diversity Article Diversity of Brazilian Troglobitic Fishes: Models of Colonization and Differentiation in Subterranean Habitats Eleonora Trajano † Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil; [email protected] † Current address: Rua Nobre Vieira, 364, São Paulo 05587-180, Brazil. Abstract: The Brazilian subterranean ichthyofauna is distinguished worldwide by high taxonomic and phylogenetic diversity, involving at least 30 exclusively subterranean (troglobitic) lineages. This may be explained by high native epigean diversty, allied to opportunities for colonization and genetic isolation in the subterranean biotope, thence originating troglobites. An updated list of Brazilian troglobitic lineages and a review of previous hypotheses on modes of colonization and differentiation in subterranean habitats are presented with fresh data and models. Colonization of and isolation in the subterranean biotope are independent processes, usually separate over time. Access to subterranean habitats varies from the (sub)horizontal through sinkholes and resurgences of base-level streams and vadose tributaries to the vertical by shallow and deep phreatic waters through the hyporheic zone. Phenotypic differentiation of subterranean populations originating troglobites may be achieved by various, non-mutually exclusive modes of genetic isolation, e.g., directly in base-level streams and upper tributaries through the extinction of epigean populations, due to drainage discontinuation in dry paleoclimatic phases (or by other causes), by topographic isolation due to a lowering of the regional base level and karst catchments or by parapatric differentiation. Differentiation may also be a consequence of transition from lotic to lentic waters in flooded caves, Citation: Trajano, E. Diversity of and from shallow to deep phreatic habitats. Brazilian Troglobitic Fishes: Models of Colonization and Differentiation in Keywords: subterranean fishes; evolution; origin of troglobites; Brazil; subterranean biology Subterranean Habitats. Diversity 2021, 13, 106. https://doi.org/10.3390/ d13030106 1. Introduction Academic Editors: Michael Wink and Raoul Manenti Subterranean (subsurface) fishes are excellent models for studies of comparative evo- lution. Due to the high taxonomic, ecological and morphological diversity, the Brazilian Received: 17 February 2021 ichthyofauna is particularly suitable for this. So far, more than 30 troglobitic fish lin- Accepted: 22 February 2021 eages (exclusively subterranean source populations—[1]) have been recognized, including Published: 1 March 2021 21 valid species described as troglobitic. Mattox et al. [2] presented a list of Brazilian troglo- bitic and troglophilic fishes (source populations in both subsurface and surface habitats, Publisher’s Note: MDPI stays neutral genetically connected by mutually commuting individuals [1]). This was subsequently with regard to jurisdictional claims in updated by Gallão and Bichuette [3] for the troglobites. Nonetheless, the discovery and published maps and institutional affil- description of novel subterranean fishes continue. Troglobites usually, but not necessarily, iations. present troglomorphisms, i.e., autapomorphies related to isolation and specialization to the subterranean life. The most frequent are the regression of visual structures and dark cutaneous pigmentation ([1,4], among others). Brazilian species of subterranean fishes are allocated into 12 genera, seven families Copyright: © 2021 by the author. and three orders, thus configuring relatively high phylogenetic diversity. In comparison, Licensee MDPI, Basel, Switzerland. the 78 species (in 20 genera) reported as troglomorphic for China [5], which has a larger This article is an open access article total karst area, are distributed in four families and two orders, and two genera concentrate distributed under the terms and ca. 70% if this species richness [5]. The troglobitic ichthyofauna from Mexico is less conditions of the Creative Commons phylogenetically diverse at lower taxonomic levels, but more so at the higher levels: the Attribution (CC BY) license (https:// 11 species recorded by Proudlove [6] are distributed in six genera and families belonging creativecommons.org/licenses/by/ to five orders. The elevated lower and higher phylogenetic levels of Brazilian subterranean 4.0/). Diversity 2021, 13, 106. https://doi.org/10.3390/d13030106 https://www.mdpi.com/journal/diversity Diversity 2021, 13, 106 2 of 19 ichthyofauna, both troglobites and troglophiles, could originate from a highly diversified and rich epigean (surface) fauna providing a large array of potential colonizers of hypogean habitats, thereby giving rise to troglophilic populations. Furthermore, karst fragmentation and paleoclimatic fluctuations would favor the isolation of these populations, thence originating troglobites. The extensive coastal karst of Mexico, propitious for marine colonizer adaptation and isolation in freshwaters ideal for originating troglobites [7], among others, explains the higher level of phylogenetic diversity. Only small Brazilian karst areas to the north of Bahia State and close enough to the current coastal line are appropriate for this. Epicontinental seas dating to the Early Cretaceous are too ancient [8]. Regular studies of Brazilian subterranean ichthyofauna started in the early 1980s, initially focusing on the blind catfish Pimelodella kronei from the Iporanga, Alto Ribeira karst area ([9–12], among others), with focus on taxonomy, morphology, ecology and behavior. Representative lineages of several genera have also been studied in detail see [13–18]. Hypotheses based on paleoclimatic models (isolation by extinction of epigean relatives during unfavorable phases—[19]) have been proposed to explain the origin of P. kronei [20] and Rhamdiopsis krugi from northeastern Brazil [21]. Topographic models were proposed for P. spelaea [22] and Ituglanis spp. [23] from the São Domingos karst area, Central Brazil. I hereby present a review of the data from these studies, prior to discussing previous hypotheses on forms of colonization and speciation in the various subterranean habitats generating troglobitic fish species in Brazil. With the aim of explaining the high diversity of subterranean ichthyofauna, former and new data were analyzed, as a means of generating novel proposals. Robust models with high predictive potential are scientifically relevant as possible indicators of areas for further research, as well as being the means of testing the generality of hypotheses. Moreover, species presenting intra-population variability, the case of most Brazilian troglobitic fishes [15], are highly propitious for testing hypotheses on the evolution (regression) of characters/features. Models emerge from the detection of congruent attributed patterns. I compared data on geographic distribution, degree of troglomorphism (primarily eye and pigmentation regression), habitat type and body shape, including hypotheses on apomorphic states related to specialized habitats and distribution. Data are mostly from both our studies and those of collaborators (sometimes unpublished). 2. Taxonomic Considerations Herein, I embraced the idea of species as separately evolving metapopulation lineages, which is the common element shared by the contemporary alternative species concepts [24]. As regards species delimitation (a separate issue) among the properties acquired by lineages during the course of divergence, viz., intrinsic reproductive isolation, monophyly and diagnosability, I followed de Queiroz [24], for whom diagnosability, i.e., the presence of an exclusive set of character states (not necessarily autapomorphic), widely used by taxonomists, is the most practical operational criterion when assessing lineage separation. Based on the comparative method, it facilitates recognition of subterranean-restricted species [1]. Due to variations in taxonomic approaches and the application of Schiner–Racovitza classification, comparisons of subterranean taxonomic richness between different coun- tries must proceed with caution. Furthermore, when differences do occur in the degree of regional richness (rich vs. poor) [25], discrimination in total diversity (trogloxenes + troglophiles + troglobites), and specifically among troglobites themselves, should be- come apparent. There are several instances of cryptic lineages within species described by traditional morphological taxonomy. Morphological stasis in highly specialized ancient lineages may be a consequence of life in a stable phreatic environment over a long period, viz., the Brazilian troglobitic fishes Rhamdiopsis krugi and Trichomycterus dali. On the other hand, in the case of isolation over relatively shorter periods (“recent troglobites”), with contemporary specialization to subterranean habitats, morphological differentiation may Diversity 2021, 13, 106 3 of 19 progress faster than molecular marker evolution, due to the accumulation of mutations in structural gene systems, viz., Ancistrus cryptophthalmus [26,27]. Due to the emphasis on Red Lists as a basis for defining protection policies, and the tendency to include therein only nominal species from traditional taxonomy, as diagnosed by morphological characters, the case of Brazil, thence leading to legal failure in protect- ing genetically distinct lineages without discernible morphological differences (cryptic diversity), the aforementioned issues pose important consequences for conservation. 3. Diversity among Brazilian Subterranean