Phylogenomic analysis of the bowfin (Amia calva) reveals unrecognized species diversity in a living fossil lineage

Wright, Jeremy J.; Bruce, Spencer A.; Sinopoli, Daniel A.; Palumbo, Jay R.; Stewart, Donald J.

doi:10.1038/s41598-022-20875-4

Cited by 18 publications

(15 citation statements)

References 63 publications

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“…Our study reveals the presence of two recently diverged sibling species of bowfins. A recent study using ddRAD data, but with very limited sampling of A. calva and A. ocellicauda, concluded that there may be up to four living species of Amia [24]. With a more inclusive sampling of populations (figure 1a), our genomic analyses consistently delimit two species of Amia.…”

Section: Resultssupporting

confidence: 57%

“…With a more inclusive sampling of populations (figure 1a), our genomic analyses consistently delimit two species of Amia. The populations within either species that exhibit the greatest genetic divergence are those of A. calva from Florida and the Gulf Coast, which were not sampled in the other study [24]. In addition, the shape of the IO and the number of dentary teeth delimit two living species of Amia (figure 1d; electronic supplementary material, table S2).…”

Section: Resultsmentioning

confidence: 99%

“…Among the species-rich fauna of North American freshwater fishes [17–19], relatively few species have geographical distributions as large as the bowfin. This wide geographical range includes many areas characterized by both high species diversity and a sizeable number of endemic freshwater fish species [20–23], enhancing the possibility of additional species diversity masquerading as Amia calva [24].

Figure 1Identification of hidden bowfin species diversity.…”

Section: Introductionmentioning

confidence: 99%

“…At the close of the nineteenth century, all of these additional species were synonymized with A. calva without justification or reference to a study of variation among the named taxa [30, p. 113]. The only studies that explore genetic variation in A. calva sample a small part of the geographical distribution [24,31], and there is no study exploring variation in morphological traits among populations of A. calva across its entire geographical distribution [2,32] (figure 1 a ).…”

Section: Introductionmentioning

confidence: 99%

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Hidden species diversity in an iconic living fossil vertebrate

et al. 2022

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Ancient, species-poor lineages persistently occur across the Tree of life. These lineages are likely to contain unrecognized species diversity masked by the low rates of morphological evolution that characterize living fossils. Halecomorphi is a lineage of ray-finned fishes that diverged from its closest relatives before 200 Ma and is represented by only one living species in eastern North America, the bowfin, Amia calva Linnaeus. Here, we use double digest restriction-site-associated DNA sequencing and morphology to illuminate recent speciation in bowfins. Our results support the delimitation of a second living species of Amia , with the timing of diversification dating to the Plio-Pleistocene. This delimitation expands the species diversity of an ancient lineage that is integral to studies of vertebrate genomics and development, yet is facing growing conservation threats driven by the caviar fishery.

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Section: Resultssupporting

confidence: 57%

Section: Resultsmentioning

confidence: 99%

Figure 1Identification of hidden bowfin species diversity.…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Hidden species diversity in an iconic living fossil vertebrate

et al. 2022

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“…Extant holosteans include seven species of Lepisosteidae (gar; (Eschmeyer 1998)) and two species of Amiidae (bowfin; (Brownstein et al 2022; Wright et al 2022)). Analyses of the spotted gar ( Lepisosteus oculatus ) genome demonstrated the potential of holostean genomes for comparative studies, providing critical insights into the evolution of vertebrate immunity, development, and the function of regulatory sequences (Braasch et al 2016).…”

Section: Introductionmentioning

confidence: 99%

A chromosome level genome assembly of longnose gar,Lepisosteus osseus

Mallik

Carlson

Wcisel

et al. 2022

Preprint

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Holosteans (gars and bowfins) represent the sister lineage to teleost fishes, the latter being a clade that comprises over half of all living vertebrates and includes important models for comparative genomics and human health. A major distinction between the evolutionary history of teleosts and holosteans is that all teleosts experienced a genome duplication event in their early evolutionary history. As holostean genomes did not undergo a round of genome duplication, they have been heralded as a means to bridge teleost models to other vertebrate genomes. However, only three species of holosteans have been genome sequenced to date and sequencing of more species is needed to fill sequence sampling gaps and provide a broader comparative basis for understanding holostean genome evolution. Here we report the first high quality reference genome assembly and annotation of the longnose gar (Lepisosteus osseus). Our final assembly consists of 22,709 scaffolds with a total length of 945 bp with contig N50of 116.6 kb. Using BRAKER2, we annotated a total of 30,068 genes. Analysis of the repetitive regions of the genome reveals the genome to contain 29.1% transposable elements, and the longnose gar to be the only other known vertebrate outside of the spotted gar to contain CR1, L2, Rex1, and Babar. These results highlight the potential utility of holostean genomes for understanding the evolution of vertebrate repetitive elements and provide a critical reference for comparative genomic studies utilizing ray-finned fish models.SignificanceOver half of all living vertebrates are teleost fishes, including numerous experimental models such as zebrafish (Danio rerio) and medaka (Oryzias latipes). However, translating research in teleost models to other organisms such as humans is often challenged by the fact that teleosts experienced a genome duplication event in their early evolutionary history. Recent genome sequencing of three holosteans, the sister lineage to teleosts that did not experience a genome duplication event, has revealed these taxa to be critical for linking homologs between teleosts and other vertebrates. Sequencing of holostean genomes remains limited, thereby impeding further comparative genomic studies. Here we fill this sampling gap through the genomic sequencing of the longnose gar (Lepisosteus osseus). This annotated reference genome will provide a useful resource for a range of comparative genomic applications that span fields as diverse as immunogenetics, developmental biology, and the understanding of regulatory sequence evolution.

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Molecular phylogenetic and population genetic relationships of a putative species of sucker (Catostomus sp.) from Surprise Valley in the Great Basin, USA

et al. 2023

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Objective The ichthyofaunal diversity of the Great Basin is incompletely characterized, with the Wall Canyon Sucker Catostomus sp. being one potential species. The Wall Canyon Sucker is limited in distribution to the Wall Canyon drainage of Surprise Valley, Washoe County, Nevada, USA. It was first documented and collected by C. L. Hubbs and R. R. Miller in 1934, and no species description has been published to date. Nonetheless, the Wall Canyon Sucker has been treated as a species and has appeared in various contexts within and outside of the scientific literature as such. Methods We conducted phylogenetic analyses and the first population genetics study of this putative species using genome‐wide sampling obtained through restriction site‐associated DNA sequencing to assess the Wall Canyon Sucker's relationships and population genetic characteristics. Result We found the Wall Canyon Sucker to be sister to the Warner Sucker C. warnerensis with high support and a median divergence time of 2.12 million years. Population genetic analyses supported that the Wall Canyon Sucker is a single genetic population with a high degree of isolation. Principal components and admixture analyses did not indicate recent admixture of the Wall Canyon Sucker with the Warner Sucker. Substantial differences in allele frequencies between the Wall Canyon and Warner suckers were apparent (genetic differentiation index FST = 0.15–0.21). Nucleotide diversity in the Wall Canyon Sucker was the lowest of all observations, and Tajima's D was greater than zero (D = 1.96), indicating population contraction and a lack of rare alleles, congruent with the desiccation of Lake Surprise and the persistence of the fish in a very restricted recent range. We undertook species delimitation with publicly available mitochondrial gene sequence data and found that a species‐level designation of the Wall Canyon Sucker is appropriate in that framework as well. Conclusion The results of this study are consistent with recognition of the Wall Canyon Sucker as a species; however, it still requires a formal taxonomic description.

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Phylogenomic analysis of the bowfin (Amia calva) reveals unrecognized species diversity in a living fossil lineage

Cited by 18 publications

References 63 publications

Hidden species diversity in an iconic living fossil vertebrate

Hidden species diversity in an iconic living fossil vertebrate

A chromosome level genome assembly of longnose gar,Lepisosteus osseus

Molecular phylogenetic and population genetic relationships of a putative species of sucker (Catostomus sp.) from Surprise Valley in the Great Basin, USA

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