The spatiotemporal and genetic architecture of extraoral taste buds in Astyanax cavefish.

Intense environmental pressures can yield both regressive and constructive traits through complex evolutionary mechanisms. Although regression is well-studied, the biological bases of constructive features are less well understood. Cave-dwelling Astyanax fish harbor prolific extraoral taste buds on their heads, which are absent in conspecific surface-dwellers. Here, we present novel ontogenetic data demonstrating extraoral taste buds appear gradually and late in life history. This appearance is similar but non-identical in different cavefish populations, where patterning has evolved to permit taste bud re-specification across the endoderm-ectoderm germ layer boundary. Quantitative genetic analyses revealed that spatially distinct taste buds on the head are primarily mediated by two different cave-dominant loci. While the precise function of this late expansion on to the head is unknown, the appearance of extraoral taste buds coincides with a dietary shift from live-foods to bat guano, suggesting an adaptive mechanism to detect nutrition in food-starved caves. This work provides fundamental insight to a constructive evolutionary feature, arising late in life history, promising a new window into unresolved features of vertebrate sensory organ development.

Identification of Late Pleistocene and Holocene fossil lizards from Hall's Cave (Kerr County, Texas) and a primer on morphological variation in North American lizard skulls.

Fossil identification practices have a profound effect on our interpretation of the past because these identifications form the basis for downstream analyses. Therefore, well-supported fossil identifications are necessary for examining the impact of past environmental changes on populations and communities. Here we apply an apomorphic identification framework in a case study identifying fossil lizard remains from Hall's Cave, a late Quaternary fossil site located in Central Texas, USA. We present images and descriptions of a broad comparative sample of North American lizard cranial elements and compile new and previously reported apomorphic characters for identifying fossil lizards. Our fossil identifications from Hall's Cave resulted in a minimum of 11 lizard taxa, including five lizard taxa previously unknown from the site. Most of the identified fossil lizard taxa inhabit the area around Hall's Cave today, but we reinforce the presence of an extirpated species complex of horned lizard. A main goal of this work is to establish a procedure for making well-supported fossil lizard identifications across North America. The data from this study will assist researchers endeavoring to identify fossil lizards, increasing the potential for novel discoveries related to North American lizards and facilitating more holistic views of ancient faunal assemblages.

Mountain caves of the central region of Veracruz: A vertebrate biodiversity reservoir in a Neotropical hotspot.

The mountain region of central Veracruz, Mexico hosts a large system of karst and volcanic caves that are unexplored. In particular, the vertebrates that inhabit these subterranean ecosystems are unknown. This study evaluated the diversity of mammals, birds, reptiles, amphibians, and fish in three environments (euphotic, disphotic, and aphotic) of 16 caves of different geological origin (12 karst caves and 4 volcanic caves) distributed along an altitudinal gradient (300-2400 m a.s.l.). We found a richness of 242 vertebrate species (184 birds, 30 mammals, 15 reptiles, 12 amphibians, and 1 fish) and an abundance of a total of 11,323 individuals (4,969 mammals, 6,483 birds, 36 reptiles, 27 amphibians, and 5 fish). The richness of all vertebrate classes was higher in karst than in volcanic caves. Vertebrate diversity was also higher at mid-altitudes between 600-899 m a.s.l. Diversity varied between environments, where bird and reptile richness was higher in the euphotic environment, while mammal and amphibian diversity was higher in the aphotic environment. The similarity in the composition of vertebrate species does not depend on the distance between karstic and volcanic caves. Volcanic and karst caves shared on average up to 70% and 55% of vertebrate species, which indicates that only 30% and 45% of species, respectively, is different in each cave type. Given the vulnerability and fragility of these subterranean ecosystems, as well as the important diversity that they contain, we recommend including the caves of the central region of Veracruz in the conservation agenda of local governments and communities. Community-based conservation can help ensure the presence of vertebrate species in the caves of this region.

Middle and Late Pleistocene Denisovan subsistence at Baishiya Karst Cave.

Genetic and fragmented palaeoanthropological data suggest that Denisovans were once widely distributed across eastern Eurasia1-3. Despite limited archaeological evidence, this indicates that Denisovans were capable of adapting to a highly diverse range of environments. Here we integrate zooarchaeological and proteomic analyses of the late Middle to Late Pleistocene faunal assemblage from Baishiya Karst Cave on the Tibetan Plateau, where a Denisovan mandible and Denisovan sedimentary mitochondrial DNA were found3,4. Using zooarchaeology by mass spectrometry, we identify a new hominin rib specimen that dates to approximately 48-32 thousand years ago (layer 3). Shotgun proteomic analysis taxonomically assigns this specimen to the Denisovan lineage, extending their presence at Baishiya Karst Cave well into the Late Pleistocene. Throughout the stratigraphic sequence, the faunal assemblage is dominated by Caprinae, together with megaherbivores, carnivores, small mammals and birds. The high proportion of anthropogenic modifications on the bone surfaces suggests that Denisovans were the primary agent of faunal accumulation. The chaîne opératoire of carcass processing indicates that animal taxa were exploited for their meat, marrow and hides, while bone was also used as raw material for the production of tools. Our results shed light on the behaviour of Denisovans and their adaptations to the diverse and fluctuating environments of the late Middle and Late Pleistocene of eastern Eurasia.

Evolution of the regulation of developmental gene expression in blind Mexican cavefish.

Developmental evolution and diversification of morphology can arise through changes in the regulation of gene expression or protein-coding sequence. To unravel mechanisms underlying early developmental evolution in cavefish of the species Astyanax mexicanus, we compared transcriptomes of surface-dwelling and blind cave-adapted morphs at the end of gastrulation. Twenty percent of the transcriptome was differentially expressed. Allelic expression ratios in cave X surface hybrids showed that cis-regulatory changes are the quasi-exclusive contributors to inter-morph variations in gene expression. Among a list of 108 genes with change at the cis-regulatory level, we explored the control of expression of rx3, which is a master eye gene. We discovered that cellular rx3 levels are cis-regulated in a cell-autonomous manner, whereas rx3 domain size depends on non-autonomous Wnt and Bmp signalling. These results highlight how uncoupled mechanisms and regulatory modules control developmental gene expression and shape morphological changes. Finally, a transcriptome-wide search for fixed coding mutations and differential exon use suggested that variations in coding sequence have a minor contribution. Thus, during early embryogenesis, changes in gene expression regulation are the main drivers of cavefish developmental evolution.

The use of carinated items in the Levantine Aurignacian-Insights from layer D, Hayonim Cave, W. Galilee, Israel.

A longstanding debate concerns the function of carinated elements in both, the Levantine, and European Aurignacian. The present study aims to contribute to this topic with the evaluation of the carinated assemblage from layer D in Hayonim Cave, Western Galilee, Israel, one of the type sites of the Levantine Aurignacian. An operational chain reconstruction with an attribute analysis is paired with a typological approach to the preparation and maintenance products based on artefacts defined as West European Aurignacian. The results of this study are investigated with multivariate statistics offering a methodological contribution. The data is subjected to a transformation into a distance matrix using the Gower distance and tested with the adonis-algorithm for significance. The results clearly indicate that the carinated items in Hayonim Cave did fully or partially function as cores. They are accompanied by diagnostic preparation- and- maintenance products known from the literature e.g. Thèmes bladelets. The statistical analysis indicates only a minor correlation with stratigraphy yet supports the techno-typological criteria applied for defining artefact categories (cores, debitage, tools), as well as the proposed differentiation of carinated 'core' types. The non-carinated cores in Hayonim Cave are characterised by a high variability in typology and reduction concepts. A curious similarity to the Levallois-concept is observed on some of the flake cores. It is therefore suggested that the frequent recycling of Middle Palaeolithic artefacts in the Levantine Aurignacian might have given the Aurignacian flint-knappers the opportunity to study the Levallois concept and apply an approximation of it in their own core reduction strategies. The notion that Palaeolithic flint-knappers actively observed former technological systems through the discarded artefacts directly opens up a new trajectory for the understanding of lithic reduction concept permanence. The conceptual diversification and variability in Hayonim Cave D indicate a highly dynamic period in the Levantine Upper Palaeolithic which increased the adaptive potential and promoted a rapid cultural change.

Are haloclines distributional barriers in anchialine ecosystems? Physiological response of cave shrimps to salinity.

Anchialine systems are coastal groundwater habitats around the world which host a unique community of cave adapted species (stygobionts). Such communities are expected to be separated by haloclines into either fresh or saline groundwater communities, hence climate changes (e.g., eustatic sea level shifts) and anthropic driven changes (e.g., salinization) may have a great impact on these stygobiont communities. Here we used cave-restricted species of Typhlatya from the Yucatan Peninsula as models to identify physiological capacities that enable the different species to thrive in marine groundwater (T. dzilamensis) or fresh groundwater (T. mitchelli and T. pearsei), and test if their distribution is limited by their salinity tolerance capacity. We used behavior, metabolic rates, indicators of the antioxidant system and cellular damage, and lactate content to evaluate the response of individuals to acute changes in salinity, as a recreation of crossing a halocline in the anchialine systems of the Yucatan Peninsula. Our results show that despite being sister species, some are restricted to the freshwater portion of the groundwater, while others appear to be euryhaline.

Bacterial diversity and geomicrobiology of Winter Wonderland ice cave, Utah, USA.

The Winter Wonderland ice cave, located at an elevation of 3140 m above sea level in the Uinta Mountains of northern Utah, USA, maintains a constant sub-zero temperature. Seasonal snowmelt and rain enter the cave, freeze on the surface of the existing ice, and contribute to a 3-m-thick layered ice mass. This ice mass contains organic matter and cryogenic cave carbonates (CCCs) that date back centuries. In this study, samples of ice, liquid water, and exposed CCCs were collected to examine the bacterial communities within the cave and to determine if these communities vary spatially and between sample types. Flow cytometry showed that cell counts are an order of magnitude higher in liquid water samples than in ice. Epifluorescence microscopy and scanning electron microscopy imaging revealed potential coccoid and bacillus microbial morphologies in water samples and putative cells or calcite spherules in the CCCs. The diversity of bacteria associated with soil, identified through sequence-based analysis, supports the hypothesis that water enters the cave by filtering through soil and bedrock. A differential abundance of bacterial taxa was observed between sample types, with the greatest diversity found in CCCs. This supports a geomicrobiological framework where microbes aggregate in the water, sink into a concentrated layer, and precipitate out of the ice with the CCCs, thereby reducing the cell counts in the ice. These CCCs may provide essential nutrients for the bacteria or could themselves be products of biomineralization.

Natural and anthropogenic impact on the microclimate and particulate matter in the UNESCO show cave.

Particulate matter concentrations (PM10, PM2.5, PM1) and microclimatic parameters (air temperature, CO2) were monitored in the Skocjan Caves (Slovenia). The effects of tourist visits on the PM concentrations and the cave's microclimate are immediate and direct, but these values normalise relatively quickly. The results showed seasonal, diurnal, and spatial differences in all parameters studied. Due to the higher number of visitors, their influence on the cave's microclimate and PM10 and PM2.5 concentrations is greater in summer than in winter. The measured PM1 levels depend on the ventilation in the cave, as air transport plays an important role in their introduction into the cave. PM consists of minerals of natural origin resulting from the re-suspension of cave sediments due to strong air currents generated by the opening of the doors to tourists and their walks. The second most common influence is the anthropogenic phases originating from maintenance work in the cave, electronic devices, cave lighting and emissions from outside the cave (aerosols from the polluted Reka River, industry, traffic, gypsum waste disposal). In order to upgrade the sustainable use of the UNESCO-listed Skocjan Caves for tourism, we propose regular monitoring of PM and a detailed characterization of individual PMs and their sources, in addition to monitoring of the cave's microclimate and biology.

Combined uranium-series and electron spin resonance dating from the Pliocene fossil sites of Aves and Milo's palaeocaves, Bolt's Farm, Cradle of Humankind, South Africa.

Bolt's Farm is the name given to a series of non-hominin bearing fossil sites that have often been suggested to be some of the oldest Pliocene sites in the Cradle of Humankind, South Africa. This article reports the results of the first combined Uranium-Series and Electron Spin Resonance (US-ESR) dating of bovid teeth at Milo's Cave and Aves Cave at Bolt's Farm. Both tooth enamel fragments and tooth enamel powder ages were presented for comparison. US-ESR, EU and LU models are calculated. Overall, the powder ages are consistent with previous uranium-lead and palaeomagnetic age estimates for the Aves Cave deposit, which suggest an age between ~3.15 and 2.61 Ma and provide the first ages for Milo's Cave dates to between ~3.1 and 2.7 Ma. The final ages were not overly dependent on the models used (US-ESR, LU or EU), which all overlap within error. These ages are all consistent with the biochronological age estimate (<3.4->2.6 Ma) based on the occurrence of Stage I Metridiochoerus andrewsi. Preliminary palaeomagnetic analysis from Milo's Cave indicates a reversal takes place at the site with predominantly intermediate directions, suggesting the deposit may date to the period between ~3.03 and 3.11 Ma within error of the ESR ages. This further suggests that there are no definitive examples of palaeocave deposits at Bolt's Farm older than 3.2 Ma. This research indicates that US-ESR dating has the potential to date fossil sites in the Cradle of Humankind to over 3 Ma. However, bulk sample analysis for US-ESR dating is recommended for sites over 3 Ma.

Combining traceological analysis and ZooMS on Early Neolithic bone artefacts from the cave of Coro Trasito, NE Iberian Peninsula: Cervidae used equally to Caprinae.

Few studies have combined the analysis of use-wear traces, traceology, and the proteomic taxonomic identification method Zooarchaeology by Mass Spectrometry (ZooMS). Traceology provides information on the usage, in this case, of bone artefacts, while ZooMS allows for taxonomic identifications where diagnostic features are otherwise gone. The approaches therefore offer complementary information on bone artefacts, allowing for insights into species selection strategies in bone tool manufacture and their subsequent use. Here we present a case study of 20 bone artefacts, mainly bone points, from the Early Neolithic cave site of Coro Trasito located on the southern slope of the Central Pyrenees. Hitherto, studies on Early Neolithic bone artefacts from the Iberian Peninsula have suggested based on morphological assessments that Ovis aries/Capra hircus constituted the majority of the bone material selected for bone tool production. However, the taxonomic identification in this study suggests that, at this site, Cervidae was selected equally to that of O. aries/C. hircus. Furthermore, bone artefacts made from Cervidae specimens seem to be utilised in a wider range of artefact types compared to O. aries/C. hircus. Coro Trasito's bone artefact species composition is probably site-specific to some degree, however, morphological assessments of bone artefacts might not be representative and could be biased towards certain species. Therefore, research on bone artefacts' usage could possibly gain new insights by implementing ZooMS in combination with traceology.

Genetic bias in repeated evolution of pigment loss in cave populations of the Asellus aquaticus species complex.

Similar phenotypes can evolve repeatedly under the same evolutionary pressures. A compelling example is the evolution of pigment loss and eye loss in cave-dwelling animals. While specific genomic regions or genes associated with these phenotypes have been identified in model species, it remains uncertain whether a bias towards particular genetic mechanisms exists. An isopod crustacean, Asellus aquaticus, is an ideal model organism to investigate this phenomenon. It inhabits surface freshwaters throughout Europe but has colonized groundwater on multiple independent occasions and evolved several cave populations with distinct ecomorphology. Previous studies have demonstrated that three different cave populations utilized common genetic regions, potentially the same genes, in the evolution of pigment and eye loss. Expanding on this, we conducted analysis on two additional cave populations, distinct either phylogenetically or biogeographically from those previously examined. We generated F2 hybrids from cave × surface crosses and tested phenotype-genotype associations, as well as conducted complementation tests by crossing individuals from different cave populations. Our findings revealed that pigment loss and orange eye pigment in additional cave populations were associated with the same genomic regions as observed in the three previously tested cave populations. Moreover, the lack of complementation across all cross combinations suggests that the same gene likely drives pigment loss. These results substantiate a genetic bias in the recurrent evolution of pigment loss in this model system. Future investigations should focus on the cause behind this bias, possibly arising from allele recruitment from ancestral surface populations' genetic variation or advantageous allele effects via pleiotropy.

Ancient and remote quartzite caves as a novel source of culturable microbes with biotechnological potential.

Quartzite caves located on table-top mountains (tepuis) in the Guyana Shield, are ancient, remote, and pristine subterranean environments where microbes have evolved peculiar metabolic strategies to thrive in silica-rich, slightly acidic and oligotrophic conditions. In this study, we explored the culturable fraction of the microbiota inhabiting the (ortho)quartzite cave systems in Venezuelan tepui (remote table-top mountains) and we investigated their metabolic and enzymatic activities in relation with silica solubilization and extracellular hydrolytic activities as well as the capacity to produce antimicrobial compounds. Eighty microbial strains were isolated with a range of different enzymatic capabilities. More than half of the isolated strains performed at least three enzymatic activities and four bacterial strains displayed antimicrobial activities. The antimicrobial producers Paraburkholderia bryophila CMB_CA002 and Sphingomonas sp. MEM_CA187, were further analyzed by conducting chemotaxonomy, phylogenomics, and phenomics. While the isolate MEM_CA187 represents a novel species of the genus Sphingomonas, for which the name Sphingomonas imawarii sp. nov. is proposed, P. bryophila CMB_CA002 is affiliated with a few strains of the same species that are antimicrobial producers. Chemical analyses demonstrated that CMB_CA002 produces ditropolonyl sulfide that has a broad range of activity and a possibly novel siderophore. Although the antimicrobial compounds produced by MEM_CA187 could not be identified through HPLC-MS analysis due to the absence of reference compounds, it represents the first soil-associated Sphingomonas strain with the capacity to produce antimicrobials. This work provides first insights into the metabolic potential present in quartzite cave systems pointing out that these environments are a novel and still understudied source of microbial strains with biotechnological potential.

Old World Fruit Bats (Pteropodidae, Chiroptera) from the Pleistocene of Vietnam.

Isolated teeth of a lesser short-nosed fruit bat Cynopterus brachyotis (Müller, 1838), a fulvous fruit bat Rousettus leschenaultii (Desmarest, 1820), and a dawn bat Eonycteris spelaea (Dobson, 1871) are described from the Middle Pleistocene Tham Hai cave locality in northern Vietnam (Lang Son Province). These are the first fossil findings of the Old World fruit bats in Vietnam. The Middle Pleistocene association of Pteropodidae from the Tham Hai locality may largely reflect the composition of species that roosted in local caves.

De novo transcriptomes of cave and surface isopod crustaceans: insights from 11 species across three suborders.

Isopods are a diverse group of crustaceans, that inhabit various environments, including terrestrial, freshwater, and marine, both on the surface and in the underground. The biological mechanisms underlying their wide range of adaptations to diverse ecological niches remain elusive. In order to unravel the molecular basis of their adaptability, we generated a comprehensive RNAseq dataset comprising 11 isopod species belonging to the three different suborders: freshwater Asellota, marine, brackish and freshwater Sphaeromatidea, and terrestrial Oniscidea, with representatives from families Asellidae, Sphaeromatidae, and Trichoniscidae, respectively. Representatives of each family were collected from both cave and surface environments, representing at least three independent cave colonization events. Three biological replicates were sequenced from each species to ensure data robustness. The 11 high-quality RNAseq datasets will serve as a valuable resource for understanding cave-specific adaptations, comparative and functional genomics, ecological annotation as well as aid in conservation efforts of these non-model organisms. Importantly, transcriptomes of eight featured species have been made publicly accessible for the first time.

Disturbance of hibernating bats due to researchers entering caves to conduct hibernacula surveys.

Estimating population changes of bats is important for their conservation. Population estimates of hibernating bats are often calculated by researchers entering hibernacula to count bats; however, the disturbance caused by these surveys can cause bats to arouse unnaturally, fly, and lose body mass. We conducted 17 hibernacula surveys in 9 caves from 2013 to 2018 and used acoustic detectors to document cave-exiting bats the night following our surveys. We predicted that cave-exiting flights (i.e., bats flying out and then back into caves) of Townsend's big-eared bats (Corynorhinus townsendii) and western small-footed myotis (Myotis ciliolabrum) would be higher the night following hibernacula surveys than on nights following no surveys. Those two species, however, did not fly out of caves more than predicted the night following 82% of surveys. Nonetheless, the activity of bats flying out of caves following surveys was related to a disturbance factor (i.e., number of researchers × total time in a cave). We produced a parsimonious model for predicting the probability of Townsend's big-eared bats flying out of caves as a function of disturbance factor and ambient temperature. That model can be used to help biologists plan for the number of researchers, and the length of time those individuals are in a cave to minimize disturbing bats.

Black surfaces on ancient leather tefillin cases and straps from the Judean Desert: Macroscopic, microscopic and spectroscopic analyses.

Tefillin are Jewish ritual artifacts consisting of leather cases, containing inscribed slips, which are affixed with leather straps to the body of the tefillin practitioner. According to current Jewish ritual law, the tefillin cases and straps are to be colored black. The present study examines seventeen ancient tefillin cases discovered among the Dead Sea Scrolls in caves in the Judean Desert. All seventeen cases display grain surfaces with a very dark, nearly black appearance. We start with a hypothesis that the cases were intentionally colored black in antiquity using either a carbon-based or iron-gall-based paint or dye. The aim of this study is to test this hypothesis by subjecting these tefillin cases to a battery of examinations to assess the presence of carbon and iron used as pigments, and of organic materials which may have been used as binding agents in a paint. The tests deployed are: (1) macroscopic and microscopic analyses; (2) multispectral imaging using infrared wavelengths; (3) Raman spectroscopy; (4) Fourier transform infrared spectroscopy (FTIR); and (5) scanning electron microscope (SEM) and energy dispersive X-ray (EDX) spectroscopy. The results of these tests found no traces of carbon-based or iron-gall-based pigments, nor of organic compounds which may have served as binders in a paint. These results suggest that our posited hypothesis is unlikely. Instead, results of the SEM examination suggest it more likely that the black color on the surfaces of the tefillin cases is the result of natural degradation of the leather through gelatinization. The Judean Desert tefillin likely represent tefillin practices prior to when the rabbinic prescription on blackening tefillin was widely practiced. Our study suggests that the kind of non-blackened tefillin which the later rabbis rejected in their own times may well have been quite common in earlier times.

Gypsum Cave Biofilm Communities are Strongly Influenced by Bat- And Arthropod-Related Fungi.

The Gypsum Karst of Sorbas, Almeria, southeast Spain, includes a few caves whose entrances are open and allow the entry and roosting of numerous bats. Caves are characterized by their diversity of gypsum speleothems, such as stalactites, coralloids, gypsum crusts, etc. Colored biofilms can be observed on the walls of most caves, among which the Covadura and C3 caves were studied. The objective was to determine the influence that bat mycobiomes may have on the fungal communities of biofilms. The results indicate that the fungi retrieved from white and yellow biofilms in Covadura Cave (Ascomycota, Mortierellomycota, Basidiomycota) showed a wide diversity, depending on their location, and were highly influenced by the bat population, the guano and the arthropods that thrive in the guano, while C3 Cave was more strongly influenced by soil- and arthropod-related fungi (Ascomycota, Mortierellomycota), due to the absence of roosting bats.

The evolution of olfactory sensitivity, preferences, and behavioral responses in Mexican cavefish is influenced by fish personality.

Animals are adapted to their natural habitats and lifestyles. Their brains perceive the external world via their sensory systems, compute information together with that of internal states and autonomous activity, and generate appropriate behavioral outputs. However, how do these processes evolve across evolution? Here, focusing on the sense of olfaction, we have studied the evolution in olfactory sensitivity, preferences, and behavioral responses to six different food-related amino acid odors in the two eco-morphs of the fish Astyanax mexicanus. To this end, we have developed a high-throughput behavioral setup and pipeline of quantitative and qualitative behavior analysis, and we have tested 489 six-week-old Astyanax larvae. The blind, dark-adapted morphs of the species showed markedly distinct basal swimming patterns and behavioral responses to odors, higher olfactory sensitivity, and a strong preference for alanine, as compared to their river-dwelling eyed conspecifics. In addition, we discovered that fish have an individual 'swimming personality', and that this personality influences their capability to respond efficiently to odors and find the source. Importantly, the personality traits that favored significant responses to odors were different in surface fish and cavefish. Moreover, the responses displayed by second-generation cave × surface F2 hybrids suggested that olfactory-driven behavior and olfactory sensitivity is a quantitative genetic trait. Our findings show that olfactory processing has rapidly evolved in cavefish at several levels: detection threshold, odor preference, and foraging behavior strategy. Cavefish is therefore an outstanding model to understand the genetic, molecular, and neurophysiological basis of sensory specialization in response to environmental change.

Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery.

The ability of organisms to adapt to sudden extreme environmental changes produces some of the most drastic examples of rapid phenotypic evolution. The Mexican Tetra, Astyanax mexicanus, is abundant in the surface waters of northeastern Mexico, but repeated colonizations of cave environments have resulted in the independent evolution of troglomorphic phenotypes in several populations. Here, we present three chromosome-scale assemblies of this species, for one surface and two cave populations, enabling the first whole-genome comparisons between independently evolved cave populations to evaluate the genetic basis for the evolution of adaptation to the cave environment. Our assemblies represent the highest quality of sequence completeness with predicted protein-coding and noncoding gene metrics far surpassing prior resources and, to our knowledge, all long-read assembled teleost genomes, including zebrafish. Whole-genome synteny alignments show highly conserved gene order among cave forms in contrast to a higher number of chromosomal rearrangements when compared with other phylogenetically close or distant teleost species. By phylogenetically assessing gene orthology across distant branches of amniotes, we discover gene orthogroups unique to A. mexicanus. When compared with a representative surface fish genome, we find a rich amount of structural sequence diversity, defined here as the number and size of insertions and deletions as well as expanding and contracting repeats across cave forms. These new more complete genomic resources ensure higher trait resolution for comparative, functional, developmental, and genetic studies of drastic trait differences within a species.