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14 results for “Amblyopsidae”
Datasets: Population genomics and mitochondrial DNA reveal cryptic diversity in North American Spring Cavefishes (Amblyopsidae, Forbesichthys)
<p>Forbesichthys_allsites.vcf: Dataset in VCF format used to perform Effective Population Size estimation.</p> <p>Forbesichthys_SNPs_NoLD.vcf: Dataset in VCF format used to perform PCA, fastStrucuture, and phylogenetic analyses.</p> <p>Files with extension .sfs contain site spectrum frequencies generated with the program easySFS.py.</p>
Data from: Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid cavefishes (Teleostei: Amblyopsidae)
The genetic mechanisms underlying regressive evolution—the degeneration or loss of a derived trait—are largely unknown, particularly for complex structures such as eyes in cave organisms. In several eyeless animals, the visual photoreceptor rhodopsin appeared to retain functional amino-acid sequences. Hypotheses to explain apparent maintenance of function include weak selection for retention of light-sensing abilities and its pleiotropic roles in circadian rhythms and thermotaxis. In contrast, we show that there has been repeated loss of functional constraint of rhodopsin in amblyopsid cavefishes, as at least three cave lineages have independently accumulated unique loss-of-function mutations over the last 10.3 My. While several cave lineages still possess functional rhodopsin, they exhibit increased rates of nonsynonymous mutations that have greater effect on the structure and function of rhodopsin compared to those in surface lineages. These results indicate that functionality of rhodopsin has been repeatedly lost in amblyopsid cavefishes. The presence of a functional copy of rhodopsin in some cave lineages is likely explained by stochastic accumulation of mutations following recent subterranean colonization.
Data from: Effects of climatic and geological processes during the Pleistocene on the evolutionary history of the northern cavefish, Amblyopsis spelaea (Teleostei: Amblyopsidae)
Open the record for dataset details and reuse information.
Data from: Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid cavefishes (Teleostei: Amblyopsidae)
Open the record for dataset details and reuse information.
Figure 6 from: Chakrabarty P, Prejean J, Niemiller M (2014) The Hoosier cavefish, a new and endangered species (Amblyopsidae, Amblyopsis) from the caves of southern Indiana. ZooKeys 412: 41-57. https://doi.org/10.3897/zookeys.412.7245
Figure 6 - Illustration of Amblyopsis hoosieri based on the holotype, INHS 106675, 75.1 mm SL. Illustration by Nathan Coussou.
Figure 5 from: Chakrabarty P, Prejean J, Niemiller M (2014) The Hoosier cavefish, a new and endangered species (Amblyopsidae, Amblyopsis) from the caves of southern Indiana. ZooKeys 412: 41-57. https://doi.org/10.3897/zookeys.412.7245
Figure 5 - Photograph of a paratype of Amblyopsis hoosieri in life, YPM ICH 25304, 60.7 mm SL. Photograph by M.L. Niemiller.
Figure 4 from: Chakrabarty P, Prejean J, Niemiller M (2014) The Hoosier cavefish, a new and endangered species (Amblyopsidae, Amblyopsis) from the caves of southern Indiana. ZooKeys 412: 41-57. https://doi.org/10.3897/zookeys.412.7245
Figure 4 - Comparative image of two similarly sized individuals of both species of Amblyopisis. Amblyopsis hoosieri, holotype, INHS 106675, 75.1 mm SL, Bronson's Cave, Lawrence Co., Indiana (A); a specimen of Amblyopsis spelaea (YPM ICH 25294) of similar SL (67 mm SL) showing the more elongate and sculpted (versus plump) body, pointed fins, less prominent myomeres and more prominent papillae on the body (B).
Figure 3 from: Chakrabarty P, Prejean J, Niemiller M (2014) The Hoosier cavefish, a new and endangered species (Amblyopsidae, Amblyopsis) from the caves of southern Indiana. ZooKeys 412: 41-57. https://doi.org/10.3897/zookeys.412.7245
Figure 3 - Plots illustrating the relationships between body depth, body width and standard length (SL). Circles in red represent specimens of Amblyopsis hoosieri, sp. n., from north of the Ohio River in Indiana; triangles in blue represent Amblyopsis spelaea from south of the Ohio River in Kentucky. (a) body depth versus standard length, (b) body width versus standard length, and (c) and body depth versus body width as proportions of standard length.
Figure 7 from: Chakrabarty P, Prejean J, Niemiller M (2014) The Hoosier cavefish, a new and endangered species (Amblyopsidae, Amblyopsis) from the caves of southern Indiana. ZooKeys 412: 41-57. https://doi.org/10.3897/zookeys.412.7245
Figure 7 - Cleared and stained image of the head of Amblyopsis hoosieri. Note lack of eye or a clearly defined bony orbit. Specimen is a paratype from INHS 40424, 71.3 mm SL.
Figure 1 from: Chakrabarty P, Prejean J, Niemiller M (2014) The Hoosier cavefish, a new and endangered species (Amblyopsidae, Amblyopsis) from the caves of southern Indiana. ZooKeys 412: 41-57. https://doi.org/10.3897/zookeys.412.7245
Figure 1 - Phylogeny of Amblyopsidae. Modified from Niemiller et al. (2013d), showing a northern lineage of Amblyopsis found north of the Ohio River in Indiana (members of the new species described herein) and a southern lineage in Kentucky (Amblyopsis spelaea sensu n.).
Figure 2 from: Chakrabarty P, Prejean J, Niemiller M (2014) The Hoosier cavefish, a new and endangered species (Amblyopsidae, Amblyopsis) from the caves of southern Indiana. ZooKeys 412: 41-57. https://doi.org/10.3897/zookeys.412.7245
Figure 2 - Distribution of Amblyopsis spp., Amblyopsis spelaea and Amblyopsis hoosieri, in the Mitchell Plain and Crawford-Mammoth Uplands of Indiana and Kentucky.
Figure 3 from: Niemiller ML, Zigler KS, Hart PB, Kuhajda BR, Armbruster JW, Ayala BN, Engel AS (2016) First definitive record of a stygobiotic fish (Percopsiformes, Amblyopsidae, Typhlichthys) from the Appalachians karst region in the eastern United States. Subterranean Biology 20: 39-50. https://doi.org/10.3897/subtbiol.20.9693
Figure 3 - Distribution of Typhlichthys subterraneus (solid circles) in southeastern Tennessee, northeastern Alabama, and northwestern Georgia. The new record at Crane Cave is denoted with a red triangle and lineage A localities are highlighted in peach. Lineage A populations that have been genetically examined are marked with an asterisk and labeled as follows: LMC – Limestone Caverns, LPC – Lost Pig Cave, LRW – Long's Rock Wall, and PCS – Pryor Cave Spring. Counties with Typhlichthys records are labeled. Karst and cave-bearing strata are shaded gray based on the U.S. karst map (Weary and Doctor 2014). The border of the Appalachian Valley and Ridge (AVR) physiographic province is denoted by the dot and dashed line.
Figure 2 from: Niemiller ML, Zigler KS, Hart PB, Kuhajda BR, Armbruster JW, Ayala BN, Engel AS (2016) First definitive record of a stygobiotic fish (Percopsiformes, Amblyopsidae, Typhlichthys) from the Appalachians karst region in the eastern United States. Subterranean Biology 20: 39-50. https://doi.org/10.3897/subtbiol.20.9693
Figure 2 - Maximum likelihood gene trees for mitochondrial ND2 (left) and nuclear S7 (right) loci. Colors correspond to genetic lineages for Typhlichthys subterraneus designated in Niemiller et al. (2012b). Bootstrap values are to the left (ND2) or right (S7) of the corresponding node with >0.70 support. Outgroup taxa include Speoplatyrhinus poulsoni and Amblyopsis hoosieri. Scale bar unit: expected substitutions per site.
Figure 1 from: Niemiller ML, Zigler KS, Hart PB, Kuhajda BR, Armbruster JW, Ayala BN, Engel AS (2016) First definitive record of a stygobiotic fish (Percopsiformes, Amblyopsidae, Typhlichthys) from the Appalachians karst region in the eastern United States. Subterranean Biology 20: 39-50. https://doi.org/10.3897/subtbiol.20.9693
Figure 1 - Typhlichthys subterraneus collected 25 November 2015 from Crane Cave (GCZ80), Catoosa County, Georgia. Photograph by B.R. Kuhajda.
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