We used molecular evidence to examine the roles that vicariance mechanisms (mountain-building and drainage changes during the Pleistocene) have played in producing phylogeographical structure within and among South American fish species of the temperate perch family Percichthyidae. The percichthyids include two South American genera, Percichthys and Percilia, each containing several species, all of which are endemic to southern Argentina and Chile (Patagonia). Maximum-likelihood phylogenies constructed using mitochondrial DNA (mtDNA) control region haplotypes and nuclear GnRH3-2 intron allele sequences support the current taxonomy at the genus level (both Percichthys and Percilia form strongly supported, monophyletic clades) but indicate that species-level designations need revision. Phylogeographical patterns at the mtDNA support the hypothesis that the Andes have been a major barrier to gene flow. Most species diversity occurs in watersheds to the west of the Andes, together with some ancient divergences among conspecific populations. In contrast, only one species (Percichthys trucha) is found east of the Andes, and little to no phylogeographical structure occurs among populations in this region. Mismatch analyses of mtDNA sequences suggest that eastern populations last went through a major bottleneck c. 188 000 bp, a date consistent with the onset of the penultimate and largest Pleistocene glaciation in Patagonia. We suggest that eastern populations have undergone repeated founder-flush events as a consequence of glacial cycles, and that the shallow phylogeny is due to mixing during recolonization periods. The area of greater diversity west of the Andes lies outside the northern limit of the glaciers. mtDNA mismatch analysis of the genus Percilia which is restricted to this area suggests a long-established population at equilibrium. We conclude that patterns of genetic diversity in these South American genera have been primarily influenced by barriers to gene flow (Andean orogeny, and to a lesser extent, isolation in river drainages), and by glacial cycles, which have resulted in population contraction, re-arrangement of some watersheds, and the temporary breakdown of dispersal barriers among eastern river systems.

We employed DNA sequence variation at two mitochondrial (control region, COI) regions from 212 individuals of Galaxias platei (Pisces, Galaxiidae) collected throughout Patagonia (25 lakes/rivers) to examine how Andean orogeny and the climatic cycles throughout the Quaternary affected the genetic diversity and phylogeography of this species. Phylogenetic analyses revealed four deep genealogical lineages which likely represent the initial division of G. platei into eastern and western lineages by Andean uplift, followed by further subdivision of each lineage into separate glacial refugia by repeated Pleistocene glacial cycles. West of the Andes, refugia were likely restricted to the northern region of Patagonia with small relicts in the south, whereas eastern refugia appear to have been much larger and widespread, consisting of separate northern and southern regions that collectively spanned most of Argentinean Patagonia. The retreat of glacial ice following the last glacial maximum allowed re-colonization of central Chile from nonlocal refugia from the north and east, representing a region of secondary contact between all four glacial lineages. Northwestern glacial relicts likely followed pro-glacial lakes into central Chilean Patagonia, whereas catastrophic changes in drainage direction (Atlantic --> Pacific) for several eastern palaeolakes were the likely avenues for invasions from the east. These mechanisms, combined with evidence for recent, rapid and widespread population growth could explain the extensive contemporary distribution of G. platei throughout Patagonia.

Changes in lake and stream habitats during the growth and retreat of Pleistocene glaciers repeatedly altered the spatial distributions and population sizes of the aquatic fauna of the southern Andes. Here, we use variation in mtDNA control region sequences to infer the temporal dynamics of two species of southern Andean fish during the past few million years. At least five important climate events were associated with major demographic changes: (i) the widespread glaciations of the mid-Pliocene (c. 3.5 Ma); (ii) the largest Patagonian glaciation (1.1 Ma); (iii) the coldest Pleistocene glaciation as indicated by stacked marine delta(18)O (c. 0.7 Ma); (iv) the last southern Patagonian glaciation to reach the Atlantic coast (180 ka); and (v) the last glacial maximum (LGM, 23-25,000 years ago). The colder-water inhabitant, Galaxias platei, underwent a strong bottleneck during the LGM and its haplotype diversity coalesces c. 0.7 Ma. In contrast, the more warm-adapted and widely distributed Percichthys trucha showed continuous growth through the last two glacial cycles but went through an important bottleneck c. 180,000 years ago, at which time populations east of the Andes may have been eliminated. Haplotype diversity of the most divergent P. trucha populations, found west of the Andes, coalesces c. 3.2 Ma. The demographic timelines obtained for the two species thus illustrate the continent-wide response of aquatic life in Patagonia to climate change during the Pleistocene, but also show how differing ecological traits and distributions led to distinctive responses.

BackgroundThe dynamic geological and climatic histories of temperate South America have played important roles in shaping the contemporary distributions and genetic diversity of endemic freshwater species. We use mitochondria and nuclear sequence variation to investigate the consequences of mountain barriers and Quaternary glacial cycles for patterns of genetic diversity in the diadromous fish Galaxias maculatus in Patagonia (~300 individuals from 36 locations).ResultsContemporary populations of G. maculatus, east and west of the Andes in Patagonia, represent a single monophyletic lineage comprising several well supported groups. Mantel tests using control region data revealed a strong positive relationship when geographic distance was modeled according to a scenario of marine dispersal. (r = 0.69, P = 0.055). By contrast, direct distance between regions was poorly correlated with genetic distance (r = -0.05, P = 0.463). Hierarchical AMOVAs using mtDNA revealed that pooling samples according to historical (pre-LGM) oceanic drainage (Pacific vs. Atlantic) explained approximately four times more variance than pooling them into present-day drainage (15.6% vs. 3.7%). Further post-hoc AMOVA tests revealed additional genetic structure between populations east and west of the Chilean Coastal Cordillera (coastal vs. interior). Overall female effective population size appears to have remained relatively constant until roughly 0.5 Ma when population size rapidly increased several orders of magnitude [100× (60×-190×)] to reach contemporary levels. Maximum likelihood analysis of nuclear alleles revealed a poorly supported gene tree which was paraphyletic with respect to mitochondrial-defined haplogroups.ConclusionsFirst diversifying in the central/north-west region of Patagonia, G. maculatus extended its range into Argentina via the southern coastal regions that join the Pacific and Atlantic oceans. More recent gene flow between northern populations involved the most ancient and most derived lineages, and was likely facilitated by drainage reversal(s) during one or more cooling events of the late Pleistocene. Overall female effective population size represents the end result of a widespread and several hundred-fold increase over approximately 0.5 Ma, spanning several climatic fluctuations of the Pleistocene. The minor influence of glacial cycles on the genetic structure and diversity of G. maculatus likely reflects the access to marine refugia during repeated bouts of global cooling. Evidence of genetic structure that was detected on a finer scale between lakes/rivers is most likely the result of both biological attributes (i.e., resident non-migratory behavior and/or landlocking and natal homing in diadromous populations), and the Coastal Cordillera as a dispersal barrier.

Aim Globally, one of the major threats to the integrity of native faunas is the loss of biodiversity that can result from the introduction of exotics. Here we document recent changes in the distribution of five common fish species that are linked to introductions in Chile.Location Chile from 28°S to 54°S. MethodsWe assess the extent of changes in distribution of galaxiid species by comparing their historical and current distributions based on the results of the most extensive survey of freshwater fishes in Chile to date, a range that encompasses the full latitudinal and elevational range of the Galaxiidae in Chile. We test for relationships of the distributions and abundances of native fishes with the incidence of introduced species. ResultsThe latitudinal range of Galaxias maculatus has declined by 26%, and most of this reduction has occurred in the northern part of its range. Aplochiton taeniatus and Brachygalaxias bullocki have experienced reductions (8-17% loss) in total drainage area occupied, and they have disappeared from, or are now extremely difficult to find, in latitudes 36°to 41°S, coincidently with areas of urban growth and intense economic activities. The distribution of Galaxias platei has, instead, increased considerably. In northern basins, G. maculatus has apparently been replaced by an introduced poeciliid Gambusia sp. High-elevation systems remain dominated by native Galaxias platei, whereas systems at intermediate elevations, especially rivers, are now dominated by introduced salmonids. Within drainages, native galaxiids remain abundant where exotic salmonid abundance is low. Main conclusionsWe suggest that negative interactions between introduced and native fish are responsible for some of the range reductions among Galaxiidae in Chile. The severity of the impacts varies with latitude and altitude and is probably related to temperature. The effects of Gambusia are restricted to warmer systems. Native fish also appear to have found temperature refugia from salmonids; impacts are low in the warmer northern and coastal systems, as well as in high-altitude relatively cold systems. Native fish also appear less vulnerable to salmonids in lakes than in rivers. This study identifies watersheds critical for the conservation of biodiversity within the Galaxiidae.

Hydropeaking dam operation and water extractions for irrigation have been broadly stated as alterations to natural flow regimes, which have also been noticed in the Biobío Watershed, in Central Chile, since 1996. In the Biobío River, most of native fish species are endemic and very little is known about them. Their ecological and social values have never been estimated, and there is lack of information about their habitat preferences. Furthermore, changes on fish habitat availability due to natural and/or man-made causes have not been evaluated. In this study, eight native fish species, in a representative reach of the Biobío River, were studied and their preferred habitats were surveyed and characterized. A hydrodynamic model was built and linked to the fish habitat simulation model CASiMiR. Fuzzy rules and fuzzy sets were developed for describing habitat preference of the native fish species. CASiMiR was then used to simulate how physical habitat conditions vary due to flow control (i.e. upstream dams). Results show how overall habitat quality, expressed as weighted usable area (WUA) and hydraulic habitat suitability (HHS), changes and fluctuates due to the dam operation and how the daily hydropeaking is influencing quantity, quality and location of different habitats. The study suggests that the analysed fish are highly susceptible to flow control, as dams are currently operated, and fish habitat improvement suggestions are proposed.

Recently, we have gained the opportunity to obtain very high-resolution imagery and topographic data of rivers using drones and novel digital photogrammetric processing techniques. The high-resolution outputs from this method are unprecedented, and provide the opportunity to move beyond river habitat classification systems, and work directly with spatially explicit continuums of data. Traditionally, classification systems have formed the backbone of physical river habitat monitoring for their ease of use, rapidity, cost efficiency, and direct comparability. Yet such classifications fail to characterize the detailed heterogeneity of habitat, especially those features which are small or marginal. Drones and digital photogrammetry now provide an alternative approach for monitoring river habitat and hydromorphology, which we review here using two case studies. First, we demonstrate the classification of river habitat using drone imagery acquired in 2012 of a 120 m section of the San Pedro River in Chile, which was at the technological limits of what could be achieved at that time. Second, we review how continuums of data can be acquired, using drone imagery acquired in 2016 from the River Teme in Herefordshire, England. We investigate the precision and accuracy of these data continuums, highlight key current challenges, and review current best practices of data collection, processing, and management. We encourage further quantitative testing and field applications. If current difficulties can be overcome, these continuums of geomorphic and hydraulic information hold great potential for providing new opportunities for understanding river systems to the benefit of both river science and management. © 2017 The Authors. WIREs Water published by Wiley Periodicals, Inc. How to cite this article:WIREs Water 2017, 4:e1222. doi: 10.1002/wat2.1222 INTRODUCTIONM onitoring the spatial and temporal variation in physical river parameters is important for understanding and improving habitat quality and distribution, especially with respect to the potential impacts of climate change. [1][2][3] Remote sensing based methods have long played a role in surveying and This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.monitoring physical river habitat and hydromorphology. 4,5 A growing body of literature demonstrates the use of digital photogrammetry 6,7 and spectraldepth correlations [8][9][10] for quantifying fluvial topography and flow depth, the computation of image textural variables and roughness of terrestrial laser scanner point clouds for quantifying fluvial substrate size, [11][12][13][14][15] and the use of multispectral imagery for mapping hydrogeomorphic units. 16 These developments have made important contributions to our abilities to map and measure physical river habitat parameters. However, few of these approaches are ca...

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