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Mark Stukel;Alexandra E. Porczak;Eric R. L. Gordon;Jason Vailionis;Diler Haji;Thomas R. Buckley;Alan R. Lemmon;Emily Moriarty Lemmon;Chris Simon; 《Systematic Entomology》2024,49(2):237-257
Rapid species radiations present difficulties for phylogenetic reconstruction due to lack of phylogenetic information and processes such as deep coalescence/incomplete lineage sorting and hybridization. Phylogenomic data can overcome some of these difficulties. In this study, we use anchored hybrid enrichment (AHE) nuclear phylogenomic data and mitochondrial genomes recovered from AHE bycatch with several concatenated and coalescent approaches to reconstruct the poorly resolved radiation of the New Zealand cicada species in the genera Kikihia Dugdale and Maoricicada Dugdale. Compared with previous studies using only three to five Sanger-sequenced genes, we find increased resolution across our phylogenies, but several branches remain unresolved due to topological conflict among genes. Some nodes that are strongly supported by traditional support measures like bootstraps and posterior probabilities still show significant gene and site concordance conflict. In addition, we find strong mito-nuclear discordance; likely the result of interspecific hybridization events in the evolutionary history of Kikihia and Maoricicada. 相似文献
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Jing-Li Xuan Sonja J. Scheffer Owen Lonsdale Brian K. Cassel Matthew L. Lewis Charles S. Eiseman Wan-Xue Liu Brian M. Wiegmann 《Systematic Entomology》2023,48(1):178-197
The genus Liriomyza Mik (Diptera: Agromyzidae) is a diverse and globally distributed group of acalyptrate flies. Phylogenetic relationships among Liriomyza species have remained incompletely investigated and have never been fully addressed using molecular data. Here, we reconstruct the phylogeny of the genus Liriomyza using various phylogenetic methods (maximum likelihood, Bayesian inference, and gene tree coalescence) on target-capture-based phylogenomic datasets (nucleotides and amino acids) obtained from anchored hybrid enrichment (AHE). We have recovered tree topologies that are nearly congruent across all data types and methods, and individual clade support is strong across all phylogenetic analyses. Moreover, defined morphological species groups and clades are well-supported in our best estimates of the molecular phylogeny. Liriomyza violivora (Spencer) is a sister group to all remaining sampled Liriomyza species, and the well-known polyphagous vegetable pests [L. huidobrensis (Blanchard), L. langei Frick, L. bryoniae. (Kaltenbach), L. trifolii (Burgess), L. sativae Blanchard, and L. brassicae (Riley)]. belong to multiple clades that are not particularly closely related on the trees. Often, closely related Liriomyza species feed on distantly related host plants. We reject the hypothesis that cophylogenetic processes between Liriomyza species and their host plants drive diversification in this genus. Instead, Liriomyza exhibits a widespread pattern of major host shifts across plant taxa. Our new phylogenetic estimate for Liriomyza species provides considerable new information on the evolution of host-use patterns in this genus. In addition, it provides a framework for further study of the morphology, ecology, and diversification of these important flies. 相似文献
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André Gomes-dos-Santos Elsa Froufe John M. Pfeiffer Nathan A. Johnson Chase H. Smith André M. Machado L. Filipe C. Castro Van Tu Do Akimasa Hattori Nicole Garrison Nathan V. Whelan Ivan N. Bolotov Ilya V. Vikhrev Alexander V. Kondakov Mohamed Ghamizi Vincent Prié Arthur E. Bogan Manuel Lopes Lima 《Molecular ecology resources》2023,23(6):1403-1422
The proliferation of genomic sequencing approaches has significantly impacted the field of phylogenetics. Target capture approaches provide a cost-effective, fast and easily applied strategy for phylogenetic inference of non-model organisms. However, several existing target capture processing pipelines are incapable of incorporating whole genome sequencing (WGS). Here, we develop a new pipeline for capture and de novo assembly of the targeted regions using whole genome re-sequencing reads. This new pipeline captured targeted loci accurately, and given its unbiased nature, can be used with any target capture probe set. Moreover, due to its low computational demand, this new pipeline may be ideal for users with limited resources and when high-coverage sequencing outputs are required. We demonstrate the utility of our approach by incorporating WGS data into the first comprehensive phylogenomic reconstruction of the freshwater mussel family Margaritiferidae. We also provide a catalogue of well-curated functional annotations of these previously uncharacterized freshwater mussel-specific target regions, representing a complementary tool for scrutinizing phylogenetic inferences while expanding future applications of the probe set. 相似文献
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Xiuguang Mao Guimei He Panyu Hua Gareth Jones Shuyi Zhang Stephen J. Rossiter 《Molecular ecology》2013,22(4):1035-1050
Phylogenetic conflicts between genetic markers can help to disentangle complex histories of phylogeography and introgression among taxa. We previously proposed that the Chinese mainland subspecies of the intermediate horseshoe bat Rhinolophus affinis himalayanus colonized Hainan Island to form the subspecies R. a. hainanus. Subsequent recolonization of the mainland formed a third taxon, R. a macrurus, and a secondary contact zone with the ancestral himalayanus. To test for historical and recurrent genetic exchange between these mainland subspecies, we sampled populations of each from two parapatric zones and undertook analyses using one mtDNA marker, three nuclear genes and 14 microsatellites. Nuclear DNA, echolocation call frequencies and morphological data all recovered two taxa; however, a mtDNA phylogeny revealed two himalayanus clades, of which one clustered with macrurus, as well as some shared or related mtDNA haplotypes in eastern populations. Isolation‐with‐migration (IM) models suggested some mtDNA gene flow from macrurus to himalayanus. However, strong population structure in himalayanus raises the possibility that macrurus captured mtDNA from a coastal population of himalayanus that has since become rare or extinct. To reconcile these two sets of results, we suggest that the IM estimates might reflect historical mtDNA gene flow among populations of himalayanus, before mtDNA was subsequently captured by macrurus. Finally, microsatellite‐based ABC analyses supported the island origin of macrurus; however, mtDNA‐based ABC analyses suggest this taxon might have evolved on the mainland. Our findings highlight the importance of understanding population history and structure for interpreting hybridization and introgression events. 相似文献
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Meng-Ting Wang Zhen-Yu Hou Chao Li Jia-Peng Yang Zhi-Tao Niu Qing-Yun Xue Wei Liu Xiao-Yu Ding 《植物分类学报：英文版》2023,61(5):790-805
Reconstructing mitochondrial genomes of angiosperms is extremely intricate due to frequent recombinations which give rise to varied sized in Dendrobium mitogenomes and their structural variations, even in most orchid species. In this study, we first sequenced two complete and five draft mitochondrial genomes of Dendrobium using next-generation and third-generation sequencing technologies. The mitochondrial genomes were 420 538–689 048 bp long, showing multipartite (multichromosomal) structures that consisted of variably sized circular or linear-mapping isoforms (chromosomes). The comparison of mitochondrial genomes showed frequent gene losses in Dendrobium species. To explore structure variations of mitochondrial genomes in vivo, we quantified copy numbers of five mitochondrial genes and DNA contents per mitochondrion. The gene copy numbers and the DNA contents showed extreme differences during Dendrobium development, suggesting dynamic structures of mitochondrial genomes. Furthermore, phylogenetic relationships of 97 accessions from 39 Dendrobium species were constructed based on 12 nuclear single-copy genes and 15 mitochondrial genes. We discovered obvious discordance between the nuclear and mitochondrial trees. Reticulate evolution was inferred from the species network analysis in Dendrobium. Our findings revealed the rapid structural evolution of Dendrobium mitochondrial genomes and the existence of hybridization events in Dendrobium species, which provided new insights into in vivo structural variations of plant mitochondrial genomes and the strong potential of mitochondrial genes in deciphering plant evolution history. 相似文献
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We investigate the pervasiveness of hybridization and mitochondrial introgression in Neodiprion Rohwer (Hymenoptera; Diprionidae), a Holarctic genus of conifer-feeding sawflies. A phylogenetic analysis of the lecontei species group revealed extensive discordance between a contiguous mitochondrial region spanning three genes (COI, tRNA-leucine, and COII) and three nuclear loci (EF1alpha, CAD, and an anonymous nuclear locus). Bayesian tests of monophyly and Shimodaira-Hasegawa (SH) tests of topological congruence were consistent with mitochondrial introgression; however, these patterns could also be explained by lineage sorting (i.e., deep coalescence). Therefore, to explicitly test the mitochondrial introgression hypothesis, we used a novel application of coalescent-based isolation with migration (IM) models to measure interspecific gene flow at each locus. In support of our hypothesis, mitochondrial gene flow was consistently higher than nuclear gene flow across 120 pairwise species comparisons (P < 1 x 10(-12)). We combine phylogenetic and coalescent evidence to identify likely cases of recent and ancient introgression in Neodiprion, and based on these observations, we hypothesize that shared hosts and/or pheromones facilitate hybridization, whereas disparate abundances between hybridizing species promote mitochondrial introgression. Our results carry implications for phylogenetic analysis, and we advocate the separation of high and low gene flow regions to inform analyses of hybridization and speciational history, respectively. 相似文献
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《昆虫分类学报》2024,46(4):319-328
枯叶蛱蝶属Kallima Doubleday,1849蝶类以模仿枯叶的翅图案而闻名,由于该属物种间表型高度相似,属内物种鉴定仍存在争议.随着枯叶蛱蝶(Kallima inachus)参考基因组的发布,基于全基因组数据的系统发育研究得以开展,从而增进了对于枯叶蛱蝶属演化关系的了解.然而,基于基因组的系统发生关系与基于形态的物种分类之间存在一些冲突.通过深入研究枯叶蛱蝶属蝶类之间的关系,检验可能的网状系统发育拓扑结构,本研究进一步探究了产生冲突的原因.基于不同的数据集(包括单拷贝基因、编码序列、中性区域和所有分析物种中均存在的单核苷酸多态性位点)构建的系统发生树呈现出不一致的拓扑结构,揭示了枯叶蛱蝶属复杂的演化历史.本研究结果表明,网状物种拓扑可能是一种普遍存在的模式,不仅存在于适应性辐射的物种中,也存在于渐进式演化的物种中,如枯叶蛱蝶属蝶类. 相似文献
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《昆虫分类学报》2024,46(4):319-328
枯叶蛱蝶属Kallima Doubleday,1849蝶类以模仿枯叶的翅图案而闻名,由于该属物种间表型高度相似,属内物种鉴定仍存在争议.随着枯叶蛱蝶(Kallima inachus)参考基因组的发布,基于全基因组数据的系统发育研究得以开展,从而增进了对于枯叶蛱蝶属演化关系的了解.然而,基于基因组的系统发生关系与基于形态的物种分类之间存在一些冲突.通过深入研究枯叶蛱蝶属蝶类之间的关系,检验可能的网状系统发育拓扑结构,本研究进一步探究了产生冲突的原因.基于不同的数据集(包括单拷贝基因、编码序列、中性区域和所有分析物种中均存在的单核苷酸多态性位点)构建的系统发生树呈现出不一致的拓扑结构,揭示了枯叶蛱蝶属复杂的演化历史.本研究结果表明,网状物种拓扑可能是一种普遍存在的模式,不仅存在于适应性辐射的物种中,也存在于渐进式演化的物种中,如枯叶蛱蝶属蝶类. 相似文献
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Anchored periplasmic expression (APEx) is a new method for the isolation of high affinity ligand-binding proteins from large combinatorial libraries (Harvey et al., 2004, Proc Natl Acad Sci USA 101(25): 9193-9198). In APEx, proteins are expressed as fusions to a membrane anchor that tethers them onto the periplasmic side of the Escherichia coli inner membrane. Conversion of the cells into spheroplasts and incubation with soluble fluorescently conjugated ligands results in the specific labeling of cells expressing ligand-binding proteins and their subsequent isolation by flow cytometry. Here we show that scFv antibody fragments expressed in the APEx format allow the binding of spheroplasts to immobilized ligands. ScFv antibodies specific for the cardiac glycoside digoxin or for the protective antigen (PA) of Bacillus anthracis as a negative control were expressed in E. coli as fusions to either N-terminal or C-terminal membrane anchoring domains. Only the C-terminally anchored fusions resulted in specific recognition and binding of spheroplasts onto TentaGel beads with immobilized antigen. Following three rounds of flow cytometric screening, spheroplasts expressing anti-digoxin scFvs were enriched 950-fold from a large excess (1,000 x) of spheroplasts expressing anti-PA antibodies. These results indicate that the APEx technology may be employed for the screening of libraries based on binding to insoluble antigens possibly including antigens on cell surfaces. 相似文献
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Oscar Alejandro Pérez-Escobar Steven Dodsworth Diego Bogarín Sidonie Bellot Juan A. Balbuena Rowan J. Schley Izai A. Kikuchi Sarah K. Morris Niroshini Epitawalage Robyn Cowan Olivier Maurin Alexandre Zuntini Tatiana Arias Alejandra Serna-Sánchez Barbara Gravendeel Maria Fernanda Torres Jimenez Katharina Nargar Guillaume Chomicki Mark W. Chase Ilia J. Leitch Félix Forest William J. Baker 《American journal of botany》2021,108(7):1166-1180
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Norberto P. Giannini Pablo A. Goloboff 《Evolution; international journal of organic evolution》2010,64(7):1885-1898
A new phylogenetic comparative method is proposed, based on mapping two continuous characters on a tree to generate data pairs for regression or correlation analysis, which resolves problems of multiple character reconstructions, phylogenetic dependence, and asynchronous responses (evolutionary lags). Data pairs are formed in two ways (tree‐down and tree‐up) by matching corresponding changes, Δx and Δy. Delayed responses (Δy occurring later in the tree than Δx) are penalized by weighting pairs using nodal or branch‐length distance between Δx and Δy; immediate (same‐node) responses are given maximum weight. All combinations of character reconstructions (or a random sample thereof) are used to find the observed range of the weighted coefficient of correlation r (or weighted slope b). This range is used as test statistic, and the null distribution is generated by randomly reallocating changes (Δx and Δy) in the topology. Unlike randomization of terminal values, this procedure complies with Generalized Monte Carlo requirements while saving considerable computation time. Phylogenetic dependence is avoided by randomization without data transformations, yielding acceptable type‐I error rates and statistical power. We show that ignoring delayed responses can lead to falsely nonsignificant results. Issues that arise from considering delayed responses based on optimization are discussed. 相似文献
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James Mallet Nora Besansky Matthew W. Hahn 《BioEssays : news and reviews in molecular, cellular and developmental biology》2016,38(2):140-149
Many groups of closely related species have reticulate phylogenies. Recent genomic analyses are showing this in many insects and vertebrates, as well as in microbes and plants. In microbes, lateral gene transfer is the dominant process that spoils strictly tree‐like phylogenies, but in multicellular eukaryotes hybridization and introgression among related species is probably more important. Because many species, including the ancestors of ancient major lineages, seem to evolve rapidly in adaptive radiations, some sexual compatibility may exist among them. Introgression and reticulation can thereby affect all parts of the tree of life, not just the recent species at the tips. Our understanding of adaptive evolution, speciation, phylogenetics, and comparative biology must adapt to these mostly recent findings. Introgression has important practical implications as well, not least for the management of genetically modified organisms in pest and disease control. 相似文献
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Maciej Matosiuk Anetta Borkowska Magdalena Świsłocka Paweł Mirski Zbigniew Borowski Kamil Krysiuk Aleksey A. Danilkin Elena Y. Zvychaynaya Alexander P. Saveljev Mirosław Ratkiewicz 《Molecular ecology》2014,23(10):2559-2572
Introgressive hybridization is a widespread evolutionary phenomenon which may lead to increased allelic variation at selective neutral loci and to transfer of fitness‐related traits to introgressed lineages. We inferred the population genetic structure of the European roe deer (Capreolus capreolus) in Poland from mitochondrial (CR and cyt b) and sex‐linked markers (ZFX, SRY, DBY4 and DBY8). Analyses of CR mtDNA sequences from 452 individuals indicated widespread introgression of Siberian roe deer (C. pygargus) mtDNA in the European roe deer genome, 2000 km from the current distribution range of C. pygargus. Introgressed individuals constituted 16.6% of the deer studied. Nearly 75% of them possessed haplotypes belonging to the group which arose 23 kyr ago and have not been detected within the natural range of Siberian roe deer, indicating that majority of present introgression has ancient origin. Unlike the mtDNA results, sex‐specific markers did not show signs of introgression. Species distribution modelling analyses suggested that C. pygargus could have extended its range as far west as Central Europe after last glacial maximum. The main hybridization event was probably associated with range expansion of the most abundant European roe deer lineage from western refugia and took place in Central Europe after the Younger Dryas (10.8–10.0 ka BP). Initially, introgressed mtDNA variants could have spread out on the wave of expansion through the mechanism of gene surfing, reaching high frequencies in European roe deer populations and leading to observed asymmetrical gene flow. Human‐mediated introductions of C. pygargus had minimal effect on the extent of mtDNA introgression. 相似文献
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John G. Phillips Danté B. Fenolio Sarah L. Emel Ronald M. Bonett 《Journal of Biogeography》2017,44(11):2463-2474