccal cavity for ∼2 weeks, resulting in a larger and rounder anterior swim bladder compartment. Comparatively, the swim bladder of gravid females is long and cylindrical. Using small beads to mimic brood weight and its effects on female buoyancy, swim bladder changes were induced that resembled those observed during brooding. Immediately after releasing their fry, brooding females swim at a positive angle of attack but correct their swimming posture to normal within 5 min, suggesting a rapid change in swim bladder gas distribution. These data provide new insights into how swim bladder morphology and swimming behavior change during mouth brooding, and suggest a compartmentalized swim bladder may be a morphological adaptation for mouth brooding.

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).

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.

Derivation of the freshwater fish fauna of Central America revisited: Myers's hypothesis in the twenty-first century.

Although attempts to understand Central American freshwater fish provincialism date to the 1960s, early efforts lacked the wealth of distributional data now available. Biogeographic work on Central American freshwater fishes has been largely descriptive and regional, and lacked a broader synthesis. Here we use parsimony analysis of endemicity (PAE) to elucidate faunistic relationships between major drainages and to delineate areas of endemism. We then perform a Brooks parsimony analysis (BPA) on the resulting areas. The PAE recovered a primary division between four Pacific and six Atlantic slope areas of endemism. In contrast, the BPA recovered two Central American geographic clades, one sharing a history with North America and the other with South America. Fish diversity is uneven across Central America, with greater diversity in areas adjacent to the more species-rich regions of North and South America. In northern and nuclear Central America, the paucity of ostariophysan freshwater fishes such as catfishes and characins (groups that dominate adjacent regions) contrasts with high species richness of poeciliids and cichlids. Results of this study are consistent with Myer's hypothesis that poeciliids and cichlids dispersed to Northern or Nuclear Middle America early in the Cenozoic, long before the Plio-Pleistocene rise of the Isthmus of Panama.

Formalizing the names of subfamilies and tribes of ponyfishes (Leiognathidae Gill 1893).

Several higher-level clades (subfamilies and tribes) of ponyfishes were introduced and diagnosed without the term "new" following the taxon names and without reference to a type genus. We correct these errors here so that the clade names comply with Articles 16.1 and 16.2, and Recommendation 16A of the Code (ICZN 2000, 4th edition), and may be formally recognized. Diagnoses for all of these clades were presented in Chakrabarty et al. (2011) and their membership updated in Sparks and Chakrabarty (2015).

Ten years later: An update on the status of collections of endemic Gulf of Mexico fishes put at risk by the 2010 Oil Spill.

The 2010 Gulf of Mexico Deepwater Horizon was the largest oil spill in human history that occurred during a 12-week period in a region less than 100 km from the coast of Louisiana; however, after more than a decade of post-spill research, few definitives can be said to be known about the long-term impacts on the development and distribution of fishes in and around the region of the disaster. Here, we examine endemic Gulf of Mexico fish species that may have been most impacted by noting their past distributions in the region of the spill and examining data of known collecting events and observations over the last twenty years (ten years prior to the spill, ten years post-spill). Five years post-spill, it was reported that 48 of the Gulf's endemic fish species had not been collected and, with expanded methods, we now report that 29 (of the 78 endemic species) have not been reported in collections since 2010 (five of these are only known from observations post-spill). Although the good news that some previously 'missing' species have been found may be cause to celebrate, the lack of information for many species remains a cause for concern given focused sampling efforts post-spill.

Checklist of the inland fishes of El Salvador.

The inland fish fauna of El Salvador and its distribution was originally described in 1925 by Samuel Hildebrand. That work has been the main source of information for freshwater fishes of El Salvador up to today. Based on the combination of an intensive literature review, electronic database searches, re-identification of museum specimens, and fieldwork, we hereby provide an updated checklist of the inland fishes of El Salvador. This checklist provides distributional data at the Salvadoran hydrographical and political (by department) levels. The checklist is systematically arranged at the ordinal and familial level and then alphabetically therein. The freshwater fish fauna of El Salvador includes 101 species divided into 64 genera, 29 families, and 14 orders. According to their supposed tolerance to salinity, 73% of these species are peripheral, 23% secondary, and only 4% are primary freshwater fishes. One species is endemic to the country, Amatitlania coatepeque. The low number of primary freshwater fishes and endemics is comparable to the Central American Pacific slope in particular, as well as northern Central America in general.