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The Astyanax species complex has two morphs: a blind, depigmented morph which inhabits caves in M&eacute, xico and an eyed, pigmented surface-dwelling morph. The eyed morph can also be found in a few caves, sometimes hybridizing with the cave morph. This species complex has arguably become the most prominent model system among cave organisms for the study of evolutionary development and genomics. Before this study, 32 caves were known to be inhabited by the cave morph, 30 of them within the El Abra region. The purpose of this study was to conduct new surveys of the area and to assess some unconfirmed reports of caves presumably inhabited by troglomorphic fish. We describe two new localities, S&oacute, tano del Toro #2 and S&oacute, tano de La Calera. These two caves comprise a single hydrologic system together with the previously described cave of S&oacute, tano del Toro. The system is inhabited by a mixed population of troglomorphic, epigeomorphic, and presumably hybrid fish. Furthermore, Astyanax cavefish and the mysid shrimp Spelaeomysis quinterensis show a phylogeographic convergence that supports the notion that the central Sierra de El Abra is a biogeographical region that has influenced the evolutionary history of its aquatic community across species. The presumptive location of the boundaries of this biogeographical region are identified.

International audience; Animals evolve their sensory systems and foraging behaviors to adapt and colonize new and challenging habitats such as the dark cave environment. Vibration attraction behavior (VAB) gives fish the ability to locate the source of a water disturbance in the darkness. VAB evolved in the blind Mexican cave tetra, Astyanax mexicanus. VAB is triggered in cavefish by vibration stimuli peaking at 35 Hz, which is within the main spectrum of water fluctuations produced by many prey crustaceans and insects. VAB has a genetic component and is correlated to an increased number of head mechanosensory neuromasts in the eye orbital region when compared to surface fish. Previous competitive prey capture assays have supported the advantage of VAB for foraging in the dark. Despite its putative adaptive function, VAB has been described as absent in some Astyanax cave populations (Tinaja and Molino) but present in others (Pachón, Piedras, Toro and Sabinos). Here we have tested the occurrence of VAB in the field and in multiple cave populations using a vibrating device in natural pools. Our results confirmed the presence of VAB in caves such as Pachón, Toro and Sabinos but showed that VAB is also present in the Tinaja and Molino cave populations, previously reported as VAB-negative in laboratory experiments. Thus, VAB is available throughout the range of hypogean A. mexicanus. However, and most notably, within a given cave the levels of VAB were highly variable among different pools. Fish at one pool may express no VAB, while fish at another nearby pool of the same cave may actively show VAB. While a variety of environmental conditions may foster this diversity, we found that individuals inhabiting pools with a high abundance of organic matter have reduced expression of VAB. In contrast, in pools with little organic debris where fish probably depend more on hunting than on scavenging, VAB is enhanced. Our results suggest that expression of VAB is a plastic trait whose variability can depend on local conditions. Such plasticity may be required within and among caves where high environmental variability between pools result in a diverse availability of food. This article is protected by copyright. All rights reserved.

The habitat of cave-adapted organisms is characterized by complete darkness and in some instances, an apparent lack of environmental distinction between day and night. It is unclear if cave-adapted organisms retain circadian rhythms that can be light-entrained. Stygobromus allegheniensis (Allegheny Cave Amphipod) is an eyeless troglobitic crustacean found in caves located in the Northeastern region of the United States. Two cave populations were examined for evidence of light-entrained circadian rhythms. The first population inhabits a small tectonic cave (Ice Caves, Sam’s Point Preserve, NY) and the second (Clarksville Cave, Clarksville, NY) inhabits a long cave system in limestone rock. Experiments conducted in both the field and the laboratory suggest that the capacity to exhibit motor rhythms has been conserved in at least some individuals of both populations. Nonetheless, their motor activity rhythms have high variability of period length between individuals and do not appear to be light-entrainable. It is thus proposed that in this species, light-entrainable circadian rhythms controlling motor activity have undergone incipient regressive evolution.

Understanding the molecular basis of repeated evolved phenotypes can yield key insights into the evolutionary process. Quantifying the amount of gene flow between populations is especially important in interpreting mechanisms of repeated phenotypic evolution, and genomic analyses have revealed that admixture is more common between diverging lineages than previously thought. In this study, we resequenced and analyzed nearly 50 whole genomes of the Mexican tetra from three blind cave populations, two surface populations, and outgroup samples. We confirmed that cave populations are polyphyletic and twoAstyanax mexicanuslineages are present in our dataset. The two lineages likely diverged ∼257k generations ago, which, assuming 1 generation per year, is substantially younger than previous mitochondrial estimates of 5-7mya. Divergence of cave populations from their phylogenetically closest surface population likely occurred between ∼161k - 191k generations ago. The favored demographic model for most population pairs accounts for divergence with secondary contact and heterogeneous gene flow across the genome, and we rigorously identified abundant gene flow between cave and surface fish, between caves, and between separate lineages of cave and surface fish. Therefore, the evolution of cave-related traits occurred more rapidly than previously thought, and trogolomorphic traits are maintained despite substantial gene flow with surface populations. After incorporating these new demographic estimates, our models support that selection may drive the evolution of cave-derived traits, as opposed to the classic hypothesis of disuse and drift. Finally, we show that a key QTL is enriched for genomic regions with very low divergence between caves, suggesting that regions important for cave phenotypes may be transferred between caves via gene flow. In sum, our study shows that shared evolutionary history via gene flow must be considered in studies of independent, repeated trait evolution.

The characiform fish Astyanaxmexicanus comes in two forms, a surface-dwelling morph which lives in the rivers of North and Central America and a blind, depigmented cave-dwelling morph which inhabits caves in Mexico. In recent years, this species has arguably become among the most influential model system for the study of evolutionary development and genomics in cave biology. While recent articles have analysed in great detail Astyanax genetics, development, physiology, phylogeny and behaviour, there have been comparatively few recent studies concerning its ecology and in particular its biogeography. Mitchell et al. (1977) reported the species inhabiting 29 caves in the Sierra de El Abra region. Despite the elapsing of over 40 years and the latest surge of interest in the model, not a single new cave locality had been described for the species. We describe here a new and 30th cave locality, Chiquitita Cave, inhabited by troglomorphic A.mexicanus. Their morphology, eye histology, 16S rRNA DNA sequence, and smelling capabilities are analysed. This cave represents the southernmost extension for the cave morph’s habitat within the Sierra de El Abra. Its name, Chiquitita Cave (Tiny Cave), was chosen in reference to a potential hydrologic connection to “Chica Cave” (small cave), which is among the most studied populations of Astyanax.

Stygobromus allegheniensis Holsinger, 1967 (Allegheny Cave Amphipod) is a troglobiotic crustacean commonly found in caves of the Northeast United States. We describe several new populations from the unique tectonic Ice Caves found in the Shawangunk Ridge in New York, USA. Results also show that despite being an eyeless species, it can detect particular wavelengths of light and individuals display scotophilia, a preference for darkness. Finally, the Ice Caves pose a challenge to any aquatic troglobiont; in the winter months, the Ice Caves freeze and the floor and walls become covered in solid ice. Our results show that S. allegheniensis may seek warmer waters within the cave, but can also survive being frozen in solid ice.

A new population of velvet worms (Onychophora) inhabiting a lava tube cave in the island of Santa Cruz, Galapagos, is reported here. The population size is large, suggesting that they may be troglophilic. Its members are darkly pigmented, with no obvious troglomorphic features. Their 16S rRNA sequence showed no differences when compared to an unidentified species of surface velvet worm from the same island, thus supporting cave and surface populations belong to the same species. Based on the 16S rRNA data, the Galapagos velvet worms derived from an Ecuadorian/Colombian clade, as would be expected of ease of dispersal from the nearest mainland to the Galapagos Islands.

In this study, we report evidence of a novel duplication of Melanocortin receptor 1 (Mc1r) in the cavefish genome. This locus was discovered following the observation of excessive allelic diversity in a ∼820 bp fragment of Mc1r amplified via degenerate PCR from a natural population of Astyanax aeneus fish from Guerrero, Mexico. The cavefish genome reveals the presence of two closely related Mc1r open reading frames separated by a 1.46 kb intergenic region. One open reading frame corresponds to the previously reported Mc1r receptor, and the other open reading frame (duplicate copy) is 975 bp in length, encoding a receptor of 325 amino acids. Sequence similarity analyses position both copies in the syntenic region of the single Mc1r locus in 16 representative craniate genomes spanning bony fish (including Astyanax) to mammals, suggesting we discovered tandem duplicates of this important gene. The two Mc1r copies share ∼89% sequence similarity and, within Astyanax, are more similar to one another compared to other melanocortin family members. Future studies will inform the precise functional significance of the duplicated Mc1r locus and if this novel copy number variant may have adaptive significance for the Astyanax lineage.

International audience; The subterranean environment is often described as "extreme" and food poor. Laboratory experiments have shown that blind Mexican tetra Astyanax mexicanus (De Filippi, 1853) cavefish are better at finding food in the dark than surface fish. Several morphological and behavioural attributes that could foster this obvious adaptive response to cave environments have been described. Nonetheless, it is currently unknown what young cavefish actually eat in their natural cave environment. Our results from the Pachón cave in México during the dry and rainy season show that fry are efficient predators in their natural cave environment. Their primary food item is aquatic crustaceans. The guts of post-larval, pre-juvenile stage individuals (n=9) contained an average of 17.9 water fleas (Cladocera), copepods, ostracods, and isopods. Thus, the fry in this cave are well-fed. The Pachón cave environment does not appear to be "food poor" for juvenile cavefish. Food regimes change between post-larval and adult stages to become more dependent on partially decomposed material, guano, or detritus from the mud. We discuss the data with regards to our current developmental and genetic understanding of cavefish morphological and behavioural evolution, particularly regarding its enhanced Vibration Attraction Behaviour (VAB).

Anelpistina californica, new species (Insecta: Zygentoma: Nicoletiidae), from the Peninsula of Baja California, Mexico, is described. We report here the 16S rRNA sequence of this new species. The information in this study will be useful in future studies of nicoletiids from Baja California, especially those that use nicoletiids to calibrate molecular clocks. Baja California populations were separated from mainland continent populations in the late Miocene to Pliocene 13–5 mya when the Gulf of California appeared.

Members of genus Speleonycta (Insecta: Zygentoma: Nicoletiidae) have only been described from caves in south-central U.S.A. The first epigean species of Speleonycta is described herein. Specimens were collected from Mount Diablo in the bay area of San Francisco, California.

The "thysanuran" (Zygentoma: Nicoletiidae) Speleonycta ozarkensis is the only troglobiotic nicoletiid from the Ozark Highlands. It was originally described with only four specimens from four different cave systems in Arkansas and Oklahoma. The scarcity of available specimens has made it difficult to determine whether morphological variation among populations represents intraspecific or interspecific variation. We examined molecular (16S rRNA) variation among populations and found no evidence that they represent a species complex. Because of its limited distribution and lack of ecological and life history data, S. ozarkensis may be a species of conservation concern. We therefore conducted a conservation status assessment. We bioinventoried 44 caves in Arkansas and Oklahoma to determine the distribution of S. ozarkensis. A new locality in Adair Co., Oklahoma, was discovered and new specimens were collected to better assess morphological variation among populations. Data on ecology and life history was gathered. We determined the conservation status of the species and identified potential threats to existing populations. Despite being known from a few localities, S. ozarkensis has a broad distribution approaching 10,000 km2. Molecular data suggest S. ozarkensis is capable of considerable dispersal and is primarily an epikarstic species, perhaps explaining why it has been infrequently collected from caves. Conservation assessments revealed that S. ozarkensis is at a slight risk of extinction. We identified seven threats impacting populations that vary in scope and severity, but only recreational caving (three caves) and development associated with urbanization (one cave) have the greatest potential to immediately impact populations.

The hydrogeology of the El Abra region has a very dynamic history. Surface and underground rivers have broadly changed their paths throughout time. A simple model for estimating the age of caves by assessing rates of uplift/erosion is proposed. It is likely that not a single one of the river caves that currently house Astyanax populations had been formed when the original wave of colonization occurred 4.6-1.12 mya (million years ago). Colonization had to occur at higher-level caves. As the zone uplifted and eroded, deeper-level cave passages formed. Capture and sequestration of the underground streams allowed the ancestral population(s) to migrate to their current localities.

Anelpistina nandalumii, new species, a nicoletiid insect, is described from Chiapas, Southeastern Mexico. Molecular and morphological data appears to indicate that the new species has close affinities with species of the Grenadine islands and Aruba, in the Caribbean.

Speleonycta anachoretes, n. sp., is described and differentiated from S. ozarkensis, known from caves in the Ozark Plateau. The new species was collected from Kartchner Caverns State Park in Arizona. Morphology and preliminary analyses using 16S rRNA corroborate that Speleonycta may be related to Texoreddellia, another nicoletiid genus from caves of Texas and northern Mexico. General information regarding its conservation status within the commercial cave is provided.

The genus Speleonycta is erected, and S. ozarkensis, n. sp., is described and separated from other species of the subfamily Cubacubaninae. The type species was collected from several caves in the Ozark Plateau, while two more species, collected from a cave in Arizona and from a cave in California, remain under study. Morphology and preliminary analyses using histone DNA indicate that the new genus may be related to Texoreddellia, another nicoletiid from caves of Texas and northern Mexico.

Anelpistina levidensis n. sp. (Insecta: Zygentoma: Nicoletiidae) from the cave of Naj Tunich, Peten, Guatemala is described. The new troglobitic species differs from other described species by its long and slim appendages.

We describe a new species of cave adapted Anelpistina from Yextla cave, Guerrero, Mexico. The species has evolved a highly modified troglobitic morphology, despite being derived from a group that was previously blind and depigmented.

Cubacubana arubana Mendes 1986, was described from only two female specimens. We describe the male morphology for the first time. Males have the diagnostic articulated submedian appendages on urosternum IV found in specimens of the genus Anelpistina, and Anelpistina arubana, n. comb., is proposed. DNA sequences of 16S rRNA also indicate that the species is widely distributed throughout caves of Aruba and not restricted to the single type locality cave.

The blind Mexican tetra fish, Astyanax mexicanus, has become the most influential model for research of cave adapted organisms. Many authors assume that the Sierra de Guatemala populations and the Sierra de El Abra populations are derived from two independent colonizations. This assumption arises in part from biogeography. The 100 m high, 100 m wide Servilleta Canyon of the Boquillas River separates both mountain ranges and is an apparent barrier for troglobite dispersion. Anelpistina quinterensis (Nicoletiidae, Zygentoma, Insecta) is one of the most troglomorphic nicoletiid silverfish insects ever described. 16S rRNA sequences support that this species migrated underground to reach both mountain ranges within less than 12,000 years. Furthermore, literature shows a plethora of aquatic and terrestrial cave restricted species that inhabit both mountain ranges. Thus, the Servilleta canyon has not been an effective biological barrier that prevented underground migration of troglobites between the Sierra de Guatemala and the Sierra de El Abra. The Boquillas River has changed its course throughout time. Caves that in the past connected the two Sierras were only recently geologically truncated by the erosion of the new river course. It is likely that, with the geological changes of the area and throughout the 2-8 million years of evolutionary history of cave Astyanax, there have been opportunities to migrate across the Servilleta canyon.

Summary A new species of the genus Prosthecina , that has structures previously used as diagnostic characters to identify Anelpistina and Mexican specimens of the genus Cubacubana , is described. Distribution within the cave environment by this new species and other species of the subfamily is also analyzed.

Background In blind cave-dwelling populations of Astyanax mexicanus, several morphological and behavioral shifts occurred during evolution in caves characterized by total and permanent darkness. Previous studies have shown that sensory systems such as the lateral line (mechanosensory) and taste buds (chemosensory) are modified in cavefish. It has long been hypothesized that another chemosensory modality, the olfactory system, might have evolved as well to provide an additional mechanism for food-searching in troglomorphic Astyanax populations. Findings During a March 2013 cave expedition to the Sierra de El Abra region of San Luís Potosi, Mexico, we tested chemosensory capabilities of the Astyanax mexicanus of the Rio Subterráneo cave. This cave hosts a hybrid population presenting a wide range of troglomorphic and epigean mixed phenotypes. During a behavioral test performed in situ in the cave, a striking correlation was observed between the absence of eyes and an increased attraction to food extract. In addition, eyeless troglomorphic fish possessed significantly larger naris size than their eyed, nontroglomorphic counterparts. Conclusions Our findings suggest that chemosensory capabilities might have evolved in cave-dwelling Astyanax mexicanus and that modulation of naris size might at least partially underlie this likely adaptive change.

While many cave-adapted organisms tend to be endemic to single locations or restricted to single karstic regions, the troglobitic silverfish insects of genus Texoreddellia can be found in scores of different cave localities that cover a range of nearly 160,000 km 2 . They are among the most important and common representatives of the cave-adapted fauna of Texas and Coahuila, in northern Mexico. Using morphological and mitochondrial gene sequence data, we have corroborated the presence of at least six different species within the genus and provided species identifications to populations inhabiting 153 different cave locations. Results show that species ranges are larger than previously reported and that ranges tend to greatly overlap with each other. We have also found that different species of Texoreddellia commonly inhabit the same cave in sympatry. Data supports that some species of Texoreddellia can easily disperse through the extensive network of cracks, fissures and smaller cavities near the surface and epikarst.

A new population of blind, cave dwelling tetra fish of the genus Astyanax was discovered in Granadas Cave, in the Balsas drainage, southern Mexico. All blind Mexican tetras previously described are from Tampico and San Luis Potosf, northern Mexico. The discovery of a new blind morph thus represents an independent colonization and convergent adaptation to the cave environment by this fish. Individuals of this population display variability of their troglomorphic features. Some individuals presented asymmetrical degeneration of the eyes, where one was normal, but the other somewhat reduced in size and complexity. Loss of pigmentation and eye reduction, although sometimes correlated, were not always linked; reduced eyes were found on pigmented fish and unpigmented fish often possessed normal eyes. Some individuals had reduced lens size or an absence of lens altogether. Retina is highly modified with photoreceptors sometimes absent. Eye reduction was correlated with a diminished size of the optic lobes and an increase of the prosencephalon. Modifications of the skull involve closing in of the circumorbital series of bones. Certain aspects of behavior are also modified.

The blind morph of Astyanax fasciatus (Pisces: Characidae) has been more thoroughly studied than any other cave inhabiting organism. Most studies of A. fasciatus have used individuals from different caves of the Sierra de El Abra, Mexico, and have assumed that each population independently evolved to live in the cave environment. We analyzed the relationships among several cave populations that delineate the Sierra de El Abra using RAPD markers. The results indicate that all cave populations are more closely related to one another than they are to the surface populations. This suggests that present day cave populations derived from a common ancestral stock, most likely due to a single colonization event, or alternatively, that strong gene flow among cave populations has occurred, raising precaution against considering each cave population as independent.