Genetic monitoring reveals temporal stability over 30 years in a small, lake-resident brown trout population

Genetic erosion in an endangered desert fish during a megadrought despite long-term supportive breeding

Human water use combined with a recent megadrought have reduced river and stream flow through the southwest United States and led to periodic drying of formerly perennial river segments. Reductions in snowmelt runoff and increased extent of drying collectively threaten short-lived, obligate aquatic species, including the endangered Rio Grande silvery minnow (Hybognathus amarus). This species is subject to boom-and-bust population dynamics, under which large fluctuations in abundance are expected to lower estimates of effective population size and erode genetic diversity over time. Rates of diversity loss are also affected by additions of hatchery-origin fish used to supplement the wild population. We used demographic and genetic data from wild and hatchery individuals to examine the relationship of genetic diversity and effective population size to abundance over the last two decades. Genetic diversity was low during the early 2000s, but diversity and demographic metrics stabilized after the hatchery program was initiated and environmental conditions improved. Yet, from 2017 onward, allelic diversity declined (Cohen's d = 1.34) and remained low despite hatchery stocking and brief wild population recovery. Across the time series, single-sample estimates of effective population size based on linkage disequilibrium (LD Ne ) were positively associated (r = 0.53) with wild abundance and total abundance, but as the proportion of hatchery-origin spawners increased, LD Ne declined (r = -0.55). Megadrought limited wild spawner abundance and precluded refreshment of hatchery brood stocks with wild fish; hence, we predict a riverine population increasingly dominated by hatchery-origin individuals and accelerated loss of genetic diversity despite supplementation. We recommend an adaptive and accelerated management plan that integrates river flow management and hatchery operations to slow the pace of genetic diversity loss exacerbated by megadrought.

New indicators for monitoring genetic diversity applied to alpine brown trout populations using whole genome sequence data

International policy recently adopted commitments to maintain genetic diversity in wild populations to secure their adaptive potential, including metrics to monitor temporal trends in genetic diversity - so-called indicators. A national programme for assessing trends in genetic diversity was recently initiated in Sweden. Relating to this effort, we systematically assess contemporary genome-wide temporal trends (40 years) in wild populations using the newly adopted indicators and whole genome sequencing (WGS). We use pooled and individual WGS data from brown trout (Salmo trutta) in eight alpine lakes in protected areas. Observed temporal trends in diversity metrics (nucleotide diversity, Watterson's ϴ and heterozygosity) lie within proposed acceptable threshold values for six of the lakes, but with consistently low values in lakes above the tree line and declines observed in these northern-most lakes. Local effective population size is low in all lakes, highlighting the importance of continued protection of interconnected systems to allow genetic connectivity for long-term viability of these populations. Inbreeding (FROH ) spans 10%-30% and is mostly represented by ancient (<1 Mb) runs of homozygosity, with observations of little change in mutational load. We also investigate adaptive dynamics over evolutionarily short time frames (a few generations); identifying putative parallel selection across all lakes within a gene pertaining to skin pigmentation as well as candidates of selection unique to specific lakes and lake systems involved in reproduction and immunity. We demonstrate the utility of WGS for systematic monitoring of natural populations, a priority concern if genetic diversity is to be protected.

Genetic structure and relatedness of brown trout (Salmo trutta) populations in the drainage basin of the Ölfusá river, South-Western Iceland

Background

Lake Þingvallavatn in Iceland, a part of the river Ölfusá drainage basin, was presumably populated by brown trout soon after it formed at the end of the last Ice Age. The genetic relatedness of the brown trout in Þingvallavatn to other populations in the Ölfusá drainage basin is unknown. After the building of a dam at the outlet of the lake in 1959 brown trout catches declined, though numbers have now increased. The aim of this study was to assess effects of geographic isolation and potential downstream gene flow on the genetic structure and diversity in brown trout sampled in several locations in the western side of the watershed of River Ölfusá. We hypothesized that brown trout in Lake Þingvallavatn constituted several local spawning populations connected by occasional gene flow before the damming of the lake. We also estimated the effective population size (NE) of some of these populations and tested for signs of a recent population bottleneck in Lake Þingvallavatn.

Methods

We sampled brown trout inhabiting four lakes and 12 rivers within and near the watershed of River Ölfusá by means of electro- and net- fishing. After stringent data filtering, 2,597 polymorphic loci obtained from ddRADseq data from 317 individuals were ascertained as putative neutral markers.

Results

Overall, the genetic relatedness of brown trout in the Ölfusá watershed reflected the connectivity and topography of the waterways. Ancestry proportion analyses and a phylogenetic tree revealed seven distinct clusters, some of which corresponded to small populations with reduced genetic diversity. There was no evidence of downstream gene flow from Lake Þingvallavatn, although gene flow was observed from much smaller mountain populations. Most locations showed low NE values (i.e., ~14.6 on average) while the putative anadromous trout from River Sog and the spawning population from River Öxará, that flows into Lake Þingvallavatn, showed notably higher NE values (i.e., 71.2 and 56.5, respectively). No signals of recent population bottlenecks were detected in the brown trout of Lake Þingvallavatn.

Discussion

This is the first time that the genetic structure and diversity of brown trout in the watershed of River Ölfusá have been assessed. Our results point towards the presence of a metapopulation in the watershed of Lake Þingvallavatn, which has been influenced by restoration efforts and is now dominated by a genetic component originated in River Öxará. Many of the locations studied represent different populations. Those that are isolated in headwater streams and lakes are genetically distinct presenting low genetic diversity, yet they can be important in increasing the genetic variation in downstream populations. These populations should be considered for conservation and direct management.

Alternative life-history strategy contributions to effective population size in a naturally spawning salmon population

Alternative life-history tactics are predicted to affect within-population genetic processes but have received little attention. For example, the impact of precocious males on effective population size (N e) has not been quantified directly in Pacific salmon Oncorhynchus spp., even though they can make up a large percentage of the total male spawners. We investigated the contribution of precocial males ("jacks") to N e in a naturally spawning population of Coho Salmon O. kisutch from the Auke Creek watershed in Juneau, Alaska. Mature adults that returned from 2009 to 2019 (~8000 individuals) were genotyped at 259 single-nucleotide polymorphism (SNP) loci for parentage analysis. We used demographic and genetic methods to estimate the effective number of breeders per year (N b). Jack contribution to N b was assessed by comparing values of N b calculated with and without jacks and their offspring. Over a range of N b values (108-406), the average jack contribution to N b from 2009 to 2015 was 12.9% (SE = 3.8%). Jacks consistently made up over 20% of the total male spawners. The presence of jacks did not seem to influence N b/N. The linkage disequilibrium N e estimate was lower than the demographic estimate, possibly due to immigration effects on population genetic processes: based on external marks and parentage data, we estimated that immigrant spawners produced 4.5% of all returning offspring. Our results demonstrate that jacks can influence N b and N e and can make a substantial contribution to population dynamics and conservation of threatened stocks.

Redundancy analysis, genome-wide association studies and the pigmentation of brown trout (Salmo trutta L.)

The association of molecular variants with phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited, use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single- and multitrait GWAS to explore the molecular basis of pigmentation variation in brown trout (Salmo trutta) belonging to wild populations impacted by hatchery fish. Based on 75,684 single nucleotide polymorphic (SNP) markers, RDA, single- and multitrait GWAS allowed the extraction of 337 independent colour patterning loci (CPLs) associated with trout pigmentation traits, such as the number of red and black spots on flanks. Collectively, these CPLs (i) mapped onto 35 out of 40 brown trout linkage groups indicating a polygenic genomic architecture of pigmentation, (ii) were found to be associated with 218 candidate genes, including 197 genes formerly mentioned in the literature associated to skin pigmentation, skin patterning, differentiation or structure notably in a close relative, the rainbow trout (Onchorhynchus mykiss), and (iii) related to functions relevant to pigmentation variation (e.g., calcium- and ion-binding, cell adhesion). Annotated CPLs include genes with well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also markers associated with genes formerly found expressed in rainbow or brown trout skins. RDA was also shown to be useful to investigate management issues, especially the dynamics of trout pigmentation submitted to several generations of hatchery introgression.

Recent Changes in Genetic Diversity, Structure, and Gene Flow in a Passerine Experiencing a Rapid Population Decline, the Dupont’s Lark (Chersophilus duponti)

Monitoring temporal dynamics in genetic diversity is of great importance for conservation, especially for threatened species that are suffering a rapid population decline and increased fragmentation. Here, we investigate temporal variation in genetic diversity, structure, and gene flow in the Dupont’s lark (Chersophilus duponti) across most of its range. This species shows increasing levels of population fragmentation, substantial population declines, and severe range contraction, so temporal losses of genetic diversity, increasing differentiation, and decreasing gene flow are expected when comparing present day data with previous situations. To address this, we resampled sites (nine regions in two countries) after 12–15 years (five-to-seven generations) and assessed changes in genetic parameters using 11 microsatellite markers. We found no substantial loss in genetic diversity over time at the species level, but we detected considerable variation among regions in the amount of allelic diversity and heterozygosity lost over time. Temporal variation in allele frequencies (common, rare, and private alleles), and changes in genetic differentiation and gene flow over time suggest a major role of connectivity for the stability of the overall metapopulation. Our results agree with the hypothesis that connectivity rescues genetic diversity via immigration and gene flow. However, evidence of recent genetic bottleneck and the substantial changes detected in some regions are clear signs of genetic erosion and may be signalling a rapid decline of the populations. Urgent actions must be carried out to stop and reverse human impacts on this threatened lark and its habitat.

Monitoring genetic diversity with new indicators applied to an alpine freshwater top predator

Genetic diversity is the basis for population adaptation and long-term survival, yet rarely considered in biodiversity monitoring. One key issue is the need for useful and straightforward indicators of genetic diversity. We monitored genetic diversity over 40 years (1970-2010) in metapopulations of brown trout (Salmo trutta) inhabiting 27 small mountain lakes representing 10 lake systems in central Sweden using >1200 fish per time point. We tested six newly proposed indicators; three were designed for broad, international use in the UN Convention on Biological Diversity (CBD) and are currently applied in several countries. The other three were recently elaborated for national use by a Swedish science-management effort and applied for the first time here. The Swedish indicators use molecular genetic data to monitor genetic diversity within and between populations (indicators ΔH and ΔF_ST , respectively) and assess the effective population size (N_e -indicator). We identified 29 genetically distinct populations, all retained over time. Twelve of the 27 lakes harboured more than one population indicating that brown trout biodiversity hidden as cryptic, sympatric populations are more common than recognized. The N_e indicator showed values below the threshold (N_e  ≤ 500) in 20 populations with five showing N_e  < 100. Statistically significant genetic diversity reductions occurred in several populations. Metapopulation structure appears to buffer against diversity loss; applying the indicators to metapopulations suggest mostly acceptable rates of change in all but one system. The CBD indicators agreed with the Swedish ones but provided less detail. All these indicators are appropriate for managers to initiate monitoring of genetic biodiversity.

Long-term monitoring of a brown trout (Salmo trutta) population reveals kin-associated migration patterns and contributions by resident trout to the anadromous run

BACKGROUND

In species showing partial migration, as is the case for many salmonid fishes, it is important to assess how anthropogenic pressure experienced by migrating individuals affects the total population. We focused on brown trout (Salmo trutta) from the Guddal River in the Norwegian Hardanger Fjord system, which encompasses both resident and anadromous individuals. Aquaculture has led to increased anthropogenic pressure on brown trout during the marine phase in this region. Fish traps in the Guddal River allow for sampling all ascending anadromous spawners and descending smolts. We analyzed microsatellite DNA markers from all individuals ascending in 2006-2016, along with all emigrating smolts in 2017. We investigated (1) if there was evidence for declines in census numbers and effective population size during that period, (2) if there was association between kinship and migration timing in smolts and anadromous adults, and (3) to what extent resident trout were parents of outmigrating smolts.

RESULTS

Census counts of anadromous spawners showed no evidence for a decline from 2006 to 2016, but were lower than in 2000-2005. Estimates of effective population size also showed no trends of declines during the study period. Sibship reconstruction of the 2017 smolt run showed significant association between kinship and migration timing, and a similar association was indicated in anadromous spawners. Parentage assignment of 2017 smolts with ascending anadromous trout as candidate parents, and assuming that unknown parents represented resident trout, showed that 70% of smolts had at least one resident parent and 24% had two resident parents.

CONCLUSIONS

The results bear evidence of a population that after an initial decline has stabilized at a lower number of anadromous spawners. The significant association between kinship and migration timing in smolts suggests that specific episodes of elevated mortality in the sea could disproportionally affect some families and reduce overall effective population size. Finally, the results based on parentage assignment demonstrate a strong buffering effect of resident trout in case of elevated marine mortality affecting anadromous trout, but also highlight that increased mortality of anadromous trout, most of which are females, may lower overall production in the system.

Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species

Developing genomic insights is challenging in nonmodel species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool-seq data to generate a de novo genome assembly for mining exons, upon which Pool-seq data are used to estimate population divergence and diversity. We do this for two pairs of sympatric populations of brown trout (Salmo trutta): one naturally sympatric set of populations and another pair of populations introduced to a common environment. We validate our approach by comparing the results to those from markers previously used to describe the populations (allozymes and individual-based single nucleotide polymorphisms [SNPs]) and from mapping the Pool-seq data to a reference genome of the closely related Atlantic salmon (Salmo salar). We find that genomic differentiation (F ST) between the two introduced populations exceeds that of the naturally sympatric populations (F ST = 0.13 and 0.03 between the introduced and the naturally sympatric populations, respectively), in concordance with estimates from the previously used SNPs. The same level of population divergence is found for the two genome assemblies, but estimates of average nucleotide diversity differ ( π ¯  ≈ 0.002 and π ¯  ≈ 0.001 when mapping to S. trutta and S. salar, respectively), although the relationships between population values are largely consistent. This discrepancy might be attributed to biases when mapping to a haploid condensed assembly made of highly fragmented read data compared to using a high-quality reference assembly from a divergent species. We conclude that the Pool-seq-only approach can be suitable for detecting and quantifying genome-wide population differentiation, and for comparing genomic diversity in populations of nonmodel species where reference genomes are lacking.

Relationship between effective and demographic population size in continuously distributed populations

Genetic monitoring of wild populations can offer insights into demographic and genetic information simultaneously. However, widespread application of genetic monitoring is hindered by large uncertainty in the estimation and interpretation of target metrics such as contemporary effective population size, Ne . We used four long-term genetic and demographic studies (≥9 years) to evaluate the temporal stability of the relationship between Ne and demographic population size (Nc ). These case studies focused on mammals that are continuously distributed, yet dispersal-limited within the spatial scale of the study. We estimated local, contemporary Ne with single-sample methods (LDNE, Heterozygosity Excess, and Molecular Ancestry) and demographic abundance with either mark-recapture estimates or catch-per-unit effort indices. Estimates of Ne varied widely within each case study suggesting interpretation of estimates is challenging. We found inconsistent correlations and trends both among estimates of Ne and between Ne and Nc suggesting the value of Ne as an indicator of Nc is limited in some cases. In the two case studies with consistent trends between Ne and Nc , FIS was more stable over time and lower, suggesting FIS may be a good indicator that the population was sampled at a spatial scale at which genetic structure is not biasing estimates of Ne . These results suggest that more empirical work on the estimation of Ne in continuous populations is needed to understand the appropriate context to use LDNe as a useful metric in a monitoring programme to detect temporal trends in either Ne or Nc .

Keeping things local: Subpopulation Nb and Ne in a stream network with partial barriers to fish migration

For organisms with overlapping generations that occur in metapopulations, uncertainty remains regarding the spatiotemporal scale of inference of estimates of the effective number of breeders (N^b) and whether these estimates can be used to predict generational N_e. We conducted a series of tests of the spatiotemporal scale of inference of estimates of N_b in nine consecutive cohorts within a long‐term study of brook trout (Salvelinus fontinalis). We also tested a recently developed approach to estimate generational N_e from N^b and compared this to an alternative approach for estimating N^e that also accounts for age structure. Multiple lines of evidence were consistent with N^b corresponding to the local (subpopulation) spatial scale and the cohort‐specific temporal scale. We found that at least four consecutive cohort‐specific estimates of N^b were necessary to obtain reliable estimates of harmonic mean N^b for a subpopulation. Generational N^e derived from cohort‐specific N^b was within 7%–50% of an alternative approach to obtain N^e, suggesting some population specificity for concordance between approaches. Our results regarding the spatiotemporal scale of inference for N_b should apply broadly to many taxa that exhibit overlapping generations and metapopulation structure and point to promising avenues for using cohort‐specific N^b for local‐scale genetic monitoring.

Temporal genetic stability in natural populations of the waterflea Daphnia magna in response to strong selection pressure

Studies monitoring changes in genetic diversity and composition through time allow a unique understanding of evolutionary dynamics and persistence of natural populations. However, such studies are often limited to species with short generation times that can be propagated in the laboratory or few exceptional cases in the wild. Species that produce dormant stages provide powerful models for the reconstruction of evolutionary dynamics in the natural environment. A remaining open question is to what extent dormant egg banks are an unbiased representation of populations and hence of the species' evolutionary potential, especially in the presence of strong environmental selection. We address this key question using the water flea Daphnia magna, which produces dormant stages that accumulate in biological archives over time. We assess temporal genetic stability in three biological archives, previously used in resurrection ecology studies showing adaptive evolutionary responses to rapid environmental change. We show that neutral genetic diversity does not decline with the age of the population and it is maintained in the presence of strong selection. In addition, by comparing temporal genetic stability in hatched and unhatched populations from the same biological archive, we show that dormant egg banks can be consulted to obtain a reliable measure of genetic diversity over time, at least in the multidecadal time frame studied here. The stability of neutral genetic diversity through time is likely mediated by the buffering effect of the resting egg bank.

Making sense of the relationships between Ne, Nb and Nc towards defining conservation thresholds in Atlantic salmon (Salmo salar)

Effective population size over a generation (Ne) or over a reproductive cycle (Nb) and the adult census size (Nc) are important parameters in both conservation and evolutionary biology. Ne provides information regarding the rate of loss of genetic diversity and can be tracked back in time to infer demographic history of populations, whereas Nb may often be more easily quantified than Nc for short-term abundance monitoring. In this study, we propose (1) an empirical context to Waples et al. (2014) who introduced a correction to bias due to overlapping generations, and (2) a mathematical relationship between Ne and Nb for direct application in Atlantic salmon populations in Québec, Canada. To achieve this, we investigate the relationships between Ne, Nb and Nc in 10 Atlantic salmon populations, Canada, for which we genotyped 100 randomly sampled young-of-the year individuals for 5 consecutive years. The results show a positive correlation between Ne, Nb and Nc, suggesting that Nb is an indicative parameter for tracking effective population size and abundance of Atlantic salmon. However, our model allows predicting Nc from Nb values at 27% that can be partly explained by high variance in Nb/Nc both among populations (37%) and among years (19%). This result illustrates the need for thorough calibration of Nb/Nc before using Nb in monitoring programs, as well as a full understanding of the limits of such an approach. Finally, we discuss the importance of these results for the management of wild populations.

High genetic diversity of common toad (Bufo bufo) populations under strong natural fragmentation on a Northern archipelago

The last decades have shown a surge in studies focusing on the interplay between fragmented habitats, genetic variation, and conservation. In the present study, we consider the case of a temperate pond-breeding anuran (the common toad Bufo bufo) inhabiting a naturally strongly fragmented habitat at the Northern fringe of the species' range: islands offshore the Norwegian coast. A total of 475 individuals from 19 populations (three mainland populations and 16 populations on seven adjacent islands) were genetically characterized using nine microsatellite markers. As expected for a highly fragmented habitat, genetic distances between populations were high (pairwise F st values ranging between 0.06 and 0.33), with however little differences between populations separated by ocean and populations separated by terrestrial habitat (mainland and on islands). Despite a distinct cline in genetic variation from mainland populations to peripheral islands, the study populations were characterized by overall high genetic variation, in line with effective population sizes derived from single-sample estimators which were on average about 20 individuals. Taken together, our results reinforce the notion that spatial and temporal scales of fragmentation need to be considered when studying the interplay between landscape fragmentation and genetic erosion.

Estimation of the variance effective population size in age structured populations

The variance effective population size for age structured populations is generally hard to estimate and the temporal method often gives biased estimates. Here, we give an explicit expression for a correction factor which, combined with estimates from the temporal method, yield approximately unbiased estimates. The calculation of the correction factor requires knowledge of the age specific offspring distribution and survival probabilities as well as possible correlation between survival and reproductive success. In order to relax these requirements, we show that only first order moments of these distributions need to be known if the time between samples is large, or individuals from all age classes which reproduce are sampled. A very explicit approximate expression for the asymptotic coefficient of standard deviation of the estimator is derived, and it can be used to construct confidence intervals and optimal ways of weighting information from different markers. The asymptotic coefficient of standard deviation can also be used to design studies and we show that in order to maximize the precision for a given sample size, individuals from older age classes should be sampled since their expected variance of allele frequency change is higher and easier to estimate. However, for populations with fluctuating age class sizes, the accuracy of the method is reduced when samples are taken from older age classes with high demographic variation. We also present a method for simultaneous estimation of the variance effective and census population size.

Mature male parr contribution to the effective size of an anadromous Atlantic salmon (Salmo salar) population over 30 years

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.