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Understanding how historical and contemporary processes lead to genetic differentiation among populations is a fundamental goal of evolutionary and conservation biology. This study focuses on Galaxias maculatus, a widely distributed fish exhibiting diadromous and freshwater resident forms. We examine the genetic differentiation among resident populations from the Manso River System, a trans-Andean system which thus went through drainage reversal following the Last Glacial Maximum (LGM), and resident and diadromous populations from the connected Puelo River that drains into the Pacific Ocean. Single nucleotide polymorphic (SNP) markers revealed that resident populations from the Manso River System are genetically distinguishable from the diadromous and resident populations from the Puelo River. This suggests that G. maculatus from the Manso River System likely colonized the area from a glacial refugium east of the Andes and did not expand downstream during drainage reversal, whereas the populations from the Puelo River colonized the area from glacial refugia west of the Andes. The populations from the Manso River exhibited lower genetic diversity than the Puelo River populations. Galaxias maculatus resident populations in Patagonia are decreasing due to anthropogenic factors. The Manso River System resident populations are susceptible to these factors and may show further decreases in genetic diversity.

The identification of closely related species with partially overlapping distributions is fundamental for effective conservation. Here we analyzed 28 sequenced microsatellites, mtDNA sequences, and morphological data, to describe the connectivity, genetic relationship, and distribution of Percilia gillissi and Percilia irwini, two endangered species inhabiting two contiguous watersheds in Chile (Itata and Biobio). We provide evidence of discordance in the spatial distribution of the two genomes (nuclear and mitochondrial). Three large clusters were identified with microsatellites, with one cluster straddling both watersheds. Three clusters were also evident in mtDNA with one cluster straddling both watersheds and the other two restricted to the Itata watershed’s northern reaches. Analyses of both microsatellite and mtDNA identified P. gillissi in the Itata watershed northern reaches and P. irwini in the Biobio watershed. Fish were detected in the Itata watershed that carried mtDNA characteristic of P. irwini but nuclear microsatellite profiles of P. gillissi suggesting an incomplete reproductive barrier between the species and connectivity between the watersheds. Additionally, fish were identified in the Itata northern reaches carrying mtDNA haplotypes sufficiently distinct from those of P. gillissi and P. irwini to suggest the existence of higher mtDNA diversity within P. gillissi than previously recognized. Finally, there was limited support for taxonomical classification based on morphological and meristic traits in this region.

Salmonid introductions for sport fishing and, more recently, for farming, have had a large impact on freshwater ecosystems in many regions worldwide. In Patagonia, both activities have contributed to the colonization of freshwater systems particularly by species such as Brown Trout (Salmo trutta) and Rainbow Trout (Oncorhynchus mykiss). The ecological impact of these species has been widely studied in continental freshwater ecosystems. There are, however, no studies of their impact in southern Patagonian fjords. Here, we evaluate the effect of the presence of Coho Salmon (Oncorhynchus kisutch) and Chinook Salmon (Oncorhynchus tshawytscha) juveniles on the diet (stomach content and isotopic niche) of the native Galaxias maculatus in lakes and estuaries associated with Patagonian fjord system. Galaxias maculatus inhabiting salmon-free lakes fed primarily on insects, while lake G. maculatus coexisting in sympatry with Coho Salmon consumed primarily benthic macroinvertebrates. In estuaries, the diet of G. maculatus and Salmon (Coho and Chinook) overlap. The isotopic niche space of G. maculatus (based on carbon, nitrogen and sulphur isotopic compositions) was larger in lake where it was found in sympatry with Coho Salmon compared to its isotopic niche space in salmonid-free lakes. Finally, in estuaries, niche spaces were similar between G. maculatus and Coho Salmon. The niche space was greater for Chinook Salmon than for G. maculatus and Coho Salmon, most probably as a consequence of their territorial behaviour and larger home ranges.

Characterizing the nature of genetic differentiation among individuals and populations and its distribution across the genome is increasingly important to inform both conservation and management of exploited species. Atlantic Halibut (Hippoglossus hippoglossus) is an ecologically and commercially important fish species, yet knowledge of population structure and genomic diversity in this species remains lacking. Here, we use restriction-site associated DNA sequencing and a chromosome-level genome assembly to identify over 86 000 single nucleotide polymorphisms mapped to 24 chromosome-sized scaffolds, genotyped in 734 individuals across the Northwest Atlantic. We describe subtle but significant genome-wide regional structuring between the Gulf of St. Lawrence and adjacent Atlantic continental shelf. However, the majority of genetic divergence is associated with a large putative chromosomal rearrangement (5.74 megabases) displaying high differentiation and linkage disequilibrium, but no evidence of geographic variation. Demographic reconstructions suggest periods of expansion coinciding with glacial retreat, and more recent declines in Ne. This work highlights the utility of genomic data to identify multiple sources of genetic structure and genomic diversity in commercially exploited marine species.

Arctic Grayling (Thymallus arcticus) are among the most widely distributed and abundant freshwater fish in the Yukon Territory of Canada, yet little information exists regarding their broad and fine‐scale population structures or the number and size of these populations. The estimation of population abundance is fundamental for robust management and conservation, yet estimating abundance in the wild is often difficult. Here, we estimated abundance of an Arctic Grayling population using multiple genetic markers and the close‐kin mark‐recapture (CKMR) method. A total of N = 1,104 Arctic Grayling collected from two systems in Yukon were genotyped at 38 sequenced microsatellites. We first identified structure and assessed genetic diversity (effective population size, N^e). Collections from one of the systems (Lubbock River) comprised adults and young‐of‐the‐year sampled independently allowing the identification of parent–offspring pairs (POPs), and thus, the estimation of abundance using CKMR. We used COLONY and CKMRsim to identify POPs and both provided similar results leading to indistinguishable estimates (95% CI) of census size, that is, N^c(COLONY) = 1858 (1259–2457) and N^c(CKMRsim)=1812 (1229–2389). The accuracy of the population abundance estimates can in the future be improved with temporal sampling and more precise age or size‐specific fecundity estimates for Arctic Grayling. Our study demonstrates that the method can be used to inform management and conservation policy for Arctic Grayling and likely also for other fish species for which the assumption of random and independent sampling of adults and offspring can be assured., We estimate population abundance of Arctic Grayling using the close‐Kin mark‐recapture method and a newly developed suite of 38 sequenced species specific microsatellite DNA markers. This is done after assessing population structure and estimating effective sizes. We suggest the approach including the added night gained by estimating the ration Ne/Nc can be added to the conservation and management toolkit for this and potentially other freshwater species where random sampling and independence of sampling of adults and potential offspring can be assured.

Despite widespread biodiversity losses, an understanding of how most taxa will respond to future climate change is lacking. Here we integrate genomics and environmental modelling to assess climate change responses in an ecologically and economically important Arctic species. Environmentally associated genomic diversity and machine learning are used to identify highly vulnerable populations of anadromous (migratory) Arctic charr, and we reconstruct estimates of effective population size spanning the twentieth century to identify past climate-associated declines. We uncover past region-wide declines in effective population size that correspond to decreases in temperature and community biomass in the Northwest Atlantic. We find vulnerable populations near the southern range limit, indicating northward shifts and a possible loss of commercially important life-history variation in response to climate change. The genomic approach used here to investigate climate change response identifies past and future declines that impact species persistence, ecosystem stability and food security in the Arctic. Genomics and environmental modelling are integrated to assess past and future changes in Arctic charr populations in response to changing climate. Southern population vulnerability suggests climate change may lead to northward shifts and the loss of important life-history variation.

The genetic underpinnings of incipient speciation, including the genomic mechanisms which contribute to morphological and ecological differentiation and reproductive isolation, remain poorly understood. The repeated evolution of consistently, phenotypically distinct morphs of Arctic Charr (Salvelinus alpinus) within the Quaternary period offer an ideal model to study the repeatability of evolution at the genomic level. Sympatric morphs of Arctic Charr are found across this species' circumpolar distribution. However, the specific genetic mechanisms driving this morph differentiation are largely unknown despite the cultural and economic importance of the anadromous morph. We used a newly designed 87k SNP chip to investigate the character and consistency of the genomic differences among sympatric morphs within three recently deglaciated and geographically proximate lakes in Labrador, Canada. We found genetically distinct small and large morph Arctic Charr in all three lakes consistent with resident and anadromous morphs, respectively. A degree of reproductive isolation among sympatric morphs is likely given genome-wide distributions of outlier SNPs and high genome-wide FST s. Across all lakes, outlier SNPs were largely nonoverlapping suggesting a lack of genetic parallelism driving morph differentiation. Alternatively, several genes and paralogous copies of the same gene consistently differentiated morphs across multiple lakes suggesting their importance to the manifestation of morphs. Our results confirm the utility of Arctic Charr as a model for investigating the predictability of evolution and support the importance of both genetic parallelism and nonparallelism to the incipient speciation of Arctic Charr morphs.

The resiliency of populations and species to environmental change is dependent on the maintenance of genetic diversity, and as such, quantifying diversity is central to combating ongoing widespread reductions in biodiversity. With the advent of next‐generation sequencing, several methods now exist for resolving fine‐scale population structure, but the comparative performance of these methods for genetic assignment has rarely been tested. Here, we evaluate the performance of sequenced microsatellites and a single nucleotide polymorphism (SNP) array to resolve fine‐scale population structure in a critically important salmonid in north eastern Canada, Arctic Charr (Salvelinus alpinus). We also assess the utility of sequenced microsatellites for fisheries applications by quantifying the spatial scales of movement and exploitation through genetic assignment of fishery samples to rivers of origin and comparing these results with a 29‐year tagging dataset. Self‐assignment and simulation‐based analyses of 111 genome‐wide microsatellite loci and 500 informative SNPs from 28 populations of Arctic Charr in north‐eastern Canada identified largely river‐specific genetic structure. Despite large differences (~4X) in the number of loci surveyed between panels, mean self‐assignment accuracy was similar with the microsatellite loci and the SNP panel (>90%). Subsequent analysis of 996 fishery‐collected samples using the microsatellite panel revealed that larger rivers contribute greater numbers of individuals to the fishery and that coastal fisheries largely exploit individuals originating from nearby rivers, corroborating results from traditional tagging experiments. Our results demonstrate the efficacy of sequence‐based microsatellite genotyping to advance understanding of fine‐scale population structure and harvest composition in northern and understudied species.

Aim The Pleistocene glaciation event prompted the allopatric divergence of multiple glacial lineages of Arctic char (Salvelinus alpinus), some of which have come into secondary contact upon their recolonization of the Holarctic. While three glacial lineages (Arctic, Atlantic, and Acadian) are known to have recolonized the western Atlantic, the degree of overlap of these three lineages is largely unknown. We sought to determine the distribution of these three glacial lineages in Labrador and Newfoundland at a fine spatial scale to assess their potential for introgression and their relative contribution to local fisheries. Location Labrador and Newfoundland, Canada. Methods We sequenced a portion of the D-loop region in over 1,000 Arctic char (S. alpinus) samples from 67 locations across Labrador and Newfoundland. Results Within Labrador, the Arctic and Atlantic lineages were widespread. Two locations (one landlocked and one with access to the sea) also contained individuals of the Acadian lineage, constituting the first record of this lineage in Labrador. Atlantic and Acadian lineage individuals were found in both eastern and western Newfoundland. Multiple sampling locations in Labrador and Newfoundland contained fish of two or more different glacial lineages, implying their introgression. Glacial lineage did not appear to dictate contemporary genetic divergence between the pale and dark morph of char present in Gander Lake, Newfoundland. Both were predominately of the Atlantic lineage, suggesting the potential for their divergence in sympatry. Main conclusions Our study reveals Labrador and Newfoundland to be a unique junction of three glacial lineages which have likely hybridized extensively in this region.

The post-glacial colonization of Gander Lake in Newfoundland, Canada, by Arctic Charr (Salvelinus alpinus) provides the opportunity to study the genomic basis of adaptation to extreme deep-water environments. Colonization of deep-water (>50 m) habitats often requires extensive adaptation to cope with novel environmental challenges from high hydrostatic pressure, low temperature, and low light, but the genomic mechanisms underlying evolution in these environments are rarely known. Here, we compare genomic divergence between a deep-water morph adapted to depths of up to 288 m and a larger, piscivorous pelagic morph occupying shallower depths. Using both a SNP array and resequencing of whole nuclear and mitochondrial genomes, we find clear genetic divergence (FST = 0.11-0.15) between deep and shallow water morphs, despite an absence of morph divergence across the mitochondrial genome. Outlier analyses identified many diverged genomic regions containing genes enriched for processes such as gene expression and DNA repair, cardiac function, and membrane transport. Detection of putative copy number variants (CNVs) uncovered 385 genes with CNVs distinct to piscivorous morphs, and 275 genes with CNVs distinct to deep-water morphs, enriched for processes associated with synapse assembly. Demographic analyses identified evidence for recent and local morph divergence, and ongoing reductions in diversity consistent with postglacial colonization. Together, these results show that Arctic Charr morph divergence has occurred through genome-wide differentiation and elevated divergence of genes underlying multiple cellular and physiological processes, providing insight into the genomic basis of adaptation in a deep-water habitat following postglacial recolonization.

The timing of reproduction influences key evolutionary and ecological processes in wild populations. Variation in reproductive timing may be an especially important evolutionary driver in the marine environment, where the high mobility of many species and few physical barriers to migration provide limited opportunities for spatial divergence to arise. Using genomic data collected from spawning aggregations of Pacific herring (Clupea pallasii) across 1600 km of coastline, we show that reproductive timing drives population structure in these pelagic fish. Within a specific spawning season, we observed isolation by distance, indicating that gene flow is also geographically limited over our study area. These results emphasize the importance of considering both seasonal and spatial variation in spawning when delineating management units for herring. On several chromosomes, we detected linkage disequilibrium extending over multiple Mb, suggesting the presence of chromosomal rearrangements. Spawning phenology was highly correlated with polymorphisms in several genes, in particularSYNE2, which influences the development of retinal photoreceptors in vertebrates.SYNE2is probably within a chromosomal rearrangement in Pacific herring and is also associated with spawn timing in Atlantic herring (Clupea harengus). The observed genetic diversity probably underlies resource waves provided by spawning herring. Given the ecological, economic and cultural significance of herring, our results support that conserving intraspecific genetic diversity is important for maintaining current and future ecosystem processes.

Summary Diadromy, the predictable movements of individuals between marine and freshwater environments, is biogeographically and phylogenetically widespread across fishes. Thus, despite the high energetic and potential fitness costs involved in moving between distinct environments, diadromy appears to be an effective life history strategy. Yet, the origin and molecular mechanisms that underpin this migratory behavior are not fully understood. In this review, we aim first to summarize what is known about diadromy in fishes; this includes the phylogenetic relationship among diadromous species, a description of the main hypotheses regarding its origin, and a discussion of the presence of non-migratory populations within diadromous species. Second, we discuss how recent research based on -omics approaches (chiefly genomics, transcriptomics, and epigenomics) is beginning to provide answers to questions on the genetic bases and origin(s) of diadromy. Finally, we suggest future directions for -omics research that can help tackle questions on the evolution of diadromy., Graphical Abstract

Changes in the genetic mechanisms that control sexual determination have occurred independently across the tree of life, and with exceptional frequency in teleost fishes. To investigate the genomic changes underlying the evolution of sexual determination, we sequenced a chromosome-level genome, multi-tissue transcriptomes, and reduced representation population data for the Atlantic halibut (Hippoglossus hippoglossus), which has an XY/XX sex determination mechanism and has recently diverged (0.9-3.8 MYA) from the Pacific halibut (Hippoglossus stenolepis), which has a ZZ/ZW system. We used frequency and coverage-based population approaches to identify a putative sex-determining factor, GSDF. We characterized regions with elevated heterozygosity and linkage disequilibrium indicating suppression of recombination across a nascent sex chromosome. We detected testis-specific expression of GSDF, the sequence of which is highly conserved across flatfishes. Based on evidence from genome-wide association, coverage, linkage disequilibrium, testis and brain transcriptomes, and sequence conservation with other flatfishes, we propose a mechanism for the recent evolution of an XY sex-determination mechanism in Atlantic halibut. Changes to the ancestral sex-determining gene DMRT1 in regulating the downstream gene GSDF likely coincided with GSDF, or a proximal regulatory element of it, becoming the primary sex-determining factor. Our results suggest changes to a small number of elements can have drastic repercussions for the genomic substrate available to sex-specific evolutionary forces, providing insight into how certain elements repeatedly evolve to control sex across taxa. Our chromosome-level assembly, multi-tissue transcriptomes, and population genomic data provide a valuable resource and understanding of the evolution of sexual systems in fishes.

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 ofP. truchais consistent with episodes of drainage reversal in multiple systems and suggests a major role for deglaciation in the genetic and indeed the geographical distribution ofP. truchain 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.

Diadromy is known for having major effects on the distribution and richness of aquatic species, and so does its loss. The loss of diadromy has led to the diversification of many species, yet research focusing on understanding its molecular basis and consequences are limited. This is particularly true for amphidromous species despite being the most abundant group of diadromous species. Galaxias maculatus, an amphidromous species and one of the most widely distributed fishes in the Southern Hemisphere, exhibits many instances of nonmigratory or resident populations. The existence of naturally replicated resident populations in Patagonia can serve as an ideal system for the study of the mechanisms that lead to the loss of the diadromy and its ecological and evolutionary consequences. Here, we studied two adjacent river systems in which resident populations are genetically differentiated yet derived from the same diadromous population. By combining a reciprocal transplant experiment with genomic data, we showed that the two resident populations followed different evolutionary pathways by exhibiting a differential response in their capacity to survive in salt water. While one resident population was able to survive salt water, the other was not. Genomic analyses provided insights into the genes that distinguished (a) migratory from nonmigratory populations; (b) populations that can vs those that cannot survive a saltwater environment; and (c) between these resident populations. This study demonstrates that the loss of diadromy can be achieved by different pathways and that environmental (selection) and random (genetic drift) forces shape this dynamic evolutionary process.

Atlantic herring (Clupea harengus), a vital ecosystem component and target of the largest Northwest Atlantic pelagic fishery, undergo seasonal spawning migrations that result in elusive sympatric population structure. Herring spawn mostly in fall or spring, and genomic differentiation was recently detected between these groups. Here we used a subset of this differentiation, 66 single nucleotide polymorphisms (SNPs) to analyze the temporal dynamics of this local adaptation and the applicability of SNP subsets in stock assessment. We showed remarkable temporal stability of genomic differentiation corresponding to spawning season, between samples taken a decade apart (2005 N = 90 vs. 2014 N = 71) in the Gulf of St. Lawrence, and new evidence of limited interbreeding between spawning components. We also examined an understudied and overexploited herring population in Bras d'Or lake (N = 97); using highly reduced SNP panels (NSNPs > 6), we verified little-known sympatric spawning populations within this unique inland sea. These results describe consistent local adaptation, arising from asynchronous reproduction in a migratory and dynamic marine species. Our research demonstrates the efficiency and precision of SNP-based assessments of sympatric subpopulations; and indeed, this temporally stable local adaptation underlines the importance of such fine-scale management practices.

Marine protected areas (MPAs) can serve as effective tools for the management and conservation of exploited marine species. The Gilbert Bay MPA in coastal Labrador was created to protect a genetically distinct population of Atlantic cod (Gadus morhua); however, decreases in abundance continue to occur potentially due to exploitation outside the MPA. We developed a single-nucleotide polymorphism (SNP) panel to identify Gilbert Bay cod in areas outside MPA boundaries where mixing with offshore cod occurs. In total, 361 individuals from Gilbert Bay, surrounding areas, and offshore were genotyped for 10 913 SNPs. Using FSTrankings and guided regularized random forest, we selected 23 SNPs that together generate 100% accuracy in individual assignment and accurately estimate the proportion of Gilbert Bay cod in fishery samples from sites outside MPA boundaries: on average, fishery samples included 17.3% Gilbert Bay cod. Estimates of effective population size for the Gilbert Bay population ranged from 655 to 1114. Our findings demonstrate the power of using genomic approaches for management of an exploited marine species and enhancing the design of MPAs.

Anadromous, resident, and landlocked Arctic char (Salvelinus alpinus) differentially experience drift and gene flow, making them ideal for studying incipient divergence. We investigated genetic divergence within and among char occupying landlocked and sea-accessible sites in Labrador, Canada, using 11 microsatellites. Unlike anadromous char, landlocked char were highly genetically differentiated. Genetic subgroups were detected within landlocked and sea-accessible sites. Within Ramah Lake (a sea-accessible site containing two subgroups), one subgroup matured at a small size, and both subgroups had equal proportions of males to females. These findings refute residency as a sneaker male tactic and instead suggest the presence of reproductively isolated resident and anadromous char. Subgroups demonstrated equal frequencies of Atlantic and Arctic lineage mtDNA haplotypes, suggesting their genetic differences were not due to allopatry during the last glacial maximum. Our results are therefore consistent with the sympatric genetic divergence of resident and anadromous Arctic char morphs.

It is well documented that hydropower plants can affect the dynamics of fish populations through landscape alterations and the creation of new barriers. Less emphasis has been placed on the examination of the genetic consequences for fish populations of the construction of dams. The relatively few studies that focus on genetics often do not consider colonization history and even fewer tend to use this information for conservation purposes. As a case study, we used a 3-pronged approach to study the influence of historical processes, contemporary landscape features, and potential future anthropogenic changes in landscape on the genetic diversity of a fish metapopulation. Our goal was to identify the metapopulation's main attributes, detect priority areas for conservation, and assess the consequences of the construction of hydropower plants for the persistence of the metapopulation. We used microsatellite markers and coalescent approaches to examine historical colonization processes, traditional population genetics, and simulations of future populations under alternate scenarios of population size reduction and gene flow. Historical gene flow appeared to have declined relatively recently and contemporary populations appeared highly susceptible to changes in landscape. Gene flow is critical for population persistence. We found that hydropower plants could lead to a rapid reduction in number of alleles and to population extirpation 50-80 years after their construction. More generally, our 3-pronged approach for the analyses of empirical genetic data can provide policy makers with information on the potential impacts of landscape changes and thus lead to more robust conservation efforts.

Understanding the evolutionary mechanisms that affect the genetic divergence between diadromous and resident populations across heterogeneous environments is a challenging task. While diadromy may promote gene flow leading to a lack of genetic differentiation among populations, resident populations tend to be affected by local adaptation and/or plasticity. Studies on these effects on genomic divergence in nonmodel amphidromous species are scarce. Galaxias maculatus, one of the most widespread fish species in the Southern Hemisphere, exhibits two life histories, an ancestral diadromous, specifically, amphidromous form, and a derived freshwater resident form. We examined the genetic diversity and divergence among 20 estuarine and resident populations across the Chilean distribution of G. maculatus and assessed the extent to which selection is involved in the differentiation among resident populations. We obtained nearly 4,400 SNP markers using a RADcap approach for 224 individuals. As expected, collections from estuarine locations typically consist of diadromous individuals. Diadromous populations are highly differentiated from their resident counterparts by both neutral and putative adaptive markers. While diadromous populations exhibit high gene flow and lack site fidelity, resident populations appear to be the product of different colonization events with relatively low genetic diversity and varying levels of gene flow. In particular, the northernmost resident populations were clearly genetically distinct and reproductively isolated from each other suggesting local adaptation. Our study provides insights into the role of life history differences in the maintenance of genetic diversity and the importance of genetic divergence in species evolution.

Funding: Marine Alliance for Science and Technology for Scotland (MASTS), which is funded by the Scottish Funding Council (grant reference HR09011) (O.E.G.). To what degree are patterns of genetic structure in fragmented systems the result of contemporary landscape vs. history? We examined the distribution of genetic diversity as a function of colonization history and contemporary landscape in four fish species inhabiting a hierarchically fragmented, unaltered system, the Kogaluk drainage (Labrador): lake trout, longnose sucker, round whitefish, and lake chub. The footprint of colonization history was still observable in the three species where this issue was examined regardless of the generations since their arrival. ABC analyses suggest colonization took place from the southwest. The species exhibit similar diversity patterns despite different Nes and generation intervals. Contemporary gene flow was largely negligible except for gene flow from a centrally located lake. These results suggest landscape has driven colonization history, which still has influence on genetic structuring. The species are widespread. Understanding how they behave in the pristine Kogaluk provides a baseline against which to evaluate how other anthropogenically perturbed systems are performing. Improved understanding of historical and contemporary processes is required to fully explain diversity patterns in complex metapopulations Postprint

High connectivity and low potential for local adaptation have been common assumptions for most marine species, given their usual high fecundity and dispersal capabilities. Recent genomic studies however, have disclosed unprecedented levels of population subdivision in what were previously presumed to be panmictic or nearly panmictic species. Here we analyzed neutral and adaptive genetic variation at the whole-genome level in Atlantic herring (Clupea harengusL.) spawning aggregations distributed across the reproductive range of the species in North America. We uncovered fine-scale population structure at putatively adaptive loci, despite low genetic differentiation at neutral loci. Our results revealed an intricate pattern of population subdivision involving two overlapping axes of divergence: a temporal axis determined by seasonal reproduction, and a spatial axis defined by a latitudinal cline establishing a steep north-south genetic break. Genetic-environment association analyses indicated that winter sea-surface temperature is the best predictor of the spatial structure observed. Thousands of outlier SNPs distributed along specific parts of the genome spanning numerous candidate genes underlined each pattern of differentiation, forming so-called “genomic regions or islands of divergence”. Our results indicate that timing of reproduction and latitudinal spawning location are features under disruptive selection leading to local adaptation in the herring. Our study highlights the importance of preserving functional and neutral intraspecific diversity, and the utility of an integrative seascape genomics approach for disentangling intricate patterns of intraspecific diversity in highly dispersive and abundant marine species.

The present distribution of Patagonian species is the result of a complex history involving Quaternary refugial populations, Holocene range expansions and demographic changes occurring during the Anthropocene. Invasive salmonids were introduced in Patagonia during the last century, occupying most rivers and lakes, preying on and competing with native species, including the fish Galaxias platei . Here, we used G. platei as a case study to understand how long-term (i.e. population differentiation during the Holocene) and short-term historical processes (salmonid introductions) affect genetic diversity. Using a suite of microsatellite markers, we found that the number of alleles is negatively correlated with the presence of salmonids (short-term processes), with G. platei populations from lakes with salmonids exhibiting significantly lower genetic diversity than populations from lakes without salmonids. Simulations (100 years backwards) showed that this difference in genetic diversity can be explained by a 99% reduction in population size. Allelic richness and observed heterozygosities were also negatively correlated with the presence of salmonids, but also positively correlated with long-term processes linked to Quaternary glaciations. Our results show how different genetic parameters can help identify processes taking place at different scales and their importance in terms of conservation.

Salmonid invasions are currently recognized as one of the main threats to the conservation of freshwater ecosystems in Patagonia. Although a number of salmonid species have been introduced to Patagonia over the last century not all species have succeeded at establishing widespread and large populations. To date, there are no reports of established self-sustaining Coho Salmon (Oncorhynchus kisutch) populations in southern Chile despite propagule pressure from aquaculture. Here, we assessed the natal origin of young-of-the-year Coho Salmon collected from estuaries and lakes associated with remote Patagonian fjords (51°S) by examining their otolith microchemical composition. Low strontium concentrations along a line transect from the otolith edge to its core in fish collected in one lake are consistent with freshwater residence until the moment of capture. Fish caught in estuaries displayed instead, relatively high strontium concentrations only at the otolith edge. This pattern suggests very recent movement from freshwater down to the estuary. Our findings are consistent with the hypothesis that the juvenile Coho Salmon collected in estuaries originated in the local freshwater system (lake) and provide the first ever evidence of recruitment and probable establishment of self-sustaining Coho Salmon population in Patagonia.

The inland water crustacean communities in southern Chilean Patagonia (46-55°S) are characterized by their marked low species number, and many recurrent species among a wide ecological and geographical gradient, that is due to oligotrophy of lakes and lagoons and the fluvial parameters (i.e., high flow velocities) in rivers. The aim of the present study was to describe the zooplankton communities in lakes and respective outflow river estuaries in Alacalufes National Reserve on islands of Chilean southern Patagonia (49-51°S). Species abundance and presence/absence were considered. The results obtained revealed the presence of a low number of species and also multiple sites in which zooplankton was not recorded at all. This is probably due the low zooplankton diversity of cold lakes at these high latitudes and the often turbulent flow of the outflow rivers studied.

Atlantic herring (Clupea harengus), a vital ecosystem component and target of the largest Northwest Atlantic pelagic fishery, undergo seasonal spawning migrations that result in elusive sympatric population structure. Herring spawn mostly in fall or spring, and genomic differentiation was recently detected between these groups. Here we used a subset of this differentiation, 66 single nucleotide polymorphisms (SNPs) to analyze the temporal dynamics of this local adaptation and the applicability of SNP subsets in stock assessment. We showed remarkable temporal stability of genomic differentiation corresponding to spawning season, between samples taken a decade apart (2005 N = 90 vs. 2014 N = 71) in the Gulf of St. Lawrence, and new evidence of limited interbreeding between spawning components. We also examined an understudied and overexploited herring population in Bras d'Or lake (N = 97); using highly reduced SNP panels (N SNPs > 6), we verified little‐known sympatric spawning populations within this unique inland sea. These results describe consistent local adaptation, arising from asynchronous reproduction in a migratory and dynamic marine species. Our research demonstrates the efficiency and precision of SNP‐based assessments of sympatric subpopulations; and indeed, this temporally stable local adaptation underlines the importance of such fine‐scale management practices.

We sequenced a portion of the D-loop region in over 1000 Arctic char (Salvelinus alpinus) samples from 67 locations across Newfoundland and Labrador to assess the extent of secondary contact among the Arctic, Atlantic, and Acadian glacial lineages in Newfoundland and Labrador. Within Labrador, the Arctic and Atlantic lineages were widespread. Two locations (one landlocked and one with access to the sea) also contained individuals of the Acadian lineage, constituting the first record of this lineage in Labrador. Atlantic and Acadian lineage individuals were found in both eastern and western Newfoundland. Multiple sampling locations in Newfoundland and Labrador contained fish of two or more different glacial lineages, implying their introgression. Glacial lineage did not appear to dictate contemporary genetic divergence between the pale and dark morph of char present in Gander Lake, Newfoundland. Both were predominately of the Atlantic lineage, suggesting the potential for their divergence in sympatry. This study reveals Newfoundland and Labrador to be a unique junction of three glacial lineages which have likely hybridized extensively in this region.

Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved or resolved haplotypes, the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq) and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in nonmodel species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g., structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently, though, no single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many nonmodel species and fields including conservation biology.

Atlantic herring is an excellent species for studying the genetic basis of adaptation in geographically distant populations because of its characteristically large population sizes and low genetic drift. In this study we compared whole-genome resequencing data of Atlantic herring populations from both sides of the Atlantic Ocean. An important finding was the very low degree of genetic differentiation among geographically distant populations (fixation index = 0.026), suggesting lack of reproductive isolation across the ocean. This feature of the Atlantic herring facilitates the detection of genetic factors affecting adaptation because of the sharp contrast between loci showing genetic differentiation resulting from natural selection and the low background noise resulting from genetic drift. We show that genetic factors associated with timing of reproduction are shared between genetically distinct and geographically distant populations. The genes for thyroid-stimulating hormone receptor (

Round whitefish is a freshwater salmonid found within northern North America and north-eastern parts of Asia. Here we describe 26 novel, and seven previously described microsatellite loci that amplified in this species. Of these 33 markers, 12 were polymorphic, exhibiting between 2 and 5 alleles each. The remaining 21 loci are monomorphic. Observed and expected heterozygosities for the polymorphic markers ranged from 0.094 to 0.625 and 0.203 to 0.768 respectively. There was no evidence of linkage disequilibrium between any locus pairs, nor was there any evidence of null alleles. There were however, seven markers deviating from Hardy–Weinberg equilibrium, a result we attribute to relatively small sample and/or population size.

Lake chub is a common freshwater cyprinid found throughout Canada and parts of the northern United States. Here we describe 36 novel microsatellite loci, 25 of which are polymorphic, exhibiting between 2 and 17 alleles each, while the remaining 11 loci are monomorphic. Observed and expected heterozygosities for the polymorphic markers ranged from 0.125 to 0.875 and 0.146 to 0.878, respectively. There was no evidence of linkage disequilibrium between any locus pairs, nor was there any evidence of null alleles. There were however, six markers deviating from Hardy–Weinberg Equilibrium, a result we attribute to relatively small sample size.

Assessment of population structure is critical to the design and implementation of sound management and conservation strategies. However, population structure must be assessed using markers attuned to population genetic processes such as genetic drift and gene flow, which reflect actual levels of reproductive isolation among putative genetic clusters. This is critical for highly exploited, commercial species that form the backbone of regional and local economies. Here, we show extremely low levels of population genetic differentiation among Greenland halibut (Reinhardtius hippoglossoides) collected from throughout the Northwest Atlantic, which cannot be statistically differentiated from panmixia using 12 species-specific polymorphic microsatellite markers. In contrast, some previous studies have demonstrated significant differences among individuals collected from various parts of the species’ range using a variety of both genetic and nongenetic techniques. In accordance with other reports and consistent with the species’ life history, we demonstrate that the most parsimonious explanation reconciling observed patterns is a repeated high degree of local differentiation of new recruits and colonizers originating from a common gene pool. Such a scenario has important conservation implications in terms of devising more appropriate strategies balancing species persistence and replenishment with sustainable resource use.

The longnose sucker (Catostomus catostomus) is a widely distributed catostomid, found throughout Canada and much of the northern United States. Although it is a species with significant ecological importance, it has been the focus of only a few studies. Here we describe 17 novel microsatellite loci, and the use of 14 previously described markers from congeneric species formerly untested on longnose sucker. Of the 31 described markers, 19 were polymorphic exhibiting between 2 and 20 alleles. Observed and expected heterozygosities ranged from 0.13 to 0.91, and 0.23 to 0.95 respectively. There was no evidence of null alleles or of deviation from Hardy–Weinberg equilibrium for any locus, and no locus pairs exhibited evidence of linkage disequilibrium.

SUMMARY 1. Freshwater systems are ideal for landscape genetics studies; they generally exhibit asymmetry in gene flow with populations arranged in a hierarchical, dendritic fashion. Such gene flow asymmetry has the potential to influence the distribution of genetic variation, with downstream populations typically exhibiting higher genetic diversity than headwater populations. 2. Lake trout (Salvelinus namaycush) are widely distributed throughout temperate North America. We examined the relationship between landscape attributes, molecular genetic diversity and differentiation among lake trout populations inhabiting a hierarchically structured freshwater system in northern Labrador (the Kogaluk River drainage). Lake trout (N = 567) collected from ten lakes in this drainage were examined for polymorphism at 12 microsatellite loci. The lakes differed in connectivity, size, elevation and position within the Kogaluk catchment. 3. We observed relatively high levels of population structure and little migration among lakes. Waterfalls were identified as a factor contributing to the observed differentiation. 4. Although a preliminary analysis suggested an isolation-by-distance pattern, a subsequent decomposed pairwise regression analysis allowed the identification of outlier lakes. Removal of these outlier lakes and of one other headwater lake, isolated from the rest by several waterfalls, led to the disappearance of the isolation-by-distance pattern, suggesting very little or no migration among lakes despite migration being physically possible. 5. Estimates of effective population size correlated with lake area but did not differ between headwater and downstream populations, nor was there a relationship with elevation, a result consistent with the evidence of very little to zero gene flow among lakes. 6. Our study is the first to describe patterns of genetic diversity among lake trout populations inhabiting a spatially fragmented system in an ecologically pristine and sensitive area of northern Canada, the barren grounds of northern Labrador.

Rocky shore intertidal communities along the cold- and warm-temperate coasts of the south-western Atlantic are dominated by small mussels of the genus Brachidontes s.l. (Mytilidae), yet the status of species occurring in the region remains unresolved. Taxonomic studies have been based on shell morphology, but high phenotypic variability has led to much confusion. Based on mitochondrial and nuclear genes (COI, 28S rDNA and ITS1) from nine localities in Uruguay and Argentina we confirmed the occurrence of three species in the south-western Atlantic: Brachidontes darwinianus and B. rodriguezii in the warmtemperate and B. purpuratus in the cold-temperate sector. The latter two species coexist in the same beds along the transition zone (41?438S). The phylogeny based on mitochondrial and nuclear genes, indicate an early divergence of B. purpuratus. At the intra-specific level, low genetic differentiation and absence of fossil record for B. purpuratus from the earlier Quaternary marine terraces of Patagonia likely result from a relatively recent (post-LGM) colonization originated from populations in the southeastern Pacific. In the case of B. rodriguezii, by contrast, genetic intraspecific differentiation, a fossil record of phenotypically-related forms going back to the Late Miocene, and phylogenetic position in the COI-based phylogeny, prompts the hypothesis that this species is derived from a local stock with a long history of occurrence in the warm-temperate region of the south-western Atlantic. While intertidal mussel beds from the south-western Atlantic are ecologically similar in appearance, their assembly involves components clearly differentiated in terms of historical biogeography and phylogeny. Fil: Trovant, Berenice. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina Fil: Ruzzante, Daniel E.. Dalhousie University Halifax. Department Of Biology. Marine Conservation Genetics; Canadá Fil: Basso, Nestor Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina Fil: Orensanz, Jose Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina

Acoustic telemetry is a useful tool to monitor the estuarine survival and behaviour of Atlantic salmon postsmolts. Most frequently, survival is reported as the static fraction of tagged postsmolts detected, and while the timing or location of mortality may be reported, covariates of survival or the relationship between migratory behaviour and survival are less often described. In this study, we used acoustic telemetry to follow Atlantic salmon smolts migrating to sea from four rivers in Nova Scotia, Canada. Further, we tested the relationship between migratory behaviour and survival and used mark–recapture models to examine the role of body length and tag-to-body mass as survival covariates. Survival was most heavily impacted in estuarine habitats closest to head-of-tide. Survival was affected by body length at three of four sites. The shape and spatial variability of the body length – survival relationship provided insight on mortality vectors, highlighting the potential roles of predation and osmotic stress. Survival was not influenced by repeated landward-seaward migratory movements; however, there was a significant correlation between residency and survival.

We describe temporal changes in the genetic composition of a small anadromous Atlantic salmon (Salmo salar) population from South Newfoundland, an area where salmon populations are considered threatened (COSEWIC 2010). We examined the genetic variability (13 microsatellite loci) in 869 out-migrating smolt and post-spawning kelt samples, collected from 1985 to 2011 for a total of 22 annual collections and a 30 year span of assigned cohorts. We estimated the annual effective number of breeders (Nb) and the generational effective population size (Ne) through genetic methods and demographically using the adult sex ratio. Comparisons between genetic and demographic estimates show that the adult spawners inadequately explain the observed Ne estimates, suggesting that mature male parr are significantly increasing Nb and Ne over the study period. Spawning as parr appears to be a viable and important strategy in the near absence of adult males.