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    Ichthyology II

    2021-07-22   13:45 - 15:30

    Moderator: Kyle Piller



    1.  13:45  IN-PERSON    Codes for Natural History Collections in Ichthyology and Herpetology. Mark Sabaj*, The Academy of Natural Sciences of Philadelphia   marksabajperez@gmail.com

    In 2020, the journal Ichthyology and Herpetology published a reasonably complete list of annotated codes for historical and modern natural history collections associated with lost and extant specimens of fossil and Recent fishes, amphibians, and reptiles. The paper included a total of 3,845 codes anchored to about 2,064 distinct collections and/or institutions in 155 countries. At least 633 of those collections are exclusively paleontological or include fossil specimens. The list was primarily derived from the scientific literature and may serve as a resource for plainly citing specimens in publications and for linking such citations to records in online databases. Due to constraints on time, this talk will not cover all 3,845 codes. Instead, it will focus on the origins and applications of collection codes and celebrate their usefulness for documenting and managing the most important specimens kept in natural history collections: fishes and herps.


    2.  14:00  IN-PERSON    Building Collections and Genomic Resources for Conservation of Imperiled Fishes. Thomas Turner*, University of New Mexico; Emily DeArmon, University of New Mexico; Alexander Cameron, University of New Mexico; David Camak, University of New Mexico; Guilherme Caeiro-Dias, University of New Mexico; Megan Osborne, University of New Mexico   turnert@unm.edu

    The utility of genomics for conservation biology is expanding rapidly. Yet, to fully realize its potential, the community needs access to samples that are sufficiently replicated in time and space to permit robust hypothesis tests and monitoring with statistical confidence. Here, we present a collective effort to build genomic resources and specimen-rich tissue archives for imperiled fishes of the American southwest through extensive partnerships with researchers, management agencies, and NGOs. Genome projects and high-throughput genetic screening tools are under development for eight species that have been systematically monitored for decades. Corresponding tissue archives bracket major environmental disturbances like drought and mega-wildfire and are valuable for understanding demographic responses and impacts of recovery actions. We discuss logistic and practical challenges to archive development including historical sample curation, funding, partner buy-in, archive systems, biological differences among species and life stages, and database integration. Because the Museum of Southwestern Biology is a project-driven collection with regional focus, we are well suited to develop and curate this critical archive that can inform future conservation actions as climate change transforms the southwestern US.


    3.  14:15  IN-PERSON    Phylogenomics of the Toothcarps (Cyprinodontiformes). Kyle Piller*, Southeastern Louisiana University; Elyse Parker, Yale University; Alan Lemmon, Florida State University; Emily Moriarty-Lemmon, Florida State University   kyle.piller@selu.edu

    The Cyprinodontiformes are a diverse and well known group of fishes that includes sixteen families inclusive of Anablepidae, Aphaniidae Aplocheilidae, Cubanichthyidae, Cyprinodontidae, Fluviphylacidae, Fundulidae, Goodeidae, Nothobranchiidae, Orestiidae, Pantanodontidae, Poeciliidae, Procatopodidae, Profundulidae, Rivulidae, and Valenciidae and more than 800 species that are globally distributed in tropical and temperate, freshwater and estuarine habitats. The evolutionary relationships among the families within the order, based on different molecular and morphologicaldata sets, have remained uncertain. Therefore, the objective of this study was to use a targeted enrichment approach known as anchored hybrid enrichment to better understand the phylogenetic relationships among the families of cyprinodontiform fishes, including several recently diagnosed families. This study included more than 100 individuals, representing all sixteen cyprinodontiform families. Two-hundred ninety-five loci were targeted with an average of 244.4 loci recovered per individual across the order. Phylogenetic analyses (RaxML and ASTRAL) recovered many of the same relationships from previous studies, but several, novel, relationships for other families also were recovered. In addition, two well-established suborders Aplocheilodei and Cyprinodontoidei were recovered and are in agreement with most previous studies. The results from this study will provide a robust, historical framework needed to investigate a plethora of questions in cyprinodontiform biogeography, taxonomy, evolutionary biology, and physiology.


    4.  14:30  IN-PERSON    Taxonomy, biogeography, phylogenetic affinities, and conservation status of recently discovered mesophotic fishes. Luiz Rocha*, California Academy of Sciences; Hudson Pinheiro, California Academy of Sciences; Bart Shepherd, California Academy of Sciences; Claudia Rocha, California Academy of Sciences; Tyler Phelps, California Academy of Sciences   lrocha@calacademy.org

    In the past 5-10 years several new species of fish have been discovered in deep reefs worldwide. This is likely a result of the increasing number of scientists exploring mesophotic coral ecosystems (MCEs) between 30 and 150m using a variety of methods. In general, these fishes belong to families that are also found in shallow reefs (especially Serranidae and Pomacentridae), and a minority are in families more typically found at deeper depths (e.g.: Callanthiidae). Patterns of phylogenetic affinities are also varied: some groups, like the genus Chromis, are mostly composed of shallow species with mesophotic species distributed through the phylogeny, whereas others, like Pseudanthias, seem to be mostly mesophotic with few species in shallow reefs. Because these depths are still unsampled in most locations, biogeographic patterns are hard to infer, but some generalizations are emerging. The number of new records for every location is consistently high, indicating that species previously described from elsewhere are often more widely distributed than initially thought. Species richness follows the general west to east diversity gradient observed in shallow reefs, however, at smaller scales (reef), diversity seems remarkably similar across vast biogeographic regions. Along with the distinctiveness of its fauna, our team has consistently observed human impacts reaching down to 150m. Plastic pollution (both coming from land and sea through fishing debris) is very common, and in most places, MCEs are not included in marine protected areas. Therefore, their uniqueness and lack of protection suggest these ecosystems should be a priority for conservation efforts worldwide.


    5.  14:45  IN-PERSON    Examining the Evolutionary Relationships of the Terapontoidei using UltraConserved Elements. William Ludt*, Natural History Museum of Los Angeles County; Kendall Clements, University of Auckland; Jean-Paul Hobbs, University of Queensland; Giacomo Bernardi, University of California Santa Cruz; Peter Unmack, University of Canberra; Prosanta Chakrabarty, Louisiana State Univeristy Museum of Natural Science   wludt@nhm.org

    The suborder Terapontoidei comprises eight families, 34 genera and 111 species. Representatives of this suborder can be found in all major ocean basins, as well as freshwater habitats, and display a variety of life history and ecological traits. The close relationship of these families is supported by a shared RLA pattern 10 nerve arrangement, and has also been recovered in recent molecular studies. However, exactly how these eight families are related to one another is still unresolved. Here we examine the relationships of this suborder using a phylogenomic approach. Concatenated and coalescent analyses using a dataset of 718 ultraconserved element loci result in three well-supported topologies that differ in the placement of the Terapontidae and the Kuhliidae. Despite overall high support values in the concatenated analysis, gene and site concordance factors reveal discrepancies in the gene trees associated with the nodes subtending these two families of interest. Filtering loci by phylogenetically and parsimony informative sites failed to clarify the placement of these families. Furthermore, AU topology tests comparing several constrained topologies, and site by site gene likelihood comparisons did not provide additional support for the coalescent-based topology. However, specific node-by-node likelihood comparisons did corroborate the sister relationships between the Terapontidae and Kuhliidae found in prior studies. While short internode branches in the Terapontoidei make estimating the relationships of these two clades difficult, relationships among the other six families are consistent across all analyses and improve our understanding of the evolutionary history in this diverse group of fishes.


    6.  15:00  IN-PERSON    Deciphering an ancient marine fish radiation: a tale of many threads. Emanuell Duarte-Ribeiro*, University of Oklahoma; Lily Hughes, University of Chicago; Guillermo Orti, George Washington University; Dahiana Arcila, University of Oklahoma; Ricardo Betancur-R., University of Oklahoma   emanuell.ribeiro@ou.edu

    The nature of the origin and propagation of higher-level taxa is an enduring question in evolution. Understanding the dynamics of early bursts of diversification is at the center of this debate. However, deciphering the historical relationships among organisms arising during periods of rapid cladogenesis is exceptionally challenging due to low levels of phylogenetic signal, severe effects of incomplete lineage sorting, or ancient reticulation events. Here, we advance our understanding of this problem by assessing the phylogenetic relationships in Carangaria, a diverse percomorph group that encompasses a disparate array of taxa such as marlins, remoras, and flatfishes. The lack of phylogenetic resolution is particularly high in Carangaria, where short internodes resulting from a period of rapid diversification in the wake of the K-Pg mass extinction have challenged recent attempts to resolve the interfamilial relationships. We assembled an extensive nucleotide sequence matrix that covers 1,111 single-copy exons and over 450 species. Our data matrix represents an increase of almost two orders of magnitude relative to previous efforts. Using a series of phylogenetic approaches, including concatenation and summary coalescent methods, we unequivocally resolve the majority of genus and family-level relationships within Carangaria. However, several nodes at the base of the tree are still poorly resolved, with low branch support estimates. For most recalcitrant nodes an equivalent number of genes and nucleotide sites favor a primary and the alternative topologies. Our results demonstrate that accounting for phylogenetic estimation uncertainty is essential for understanding the factors shaping the origin and propagation of ancient radiations.


    7.  15:15  IN-PERSON    Using Gene-Capture to Create a Robust Phylogeny Resolving the Lineages of the Family Gobiidae. Kendall Johnson*, Texas A&M University - Corpus Christi; Chenhong Li, Shanghai Ocean University; Luke Tornabene, University of Washington; Frank Pezold, Texas A&M University - Corpus Christi   kjohnson47@islander.tamucc.edu

    Gobies (Gobiidae+Oxudercidae) (suborder Gobioidei) are one of the most diverse and complex groups of teleosts, due to an early period of rapid diversification that led to the evolution of a remarkable variety of ecologies and morphologies. This diversity makes them ideal subjects for the study of many topics of ecology and evolution, including the evolution of behavior and life history traits, ecological and morphological adaptation, and species diversification. However, relationships of clades within the family Gobiidae remained poorly-understood as those bursts of speciation have made it impossible for traditional genetic markers to confidently resolve them, greatly limiting our ability to understand and study these topics in gobies. Therefore, we used gene-capture to obtain sequence data for hundreds of protein-coding loci to create a high-resolution phylogeny of Gobiidae which confidently resolved its internal structure. There remains some ambiguity regarding the placement of the Gobiosomatini in relation to the other gobiid lineages, which was investigated using ΔGLS and ΔSLS topology tests to identify what genes are responsible for its conflicting placement. This represents a breakthrough not only for gobies, but serves as a model for how gene-capture can resolve the taxonomy of problematic groups.




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