Phylogeny of finescale shiners of the genus Lythrurus (Cypriniformes: Cyprinidae) inferred from four mitochondrial genes

Pramuk, Jennifer B.; Grose, Michael J.; Clarke, Anna L.; Greenbaum, Eli; Bonaccorso, Elisa; Guayasamín, Juan M.; Smith-Pardo, Allan H.; Benz, Brett W.; Harris, Bethany; Siegfreid, Eric; Reid, Yana R.; Holcroft-Benson, Nancy; Wiley, E. O.

doi:10.1016/j.ympev.2006.06.008

Cited by 12 publications

(5 citation statements)

References 29 publications

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“…Lythrurus has long been considered monophyletic ( Snelson, 1972 ; Schmidt, Bielawski & Gold, 1998 ; Mayden et al, 2006 ; Pramuk et al, 2007 ), and our study also supports the monophyly of this group (BS 100, PP 1). What has been more problematic, however, is determining the clade’s relationship to other genera.…”

Section: Discussionsupporting

confidence: 83%

Phylogenomics and classification ofNotropisand related shiners (Cypriniformes: Leuciscidae) and the utility of exon capture on lower taxonomic groups

Stout

Schönhuth

Mayden

et al. 2022

PeerJ

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North American minnows of the Shiner Clade, within the family Leuciscidae, represent one of the most taxonomically complex clades of the order Cypriniformes due to the large number of taxa coupled with conserved morphologies. Species within this clade were moved between genera and subgenera until the community decided to lump many of the unclassified taxa with similar morphologies into one genus, Notropis, which has held up to 325 species. Despite phylogentic studies that began to re-elevate some genera merged into Notropis, such as Cyprinella, Luxilus, Lythrurus, and Pteronotropis, the large genus Notropis remained as a taxonomic repository for many shiners of uncertain placement. Recent molecular advances in sequencing technologies have provided the opportunity to re-examine the Shiner Clade using phylogenomic markers. Using a fish probe kit, we sequenced 90 specimens in 87 species representing 16 genera included in the Shiner Clade, with a resulting dataset of 1,004 loci and 286,455 base pairs. Despite the large dataset, only 32,349 bp (11.29%) were phylogenetically informative. In our maximum likelihood tree, 78% of nodes are 100% bootstrap supported demonstrating the utility of the phylogenomic markers at lower taxonomic levels. Unsurprisingly, species within Notropis as well as Hudsonius, Luxilus, and Alburnops are not resolved as monophyletic groups. Cyprinella is monophyletic if Cyprinella callistia is excluded, and Pteronotropis is monophyletic if it includes Hudsonius cummingsae. Taxonomic changes we propose are: restriction of species included in Alburnops and Notropis, elevation of the subgenus Hydrophlox, expansion of species included in Miniellus, movement of Hudsonius cummingsae to Pteronotropis, and resurrection of the genera Coccotis and Paranotropis. We additionally had two specimens of three species, Notropis atherinoides, Ericymba amplamala, and Pimephales vigilax and found signficant differences between the localities (1,086, 1,424, and 845 nucleotides respectively).

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Section: Discussionsupporting

confidence: 83%

Phylogenomics and classification ofNotropisand related shiners (Cypriniformes: Leuciscidae) and the utility of exon capture on lower taxonomic groups

Stout

Schönhuth

Mayden

et al. 2022

PeerJ

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“…Evidence consistent with taxon‐cycle predictions is present throughout highland‐fish literature. For example, ancestral Campostoma spadiceum and Lythrurus snelsoni of the Ouachita highlands (Pramuk et al ., ; Blum et al ., ; Cashner et al ., ) are putative stage 4 species that possibly originated in the late Tertiary when the Ouachita highlands were unroofed and Ouachita streams became isolated. These species are confined to highland‐type habitats and have parapatric distributions with younger, widespread (putative stage 1) Campostoma plumbeum and Lythrurus umbratilis , respectively (Taylor & Lienesch, ; Cashner et al ., ).…”

Section: Discussionmentioning

confidence: 99%

Miocene rivers and taxon cycles clarify the comparative biogeography ofNorthAmerican highland fishes

Hoagstrom

Ung

Taylor³

2013

Journal of Biogeography

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Aim Our aims were: (1) to use recently published phylogenies of six widely distributed clades of highland-type fishes in a comparative analysis that investigates relationships among North American highlands; (2) to construct a map of relevant (pre-historic) river geography; and (3) to apply ecological paradigms to interpret patterns of highland-fish cladogenesis. Our principal questions were: (1) does highland endemism correspond to pre-historic river drainages; and (2) do patterns of speciation conform to any relevant paradigm?Location Twenty-two North American highlands, east to west from Appalachia to the Basin and Range, north to south from the Canadian Shield to the Mesa Central.Methods We used three-item analysis to find shared highland-area relationships, and we used dated phylogenies and geological literature to construct a map of relevant, pre-historic river drainages. We applied the taxon-cycle concept to interpret results.Results Three-item analysis identified 375 most-parsimonious trees with a retention index of 80.4%. An intersection tree reconstructed from shared three-area statements had a completeness index of 80.3%. Nodes on the tree identified seven major branches of one to eight highland areas each that were congruent with late Miocene river drainage patterns. Sister-area relationships within nodes were congruent with Plio-Pleistocene events. Older taxa have restricted distributions and some younger members of each clade are broadly distributed, consistent with predictions of the taxon cycle.Main conclusions Progenitors of highland endemics were widespread across an aggraded, alluvial landscape by the early Miocene. Middle Miocene drainage rearrangements facilitated further range expansion. Accelerated erosion in the middle Miocene, caused by tectonic uplift and climate change, created highland-type (sediment-starved) habitats. Parallel colonization and adaptation to these habitats and geographical isolation in the late Miocene and early Pliocene led to speciation of highland endemics. Plio-Pleistocene drainage rearrangements allowed populations of tolerant (derivative) taxa to expand again and colonize highland areas, including emerging ones.

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“…1) resulted in peripheral isolation of the upland E. nuchale from the widespread Coastal Plain species E. swaini, a pattern of speciation common among other upper Black Warrior River endemic darters (Bart and Taylor 1999;Porter et al 2002) and minnows of the genus Lythrurus (Pramuk et al 2007). Our ND2 phylogeny supports this hypothesis, but revealed peripheral isolation of an upland group containing both E. swaini populations from above the Fall Line (WC, WF and LY) and E. nuchale (clade 6) from lowland E. swaini.…”

Section: Historical Biogeographymentioning

confidence: 99%

Low genetic diversity and small long-term population sizes in the spring endemic watercress darter, Etheostoma nuchale

et al. 2010

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Species endemic to coldwater springs in the southeastern United States are some of the rarest and most imperiled in this region, yet little is known about their genetic composition and conservation needs. Here, microsatellite based levels of genetic diversity and estimates of effective population size (N e ) were compared between a narrow spring endemic fish, Etheostoma nuchale, and its widespread stream-dwelling relative, E. swaini. We applied several analytical methods to assess how demographic history is reflected in contemporary levels of genetic diversity for populations of E. nuchale. Phylogenetic analyses based on mitochondrial and nuclear DNA sequence data revealed a complex history among E. nuchale and E. swaini, but suggested ancient divergence and historic periods of isolation since colonization of spring habitats by E. nuchale. Populations of E. nuchale have levels of genetic diversity approximately one-half that of E. swaini, a result most likely due to founder effects and recent bottlenecks. Statistically significant F st values (0.05-0.27) and STRUCTURE analyses implied high levels of differentiation among E. nuchale populations. Estimates of current N e suggest relatively consistent levels across populations of E. nuchale, but one population may suffer from habitat degradation. We suggest that high levels of population structure and low levels of genetic diversity may be typical in other spring endemics inhabiting this region. Therefore, effective management planning for these unique species will require a detailed knowledge of the genetic and demographic history of each population.

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Phylogeny of finescale shiners of the genus Lythrurus (Cypriniformes: Cyprinidae) inferred from four mitochondrial genes

Cited by 12 publications

References 29 publications

Phylogenomics and classification ofNotropisand related shiners (Cypriniformes: Leuciscidae) and the utility of exon capture on lower taxonomic groups

Phylogenomics and classification ofNotropisand related shiners (Cypriniformes: Leuciscidae) and the utility of exon capture on lower taxonomic groups

Miocene rivers and taxon cycles clarify the comparative biogeography ofNorthAmerican highland fishes

Low genetic diversity and small long-term population sizes in the spring endemic watercress darter, Etheostoma nuchale

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