Next generation phylogeography of cave and surface Astyanax mexicanus

Coghill, Lyndon M.; Hulsey, C. Darrin; Chaves‐Campos, Johel; León, Francisco J. Garcı́a de; Johnson, Steven G.

doi:10.1016/j.ympev.2014.06.029

Cited by 70 publications

(70 citation statements)

References 40 publications

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“…2), which is independently derived in multiple, independent cave invasions2323. In cavefish, early eye development is largely similar to the eye development in surface fish in that lens vesicles and optic cups form, albeit, they are smaller in cavefish even at very early stages (14 h.p.f., hours post fertilization24).…”

Section: Resultsmentioning

confidence: 98%

“…Specifically, surface forms of the Mexican tetra, Astyanax mexicanus , colonized multiple caves in northeastern Mexico and evolved extreme cave-associated traits at least four independent times over the past 2–3 Myr (refs 2, 3). Cavefish populations exhibit repeated morphological evolution for a variety of traits including eye degeneration24, pigment loss56, increased size and number of specialized mechanosensory organs called neuromasts7 and increased numbers of taste buds4.…”

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confidence: 99%

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The cavefish genome reveals candidate genes for eye loss

et al. 2014

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Natural populations subjected to strong environmental selection pressures offer a window into the genetic underpinnings of evolutionary change. Cavefish populations, Astyanax mexicanus (Teleostei: Characiphysi), exhibit repeated, independent evolution for a variety of traits including eye degeneration, pigment loss, increased size and number of taste buds and mechanosensory organs, and shifts in many behavioural traits. Surface and cave forms are interfertile making this system amenable to genetic interrogation; however, lack of a reference genome has hampered efforts to identify genes responsible for changes in cave forms of A. mexicanus. Here we present the first de novo genome assembly for Astyanax mexicanus cavefish, contrast repeat elements to other teleost genomes, identify candidate genes underlying quantitative trait loci (QTL), and assay these candidate genes for potential functional and expression differences. We expect the cavefish genome to advance understanding of the evolutionary process, as well as, analogous human disease including retinal dysfunction.

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Section: Resultsmentioning

confidence: 98%

mentioning

confidence: 99%

The cavefish genome reveals candidate genes for eye loss

et al. 2014

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“…However, the Molino, Tinaja, Los Sabinos and commercial Chica cavefish populations were not sensitive to lateral line ablation, highlighting mechanistic differences in the evolution of sleep loss between cavefish populations. Of the lineages tested for sleep, the Molino population is most distantly related to Pachón, originating from a geographically distinct region of Mexico and a more recent surface fish invasion compared with the older stocks of the Sierra del Abra region that include Pachón, Tinaja, Los Sabinos and Chica (Bradic et al, 2012;Coghill et al, 2014;Strecker et al, 2012). Despite close evolutionary relationships between older populations of Sierra del Abra cavefish, many ecological factors differ between subterranean populations.…”

Section: Mechanistic Differences In Sleep Loss Between Cavefish Populmentioning

confidence: 99%

“…The defined ecological habitat and evolutionary history provide a powerful model for investigating the mechanisms that underlie changes in sleep and sensory processing (Bibliowicz et al, 2013;Duboué et al, 2011;Varatharasan et al, 2009;Yoshizawa et al, 2010). Within the past 2-5 million years, at least five independent colonization events by two different migration waves of eyed surface fish have established independent cavefish populations in northeastern Mexico (Bradic et al, 2012;Coghill et al, 2014;Ornelas-García et al, 2008;Strecker et al, 2012). Despite this isolation, A. mexicanus surface fish and cavefish are interfertile, providing the opportunity to generate surface×cave and cave×cave hybrids that enable investigation of the genetic relationship between behavioral and physiological traits (Borowsky, 2008a;Wilkins, 1971Wilkins, , 1988.…”

Section: Introductionmentioning

confidence: 99%

The lateral line confers evolutionarily derived sleep loss in the Mexican cavefish

Jaggard

Robinson

Stahl

et al. 2017

Journal of Experimental Biology

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Sleep is an essential behavior exhibited by nearly all animals, and disruption of this process is associated with an array of physiological and behavioral deficits. Sleep is defined by changes in sensory gating that reduce sensory input to the brain, but little is known about the neural basis for interactions between sleep and sensory processing. Blind Mexican cavefish comprise an extant surface dwelling form and 29 cave morphs that have independently evolved increased numbers of mechanoreceptive lateral line neuromasts and convergent evolution of sleep loss. Ablation of the lateral line enhanced sleep in the Pachoń cavefish population, suggesting that heightened sensory input underlies evolutionarily derived sleep loss. Targeted lateral line ablation and behavioral analysis localized the wake-promoting neuromasts in Pachoń cavefish to superficial neuromasts of the trunk and cranial regions. Strikingly, lateral line ablation did not affect sleep in four other cavefish populations, suggesting that distinct neural mechanisms regulate the evolution of sleep loss in independently derived cavefish populations. Cavefish are subject to seasonal changes in food availability, raising the possibility that sensory modulation of sleep is influenced by metabolic state. We found that starvation promotes sleep in Pachoń cavefish, and is not enhanced by lateral line ablation, suggesting that functional interactions occur between sensory and metabolic regulation of sleep. Taken together, these findings support a model where sensory processing contributes to evolutionarily derived changes in sleep that are modulated in accordance with food availability.

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“…RAD-Seq provides high-resolution data that enable the identification of potentially thousands of these genetic markers across individuals and populations that can be employed for further analyses (Davey & Blaxter, 2010;Peterson et al, 2012). For example, Coghill et al (2014) used RAD-Seq to trace the colonization of caves by the blind Mexican cavefish Astyanax mexicanus. This methodology enabled them to find over 2,000 SNPs across the examined populations and provided evidence for at least four independent colonization events from surface populations to the caves, which suggests parallel evolution of the cave phenotypes observed in these stygobitic fish.…”

Section: International Journal Of Speleology 45 (2) 149-170 Tampamentioning

confidence: 99%

Life in the Underworld: Anchialine cave biology in the era of speleogenomics

Pérez‐Moreno

Iliffe²,

Bracken‐Grissom³

2016

IJS

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Abstract:Anchialine caves contain haline bodies of water with underground connections to the ocean and limited exposure to open air. Despite being found on islands and peninsular coastlines around the world, the isolation of anchialine systems has facilitated the evolution of high levels of endemism among their inhabitants. The unique characteristics of anchialine caves and of their predominantly crustacean biodiversity nominate them as particularly interesting study subjects for evolutionary biology. However, there is presently a distinct scarcity of modern molecular methods being employed in the study of anchialine cave ecosystems. The use of current and emerging molecular techniques, e.g., next-generation sequencing (NGS), bestows an exceptional opportunity to answer a variety of long-standing questions pertaining to the realms of speciation, biogeography, population genetics, and evolution, as well as the emergence of extraordinary morphological and physiological adaptations to these unique environments. The integration of NGS methodologies with traditional taxonomic and ecological methods will help elucidate the unique characteristics and evolutionary history of anchialine cave fauna, and thus the significance of their conservation in face of current and future anthropogenic threats. Here we review previous contributions to our understanding of anchialine biodiversity and evolution, and discuss the potential of "speleogenomic" methods for future research in these threatened systems.

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Next generation phylogeography of cave and surface Astyanax mexicanus

Cited by 70 publications

References 40 publications

The cavefish genome reveals candidate genes for eye loss

The cavefish genome reveals candidate genes for eye loss

The lateral line confers evolutionarily derived sleep loss in the Mexican cavefish

Life in the Underworld: Anchialine cave biology in the era of speleogenomics

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