Trophic consequences of non‐native species for commercial fish in a backwater bay of the Three Gorges Reservoir,Southwest China

Trophic niche overlap in native and alien fish species can lead to competitive interactions whereby non‐native fishes outcompete indigenous individuals and eventually affect the viability of natural populations. The species Erythroculter mongolicus and Erythroculter ilishaeformis (belonging to the Culterinae), which are two commercially important fish species in the backwater bay of the Pengxi River in the Three Gorges Reservoir (TGR), were threatened by competition from the non‐native Coilia ectenes (lake anchovy). The latter is an alien species introduced into the lower reaches of the Yangtze River in China and now widespread in the TGR. The trophic consequences of non‐native lake anchovy invasion for E. mongolicus and E. ilishaeformis were assessed using stable isotope analysis (δ¹³C and δ¹⁵N) and associated metrics including the isotopic niche, measured as the standard ellipse area. The trophic niche of native E. mongolicus had little overlap (<15%) with the alien fish species and was significantly reduced in size after invasion by lake anchovy. This suggests that E. mongolicus shifted to a more specialized diet after invasion by lake anchovy. In contrast, the trophic niche overlap of native fish E. ilishaeformis with the alien fish species was larger (>50%) and the niche was obviously increased, implying that fish in this species exploited a wider dietary base to maintain their energetic requirements. Thus, marked changes for the native E. mongolicus and E. ilishaeformis were detected as the trophic consequences of invasion of non‐native lake anchovy.     

The effect of top‐predator presence and phenotype on aquatic microbial communities

The presence of predators can impact a variety of organisms within the ecosystem, including microorganisms. Because the effects of fish predators and their phenotypic differences on microbial communities have not received much attention, we tested how the presence/absence, genotype, and plasticity of the predatory three‐spine stickleback (Gasterosteus aculeatus) influence aquatic microbes in outdoor mesocosms. We reared lake and stream stickleback genotypes on contrasting food resources to adulthood, and then added them to aquatic mesocosm ecosystems to assess their impact on the planktonic bacterial community. We also investigated whether the effects of fish persisted following the removal of adults, and the subsequent addition of a homogenous juvenile fish population. The presence of adult stickleback increased the number of bacterial OTUs and altered the size structure of the microbial community, whereas their phenotype affected bacterial community composition. Some of these effects were detectable after adult fish were removed from the mesocosms, and after juvenile fish were placed in the tanks, most of these effects disappeared. Our results suggest that fish can have strong short‐term effects on microbial communities that are partially mediated by phenotypic variation of fish.     

Phylogeography of the freshwater red alga B atrachospermum viride‐brasiliense (Rhodophyta,Batrachospermales)

Phylogeography of B atrachospermum viride‐brasiliense was investigated using two mitochondrial regions: the cox2‐3 spacer and the barcode region of cox1 gene. Eighty‐seven individuals were analyzed from nine stream segments throughout its distribution in Brazil. Ten cox2‐3 spacer and nine cox1 haplotypes were observed among the individuals studied (87 vs. 43, respectively). Divergences among haplotypes were relatively low (≤2.4% for cox2‐3 and ≤1.8% for cox1). Most locations have a single haplotype, whereas only two locations had two haplotypes for both markers. The haplotype network for cox2‐3 showed a phylogeographic trend from the south towards the southeast with haplotypes from the southeast more closely related. For cox1 a trend from the southeast spreading towards the south and north was revealed, with the southern haplotypes more closely associated. Results clearly indicated that B . viride‐brasiliense represents a single species and the phylogeographic pattern consisted of a closely connected group of haplotypes from southern and southeastern Brazil. Levels of intra‐ and inter‐population variation were similar for the two markers with slightly higher values for cox2‐3. The trend observed in this study is similar to that in other members of Batrachospermales with little variation within a stream segment (one or two haplotypes) and more distant haplotypes showing higher divergences. This pattern could be attributed to the fact that colonization of a site might be rare by a single event with subsequent proliferation of the population. The geographic distribution of B . viride‐brasiliense was interpreted according to the biogeographic models proposed for South America being limited to three morpho‐climatic domains or biogeographic provinces: tropical Atlantic rainforest, sub‐tropical rainforest and cerrado (Brazilian savannah).     

A wide window of migration phenology captures inter‐annual variability of favourable conditions: Results of a whole‐lake experiment with juvenile Pacific salmon

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Demography and genome divergence of lake and stream populations of an East African cichlid fish

Disentangling the processes and mechanisms underlying adaptive diversification is facilitated by the comparative study of replicate population pairs that have diverged along a similar environmental gradient. Such a setting is realized in a cichlid fish from southern Lake Tanganyika, Astatotilapia burtoni, which occurs within the lake proper as well as in various affluent rivers. Previously, we demonstrated that independent lake and stream populations show similar adaptations to the two habitat regimes. However, little is known about the evolutionary and demographic history of the A. burtoni populations in question and the patterns of genome divergence among them. Here, we apply restriction site‐associated DNA sequencing (RADseq) to examine the evolutionary history, the population structure and genomic differentiation of lake and stream populations in A. burtoni. A phylogenetic reconstruction based on genome‐wide molecular data largely resolved the evolutionary relationships among populations, allowing us to re‐evaluate the independence of replicate lake–stream population clusters. Further, we detected a strong pattern of isolation by distance, with baseline genomic divergence increasing with geographic distance and decreasing with the level of gene flow between lake and stream populations. Genome divergence patterns were heterogeneous and inconsistent among lake‐stream population clusters, which is explained by differences in divergence times, levels of gene flow and local selection regimes. In line with the latter, we only detected consistent outlier loci when the most divergent lake–stream population pair was excluded. Several of the thus identified candidate genes have inferred functions in immune and neuronal systems and show differences in gene expression between lake and stream populations.     

Identification of the maternal source of young‐of‐the‐year Arctic charr in Lake Hazen,Canada

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Long‐term panmixia in a cosmopolitan Indo‐Pacific coral reef fish and a nebulous genetic boundary with its broadly sympatric sister species

Phylogeographical studies have shown that some shallow‐water marine organisms, such as certain coral reef fishes, lack spatial population structure at oceanic scales, despite vast distances of pelagic habitat between reefs and other dispersal barriers. However, whether these dispersive widespread taxa constitute long‐term panmictic populations across their species ranges remains unknown. Conventional phylogeographical inferences frequently fail to distinguish between long‐term panmixia and metapopulations connected by gene flow. Moreover, marine organisms have notoriously large effective population sizes that confound population structure detection. Therefore, at what spatial scale marine populations experience independent evolutionary trajectories and ultimately species divergence is still unclear. Here, we present a phylogeographical study of a cosmopolitan Indo‐Pacific coral reef fish Naso hexacanthus and its sister species Naso caesius, using two mtDNA and two nDNA markers. The purpose of this study was two‐fold: first, to test for broad‐scale panmixia in N. hexacanthus by fitting the data to various phylogeographical models within a Bayesian statistical framework, and second, to explore patterns of genetic divergence between the two broadly sympatric species. We report that N. hexacanthus shows little population structure across the Indo‐Pacific and a range‐wide, long‐term panmictic population model best fit the data. Hence, this species presently comprises a single evolutionary unit across much of the tropical Indian and Pacific Oceans. Naso hexacanthus and N. caesius were not reciprocally monophyletic in the mtDNA markers but showed varying degrees of population level divergence in the two nuclear introns. Overall, patterns are consistent with secondary introgression following a period of isolation, which may be attributed to oceanographic conditions of the mid to late Pleistocene, when these two species appear to have diverged.     

Quantification of Tetradesmus obliquus (Chlorophyceae) cell size and lipid content heterogeneity at single‐cell level

Much of our current knowledge of microbial growth is obtained from studies at a population level. Driven by the realization that processes that operate within a population might influence a population's behavior, we sought to better understand Tetradesmus obliquus (formerly Scenedesmus obliquus ) physiology at the cellular level. In this work, an accurate pretreatment method to quantitatively obtain single cells of T. obliquus , a coenobia‐forming alga, is described. These single cells were examined by flow cytometry for triacylglycerol (TAG ), chlorophyll, and protein content, and their cell sizes were recorded by coulter counter. We quantified heterogeneity of size and TAG content at single‐cell level for a population of T. obliquus during a controlled standard batch cultivation. Unexpectedly, variability of TAG content per cell within the population increased throughout the batch run, up to 400 times in the final stage of the batch run, with values ranging from 0.25 to 99 pg · cell^?1. Two subpopulations, classified as having low or high TAG content per cell, were identified. Cell size also increased during batch growth with average values from 36 to 70 μm³ · cell^?1; yet cell size variability increased only up to 16 times. Cell size and cellular TAG content were not correlated at the single‐cell level. Our data show clearly that TAG production is affected by cell‐to‐cell variation, which suggests that its control and better understanding of the underlying processes may improve the productivity of T. obliquus for industrial processes such as biodiesel production.     

Retention of a chromosomal inversion from an anadromous ancestor provides the genetic basis for alternative freshwater ecotypes in rainbow trout

Migratory behaviour patterns in animals are controlled by a complex genetic architecture. Rainbow trout (Oncorhynchus mykiss) is a salmonid fish that spawns in streams but exhibits three primary life history pathways: stream‐resident (fluvial), lake‐migrant (adfluvial) and ocean‐migrant (anadromous). Previous studies examining fluvial and anadromous O. mykiss have identified several genes associated with life history divergence including the presence of an inversion complex within chromosome 5 (Omy05) that appears to maintain a suite of linked genes controlling migratory behaviour. However, adfluvial trout are migratory without being anadromous, and the genetic basis for this life history has not been investigated from evolutionary perspectives. We sampled wild, native nonanadromous rainbow trout occupying connected stream and lake habitats in a southwest Alaskan watershed to determine whether these fish exhibit genetic divergence between fluvial and adfluvial ecotypes, and whether that divergence parallels that documented in fluvial and anadromous O. mykiss. Data from restriction site‐associated DNA (RAD) sequencing revealed an association between frequencies of both the Omy05 inversion complex and other single nucleotide polymorphisms (SNPs) with habitat type (stream or lake), supporting the genetic divergence of fluvial and adfluvial individuals in sympatry. The presence of a genetic basis for migration into lakes, analogous to that documented for anadromy, indicates that the adfluvial ecotype must be recognized separately from the fluvial form of O. mykiss even though neither is anadromous. These results highlight the genetic architecture underlying migration and the importance of chromosomal inversions in promoting and sustaining intraspecific diversity.     

Estimating population size using single‐nucleotide polymorphism‐based pedigree data

Reliable population estimates are an important aspect of sustainable wildlife management and conservation but can be difficult to obtain for rare and elusive species. Here, we test a new census method based on pedigree reconstruction recently developed by Creel and Rosenblatt (2013). Using a panel of 96 single‐nucleotide polymorphisms (SNPs), we genotyped fecal samples from two Swedish brown bear populations for pedigree reconstruction. Based on 433 genotypes from central Sweden (CS) and 265 from northern Sweden (NS), the population estimates (N = 630 for CS, N = 408 for NS) fell within the 95% CI of the official estimates. The precision and accuracy improved with increasing sampling intensity. Like genetic capture–mark–recapture methods, this method can be applied to data from a single sampling session. Pedigree reconstruction combined with noninvasive genetic sampling may thus augment population estimates, particularly for rare and elusive species for which sampling may be challenging.     

Evidence for genetic differentiation in timing of maturation among nine‐spined stickleback populations

Timing of maturation is an important life‐history trait that is likely to be subjected to strong natural selection. Although population differences in timing of maturation have been frequently reported in studies of wild animal populations, little is known about the genetic basis of this differentiation. Here, we investigated population and sex differences in timing of maturation within and between two nine‐spined stickleback (Pungitius pungitius) populations in a laboratory breeding experiment. We found that fish from the high‐predation marine population matured earlier than fish from the low‐predation pond population and males matured earlier than females. Timing of maturation in both reciprocal hybrid crosses between the two populations was similar to that in the marine population, suggesting that early timing of maturation is a dominant trait, whereas delayed timing of maturation in the pond is a recessive trait. Thus, the observed population divergence is suggestive of strong natural selection against early maturation in the piscine‐predator‐free pond population.     

Validation of mark‐recapture population estimates for invasive common carp,Cyprinus carpio,in Lake Crescent,Tasmania

A mark‐recapture study based on the Petersen method was implemented in 1998 to estimate the abundance of the invasive common carp, Cyprinus carpio L., in Lake Crescent, Tasmania. Multiple gear types were employed to minimise capture bias, with multiple capture and recapture events providing an opportunity to compute and compare Petersen and Schnabel estimates. A single Petersen estimate on recapture data and two Schnabel estimates – one each on mark (forward‐Schnabel estimate) and recapture (reverse‐Schnabel estimate) data – were conducted. An independent long‐term double tag study facilitated estimation of the annual natural mortality. Subsequent fish‐down of the population suggests that, in all likelihood, the carp have been eradicated from the lake, providing an unprecedented opportunity to verify the forward population estimates carried out in 1998. Results suggest that all three estimates were close to the true population size, with the reverse‐Schnabel estimate being the most accurate and within 1% of the true population in this relatively large lake (～2365 ha). Greater accuracy of the reverse‐Schnabel approach can be attributed to either minimised fish behavioural (i.e. gear susceptibility or avoidance) or computational bias associated with the forward‐Schnabel and Petersen approaches, respectively. While the original estimates served as a guide in eradication of carp from the lake, the ultimate validation provides a reliable framework for abundance estimation of this invasive fish in relatively large water bodies elsewhere.     

Food web de‐synchronization in England's largest lake: an assessment based on multiple phenological metrics

Phenological changes have been observed globally for marine, freshwater and terrestrial species, and are an important element of the global biological ‘fingerprint’ of climate change. Differences in rates of change could desynchronize seasonal species interactions within a food web, threatening ecosystem functioning. Quantification of this risk is hampered by the rarity of long‐term data for multiple interacting species from the same ecosystem and by the diversity of possible phenological metrics, which vary in their ecological relevance to food web interactions. We compare phenological change for phytoplankton (chlorophyll a), zooplankton (Daphnia) and fish (perch, Perca fluviatilis) in two basins of Windermere over 40 years and determine whether change has differed among trophic levels, while explicitly accounting for among‐metric differences in rates of change. Though rates of change differed markedly among the nine metrics used, seasonal events shifted earlier for all metrics and trophic levels: zooplankton advanced most, and fish least, rapidly. Evidence of altered synchrony was found in both lake basins, when combining information from all phenological metrics. However, comparisons based on single metrics did not consistently detect this signal. A multimetric approach showed that across trophic levels, earlier phenological events have been associated with increasing water temperature. However, for phytoplankton and zooplankton, phenological change was also associated with changes in resource availability. Lower silicate, and higher phosphorus, concentrations were associated with earlier phytoplankton growth, and earlier phytoplankton growth was associated with earlier zooplankton growth. The developing trophic mismatch detected between the dominant fish species in Windermere and important zooplankton food resources may ultimately affect fish survival and portend significant impacts upon ecosystem functioning. We advocate that future studies on phenological synchrony combine data from multiple phenological metrics, to increase confidence in assessments of change and likely ecological consequences.     

Species‐specific separation of lake plankton reveals divergent food assimilation patterns in rotifers

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Long‐term impacts of invasive species on a native top predator in a large lake system

1. Declining abundances of forage fish and the introduction and establishment of non‐indigenous species have the potential to substantially alter resource and habitat exploitation by top predators in large lakes. 2. We measured stable isotopes of carbon (δ¹³C) and nitrogen (δ¹⁵N) in field‐collected and archived samples of Lake Ontario lake trout (Salvelinus namaycush) and five species of prey fish and compared current trophic relationships of this top predator with historical samples. 3. Relationships between δ¹⁵N and lake trout age were temporally consistent throughout Lake Ontario and confirmed the role of lake trout as a top predator in this food web. However, δ¹³C values for age classes of lake trout collected in 2008 ranged from 1.0 to 3.9‰ higher than those reported for the population sampled in 1992. 4. Isotope mixing models predicted that these changes in resource assimilation were owing to the replacement of rainbow smelt (Osmerus mordax) by round goby (Neogobius melanostomus) in lake trout diet and increased reliance on carbon resources derived from nearshore production. This contrasts with the historical situation in Lake Ontario where δ¹³C values of the lake trout population were dominated by a reliance on offshore carbon production. 5. These results indicate a reduced capacity of the Lake Ontario offshore food web to support the energetic requirements of lake trout and that this top predator has become increasingly reliant on prey resources that are derived from nearshore carbon pathways.     

The role of local adaptation in shaping fish‐mussel coevolution

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Seasonal dynamics and co‐occurrence patterns of honey bee pathogens revealed by high‐throughput RT‐qPCR analysis

The health of the honey bee Apis mellifera is challenged by introduced parasites that interact with its inherent pathogens and cause elevated rates of colony losses. To elucidate co‐occurrence, population dynamics, and synergistic interactions of honey bee pathogens, we established an array of diagnostic assays for a high‐throughput qPCR platform. Assuming that interaction of pathogens requires co‐occurrence within the same individual, single worker bees were analyzed instead of collective samples. Eleven viruses, four parasites, and three pathogenic bacteria were quantified in more than one thousand single bees sampled from sixteen disease‐free apiaries in Southwest Germany. The most abundant viruses were black queen cell virus (84%), Lake Sinai virus 1 (42%), and deformed wing virus B (35%). Forager bees from asymptomatic colonies were infected with two different viruses in average, and simultaneous infection with four to six viruses was common (14%). Also, the intestinal parasites Nosema ceranae (96%) and Crithidia mellificae/Lotmaria passim (52%) occurred very frequently. These results indicate that low‐level infections in honey bees are more common than previously assumed. All viruses showed seasonal variation, while N. ceranae did not. The foulbrood bacteria Paenibacillus larvae and Melissococcus plutonius were regionally distributed. Spearman's correlations and multiple regression analysis indicated possible synergistic interactions between the common pathogens, particularly for black queen cell virus. Beyond its suitability for further studies on honeybees, this targeted approach may be, due to its precision, capacity, and flexibility, a viable alternative to more expensive, sequencing‐based approaches in nonmodel systems.     

Fine‐scale habitat use in Indo‐Pacific humpback dolphins,Sousa chinensis,may be more influenced by fish rather than vessels in the Pearl River Estuary,China

Shifts in habitat use and distribution patterns in dolphins are often concerns that can result from habitat degradation. We investigated how potential changes to a habitat from human activity may alter dolphin distributions within Lingding Bay in the Pearl River Estuary, China, by studying the relationship between fish choruses, vessel presence and Indo‐Pacific humpback dolphin (Sousa chinensis) detection rates. Analyses revealed temporal and spatial variation within fish choruses, vessel presence and dolphin detection rates. After accounting for any temporal autocorrelation, correlations between fish choruses and dolphin detection rates were also found; however, no relationship between fish choruses and vessel presence or dolphin detection rates and vessel presence were observed. Furthermore, fewer dolphins were detected at sites where fish activity was less intense. Thus fish activity, rather than vessels, may be a key factor influencing the distribution of the dolphins within the estuary. These findings emphasize the risk of potential shifts in habitat use for Indo‐Pacific humpback dolphins due to detrimental changes to prey availability and dolphin feeding grounds from human activity, such as overfishing and coastal developments, within the estuary. This is a critical conservation issue for this dolphin population that is facing intense anthropogenic pressure.     

Carbon sources and trophic structure in a macrophyte‐dominated polyculture pond assessed by stable‐isotope analysis

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