Gene flow and maintenance of genetic diversity in invasive mosquitofish (Gambusia holbrooki)

Population genetic structure and demographic history reconstruction of introduced flathead catfish (Pylodictis olivaris) in two US Mid-Atlantic rivers

Population genetic analysis of invasive populations can provide valuable insights into the source of introductions, pathways for expansion, and their demographic histories. Flathead catfish (Pylodictis olivaris) are a prolific invasive species with high fecundity, long-distance dispersal, and piscivorous feeding habits that can lead to declines in native fish populations. In this study, we analyse the genetics of invasive P. olivaris in the Mid-Atlantic region to assess their connectivity and attempt to reconstruct the history of introduced populations. Based on an assessment across 13 microsatellite loci, P. olivaris from the Susquehanna River system (N = 537), Schuylkill River (N = 33), and Delaware River (N = 1) have low genetic diversity (global Hobs = 0.504), although we detected no evidence of substantial inbreeding (FIS = -0.083 to 0.022). P. olivaris from these different river systems were genetically distinct, suggesting separate introductions. However, population structure was much weaker within each river system and exhibited a pattern of high connectivity, with some evidence of isolation by distance. P. olivaris from the Susquehanna and Schuylkill rivers showed evidence for recent genetic bottlenecks, and demographic models were consistent with historical records, which suggest that populations were established by recent founder events consisting of a small number of individuals. Our results show the risk posed by small introductions of P. olivaris, which can spread widely once a population is established, and highlight the importance of prevention and sensitive early detection methods to prevent the spread of P. olivaris in the future.

A systematic review of poeciliid fish invasions in Africa

BACKGROUND

This review compiles and synthesises the existing information concerning non-native poeciliid introductions to Africa. The recent upsurge in research on invasive poeciliids has revealed their widespread occurrence in Africa.

RESULTS

Within the 87 relevant articles, 74% reported on the presence of Gambusia spp., 33% on P. reticulata, 19% on X. hellerii, 11% on X. maculatus, and 5% on other ornamental poeciliids. Overall, poeciliids have been documented as introduced to 25 different countries in Africa. With Gambusia spp. being introduced to 16 countries and P. reticulata to 19 countries. Our results are representative of the current state of research on invasive poeciliids in Africa. There was a concentration of studies in South Africa, with limited research elsewhere. Current distribution data is relatively patchy, although widespread surveys of multiple river systems in Morocco and South Africa, confirmed widespread and abundant established poeciliid populations. The ecological impacts of invasive poeciliids in Africa remain understudied but evidence indicates deleterious effects on native fish, invertebrates, and amphibians, many of which are critically endangered or endemic.

CONCLUSION

Current research is limited in reporting from certain countries and ecological impacts. An increased effort to monitor species composition in vulnerable waterbodies, especially in the many African countries where invasive poeciliids are reported, should be completed to reveal further established populations. Future research should prioritise quantifying the ecological impacts of invasive poeciliids in the field and identifying both vulnerable and resistant native ecosystems to guide future management decisions.

Limited population structure but signals of recent selection in introduced African Fig Fly (Zaprionus indianus) in North America

Invasive species have devastating consequences for human health, food security, and the environment. Many invasive species adapt to new ecological niches following invasion, but little is known about the early steps of adaptation. Here we examine population genomics of a recently introduced drosophilid in North America, the African Fig Fly, Zaprionus indianus. This species is likely intolerant of subfreezing temperatures and recolonizes temperate environments yearly. We generated a new chromosome-level genome assembly for Z. indianus. Using resequencing of over 200 North American individuals collected over four years in temperate Virginia, plus a single collection from subtropical Florida, we tested for signatures of recolonization, population structure, and adaptation within invasive populations. We show founding populations are sometimes small and contain close genetic relatives, yet temporal population structure and differentiation of populations is mostly absent across recurrent recolonization events. Although we find limited signals of genome-wide spatial or temporal population structure, we identify haplotypes on the X chromosome that are repeatedly differentiated between Virginia and Florida populations. These haplotypes show signatures of natural selection and are not found in African populations. We also find evidence for several large structural polymorphisms segregating within North America populations and show X chromosome evolution in invasive populations is strikingly different from the autosomes. These results show that despite limited population structure, populations may rapidly evolve genetic differences early in an invasion. Further uncovering how these genomic regions influence invasive potential and success in new environments will advance our understanding of how organisms evolve in changing environments.

Habitat structural complexity predicts cognitive performance and behaviour in western mosquitofish

Urban stream syndrome alters stream habitat complexity. We define habitat complexity as the degree of variation in physical habitat structure, with increasing variation equating to higher complexity. Habitat complexity affects species composition and shapes animal ecology, physiology, behaviour and cognition. We used a delayed detour test to measure whether cognitive processes (motor self-regulation) and behaviour (risk-taking) of female Western mosquitofish, Gambusia affinis, varied with habitat structural complexity (low, moderate and high) that was quantified visually for nine populations. We predicted that motor self-regulation and risk-taking behaviour would increase with increasing habitat complexity, yet we found support for the opposite. Lower complexity habitats offer less refuge potentially leading to higher predation pressure and selecting for greater risk-taking by fish with higher motor self-regulation. Our findings provide insight into how habitat complexity can shape cognitive processes and behaviour and offers a broader understanding of why some species may tolerate conditions of urbanized environments.

Population Genetics Reveals Invasion Origin of Coilia brachygnathus in the Three Gorges Reservoir of the Yangtze River, China

Non-indigenous fish invasions have posed a serious threat to global fish diversity and aquatic ecosystem security. Studying the invasion sources, pathways, and genetic mechanisms by means of population genetics is helpful in the management and control of non-indigenous fishes. In this study, we used mitochondrial Cyt b gene, D-Loop region and microsatellite markers to analyze the genetic diversity and population structure of 12 Coilia brachygnathus populations from the native and invaded regions of the Yangtze River Basin in order to explore the invasion sources, pathways, and genetic mechanisms of C. brachygnathus in the Three Gorges Reservoir. The results showed that the main invasion sources of C. brachygnathus in the Three Gorges Reservoir were the Poyanghu Lake, Dongtinghu Lake, Changhu Lake, and other populations in the middle reaches of the Yangtze River. The invasion pathway may have involved moving upstream through the operation of ship locks. The genetic diversity of C. brachygnathus in the invasive populations was significantly smaller than in the native populations, indicating a founder effect. The low genetic diversity did not affect the successful invasion, confirming that genetic diversity and successful invasion do not always have a simple causal relationship. These results can provide basic data for the prevention and control of C. brachygnathus in the Three Gorges Reservoir and study case for understanding the mechanism of invasion genetics.

Chromosome-level genome assembly of the female western mosquitofish (Gambusia affinis)

BACKGROUND

The western mosquitofish (Gambusia affinis) is a sexually dimorphic poeciliid fish known for its worldwide biological invasion and therefore an important research model for studying invasion biology. This organism may also be used as a suitable model to explore sex chromosome evolution and reproductive development in terms of differentiation of ZW sex chromosomes, ovoviviparity, and specialization of reproductive organs. However, there is a lack of high-quality genomic data for the female G. affinis; hence, this study aimed to generate a chromosome-level genome assembly for it.

RESULTS

The chromosome-level genome assembly was constructed using Oxford nanopore sequencing, BioNano, and Hi-C technology. G. affinis genomic DNA sequences containing 217 contigs with an N50 length of 12.9 Mb and 125 scaffolds with an N50 length of 26.5 Mb were obtained by Oxford nanopore and BioNano, respectively, and the 113 scaffolds (90.4% of scaffolds containing 97.9% nucleotide bases) were assembled into 24 chromosomes (pseudo-chromosomes) by Hi-C. The Z and W chromosomes of G. affinis were identified by comparative genomic analysis of female and male G. affinis, and the mechanism of differentiation of the Z and W chromosomes was explored. Combined with transcriptome data from 6 tissues, a total of 23,997 protein-coding genes were predicted and 23,737 (98.9%) genes were functionally annotated.

CONCLUSIONS

The high-quality female G. affinis reference genome provides a valuable omics resource for future studies of comparative genomics and functional genomics to explore the evolution of Z and W chromosomes and the reproductive developmental biology of G. affinis.

Genetic Diversity and Population Structure of Nutria (Myocastor coypus) in South Korea

The nutria (Myocastor coypus) is an invasive alien species that have had major adverse effects on biodiversity and the agricultural economy in wetland habitats. Since 2014, the Ministry of Environment in South Korea has been carrying out the Nutria Eradication Project, and we investigated nutria distribution and genetic diversity of nutria populations in South Korea. We estimated that 99.2% of nutria habitats are in the mid-lower Nakdong River regions. To further analyze the genetic diversity in eight major nutria populations, we performed a genetic analysis using microsatellite markers. Genetic diversity levels of the eight nutria populations in South Korea were relatively lower than those in other countries. The probability of migration direction among nutria populations was predicted from genetic distance analysis. Genetic structure analysis showed little difference among the nutria populations in South Korea. These results suggest that nutrias in South Korea originated from a single population. Our results provide important data for establishing management strategies for the successful eradication of nutria populations in South Korea, as well as in other countries with alien invasive species.

Effects of water pollution and river fragmentation on population genetic structure of invasive mosquitofish

We analyzed variation at the GPI-2 locus and eleven microsatellite loci of eastern mosquitofish Gambusia holbrooki populations introduced to the Ebro River (Spain), sampling above and below a dam (Flix Reservoir) where severe chronic pollution has been well documented. Allele frequency changes at the GPI-2 locus in the sites nearest to the polluted sediments agree with previous results from studies in mercury-exposed populations of this highly invasive fish. Genetic distinction of the mosquitofish collected close to the polluted sediments was detected at the GPI locus but also at the presumptive neutral microsatellite loci. Recent migration rates estimated from microsatellites indicated that around 30% of fish collected in a specific location were immigrants from upstream and downstream sources. Such high migration rates probably contribute to the mosquitofish's invasive success and suggest that the consequences on the mosquitofish regional genetic structured of high levels of water toxicants could be mediated by immigration from other sites, but the effect of pollutants on local diversity might be higher than observed here.

Contrasting life histories contribute to divergent patterns of genetic diversity and population connectivity in freshwater sculpin fishes

BACKGROUND

Life history characteristics are considered important factors influencing the evolutionary processes of natural populations, including the patterns of population genetic structure of a species. The sister species Cottus hangiongensis and C. koreanus are small bottom-dwelling freshwater sculpin fishes from South Korea that display marked life history divergence but are morphologically nearly indistinguishable. Cottus hangiongensis evolved an 'amphidromous' life history with a post-hatching pelagic larval phase. They spawn many small eggs in the low reaches of rivers, and hatched larvae migrate to the sea before returning to grow to maturity in the river mouth. In contrast, C. koreanus evolved a 'fluvial' landlocked type with benthic larvae. They release a smaller number of larger eggs, and the larvae undergo direct development, remaining benthic in the upstream rivers throughout their entire lives. We tested whether there were differences in patterns and levels of within-population genetic diversities and spatial population structure between the two closely related Korean sculpins using mitochondrial DNA control region sequences and seven nuclear microsatellite loci.

RESULTS

The combined analyses of both marker sets revealed that C. hangiongensis harboured considerably higher levels of within-population genetic diversities (e.g. haplotype/allelic richness, heterozygosities) than C. koreanus. In contrast, the fluvial sculpin exhibited noticeably more spatial population structure than did the amphidromous sculpin, as suggested by pairwise F_ST statistics. The finding that C. hangiongensis individuals comprised a single random mating population across the east-flowing river basins in the Korean Peninsula, whereas C. koreanus individuals comprised genetically discrete individual populations, was further supported by an individual-based Bayesian population assignment and also factorial correspondence analyses.

CONCLUSIONS

The higher genetic diversity, but lower population structure, of the amphidromous sculpin relative to the fluvial sculpin may have resulted from its greater larval dispersal and also possibly, higher fecundity accompanied by an amphidromous life history. Hence, we conclude that contrasting early life histories - including the presence or absence of the pelagic larval phase - may have led to divergent patterns of within-population genetic diversities and spatial population structure between the sister Cottus species following speciation from a common ancestor of marine sculpin.

Microsatellite evidence of dispersal mechanism of red swamp crayfish (Procambarus clarkii) in the Pearl River basin and implications for its management

Discerning the dispersal patterns of invasive species is critically important for the design of effective management strategies and the development of appropriate theoretical models predicting the spatial expansion of introduced populations. Post-introduction dispersal may occur naturally or via human transport, but for many organisms, assessing the relative contribution of each of these factors is difficult using traditional methods. Here, we explored the genetic patterns associated with the spread of red swamp crayfish (Procambarus clarkii) among 21 populations in the Pearl River basin and 2 peripheral populations in the Yangtze River basin. We found the genetic diversity of P. clarkii in the Pearl River basin was somewhat lower than in the Yangtze River basin. We also found (1) there was significant genetic differentiation between populations, (2) genetic differentiation was not related to geographic distance (i.e., isolation by distance), and (3) a Bayesian assignment analysis revealed three distinct genetic clusters and genetic admixture. Our results therefore provide evidence that human-mediated multiple introductions occurred in the Pearl River basin. Anthropogenic activities such as commercial transportation were likely responsible for the long-distance dispersal of P. clarkii. This study provides useful information for developing management strategies.

Genomic survey provides insights into the evolutionary changes that occurred during European expansion of the invasive mosquitofish (Gambusia holbrooki)

Biological invasions rank among the main global threats for biodiversity. The Eastern mosquitofish (Gambusia holbrooki) is considered one of the 100 world worst invasive species due to its high adaptation capability to new environments. Using the restriction-site-associated DNA tags (RADtags), introduced European locations were compared against native US mosquitofish populations to analyse genomic changes that occurred during invasive process of European locations. After filtering, 7724 RADtags containing only one SNP were retained for population studies. Comparative genomics indicated that 186 of these RADtags matched sequences in the transcriptome of Xyphophorus maculatus, the most closely related genome available. Genomic analyses showed that invasive populations show high reductions in diversity. Further, analyses of population structuring based on these data are concordant with previous analyses based on microsatellites. It is concluded that during the invasion process genetic drift was the main evolutionary force affecting patterns of diversity and population structure. While recognizing that positive selection could be masked by the strong drift during founder events, adaptive processes were evidenced in a reduced number of RADtags (<2%), with only one of these in a putative coding region. Surprisingly, balancing selection was detected in several coding RADtags, suggesting that the preservation of polymorphism in specific genes could be more important than the average population diversity for the population maintenance at any location, particularly for the survival of introduced populations.

Queen execution increases relatedness among workers of the invasive Argentine ant, Linepithema humile

Polygyny in social insects can greatly reduce within‐nest genetic relatedness. In polygynous ant species, potential rival queens in colonies with multiple queens are often executed by other queens, workers, or both. The Argentine ant, Linepithema humile, native to South America, forms a “supercolony” that is composed of a large number of nests and is considered to contribute to the ant's invasion success. Currently, four mutually antagonistic supercolonies are contiguously distributed within a small area of Japan. Here, we analyzed the genetic structure and relatedness within and among the four supercolonies using microsatellite markers to clarify how L. humile maintains its supercoloniality. The results of AMOVA and BASP, the F_ST values, and the existence of several private alleles indicated that the L. humile population in the Kobe area had a characteristic genetic structure. Within a given supercolony, there was significant genetic differentiation (F_ST) among workers collected in May and those collected in September. The significant deviation from Hardy–Weinberg equilibrium increased, and the relatedness among workers significantly increased from May to September in all supercolonies. This result suggested that the supercolonies replaced old queens with new ones during the reproductive season, thus supporting the plausibility of queen execution. From the perspective of kin selection, workers collectively eliminate queens, thereby increasing their own inclusive fitness. Restricted gene flow among supercolonies, together with mating with sib and queen execution, could help to maintain the unique social structure of L. humile, the distribution of which is expanding worldwide.

Using Massive Parallel Sequencing for the development, validation, and application of population genetics markers in the invasive bivalve zebra mussel (Dreissena polymorpha)

The zebra mussel (Dreissena polymorpha, Pallas, 1771) is one of the most invasive species of freshwater bivalves, due to a combination of biological and anthropogenic factors. Once this species has been introduced to a new area, individuals form dense aggregations that are very difficult to remove, leading to many adverse socioeconomic and ecological consequences. In this study, we identified, tested, and validated a new set of polymorphic microsatellite loci (also known as SSRs, Single Sequence Repeats) using a Massive Parallel Sequencing (MPS) platform. After several pruning steps, 93 SSRs could potentially be amplified. Out of these SSRs, 14 were polymorphic, producing a polymorphic yield of 15.05%. These 14 polymorphic microsatellites were fully validated in a first approximation of the genetic population structure of D. polymorpha in the Iberian Peninsula. Based on this polymorphic yield, we propose a criterion for establishing the number of SSRs that require validation in similar species, depending on the final use of the markers. These results could be used to optimize MPS approaches in the development of microsatellites as genetic markers, which would reduce the cost of this process.

Out of the Black Sea: phylogeography of the invasive killer shrimp Dikerogammarus villosus across Europe

The amphipod Dikerogammarus villosus has colonized most of the European main inland water bodies in less than 20 years, having deteriorating effect on the local benthic communities. Our aim was to reveal the species phylogeography in the native Black Sea area, to define the source populations for the colonization routes in continental Europe and for the newly established UK populations. We tested for the loss of genetic diversity between source and invasive populations as well as along invasion route. We tested also for isolation by distance. Thirty three native and invasive populations were genotyped for mtDNA (COI, 16S) and seven polymorphic nuclear microsatellites to assess cryptic diversity (presence of deeply divergent lineages), historical demography, level of diversity within lineage (e.g., number of alleles), and population structure. A wide range of methods was used, including minimum spanning network, molecular clock, Bayesian clustering and Mantel test. Our results identified that sea level and salinity changes during Pleistocene impacted the species phylogeography in the Black Sea native region with four differentiated populations inhabiting, respectively, the Dnieper, Dniester, Danube deltas and Durungol liman. The invasion of continental Europe is associated with two sources, i.e., the Danube and Dnieper deltas, which gave origin to two independent invasion routes (Western and Eastern) for which no loss of diversity and no isolation by distance were observed. The UK population has originated in the Western Route and, despite very recent colonization, no drastic loss of diversity was observed. The results show that the invasion of the killer shrimp is not associated with the costs of loosing genetic diversity, which may contribute to the success of this invader in the newly colonized areas. Additionally, while it has not yet occurred, it might be expected that future interbreeding between the genetically diversified populations from two independent invasion routes will potentially even enhance this success.