Invasion genomics of lionfish in the Mediterranean Sea

Microplastic distribution, abundance, and composition in the sediments, water, and fishes of the Red and Mediterranean seas, Egypt

Bacteriochlorophyll a-containing aerobic anoxygenic phototrophs (AAnP) have been proposed to account for up to 11% of the total surface water microbial community and to potentially have great ecological importance in the world's oceans. Recently, environmental and genomic data based on analysis of the pufM gene identified the existence of alpha-proteobacteria as well as possible gamma-like proteobacteria among AAnP in the Pacific Ocean. Here we report on analyses of environmental samples from the Red and Mediterranean Seas by using pufM as well as the bchX and bchL genes as molecular markers. The majority of photosynthesis genes retrieved from these seas were related to Roseobacter-like AAnP sequences. Furthermore, the sequence of a novel photosynthetic operon organization from an uncultured Roseobacter-like bacterial artificial chromosome retrieved from the Red Sea is described. The data show the presence of Roseobacter-like bacteria in Red and Mediterranean Sea AAnP populations in the seasons analyzed.

Molecular evaluations of successful invaders are common, however studies of introduced species that have had limited invasion success, or have died out completely, are rare. We studied an introduced population of speckled dace (Rhinichthys osculus) from northern California, USA that has rapidly increased in abundance but remained restricted to a 25-km stretch of river since its introduction in the mid-1980s. Field and laboratory analyses indicate that invasion success of speckled dace is constrained by the combined effects of multiple predators. The role of bottleneck effects associated with the introduction has not been studied. We assayed variation in seven microsatellite loci and one mitochondrial DNA gene in the introduced population and nine putative source populations to identify the source population and evaluate bottleneck effects. The Trinity River system was supported as the source owing to its genetic similarity and geographic proximity to the introduced population. Consistent with a bottleneck, the introduced population exhibited reduced allelic and haplotype richness in comparison to source populations. Estimates of the genetically effective number of individuals founding the introduced population using nuclear coalescent analyses and a mitochondrial simulation procedure were highly concordant in suggesting that the initial colonizing group was comprised of about 10 individuals. A bottleneck effect in an exotic species exhibiting limited invasion success has rarely been documented and thus introduction of speckled dace represents an important model system for future investigation. Establishing a relationship between genetic diversity and factors limiting invasion success in this system (e.g., predator avoidance) will help determine the extent to which genetic diversity loss has constrained invasion success in speckled dace.

Organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) residues were studied in different mollusk species from the Egyptian Mediterranean and Red Sea coasts. The average levels of OCPs in mollusks comprised chlordanes, dieldrins, total endrin, endosulfan compounds, and methoxychlor (DECEM), dichlorodiphenyltrichloroethanes (DDTs), and, hexachlorocyclohexanes (HCHs). The averages of HCHs, DDTs, and polychlorinated biphenyls (PCBs) in mollusks from the Mediterranean Sea were 1.13±1.21, 1.30±1.27, and 1.40±0.93 ng/g, respectively; from the Red Sea, they were 0.62±0.90, 1.77±1.82, and 6.44±5.05 ng/g, respectively. The analysis of HCHs, DDTs, and PCBs in mollusks indicates a new usage of lindane, PCB congeners, and the input of technical HCH and aged DDT. The data showed that the Red Sea Coast was more affected by PCBs congeners than the Mediterranean Sea Coast, which may be attributed to the different activities along the two coastal areas. Mollusks in the Mediterranean Sea had higher dieldrins, total endrin, endosulfan compounds, and methoxychlor contents than those in the Red Sea. Interestingly, HCHs, DDTs, and PCBs levels were lower than those recommended for Swedish Food Regulation and U.S. Food and Drug Administration, which means that mollusks from these two coastal areas are safe as food.

The present work utilized partial sequences of cytochrome c oxidase subunit I (COI) to study Red Sea populations of threadfin breams (Nemipteridae), and compare their genetic diversity to that of Mediterranean Sea (Nemipterus randalli only) and Indo-Pacific populations. A Maximum Likelihood tree separated four fish species - N. randalli, N. japonicus, N. bipunctatus, and N. zysron - into four clades. Haplotype analyses revealed a strong case of the founder effect for the Lessepsian migrant N. randalli: Three haplotypes represented all sampled geographical ranges in the Mediterranean Sea and only one haplotype was shared with a Red Sea individual, presenting evidence that the colonizing population was founded by a small number of migrants. The Red Sea population of N. japonicus shared haplotypes with Persian Gulf and Indian Ocean populations, but South China Sea populations remained fully isolated. The haplotype networks of N. randalli and N. bipunctatus also revealed haplotype sharing between Red Sea and Indian Ocean populations. For N. zysron, one haplotype was shared between Indonesia and the Persian Gulf. We discuss the impact of continued usage of public database sequences of initially misidentified organisms and provide recommendations for avoiding distribution of sequences with incorrect scientific names.

Invasive alien species are a major threat to global biodiversity, thus recent work has aimed to identify traits of successful invaders to better inform management efforts and predictions of future invasions. Personality and intraspecific behavioral variation are important characteristics that may mediate individuals’ and species’ invasion success. However, to the best of our knowledge, no study to date has looked at the personality differences between an invasive species in its native and invasive ranges. Here, we filled this gap by studying the sociality and self-grooming behavior of eastern gray squirrels ( Sciurus carolinensis ) in their native range in Northeastern USA and in their invasive range in Italy. We used the open field and mirror-image stimulation tests to assess the personality of 466 unique gray squirrels, including 271 individuals from the native population and 195 from the invasive population. We found that both the distribution and the median value of sociality significantly differed between populations, with a higher median value of sociality among invasive squirrels, while the distribution and median of self-grooming, a proxy for stress-coping ability, did not significantly differ between populations. Overall, we demonstrate that certain personality traits differ between native and invasive populations, highlighting the importance of considering intraspecific behavioral diversity for the prediction and management of invasive alien species. We urge further work to elucidate the mechanisms behind such personality differences.

Plant–soil biota interactions of an invasive species in its native and introduced ranges: Implications for invasion success

Follow-up analyses of the AFLP data published in Lachmuth et al. (2010) revealed that wrong peak height thresholds had been applied during genotyping of one of the AFLP primer combinations. This resulted in erroneous presences or absences at some loci. We have subsequently resubmitted a corrected AFLP data set to DRYAD (http://dx.doi.org/10.5061/dryad.1813.2). Re-analyses of the corrected data brought about changes in the results and the design of the structure analyses as well as slight changes in the absolute values of measures of genetic diversities and parameter estimates of all statistical analyses. Despite these changes, all statistical analyses yielded qualitatively the same results as reported in the original publication. Consequently, the major interpretations and conclusions of this publication remain unaltered. Re-analyses of the corrected data yielded slight changes in the measures of genetic diversity (see Original Table 1 and New Table 1) and in the structure results. For the European range, only two clusters were identified, which contain the introduction sites Mazamet and Verviers, and their presumable descendent populations, respectively. The introduction site Calais is now largely assigned to the Mazamet cluster, whereas the Bremen introduction centre is completely allocated to the Verviers route. The four historically documented introductions to Verviers, Mazamet, Bremen and Calais thus show even stronger differences in invasion success than reported in Lachmuth et al. (2010). In all subsequent statistical analyses (Isolation by distance, amova, variation in genetic diversity), the absolute values of parameter estimates and sometimes P-values changed. However, the analyses yielded qualitatively the same results as in the original publication (all effects that were previously significant at P < 0.05 remain significant). The main interpretations and conclusions of the original publication thus remain unaltered. After correction of the AFLP absence–presence data, the following results changed between the original analyses and the re-analyses of the data. For the European range (structure analysis 3, see Original Fig. 1 and New Fig. 1), only two clusters (K = 2) were identified, which contain the introduction sites Mazamet (a subset of cluster B in analysis 1, Europe-S) and Verviers (a subset of cluster C in analysis 1, Europe-N), and their presumable descendent populations, respectively (New Fig. 1, New Fig. 2D, E). The introduction site Calais was largely assigned to the Mazamet cluster, but shows higher assignment to the Verviers cluster than the populations descending from Mazamet. The Bremen introduction centre is assigned completely to the Verviers route. Thus, only two separate clusters (see New Table 1; see Original Fig. 2 and New Fig. 2) were distinguished as random effect in subsequent analyses. Also, with the updated AFLP genotyping, structure analysis 3 no longer identified four strongly bottlenecked populations (Deggendorf, Genthod, Lausanne, Vilette) as separate clusters. This means that the previous structure analysis 4 (without these bottlenecked populations) was no longer necessary. However, these populations still have low values of genetic diversity (see New Table 1). Interpretation: The four historically documented introductions to Verviers, Mazamet, Bremen and Calais show even stronger differences in invasion success than reported in Lachmuth et al. (2010). The previously identified 'strongly bottlenecked' populations still have low genetic diversity, but seem less differentiated from the other populations. Old result: In the African range, the probability of population assignment (Q) to cluster C increases as minimum winter temperature decreases (F1,17 = 14.1, P < 0.01, Akaike's information criterion AIC: −10.8, Original Fig. 3). New result: In the African range, the probability of population assignment (Q) to cluster C increases as minimum winter temperature decreases (F1,17 = 4.7, P < 0.05, Akaike's information criterion AIC: −19.6, New Fig. 3). Interpretation: As in the original study, we find a significant relationship between the assignment probability of native populations to cluster C and minimum winter temperature. Original results: Entire African sample, r = 0.6, Mantel-P < 0.01, slope = 0.0001; Africa-N region, r = 0.4, Mantel-P < 0.01, slope = 0.0002; Entire European sample: r = 0.3, Mantel-P < 0.05, slope = 0.00006; Europe-N region, r = 0.3, Mantel-P < 0.05, slope = 0.00005. New results: Entire African sample, r = 0.6, Mantel-P < 0.01, slope = 0.0002; Africa-N region, r = 0.4, Mantel-P < 0.01, slope = 0.0004; European sample, r = 0.3, Mantel-P < 0.05, slope = 0.0001; Europe-N region, r = 0.3, Mantel-P < 0.01, slope = 0.0001. Interpretation: As in the original study, all regions show patterns of isolation by distance. See Original Table 2 and New Table 2. Interpretation: Although the absolute values change slightly, the interpretation of amova results remains unaltered. Old values: Africa-N, 0; Africa-S, 4; Europe-N, 1; Europe-S, 1. New values: Africa-N, 0; Africa-S, 3; Europe-N, 2; and Europe-S, 1. Interpretation: Numbers of private alleles for the different subregions were low in both the original analysis and the re-analysis. Thus, population differentiation mainly resulted from shifts in band frequencies. Original results: Genetic diversity of populations (Hj, PLP and Br) varied between 0.12–0.23 (mean 0.18), 0.23–0.58 (mean 0.41) and 1.20–1.44 (mean 1.33) per population, respectively (Original Table 1). European populations showed a decrease in Hj and Br compared to the Africa-N source populations (Hj: F1,45 = 16.3, P < 0.001, Br: F1,45 = 14.6, P < 0.001, see also Original Fig. 4A). This also held after omitting the four strongly bottlenecked European populations (Deggendorf, Genthod, Lausanne, Vilette, Table 1). In contrast, PLP did not differ significantly between native and invasive populations (F1,45 = 0.4, P > 0.05, see also Original Fig. 4B). Within Africa, the lowland populations (Africa-S) were slightly more diverse than the highland populations (Africa-N), but the difference was not significant. In Europe, southern populations (Europe-S) were significantly less diverse than the Central European (Europe-N) ones except for PLP (Hj: F1,30 = 6.2, P < 0.05, Br: F1,30 = 4.7, P < 0.05, PLP: F1,30 = 3.2, P > 0.05; Original Fig. 4). The different diversity measures showed the same temporal development along the four European invasion routes. All of them increased with population age (Hj: χ2 (1) = 9.4, P < 0.01, Br: χ2 (1) = 11.7, P < 0.001, PLP: χ2 (1) = 11.5, P < 0.001, Original Fig. 5A, B), whereas spread rate was dropped from the minimum adequate model. A comparison of models containing either log-transformed population age or spread rate as explanatory variable further established the higher explanatory power of population age for all three measures (AIC differences: Hj: 2.4, Br: 4.1, PLP: 5.6, note that population age and spread rate were correlated (Spearman rho = −0.63, P > 0.001)). Still, spread rate as a single explanatory variable did have a significant negative effect on genetic diversity (Hj: χ2(1) = 9.4, P < 0.01, Br: χ2(1) = 11.7, P < 0.001, PLP: χ2(1) = 5.86, P < 0.05, Original Fig. 5C, D). New results: Genetic diversity of populations (Hj, PLP and Br) varied between 0.11–0.22 (mean 0.17), 0.21–0.57 (mean 0.39) and 1.18–1.42 (mean 1.31) per population, respectively (New Table 1). European populations showed a decrease in Hj and Br compared to the Africa-N source populations (Hj: F1,45 = 15.2, P < 0.001, Br: F1,45 =14.8, P < 0.001, see also New Fig. 4A). In contrast, PLP did not differ significantly between native and invasive populations (F1,45 = 0.66, P > 0.05, see also New Fig. 4B). Within Africa, the lowland populations (Africa-S) were more diverse than the highland populations in terms of Br (Africa-N, (F1,17 = 5.8, P < 0.05). In Europe, southern populations (Europe-S) were significantly less diverse than the Central European (Europe-N) ones except for PLP (Hj: F1,30 = 5.3, P < 0.05, Br: F1,30 = 4.6, P < 0.05, PLP: F1,30 = 2.7, P > 0.05; New Fig. 4). The different diversity measures showed the same temporal development along the two European invasion routes. All of them increased with population age (Hj: χ2(1) = 9.0, P < 0.01, Br: χ2 (1) = 11.6, P < 0.001, PLP: χ2 (1) = 11.9, P < 0.001, New Fig. 5A, B), whereas spread rate was dropped from the minimum adequate model. A comparison of models containing either log-transformed population age or spread rate as explanatory variable further established the higher explanatory power of population age for all three measures (AIC differences: Hj: 1.0, Br: 3.9, PLP:4.6, note that population age and spread rate were correlated (Spearman rho =−0.63, P > 0.001)). Still, spread rate as a single explanatory variable did have a significant negative effect on genetic diversity (Hj: χ2(1) = 8.0, P < 0.01, Br: χ2 (1) = 8.6, P < 0.01, PLP: χ2 (1) = 7.4, P < 0.01, New Fig. 5C, D). Interpretation: The interpretation remains the same as in the original study.

This collection of benthic Polychaeta from the eastern bank of the Suez Canal contains 55 species. Thirty-eight of them are new records for the Suez Canal. Of these, 22 probably originate as follows: Red Sea, 13; Mediterranean, four; species common to the Red Sea and the Mediterranean, five. Seven possible new species belonging to the families Phyllodocidae, Syllidae and Eunicidae are described. The 38 new records, added to those reported by the Cambridge Expedition of 1924, bring the total number of Errantia species for the Suez Canal to 81. Two species are added to the list of Red Sea Polychaeta which have migrated into the eastern Mediterranean: Glycinde bonhourei, a rare species, reported from the Great Bitter Lake and the Mediterranean coast of the Sinai peninsula (El 'Arish); and Eunice indica, reported from the Suez Canal and from the Mediterranean coasts of Sinai and Israel. Branchiosyllis uncinigera, a Red Sea species recently found on the Israel coast, is now reported from the Suez Canal.

The trace element contamination levels in mollusks were evaluated for different marine coastal sites in the Mediterranean (Israeli coast), Red (Israeli coast) and North (German coast) Seas. Three bivalve species (Mactra corallina, Donax sp, and Mytilusedulis) and two gastropod species (Patella sp.and Cellana rota) were sampled at polluted and relatively clean sites, and their soft tissue analyzed for Hg, Cd, Zn, Cu, Mn and Fe concentrations. Representative samples were screened for organic contaminants [(DDE), polychlorinated biphenyls PCBs and polycyclic aromatic hydrocarbons (PAHs)] which exhibited very low concentrations at all sites. In the Red Sea, the gastropod C. rota showed low levels of Hg (below detection limit) and similar Cd concentrations at all the examined sites, while other trace elements (Cu, Zn, Mn, Fe) were slightly enriched at the northern beach stations. Along the Mediterranean coast of Israel, Hg and Zn were enriched in two bivalves (M. corallina and Donax sp.) from Haifa Bay, both species undergoing a long-term decrease in Hg based on previous studies. Significant Cd and Zn enrichment was detected in Patella sp. from the Kishon River estuary at the southern part of Haifa Bay. In general, Patella sp. and Donax sp. specimens from Haifa Bay exhibited higher levels of Cd compared to other sites along the Israeli Mediterranean coast, attributed to the enrichment of Cd in suspended particulate matter. Along the German coast (North Sea) M. edulis exhibited higher concentrations of Hg and Cd at the Elbe and Eider estuaries, but with levels below those found in polluted sites elsewhere.

Marine organisms that enter the Mediterranean from the Red Sea via the Suez Canal are known as Lessepsian bioinvaders. In general, genetic studies of Lessepsian fishes have shown little structure between Red Sea and Mediterranean populations. Yet notable exceptions suggest the importance of life-history factors that may influence patterns of spatial genetic variation. In this study, by sampling two invasive fishes with different life histories (the rabbitfish Siganus rivulatus and the filefish Stephanolepis diaspros), we looked at evidence of population structure and selection at the boundary between the Red Sea and the Mediterranean (the Suez Canal), using thousands of molecular markers. Results illustrate two divergent patterns of genetic patterns, with little genetic structure in S. rivulatus and strong population structure in S. diaspros, even at such small spatial scale. We discuss differences in ecological characteristics between the two species to account for such differences. In addition, we report that in the face of both high (S. rivulatus) and low (S. diaspros) gene flow, loci under selection were uncovered, and some protein coding genes were identified as being involved with osmoregulation, which seems to be an important feature of individuals crossing the salinity-variable Suez Canal. The presence of genes under selection in populations near the Suez Canal supports the idea that selection may be active and essential for successful invasions right out of the gate.

Eco-evolutionary litter feedback as a driver of exotic plant invasion

BackgroundThe influence of introduction history and post-introduction dynamics on genetic diversity and structure has been a major research focus in invasion biology. However, genetic diversity and structure in the invasive range can also be affected by human-mediated processes in the native range prior to species introductions, an aspect often neglected in invasion biology. Here we aim to trace the native provenance of the invasive tree Acacia pycnantha by comparing the genetic diversity and structure between populations in the native Australian range and the invasive range in South Africa. This approach also allowed us to explore how human actions altered genetic structure before and after the introduction of A. pycnantha into South Africa. We hypothesized that extensive movement and replanting in A. pycnantha’s Australian range prior to its introduction to South Africa might result in highly admixed genotypes in the introduced range, comparable genetic diversity in both ranges, and therefore preclude an accurate determination of native provenance(s) of invasive populations.ResultsIn the native range Bayesian assignment tests identified three genetic clusters with substantial admixture and could not clearly differentiate previously identified genetic entities, corroborating admixture as a result of replantings within Australia. Assignment tests that included invasive populations from South Africa indicated similar levels of admixture compared to Australian populations and a lack of genetic structure. Invasive populations of A. pycnantha in South Africa are as genetically diverse as native populations, and could not be assigned to particular native range regions.ConclusionsOur results indicate that the genetic structure of A. pycnantha in Australia has been greatly altered through various planting initiatives. Specifically, there is little geographic structure and high levels of admixture. While numerous introduction history scenarios may explain the levels of admixture observed in South Africa, planting records of A. pycnantha in Australia suggest that populations were probably already admixed before propagules were introduced to South Africa. These findings have important implications for the management of invasive A. pycnantha populations in South Africa, especially for classical biological control, and more broadly, for studies that aim to understand the evolutionary dynamics of the invasion process.

AimsGermination is the earliest life-history transition of a plant species. It determines the ecological breadth and geographic ranges of a species and has major effects on its invasion potential. The largest spread of the invasive salt-marsh cordgrass Spartina alterniflora in China, where it extends to latitudes lower than its native range in North America, provides an opportunity to examine germination trait variation across latitudes within and among its invasive and native ranges.MethodsWe studied seed germination traits of S. alterniflora using seeds collected from 10 locations across latitudes in its invasive range (China, 20°–40° N) and 16 locations across latitudes in its native range (USA, 27°–43° N) in growth chambers with 0 PSU sterilized distilled water. We further evaluated how climate and tide range in the original locations influenced germination traits.Important FindingsNative populations showed higher (~10%) germination percentage and significantly higher (~20%) germination index than invasive populations did, but invasive populations germinated significantly earlier (~3 days) than native populations. Germination percentage and germination index increased with latitude in the invasive range but decreased with latitude in the native range. The mean germination time decreased with latitude in the invasive range and paralleled that in the native range. Germination percentage and germination index were negatively correlated with mean daily temperature (Tmean), mean daily maximum temperature (Tmax) and mean daily minimum temperature (Tmin), and inversely correlated with Tmean, Tmax and Tmin in the native range. However, the mean germination time was positively correlated with Tmean, Tmax and Tmean in both ranges. Our results demonstrate that invasive and native populations have evolved different latitudinal clines in germination percentage and index, but the mean germination time of the invasive population mirrored the latitudinal cline observed in the native range, suggesting that germination strategy across latitudes may change during invasion process.

The bioaccumulation of Hg, Cd, Zn, Cu, Mn and Fe was evaluated in the muscle and liver tissue of four fish species (Siganus rivulatus, Diplodus sargus, Lithognatus mormyrus and Plathychtis flesus) from clean and polluted marine coastal sites in the Red Sea, Mediterranean Sea and North Sea within the framework of the MARS 1 program. Representative liver samples were screened for organic contaminants (DDE, PCBs and PAHs) which exhibited very low concentrations. The levels of Cd, Cu, Zn, Fe and Mn found in the muscle tissue in this study were similar among the four species and within the naturally occurring metal ranges. However, differences were found among the sites. In the Red Sea, Cu was higher in the muscle of S. rivulatus at Ardag and Zn at the Observatory (OBS). Cu, Zn and Mn were higher in the Red Sea than in the specimens from the Mediterranean. The differences were attributed to different diets derived from distinctively different natural environments. D. sargus from Haifa Bay (HB) had higher Cd, Cu and Mn values than specimens from Jaffa (JFA), and L. mormyrus higher Cd, Fe and Mn in HB, corresponding to the polluted environmental status of the Bay. No differences in metal levels were found among the North Sea sites, except for Fe that was lower at the Eider station. Hg was low in all the specimens, but the values varied with species and sites. The lowest Hg values were found in S. rivulatus, the herbivorous species, as expected from its trophic level. Hg in P. flesus was higher than in S. rivulatus but still low. Higher Hg values were found in the muscle tissue of L. mormyrus,with the highest values in D. sargus, both carnivorous species from the same family. Hg in D. sargus was higher in HB than in JFA, as expected, but in the larger specimens of L. mormyrus from JFA values were higher, while in the small specimens there were no differences in Hg values. The levels of all metals were higher in the liver than in the muscle, with enrichment factors ranging from 3 to 104, depending on species and sites. The lowest enrichment values were found for Hg. Based on liver values, the specimens of S. rivulatus from the OBS had the highest levels, as well as D. sargus and L. mormyrus from JFA, contrary to the known relative environmental status of the sites.