Isolation and characterization of polymorphic microsatellite DNA markers in topmouth gudgeon,Pseudorasbora (Teleostei: Cyprinidae)

Due to accidental introductions, the distribution of the east Asian topmouth gudgeon, Pseudorasbora parva, has rapidly expanded over recent years, thereby threatening the endangered Japanese species, P. pumila pumila. Sixteen microsatellite loci were isolated and characterized for P. parva, 14 being highly polymorphic (mean H_E = 0.58, mean number of alleles = 4.4). Successful characterization of 10 of these loci was also achieved for P. pumila pumila. These markers should be useful in future investigation of colonization of P. parva and the development of conservation strategies for P. pumila pumila.     

Genomic signatures of rapid adaptive evolution in the bluespotted cornetfish,a Mediterranean Lessepsian invader

Biological invasions are increasingly creating ecological and economical problems both on land and in aquatic environments. For over a century, the Mediterranean Sea has steadily been invaded by Indian Ocean/Red Sea species (called Lessepsian invaders) via the Suez Canal, with a current estimate of ~450 species. The bluespotted cornetfish, Fistularia commersonii, considered a ‘Lessepsian sprinter’, entered the Mediterranean in 2000 and by 2007 had spread through the entire basin from Israel to Spain. The situation is unique and interesting both because of its unprecedented rapidity and by the fact that it took this species c. 130 years to immigrate into the Mediterranean. Using genome scans, with restriction site‐associated DNA (RAD) sequencing, we evaluated neutral and selected genomic regions for Mediterranean vs. Red Sea cornetfish individuals. We found that few fixed neutral changes were detectable among populations. However, almost half of the genes associated with the 47 outlier loci (potentially under selection) were related to disease resistance and osmoregulation. Due to the short time elapsed from the beginning of the invasion to our sampling, we interpret these changes as signatures of rapid adaptation that may be explained by several mechanisms including preadaptation and strong local selection. Such genomic regions are therefore good candidates to further study their role in invasion success.     

基于Maxent的两种入侵性鱼类(麦穗鱼和鲫)的全球适生区预测

受引种、贸易等人类活动的影响, 麦穗鱼(Pseudorasbora parva)和鲫(Carassius auratus)在全球范围内已经广泛分布并造成巨大的生态危害。根据野外采样和文献记录, 本文系统整理了麦穗鱼和鲫在世界各地的分布情况, 以高达2.5弧分分辨率的环境数据底图, 利用Maxent模型预测了麦穗鱼和鲫在全球的适生区, 以期为防控麦穗鱼和鲫的入侵提供早期预警。结果表明麦穗鱼和鲫在全球范围的分布区非常广泛, 除南极洲外的各个大洲均有其适生区, 因此这两种鱼还有继续扩散的潜力, 并可能在美国、巴西和阿根廷等国家出现由生物入侵导致的生态学问题。麦穗鱼的适生区主要集中在15º–55º N之间, 欧洲是麦穗鱼入侵的重灾区, 尤其是法国、荷兰周边的西欧国家和匈牙利、塞尔维亚周边的东欧国家; 而美国中部的密西西比河流域、东部及南部沿海, 以及西雅图至加拿大的温哥华之间是麦穗鱼潜在入侵风险性极高的区域。鲫自然分布于欧洲至东亚的广大地区, 目前已经在澳大利亚、加拿大、美国、马达加斯加、印度和越南等国家有分布, 未来还可能进一步扩散至大洋洲的新西兰和新喀里多尼亚, 北美洲的墨西哥至南美洲的阿根廷, 以及非洲的塞内加尔、几内亚和南非等国家; 尤其是南美洲的阿根廷和巴西, 非洲西部的几内亚、喀麦隆等国家将是鲫入侵风险极高的区域。     

Phenotypic variability of rusty crayfish (Faxonius rusticus) at the leading edge of its riverine invasion

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Population genomic analysis uncovers African and European admixture in Drosophila melanogaster populations from the south‐eastern United States and Caribbean Islands

Drosophila melanogaster is postulated to have colonized North America in the past several 100 years in two waves. Flies from Europe colonized the east coast United States while flies from Africa inhabited the Caribbean, which if true, make the south‐east US and Caribbean Islands a secondary contact zone for African and European D. melanogaster. This scenario has been proposed based on phenotypes and limited genetic data. In our study, we have sequenced individual whole genomes of flies from populations in the south‐east US and Caribbean Islands and examined these populations in conjunction with population sequences from the west coast US, Africa, and Europe. We find that west coast US populations are closely related to the European population, likely reflecting a rapid westward expansion upon first settlements into North America. We also find genomic evidence of African and European admixture in south‐east US and Caribbean populations, with a clinal pattern of decreasing proportions of African ancestry with higher latitude. Our genomic analysis of D. melanogaster populations from the south‐east US and Caribbean Islands provides more evidence for the Caribbean Islands as the source of previously reported novel African alleles found in other east coast US populations. We also find the border between the south‐east US and the Caribbean island to be the admixture hot zone where distinctly African‐like Caribbean flies become genomically more similar to European‐like south‐east US flies. Our findings have important implications for previous studies examining the generation of east coast US clines via selection.     

When invasion may not be harmful: niche relations in a lizard assemblage

Some studies have suggested that non‐native species invasions may threaten local diversity by creating homogenized environments. However, many studies have been based on limited or anecdotal data, and/or have failed to consider the influence of habitat modification together with possible influences of non‐native species on native ones. Hemidactylus mabouia (Squamata, Gekkonidae) likely invaded natural environments in Brazil hundreds of years ago. Yet, little is known about whether it affects native lizard fauna. We tested whether H. mabouia negatively influences native lizard species richness and abundance on a regional scale and locally through niche overlap. We analyzed species abundance and richness of nine lizard assemblages, in five of which H. mabouia occurred. We evaluated niche overlap of species in a lizard assemblage with high H. mabouia abundance through null models. Niche axes included spatial use, temporal activity and diet. Although species abundance did not differ among sites with and without the invasive species, the presence of H. mabouia seems constrained to the richer assemblages sampled. We observed significantly higher niche overlap in spatial (?_obs = 0.63; ?_exp = 0.37; P_obs ≥ P_exp = 0.0002) and trophic axes (?_obs = 0.46; ?_exp = 0.17; P_obs ≥ P_exp < 0.001), but not in activity. When we considered all axes (three‐dimensional niche), there was no overlapping among the lizard species. Our findings did not support the hypothesis that this non‐native species negatively influences other sympatric lizard species.     

Genomic differentiation and patterns of gene flow between two long‐tailed tit species (Aegithalos)

Patterns of heterogeneous genomic differentiation have been well documented between closely related species, with some highly differentiated genomic regions (“genomic differentiation islands”) spread throughout the genome. Differential levels of gene flow are proposed to account for this pattern, as genomic differentiation islands are suggested to be resistant to gene flow. Recent studies have also suggested that genomic differentiation islands could be explained by linked selection acting on genomic regions with low recombination rates. Here, we investigate genomic differentiation and gene‐flow patterns for autosomes using RAD‐seq data between two closely related species of long‐tailed tits (Aegithalos bonvaloti and A. fuliginosus) in both allopatric and contact zone populations. The results confirm recent or ongoing gene flow between these two species. However, there is little evidence that the genomic regions that were found to be highly differentiated between the contact zone populations are resistant to gene flow, suggesting that differential levels of gene flow is not the cause of the heterogeneous genomic differentiation. Linked selection may be the cause of genomic differentiation islands between the allopatric populations with no or very limited gene flow, but this could not account for the heterogeneous genomic differentiation between the contact zone populations, which show evidence of recent or ongoing gene flow.     

Weak photoperiodic response facilitates the biological invasion of the harlequin ladybird Harmonia axyridis (Pallas) (Coleoptera: Coccinellidae)

Photoperiodic regulation of reproductive diapause in two invasive and two native populations of Harmonia axyridis and in one native population of Harmonia yedoensis was investigated in laboratory at 20°C, five photoperiods (day length of 10, 12, 14, 16 and 18 h) and two diets: (i) eggs of the Angoumois grain moth Sitotroga cerealella and (ii) the green peach aphid, Myzus persicae. Laboratory strains originated from native populations of H. axyridis from Irkutsk province of Siberia and H. yedoensis from South Korea showed a strong photoperiodic response: under short photoperiods (10–14 h and 10–12 h for H. axyridis and H. yedoensis, correspondingly), all females which fed on eggs and most of those fed on aphids did not start to lay eggs during 40 days after emergence, while under long photoperiods, all females fed on aphids and most of those fed on eggs oviposited. The photoperiodic response of H. axyridis from South Korea was less strong: on the both diets, the range of the photoperiodic response (the difference in the proportion of ovipositing females between the treatments with long and short days) was ca 40%. In the European (Czech Republic) and in the Caucasian (Sochi region, Russia) invasive populations of H. axyridis, the photoperiodic response was very weak: the proportion of females that started oviposition (when fed on aphids) or at least reproductive maturation (when fed on eggs) during 40 days after emergence was close to 100%, independently of the photoperiodic conditions. Obviously, instead of a rapid micro‐evolutionary adaptation of the critical day length to a new climate, the invasive populations of the harlequin ladybird decrease their dependence on photoperiod and thus the weak photoperiodic response of SE Asian population of H. axyridis can be considered as a pre‐adaptation further developed during the invasion.     

Genomic islands of divergence in the Yellow Tang and the Brushtail Tang Surgeonfishes

The current ease of obtaining thousands of molecular markers challenges the notion that full phylogenetic concordance, as proposed by phylogenetic species concepts, is a requirement for defining species delimitations. Indeed, the presence of genomic islands of divergence, which may be the cause, or in some cases the consequence, of speciation, precludes concordance. Here, we explore this issue using thousands of RAD markers on two sister species of surgeonfishes (Teleostei: Acanthuridae), Zebrasoma flavescens and Z. scopas, and several populations within each species. Species are readily distinguished based on their colors (solid yellow and solid brown, respectively), yet populations and species are neither distinguishable using mitochondrial markers (cytochrome c oxidase 1), nor using 5193 SNPs (pairwise Φst = 0.034). In contrast, when using outlier loci, some of them presumably under selection, species delimitations, and strong population structure follow recognized taxonomic positions (pairwise Φst = 0.326). Species and population delimitation differences based on neutral and selected markers are likely due to local adaptation, thus being consistent with the idea that these genomic islands of divergence arose as a consequence of isolation. These findings, which are not unique, raise the question of a potentially important pathway of divergence based on local adaptation that is only evident when looking at thousands of loci.     

Evidence for a recent horizontal transmission and spatial spread of Wolbachia from endemic Rhagoletis cerasi (Diptera: Tephritidae) to invasive Rhagoletis cingulata in Europe

The widespread occurrence of Wolbachia in arthropods and nematodes suggests that this intracellular, maternally inherited endosymbiont has the ability to cross species boundaries. However, direct evidence for such a horizontal transmission of Wolbachia in nature is scarce. Here, we compare the well‐characterized Wolbachia infection of the European cherry fruit fly, Rhagoletis cerasi, with that of the North American eastern cherry fruit fly, Rhagoletis cingulata, recently introduced to Europe. Molecular genetic analysis of Wolbachia based on multilocus sequence typing and the Wolbachia surface protein wsp showed that all R. cingulata individuals are infected with wCin2 identical to wCer2 in R. cerasi. In contrast, wCin1, a strain identical to wCer1 in R. cerasi, was present in several European populations of R. cingulata, but not in any individual from the United States. Surveys of R. cingulata from Germany and Hungary indicated that in some populations, the frequency of wCin1 increased significantly in just a few years with at least two independent horizontal transmission events. This is corroborated by the analysis of the mitochondrial cytochrome oxidase II gene that showed association of wCin1 with two distinct haplotypes in Germany, one of which is also infected with wCin1 in Hungary. In summary, our study provides strong evidence for a very recent inter‐specific Wolbachia transmission with a subsequent spatial spread in field populations.     

Population genetics and sympatric divergence of the freshwater gudgeon,Gobiobotia filifer,in the Yangtze River inferred from mitochondrial DNA

The ecosystem and Pleistocene glaciations play important roles in population demography. The freshwater gudgeon, Gobiobotia filifer, is an endemic benthic fish in the Yangtze River and is a good model for ecological and evolutionary studies. This study aimed to decode the population structure of G. filifer in the Yangtze River and reveal whether divergence occurred before or after population radiation. A total of 292 specimens from eight locations in the upper and middle reaches of the Yangtze River were collected from 2014 to 2016 and analyzed via mitochondrial DNA Cyt b gene sequencing. A moderately high level of genetic diversity was found without structures among the population. However, phylogenetic and network topology showed two distinct haplotype groups, and each group contained a similar proportion of individuals from all sampled sites. This suggested the existence of two genetically divergent source populations in G. filifer. We deduced that a secondary contact of distinct glacial refugia was the main factor creating sympatric populations of G. filifer, and climate improvement promoted population expansion and colonization.     

Holostephanus metorchis (Digenea: Cyathocotylidae) from chicks experimentally infected with metacercariae from a fish, Pseudorasbora parva, in the Republic of Korea

Holostephanus metorchis (Digenea: Cyathocotylidae) is a parasite of birds, transmitted by freshwater fishes. H. metorchis adults were recovered from chicks experimentally infected with metacercariae collected from freshwater fishes, Pseudorasbora parva. The metacercariae were oval, surrounded with thick fibrous capsules. In adult flukes, the holdfast organ occupied the ventral concavity, and the anterior testis did not reach the level of the ventral sucker. Based on these morphological characteristics, these flukes were identified as H. metorchis.     

A layover in Europe: Reconstructing the invasion route of asexual lineages of a New Zealand snail to North America

Non‐native invasive species are threatening ecosystems and biodiversity worldwide. High genetic variation is thought to be a critical factor for invasion success. Accordingly, the global invasion of a few clonal lineages of the gastropod Potamopyrgus antipodarum is thus both puzzling and has the potential to help illuminate why some invasions succeed while others fail. Here, we used SNP markers and a geographically broad sampling scheme (N = 1617) including native New Zealand populations and invasive North American and European populations to provide the first widescale population genetic assessment of the relationships between and among native and invasive P. antipodarum. We used a combination of traditional and Bayesian molecular analyses to demonstrate that New Zealand populations harbour very high diversity relative to the invasive populations and are the source of the two main European genetic lineages. One of these two European lineages was in turn the source of at least one of the two main North American genetic clusters of invasive P. antipodarum, located in Lake Ontario. The other widespread North American group had a more complex origin that included the other European lineage and two New Zealand clusters. Altogether, our analyses suggest that just a small handful of clonal lineages of P. antipodarum were responsible for invasion across continents. Our findings provide critical information for prevention of additional invasions and control of existing invasive populations and are of broader relevance towards understanding the establishment and evolution of asexual populations and the forces driving biological invasion.     

Genomic studies on the nature of species: adaptation and speciation in Mimulus

Evolutionary biology is in an exciting era, in which powerful genomic tools make the answers accessible to long‐standing questions about variation, adaptation and speciation. The availability of a suite of genomic resources, a shared knowledge base and a long history of study have made the phenotypically diverse plant genus Mimulus an important system for understanding ecological and evolutionary processes. An international Mimulus Research Meeting was held at Duke University in June 2014 to discuss developments in ecological and evolutionary genetic studies in Mimulus. Here, we report major recent discoveries presented at the meeting that use genomic approaches to advance our understanding of three major themes: the parallel genetic basis of adaptation; the ecological genomics of speciation; and the evolutionary significance of structural genetic variation. We also suggest future research directions for studies of Mimulus and highlight challenges faced when developing new ecological and evolutionary model systems.