Genetic signs of multiple colonization events in Baltic ciscoes with radiation into sympatric spring‐ and autumn‐spawners confined to early postglacial arrival

Presence of sympatric populations may reflect local diversification or secondary contact of already distinct forms. The Baltic cisco (Coregonus albula) normally spawns in late autumn, but in a few lakes in Northern Europe sympatric autumn and spring‐ or winter‐spawners have been described. So far, the evolutionary relationships and taxonomic status of these main life history forms have remained largely unclear. With microsatellites and mtDNA sequences, we analyzed extant and extinct spring‐ and autumn‐spawners from a total of 23 Swedish localities, including sympatric populations. Published sequences from Baltic ciscoes in Germany and Finland, and Coregonus sardinella from North America were also included together with novel mtDNA sequences from Siberian C. sardinella. A clear genetic structure within Sweden was found that included two population assemblages markedly differentiated at microsatellites and apparently fixed for mtDNA haplotypes from two distinct clades. All sympatric Swedish populations belonged to the same assemblage, suggesting parallel evolution of spring‐spawning rather than secondary contact. The pattern observed further suggests that postglacial immigration to Northern Europe occurred from at least two different refugia. Previous results showing that mtDNA in Baltic cisco is paraphyletic with respect to North American C. sardinella were confirmed. However, the inclusion of Siberian C. sardinella revealed a more complicated pattern, as these novel haplotypes were found within one of the two main C. albula clades and were clearly distinct from those in North American C. sardinella. The evolutionary history of Northern Hemisphere ciscoes thus seems to be more complex than previously recognized.     

Asynchronous spawning in sympatric populations of a hard coral reveals cryptic species and ancient genetic lineages

Genetic subdivision within a species is a vital component of the evolution of biodiversity. In some species of Acropora corals in Western Australia, conspecific individuals spawn in two seasons 6 months apart, which has the potential to impede gene flow and result in genetic divergence. Genetic comparison of sympatric spring and autumn spawners of Acropora samoensis was conducted to assess the level of reproductive isolation and genetic divergence between the spawning groups based on multiple loci (13 microsatellite loci, the mitochondrial control region and two nuclear introns). Bayesian clustering and principal coordinate analysis of the microsatellite loci showed a high level of genetic differentiation between the spawning groups (F’_ST = 0.30; P < 0.001), as did the sequence data from PaxC and Calmodulin (Φ_ST = 0.97 and 0.31, respectively). At the PaxC locus, the autumn and spring spawners were associated with two divergent lineages that were separated by an evolutionary distance of 1.7% and statistical tests indicate divergent selection in PaxC, suggesting this gene may play a role in coral spawning. This study indicates that the autumn and spring spawners represent two cryptic species, and highlights the importance of asynchronous spawning as a mechanism influencing speciation in corals.     

Outlier Loci Detect Intraspecific Biodiversity amongst Spring and Autumn Spawning Herring across Local Scales

Herring, Clupea harengus, is one of the ecologically and commercially most important species in European northern seas, where two distinct ecotypes have been described based on spawning time; spring and autumn. To date, it is unknown if these spring and autumn spawning herring constitute genetically distinct units. We assessed levels of genetic divergence between spring and autumn spawning herring in the Baltic Sea using two types of DNA markers, microsatellites and Single Nucleotide Polymorphisms, and compared the results with data for autumn spawning North Sea herring. Temporally replicated analyses reveal clear genetic differences between ecotypes and hence support reproductive isolation. Loci showing non-neutral behaviour, so-called outlier loci, show convergence between autumn spawning herring from demographically disjoint populations, potentially reflecting selective processes associated with autumn spawning ecotypes. The abundance and exploitation of the two ecotypes have varied strongly over space and time in the Baltic Sea, where autumn spawners have faced strong depression for decades. The results therefore have practical implications by highlighting the need for specific management of these co-occurring ecotypes to meet requirements for sustainable exploitation and ensure optimal livelihood for coastal communities.     

Habitat coupling in a large lake system: delivery of an energy subsidy by an offshore planktivore to the nearshore zone of Lake Superior

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The growth of charr, Salvelinus willughbii Günther, in Windermere

The growth of charr ( Salvelinus willughbii Günther ) caught in Windermere from 1941–1952 has been studied. Scales were used for determination of age and back-calculation of length for age. Autumn and spring spawners, males and females, and charr of normal and dwarf growth were treated separately. In fish of normal growth, the spring spawners were significantly smaller than the autumn spawners at ages 1 and 2 years, and significantly larger from age 4 years onwards. There was little difference in growth between males and females within the two spawning populations. Charr of lengths of less than 200 mm at age 4 years were considered to be dwarfs. Mean lengths at capture of male charr were: autumn spawners normal growth 272 mm, dwarf 218 mm; spring spawners normal growth 327 mm, dwarf 194 mm. The oldest recorded age was 8 years.     

New insights into patterns of coral spawning on Western Australian reefs

On reefs around Australia, coral mass spawning typically occurs during the austral spring (October/November) on the east coast, and during autumn (March/April) on the west coast. However, to investigate the incidence of a secondary spawning event in spring on the west coast, the reproductive state of corals was assessed on two reefs. The results indicated that of the 29 species of Acropora investigated, multiple colonies of 11 species spawned in late spring or in early summer, in contrast to previous reports of spawning during autumn. Additionally, of four species that were followed through time at one reef, two spawned in both spring and autumn, however, individual colonies had only one gametogenic cycle. Within a single site, conspecific colonies were reproductively isolated and may not interbreed, potentially representing the initial stage of sympatric speciation in these populations.     

Migratory behaviour of adult cisco, Coregonus albula L., in the Bothnian Bay

The population of adult cisco in the Bothnian Bay consists of a number of spawning populations. Each one of these returns to the same inshore area for spawning every autumn. In the summer these populations are mixed and occur mainly offshore. These are the main conclusions of an experiment in which cisco were marked with Carlin-type tags. The cisco were caught mainly in fyke nets both in the summer and in the autumn and released after tagging in the area where they had been caught. Fish tagged in the autumn and recaptured in the autumn one or more years later showed a strong affinity to the point of release, while fish from the same group recaptured in the summer had migrated far from the release site. The distribution of cisco that were tagged in the summer and caught in the autumn showed no correlation with the release site.     

Segregation in spawning and early life history among polymorphic Arctic charr, Salvelinus alpinus, in Thingvallavatn, Iceland

The relationships among time of spawning, incubation temperature, timing of first feeding and early growth were examined in four sympatric morphs of Arctic charr in Thingvallavatn, Iceland. Large benthivorous charr spawn in July-August at sites with cold ground-water flow. Planktivorous and piscivorous charr spawn in September-November and are not confined to ground-water sites. The spawning of small benthivorous charr overlaps with that of other morphs. Progeny of large benthivorous charr start feeding 2-3 months earlier than the progeny of autumn spawners. This results in differential size distribution and growth rates of young in the spring.     

Timing matters: species‐specific interactions between spawning time,substrate quality,and recruitment success in three salmonid species

Substratum quality and oxygen supply to the interstitial zone are crucial for the reproductive success of salmonid fishes. At present, degradation of spawning grounds due to fine sediment deposition and colmation are recognized as main factors for reproductive failure. In addition, changes in water temperatures due to climate change, damming, and cooling water inlets are predicted to reduce hatching success. We tested the hypothesis that the biological effects of habitat degradation depend strongly on the species‐specific spawning seasons and life‐history strategies (e.g., fall‐ vs. spring‐spawners, migratory vs. resident species) and assessed temperature as an important species‐specific factor for hatching success within river substratum. We studied the species‐specific differences in their responses to such disturbances using egg‐to‐fry survival of Danube Salmon (Hucho hucho), resident brown trout (Salmo trutta fario), and migratory brown trout (Salmo trutta lacustris) as biological endpoint. The egg incubation and hatching success of the salmonids and their dependence on temperature and stream substratum quality were compared. Hatching rates of Danube salmon were lower than of brown trout, probably due to higher oxygen demands and increased interstitial respiration in spring. Increases in maximum water temperature reduced hatching rates of resident and migratory brown trout (both fall‐spawners) but were positively correlated with hatching rates of Danube salmon (a spring‐spawner). Significantly longer incubation periods of resident and migratory brown trout coincided with relatively low stream substratum quality at the end of the egg incubation. Danube salmon seem to avoid low oxygen concentrations in the hyporheic zone by faster egg development favored by higher water temperatures. Consequently, the prediction of effects of temperature changes and altered stream substratum properties on gravel‐spawning fishes and biological communities should consider the observed species‐specific variances in life‐history strategies to increase conservation success.     

Effect of spatial differences in growth on distribution of seasonally co‐occurring herring Clupea harengus stocks

The mechanisms most likely to determine the distribution of the two major herring Clupea harengus stocks in their common early summer feeding ground in the eastern North Sea, Skagerrak and Kattegat were investigated through analysis of acoustic survey data from six consecutive years. No change was detected in biomass of North Sea autumn spawning C. harengus (NSAS) over time, whereas the biomass of western Baltic spring spawning C. harengus (WBSS) declined severely. Analyses of centre of abundance by stock showed no change in NSAS distribution, whereas the WBSS changed to a more western distribution over time. Contrary to previous perception of the juvenile migration, NSAS were found to leave the study area at the age between 1 and 2 years and WBSS 1 year olds were encountered in the Skagerrak. The estimated parameters of von Bertalanffy growth equations showed marked differences between areas with fish in the eastern part of the area having the lowest size at age at all ages. Further, their growth conditions appeared to deteriorate progressively over the period studied. Both NSAS and WBSS showed the highest condition in the North Sea and Skagerrak while condition was substantially lower in age Kattegat. The westward movement of spring spawners over time suggests that growth rate and possibly density of conspecifics influence the migration pattern and distribution of C. harengus in the area. In contrast, there was no evidence to suggest that distribution was constant over time within stocks or that distribution reflected size‐dependent limitations on migration distance.     

Patterns of morphological changes and hybridization between sympatric whitefish morphs (Coregonus spp.) in a Swiss lake: a role for eutrophication?

Whitefish, genus Coregonus, show exceptional levels of phenotypic diversity with sympatric morphs occurring in numerous postglacial lakes in the northern hemisphere. Here, we studied the effects of human‐induced eutrophication on sympatric whitefish morphs in the Swiss lake, Lake Thun. In particular, we addressed the questions whether eutrophication (i) induced hybridization between two ecologically divergent summer‐spawning morphs through a loss of environmental heterogeneity, and (ii) induced rapid adaptive morphological changes through changes in the food web structure. Genetic analysis based on 11 microsatellite loci of 282 spawners revealed that the pelagic and the benthic morph represent highly distinct gene pools occurring at different relative proportions on all seven known spawning sites. Gill raker counts, a highly heritable trait, showed nearly discrete distributions for the two morphs. Multilocus genotypes characteristic of the pelagic morph had more gill rakers than genotypes characteristic of benthic morph. Using Bayesian methods, we found indications of recent but limited introgressive hybridization. Comparisons with historical gill raker data yielded median evolutionary rates of 0.24 haldanes and median selection intensities of 0.27 for this trait in both morphs for 1948–2004 suggesting rapid evolution through directional selection at this trait. However, phenotypic plasticity as an alternative explanation for this phenotypic change cannot be discarded. We hypothesize that both the temporal shifts in mean gill raker counts and the recent hybridization reflect responses to changes in the trophic state of the lake induced by pollution in the 1960s, which created novel selection pressures with respect to feeding niches and spawning site preferences.     

In the shadows of snow leopards and the Himalayas: density and habitat selection of blue sheep in Manang,Nepal

There is a growing agreement that conservation needs to be proactive and pay increased attention to common species and to the threats they face. The blue sheep (Pseudois nayaur) plays a key ecological role in sensitive high‐altitude ecosystems of Central Asia and is among the main prey species for the globally vulnerable snow leopard (Panthera uncia). As the blue sheep has been increasingly exposed to human pressures, it is vital to estimate its population dynamics, protect the key populations, identify important habitats, and secure a balance between conservation and local livelihoods. We conducted a study in Manang, Annapurna Conservation Area (Nepal), to survey blue sheep on 60 transects in spring (127.9 km) and 61 transects in autumn (134.7 km) of 2019, estimate their minimum densities from total counts, compare these densities with previous estimates, and assess blue sheep habitat selection by the application of generalized additive models (GAMs). Total counts yielded minimum density estimates of 6.0–7.7 and 6.9–7.8 individuals/km² in spring and autumn, respectively, which are relatively high compared to other areas. Elevation and, to a lesser extent, land cover indicated by the normalized difference vegetation index (NDVI) strongly affected habitat selection by blue sheep, whereas the effects of anthropogenic variables were insignificant. Animals were found mainly in habitats associated with grasslands and shrublands at elevations between 4,200 and 4,700 m. We show that the blue sheep population size in Manang has been largely maintained over the past three decades, indicating the success of the integrated conservation and development efforts in this area. Considering a strong dependence of snow leopards on blue sheep, these findings give hope for the long‐term conservation of this big cat in Manang. We suggest that long‐term population monitoring and a better understanding of blue sheep–livestock interactions are crucial to maintain healthy populations of blue sheep and, as a consequence, of snow leopards.     

Homing precision of roach Rutilus rutilus in Lake Arungen,Norway

Synopsis The present study tests the precision of repeat homing of roach, Rutilus rutilus, to two tributaries of a small Norwegian Lake, Årungen. A sample of 19 959 spawners was tagged or marked in the spawning area. After spawning the roach intermingled with other spawning demes in the lake. The year after marking, 2515 (12.6%) roach were recaptured during spawning in the five tributaries, 340 (13.5) of these were strayers. This straying is considerably larger than found in comparable autumn spawning species, but approximately the same as reported for other spring spawning species. The recapture rate was lower for females than for males, probably due to increased female mortality induced by the tagging manipulation.     

Biannual Spawning and Temporal Reproductive Isolation in Acropora Corals

Coral spawning on the oceanic reef systems of north-western Australia was recently discovered during autumn and spring, but the degree to which species and particularly colonies participated in one or both of these spawnings was unknown. At the largest of the oceanic reef systems, the participation by colonies in the two discrete spawning events was investigated over three years in 13 species of Acropora corals (n = 1,855 colonies). Seven species spawned during both seasons; five only in autumn and one only in spring. The majority of tagged colonies (n = 218) spawned once a year in the same season, but five colonies from three species spawned during spring and autumn during a single year. Reproductive seasonality was not influenced by spatial variation in habitat conditions, or by Symbiodinium partners in the biannual spawner Acropora tenuis. Colonies of A. tenuis spawning during different seasons separated into two distinct yet cryptic groups, in a bayesian clustering analysis based on multiple microsatellite markers. These groups were associated with a major genetic divergence (G”_ST = 0.469), despite evidence of mixed ancestry in a small proportion of individuals. Our results confirm that temporal reproductive isolation is a common feature of Acropora populations at Scott Reef and indicate that spawning season is a genetically determined trait in at least A. tenuis. This reproductive isolation may be punctuated occasionally by interbreeding between genetic groups following favourable environmental conditions, when autumn spawners undergo a second annual gametogenic cycle and spawn during spring.     

Otolith shape: a population marker for Atlantic herring Clupea harengus

Otolith shape variation of seven Atlantic herring Clupea harengus populations from Canada, the Faroe Islands, Iceland, Ireland, Norway and Scotland, U.K., covering a large area of the species' distribution, was studied in order to see if otolith shape can be used to discriminate between populations. The otolith shape was obtained using quantitative shape analysis, transformed with Wavelet and analysed with multivariate methods. Significant differences were detected among the seven populations, which could be traced to three morphological structures in the otoliths. The differentiation in otolith shape between populations was not only correlated with their spawning time, indicating a strong environmental effect, but could also be due to differing life‐history strategies. A model based on the shape differences discriminates with 94% accuracy between Icelandic summer spawners and Norwegian spring spawners, which are known to mix at feeding grounds. This study shows that otolith shape could become an accurate marker for C. harengus population discrimination.     

Temporal and spatial segregation of spawning in sympatric populations of Atlantic salmon, Salmo salar L., and brown trout, Salmo trutta L.

Based on data from Norwegian streams with sympatric populations of Atlantic salmon and brown trout, it is suggested that temporal segregation is the main mechanism segregating Atlantic salmon and brown trout during spawning. Peak spawning of trout was about 15 days earlier than that of salmon. Physical factors, such as water depth, water velocity and distance from the river banks segregate spawning sites of salmon and trout poorly. Gravel sizes of the redds of salmon and trout were significantly different, though with a considerable overlap, and mean egg depth of salmon and trout were 0.18 and 0.12 m, respectively, probably attributable to the different size of spawners of salmon and trout. None of the temporal or spatial parameters analysed segregate spawners of salmon and trout completely. Species determination of eggs and alevins from the redds showed no interspecific superimposition of redds. It is, therefore, concluded that low survival of hybrids after hatching does not explain the low frequency of hybrids observed in sympatric populations of salmon and trout.     

Dynamic micro-geographic and temporal genetic diversity in vertebrates: the case of lake-spawning populations of brown trout (Salmo trutta)

Conservation of species should be based on knowledge of effective population sizes and understanding of how breeding tactics and selection of recruitment habitats lead to genetic structuring. In the stream‐spawning and genetically diverse brown trout, spawning and rearing areas may be restricted source habitats. Spatio–temporal genetic variability patterns were studied in brown trout occupying three lakes characterized by restricted stream habitat but high recruitment levels. This suggested non‐typical lake‐spawning, potentially representing additional spatio–temporal genetic variation in continuous habitats. Three years of sampling documented presence of young‐of‐the‐year cohorts in littoral lake areas with groundwater inflow, confirming lake‐spawning trout in all three lakes. Nine microsatellite markers assayed across 901 young‐of‐the‐year individuals indicated overall substantial genetic differentiation in space and time. Nested gene diversity analyses revealed highly significant (≤P = 0.002) differentiation on all hierarchical levels, represented by regional lakes (F_LT = 0.281), stream vs. lake habitat within regional lakes (F_HL = 0.045), sample site within habitats (F_SH = 0.010), and cohorts within sample sites (F_CS = 0.016). Genetic structuring was, however, different among lakes. It was more pronounced in a natural lake, which exhibited temporally stable structuring both between two lake‐spawning populations and between lake‐ and stream spawners. Hence, it is demonstrated that lake‐spawning brown trout form genetically distinct populations and may significantly contribute to genetic diversity. In another lake, differentiation was substantial between stream‐ and lake‐spawning populations but not within habitat. In the third lake, there was less apparent spatial or temporal genetic structuring. Calculation of effective population sizes suggested small spawning populations in general, both within streams and lakes, and indicates that the presence of lake‐spawning populations tended to reduce genetic drift in the total (meta‐) population of the lake.     

An electrophoretic and biometric study of Arctic charr, Salvelinm alpinus (L.), from ten British lakes

Samples of Arctic charr, Salvelinus alpinus (L.), were collected from the eight Cumbrian lakes containing all the known English populations. Comparative material was obtained from North Wales and southern Scotland. Comparisons were performed using otolith ages, meristic and morphological characters and by assessing allele frequencies for serum esterase and for skeletal muscle malate dehydrogenase. The results confirm that both basins of Windermere contain spring and autumn spawning races of charr. As well as differing genetically and exhibiting differing growth rates, the two races have different mean gill raker numbers and mean gill raker lengths. The latter two variables were used to derive a discriminant function which enables individual charr to be ascribed to the correct race with 94-96% accuracy. Within both principal races there were further significant differences between charr from the north and south basins of the lake and possibly also between different spawning grounds within each basin. Variation between six of the remaining seven Cumbrian populations is significant but generally no greater than that between the Windermere spring and autumn spawners. The exception is the Ennerdale charr which stands out on morphological, meristic and genetic characters, has a rapid growth rate despite its oligotrophic environment, and is a river rather than a lake spawner. The charr from North Wales and southern Scotland were clearly distinct, both from each other and from the English populations.     

Temporal stability and assignment power of adaptively divergent genomic regions between herring (Clupea harengus) seasonal spawning aggregations

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.     

Alternative tactics in spawning site selection by brook trout (Salvelinus fontinalis) related to incubation microhabitats in a harsh winter environment

1. Species with distributions that span a broad range of latitudes may have populations that exhibit distinct life history traits associated with environmental gradients. The majority of previous studies have indicated a strong association between spawning site selection by brook trout (Salvelinus fontinalis) and the presence of upwelling groundwater, but does this generalisation extend to the thermal regimes experienced at northern sites? 2. We investigated the role of hyporheic flow in redd site selection by brook trout in a relatively high‐latitude boreal system. Hyporheic flows through streambed substratums can be dominated by groundwater or surface water and may be influenced by the presence of morphological features. For autumn spawners such as brook trout, embryos situated in microhabitats where hyporheic flow in the shallow substratum is groundwater dominant (i.e. warmer in winter) are likely to experience accelerated development rates relative to embryos in redds where there is downwelling surface water (i.e. colder in winter). 3. We measured vertical hydraulic gradients (VHG) at the microhabitat scale and spatial and temporal variation in upwelling/downwelling flow and thermal regimes in brook trout spawning/incubation habitats. Additionally, we noted the proximity of redd sites to stream morphological features (e.g. riffle crests). 4. Our results indicate that upwelling flow was not a decisive cue in redd site selection at the microhabitat scale (10⁰ m) as an approximately equal number of redds were situated in microhabitats with upward flow as compared to microhabitats with downward flow through the redd. Redds situated on bedforms with convex longitudinal profiles (e.g. riffle crests, log steps) were associated with downward flow, whereas redds not immediately adjacent to these bedform features were associated with upward flow. Winter streambed temperatures confirmed that both sites with steady upwelling (i.e. warm incubation regime) and downwelling (i.e. cold incubation regime) were indeed selected by spawners. 5. Our observations that spawners utilised both cold‐regime and warm‐regime sites suggests the existence of distinct reproductive tactics related to hyporheic flow patterns in this boreal system. As temperature is the dominant factor controlling rates of embryonic development, the use of spawning microhabitats with distinct thermal regimes implies substantial differences in the timing of hatching and the phenology of emergence.