We present here a framework for the study of molecular variation within a single species. Information on DNA haplotype divergence is incorporated into an analysis of variance format, derived from a matrix of squared-distances among all pairs of haplotypes. This analysis of molecular variance (AMOVA) produces estimates of variance components and F-statistic analogs, designated here as phi-statistics, reflecting the correlation of haplotypic diversity at different levels of hierarchical subdivision. The method is flexible enough to accommodate several alternative input matrices, corresponding to different types of molecular data, as well as different types of evolutionary assumptions, without modifying the basic structure of the analysis. The significance of the variance components and phi-statistics is tested using a permutational approach, eliminating the normality assumption that is conventional for analysis of variance but inappropriate for molecular data. Application of AMOVA to human mitochondrial DNA haplotype data shows that population subdivisions are better resolved when some measure of molecular differences among haplotypes is introduced into the analysis. At the intraspecific level, however, the additional information provided by knowing the exact phylogenetic relations among haplotypes or by a nonlinear translation of restriction-site change into nucleotide diversity does not significantly modify the inferred population genetic structure. Monte Carlo studies show that site sampling does not fundamentally affect the significance of the molecular variance components. The AMOVA treatment is easily extended in several different directions and it constitutes a coherent and flexible framework for the statistical analysis of molecular data.

We describe "universal" DNA primers for polymerase chain reaction (PCR) amplification of a 710-bp fragment of the mitochondrial cytochrome c oxidase subunit I gene (COI) from 11 invertebrate phyla: Echinodermata, Mollusca, Annelida, Pogonophora, Arthropoda, Nemertinea, Echiura, Sipuncula, Platyhelminthes, Tardigrada, and Coelenterata, as well as the putative phylum Vestimentifera. Preliminary comparisons revealed that these COI primers generate informative sequences for phylogenetic analyses at the species and higher taxonomic levels.

The most extensively studied group of Darwin's finches is the genus Geospiza, the ground finches, and yet little is known about the evolutionary history and genetic relationships of these birds. Studies using either allozyme or morphological data have been unable to resolve relationships between the six species and numerous populations of ground finches. In this paper we report the results of a study using mitochondrial control region and nuclear internal transcribed spacer (ITS) 1 sequence data. The differentiation of the ground finch species based on morphological data is not reflected in either mitochondrial or nuclear DNA sequence phylogenies. Furthermore, there is little concordance between the mitochondrial haplotypes and ITS alleles found within individuals. We suggest that the absence of species-specific lineages can be attributed to ongoing hybridization involving all six species of Geospiza. There are no long term selective pressures against hybridization within this genus, and therefore a genetically homogenous genus may be maintained indefinitely. Hybridization has apparently played a role in the adaptive radiation of Darwin's finches.© 1999 The Society for the Study of Evolution.

Genetic variation facilitates both natural range expansions and anthropogenic invasions. Contrary to expectations, hybridization does not always impact negatively on biodiversity. Increasing evidence indicates advantageous roles for introgressive hybridization in maintaining standing genetic variation. Hypothesizing that hybridization may contribute to the evolutionary and invasive success of a diverse group of freshwater snails (Ampullariidae, commonly known as apple snails), we estimated the frequency of hybridization between two globally invasive species of, (Lamarck, 1822) and Perry, 1810, in their native range. While previous work in Asia has uncovered the occurrence of extensive hybridization, we provide the first phylogenetic evidence of a high degree of hybridization (30%) between these species in Uruguay and Brazil. Hybrids carried both heterozygous and homozygous combinations of elongation factor 1-α (EF1α) nuclear alleles in both mating directions, indicating that hybridization has occurred over multiple generations and likely preceded introductions outside the native range. Among the five sites in Brazil previously documented as containing only, one far northern population (Careiro Castanho), which is thousands of kilometres from the northern range of, unexpectedly contained hybrids. This may be the result of human-facilitated introductions. Together with recent work from Asia, our investigations in the native range of apple snails support a reframing of historical perspectives of hybridization as a driver of extinction and diversity loss towards a modern paradigm where hybridization may promote diversification and contribute to the survival of evolutionary lineages such as molluscs.© The Author(s) 2020. Published by Oxford University Press on behalf of The Malacological Society of London, all rights reserved. For Permissions, please email: journals.permissions@oup.com.

Understanding the mechanisms of rapid adaptive radiation has been a central problem of evolutionary ecology. Recently, there is a growing recognition that hybridization between different evolutionary lineages can facilitate adaptive radiation by creating novel phenotypes. Yet, theoretical plausibility of this hypothesis remains unclear because, for example, hybridization can negate pre-existing species richness. Here, we theoretically investigate whether and under what conditions hybridization promotes ecological speciation and adaptive radiation using an individual-based model to simulate genome evolution following hybridization between two allopatrically evolved lineages. The model demonstrated that transgressive segregation through hybridization can facilitate adaptive radiation, most powerfully when novel vacant ecological niches are highly dissimilar, phenotypic effect size of mutations is small and there is moderate genetic differentiation between parental lineages. These results provide a theoretical basis for the effect of hybridization facilitating adaptive radiation.© 2017 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data.Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.

The golden apple snail, Pomacea canaliculata, is one of the world's 100 most notorious invasive alien species. Knowledge about the critical climate variables that limit the global distribution range of the snail, as well as predictions of future species distributions under climate change, is very helpful for management of snail. In this study, the climatically suitable habitats for this kind of snail under current climate conditions were modeled by biomod2 and projected to eight future climate scenarios (2 time periods [2050s, 2080s] × 2 Representative Concentration Pathways [RCPs; RCP2.6, RCP8.5] × 2 atmospheric General Circulation Models [GCMs; Canadian Centre for Climate Modelling and Analysis (CCCMA), Commonwealth Scientific and Industrial Research Organisation (CSIRO)]). The results suggest that the lowest temperature of coldest month is the critical climate variable to restrict the global distribution range of P. canaliculata. It is predicted that the climatically suitable habitats for P. canaliculata will increase by an average of 3.3% in 2050s and 3.8% in 2080s for the RCP2.6 scenario, while they increase by an average of 8.7% in 2050s and 10.3% in 2080s for the RCP8.5 scenario. In general, climate change in the future may promote the global invasion of the invasive species. Therefore, it is necessary to take proactive measures to monitor and preclude the invasion of this species.

钩手水母(Gonionemus vertens)为大西洋和太平洋广布种, 是我国习见的有毒水母种类之一。本文对采自黄渤海海域4个地理群体的104个钩手水母线粒体COI基因序列进行扩增, 并结合GenBank上其他182个钩手水母同源序列进行序列变异分析。在286个基因序列中共检测出52个多态位点, 定义了14种单倍型。总群体的单倍型多样性和核苷酸多样性分别为0.743 ± 0.012和1.046% ± 0.097%, 与其他几种大型水母相比, 钩手水母总群体的遗传多样性处于较高水平。AMOVA结果显示, 60.17%的分子变异源于群组间, 13.37%的分子变异源于群体内, 26.46%的分子变异源于组内群体间, 群组间、群体内和组内群体间的遗传分化均极显著。F_st值统计检验表明, 中国厦门群体与乐亭、东营、烟台、大连群体间存在显著的遗传分化, 大连与东营、烟台群体间也存在显著的遗传分化。系统分析结果显示, 钩手水母群体间存在2个明显的单倍型谱系分支。不同的钩手水母地理群体间具有复杂的遗传模式, 钩手水母复杂的生活史、扩散能力、地理隔离和海流分布可能是影响钩手水母遗传结构的重要因素。

Since the mid 1990s populations of non-native apple snails (Ampullariidae) have been discovered with increasing frequency in the continental United States. Given the dramatic effects that introduced apple snails have had on both natural habitats and agricultural areas in Southeast Asia, their introduction to the mainland U.S. is cause for concern. We combine phylogenetic analyses of mtDNA sequences with examination of introduced populations and museum collections to clarify the identities, introduced distributions, geographical origins, and introduction histories of apple snails.Based on sampling to date, we conclude there are five species of non-native apple snails in the continental U.S. Most significantly, we recognize three species within what has been called the channeled apple snail: Pomacea canaliculata (California and Arizona), Pomacea insularum, (Florida, Texas, and Georgia) and Pomacea haustrum (Florida). The first established populations of P. haustrum were discovered in the late 1970s in Palm Beach County Florida, and have not spread appreciably in 30 years. In contrast, populations of P. insularum were established in Texas by 1989, in Florida by the mid to late 1990s, and in Georgia by 2005, and this species continues to spread rapidly. Most introduced P. insularum haplotypes are a close match to haplotypes from the Río Uruguay near Buenos Aires, indicating cold tolerance, with the potential to spread from Florida, Georgia, and Texas through Louisiana, Alabama, Mississippi, and South Carolina. Pomacea canaliculata populations were first discovered in California in 1997. Haplotypes of introduced P. canaliculata match native-range haplotypes from near Buenos Aires, Argentina, also indicating cold tolerance and the potential to establish farther north.The term "channeled apple snail" is descriptive of a morphology found in many apple snail species. It does not identify a single species or a monophyletic group. Clarifying species identifications permits a more accurate assessment of introduction histories and distributions, and provides a very different picture of the tempo and pattern of invasions than was inferred when the three species with channeled sutures were considered one. Matching introduced and native-range haplotypes suggests the potential for range expansion, with implications for native aquatic ecosystems and species, agriculture, and human health.

MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types-e.g. morphological, nucleotide, and protein-and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.

We present version 6 of the DNA Sequence Polymorphism (DnaSP) software, a new version of the popular tool for performing exhaustive population genetic analyses on multiple sequence alignments. This major upgrade incorporates novel functionalities to analyze large data sets, such as those generated by high-throughput sequencing technologies. Among other features, DnaSP 6 implements: 1) modules for reading and analyzing data from genomic partitioning methods, such as RADseq or hybrid enrichment approaches, 2) faster methods scalable for high-throughput sequencing data, and 3) summary statistics for the analysis of multi-locus population genetics data. Furthermore, DnaSP 6 includes novel modules to perform single- and multi-locus coalescent simulations under a wide range of demographic scenarios. The DnaSP 6 program, with extensive documentation, is freely available at http://www.ub.edu/dnasp.© The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Invasive species are expected to undergo a reduction in genetic diversity due to founder effects, which should limit their ability to adapt to new habitats. Still, many invasive species achieve widespread distributions and dense populations. This paradox of invasions could potentially be overcome through multiple introductions or hybridization, both of which increase genetic diversity. We conducted a population genomics study of Japanese knotweed (Reynoutria japonica), which is a polyploid, clonally reproducing invasive species that has been notoriously successful worldwide despite supposedly low genetic diversity.We used genotyping by sequencing to collect 12,912 SNP markers from 88 samples collected at 38 locations across North America for the species complex. We used alignment-free k-mer hashing analysis in addition to traditional population genetic analyses to account for the challenges of genotyping polyploids.Genotypes conformed to three genetic clusters, likely representing Japanese knotweed, giant knotweed, and hybrid bohemian knotweed. We found that, contrary to previous findings, the Japanese knotweed cluster had substantial genetic diversity, though it had no apparent genetic structure across the landscape. In contrast, giant knotweed and hybrids showed distinct population groups. We did not find evidence of isolation by distance in the species complex, likely reflecting the stochastic introduction history of this species complex.The results indicate that clonal invasive species can show substantial genetic diversity and can be successful at colonizing a variety of habitats without showing evidence of local adaptation or genetic structure.© 2021 Botanical Society of America.

Due to the similarities of overall shell morphology among apple snail species and considerable variability within species, substantial taxonomic confusion has plagued the accurate identification of Pomacea species. Many invasive apple snails have been mistakenly identified as P. canaliculata since their introduction to Asia around 1980. In 2008, three other introduced species in addition to P. canaliculata were recognized. In 2013, a fifth, previously unrecognized lineage was reported from China, indicating that despite the taxonomic clarity brought by previous work, continued surveys and taxonomic research are necessary to prevent additional introductions and continued spread, as well as to develop effective management strategies.Phylogenetic analysis of mitochondrial COI sequences confirmed the presence of a widespread unidentified Pomacea lineage in China. All sequences from samples of this newly documented lineage were recovered in a monophyletic clade delineated from closely related species; however, different DNA barcoding methods yielded inconsistent species boundaries. Additionally, nuclear EF1α sequences indicated incomplete lineage sorting or recent hybridization of the unidentified lineage with the other two established species.Barcoding is a valuable tool for species discovery, and a powerful approach for delineating introduced species. However, determining the identity of the newly discovered invasive lineage in China will require an integrated taxonomic approach incorporating individuals from the native range, and examination of natural history collections at museums around the world. To manage and prevent additional spread of already established species, and to stop the introduction of new taxa, continued monitoring and rigorous taxonomic assessments must be undertaken. © 2018 Society of Chemical Industry.© 2018 Society of Chemical Industry.

Species of Pomacea, commonly known as apple snails, are native to South America, and have become widely distributed agricultural and environmental pests in southern China since their introduction in the 1980s. However, only since 2010 have researchers recognized that at least two species, P. canaliculata and P. maculata, are present in China. Although impacts of apple snails have been extensively documented, confusion still persists regarding current distributions and origin of the species in China. To resolve this confusion, we used phylogenetic and phylogeographic methods to analyze 1464 mitochondrial COI sequences, including 349 new sequences from samples collected in southern China and 1115 publicly available sequences from snails collected in the native and introduced ranges. Pomacea canaliculata was found at all sampled localities, while P. maculata was found at only five sampled localities in the Sichuan basin and Zhejiang province. Our data indicate that Chinese populations of P. canaliculata share an Argentinian origin, consistent with multiple introductions of this species elsewhere in Asia. In addition, just a single lineage ofP. maculata is established in China, which shares with populations in Brazil.

Golden apple snails seriously damage crops and aquatic ecosystem in China. Two invasive apple snail species, Pomacea canaliculata and P. maculata, have been reported in China since 2010. Only the distribution of P. canaliculata was reported in Zhejiang Province. It is difficult to distinguish the two species due to their close morphological characteristics and high diversity of shell morphology, which are influenced by both environmental factors and food types. We collected samples from seven localities from Zhejiang Province and sequenced 101 individuals of mitochondrial COI fragments of the DNA barcode region. We also downloaded 55 sequences of five species of the P. canaliculata group, which included all public sequences of P. lineata, P. dolioides, and P. paludosa, and South American sample sequences of P. canaliculata and P. maculata. Analyses including similarity alignments, DNA barcoding gaps, and phylogenetic relationships, revealed that COI sequences were effective to distinguish apple snail species. We detected P. canaliculata and P. maculata distributed in the Jianggan region of Hangzhou, while only P. canaliculata was distributed in the Putuo region of Zhoushan, the Shanyu and Xinchang regions of Shaoxing, the Ouhai region of Wenzhou and the Xihu regoin of Hangzhou. P. canaliculata revealed a much wider distribution range. P. canaliculata and P. maculata were collapsed into 4 haplotypes and 2 haplotypes, respectively. There were 1 to 3 haplotypes in each locality, which indicated a low genetic diversity. The phylogenetic analyses deduced that P. canaliculata and P. maculata were probably introduced from Argentina and Brazil, respectively.

外来入侵福寿螺对我国农业生产和水生生态系统平衡等造成严重危害。2010年, 种类鉴定研究首次揭示我国外来入侵福寿螺包括Pomacea canaliculata和P. maculata两个种, 而浙江省仅见P. canaliculata一种报道。P. canaliculata和P. maculata种间形态近似, 且受环境、食物源等因素影响, 同种内外壳形态特征多样, 因而基于形态特征进行种类的准确鉴定极为困难。本研究在采集浙江省7个区县的福寿螺样本的基础上, 利用DNA条形码技术扩增了101个不同个体的COI序列, 并从BOLD数据库下载了“P. canaliculata种团”的5个近缘种的55条COI序列用于分析, 其中包括P. lineata, P. dolioides和P. paludosa所有已发表序列, 以及P. canaliculata和P. maculata的南美洲样品的序列等。序列相似度比对、DNA条形码间隙和系统发育树等分析表明, COI序列可以实现近缘福寿螺的有效鉴别。待测的浙江省福寿螺样品中, 杭州江干区检测到P. canaliculata和P. maculata两种, 而舟山普陀区、绍兴上虞区和新昌县、温州瓯海区及杭州西湖区仅检测到P. canaliculata, 表明P. canaliculata在浙江省具有更广的分布范围。P. canaliculata和P. maculata分别形成4种和2种单倍型, 各区县样点分别包含1-3种单倍型, 浙江省各发生地呈现较低的遗传多样性。依据系统发育关系推测, 浙江省分布的P. canaliculata和P. maculata分别可能来源于阿根廷和巴西。

Pomacea canaliculata is one of the 100 worst invasive alien species in the world, which has significant effects and harm to native species, ecological environment, human health, and social economy. Climate change is one of the major causes of species range shifts. With recent climate change, the distribution of P. canaliculata has shifted northward. Understanding the potential distribution under current and future climate conditions will aid in the management of the risk of its invasion and spread. Here, we used species distribution modeling (SDM) methods to predict the potential distribution of P. canaliculata in China, and the jackknife test was used to assess the importance of environmental variables for modeling. Our study found that precipitation of the warmest quarter and maximum temperature in the coldest months played important roles in the distribution of P. canaliculata. With global warming, there will be a trend of expansion and northward movement in the future. This study could provide recommendations for the management and prevention of snail invasion and expansion.