Population genomic analysis of the Speckled Dace species complex identifies three distinct lineages in California

Su, Yingxin; Moyle, Peter B.; Campbell, Matthew A.; Finger, Amanda J.; O’Rourke, Sean; Baumsteiger, Jason; Miller, Michael R.

doi:10.1002/tafs.10388

Cited by 4 publications

(32 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Taxonomic distinctness is supported by genomic and other genetic studies. Our assumption is that the evolutionary distances among populations provide support for designation of species and subspecies within the Speckled Dace complex (Su et al 2022). Genetic/genomic studies should indicate if there is evidence for inbreeding with other populations and if such interbreeding has played a role in a dace population's evolution, especially prior to the invasion of Euro-American people into western North America.…”

Section: Designation Of Species and Subspeciesmentioning

confidence: 99%

“…To determine evolutionary lineages within California populations, Su et al (2022) collected samples from 38 locations in the western USA, with a focus on California. They used RAD sequencing to extract thousands of SNPs across the genome to identify genetic differences among all the samples.…”

Section: Geneticsmentioning

confidence: 99%

“…We therefore find it appropriate to label lineages with broad genomic differences from other lineages as species and geographically isolated lineages with less genomic differentiation as subspecies or distinct population segments. This is possible in part because the improved genetic techniques used here make no assumptions that species must be morphologically distinct from one another if genetic differences are large (Su et al 2022). In any case, our designations of species and subspecies are not solely based on genomics, but on other criteria as well, as mentioned.…”

Section: Geneticsmentioning

confidence: 99%

“…Moyle (2002) and Moyle et al (2015) list seven dace taxa as present in California, all considered to be subspecies of R. osculus although five are not formally described. A recent genome-based analysis (Su et al 2022) shows that there are three lineages of dace in California that can be recognized as distinct population segments; these lineages are more or less in concordance with lineages described in Oakey et al (2004). Formal recognition is important because species/subspecies that lack scientific names are much less likely to be the focus of conservation actions under federal and state Endangered Species Acts.…”

Section: Introductionmentioning

confidence: 99%

“…The purpose of this study is to examine the taxonomy of Speckled Dace in California and to describe the three species (one new, two elevated to species level) and six subspecies (three new) that we found to be present. To do this, we (a) discuss the history of Speckled Dace taxonomy in California, (b) describe how we determined species and subspecies, (c) summarize the new genomic findings (Su et al 2022) that supports the revised taxonomy in this study and (d) present a revision of the taxonomy of dace populations in California. We focus on California because it is an immense state with diverse habitats that have been the end point of colonization events as dace spread slowly from their presumptive ancestral home in the Columbia River basin.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Taxonomy of the Speckled Dace Species Complex (Cypriniformes: Leuciscidae, Rhinichthys) in California, USA

Moyle¹,

Buckmaster

2023

Zootaxa

View full text Add to dashboard Cite

The Speckled Dace, Rhinichthys osculus (Girard), is a small species of fish (Cypriniformes, Leuciscidae) that has the widest geographic range of any freshwater dispersing fish in western North America. The dynamic geologic history of the region has produced many isolated watersheds with endemic fish species. However, Speckled Dace from these watersheds cannot be differentiated readily by morphometrics and meristics. This has led to the widely accepted hypothesis that the dace’s adaptability and ability to cross geologic barriers has resulted in interbreeding among neighboring populations, maintaining the dace as a single species. We investigate this hypothesis by looking at Speckled Dace populations in California which are the result of at least three separate colonization events of isolated watersheds. We synthesize results from taxonomic, genetic, and zoogeographic studies in combination with the findings of a recent genomics study, to show that there are distinctive evolutionary lineages within the Speckled Dace complex. These lineages are used to designate multiple species and subspecies. We back up these designations by examining how well these lineages fit with the geologic history of the isolated basins they inhabit and with the presence of other endemic fishes. We conclude the following nine taxa can be recognized within the Speckled Dace complex in California.

show abstract

Section: Designation Of Species and Subspeciesmentioning

confidence: 99%

Section: Geneticsmentioning

confidence: 99%

Section: Geneticsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Taxonomy of the Speckled Dace Species Complex (Cypriniformes: Leuciscidae, Rhinichthys) in California, USA

Moyle¹,

Buckmaster

2023

Zootaxa

View full text Add to dashboard Cite

show abstract

Genetic approaches reveal a healthy population and an unexpectedly recent origin for an isolated desert spring fish

Sidlauskas

Mathur

Aydoğan

et al. 2023

Preprint

View full text Add to dashboard Cite

Foskett Spring in Oregon's desert harbors a historically threatened population of Western Speckled Dace (Rhinichthys klamathensis). Though recently delisted, the dace's recruitment depends upon regular removal of encroaching vegetation. Previous studies assumed that Foskett Dace separated from others in the Warner Valley about 10,000 years ago, thereby framing an enigma about the population's surprising ability to persist for so long in a tiny habitat easily overrun by plants. To investigate the phenomenon of persistence and the effectiveness of interventions to augment population size, we assessed genetic diversity among daces inhabiting Foskett Spring, a refuge at Dace Spring, and three nearby streams. Analysis revealed a robust effective population size (Ne) of nearly 5,000 within Foskett Spring, though Ne in the Dace Spring refuge is just 10% of that value. Heterozygosity is slightly lower than expected based on random mating at all five sites, indicating mild inbreeding, but not at a level of concern. These results confirm the genetic health of Foskett Dace. Unexpectedly, genetic differentiation reveals closer similarity between Foskett Dace and a newly discovered population from Nevada's Coleman Creek than between Foskett Dace and dace elsewhere in Oregon. Demographic modeling inferred Coleman Creek as the ancestral source of Foskett Dace just 600 years ago, much more recently than previously suspected and coincident with the arrival of large herbivores whose grazing may have maintained open water suitable for reproduction. These results solve the enigma of persistence by greatly shortening the duration over which Foskett Dace have inhabited their isolated spring.

show abstract

Genetic approaches reveal a healthy population and an unexpectedly recent origin for an isolated desert spring fish

Sidlauskas,

Mathur,

Aydoğan

et al. 2024

BMC Ecol Evo

View full text Add to dashboard Cite

Foskett Spring in Oregon’s desert harbors a historically threatened population of Western Speckled Dace (Rhinichthys klamathensis). Though recently delisted, the dace’s recruitment depends upon regular removal of encroaching vegetation. Previous studies assumed that Foskett Dace separated from others in the Warner Valley about 10,000 years ago, thereby framing an enigma about the population’s surprising ability to persist for so long in a tiny habitat easily overrun by plants. To investigate that persistence and the effectiveness of interventions to augment population size, we assessed genetic diversity among daces inhabiting Foskett Spring, a refuge at Dace Spring, and three nearby streams. Analysis revealed a robust effective population size (Ne) of nearly 5000 within Foskett Spring, though Ne in the Dace Spring refuge is just 10% of that value. Heterozygosity is slightly lower than expected based on random mating at all five sites, indicating mild inbreeding, but not at a level of concern. These results confirm the genetic health of Foskett Dace. Unexpectedly, genetic differentiation reveals closer similarity between Foskett Dace and a newly discovered population from Nevada’s Coleman Creek than between Foskett Dace and dace elsewhere in Oregon. Demographic modeling inferred Coleman Creek as the ancestral source of Foskett Dace fewer than 1000 years ago, much more recently than previously suspected and possibly coincident with the arrival of large herbivores whose grazing may have maintained open water suitable for reproduction. These results solve the enigma of persistence by greatly shortening the duration over which Foskett Dace have inhabited their isolated spring.

show abstract

Population genomic analysis of the Speckled Dace species complex identifies three distinct lineages in California

Cited by 4 publications

References 33 publications

Taxonomy of the Speckled Dace Species Complex (Cypriniformes: Leuciscidae, Rhinichthys) in California, USA

Taxonomy of the Speckled Dace Species Complex (Cypriniformes: Leuciscidae, Rhinichthys) in California, USA

Genetic approaches reveal a healthy population and an unexpectedly recent origin for an isolated desert spring fish

Genetic approaches reveal a healthy population and an unexpectedly recent origin for an isolated desert spring fish

Contact Info

Product

Resources

About