Extremely low genetic diversity across mangrove taxa reflects past sea level changes and hints at poor future responses

The projected increases in sea levels are expected to affect coastal ecosystems. Tropical communities, anchored by mangrove trees and having experienced frequent past sea level changes, appear to be vibrant at present. However, any optimism about the resilience of these ecosystems is premature because the impact of past climate events may not be reflected in the current abundance. To assess the impact of historical sea level changes, we conducted an extensive genetic diversity survey on the Indo‐Malayan coast, a hotspot with a large global mangrove distribution. A survey of 26 populations in six species reveals extremely low genome‐wide nucleotide diversity and hence very small effective population sizes (N_e) in all populations. Whole‐genome sequencing of three mangrove species further shows the decline in N_e to be strongly associated with the speed of past changes in sea level. We also used a recent series of flooding events in Yalong Bay, southern China, to test the robustness of mangroves to sea level changes in relation to their genetic diversity. The events resulted in the death of half of the mangrove trees in this area. Significantly, less genetically diverse mangrove species suffered much greater destruction. The dieback was accompanied by a drastic reduction in local invertebrate biodiversity. We thus predict that tropical coastal communities will be seriously endangered as the global sea level rises. Well‐planned coastal development near mangrove forests will be essential to avert this crisis.     

Sweepstakes reproductive success is absent in a New Zealand snapper (Chrysophrus auratus) population protected from fishing despite “tiny” Ne/N ratios elsewhere

A landmark study published in 2002 estimated a very small N_e/N ratio (around 10^–5) in a population of pink snapper (Chrysophrys auratus, Forster, 1801) in the Hauraki Gulf in New Zealand. It epitomized the tiny N_e/N ratios (<10^–3) reported in marine species due to the hypothesized operation of sweepstakes reproductive success (SRS). Here we re‐evaluate the occurrence of SRS in marine species and the potential effect of fishing on the N_e/N ratio by studying the same species in the same region, but in a population that has been protected from fishing since 1975. We combine empirical, simulation and model‐based approaches to estimate N_e (and N_b) from genotypes of 1,044 adult fish and estimate N using recapture‐probabilities. The estimated N_e/N ratio was much larger (0.33, SE: 0.14) than expected. The magnitude of estimates of population‐wide variance in individual lifetime reproductive success (10–18) suggested that the sweepstakes effect was negligible in the study population. After evaluating factors that could explain the contrast between studies – experimental design, life history differences, environmental effects and the influence of exploitation on the N_e/N ratio – we conclude that the low N_e of the Hauraki Gulf population is associated with demographic instability in the harvested compared to the protected population despite circumstantial evidence that the 2002 study may have underestimated N_e. This study has broad implications for the prevailing view that reproductive success in the sea is largely driven by chance, and for genetic monitoring of populations using the N_e/N ratio and N_b.     

Recruitment and growth of two small‐bodied resident fish species (Gobiidae and Atherinidae) in oligohaline,seasonally open lagoons

Spatio‐temporal recruitment patterns, growth and survival of the Swan River goby Pseudogobius olorum and western hardyhead Leptatherina wallacei are described from two small, coastal lagoons on the south coast of Western Australia. In these lagoons, estuarine salinity dynamics were relatively stable over much of the autumn–spring period when freshwater inputs from rivers were reduced and there was no oceanic connection. Preflexion and flexion stages of both fish species contributed strongly to population size structure in downstream reaches, whereas upstream reaches were dominated by postflexion larvae and juvenile stages. Spawning of both species was protracted and largely asynchronous, although the episodic presence of stronger preflexion and flexion cohorts suggested some synchronized spawning had occurred. Comparison with estuarine conditions over this period provided evidence that synchronized spawning may be related to temperature and salinity variations from a combination of freshwater inputs and periods of marine exchange. Uninterrupted growth and the progression of cohorts through to juvenile stages were consistent with the generally stable estuarine conditions. Larval and juvenile stages of both species were also tolerant of abrupt changes in salinity and temperature, which occurred due to a non‐seasonal oceanic connection. These findings were consistent with the euryhaline nature of adults of both species.     

Genetic effective size,Ne, tracks density in a small freshwater cyprinid,Pecos bluntnose shiner (Notropis simus pecosensis)

Genetic monitoring tracks changes in measures of diversity including allelic richness, heterozygosity and genetic effective size over time, and has emerged as an important tool for understanding evolutionary consequences of population management. One proposed application of genetic monitoring has been to estimate abundance and its trajectory through time. Here, genetic monitoring was conducted across five consecutive year for the Pecos bluntnose shiner, a federally threatened minnow. Temporal changes in allele frequencies at seven microsatellite DNA loci were used to estimate variance effective size (N_eV) across adjacent years in the time series. Likewise, effective size was computed using the linkage disequilibrium method (N_eD) for each sample. Estimates of N_e were then compared to estimates of adult fish density obtained from traditional demographic monitoring. For Pecos bluntnose shiner, density (catch‐per‐unit‐effort), N_eV and N_eD were positively associated across this time series. Results for Pecos bluntnose shiner were compared to a related and ecologically similar species, the Rio Grande silvery minnow. In this species, density and N_eV were negatively associated, which suggested decoupling of abundance and effective size trajectories. Conversely, density and N_eD were positively associated. For Rio Grande silvery minnow, discrepancies among estimates of N_e and their relationships with adult fish density could be related to effects of high variance in reproductive success in the wild and/or effects of supplementation of the wild population with captive‐bred and reared fish. The efficacy of N_e as a predictor of density and abundance may depend on intrinsic population dynamics of the species and how these dynamics are influenced by the landscape features, management protocols and other factors.     

Length–weight and length–length relationships for some continental fishes of northwestern Baja California, México

Length–weight and length–length relationships were estimated for 10 freshwater, estuarine and marine fish species caught at the mouths of coastal sterams from northwestern Baja California (Mexico). The parameter b estimated by nonlinear least squares of weight and length data, ranged from 2.50 to 3.61. Size conversions (calculated total length from standard length) can be used in fishery for understanding several aspects of population dynamics.     

Estuarine colonization, population structure and nursery functioning for 0-group sea bass (Dicentrarchus labrax), flounder (Platichthys flesus) and sole (Solea solea) in a mesotidal temperate estuary

The function of the Mondego estuary as a fish nursery habitat was investigated from June 2003 to June 2004 by comparing the timing of estuarine colonization with juveniles of sea bass Dicentrarchus labrax, flounder Platichthys flesus, and sole Solea solea, while also analysing their population structure, growth and diet composition. Differences in the onset of estuarine colonization were observed, since sole juveniles were the first to enter the estuary (in January), followed by flounder in April and sea bass in June. The estuarine population of these species consisted of several age‐groups, although the majority of individuals belonged to age‐groups 0 and 1. The growth rates determined for 0‐group fish were within the range of those reported for other European estuarine systems. Some differences were also recognized regarding the timing of estuarine colonization and the length of the growing season. Diet of 0‐group sea bass consisted mainly of Crustacea, Polychaeta and Mollusca. Flounder juveniles fed chiefly on Amphipoda (especially Corophium spp.), with Polychaeta, Isopoda and Decapoda also being common prey. The diet of 0‐group sole was dominated by Polychaeta, with Amphipoda, Mollusca and Decapoda ranking highest, with other important benthic organisms also being present. Dietary overlap among these species was relatively low.     

Puny males punch above their weight to preserve genetic diversity in a declining Atlantic salmon population

Many salmonid fish populations have anadromous (i.e. migratory) and nonanadromous individuals co‐existing in sympatry. The nonanadromous individuals, frequently males, mature at a much smaller size in freshwater without undergoing marine migrations and often successfully fertilize many eggs laid by anadromous females. Because these small males do not recruit to fisheries, they are often not regarded in high esteem by fishers. In this issue of Molecular Ecology, Johnstone et al. ( 2013 ) demonstrate that by substantially contributing to reproduction, such males help maintain genetic diversity in a declining population of Atlantic salmon (Salmo salar). Their results show that estimates of effective population size (N_e), obtained by counting the number of anadromous adults returning from sea and correcting for unequal sex ratios, are lower than estimates generated from genetic markers. Many mechanisms are expected to reduce N_e below the adult census population size (N); the opposite pattern of N_e > N observed by Johnstone et al. ( 2013 ) is difficult to explain unless the reproductive effort of nonanadromous males is accounted for. The results have important implications for the conservation of small populations and highlight the challenges of relating N_e to N in organisms with complex life histories.     

Low interbasin connectivity in a facultatively diadromous fish: evidence from genetics and otolith chemistry

Southern smelts (Retropinna spp.) in coastal rivers of Australia are facultatively diadromous, with populations potentially containing individuals with diadromous or wholly freshwater life histories. The presence of diadromous individuals is expected to reduce genetic structuring between river basins due to larval dispersal via the sea. We use otolith chemistry to distinguish between diadromous and nondiadromous life histories and population genetics to examine interbasin connectivity resulting from diadromy. Otolith strontium isotope (⁸⁷Sr:⁸⁶Sr) transects identified three main life history patterns: amphidromy, freshwater residency and estuarine/marine residency. Despite the potential for interbasin connectivity via larval mixing in the marine environment, we found unprecedented levels of genetic structure for an amphidromous species. Strong hierarchical structure along putative taxonomic boundaries was detected, along with highly structured populations within groups using microsatellites (F_ST = 0.046–0.181), and mtDNA (Φ_ST = 0.498–0.816). The presence of strong genetic subdivision, despite the fact that many individuals reside in saline water during their early life history, appears incongruous. However, analysis of multielemental signatures in the otolith cores of diadromous fish revealed strong discrimination between river basins, suggesting that diadromous fish spend their early lives within chemically distinct estuaries rather than the more homogenous marine environment, thus avoiding dispersal and maintaining genetic structure.     

PSMC analysis of effective population sizes in molecular ecology and its application to black‐and‐white Ficedula flycatchers

Climatic fluctuations during the Quaternary period governed the demography of species and contributed to population differentiation and ultimately speciation. Studies of these past processes have previously been hindered by a lack of means and genetic data to model changes in effective population size (N_e) through time. However, based on diploid genome sequences of high quality, the recently developed pairwise sequentially Markovian coalescent (PSMC) can estimate trajectories of changes in N_e over considerable time periods. We applied this approach to resequencing data from nearly 200 genomes of four species and several populations of the Ficedula species complex of black‐and‐white flycatchers. N_e curves of Atlas, collared, pied and semicollared flycatcher converged 1–2 million years ago (Ma) at an N_e of ≈ 200 000, likely reflecting the time when all four species last shared a common ancestor. Subsequent separate N_e trajectories are consistent with lineage splitting and speciation. All species showed evidence of population growth up until 100–200 thousand years ago (kya), followed by decline and then start of a new phase of population expansion. However, timing and amplitude of changes in N_e differed among species, and for pied flycatcher, the temporal dynamics of N_e differed between Spanish birds and central/northern European populations. This cautions against extrapolation of demographic inference between lineages and calls for adequate sampling to provide representative pictures of the coalescence process in different species or populations. We also empirically evaluate criteria for proper inference of demographic histories using PSMC and arrive at recommendations of using sequencing data with a mean genome coverage of ≥18X, a per‐site filter of ≥10 reads and no more than 25% of missing data.     

Why are there so few freshwater fish species in most estuaries?

The freshwater fish assemblage in most estuaries is not as species rich as the marine assemblage in the same systems. Coupled with this differential richness is an apparent inability by most freshwater fish species to penetrate estuarine zones that are mesohaline (salinity: 5·0–17·9), polyhaline (salinity: 18·0–29·9) or euhaline (salinity: 30·0–39·9). The reason why mesohaline waters are avoided by most freshwater fishes is difficult to explain from a physiological perspective as many of these species would be isosmotic within this salinity range. Perhaps, a key to the poor penetration of estuarine waters by freshwater taxa is an inability to develop chloride cells in gill filament epithelia, as well as a lack of other osmoregulatory adaptations present in euryhaline fishes. Only a few freshwater fish species, especially some of those belonging to the family Cichlidae, have become fully euryhaline and have successfully occupied a wide range of estuaries, sometimes even dominating in hyperhaline systems (salinity 40+). Indeed, this review found that there are few fish species that can be termed holohaline (i.e. capable of occupying waters with a salinity range of 0–100+) and, of these taxa, there is a disproportionally high number of freshwater species (e.g. Cyprinodon variegatus, Oreochromis mossambicus and Sarotherodon melanotheron). Factors such as increased competition for food and higher predation rates by piscivorous fishes and birds may also play an important role in the low species richness and abundance of freshwater taxa in estuaries. Added to this is the relatively low species richness of freshwater fishes in river catchments when compared with the normally higher diversity of marine fish species for potential estuarine colonization from the adjacent coastal waters. The almost complete absence of freshwater fish larvae from the estuarine ichthyoplankton further reinforces the poor representation of this guild within these systems. An explanation as to why more freshwater fish species have not become euryhaline and occupied a wide range of estuaries similar to their marine counterparts is probably due to a combination of the above described factors, with physiological restrictions pertaining to limited salinity tolerances probably playing the most important role.     

Volatility in the effective size of a freshwater gastropod population

Despite the utility of gastropod models for the study of evolutionary processes of great generality and importance, their effective population size has rarely been estimated in the field. Here, we report allele frequency variance at three allozyme‐encoding loci monitored over 7 years in a population of the invasive freshwater pulmonate snail Physa acuta (Draparnaud 1805), estimating effective population size with both single‐sample and two‐sample approaches. Estimated N_e declined from effectively infinite in 2009 to approximately 40–50 in 2012 and then rose back to infinity in 2015, corresponding to a striking fluctuation in the apparent census size of the population. Such volatility in N_e may reflect cryptic population subdivision.     

Whole‐genome resequencing reveals the pleistocene temporal dynamics of Branchiostoma belcheri and Branchiostoma floridae populations

Global climatic fluctuations governed the ancestral demographic histories of species and contributed to place the current population status into a more extensive ecological and evolutionary context. Genetic variations will leave unambiguous signatures in the patterns of intraspecific genetic variation in extant species since the genome of each individual is an imperfect mosaic of the ancestral genomes. Here, we report the genome sequences of 20 Branchiostoma individuals by whole‐genome resequencing strategy. We detected over 140 million genomic variations for each Branchiostoma individual. In particular, we applied the pairwise sequentially Markovian coalescent (PSMC) method to estimate the trajectories of changes in the effective population size (N_e) of Branchiostoma population during the Pleistocene. We evaluated the threshold of sequencing depth for proper inference of demographic histories using PSMC was ≥25×. The PSMC results highlight the role of historical global climatic fluctuations in the long‐term population dynamics of Branchiostoma. The inferred ancestral N_e of the Branchiostoma belcheri populations from Zhanjiang and Xiamen (China) seawaters was different in amplitude before the first (mutation rate = 3 × 10^?9) or third glaciation (mutation rate = 9 × 10^?9) of the Pleistocene, indicating that the two populations most probably started to evolve in isolation in their respective seas after the first or third glaciation of the Pleistocene. A pronounced population bottleneck coinciding with the last glacial maximum was observed in all Branchiostoma individuals, followed by a population expansion occurred during the late Pleistocene. Species that have experienced long‐term declines may be especially vulnerable to recent anthropogenic activities. Recently, the industrial pollution and the exploitation of sea sand have destroyed the harmonious living environment of amphioxus species. In the future, we need to protect the habitat of Branchiostoma and make full use of these detected genetic variations to facilitate the functional study of Branchiostoma for adaptation to local environments.     

Consequences of multiple mating‐system shifts for population and range‐wide genetic structure in a coastal dune plant

Evolutionary transitions from outcrossing to selfing can strongly affect the genetic diversity and structure of species at multiple spatial scales. We investigated the genetic consequences of mating‐system shifts in the North American, Pacific coast dune endemic plant Camissoniopsis cheiranthifolia (Onagraceae) by assaying variation at 13 nuclear (n) and six chloroplast (cp) microsatellite (SSR) loci for 38 populations across the species range. As predicted from the expected reduction in effective population size (N_e) caused by selfing, small‐flowered, predominantly selfing (SF) populations had much lower nSSR diversity (but not cpSSR) than large‐flowered, predominantly outcrossing (LF) populations. The reduction in nSSR diversity was greater than expected from the effects of selfing on N_e alone, but could not be accounted for by indirect effects of selfing on population density. Although selfing should reduce gene flow, SF populations were not more genetically differentiated than LF populations. We detected five clusters of nSSR genotypes and three groups of cpSSR haplotypes across the species range consisting of parapatric groups of populations that usually (but not always) differed in mating system, suggesting that selfing may often initiate ecogeographic isolation. However, lineage‐wide genetic variation was not lower for selfing clusters, failing to support the hypothesis that selection for reproductive assurance spurred the evolution of selfing in this species. Within three populations where LF and SF plants coexist, we detected genetic differentiation among diverged floral phenotypes suggesting that reproductive isolation (probably postzygotic) may help maintain the striking mating‐system differentiation observed across the range of this species.     

Fine‐scale habitat preferences influence within‐river population connectivity: a case‐study using two sympatric New Zealand Galaxias fish species

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Looking into the past – the reaction of three grouse species to climate change over the last million years using whole genome sequences

Tracking past population fluctuations can give insight into current levels of genetic variation present within species. Analysing population dynamics over larger timescales can be aligned to known climatic changes to determine the response of species to varying environments. Here, we applied the Pairwise Sequentially Markovian Coalescent (psmc ) model to infer past population dynamics of three widespread grouse species; black grouse, willow grouse and rock ptarmigan. This allowed the tracking of the effective population size (N_e) of all three species beyond 1 Mya, revealing that (i) early Pleistocene cooling (~2.5 Mya) caused an increase in the willow grouse and rock ptarmigan populations, (ii) the mid‐Brunhes event (~430 kya) and following climatic oscillations decreased the N_e of willow grouse and rock ptarmigan, but increased the N_e of black grouse and (iii) all three species reacted differently to the last glacial maximum (LGM) – black grouse increased prior to it, rock ptarmigan experienced a severe bottleneck and willow grouse was maintained at large population size. We postulate that the varying psmc signal throughout the LGM depicts only the local history of the species. Nevertheless, the large population fluctuations in willow grouse and rock ptarmigan indicate that both species are opportunistic breeders while black grouse tracks the climatic changes more slowly and is maintained at lower N_e. Our results highlight the usefulness of the psmc approach in investigating species’ reaction to climate change in the deep past, but also that caution should be taken in drawing general conclusions about the recent past.     

Effective size of density‐dependent two‐sex populations: the effect of mating systems

Density dependence in vital rates is a key feature affecting temporal fluctuations of natural populations. This has important implications for the rate of random genetic drift. Mating systems also greatly affect effective population sizes, but knowledge of how mating system and density regulation interact to affect random genetic drift is poor. Using theoretical models and simulations, we compare N_e in short‐lived, density‐dependent animal populations with different mating systems. We study the impact of a fluctuating, density‐dependent sex ratio and consider both a stable and a fluctuating environment. We find a negative relationship between annual N_e/N and adult population size N due to density dependence, suggesting that loss of genetic variation is reduced at small densities. The magnitude of this decrease was affected by mating system and life history. A male‐biased, density‐dependent sex ratio reduces the rate of genetic drift compared to an equal, density‐independent sex ratio, but a stochastic change towards male bias reduces the N_e/N ratio. Environmental stochasticity amplifies temporal fluctuations in population size and is thus vital to consider in estimation of effective population sizes over longer time periods. Our results on the reduced loss of genetic variation at small densities, particularly in polygamous populations, indicate that density regulation may facilitate adaptive evolution at small population sizes.     

A genetic demographic analysis of Lake Malawi rock‐dwelling cichlids using spatio‐temporal sampling

We estimated the effective population sizes (N_e) and tested for short‐term temporal demographic stability of populations of two Lake Malawi cichlids: Maylandia benetos, a micro‐endemic, and Maylandia zebra, a widespread species found across the lake. We sampled a total of 351 individuals, genotyped them at 13 microsatellite loci and sequenced their mitochondrial D‐loop to estimate genetic diversity, population structure, demographic history and effective population sizes. At the microsatellite loci, genetic diversity was high in all populations. Yet, genetic diversity was relatively low for the sequence data. Microsatellites yielded mean N_e estimates of 481 individuals (±99 SD) for M. benetos and between 597 (±106.3 SD) and 1524 (±483.9 SD) individuals for local populations of M. zebra. The microsatellite data indicated no deviations from mutation–drift equilibrium. Maylandia zebra was further found to be in migration–drift equilibrium. Temporal fluctuations in allele frequencies were limited across the sampling period for both species. Bayesian Skyline analyses suggested a recent expansion of M. zebra populations in line with lake‐level fluctuations, whereas the demographic history of M. benetos could only be estimated for the very recent past. Divergence time estimates placed the origin of M. benetos within the last 100 ka after the refilling of the lake and suggested that it split off the sympatric M. zebra population. Overall, our data indicate that micro‐endemics and populations in less favourable habitats have smaller N_e, indicating that drift may play an important role driving their divergence. Yet, despite small population sizes, high genetic variation can be maintained.     

Comparison of inshore and offshore fish larval assemblages within the wider Yangtze River estuary (China)

It is hypothesized that fish larvae undertake vertical movements in estuarine waters. To test this hypothesis, a sampling period was selected during times when many spring‐spawning fish reach maximum abundance in coastal waters so that spring and summer variations in larval fish assemblages could be determined in the Yangtze River estuary. Six oceanographic surveys were conducted across the salinity gradient of an inshore (freshwater) and offshore area (brackish intersection) during spring (May) and summer (August) between 2010 and 2012. The fish larval community was dominated by species of Engraulidae, Gobiidae, Champsodontidae and Mugilidae. The pre‐flexion and flexion larval stages of euryhaline marine species, which are dependent on estuaries as nursery areas, were common. The brackish and marine larval assemblage was the most abundant with taxa such as Coilia mystus and Engraulis japonicus accounting for more than 57.3% of the total catch. Spatial differences in the taxonomic composition of larval fish assemblages were evident between the inshore and offshore areas. Additionally, the Yangtze River runoff regulatory functions as affected by the Three Gorges Reservoir operational mode (hydrological alternating operations) showed weak influences on fish and habitat environments. Low salinities from high freshwater inflow limited bay anchovy production in the inshore area.     

Salmonella spp., Vibrio spp., Clostridium perfringens, and Plesiomonas shigelloides in Marine and Freshwater Invertebrates from Coastal California Ecosystems

The coastal ecosystems of California are highly utilized by humans and animals, but the ecology of fecal bacteria at the land–sea interface is not well understood. This study evaluated the distribution of potentially pathogenic bacteria in invertebrates from linked marine, estuarine, and freshwater ecosystems in central California. A variety of filter-feeding clams, mussels, worms, and crab tissues were selectively cultured for Salmonella spp., Campylobacter spp., Escherichia coli-O157, Clostridium perfringens, Plesiomonas shigelloides, and Vibrio spp. A longitudinal study assessed environmental risk factors for detecting these bacterial species in sentinel mussel batches. Putative risk factors included mussel collection near higher risk areas for livestock or human sewage exposure, adjacent human population density, season, recent precipitation, water temperature, water type, bivalve type, and freshwater outflow exposure. Bacteria detected in invertebrates included Salmonella spp., C. perfringens, P. shigelloides, Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio alginolyticus. Overall, 80% of mussel batches were culture positive for at least one of the bacterial species, although the pathogens Campylobacter, E. coli-O157, and Salmonella were not detected. Many of the same bacterial species were also cultured from upstream estuarine and riverine invertebrates. Exposure to human sewage sources, recent precipitation, and water temperature were significant risk factors for bacterial detection in sentinel mussel batches. These findings are consistent with the hypothesis that filter-feeding invertebrates along the coast concentrate fecal bacteria flowing from land to sea and show that the relationships between anthropogenic effects on coastal ecosystems and the environmental niches of fecal bacteria are complex and dynamic.     

A review of the influence of biogeography,riverine linkages,and marine connectivity on fish assemblages in evolving lagoons and lakes of coastal southern Africa

The Holocene evolution of eight South African coastal lakes and lagoons is examined and related to changes in fish composition over that period. Historical and current connectivity with riverine and marine environments are the primary determinants of present‐day fish assemblages in these systems. A small and remarkably consistent group of relict estuarine species have persisted in these coastal lakes and lagoons. The loss or reduction of connectivity with the sea has impacted on the diversity of marine fishes in all eight study systems, with no marine fishes occurring in those water bodies where connectivity has been completely broken (e.g. Sibaya, Groenvlei). In systems that have retained tenuous linkages with the sea (e.g., Verlorenvlei, Wilderness lakes), elements of the marine fish assemblage have persisted, especially the presence of facultative catadromous species. Freshwater fish diversity in coastal lakes and lagoons is a function of historical and present biogeography and salinity. From a freshwater biogeography perspective, the inflowing rivers of the four temperate systems reviewed here contain three or fewer native freshwater fishes, while the subtropical lakes that are fed by river systems contain up to 40 freshwater fish species. Thus, the significantly higher fish species diversity in subtropical versus temperate coastal lakes and lagoons comes as no surprise. Fish species diversity has been increased further in some systems (e.g., Groenvlei) by alien fish introductions. However, the impacts of fish introductions and translocations have not been studied in the coastal lakes and lagoons of South Africa. In these closed systems, it is probable that predation impacts on small estuarine fishes are significant. The recent alien fish introductions is an example of the growing threats to these systems during the Anthropocene, a period when human activities have had significant negative impacts and show potential to match the changes recorded during the entire Holocene.