Lake Ecotypes Research Articles

Unravelling the identity of lake ecotype of brown trout (Salmo trutta) in Slovenia: genetic insights and conservation implications

Abstract The genetic identity and conservation status of lake ecotype of brown trout (Salmo trutta) populations in Slovenia’s Alpine lakes Bled and Bohinj have been subjected to changes due to historical stocking practices. We aimed to evaluate the genetic differentiation and origins of these populations to advise for correct conservation strategies. Using microsatellite and mitochondrial DNA analysis on 365 trout specimens, we explored the genetic diversity and structure of these populations, comparing them with potential originators. Results revealed distinct genetic profiles between Bled and Bohinj lake trout, with Bohinj lake trout closely aligned with the native Danubian lineage and Bled lake trout showing a hybrid composition, significantly influenced by hatchery-introduced Atlantic lineage strains. The genetic distinction between these populations underscores the complexity of their conservation, showcasing the impact of human-mediated introductions on natural populations. The urgent need for conservation measures to preserve the Bohinj population’s native genetic pool is highlighted, underlining the must to prevent the transfer of individuals from Lake Bled or elsewhere and to reconsider stocking practises in order to prevent further genetic dilution of these iconic European lake dwellers.

The genomics of phenotypically differentiated Asellus aquaticus cave, surface stream and lake ecotypes.

Organisms well suited for the study of ecotype formation have wide distribution ranges, where they adapt to multiple drastically different habitats repeatedly over space and time. Here we study such ecotypes in a Crustacean model, Asellus aquaticus, a commonly occurring isopod found in freshwater habitats as diverse as streams, caves and lakes. Previous studies focusing on cave vs. surface ecotypes have attributed depigmentation, eye loss and prolonged antennae to several south European cave systems. Likewise, surveys across multiple Swedish lakes have identified the presence of dark-pigmented "reed" and light-pigmented "stonewort" ecotypes, which can be found within the same lake. In this study, we sequenced the first draft genome of A. aquaticus, and subsequently use this to map reads and call variants in surface stream, cave and two lake ecotypes. In addition, the draft genome was combined with a RADseq approach to perform a quantitative trait locus (QTL) mapping study using a laboratory bred F2 and F4 cave×surface intercross. We identified genomic regions associated with body pigmentation, antennae length and body size. Furthermore, we compared genome-wide differentiation between natural populations and found several genes potentially associated with these habitats. The assessment of the cave QTL regions in the light-dark comparison of lake populations suggests that the regions associated with cave adaptation are also involved with genomic differentiation in the lake ecotypes. These demonstrate how troglomorphic adaptations can be used as a model for related ecotype formation.

Assessing thermal adaptation using family-based association and FST outlier tests in a threatened trout species.

Discovering genetic markers associated with phenotypic or ecological characteristics can improve our understanding of adaptation and guide conservation of key evolutionary traits. The Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) of the northern Great Basin Desert, USA, demonstrated exceptional tolerance to high temperatures in the desert lakes where it resided historically. This trait is central to a conservation hatchery effort to protect the genetic legacy of the nearly extinct lake ecotype. We genotyped full-sibling families from this conservation broodstock and samples from the only two remaining, thermally distinct, native lake populations at 4,644 new single nucleotide polymorphisms (SNPs). Family-based genome-wide association testing of the broodstock identified nine and 26 SNPs associated with thermal tolerance (p<0.05 and p<0.1), measured in a previous thermal challenge experiment. Genes near the associated SNPs had complex functions related to immunity, growth, metabolism and ion homeostasis. Principal component analysis using the thermotolerance-related SNPs showed unexpected divergence between the conservation broodstock and the native lake populations at these loci. FST outlier tests on the native lake populations identified 18 loci shared between two or more of the tests, with two SNPs identified by all three tests (p<0.01); none overlapped with loci identified by association testing in the broodstock. A recent history of isolation and the complex genetic and demographic backgrounds of Lahontan cutthroat trout probably limited our ability to find shared thermal tolerance loci. Our study extends the still relatively rare application of genomic tools testing for markers associated with important phenotypic or environmental characteristics in species of conservation concern.

Life at the top: Lake ecotype influences the foraging pattern, metabolic costs and life history of an apex fish predator.

We used acoustic telemetry and acceleration sensors to compare population-specific measures of the metabolic costs of an apex fish predator living in four separate lakes. We chose our study species and populations to provide a strong test of recent theoretical predictions that optimal foraging by an apex fish predator in a typical aquatic environment would be consistent with feeding to satiation rather than continuous feeding. We chose four populations where the primary prey type differed along a body size gradient (from small invertebrates to large planktivorous fish) and along a thermal accessibility gradient (from easily accessible cold-water pelagic prey to less accessible warm-water epilimnetic and littoral prey). We expected that these gradients in prey type would evoke distinctly different activity gradients depending on whether predators fed to satiation (e.g., less frequent "rest" detections where primary prey are smaller/less accessible) or fed continuously (e.g., fixed level of "rest" detections under all prey conditions). Our study organism was a fall spawning, cold-water visual apex predator (lake trout). Therefore, we focused our study on diel (early night, dawn, day, dusk, late night) changes in metabolic costs associated with summer feeding behaviour. The duration (~20days) and fine temporal scale (~30min) of our behavioural data provided a uniquely detailed picture of intra- and inter-population differences in activity patterns over a critical period in the annual growing season. In all populations, diel shifts in activity were qualitatively consistent with that expected of a visual predator (e.g., resting state detections were most frequent at night). Between-lake differences in daytime thermal experience were qualitatively consistent with between-lake differences in the location of primary prey (e.g., excursions to warm habitats were common in lakes with epilimnetic/littoral fish as primary prey and relatively rare in lakes with pelagic cold-water invertebrates/fish as primary prey). Daytime activity patterns were more consistent with the feeding pattern expected from feeding to satiation rather than continuous feeding: (a) individuals in all four populations exhibited clearly delineated bouts of resting behaviour and active behaviour; (b) the frequency of resting bouts and the resultant overall cost of daily activity were strongly associated with the size and accessibility of prey-in lakes with smaller and/or less accessible prey, predators rested less frequently, exhibited marginally higher costs when active and had higher overall daytime activity costs. Within each lake, similar changes in activity occurred concurrently with diel changes in prey accessibility/relative density.

Female assortative mate choice functionally validates synthesized male odours of evolving stickleback river-lake ecotypes.

During mate choice decisions, females of many vertebrates use male olfactory cues to achieve immunogenetic optimality of their offspring. Three-spined sticklebacks (Gasterosteus aculeatus) populating habitats that differ in their parasite communities evolve locally adapted combinations of genetic variants encoded at the major histocompatibility complex (MHC). Such adaptation confers optimal resistance to the local parasite fauna. Immunogenetic signatures co-evolved with local parasites favour population-specific assortative mate choice behaviour. Previous studies have shown that female sticklebacks evaluate male MHC-associated olfactory cues during the process of mate choice, but how habitat-specific information is exchanged between males and females has remained elusive. Here, we directly demonstrate the molecular nature of the olfactory cue providing habitat-specific information. Under controlled laboratory conditions, females that are ready to mate prefer mixtures of synthetic MHC peptide ligands mimicking the optimal allele number of their original population. These results imply that female sticklebacks can determine the number of MHC alleles of their prospective mates, compare it to their own immunogenetic status, and, if optimal with respect to the immunogenetic complementarity, accept the male as mate. Our results suggest a potentially common mechanism of ecological speciation in vertebrates that is based on the olfactory assessment of habitat-specific immunogenetic diversity.

Genetic variation and the relationship between stream and lake ecotypes of a threatened desert Catostomid, the Warner sucker (Catostomus warnerensis)

AbstractMany fish species exhibit diverse life history strategies that help maintain population viability. An understanding of the relationships among these strategies is crucial for prioritising conservation actions. The Warner sucker, endemic to the Warner Lakes Basin in southern Oregon, USA, is one example of a taxon where a lack of information regarding relationships among life history strategies has hampered conservation efforts. Warner suckers have two distinct life history types: stream‐type fish that have a fluvial life history and lake‐type fish that have an adfluvial life history. There are advantages and disadvantages associated with each life history, and presently the relationship between life history types is not well understood. Our objectives were to determine the amount of genetic variation within and among tributary populations of Warner suckers and to determine the origins of suckers collected in the Warner Lakes. We collected individuals from four tributary populations, a refugial population, and Hart and Crump lakes and genotyped them at 16 microsatellite loci. Estimates of genetic variation among populations suggested low levels of gene flow (FST = 0.153) and genetic variation among populations seemed to be influenced by population and habitat characteristics. Nearly all of the individuals collected in Hart and Crump lakes originated in a single tributary, Deep Creek, which likely reflects reduced habitat connectivity between most other tributaries and the Warner Lakes. Data presented in this study are useful for evaluating the status of Warner sucker populations and for prioritising conservation actions such as the removal and modification of barriers.

The association of feeding behaviour with the resistance and tolerance to parasites in recently diverged sticklebacks.

Divergent natural selection regimes can contribute to adaptive population divergence, but can be sensitive to human-mediated environmental change. Nutrient loading of aquatic ecosystems, for example, might modify selection pressures by altering the abundance and distribution of resources and the prevalence and infectivity of parasites. Here, we used a mesocosm experiment to test for interactive effects of nutrient loading and parasitism on host condition and feeding ecology. Specifically, we investigated whether the common fish parasite Gyrodactylus sp. differentially affected recently diverged lake and stream ecotypes of three-spined stickleback (Gasterosteus aculeatus). We found that the stream ecotype had a higher resistance to Gyrodactylus sp. infections than the lake ecotype, and that both ecotypes experienced a cost of parasitism, indicated by negative relationships between parasite load and both stomach fullness and body condition. Overall, our results suggest that in the early stages of adaptive population divergence of hosts, parasites can affect host resistance, body condition and diet.

Three routes to crypsis: Stasis, convergence, and parallelism in the Mastigias species complex (Scyphozoa, Rhizostomeae)

Evolutionary inference can be complicated by morphological crypsis, particularly in open marine systems that may rapidly dissipate signals of evolutionary processes. These complications may be alleviated by studying systems with simpler histories and clearer boundaries, such as marine lakes—small bodies of seawater entirely surrounded by land. As an example, we consider the jellyfish Mastigias spp. which occurs in two ecotypes, one in marine lakes and one in coastal oceanic habitats, throughout the Indo-West Pacific (IWP). We tested three evolutionary hypotheses to explain the current distribution of the ecotypes: (H1) the ecotypes originated from an ancient divergence; (H2) the lake ecotype was derived recently from the ocean ecotype during a single divergence event; and (H3) the lake ecotype was derived from multiple, recent, independent, divergences. We collected specimens from 21 locations throughout the IWP, reconstructed multilocus phylogenetic and intraspecific relationships, and measured variation in up to 40 morphological characters. The species tree reveals three reciprocally monophyletic regional clades, two of which contain ocean and lake ecotypes, suggesting repeated, independent evolution of coastal ancestors into marine lake ecotypes, consistent with H3; hypothesis testing and an intraspecific haplotype network analysis of samples from Palau reaffirms this result. Phylogenetic character mapping strongly correlates morphology to environment rather than lineage (r=0.7512, p<0.00001). Considering also the deeper relationships among regional clades, morphological similarity in Mastigias spp. clearly results from three separate patterns of evolution: morphological stasis in ocean medusae, convergence of lake morphology across distinct species and parallelism between lake morphologies within species. That three evolutionary routes each result in crypsis illustrates the challenges of interpreting evolutionary processes from patterns of biogeography and diversity in the seas. Identifying cryptic species is only the first step in understanding these processes; an equally important second step is exploring and understanding the processes and patterns that create crypsis.

Dissimilatory nitrate reduction pathways in an oligotrophic freshwater ecosystem: spatial and temporal trends

Elevated nitrate (NO3 � ) concentrations can cause eutrophication, which may lead to harmful algal blooms, loss of habitat and reduction in biodiversity. Denitrification, a dissimilatory process that removes NO3 � mainly as dinitrogen gas (N2), is believed to be the dominant NO3 � re- moval pathway in aquatic ecosystems. Evidence suggests that a less well-studied process, dissimila- tory nitrate reduction to ammonium (DNRA), which retains nitrogen (N) in the system, may also be important under favorable conditions. Using stable isotope tracers in sealed microcosms, we mea- sured the potential for NO3 � losses due to DNRA and denitrification in an oligotrophic freshwater ecosystem. We took sediment and water samples at runoff and baseflow, across several ecotypes. Our objective was to quantify the relative importance of DNRA compared to denitrification with changes in ecotype and season. Potential denitrification rates ranged from 0 to 0.14 ± 0.03 µgN gAFDM �1 d �1 . Potential DNRA rates ranged from 0 to 0.0051 ± 0.0008 µgN gAFDM �1 d �1 . Denitrifica- tion losses peaked at the inflow stream ecotype at 96.2% of total dissimilatory NO3 � removal, whereas losses due to DNRA peaked in the lake ecotype at 34.4%. When averaged over the entire system, denitrification peaked at baseflow (31.2%), while DNRA peaked at runoff (2.9%). Although NO3 � transformations due to denitrification were higher than DNRA in all ecotype and temporal comparisons, our results suggest that DNRA is also important under favorable conditions.

Population genomics of parallel phenotypic evolution in stickleback across stream–lake ecological transitions

Understanding the genetics of adaptation is a central focus in evolutionary biology. Here, we use a population genomics approach to examine striking parallel morphological divergences of parapatric stream-lake ecotypes of threespine stickleback fish in three watersheds on the Haida Gwaii archipelago, western Canada. Genome-wide variation at greater than 1000 single nucleotide polymorphism loci indicate separate origin of giant lake and small-bodied stream fish within each watershed (mean F(ST) between watersheds = 0.244 and within = 0.114). Genome scans within watersheds identified a total of 21 genomic regions that are highly differentiated between ecotypes and are probably subject to directional selection. Most outliers were watershed-specific, but genomic regions undergoing parallel genetic changes in multiple watersheds were also identified. Interestingly, several of the stream-lake outlier regions match those previously identified in marine-freshwater and benthic-limnetic genome scans, indicating reuse of the same genetic loci in different adaptive scenarios. We also identified multiple new outlier loci, which may contribute to unique aspects of differentiation in stream-lake environments. Overall, our data emphasize the important role of ecological boundaries in driving both local and broadly occurring parallel genetic changes during adaptation.

Parasite diversity, patterns of MHC II variation and olfactory based mate choice in diverging three-spined stickleback ecotypes

Ecological speciation has been the subject of intense research in evolutionary biology but the genetic basis of the actual mechanism driving reproductive isolation has rarely been identified. The extreme polymorphism of the major histocompatibility complex (MHC), probably maintained by parasite-mediated selection, has been proposed as a potential driver of population divergence. We performed an integrative field and experimental study using three-spined stickleback river and lake ecotypes. We characterized their parasite load and variation at MHC class II loci. Fish from lakes and rivers harbor contrasting parasite communities and populations possess different MHC allele pools that could be the result of a combined action of genetic drift and parasite-mediated selection. We show that individual MHC class II diversity varies among populations and is lower in river ecotypes. Our results suggest the action of homogenizing selection within habitat type and diverging selection between habitat types. Finally, reproductive isolation was suggested by experimental evidence: in a flow channel design females preferred assortatively the odor of their sympatric male. This demonstrates the role of olfactory cues in maintaining reproductive isolation between diverging fish ecotypes.

Evolutionary diversification of opercle shape in Cook Inlet threespine stickleback

We investigated the evolution of a large facial bone, the opercle (OP), in lake populations of the threespine stickleback that were founded by anadromous ancestors, in Cook Inlet, Alaska. Recent studies characterized OP variation among marine and lake populations and mapped a quantitative trait locus with a large influence on OP shape. Using populations from diverse environments and independent evolutionary histories, we examined divergence of OP shape from that of the anadromous ancestor. We report preliminary evidence for divergence between benthic and generalist lake ecotypes, necessitating further investigation. Furthermore, rapid divergence of OP shape has occurred in a lake population that was founded by anadromous stickleback in the 1980s, which is consistent with divergence of other phenotypic traits and with OP diversification in other lake populations. By contrast, there has been limited evolution of OP shape in a second lake population that may have experienced a genetic bottleneck early in its history and lacks genetic variation for OP divergence. Taken together, the results obtained from these two populations are consistent with studies of other stickleback phenotypic traits that implicate ancestral variation in postglacial adaptive radiation of threespine stickleback in fresh water. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 832–844.

Vegetation communities of British lakes: a revised classification scheme for conservation

AbstractA revised classification scheme is described for standing waters in Britain, based on the TWINSPAN analysis of a dataset of aquatic plant records from 3447 lakes in England, Wales and Scotland, which is held by the Joint Nature Conservation Committee.Separate ecological descriptions of 11 distinct lake groups (A–J) are presented with summary environmental data, macrophyte constancy tables and maps showing their distribution. These lake groups include small dystrophic waters dominated bySphagnumspp.; large, acid, upland lakes supporting a diversity of plant species, includingJuncus bulbosus,Littorella uniflora,Lobelia dortmannaandMyriophyllum alterniflorum; low‐altitude, above‐neutral lakes with a high diversity of plant species, characterized by the presence ofPotamogetonspp.,Charaspp. or water‐lilies and other floating‐leaved vegetation; and coastal, brackish lakes, with macroalgae.The Plant Lake Ecotype Index (PLEX) is presented as an indicator of changing lake environments. PLEX scores reflecting the new classification scheme have been developed for individual plant species and lakes. Applications of the index are demonstrated.There is discussion of possible applications of the data collected and the resultant classification, in the context of the Habitats Directive, the Water Framework Directive and other conservation requirements.© Crown copyright 2006. Reproduced with the permission of Her Majesty's Stationery Office. Published by John Wiley &amp; Sons, Ltd.

Ecological growth response specificity of two Douglas-fir ecotypes inoculated with coexistent beneficial rhizosphere bacteria

The influence of inoculation with rhizosphere bacteria on Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) seedling emergence in a controlled environment and on survival and growth in the field was investigated. Seed or seedlings of interior and coastal Douglas-fir ecotypes originating from the vicinity of Williams Lake and Chilliwack, British Columbia, Canada, respectively, were inoculated with two strains of rhizosphere bacteria, Arthrobacter oxydans strain N74 and Pseudomonas aureofaciens strain K23. These strains were previously isolated from naturally regenerating Douglas-fir seedlings collected from the Williams Lake and Chilliwack sites, respectively. Seed inoculation with either strain of bacteria, K23 or N74, stimulated the rate of seedling emergence, but these effects were not ecotype specific. While inoculation did not affect germination percentage, ecotype-specific seedling growth responses were detected 13 months after field planting. Arthrobacter oxydans strain N74 significantly stimulated seedling branching and enhanced root and shoot dry weight of the Williams Lake ecotype but had no significant stimulatory effect on growth of the Chilliwack ecotype. Pseudomonas aureofaciens strain K23 significantly stimulated shoot branching and root dry weight of Chilliwack Douglas-fir but had no significant stimulatory effect on growth of that from Williams Lake. When treatments of Douglas-fir seedlings and rhizosphere bacteria that originated from the same geographic site were pooled and compared with uninoculated controls, significant increases in shoot branch number and root dry weight were also detected. No significant difference in seedling growth was detected when treatments of seedlings and bacteria that originated from different sites were pooled and compared with uninoculated controls. Based on these results, we hypothesize that plant–microbe specificity may be an important component of Douglas-fir – beneficial rhizosphere bacteria interactions in the field. Key words: Douglas-fir seedlings, emergence, growth, rhizosphere bacteria, inoculation.