Phylogeography of the ancient catfish family Diplomystidae: biogeographic, systematic, and conservation implications

Species tree analyses and speciation-based species delimitation support new species in the relict catfish family Diplomystidae and provide insights on recent glacial history in Patagonia

Diplomystidae is an early-diverged family of freshwater catfish endemic to southern South America. We have recently collected five juvenile specimens belonging to this family from the Bueno River Basin, a basin which the only previous record was a single juvenile specimen collected in 1996. This finding confirms the distribution of the family further South in northern Patagonia, but poses new questions about the origin of this population in an area with a strong glacial history. We used phylogenetic analyses to evaluate three different hypotheses that could explain the origin of this population in the basin. First, the population could have originated in Atlantic basins (East of the Andes) and dispersed to the Bueno Basin after the Last Glacial Maximum (LGM) via river reversals, as it has been proposed for other population of Diplomystes as well as for other freshwater species from Patagonia. Second, the population could have originated in the geographically close Valdivia Basin (West of the Andes) and dispersed south to its current location in the Bueno Basin. Third, regardless of its geographic origin (West or East of the Andes), the Bueno Basin population could have a longer history in the basin, surviving in situ through the LGM. In addition, we conducted species delimitation analyses using a recently developed method that uses a protracted model of speciation. Our goal was to test the species status of the Bueno Basin population along with another controversial population in Central Chile (Biobío Basin), which appeared highly divergent in previous studies with mtDNA. The phylogenetic analyses showed that the population from the Bueno Basin is more related to Atlantic than to Pacific lineages, although with a deep divergence that predated the LGM, supporting in situ survival rather than postglacial dispersal. In addition, these analyses also showed that the species D. nahuelbutaensis is polyphyletic, supporting the need for a taxonomic reevaluation. The species delimitation analyses supported two new species which are described using molecular diagnostic characters: Diplomystes arratiae sp. nov. from the Biobío, Carampangue, and Laraquete basins, maintaining D. nahuelbutaensis valid only for the Imperial Basin, and Diplomystes habitae sp. nov. from the Bueno Basin. This study greatly increases the number of species within both the family Diplomystidae and Patagonia, and contributes substantially to the knowledge of the evolution of southern South American freshwater biodiversity during its glacial history. Given the important contribution to the phylogenetic diversity of the family, we recommend a high conservation priority for both new species. Finally, this study highlights an exemplary scenario where species descriptions based only on DNA data are particularly valuable, bringing additional elements to the ongoing debate on DNA-based taxonomy.

Taxonomic and Functional Responses of Species-Poor Riverine Fish Assemblages to the Interplay of Human-Induced Stressors

The effects of human-induced stressors on riverine fish assemblages are still poorly understood, especially in species-poor assemblages such as those of temperate South American rivers. In this study we evaluated the effects of human-induced stressors on the taxonomic and functional facets of fish assemblages of two central-southern Chilean rivers: the Biobío River (flow regulated by multiple dams) and the Valdivia River (free-flowing). The study design considered reference condition, urban polluted, and urban-industrial polluted sites. To evaluate the effects of stressors on fish assemblages we assessed: (i) components of beta diversity; (ii) spatial and temporal patterns of fish structure using a multivariate approach; and (iii) functional diversity (specialization, originality, dispersion, and entropy) using linear models. We found a strong association between taxonomic and functional fish assemblage facets with a predominance of natural processes in the Valdivia River reflected in marked temporal dynamics. In contrast, the Biobío River showed a clear loss of association with seasonal pattern, and both taxonomic and functional facets appeared to respond significantly to pollution zones. Implementation of stricter environmental policies and integrated river basin management are instrumental for conserving species-poor fish assemblages in Chilean temperate rivers characterized by low functional traits redundancy.

Phylogeography and molecular species delimitation reveal cryptic diversity in Potamolithus (Caenogastropoda: Tateidae) of the southwest basin of the Andes

The species of the genus Potamolithus inhabiting the southwestern basin of the Andes are difficult to distinguish due to small size and similar shell morphology. Only Potamolithus australis and Potamolithus santiagensis have been traditionally recognized in this region, but the occurrence of several morphologically similar undescribed populations could increase the regional richness. Here we delimit described and potentially undescribed cryptic species of the genus using partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Network analysis and diversity indices inferred six highly differentiated haplogroups, many of them sympatric and widespread in the study area. Phylogeographic analyses suggest a scenario of recent diversification and the occurrence of multiple refuges during the successive Pleistocene glaciations. Phylogenetic analysis also recovered six major clades that showed no relationship with physiography. Species delimitation analyses consistently recognized three or four candidate species apart from P. australis and P. santiagensis. Divergence times indicate that speciation of Chilean Potamolithus began at the end of the Pliocene, probably driven by climatic rather than geographic events. Considering the high inter- and intra-basin genetic diversity, conservation efforts should be focused on protecting sympatric taxa in the basins with the highest species richness.

Evolving in islands of mud: old and structured hidden diversity in an endemic freshwater crayfish from the Chilean hotspot

Parastacus is a genus of South American freshwater crayfishes disjunctively distributed in southern Chile, Northern Argentina, Uruguay and Southeastern Brazil. Parastacus pugnax is a Chilean endemic distributed along 700 km of latitude in central-southern Chile from the Pacific coast to the Andean piedmont, which is intensively captured for consumption for local communities. Considering the habitat (wet meadows) and natural history (primary burrower, non-migrant) of the species, we tested a hypothesis of highly structured genetic diversity using mtDNA of 465 specimens gathered at 56 localities across the species range. The crown age of P. pugnax was estimated at 38 Ma, predating the main Andean uplift. The genetic variation of P. pugnax is large and geographically structured. In some cases, genetic groups do not match basin limits, suggesting a previous to current dynamic of basin evolution. The uncovered intraspecific main lineages have different demographic histories. A latitudinal cline in past effective population size reduction suggests environmental singularities with a glacial effect in the southern populations. We suggest adding morphologic and more genetic data in order to assess species limits. Our results contribute to improve future conservation actions for this taxon, providing basic information to delimit conservation units.

Connection, isolation and reconnection: Quaternary climatic oscillations and the Andes shaped the phylogeographical patterns of the Patagonian bee Centris cineraria (Apidae)

The joint effect of the Andes as a geographical barrier and the Quaternary glaciations as promoters of genetic divergence remains virtually unexplored in southern South America. To help fill this knowledge gap, in this study we investigated the demographic history of Centris cineraria, a solitary bee mainly distributed in Patagonia. We used mitochondrial and nuclear markers and performed phylogeographical and dating analyses, adjusted spatio-temporal diffusion and species distribution models, and used Approximate Bayesian Computation to identify likely historical demographic scenarios. Our results revealed that during glacial periods the Andes represented a barrier due to the extent of the ice-sheets and the occurrence of unsuitable habitats, while interglacials allowed for gene flow across the Andes. Secondary contact between previously isolated lineages was evident across at least two low-altitude Andean areas, the northern one being a putative glacial refugium. Our findings also suggest that C. cineraria has persisted in situ in four periglacial refugia located along a north–south transect, congruent with the maximum extent of the ice sheet during the Greatest Patagonian Glaciation. As the first phylogeographical study of Patagonian insects, our work reveals that the interaction between Quaternary climatic oscillations and the Andes as a barrier was the main driver of the spatial and demographic history of C. cineraria.

Contrasting evolutionary responses in two co-distributed species of Galaxias (Pisces, Galaxiidae) in a river from the glaciated range in Southern Chile

Life-history traits are among the most important factors affecting population abundance and genetic diversity of species. Here, we analysed the genetic patterns of two Galaxias species with different life-history traits to investigate how these biological differences impacted their evolution in the Valdivia River basin, Southern Chile. We analysed mitochondrial DNA (mtDNA) sequences from 225 individuals of Galaxias maculatus and 136 of G. platei to compare patterns of genetic diversity, structure and demographic growth across the basin. Galaxias maculatus presented higher genetic diversity and higher genetic structure than G. platei. Demographic analyses showed G. maculatus kept a higher population size over time, with a signal of demographic expansion in the last 250 kyr. Whereas Galaxias platei, exhibited lower, but constant population size over time. Furthermore, haplotype networks revealed higher lineage diversity in G. maculatus with a tendency to occupy different areas of the basin. Coalescent simulations ruled out that genetic differences between species could be explained by stochastic processes (genetic drift), suggesting species-specific biological differences as responsible for the observed genetic differences. We discuss how differences in life-history traits and past glaciations interact to shape the evolutionary history of the two Galaxias species.

Multiple drainage reversal episodes and glacial refugia in a Patagonian fish revealed by sequenced microsatellites

The rise of the southern Andes and the Quaternary glacial cycles influenced the landscape of Patagonia, affecting the phylogeographic and biogeographic patterns of its flora and fauna. Here, we examine the phylogeography of the freshwater fish, Percichthys trucha, using 53 sequenced microsatellite DNA markers. Fish (n= 835) were collected from 16 river systems (46 locations) spanning the species range on both sides of the Andes. Eleven watersheds drain to the Pacific, five of which are trans-Andean (headwaters east of Andes). The remaining five drainages empty into the Atlantic. Three analytical approaches (neighbour-joining tree, hierarchical AMOVAs, Structure) revealed evidence of historic drainage reversals: fish from four of the five trans-Andean systems (Puelo, Futalaufquen/Yelcho, Baker, Pascua) exhibited greater genetic similarity with Atlantic draining systems than with Pacific systems with headwaters west of Andes. Present-day drainage (Pacific versus Atlantic) explained only 5% of total genetic variance, while ancestral drainage explained nearly 27% of total variance. Thus, the phylogeographic structure of P. trucha is consistent with episodes of drainage reversal in multiple systems and suggests a major role for deglaciation in the genetic and indeed the geographical distribution of P. trucha in Patagonia. The study emphasizes the significant role of historical processes in the current pattern of genetic diversity and differentiation in a fish from a southern temperate region.

Revalidation of the Argentinian pouched lamprey Geotria macrostoma (Burmeister, 1868) with molecular and morphological evidence

BACKGROUND

The Argentinian pouched lamprey, classified as Petromyzon macrostomus Burmeister, 1868 was first described in 1867 in De La Plata River, in Buenos Aires, Argentina, and subsequently recorded in several rivers from Patagonia. Since its original description, the validity of P. macrostomus was questioned by several ichthyologists and 36 years after its original discovery it was considered a junior synonym of Geotria australis Gray, 1851. For a long time, the taxonomic status of G. australis has been uncertain, largely due to the misinterpretations of the morphological alterations that occur during sexual maturation, including the arrangement of teeth, size and position of fins and cloaca, and the development of an exceptionally large gular pouch in males. In this study, the taxonomic status of Geotria from across the "species" range was evaluated using both molecular analysis and examination of morphological characteristics.

METHODOLOGY/PRINCIPAL FINDINGS

Phylogenetic and species delimitation analyses based on mitochondrial DNA sequences of Cytochrome b (Cyt b) and Cytochrome C Oxidase Subunit 1 (COI) genes, along with morphological analysis of diagnostic characters reported in the original descriptions of the species were used to assess genetic and morphological variation within Geotria and to determine the specific status of the Argentinian lamprey. These analyses revealed that Geotria from Argentina constitutes a well differentiated lineage from Chilean and Australasian populations. The position of the cloaca and the distance between the second dorsal and caudal fins in sub-adult individuals, and at previous life stages, can be used to distinguish between the two species. In addition, the genetic distance between G. macrostoma and G. australis for the COI and Cyt b mitochondrial genes is higher than both intra- and inter-specific distances reported for other Petromyzontiformes.

CONCLUSIONS/SIGNIFICANCE

Our results indicate that the Argentinian pouched lamprey, found along a broad latitudinal gradient on the south-west Atlantic coast of South America, should be named as Geotria macrostoma (Burmeister, 1868) and not as G. australis Gray 1851, returning to its earliest valid designation in Argentina. Geotria macrostoma can now be considered as the single lamprey species inhabiting Argentinian Patagonia, with distinct local adaptations and evolutionary potential. It is essential that this distinctiveness is recognized in order to guide future conservation and management actions against imminent threats posed by human actions in the major basins of Patagonia.

A Century after! Rediscovery of the ancient catfish Diplomystes Bleeker 1858 (Siluriformes: Diplomystidae) in coastal river basins of Chile and its implications for conservation

ABSTRACT The ancient catfish family Diplomystidae, with seven species endemic to rivers of southern South America, represents one of the oldest branches of the diverse order Siluriformes. With most species endangered, new reports of these species become extremely valuable for conservation. Currently, it is assumed that Diplomystes species inhabit only Andean (large) basins, and that they are extinct from coastal (small) basins from which their presence have not been recorded since 1919. Here, we document new records of the family Diplomystidae in the Laraquete and Carampangue basins, two coastal basins from the Nahuelbuta Coast Range, Chile, with no previous reports. This finding represents the rediscovery of the genus in coastal basins in more than a Century. Based on analysis of mitochondrial DNA sequences, the collected specimens were found to be closely related to Diplomystes nahuelbutaensis from the Andean Biobío Basin, but sufficiently differentiated to suggest that coastal basin populations are a different management unit. These populations are important because, contrary to previous thoughts, they prove these catfish can survive in small river networks, providing unique opportunities for research and conservation. The conservation category of Critically Endangered (CE) is recommended for the populations from the Laraquete and Carampangue basins.

Movement patterns and home range in Diplomystes camposensis (Siluriformes: Diplomystidae), an endemic and threatened species from Chile

ABSTRACT We document movement patterns and home range of Diplomystes camposensis, an endemic and threatened freshwater catfish from Chile. We tracked the movements of seven individuals of different body size (13.5 to 19 cm SL) using portable radio telemetry equipment to investigate movement patterns in relation to day/night activity and habitat use in the San Pedro River (Valdivia Basin). Tracked movements and model-based analyses revealed that D. camposensis has a large home range and high mobility. The average home range was 0.068163 ± 0.033313 km2, and the average area of higher activity was 0.005646 ± 0.011386 km2. The mean linear home range was 387.4 m. The results also showed that movements were longer during the night, supporting nocturnal habits. Movements tended to be in an upstream direction for some individuals, although these differences were not significant when data was pooled. Large home range and movements suggest that the species may require large river areas to meet ecological demands, an aspect that could be severely affected by fragmentation. These results, along with previously published genetic data, suggest that the conservation of D. camposensis would be seriously threatened by hydromorphological alterations (e.g. lack of connectivity), such as those resulting from dam building.

Understanding morphological variability in a taxonomic context in Chilean diplomystids (Teleostei: Siluriformes), including the description of a new species

Following study of the external morphology and its unmatched variability throughout ontogeny and a re-examination of selected morphological characters based on many specimens of diplomystids from Central and South Chile, we revised and emended previous specific diagnoses and consider Diplomystes chilensis, D. nahuelbutaensis, D. camposensis, and Olivaichthys viedmensis (Baker River) to be valid species. Another group, previously identified as Diplomystes sp., D. spec., D. aff. chilensis, and D. cf. chilensis inhabiting rivers between Rapel and Itata Basins is given a new specific name (Diplomystes incognitus) and is diagnosed. An identification key to the Chilean species, including the new species, is presented. All specific diagnoses are based on external morphological characters, such as aspects of the skin, neuromast lines, and main lateral line, and position of the anus and urogenital pore, as well as certain osteological characters to facilitate the identification of these species that previously was based on many internal characters. Diplomystids below 150 mm standard length (SL) share a similar external morphology and body proportions that make identification difficult; however, specimens over 150 mm SL can be diagnosed by the position of the urogenital pore and anus, and a combination of external and internal morphological characters. According to current knowledge, diplomystid species have an allopatric distribution with each species apparently endemic to particular basins in continental Chile and one species (O. viedmensis) known only from one river in the Chilean Patagonia, but distributed extensively in southern Argentina.

Mimics here and there, but not everywhere: Müllerian mimicry in Ceroglossus ground beetles?

The ground beetle genus Ceroglossus contains co-distributed species that show pronounced intraspecific diversity in the form of geographical colour morphs. While colour morphs among different species appear to match in some geographical regions, in others, there is little apparent colour matching. Mimicry is a potential explanation for covariation in colour patterns, but it is not clear whether the degree of sympatric colour matching is higher than expected by chance given the obvious mismatches among morphs in some regions. Here, we used reflectance spectrometry to quantify elytral coloration from the perspective of an avian predator to test whether colour similarity between species is, indeed, higher in sympatry. After finding no significant phylogenetic signal in the colour data, analyses showed strong statistical support for sympatric colour similarity between species despite the apparent lack of colour matching in some areas. We hypothesize Müllerian mimicry as the responsible mechanism for sympatric colour similarity in Ceroglossus and discuss potential explanations and future directions to elucidate why mimicry has not developed similar levels of interspecific colour resemblance across space.

Freshwater fishes of Patagonia: conservation and fisheries

The absence of much literature on the Patagonian fish fauna in comparison with that of the neotropics, has previously been blamed on its poor species diversity. Knowledge of the fishes of Patagonia, however, rose sharply at the beginning of the present century, allowing for an understanding of the complex biogeographical history that has led to the present diversity and distribution patterns. There are several new and potential threats to biodiversity and conservation of Patagonian fishes, such as the introduction of exotic species, damming, climate change and changes geared to safeguard economic interests, often acting synergistically. A great amount of new information is now available and the aim of the present review is to articulate this knowledge in a comprehensive way in order to aid in the development of tools to face the increasing challenges posed by environmental change and human activity. Knowledge about fishes of Patagonia has grown at the same time as human actions, and presence.

Low Genetic Diversity in Diplomystes camposensis, an Endemic and Endangered Catfish from South Chile

Carlos P. Muñoz-Ramírez, Evelyn Habit, Peter J. Unmack, Jerald B. Johnson, and Pedro F. Victoriano (2016) Despite the fundamental importance of the family Diplomystidae for understanding catfish evolution, its species are poorly known and most of them endangered. Diplomystes camposensis, restricted to a single river basin in southern Chile, is perhaps the most vulnerable species due to its small geographic range and imminent habitat alterations by dam constructions. Using mitochondrial DNA sequences, we describe the genetic diversity across its entire distribution in the Valdivia basin and test hypotheses related to the impact of glacial cycles on the genetic diversity and structure. We found that Diplomystes camposensis has low genetic diversity and structure across the entire Valdivia basin along with a pattern of decreasing nucleotide and haplotype diversity from West to East. Demographic analyses showed evidence of population expansion in agreement with the glaciated history of the basin. Analyses of population structure showed no evidence of population subdivision. However, coalescent analyses indicated that very recent subdivision (in the last 50 years) cannot be ruled out. Low genetic diversity and genetic structure across the entire basin suggest that the species might be highly vulnerable to habitat fragmentation. Thus, the imminent construction of hydropower dams represents a serious threat to its conservation. Our results suggest that the low genetic diversity can be the product of the glaciated history of the basin, although the influence of species-specific biological traits may also add to this condition. Despite the overall low genetic diversity, higher diversity was found in the central portion of the basin suggesting high priority of conservation for this area as it might be used as a source population in case translocations are required among potential management plans.