The role of founder effects on the genetic structure of the invasive bullfrog (Lithobates catesbeianaus) in China

Variations in Genetic Diversity of Invasive Species Lithobates catesbeianus in China

The introduction and subsequent range expansion of the American bullfrog (Lithobates catesbeianus) is part of a rising trend of troublesome biological invasions happening in China. This detrimental amphibious invasive species has strong adaptability. After its introduction and spread, it established its own ecological niche in many provinces of China, and its range has continued to expand to more areas. Previous studies recorded the introduction time of bullfrogs and calculated the changes in their genetic diversity in China using mitochondria, but the specific introduction route in China is still unknown. Expanding upon previous research, we employed whole-genome scans (utilizing 2b-RAD genomic sequencing) to examine single nucleotide polymorphisms (SNPs) and microsatellites within Lithobates catesbeianus to screen the genomes of these invasive amphibian species from eight Chinese provinces and two U.S. states, including Kansas, where bullfrogs originate. A total of 1,336,475 single nucleotide polymorphic loci and 17 microsatellite loci were used to calculate the genetic diversity of bullfrogs and their migration pathways. Our results suggest that the population in Hunan was the first to be introduced and to spread, and there may have been multiple introductions of subpopulations. Additionally, the genetic diversity of both the SNP and microsatellite loci in the Chinese bullfrog population was lower than that of the US population due to bottleneck effects, but the bullfrogs can adapt and spread rapidly. This study will offer crucial insights for preventing and controlling future introductions into the natural habitats in China. Additionally, it will assist in devising more precise strategies to manage the existing populations and curtail their continued expansion, as well as aim to improve clarity and originality while mitigating plagiarism risk.

Conservation genomics of an endangered montane amphibian reveals low population structure, low genomic diversity and selection pressure from disease

Wildlife diseases are a major global threat to biodiversity. Boreal toads (Anaxyrus [Bufo] boreas) are a state-endangered species in the southern Rocky Mountains of Colorado and New Mexico, and a species of concern in Wyoming, largely due to lethal skin infections caused by the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd). We performed conservation and landscape genomic analyses using single nucleotide polymorphisms from double-digest, restriction site-associated DNA sequencing in combination with the development of the first boreal toad (and first North American toad) reference genome to investigate population structure, genomic diversity, landscape connectivity and adaptive divergence. Genomic diversity (π = 0.00034-0.00040) and effective population sizes (Ne = 8.9-38.4) were low, likely due to post-Pleistocene founder effects and Bd-related population crashes over the last three decades. Population structure was also low, likely due to formerly high connectivity among a higher density of geographically proximate populations. Boreal toad gene flow was facilitated by low precipitation, cold minimum temperatures, less tree canopy, low heat load and less urbanization. We found >8X more putatively adaptive loci related to Bd intensity than to all other environmental factors combined, and evidence for genes under selection related to immune response, heart development and regulation and skin function. These data suggest boreal toads in habitats with Bd have experienced stronger selection pressure from disease than from other, broad-scale environmental variations. These findings can be used by managers to conserve and recover the species through actions including reintroduction and supplementation of populations that have declined due to Bd.

Pathogenic selection promotes adaptive immune variations against serious bottlenecks in early invasions of bullfrogs

Adaptive genetic variations are key for understanding evolutionary processes influencing invasions. However, we have limited knowledge on how adaptive genetic diversity in invasive species responds to new pathogenic environments. Here, we compared variations in immune major histocompatibility complex (MHC) class-II β gene and neutral loci in relation to pathogenic chytrid fungus (Batrachochytrium dendrobatidis, Bd) infection across invasive and native populations of American bullfrog between China and United States (US). Chinese invasive populations show a 60% reduction in neutral cytb variations relative to US native populations, and there were similar MHC variation and functional diversity between them. One MHC allele private to China was under recent positive selection and associated with decreased Bd infection, partly explaining the lower Bd prevalence for Chinese populations than for native US populations. These results suggest that pathogen-mediated selection favors adaptive MHC variations and functional diversity maintenance against serious bottlenecks during the early invasions (within 15 generations) of bullfrogs.

Invasive American Bullfrogs Age, Body Size, and Sexual Size Dimorphism Geographical Variation in Northwestern China

Invasive species impact both the local biota and human economies and are a very serious threat to biodiversity. The American bullfrog was initially introduced into northwestern China and many other sites for aquacultural purposes. Then, the frogs escaped and established feral populations. Here, we investigated the variations in age, body size, and sexual size dimorphism of two breeding populations inhabiting the southern (warm and dry) and northern (cold and wet) regions of Xinjiang province in northwestern China. Both populations originated from a single source that was introduced into Xinjiang 54 years ago. In both populations, males were significantly smaller than females, indicating significant sexual size dimorphism. The mean age and body size of both sexes in the population in the colder region were lower than those of the population in the warmer region. Bullfrogs in the southern population had a higher degree of sexual size dimorphism. These results increase our understanding of the American bullfrog, which could help in the development of strategies to control this invasive species.

Complex origins indicate a potential bridgehead introduction of an emerging amphibian invader (Eleutherodactylus planirostris) in China

Identifying the origins of established alien species is important to prevent new introductions in the future. The greenhouse frog (Eleutherodactylus planirostris), native to Cuba, the Bahamas, and the Cayman Islands, has been widely introduced to the Caribbean, North and Central America, Oceania and Asia. This invasive alien amphibian was recently reported in Shenzhen, China, but the potential introduction sources remain poorly understood. Based on phylogenetic analysis using mitochondrial 16S, COI and CYTB sequences, we detected a complex introduction origin of this species, which may be from Hong Kong, China, the Philippines, Panama and Florida, USA, all pointing to a bridgehead introduction. In addition, the nursery trade between the four countries or regions and mainland China from 2011 to 2020 was also significantly higher than other areas with less likelihood of introductions, which supported the molecular results. Our study provides the first genetic evidence of the potential sources of this emerging amphibian invader in mainland China, which may help develop alien species control strategies in the face of growing trade through globalization.

Invasive Bullfrogs Maintain MHC Polymorphism Including Alleles Associated with Chytrid Fungal Infection

Maintenance of genetic diversity at adaptive loci may facilitate invasions by non-native species by allowing populations to adapt to novel environments, despite the loss of diversity at neutral loci that typically occurs during founder events. To evaluate this prediction, we compared genetic diversity at major histocompatibility complex (MHC) and cytochrome b (cytb) loci from 20 populations of the American bullfrog (Rana catesbeiana) across theinvasive and native ranges in North America and quantified the presence of the pathogen Batrachochytrium dendrobatidis (Bd). Compared to native populations, invasive populations had significantly higher Bd prevalence and intensity, significantly higher pairwise MHC and cytb FST, and significantly lower cytb diversity, but maintained similar levels of MHC diversity. The two most common MHC alleles (LiCA_B and Rapi_33) were associated with a significant decreased risk of Bd infection, and we detected positive selection acting on four peptide binding residues. Phylogenetic analysis suggested invasive populations likely arose from a single founding population in the American Midwest with a possible subsequent invasion in the northwest. Overall, our study suggests that the maintenance of diversity at adaptive loci may contribute to invasion success and highlights the importance of quantifying diversity at functional loci to assess the evolutionary potential of invasive populations.

Genetic structure of American bullfrog populations in Brazil

Non-native species are a major problem affecting numerous biomes around the globe. Information on their population genetics is crucial for understanding their invasion history and dynamics. We evaluated the population structure of the non-native American bullfrog, Aquarana catesbeiana, in Brazil on the basis of 324 samples collected from feral and captive groups at 38 sites in seven of the nine states where feral populations occur. We genotyped all samples using previously developed, highly polymorphic microsatellite loci and performed a discriminant analysis of principal components together with Jost’s D index to quantify pairwise differentiation between populations. We then amplified 1,047 base pairs of the mitochondrial cytochrome b (cytb) gene from the most divergent samples from each genetic population and calculated their pairwise differences. Both the microsatellite and cytb data indicated that bullfrogs comprise two populations. Population grouping 1 is widespread and possesses two cytb haplotypes. Population grouping 2 is restricted to only one state and possesses only one of the haplotypes from Population grouping 1. We show that there were two imports of bullfrogs to Brazil and that there is low genetic exchange between population groupings. Also, we find that there is no genetic divergence among feral and captive populations suggesting continuous releases. The limited genetic variability present in the country is associated to the small number of introductions and founders. Feral bullfrogs are highly associated to leaks from farms, and control measures should focus on preventing escapes using other resources than genetics, as feral and captive populations do not differ.

Genetic analysis of hog deer (Axis porcinus) in Victoria, Australia, and its applications to invasive species and game management

Hog deer were introduced to Australia in the 1860s, where they have spread across the Gippsland region of Victoria. Due to its status as an introduced species and an important game animal within Victoria, management of the species is complex. Given this complexity, genetic studies can provide important information regarding population structure and diversity which can assist in controlling problematic populations of hog deer, while also ensuring viable game stock in sites managed as game reserves. The aim of this study was to investigate the population genetic structure and diversity of the Victorian hog deer 150 years after introduction using short tandem repeats (STRs). Hog deer samples were collected across 15 sites of differing management regimes in the Gippsland region of Victoria and genotyped for 13 polymorphic STR loci. Up to four distinct genetic clusters were identified across the sites sampled, suggesting that despite low observed genetic diversity, population structure is present across their range. It was also possible to detect evidence of recent translocations among populations. This study suggests that the presence of distinct genetic clusters may enable management of separate genetic units, considering invasive species and game management objectives.

Vibrio cholerae was found in cultured bullfrog

Bullfrog is one of the most important economic aquatic animals in China that is widely cultured in southern China and is a key breed recommended as an industry of poverty alleviation in China. During recent years, a fatal bacterial disease has often been found in cultured bullfrogs. The clinical manifestations of the diseased bullfrogs were severe intestinal inflammation and an anal prolapse. A bacterial pathogen was isolated from the diseased bullfrog intestines. The bacterium was identified as Vibrio cholerae using morphological, biochemical and 16S rRNA phylogenetic analysis. In this study, V. cholerae was isolated and identified in diseased bullfrogs for the first time, providing a basis for the diagnosis and control of the disease. Therefore, attention should be paid to the modes of transmission of V. cholerae from bullfrog and formulate reasonable safety measures.

Genetic diversity of Procambarus clarkii populations based on mitochondrial DNA and microsatellite markers in different areas of Guangxi, China

The red swamp crayfish (Procambarus clarkii) is a famous invasive species. However, it has become one of the most important freshwater aquaculture resources in China. Herein, we focus on five artificial cultured populations of P. clarkii in Guangxi, southern China to investigate the genetic diversity based on mitochondrial DNA and microsatellites. The results revealed that the genetic diversity of P. clarkii populations in southern Guangxi (NN and DT) was lower than in central (LZ and LB) and northern (RS) Guangxi. A total of 17 haplotypes were captured from 100 individuals and haplotype 2 mainly existed, and the number of haplotype in NN and DT was less than other populations. The AMOVA showed that genetic variation was determined by within populations. The observed mismatch distribution of overall populations fit the expected distributions, indicating that no obvious demographic expansion, but unimodal was observed in RS, LZ and LB. Fst among most of groups exhibited moderate differentiation. Nevertheless, the gene flow demonstrated there had extensive gene exchanges between different populations, particularly between LZ and LB. UPGMA tree revealed that NN and DT belonged to the same clade, whereas the remaining populations were in the other clade. According to the genetic diversity, there is a need to improve the germplasm resources of P. clarkii in southern Guangxi.

Propagule pressure and hunting pressure jointly determine genetic evolution in insular populations of a global frog invader

Islands are often considered to be more susceptible to biological invasions and to suffer greater impacts from invaders than mainland areas, and this difference is generally attributed to differences in species introductions, ecological factors or human activities between islands and mainland areas. Genetic variation, as a good estimate of evolutionary potential, can influence the invasion process and impacts of alien species. However, few studies have compared the genetic diversity of alien species between islands and a corresponding mainland. Here, we examined the genetic variation and differentiation in feral populations (30 sampled individuals/population) of a globally invasive species (the American bullfrog, Lithobates catesbeianus) that was extensively farmed on 14 islands in the Zhoushan Archipelago of China and in three nearby regions on the mainland. We quantified the relative importance of propagule pressure and hunting pressures on the genetic variation of bullfrog populations and found that insular populations have greater genetic variation than their mainland counterparts. Although genetic differentiation between the populations was observed, no evidence of recent bottlenecks or population expansion in any of the tested population was found. Our results suggest that the propagule pressures of bullfrogs escaping from farms, multiple releases and hunting pressure influence the genetic variation among bullfrog populations. These results might have important implications for understanding the establishment and evolution of alien species on islands and for the management of invasive species.

Biology, taxonomy, and IPM strategies of Bactrocera tau Walker and complex species (Diptera; Tephritidae) in Asia: a comprehensive review

Bactrocera flies are the serious pests of fruit, vegetables, and nuts over the world. Bactrocera tau Walker is an economically important pest of agricultural crops. In Asia, approximately 30-40% losses of agricultural products are caused by B. tau infestation every year. In Asia, the B. tau contains a complex of sibling species that called the tau complex. However, the basic studies of B. tau and complex species are very important for integrated management. A comprehensive review of the B. tau and complex species has not been provided elsewhere. So, considering the importance of B. tau and complex species, this study provides the published information on ecology, nomenclature, identification tools, geographical distribution, potential invasion, and IPM tactics of B. tau and complex species, which would be more informative for publication facilitating related to integrated pest management (IPM) strategies of B. tau and complex species. In IPM of B. tau and complex species, the phytochemical and biological controls have not been applied successfully in Asia; there is an urgent need to study and applications of these two mentioned control techniques against the B. tau and complex species in Asia.

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.

ORIGINS AND GENETIC DIVERSITY OF INTRODUCED POPULATIONS OF THE PUERTO RICAN RED-EYED COQUÍ, ELEUTHERODACTYLUS ANTILLENSIS, IN SAINT CROIX (U.S. VIRGIN ISLANDS) AND PANAMÁ

The Red-eyed Coquí, Eleutherodactylus antillensis, is a terrestrial frog endemic to the Puerto Rican Bank (Puerto Rico and numerous islands and cays off its eastern coast), in the eastern Caribbean Sea. The species was likely introduced in Saint Croix, an island c. 100 km southeast of Puerto Rico, in the late 1930s, and in Panamá City, Panamá, in the late 1950s or early 1960s, but the source(s) of these introductions are unknown. We analyzed sequence data from one mtDNA locus and four nuDNA introns to infer the origin(s) of the Saint Croix and Panamá City populations and quantify their genetic diversity. Saint Croix and Panamanian populations do not share any haplotypes, and they cluster with different native populations, suggesting that they are derived from separate sources in the Puerto Rican Bank. Patterns of population structure trace the probable sources of E. antillensis in Saint Croix to islands off Puerto Rico's eastern coast, which include Vieques, Culebra, Saint Thomas, Saint John, Tortola, and Virgin Gorda, and possibly to eastern Puerto Rico as well. In contrast, Panamá City E. antillensis probably originated from either western or eastern Puerto Rico. Genetic diversity in the introduced populations is similar to or lower than in populations in the species' native range, indicating that genetic diversity has not increased in the alien frogs. Our findings may facilitate the development of preventive measures to minimize introductions of non-native amphibians in the Caribbean and Central America.

Genetic reconstruction of a bullfrog invasion to elucidate vectors of introduction and secondary spread

Reconstructing historical colonization pathways of an invasive species is critical for uncovering factors that determine invasion success and for designing management strategies. The American bullfrog (Lithobates catesbeianus) is endemic to eastern North America, but now has a global distribution and is considered to be one of the worst invaders in the world. In Montana, several introduced populations have been reported, but little is known of their sources and vectors of introduction and secondary spread. We evaluated the genetic composition of introduced populations at local (Yellowstone River floodplain) and regional (Montana and Wyoming) scales in contrast to native range populations. Our objectives were to (1) estimate the number of introductions, (2) identify probable native sources, (3) evaluate genetic variation relative to sources, and (4) characterize properties of local‐ and regional‐scale spread. We sequenced 937 bp of the mitochondrial cytochrome b locus in 395 tadpoles collected along 100 km of the Yellowstone River, from three additional sites in MT and a proximate site in WY. Pairwise Φ_ST revealed high divergence among nonnative populations, suggesting at least four independent introductions into MT from diverse sources. Three cyt b haplotypes were identical to native haplotypes distributed across the Midwest and Great Lakes regions, and AMOVA confirmed the western native region as a likely source. While haplotype (H_d = 0.69) and nucleotide diversity (π = 0.005) were low in introduced bullfrogs, the levels of diversity did not differ significantly from source populations. In the Yellowstone, two identified haplotypes implied few introduction vectors and a significant relationship between genetic and river distance was found. Evidence for multiple invasions and lack of subsequent regional spread emphasizes the importance of enforcing legislation prohibiting bullfrog importation and the need for continuing public education to prevent transport of bullfrogs in MT. More broadly, this study demonstrates how genetic approaches can reveal key properties of a biological invasion to inform management strategies.

Different evolutionary processes in shaping the genetic composition of Dendrobium nobile in southwest China

Knowledge of population genetic structure and intrapopulation genetic variation is important for understanding population dynamics and evolutionary processes. Dendrobium nobile is an endangered traditional Chinese tonic medicine. In order to analyze the population differentiation and genetic diversity in D. nobile and propose proper conservation measurements, we genotyped 102 individual plants from 7 natural populations distributed across southwest China at 9 microsatellite loci. Seven pairs of genomic SSR primers were newly designed, and two pairs were chosen from the EST-SSRs. According to the results, the genetic process of D. nobile on Hainan Island and the Chinese mainland might be affected by different evolutionary processes, the genetic drift caused by founder effect has played an important role in shaping the genetic constitution of the Island population. The population of D. nobile in Hainan Island was highly differentiated and displayed low levels of genetic diversity. For the conservation management plans of D. nobile, we propose that individuals in Hainan Island with rare alleles need to be conserved with top priority, and those individuals with rare alleles and the most common alleles also should be concerned. The seven new microsatellite loci may be informative for further evaluation and conservation of the genetic diversity of D. nobile.

Population genetics suggest that multiple invasion processes need to be addressed in the management plan of a plant disease vector

The use of a multidisciplinary approach is becoming increasingly important when developing management strategies that mitigate the economic and biological costs associated with invasive pests. A framework of simulated dispersal is combined with life-history information and analyses of population genetic structure to investigate the invasion dynamics of a plant disease vector, the island sugarcane planthopper (Eumetopina flavipes), through an archipelago of significant Australian quarantine concern. Analysis of eight microsatellite loci from 648 individuals suggests that frequent, wind-assisted immigration from multiple sources in Papua New Guinea contributes significantly to repeated colonization of far northern islands. However, intermittent wind-assisted immigration better explains patterns of genetic diversity and structure in the southern islands and on the tip of mainland Australia. Significant population structuring associated with the presence of clusters of highly related individuals results from breeding in-situ following colonization, with little postestablishment movement. Results also suggest that less important secondary movements occur between islands; these appear to be human mediated and restricted by quarantine zones. Control of the planthopper may be very difficult on islands close to Papua New Guinea given the apparent propensity for multiple invasion, but may be achievable further south where local populations appear highly independent and isolated.