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The Neotropical region hosts 4225 freshwater fish species, ranking first among the world's most diverse regions for freshwater fishes. Our NEOTROPICAL FRESHWATER FISHES data set is the first to produce a large-scale Neotropical freshwater fish inventory, covering the entire Neotropical region from Mexico and the Caribbean in the north to the southern limits in Argentina, Paraguay, Chile, and Uruguay. We compiled 185,787 distribution records, with unique georeferenced coordinates, for the 4225 species, represented by occurrence and abundance data. The number of species for the most numerous orders are as follows: Characiformes (1289), Siluriformes (1384), Cichliformes (354), Cyprinodontiformes (245), and Gymnotiformes (135). The most recorded species was the characid Astyanax fasciatus (4696 records). We registered 116,802 distribution records for native species, compared to 1802 distribution records for nonnative species. The main aim of the NEOTROPICAL FRESHWATER FISHES data set was to make these occurrence and abundance data accessible for international researchers to develop ecological and macroecological studies, from local to regional scales, with focal fish species, families, or orders. We anticipate that the NEOTROPICAL FRESHWATER FISHES data set will be valuable for studies on a wide range of ecological processes, such as trophic cascades, fishery pressure, the effects of habitat loss and fragmentation, and the impacts of species invasion and climate change. There are no copyright restrictions on the data, and please cite this data paper when using the data in publications.

Ecological interactions among multiple invaders can aggravate their effects on invaded systems. Many salmonids including rainbow trout Oncorhynchus mykiss and Chinook salmon O. tshawytscha have established naturalized populations and co-occur in rivers worldwide. Predation of eggs and juveniles has been well documented among salmonids in their native range in the Northern Hemisphere. It has been unclear to what extent these interactions exist in invaded rivers of the Patagonia. Here, we report and quantify rainbow trout predation of Chinook salmon eggs in the Cisnes River Basin, southern Chile. We used hook and line angling to sample rainbow trout (n = 80) around salmon spawning areas before, during, and after the spawning season of Chinook salmon. Stomach contents obtained during two consecutive years show consistent evidence that rainbow trout opportunistically prey on Chinook salmon eggs. Salmon eggs occurred in 75 and 50% of the trout stomachs analyzed in 2019 and 2020, respectively. The number of salmon eggs (mean ± SD) per trout stomach ranged between 17.95 ± 24.29 in 2019 and 7.45 ± 12.90 in 2020. We assumed that consumed eggs were primarily non-viable or would have had low probabilities of survival suggesting a synergistic interaction between rainbow trout and Chinook salmon. Our findings provide baseline information that contribute to demographic studies and the management of invasive salmonids in rivers of this region and elsewhere.

Thouarella Gray, 1870, is one of the most speciose genera among gorgonians of the family Primnoidae (Cnidaria : Octocorallia : Anthozoa), being remarkably diverse in the Antarctic and sub-Antarctic seafloor. However, their diversity in the Southern Ocean is likely underestimated. Phylogenetic analyses of mitochondrial and nuclear DNA markers were integrated with species delimitation approaches as well as morphological colonial and polyps features and skeletal SEM examinations to describe and illustrate three new species within Thouarella, from the Weddell Sea, Southern Ocean: T. amundseni sp. nov., T. dolichoespinosa sp. nov. and T. pseudoislai sp. nov. Our species delimitation results suggest, for the first time, the potential presence of Antarctic and sub-Antarctic cryptic species of primnoids, based on the likely presence of sibling species within T. undulata and T. crenelata. With the three new species here described, the global diversity of Thouarella has increased to 41 species, 15 of which are endemic to the Antarctic and sub-Antarctic waters. Consequently, our results provide new steps for uncovering the shelf benthonic macrofauna’s hidden diversity in the Southern Ocean. Finally, we recommend using an integrative taxonomic framework in this group of organisms and species delimitation approaches because the distinctions between some Thouarella species based only on a superficial examination of their macro- and micromorphological features is, in many cases, limited.

Chinook salmon (Oncorhynchus tshawytscha) are widely distributed across the globe, with native stocks in the North Pacific Ocean and self-sustained populations in both the Northern and Southern hemispheres. In their native range, Chinook salmon face many conservation and management challenges, including depleted stocks, loss of genetic diversity, and hatchery influences, whereas naturalized range expansion poses a threat to novel ecosystems. Therefore, ways to improve stock discrimination would be a useful tool for fishery managers. Here, we evaluated otolith shape variation in Chinook salmon as a potential tool for stock discrimination using wavelet coefficients and Fourier harmonics in three case studies at multiple spatial scales. We adopted a simple Classification Tree model that used otolith shape variation to separate Chinook salmon groups. We found best performance of the model occurring between hemispheres, followed by Oregon basins, within-watershed Elk River, Oregon, and lastly among South American basins. Otolith shape analysis is a promising tool for stock discrimination if used in conjunction with other methods to better understand plasticity of anadromous species that use pan-environmental systems.

The Cape Horn Biosphere Reserve, one of the last wild areas of the planet, is not exempt from the pressures of global change, such as non-native species introductions. During 2018 and 2019 we studied the Robalo river basin in order to update the diversity and distribution of fishes. Here, we report for the first time the native and endangered "Peladillas" Aplochiton taeniatus and the non-native coho salmon Oncorhynchus kisutch. The coexistence of native and non-native fishes poses a challenge for the management and conservation of aquatic biota from the Cape Horn Biosphere Reserve.

Different pathways of propagation and dispersal of non‐native species into new environments may have contrasting demographic and genetic impacts on established populations. Repeated introductions of rainbow trout (Oncorhynchus mykiss) to Chile in South America, initially through stocking and later through aquaculture escapes, provide a unique setting to contrast these two pathways. Using a panel of single nucleotide polymorphisms, we found contrasting genetic metrics and patterns among naturalized trout in Lake Llanquihue, Chile's largest producer of salmonid smolts for nearly 50 years, and Lake Todos Los Santos (TLS), a reference lake where aquaculture has been prohibited by law. Trout from Lake Llanquihue showed higher genetic diversity, weaker genetic structure, and larger estimates for the effective number of breeders (Nb) than trout from Lake TLS. Trout from Lake TLS were divergent from Lake Llanquihue and showed marked genetic structure and a significant isolation‐by‐distance pattern consistent with secondary contact between documented and undocumented stocking events in opposite shores of the lake. Multiple factors, including differences in propagule pressure, origin of donor populations, lake geomorphology, habitat quality or quantity, and life history, may help explain contrasting genetic metrics and patterns for trout between lakes. We contend that high propagule pressure from aquaculture may not only increase genetic diversity and Nb via demographic effects and admixture, but also may impact the evolution of genetic structure and increase gene flow, consistent with findings from artificially propagated salmonid populations in their native and naturalized ranges.

The phylogenetic resolution provided by genome-wide data has demonstrated the usefulness of RAD sequencing to tackle long-standing taxonomic questions. Cnidarians have recently become a model group in this regard, yet species delimitation analyses have been mostly performed in octocorals. In this study, we used RAD sequencing to test the species hypotheses in a wide-spread complex of sea anemones (genus Anthothoe), contrasting this new line of evidence with their current classification. The alternative hypotheses were tested using a Bayes Factors delimitation method, and the most probable species tree was then evaluated under different biogeographic scenarios. Our results decisively rejected the current morphology-informed delimitation model and infer the presence of several cryptic species associated with distinct marine ecoregions. This spatial pattern was remarkably consistent throughout the study, highlighting the role of geographic distribution as a powerful explanatory variable of lineages diversification. The southern Gondwana pattern with episodic, jump dispersal events is the biogeographic historical representation that best fits the Anthothoe species tree. The high population differentiation possibly amplified by the occurrence of asexual reproduction makes it difficult to identify genes responsible for local adaptation, however, these seem to be mainly associated with cellular and metabolic processes. We propose a new set of species hypotheses for the Southern Hemispheric Anthothoe clade, based on the pronounced genomic divergence observed among lineages. Although the link between the genetic and phenotypic differentiation remains elusive, newer sequencing technologies are bringing us closer to understanding the evolution of sea anemone diversity and, therefore, how to appropriately classify them. Fil: Spano, Carlos A.. Universidad de Concepción; Chile Fil: Häussermann, Vreni. Pontificia Universidad Católica de Valparaíso; Chile. Huinay Scientific Field Station; Chile Fil: Acuña, Fabian Horacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; Argentina Fil: Griffiths, Charles. University Of Cape Town; Sudáfrica Fil: Seeb, Lisa W.. University Of Washington. School Of Aquatic And Fisheries Sciences; Estados Unidos Fil: Gomez-Uchida, Daniel. Universidad de Concepción; Chile

Genetics data have provided unprecedented insights into evolutionary aspects of colonization by non-native populations. Yet, our understanding of how artificial (human-mediated) and natural dispersal pathways of non-native individuals influence genetic metrics, evolution of genetic structure, and admixture remains elusive. We capitalize on the widespread colonization of Chinook salmon Oncorhynchus tshawytscha in South America, mediated by both dispersal pathways, to address these issues using data from a panel of polymorphic SNPs. First, genetic diversity and the number of effective breeders (Nb) were higher among artificial than natural populations. Contemporary gene flow was common between adjacent artificial and natural and adjacent natural populations, but uncommon between geographically distant populations. Second, genetic structure revealed four distinct clusters throughout the Chinook salmon distributional range with varying levels of genetic connectivity. Isolation by distance resulted from weak differentiation between adjacent artificial and natural and between natural populations, with strong differentiation between distant Pacific Ocean and Atlantic Ocean populations, which experienced strong genetic drift. Third, genetic mixture analyses revealed the presence of at least six donor geographic regions from North America, some of which likely hybridized as a result of multiple introductions. Relative propagule pressure or the proportion of Chinook salmon propagules introduced from various geographic regions according to government records significantly influenced genetic mixtures for two of three artificial populations. Our findings support a model of colonization in which high-diversity artificial populations established first; some of these populations exhibited significant admixture resulting from propagule pressure. Low-diversity natural populations were likely subsequently founded from a reduced number of individuals. Fil: Gomez Uchida, Daniel. Núcleo Milenio Invasal; Chile. Universidad de Concepción; Chile Fil: Cañas Rojas, Diego. Núcleo Milenio Invasal; Chile. Universidad de Concepción; Chile Fil: Riva Rossi, Carla Marcela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; Argentina Fil: Ciancio Blanc, Javier Ernesto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Centro para el Estudio de Sistemas Marinos; Argentina Fil: Pascual, Miguel Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico para el Estudio de los Ecosistemas Continentales; Argentina Fil: Ernst, Billy. Universidad de Concepción; Chile. Núcleo Milenio Invasal; Chile Fil: Aedo, Eduardo. Universidad Austral de Chile; Chile Fil: Musleh, Selim S.. Universidad de Concepción; Chile. Núcleo Milenio Invasal; Chile Fil: Valenzuela Aguayo, Francisca. Universidad de Concepción; Chile Fil: Quinn, Thomas P.. Núcleo Milenio Invasal; Chile. University of Washington; Estados Unidos Fil: Seeb, James E.. Núcleo Milenio Invasal; Chile. University of Washington; Estados Unidos Fil: Seeb, Lisa W.. Núcleo Milenio Invasal; Chile. University of Washington; Estados Unidos

Numerous empirical studies have reported lack of migration–drift equilibrium in wild populations. Determining the causes of nonequilibrium population structure is challenging because different evolutionary processes acting at a variety of spatiotemporal scales can produce similar patterns. Studies of contemporary populations in northern latitudes suggest that nonequilibrium population structure is probably caused by recent colonization of the region after the last Pleistocene ice age ended ~13 000 years ago. The chum salmon's (Oncorhynchus keta) range was fragmented by dramatic environmental changes during the Pleistocene. We investigated the population structure of chum salmon on the North Alaska Peninsula (NAP) and, using both empirical data and simulations, evaluated the effects of colonization timing and founder population heterogeneity on patterns of genetic differentiation. We screened 161 single nucleotide polymorphisms and found evidence of nonequilibrium population structure when the slope of the isolation-by-distance relationship was examined at incremental spatial scales. In addition, simulations suggested that this pattern closely matched models of recent colonization of the NAP by secondary contact. Our results agree with geological and archaeological data indicating that the NAP was a dynamic landscape that may have been more recently colonized than during the last deglaciation because of dramatic changes in coastal hydrology over the last several thousand years.

Salmonids are an important cultural and ecological resource exhibiting near worldwide distribution between their native and introduced range. Previous research has generated linkage maps and genomic resources for several species as well as genome assemblies for two species. We first leveraged improvements in mapping and genotyping methods to create a dense linkage map for Chinook salmon Oncorhynchus tshawytscha by assembling family data from different sources. We successfully mapped 14 620 SNP loci including 2336 paralogs in subtelomeric regions. This improved map was then used as a foundation to integrate genomic resources for gene annotation and population genomic analyses. We anchored a total of 286 scaffolds from the Atlantic salmon genome to the linkage map to provide a framework for the placement 11 728 Chinook salmon ESTs. Previously identified thermotolerance QTL were found to colocalize with several candidate genes including HSP70, a gene known to be involved in thermal response, as well as its inhibitor. Multiple regions of the genome with elevated divergence between populations were also identified, and annotation of ESTs in these regions identified candidate genes for fitness related traits such as stress response, growth and behaviour. Collectively, these results demonstrate the utility of combining genomic resources with linkage maps to enhance evolutionary inferences.

We genotyped nuclear and mitochondrial single nucleotide polymorphisms (SNPs) in six paired archived and contemporary collections of Alaskan sockeye salmon ( Oncorhynchus nerka ) to evaluate the stability of allele frequencies over 25–42 years (4.9–8.4 generations). First, our results show that temporal changes were dramatically (between 40- and 250-fold) smaller than spatial differences in allele frequencies when based on nuclear SNPs. Second, the magnitude of temporal change was consistent with a model of genetic drift: (i) SNPs with high levels of differentiation (large θ) and candidates for diversifying selection were not more likely to show significant temporal changes than small-θ SNPs; and (ii) the fraction of single-locus significant tests was consistent with theoretical predictions relating sample size and the annual number of breeders (Nb). Third, estimates of Nbwere bound by infinitely large upper 95% confidence intervals, except for one paired collection with unique life-history attributes of both a smoltification phase and generation time shorter than the other paired collections. Use of multigenerational SNP data sets seems a safe practice in management of Alaska sockeye salmon that could be extended to other large, wild aquatic populations.

The Southern Darwin’s frog Rhinoderma darwinii is a charismatic, mouth-brooding amphibian endemic to temperate forests of South America with a Vulnerable conservation status according to the IUCN Red List. We developed microsatellite markers from next generation sequence data that will aid genetic monitoring during and after re-introduction efforts. Using bioinformatics we characterized 3,521 perfect microsatellite repeats and designed primers for 35 of them. From these, 23 were polymorphic and amplified reliably. Number of alleles varied between 2 and 15, allele sizes varied between 84 and 299 bp, and observed heterozygosities varied between 0.105 and 0.904. These microsatellites represent a valuable resource to aid recovery of threatened Southern Darwin’s frog populations.

The black rockfish (Sebastes melanops) is a long-lived (≤50 years) viviparous species with an extended pelagic larval period (3–5 months) and a broad continental distribution. Prolonged larval periods have been assumed to lead to widespread dispersal resulting in minimal population structure. We tested this assumption by comparing otolith microchemistry and microsatellite DNA of adult black rockfish from four locations in Oregon and Washington. We observed significant differences among locations in element-to-Ca ratios (Mg:Ca, Mn:Ca, Zn:Ca, Sr:Ca, and Ba:Ca) at the otolith edge, which represented the last year of life. Discriminant function analysis, based on otolith element-to-Ca ratios classified, on average, 64% of the fish to collection location, suggesting that the majority of individuals from these locations did not mix. Using microsatellite DNA, we observed significant genetic differences among adults collected 340–460 km apart (FST = 0.018 ± 0.004). Using five and seven loci, 63% and 75% of the fish, respectively, were correctly assigned to collection location. These two techniques provided corroborative and complementary information on the population structure of S. melanops.

By pooling or removing samples of small size, we investigated how results from microsatellite analyses of spatial genetic structure in darkblotched rockfish (Sebastes crameri) were affected. Genotypes from six and seven microsatellite loci from 1206 specimens collected offshore from Washington to California were employed in the analy- ses. Sample sizes varied greatly among locations (n = 11-114). When adjacent samples of n 100) and further in- creased the correlation, although this strategy did not raise overall FST. These results indicate that under genetic isola- tion by distance, excessive pooling might not enhance the overall genetic differentiation among populations. The regression slope in isolation by distance plots was robust throughout all treatments, and its value suggests limited dis- persal distance on this species. Resume : Nous avons etudie comment les resultats d'analyses des microsatellites sur la structure genetique spatiale chez le sebaste tachete (Sebastes crameri) sont affectes par la fusion et le retrait d'echantillons de petite taille. Des genotypes de six et sept locus microsatellites chez 1206 specimens recoltes du Washington a la Californie ont servi aux analyses. Les tailles des echantillons varient considerablement selon les sites (n = 11-114). Lorsque des echantillons adjacents de n < 25 sont fusionnes a l'aide d'une distance genetique absolue (FST ≤ 0), la correlation entre les distances genetique et geographique calculees dans les donnees originales double presque et le FST (intervalle de confiance de 95 %) global augmente de 0,001 (0,000-0,002) a 0,002 (0,001-0,003). Le retrait des echantillons de n <

We deep-sequenced the transcriptome of Chinook salmon (Oncorhynchus tshawytscha) that yielded 2.5 million high-quality reads (combined for four fish) with an average length of 378 bp. De novo assembly resulted in 44,264 contigs with an average length of 567 bp and an average depth of 29 reads. Nearly half (42 %) of the contigs were annotated through alignment against protein, gene ontology (GO) and taxonomic databases using BLASTX. Overrepresented GO categories included metabolism (32 %), biosynthesis (11 %), transport (7 %), transcription (5 %) and other important pathways (response to stress, lipid metabolism and reproduction: 3 %). We identified 3,793 putative single nucleotide polymorphisms (SNPs) in silico, of which 718 were annotated. We characterized a sample of 54 annotated SNPs within contigs with transition-to-transversion ratios

Landscape genetics holds promise for the forecasting of spatial patterns of genetic diversity based on key environmental features. Yet, the degree to which inferences based on single species can be extended to whole communities is not fully understood. We used a pristine and spatially structured community of three landlocked salmonids (Salvelinus fontinalis, Salmo salar, and Salvelinus alpinus) from Gros Morne National Park (Newfoundland, Canada) to test several predictions on the interacting effects of landscape and life history variation on genetic diversity, neutral divergence, and gene flow (m, migration rate). Landscape factors consistently influenced multispecies genetic patterns: (i) waterfalls created strong dichotomies in genetic diversity and divergence between populations above and below them in all three salmonids; (ii) contemporary m decreased with waterway distance in all three species, while neutral genetic divergence (h) increased with waterway distance, albeit in only two taxa; (iii) river flow generally produced downstream-biased m between populations when waterfalls separated these, but not otherwise. In contrast, we expected differential life history to result in a hierarchy of neutral divergence (S. salar > S. fontinalis > S. alpinus) based on disparities in dispersal abilities and population size from previous mark-recapture studies. Such hierarchy additionally matched varying degrees of spatial genetic structure among species revealed through individual-based analyses. We conclude that, whereas key landscape attributes hold power to predict multispecies genetic patterns in equivalent communities, they are likely to interact with species-specific life history attributes such as dispersal, demography, and ecology, which will in turn affect holistic conservation strategies.

Background Disentangling the roles of geography and ecology driving population divergence and distinguishing adaptive from neutral evolution at the molecular level have been common goals among evolutionary and conservation biologists. Using single nucleotide polymorphism (SNP) multilocus genotypes for 31 sockeye salmon (Oncorhynchus nerka) populations from the Kvichak River, Alaska, we assessed the relative roles of geography (discrete boundaries or continuous distance) and ecology (spawning habitat and timing) driving genetic divergence in this species at varying spatial scales within the drainage. We also evaluated two outlier detection methods to characterize candidate SNPs responding to environmental selection, emphasizing which mechanism(s) may maintain the genetic variation of outlier loci. Results For the entire drainage, Mantel tests suggested a greater role of geographic distance on population divergence than differences in spawn timing when each variable was correlated with pairwise genetic distances. Clustering and hierarchical analyses of molecular variance indicated that the largest genetic differentiation occurred between populations from distinct lakes or subdrainages. Within one population-rich lake, however, Mantel tests suggested a greater role of spawn timing than geographic distance on population divergence when each variable was correlated with pairwise genetic distances. Variable spawn timing among populations was linked to specific spawning habitats as revealed by principal coordinate analyses. We additionally identified two outlier SNPs located in the major histocompatibility complex (MHC) class II that appeared robust to violations of demographic assumptions from an initial pool of eight candidates for selection. Conclusions First, our results suggest that geography and ecology have influenced genetic divergence between Alaskan sockeye salmon populations in a hierarchical manner depending on the spatial scale. Second, we found consistent evidence for diversifying selection in two loci located in the MHC class II by means of outlier detection methods; yet, alternative scenarios for the evolution of these loci were also evaluated. Both conclusions argue that historical contingency and contemporary adaptation have likely driven differentiation between Kvichak River sockeye salmon populations, as revealed by a suite of SNPs. Our findings highlight the need for conservation of complex population structure, because it provides resilience in the face of environmental change, both natural and anthropogenic.