Tracing invasion routes of Cuban treefrogs into Louisiana using mitochondrial DNA

Background: Walleye (Sander vitreus), a valuable sportfish and an important ecological apex predator, exhibits genetic structuring across their range and localized structuring as a result of stocking. Methods: Walleye from 17 sampling locations across West Virginia were sequenced using a ddRAD protocol, generating various SNP datasets to assess population structuring and genomic diversity, with specific emphasis on the native Eastern Highlands strain. Different minor allele frequency filter thresholds were tested to assess impacts on genetic diversity and differentiation metrics. Results: High genetic differentiation was observed between the Eastern Highlands and Great Lakes strains, with further sub-structuring within the Eastern Highlands strain between the Ohio River populations and the other populations. Increasing MAF thresholds generally reduced the distinctiveness of clusters, but the overall inference of the number of clusters was minimally impacted. Genetic diversity metrics indicated some variability among Eastern Highlands walleye populations, with isolated populations, including the New River and Summersville Lake, showing higher inbreeding coefficients. MAF filters generally increased diversity metrics, but the trend of diversity metrics among populations remained relatively consistent. Several SNPs were found to be potentially undergoing selection, with the minor allele frequencies of these SNPs being found to be highest in Summersville Lake, highlighting potential adaptive divergence between the riverine populations and a large lentic system. Conclusions: The use of any MAF filter generated the same trends of population structuring and genomic diversity inferences regardless of the MAF threshold used. Further management of Eastern Highlands walleye in West Virginia needs to emphasize protecting the genetic integrity of the Kanawha River population and ongoing genomic screening of broodstock to conserve native genetic diversity.

Species introductions often bring together genetically divergent source populations, resulting in genetic admixture. This geographic reshuffling of diversity has the potential to generate favourable new genetic combinations, facilitating the establishment and invasive spread of introduced populations. Observational support for the superior performance of admixed introductions has been mixed, however, and the broad importance of admixture to invasion questioned. Under most underlying mechanisms, admixture's benefits should be expected to increase with greater divergence among and lower genetic diversity within source populations, though these effects have not been quantified in invaders. We experimentally crossed source populations differing in divergence in the invasive plant Centaurea solstitialis. Crosses resulted in many positive (heterotic) interactions, but fitness benefits declined and were ultimately negative at high source divergence, with patterns suggesting cytonuclear epistasis. We explored the literature to assess whether such negative epistatic interactions might be impeding admixture at high source population divergence. Admixed introductions reported for plants came from sources with a wide range of genetic variation, but were disproportionately absent where there was high genetic divergence among native populations. We conclude that while admixture is common in species introductions and often happens under conditions expected to be beneficial to invaders, these conditions may be constrained by predictable negative genetic interactions, potentially explaining conflicting evidence for admixture's benefits to invasion.

Tadpoles have many predators in the wild and are able to escape from them because the structure of their tail allows it to tear off if attacked. We examined the effects of tail damage in the early tadpole stages on the leaping and swimming abilities of Cuban tree frogs after metamorphosis. We obtained 120 Cuban tree frogs, and to simulate predation, we initially removed a piece of the top of the tadpole tails in one experimental group, cut off a piece of the bottom of the tadpole tails in the second experimental group, and did not make any cuts to tails of the control group. Following tail regeneration by all tadpoles in both experimental groups, we treated all experimental tadpoles as one group, and simulated a second predation event by removing 10% of the distal tip of the tail. After tadpoles completed metamorphosis, they were subjected to a swimming endurance test and subsequent measurement of their leaping abilities. We found no significant effect of tail damage on the leaping abilities of frogs after metamorphosis, and no significant difference in body size at metamorphosis among the groups. The experiment was then replicated and tested tadpole corticosterone (CORT) levels to determine if tadpoles exhibited stress from the tail damage. We found significantly elevated CORT levels in tadpoles with tail damage compared to the tadpoles without tail damage. We conclude that the regeneration abilities of the Cuban tree frog tadpoles afford them the opportunity to survive minor predation events and recover with no apparent long-lasting ill effects even though they were physiologically stressed from the damage. These abilities likely contribute to the Cuban tree frogs' success as an invasive species throughout the Florida peninsula.

Aim Invasive alien species usually exhibit very high adaptation and rapid evolution in a new environment, but they often have low levels of genetic diversity (invasive species paradox). Genetic variation and population genetic structure of feral American mink, Neovison vison, in Poland was investigated to explain the invasion paradox and to assess current gene flow. Furthermore, the influence of mink farming on adaptation of the feral population was evaluated by comparing the genetic structure of feral and ranch mink.Location Samples from feral mink were collected in 11 study areas in northern and central Poland and from ranch mink at 10 farms distributed throughout the country.Methods A 373‐bp‐long mtDNA control region fragment was amplified from 276 feral and 166 ranch mink.Results Overall, 31 haplotypes, belonging to two groups from genetically diverse sources, were detected: 11 only in feral mink, 12 only in ranch mink and eight in both. The genetic differentiation of feral mink from the trapping sites was high, while that among ranch mink from various farms was moderate. There was no significant relationship between genetic and geographic distance. The number of trapping sites where given haplotypes occurred correlated with the number of farms with these haplotypes. The mink from two sites were the most divergent, both from all other feral mink and from ranch mink. Comparison of mtDNA and microsatellite differentiation suggests male‐biased dispersal in this species.Main conclusions American mink in Poland exhibit high genetic diversity and originate from different source populations of their native range. The process of colonization was triggered by numerous escapees from various farms and by immigrants from Belarus. The genetic structure of local feral mink populations was shaped by the founder effect and multiple introductions. The genomic admixture that occurred during mixing of different populations might have increased the fitness of individuals and accelerated the invasiveness of this species.

Lao Pa Koi (LPK) chicken is a popular fighting breed in Thailand, prized for (its unique characteristics acquired by selective breeding), and a valuable model for exploring the genetic diversity and admixture of red junglefowls and domestic chickens. In this study, genetic structure and diversity of LPK chicken were assessed using 28 microsatellite markers and mitochondrial DNA (mtDNA) D-loop sequences, and the findings were compared to a gene pool library from “The Siam Chicken Bioresource Project”. High genetic variability was observed in LPK chickens using mtDNA D-loop haplotype analysis, and six haplotypes were identified. Microsatellite data revealed 182 alleles, with an average of 6.5 alleles per locus. These results confirmed the occurrence of genetic admixture of red junglefowl and Thai domestic chickens in LPK chicken breed. A maximum entropy modeling approach was used to analyze the spatial suitability and to assess the adaptive evolution of LPK chickens in diverse local environments. The model identified 82.52% of the area studied as unsuitable, and 9.34%, 7.11%, and 2.02% of the area indicated moderate, low, and high suitability, respectively. The highest contribution rate to land suitability for LPK chickens was found at an elevation of 100–250 m, suggesting the importance of elevation for their potential distribution. The results of this study provide valuable insights into the genetic origin of LPK chicken breed and identify resources for future genetic improvement.

The brown treesnake (Boiga irregularis) population on the Pacific island of Guam has reached iconic status as one of the most destructive invasive species of modern times, yet no published works have used genetic data to identify a source population. We used DNA sequence data from multiple genetic markers and coalescent-based phylogenetic methods to place the Guam population within the broader phylogeographic context of B. irregularis across its native range and tested whether patterns of genetic variation on the island are consistent with one or multiple introductions from different source populations. We also modeled a series of demographic scenarios that differed in the effective size and duration of a population bottleneck immediately following the invasion on Guam, and measured the fit of these simulations to the observed data using approximate Bayesian computation. Our results exclude the possibility of serial introductions from different source populations, and instead verify a single origin from the Admiralty Archipelago off the north coast of Papua New Guinea. This finding is consistent with the hypothesis that B. irregularis was accidentally transported to Guam during military relocation efforts at the end of World War II. Demographic model comparisons suggest that multiple snakes were transported to Guam from the source locality, but that fewer than 10 individuals could be responsible for establishing the population. Our results also provide evidence that low genetic diversity stemming from the founder event has not been a hindrance to the ecological success of B. irregularis on Guam, and at the same time offers a unique ‘genetic opening’ to manage snake density using classical biological approaches.

The introduction of invasive Cichla spp. was followed by the several reports regarding the decline of local freshwater native species in Malaysia. The purpose of this research was to generate information concerning the introduction history of Cichla spp. in Malaysia. Studies on genetic diversity and structure provides the essential baseline data for monitoring and conservation of invasive species. This will help to clearly understand the propagule pressure and genetic distribution of Cichla spp. in the invaded freshwaters of Malaysia. A total of 61 samples of Cichla spp. were collected from 9 sampling location in Malaysia for mitochondrial DNA (control region) analysis. Overall samples showed high genetic diversity (Hd, 0.6700; π, 0.0254) and yielded 9 haplotypes resulted from different Cichla spp. present. The maximum likelihood tree with strong bootstrap support revealed that Cichla spp. forms 3 clusters, and confirmed to be C. monocoulus, C. occelaris and C. temensis. Except for Malacca populations, other populations were largely dominated by either C. monocoulus or C. occelaris. The current study suggesting that more than one introduction event of invasive Cichla spp. occurred in Malaysia. HIGHLIGHTS One of the common problem in the conservation effort for Malaysia’s freshwater aquatic ecosystem is failure to understand the introduction events of invasive species (Cichla) Mitochondrial DNA analysis (control region) conducted in order to find the genetic diversity and genetic structure of invasive Cichla across freshwater habitats in Malaysia High genetic diversity was observed, suggesting multiple introduction occurance of invasive Cichla in the country GRAPHICAL ABSTRACT

The maintenance of genetic diversity is thought to be fundamental for the conservation of threatened species. It is therefore important to understand how genetic diversity is affected by the re-introduction of threatened species. We use establishment history and genetic data from the remnant and re-introduced populations of a New Zealand endemic bird, the hihi Notiomystis cincta, to understand genetic diversity loss and quantify the genetic effects of re-introduction. Our data do not support any recent bottleneck events in the remnant population. Furthermore, all genetic diversity measures indicate the remnant hihi population has retained high levels of genetic diversity relative to other New Zealand avifauna with similar histories of decline. Genetic diversity (N(A) , alleles per locus, allelic richness, F(IS) and H(S) ) did not significantly decrease in new hihi populations founded through re-introduction when compared to their source populations, except in the Kapiti Island population (allelic richness and H(S) ) which had very slow post-re-introduction population growth. The N(e) /N(c) ratio in the remnant population was high, but decreased in first-level re-introductions, which together with significant genetic differentiation between populations (F(ST) & Fisher's exact tests) suggest that extant populations are diverging as a result of founder effects and drift. Importantly, simulations of future allele loss predict that the number of alleles lost will be higher in populations with a slow population growth, fewer founding individuals and with nonrandom mating. Interestingly, this species has very high levels of extra-pair paternity which may reduce reproductive variance by allowing social and floater males to reproduce a life history trait that together with a large remnant population size may help maintain higher levels of genetic diversity than expected.

Genetic consequences of seed dispersal to sleeping trees by white-bellied spider monkeys

Habitat loss and overexploitation extirpated American black bears (Ursus americanus) from most of the Central Appalachians, USA, by the early 20th Century. To attempt to restore bears to the southwestern portion of this region, 2 reintroductions that used small founder groups (n = 27 and 55 bears), but different release methods (hard vs. soft), were conducted during the 1990s. We collected hair samples from black bears during 2004–2016 in the reintroduced Big South Fork (BSF) and Kentucky–Virginia populations (KVP), their respective Great Smoky Mountains (GSM) and Shenandoah National Park (SNP) source populations, and a neighboring population in southern West Virginia (SWV) to investigate the early genetic outcomes of bear reintroduction. Despite having undergone genetic bottlenecks, genetic diversity remained similar between reintroduced populations and their sources approximately 15 years after the founder events (ranges: AR = 4.86–5.61; HO = 0.67–0.75; HE = 0.65–0.71). Effective population sizes of the reintroduced KVP and BSF (NE = 31 and 36, respectively) were substantially smaller than their respective SNP and GSM sources (NE = 119 and 156, respectively), supporting founder effects. Genetic structure analysis indicated that the hard-released (i.e., no acclimation period) KVP founder group likely declined considerably, whereas the soft-released BSF founder group remained mostly intact, suggesting superior effectiveness of soft releases. Asymmetrical gene flow via immigration from the SWV has resulted in the KVP recovering from the initial founder group reduction. Sustained isolation, small NE, and small population size of the BSF may warrant continued genetic monitoring to determine if gene flow from neighboring populations is established or NE declines. For future bear reintroductions, we suggest managers consider sourcing founders from populations with high genetic diversity and soft-releasing bears to locales that are, if possible, within the dispersal capability of extant populations to mitigate the potential consequences of founder effects and isolation.

Studies in ecological and community genetics have advanced our understanding of the role of intraspecific diversity in structuring communities and ecosystems. However, in near-shore marine communities, these studies have mostly been restricted to seagrasses, marsh plants, and oysters. Yet, macroalgae are critically important ecosystem engineers in these communities. Greater intraspecific diversity in a macroalgal ecosystem engineer should result in higher primary and secondary production and community resilience. The paucity of studies investigating the consequences of macroalgal intraspecific genetic variation might be due, in part, to the complexity of macroalgal life cycles. The majority of macroalgae have seemingly subtle, but in actuality, profoundly different life cycles than the more typical animal and angiosperm models. Here, we develop a novel genetic diversity metric, PHD , that incorporates the ratio of gametophytic to sporophytic thalli in natural populations. This metric scales from 0 to 1 like many common genetic diversity metrics, such as genotypic richness, enabling comparisons among metrics. We discuss PHD and examples from the literature, with specific reference to the widespread, red seaweed Agarophyton vermiculophyllum. We also discuss a sex diversity metric, PFM , which also scales from 0 to 1, but fewer studies have identified males and females in natural populations. Nevertheless, by incorporating these novel metrics into the repertoire of diversity metrics, we can explore the role of genetic diversity in community and ecosystem dynamics with an emphasis on the unique biology of many macroalgae, as well as other haplodiplontic taxa such as ferns, foraminiferans, and some fungi.

To relate base populations in genomic evaluations, the theory of metafounders has been developed during the last decade. From this theory, relationships within and between populations can be estimated with the gamma parameter. Recently, it has been demonstrated that several genetic diversity metrics such as fixation index (Fst), Nei’s minimum genetic distance (D), and population inbreeding coefficients based on homozygosity (Fhom), drift (Fdrift) or average heterozygosity (Fb) can be estimated based on this gamma matrix. However, how these derived formulas behave in real populations, compared to their traditionally estimated counterparts, has not yet been studied. Therefore, the objective of this study is to compare traditional and gamma-based genetic diversity parameters. For this purpose, we will apply formulas found in Table 1 to different cattle populations. Formulas derived from the gamma parameter assume allelic frequencies of 0.5 in the base population. Unless the formulas are more robust to changes in allelic frequencies than expected, we should probably expect different results between the traditional and novel metrics based on gamma.

A simulation study shows impacts of genetic diversity on establishment success of digital invaders in heterogeneous environments

The Old World bollworm, Helicoverpa armigera (Hubner) (Lepidoptera: Noctuidae), is a globally distributed agricultural and horticultural insect pest. Despite the economic importance of this insect in Ethiopia, its genetic diversity and demographic history are poorly understood. We examined the nucleotide variation of the mitochondrial cytochrome c oxidase subunit I (COI) gene fragment of 74 H. armigera individuals from six collection sites in Ethiopia. We recorded 15 COI haplotypes in H. armigera, ten globally shared and five exclusive to Ethiopia (HaET15, HaET14, HaET10, HaET7, and HaET4). Haplotype HaET1 was the most widely geographically distributed and frequent (71.62%). Analysis of molecular variance (AMOVA) revealed a high and significant level of variation within H. armigera populations (θST = −0.0135). Negative values of the neutrality test and nonsignificant index of mismatch distribution supported the demographic expansion of H. armigera populations in Ethiopia; furthermore, this was also supported by the nonsignificant values of the sum of squared deviations (SSD) and raggedness index (r). The high genetic variation and population expansion of H. armigera have immense implications for devising locally adapted management strategies in area‐wide integrated pest management IPM programs. However, a comprehensive study of H. armigera genetic diversity and population structure using various molecular markers is needed for future confirmation.

The link between the successful establishment of alien species and propagule pressure is well-documented. Less known is how humans influence the post-introduction dynamics of invasive alien populations. The latter requires studying parallel invasions by the same species in habitats that are differently impacted by humans. We analysed microsatellite and genome size variation, and then compared the genetic diversity and structure of invasive Poa annua L. on two sub-Antarctic islands: human-occupied Marion Island and unoccupied Prince Edward Island. We also carried out niche modelling to map the potential distribution of the species on both islands. We found high levels of genetic diversity and evidence for extensive admixture between genetically distinct lineages of P. annua on Marion Island. By contrast, the Prince Edward Island populations showed low genetic diversity, no apparent admixture, and had smaller genomes. On both islands, high genetic diversity was apparent at human landing sites, and on Marion Island, also around human settlements, suggesting that these areas received multiple introductions and/or acted as initial introduction sites and secondary sources (bridgeheads) for invasive populations. More than 70years of continuous human activity associated with a meteorological station on Marion Island led to a distribution of this species around human settlements and along footpaths, which facilitates ongoing gene flow among geographically separated populations. By contrast, this was not the case for Prince Edward Island, where P. annua populations showed high genetic structure. The high levels of genetic variation and admixture in P. annua facilitated by human activity, coupled with high habitat suitability on both islands, suggest that P. annua is likely to increase its distribution and abundance in the future.