Small founding number and low genetic diversity in an introduced species exhibiting limited invasion success (speckled dace, Rhinichthys osculus)

Uniparental and biparental markers unravel invasion pathways, population admixture, and genetic structure in naturalized rainbow trout (Oncorhynchus mykiss)

The present study combined uniparental mtDNA and biparental SNPs to illuminate the invasion and colonization pathways of rainbow trout, Oncorhynchus mykiss, one of the world's most widespread invasive fishes, that has been intensively propagated in Chile, South America. The specific aims of the study were (i) to evaluate potential donor populations, which could be either from the species' native range in North America or from introduced populations in Europe, by comparing mtDNA D-loop/control region haplotypes; and (ii) to assess the factors that have shaped genetic diversity and contemporary genetic structure of rainbow trout populations introduced to Chile through SNP genotyping. The authors comprehensively sampled 24 sites in 12 basins ranging from the High Andean Plateau (Altiplano, 18° S) to northern Patagonia (41° S). Results of the mtDNA data of naturalized trout populations from rivers in the Altiplano (northern Chile) differed from those collected in central and southern Chile, suggesting an origin from North American hatcheries. Naturalized trout populations in central and southern Chile, on the contrary, shared haplotypes with specimens found in European hatcheries. The southern and central Chile populations also contained rare haplotypes, possibly indicating potential spread through aquaculture escapes. Results of the SNP analysis revealed higher allelic richness for trout sampled in sites influenced by commercial aquaculture than sites without commercial aquaculture, likely due to increased admixture between aquaculture broodstock and naturalized trout. The analysis further uncovered some complex patterns of divergent trout populations with low genetic diversity as well as increased relatedness between individuals from isolated sites, suggesting possible local populations. A comprehensive characterization of genetic diversity and structure of rainbow trout should help identify management areas that may augment socioeconomic benefits while preventing the spread and further impacts on biodiversity.

Population genetic structure of the globally introduced big-headed ant in Taiwan

Global commerce and transportation facilitate the spread of invasive species. The African big-headed ant, Pheidole megacephala (Fabricius), has achieved worldwide distribution through globalization. Since the late 19th century, Taiwan has served as a major seaport because of its strategic location. The population genetic structure of P. megacephala in Taiwan is likely to be shaped by international trade and migration between neighboring islands. In this study, we investigated the population genetics of P. megacephala colonies sampled from four geographical regions in Taiwan and elucidated the population genetic structures of P. megacephala sampled from Taiwan, Okinawa, and Hawaii. We observed a low genetic diversity of P. megacephala across regions in Taiwan. Moreover, we noted low regional genetic differentiation and did not observe isolation by distance, implying that long-distance jump dispersal might have played a crucial role in the spread of P. megacephala. We sequenced the partial cytochrome oxidase I gene and observed three mitochondrial haplotypes (TW1-TW3). TW1 and TW3 most likely originated from populations within the species' known invasive range, suggesting that secondary introduction is the predominant mode of introduction for this invasive ant. TW2 represents a novel haplotype that was previously unreported in other regions. P. megacephala populations from Taiwan, Okinawa, and Hawaii exhibited remarkable genetic similarity, which may reflect their relative geographic proximity and the historical connectedness of the Asia-Pacific region.

Substantial rearrangements, single nucleotide frameshift deletion and low diversity in mitogenome of Wolbachia-infected strepsipteran endoparasitoid in comparison to its tephritid hosts

Insect mitogenome organisation is highly conserved, yet, some insects, especially with parasitic life cycles, have rearranged mitogenomes. Furthermore, intraspecific mitochondrial diversity can be reduced by fitness-affecting bacterial endosymbionts like Wolbachia due to their maternal coinheritance with mitochondria. We have sequenced mitogenomes of the Wolbachia-infected endoparasitoid Dipterophagus daci (Strepsiptera: Halictophagidae) and four of its 22 known tephritid fruit fly host species using total genomic extracts of parasitised flies collected across > 700 km in Australia. This halictophagid mitogenome revealed extensive rearrangements relative to the four fly mitogenomes which exhibited the ancestral insect mitogenome pattern. Compared to the only four available other strepsipteran mitogenomes, the D. daci mitogenome had additional transpositions of one rRNA and two tRNA genes, and a single nucleotide frameshift deletion in nad5 requiring translational frameshifting or, alternatively, resulting in a large protein truncation. Dipterophagus daci displays an almost completely endoparasitic life cycle when compared to Strepsiptera that have maintained the ancestral state of free-living adults. Our results support the hypothesis that the transition to extreme endoparasitism evolved together with increased levels of mitogenome changes. Furthermore, intraspecific mitogenome diversity was substantially smaller in D. daci than the parasitised flies suggesting Wolbachia reduced mitochondrial diversity because of a role in D. daci fitness.

Genomics-informed models reveal extensive stretches of coastline under threat by an ecologically dominant invasive species

Explaining why some species are widespread, while others are not, is fundamental to biogeography, ecology, and evolutionary biology. A unique way to study evolutionary and ecological mechanisms that either limit species' spread or facilitate range expansions is to conduct research on species that have restricted distributions. Nonindigenous species, particularly those that are highly invasive but have not yet spread beyond the introduced site, represent ideal systems to study range size changes. Here, we used species distribution modeling and genomic data to study the restricted range of a highly invasive Australian marine species, the ascidian Pyura praeputialis This species is an aggressive space occupier in its introduced range (Chile), where it has fundamentally altered the coastal community. We found high genomic diversity in Chile, indicating high adaptive potential. In addition, genomic data clearly showed that a single region from Australia was the only donor of genotypes to the introduced range. We identified over 3,500 km of suitable habitat adjacent to its current introduced range that has so far not been occupied, and importantly species distribution models were only accurate when genomic data were considered. Our results suggest that a slight change in currents, or a change in shipping routes, may lead to an expansion of the species' introduced range that will encompass a vast portion of the South American coast. Our study shows how the use of population genomics and species distribution modeling in combination can unravel mechanisms shaping range sizes and forecast future range shifts of invasive species.

Recent, small beginnings: genetic analysis suggests Catostomus rimiculus (Klamath smallscale sucker) in the Smith River, California, are introduced

Identification of introduced species can be important to understanding ecological systems and meeting conservation and management goals, but the process can be surprisingly challenging. The Klamath smallscale sucker Catostomus rimiculus seems likely to be native to the Smith River because the drainage separates two basins believed to be within the fish's native range, the Rogue and Klamath rivers. Further, C. rimiculus is broadly distributed in the Smith River, and the indigenous Dee-ni' People of the Smith River have a unique word for sucker. Nonetheless, a historical survey of fishes that described C. rimiculus from the Rogue and Klamath rivers did not include C. rimiculus among the fishes of the Smith River. To determine whether the genetic structure of the Smith River C. rimiculus reflects expectations for a native sucker population, the authors of this study examined variation in microsatellite and mitochondrial genetic markers from the Smith River and surrounding drainages. The genetic analyses revealed a pattern consistent with extreme founder effects in Smith River C. rimiculus, as would be expected from a single introduction of six or fewer effective individuals. The sharing of a high-frequency haplotype between the Smith River and Klamath River that is not detected in the Rogue River suggests the Klamath River as the likely source for the introduction. The findings highlight that local-scale introductions can be easily overlooked because the newly established populations can appear to be parts of contiguous natural distributions.

Not in the Least Concern: anthropogenic influences on a South-east Asian apple snail Pila scutata (Ampullariidae)

South-east Asian apple snails, Pila spp., have been declining since the introduction of globally invasive, confamilial South American Pomacea spp., yet Pila ecology remains poorly studied, with most occurrence records unconfirmed. Pila scutata, a previously widespread species, presumed native to the Malay peninsula and assessed as Least Concern in the IUCN Red List, was formerly harvested for food, and may have experienced anthropogenic translocations. We surveyed the Malay peninsula (specifically Peninsular Malaysia and Singapore) to investigate the current distribution and genetic diversity of P. scutata. Six populations were found in Singapore, but only one in Peninsular Malaysia. Mitochondrial COI and 16S sequencing revealed that the Malaysian population shared a single haplotype of both genes with the Singapore populations (500 km distant). This low genetic diversity could stem from a recent anthropogenic introduction, which brings into question the true native range of P. scutata and, coupled with poorly resolved taxonomy of the genus, necessitates a reassessment of its IUCN Red List status. Introduced populations pose a dilemma, and the lack of genetic diversity is of concern in light of Pila decline throughout South-east Asia. Our results highlight that conservation management of P. scutata and its congeners must therefore be better informed by greater taxonomic resolution and more comprehensive investigations of their ecology, both in native and introduced ranges.

Gene flow and genetic structure in Nile perch, Lates niloticus, from African freshwater rivers and lakes

BACKGROUND

Geological evolution of the African continent has been subject to complex processes including uplift, volcanism, desert formation and tectonic rifting. This complex geology has created substantial biogeographical barriers, and coupled with anthropogenic introductions of freshwater fishes, has influenced the genetic diversity, connectivity and sub-structuring of the teleost fauna. Nile perch, Lates niloticus, is an iconic fish in Africa and is of high commercial importance, both in the species' native range and where it has been translocated. However, the species is in decline and there is a need to understand its population genetic structure to facilitate sustainable management of the fishery and aquaculture development.

METHODOLOGY

Nile perch tissue samples were acquired from two West and four East (Lakes; Albert, Kyoga, Victoria and Turkana) African locations. Nineteen polymorphic microsatellite loci were used to study the genetic variation among populations across regions (West and East Africa), as well as between native and introduced environments within East Africa.

PRINCIPAL FINDINGS AND THEIR SIGNIFICANCE

Results revealed strong and significant genetic structuring among populations across the sampled distribution (divergence across regions, FCT = 0.26, P = 0.000). STRUCTURE analysis at a broad scale revealed K = 2 clusters, the West African individuals were assigned to one cluster, while all individuals from the East African region, regardless of whether native or introduced, were assigned to another cluster. The distinct genetic clusters identified in the current study between the West and East African Nile perch, appear to have been maintained by presence of biogeographic barriers and restricted gene flow between the two regions. Therefore, any translocations of Nile perch should be carefully considered across the regions of West and East Africa. Further analysis at a regional scale revealed further structuring of up to K = 3 genetic clusters in East African Nile perch. Significantly (P < 0.05) lower genetic diversity based on analysis of allelic richness (AR) was obtained for the two translocated populations of Lake Kyoga (AR = 3.61) and Lake Victoria (AR = 3.52), compared to Nile perch populations from their putative origins of Lakes Albert (AR = 4.12) and Turkana (AR = 4.43). The lower genetic diversity in the translocated populations may be an indication of previous bottlenecks and may also indicate a difficulty for these populations to persist and adapt to climatic changes and anthropogenic pressures that are currently present in the East African region.

Genetic signals of artificial and natural dispersal linked to colonization of South America by non-native Chinook salmon (Oncorhynchus tshawytscha)

Genetics data have provided unprecedented insights into evolutionary aspects of colonization by non-native populations. Yet, our understanding of how artificial (human-mediated) and natural dispersal pathways of non-native individuals influence genetic metrics, evolution of genetic structure, and admixture remains elusive. We capitalize on the widespread colonization of Chinook salmon Oncorhynchus tshawytscha in South America, mediated by both dispersal pathways, to address these issues using data from a panel of polymorphic SNPs. First, genetic diversity and the number of effective breeders (Nb) were higher among artificial than natural populations. Contemporary gene flow was common between adjacent artificial and natural and adjacent natural populations, but uncommon between geographically distant populations. Second, genetic structure revealed four distinct clusters throughout the Chinook salmon distributional range with varying levels of genetic connectivity. Isolation by distance resulted from weak differentiation between adjacent artificial and natural and between natural populations, with strong differentiation between distant Pacific Ocean and Atlantic Ocean populations, which experienced strong genetic drift. Third, genetic mixture analyses revealed the presence of at least six donor geographic regions from North America, some of which likely hybridized as a result of multiple introductions. Relative propagule pressure or the proportion of Chinook salmon propagules introduced from various geographic regions according to government records significantly influenced genetic mixtures for two of three artificial populations. Our findings support a model of colonization in which high-diversity artificial populations established first; some of these populations exhibited significant admixture resulting from propagule pressure. Low-diversity natural populations were likely subsequently founded from a reduced number of individuals.

Urban landscape genomics identifies fine-scale gene flow patterns in an avian invasive

Invasive species exert a serious impact on native fauna and flora and have been the target of many eradication and management efforts worldwide. However, a lack of data on population structure and history, exacerbated by the recency of many species introductions, limits the efficiency with which such species can be kept at bay. In this study we generated a novel genome of high assembly quality and genotyped 4735 genome-wide single nucleotide polymorphic (SNP) markers from 78 individuals of an invasive population of the Javan Myna Acridotheres javanicus across the island of Singapore. We inferred limited population subdivision at a micro-geographic level, a genetic patch size (~13-14 km) indicative of a pronounced dispersal ability, and barely an increase in effective population size since introduction despite an increase of four to five orders of magnitude in actual population size, suggesting that low population-genetic diversity following a bottleneck has not impeded establishment success. Landscape genomic analyses identified urban features, such as low-rise neighborhoods, that constitute pronounced barriers to gene flow. Based on our data, we consider an approach targeting the complete eradication of Javan Mynas across Singapore to be unfeasible. Instead, a mixed approach of localized mitigation measures taking into account urban geographic features and planning policy may be the most promising avenue to reducing the adverse impacts of this urban pest. Our study demonstrates how genomic methods can directly inform the management and control of invasive species, even in geographically limited datasets with high gene flow rates.

Contrasting genetic metrics and patterns among naturalized rainbow trout (Oncorhynchus mykiss) in two Patagonian lakes differentially impacted by trout aquaculture

Different pathways of propagation and dispersal of non‐native species into new environments may have contrasting demographic and genetic impacts on established populations. Repeated introductions of rainbow trout (Oncorhynchus mykiss) to Chile in South America, initially through stocking and later through aquaculture escapes, provide a unique setting to contrast these two pathways. Using a panel of single nucleotide polymorphisms, we found contrasting genetic metrics and patterns among naturalized trout in Lake Llanquihue, Chile's largest producer of salmonid smolts for nearly 50 years, and Lake Todos Los Santos (TLS), a reference lake where aquaculture has been prohibited by law. Trout from Lake Llanquihue showed higher genetic diversity, weaker genetic structure, and larger estimates for the effective number of breeders (N_b) than trout from Lake TLS. Trout from Lake TLS were divergent from Lake Llanquihue and showed marked genetic structure and a significant isolation‐by‐distance pattern consistent with secondary contact between documented and undocumented stocking events in opposite shores of the lake. Multiple factors, including differences in propagule pressure, origin of donor populations, lake geomorphology, habitat quality or quantity, and life history, may help explain contrasting genetic metrics and patterns for trout between lakes. We contend that high propagule pressure from aquaculture may not only increase genetic diversity and N_b via demographic effects and admixture, but also may impact the evolution of genetic structure and increase gene flow, consistent with findings from artificially propagated salmonid populations in their native and naturalized ranges.

Rapid expansion of the invasive oyster Crassostrea gigas at its northern distribution limit in Europe: Naturally dispersed or introduced?

The Pacific oyster, Crassostrea gigas, was introduced to Europe for aquaculture purposes, and has had a rapid and unforeseen northward expansion in northern Europe. The recent dramatic increase in number of C. gigas populations along the species’ northern distribution limit has questioned the efficiency of Skagerrak as a dispersal barrier for transport and survival of larvae. We investigated the genetic connectivity and possible spreading patterns between Pacific oyster populations on the southern Norwegian coast (4 localities) and Swedish and Danish populations by means of DNA microsatellite analysis of adult oysters, and by simulating larvae drift. In the simulations we used a 3D oceanographic model to explore the influence of recent climate change (1990–2010) on development, survival, and successful spreading of Danish and Swedish Pacific oyster larvae to Norwegian coastal waters. The simulations indicated adequate temperature conditions for development, survival, and settlement of larvae across the Skagerrak in warm years since 2000. However, microsatellite genotyping revealed genetic differences between the Norwegian populations, and between the Norwegian populations and the Swedish and Danish populations, the latter two populations being more similar. This patchwork pattern of genetic dissimilarity among the Norwegian populations points towards multiple local introduction routes rather than the commonly assumed unidirectional entry of larvae drifted from Denmark and Sweden. Alternative origins of introduction and implications for management, such as forecasting and possible mitigation actions, are discussed.

Evidence of natural reproduction of Atlantic sturgeon in the Connecticut River from unlikely sources

Atlantic Sturgeon is listed under the U.S. Endangered Species Act as five Distinct Population Segments (DPS). The "endangered" New York Bight (NYB) DPS is thought to only harbor two populations; one in the Hudson River and a second smaller one in the Delaware River. Historically, the Connecticut River probably supported a spawning population of Atlantic Sturgeon that was believed extirpated many decades ago. In 2014, we successfully collected pre-migratory juvenile specimens from the lower Connecticut River which were subjected to mitochondrial DNA (mtDNA) control region sequence and microsatellite analyses to determine their genetic relatedness to other populations coastwide. Haplotype and allelic frequencies differed significantly between the Connecticut River collection and all other populations coastwide. Sibship analyses of the microsatellite data indicated that the Connecticut River collection was comprised of a small number of families that were likely the offspring of a limited number of breeders. This was supported by analysis of effective population size (Ne) and number of breeders (Nb). STRUCTURE analysis suggested that there were 11 genetic clusters among the coastwide collections and that from the Connecticut River was distinct from those in all other rivers. This was supported by UPGMA analyses of the microsatellite data. In AMOVA analyses, among region variation was maximized, and among population within regions variation minimized when the Connecticut River collection was separate from the other two populations in the NYB DPS indicating the dissimilarity between the Connecticut River collection and the other two populations in the NYB DPS. Use of mixed stock analysis indicated that the Connecticut River juvenile collection was comprised of specimens primarily of South Atlantic and Chesapeake Bay DPS origins. The most parsimonious explanation for these results is that the Connecticut River hosted successful natural reproduction in 2013 and that its offspring were descendants of a small number of colonizers from populations south of the NYB DPS, most notably the South Atlantic DPS. Our results run contrary to the belief that re-colonizers of extirpated populations primarily originate in proximal populations.

Genetic variation in the invasive weed Mikania micrantha (Asteraceae) suggests highways as corridors for its dispersal in southern China

BACKGROUND AND AIMS

Roads as corridors of seed or fruit spatial dispersal have major impacts on the establishment and spread of invasive species, but their precise role in population genetic variation remains poorly understood. The South American weed Mikania micrantha has spread rapidly across southern China since its introduction to the Shenzhen area in 1984. This study investigated how its genetic diversity is distributed along highways, and whether highways have acted as corridors for the rapid expansion of M. micrantha METHODS: Twenty-seven roadside populations were sampled along four highways in southern China, and 787 samples were examined using 12 microsatellite markers. Variation in genetic diversity among populations was quantified and patterns of genetic differentiation were analysed.

KEY RESULTS

A high level of genetic diversity was found at both the species and the population levels in this self-incompatible plant (expected heterozygosity = 0·497 and 0·477, respectively; allelic richness = 2·580 and 2·521, respectively). The Wright F-statistic value among populations (0·044, P < 0·01) and the analysis of molecular variance (91 % of genetic variation residing within populations, 9 % among populations within highways and 0 % among the four highways) showed a relatively low level of genetic differentiation among populations, while the principal coordinate and cluster analyses also indicated a lack of clear geographical genetic structure among populations. The calculated N_m value of 5·5 signifies strong gene flow.

CONCLUSIONS

The pattern of genetic variation is consistent with facilitated dispersal along highways. The genetic admixtures among the roadside populations imply the occurrence of multiple population introductions during colonization. The long-distance dispersal of seeds associated with vehicular transportation on highways may have played important roles in shaping the genetic variation. This finding highlights the importance of highways as corridors for the spread of M. micrantha in southern China.