Molecular Phylogenetics and Evolution最新文献

{"title":"Phylogenomic analyses of the pantropical Platycerium Desv. (Platycerioideae) reveal their complex evolution and historical biogeography","authors":"Jing Zhao ,&nbsp;Chuan-Jie Huang ,&nbsp;Li-Ju Jiang ,&nbsp;Zhao-Rong He ,&nbsp;Shuai Yang ,&nbsp;Zhang-Ming Zhu ,&nbsp;Liang Zhang ,&nbsp;Hong Yu ,&nbsp;Xin-Mao Zhou ,&nbsp;Jia-Guan Wang","doi":"10.1016/j.ympev.2024.108213","DOIUrl":"10.1016/j.ympev.2024.108213","url":null,"abstract":"<div><div><em>Platycerium</em> is a genus of pantropical epiphytic ferns consisting of ca. 18 species and are highly sought after by horticultural enthusiasts. Although the monophyly of this genus has been well supported in previous molecular studies, as an intercontinentally disjunct genus, the origin and distribution pattern of <em>Platycerium</em> were elusive and controversial. This is mainly due to limited taxon sampling, a plastid representing only a single coalescent history, the lack of fossil evidence, and so on. Here, by utilizing genome-skimming sequencing, transcriptome sequencing, and flow cytometry, we integrated chloroplast genomes, data of single-copy nuclear genes, ploidy levels, morphology, and geographic distribution to understand the species phylogeny and the evolutionary and biogeographic history of <em>Platycerium</em>. Our major results include: (1) based on both plastid and nuclear datasets, <em>Platycerium</em> is consistently resolved into three fully supported clades: the Afro-American (AA) clade, the Javan-Australian (JA) clade, and the Malayan-Asian (MA) clade. The AA clade and MA clade are further divided into three and two subclades, respectively; (2) a large amount of gene tree conflict, as well as cytonuclear discordance, was found and can be explained by hybridization and incomplete lineage sorting, and most of the hybridization hypotheses represented ancient hybridization events; (3) through molecular dating, the crown age of <em>Platycerium</em> is determined to be at approximately 32.79 Ma based on the plastid dataset or 29.08 Ma based on the nuclear dataset in the Middle Oligocene; (4) ancestral area reconstruction analysis from different datasets showed that <em>Platycerium</em> most likely originated from Indochina; (5) current distribution patterns are resultant from long-distance dispersals, ancient orogeny, and an ancient climate event; and (6) species diversification was driven by polyploidization, dispersal, and hybridization. This study presented here will help understand the evolution of tropical plant flora and provide a reference for the cultivation and breeding of staghorn ferns.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108213"},"PeriodicalIF":3.6,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142407275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Imperiled wanderlust lichens in steppe habitats of western North America comprise geographically structured mycobiont lineages and a reversal to sexual reproduction within this asexual clade","authors":"Robert Hadfield ,&nbsp;Teagan Mulford ,&nbsp;Makani L. Fisher ,&nbsp;Abigail Borgmeier ,&nbsp;Diego A. Ardon ,&nbsp;Andrew D. Suchomel ,&nbsp;Judicaël Fomekong-Lontchi ,&nbsp;Laura Sutherland ,&nbsp;Madison Huie ,&nbsp;Pungki Lupiyaningdyah ,&nbsp;Sierra Nichols ,&nbsp;Ying Fei Lin ,&nbsp;Nopparat Anantaprayoon ,&nbsp;Steven D. Leavitt","doi":"10.1016/j.ympev.2024.108212","DOIUrl":"10.1016/j.ympev.2024.108212","url":null,"abstract":"<div><div>The northern North American Cordillera is a globally significant center of endemism. In western North America, imperiled arid steppe habitats support a number of unique species, including several endemic lichens. However, processes driving diversification and endemism in this region remain unclear. In this study, we investigate diversity and phylogeography of the threatened wanderlust lichens (mycobiont = <em>Rhizoplaca</em> species) which occur unattached on calcareous soils in steppe habitats. Wanderlust lichens comprise three species of lichen-forming fungi (LFF) – <em>Rhizoplaca arbuscula</em>, <em>R. haydenii</em>, and <em>R. idahoensis</em> (endangered, IUCN Red List) – which occur in fragmented populations in Idaho and Wyoming, with more limited populations in southern Montana and northern Utah. These lichens reproduce almost exclusively via large, asexual vegetative propagules. Here, our aims were to (i) assess the evolutionary origin of this group and identify phylogeographic structure, (ii) infer ancestral geographic distributions for lineages within this clade, and (iii) use species distribution modeling to better understand the distribution of contemporary populations. Using a genome-skimming approach, we generated a 19.1Mb alignment, spanning ca. half of the complete LFF genome, from specimens collected throughout the entire range of wanderlust lichens. Based on this phylogeny, we investigated phylogeographic patterns using RASP. Finally, we used MaxEnt to estimate species distribution models for <em>R. arbuscula</em> and <em>R. haydenii</em>. We inferred a highly structured topology, with clades corresponding to distinct geographic regions and morphologies collected throughout the group’s distribution. We found that <em>R. robusta</em>, a sexually reproducing taxon, is clearly nested within the vagrant <em>Rhizoplaca</em> clade. Phylogeographic analyses suggest that both dispersal and vicariance played significant roles throughout the evolutionary history of the vagrant <em>Rhizoplaca</em> clade, with most of the dispersal events originating from the Salmon Basin in eastern Idaho – the center of diversity for this group. Despite the fact that wanderlust lichens are dispersal limited due to large, unspecialized vegetative propagules, we inferred multiple dispersal events crossing the Continental Divide. Comparing herbarium records with species distribution models suggests that wanderlust lichens don’t fully occupy the areas of highest distribution probability. In fact, documented records often occur in areas predicted to be only marginally suitable. These data suggest a potential mismatch between contemporary habitats outside of the center of diversity in eastern Idaho with the most suitable habitat, adding to the vulnerability of this imperiled complex of endemic lichens.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108212"},"PeriodicalIF":3.6,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The genetic consequences of historic climate change on the contemporary population structure of a widespread temperate North American songbird","authors":"Alison Cloutier ,&nbsp;David Tsz Chung Chan,&nbsp;Emily Shui Kei Poon ,&nbsp;Simon Yung Wa Sin","doi":"10.1016/j.ympev.2024.108216","DOIUrl":"10.1016/j.ympev.2024.108216","url":null,"abstract":"<div><div>Studies of widely distributed species can inform our understanding of how past demographic events tied to historic glaciation and ongoing population genetic processes interact to shape contemporaneous patterns of biodiversity at a continental scale. In this study, we used whole-genome resequencing to investigate the current population structure and genetic signatures of past demographic events in the widespread migratory American goldfinch (<em>Spinus tristis</em>). Phylogenetic relationships inferred from whole mitochondrial genomes were poorly resolved. In contrast, a genome-wide panel of &gt; 4.5 million single nucleotide polymorphisms (SNPs) strongly supported the existence of eastern and western populations separated by western mountain ranges and additional population structuring within the western clade. Demographic modeling estimated that the eastern and western populations diverged approximately one million years ago, and both populations experienced subsequent population bottlenecks during the last glacial period. Species distribution models showed a severe contraction of suitable habitat for the American goldfinch during this period, with predicted discontinuities that are consistent with multiple, isolated glacial refugia that coincide with present-day population structure. Low overall genetic differentiation between the eastern and western populations (F_ST ∼ 0.01) suggests ongoing gene flow accompanied divergence, and individuals with admixed genomic signatures were sampled along a potential contact zone. Nevertheless, outlier SNPs were identified near genes associated with feather color, song, and migratory behavior and provide strong candidates for further study of the mechanisms underlying reproductive isolation and speciation in birds.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108216"},"PeriodicalIF":3.6,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395623","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Back together: Over 1000 single-copy nuclear loci and reproductive features support the holoendoparasitic Apodanthaceae and Rafflesiaceae as sister lineages in the order Malpighiales","authors":"Juan F. Alzate ,&nbsp;Favio A. González ,&nbsp;Natalia Pabón-Mora","doi":"10.1016/j.ympev.2024.108217","DOIUrl":"10.1016/j.ympev.2024.108217","url":null,"abstract":"<div><div>The systematics of the holoendoparasitic flowering plant families Apodanthaceae and Rafflesiaceae has been discussed for over two centuries. The morphological reduction of roots, shoots and leaves in all members of both families, resulting in a cryptic mycelium-like vegetative body, has been interpreted either as a key common feature, or as a result of convergent evolution due to full dependence upon their hosts. Historically, the two families have been placed together due to similar morphological features, but recent analyses based on few mitochondrial and ribosomal gene markers placed them in the distantly related orders Cucurbitales and Malpighiales. Here we reevaluate the affinities of the Apodanthaceae and the Rafflesiaceae using a phylogenomic approach. We present (1) a historical account on their affinities over the last 200 years; (2) phylogenetic analyses reinstating their sister group relationship as part of the order Malpighiales, based on over 1000 single-copy nuclear protein-coding loci; and (3) a comprehensive list of putative morphoanatomical and developmental synapomorphies in light of the phylogenomic results, with emphasis on shared reproductive traits regardless of dramatic differences in floral size.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108217"},"PeriodicalIF":3.6,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Scaling the high latitudes: evolution, diversification, and dispersal of Coryphella nudibranchs across the Northern Hemisphere","authors":"Irina A. Ekimova ,&nbsp;Dimitry M. Schepetov ,&nbsp;Brenna Green ,&nbsp;Maria V. Stanovova ,&nbsp;Tatiana I. Antokhina ,&nbsp;Terrence Gosliner ,&nbsp;Manuel Antonio E. Malaquias ,&nbsp;Ángel Valdés","doi":"10.1016/j.ympev.2024.108214","DOIUrl":"10.1016/j.ympev.2024.108214","url":null,"abstract":"<div><div>Nudibranch molluscs <em>Coryphella</em> are widely distributed and species-rich gastropod group lacking fossil record and displaying a complex distribution across both Southern and Northern hemispheres. In this paper we provide a detailed review of the morphology, ecology, and distribution of <em>Coryphella,</em> estimation of divergence times between species, an ancestral area reconstruction, and a population analysis of widely distributed trans-Arctic species <em>Coryphella verrucosa</em> to investigate the evolution, phylogeographic patterns and reconstruct possible historical routes of oceanic dispersal. The inclusion of a larger sample size and five molecular markers has revealed a complex evolutionary history of <em>Coryphella</em>, shaped by transgression, vicariance, and dietary shifts, and overall driven by the pervasive effect of glacial cycles. We also revealed the presence of additional cryptic diversity, which suggests that further sampling may produce additional species in this group of nudibranchs. Tree calibration indicates the genus <em>Coryphella</em> originates in the middle Miocene in the Pacific Ocean and the early divergence within this group also occurred in the Pacific, specifically in different regions of the North Pacific. The ancestral area reconstruction inferred five independent instances of transgression from the Pacific Ocean to the Atlantic via different migration routes, including the Panamanian seaway and the Bering Strait. Among them, we identified three cases of successful transition to the Arctic waters from the North Pacific via the Bering Strait, associated with interglacial conditions of middle Pleistocene. Consequently, Pleistocene glacial cycles likely prompted pulses of boreal faunal elements to disperse southwards followed by range disjunction and temporary isolation of distant populations and resulting in allopatric speciation. Evidence from the population structure of contemporary trans-Arctic species suggests an occurrence of independent recolonization pathways of Arctic waters from both southernly and northernly refugia after the Last Glacial Maximum.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108214"},"PeriodicalIF":3.6,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142382493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular phylogenetic and estimation of evolutionary divergence and biogeography of the family Schizoparmaceae and allied families (Diaporthales, Ascomycota)","authors":"Taichang Mu ,&nbsp;Yongsheng Lin ,&nbsp;Huili Pu ,&nbsp;Nemat O. Keyhani ,&nbsp;Yuxiao Dang ,&nbsp;Huajun Lv ,&nbsp;Zhiying Zhao ,&nbsp;Zhiang Heng ,&nbsp;Ziyi Wu ,&nbsp;Chengjie Xiong ,&nbsp;Longbing Lin ,&nbsp;Yuxi Chen ,&nbsp;Hailan Su ,&nbsp;Xiayu Guan ,&nbsp;Junzhi Qiu","doi":"10.1016/j.ympev.2024.108211","DOIUrl":"10.1016/j.ympev.2024.108211","url":null,"abstract":"<div><div>The Diaporthales includes 32 families, many of which are important plant pathogens, endophytes and saprobes, e.g., members of the families Pseudoplagiostomataceae, Pyrisporaceae and Schizoparmaceae. Nucleotide sequences derived from five genetic loci including: ITS, LSU, TEF1-α, TUB2 and RPB2 were used for Bayesian evolutionary analysis to determine divergence times and evolutionary relationships within the Schizoparmaceae. Molecular clock analyses revealed that the ancestor of Schizoparmaceae split during the Upper Cretaceous period approximately 75.7 Mya (95 % highest posterior density of 60.3–91.3 Mya). Reconstructing ancestral state in phylogenies (RASP) with using the Bayesian Binary Markov chain Monte Carlo (BBM) Method to reconstruct the historical biogeography for the family Schizoparmaceae indicated its most likely origin in Africa. Based on taxonomic and phylogenetic analyses, the Pseudoplagiostomataceae and Pyrisporaceae relationships were clarified and a total of four species described herein. For Pseudoplagiostomataceae, three new species and one known species that include, <em>Pseudoplagiostoma fafuense</em> sp. nov., <em>Ps. ilicis</em> sp. nov., <em>Ps. sanmingense</em> sp. nov. and <em>Ps. bambusae</em> are described and a key of Pseudoplagiostomataceae is provided. With respect to Pyrisporaceae, we considered <em>Pseudoplagiostoma castaneae</em> to be a synonym of <em>Pyrispora castaneae</em>. In addition, a new species of Schizoparmaceae, <em>Coniella fujianensis</em> sp. nov. is described and illustrated.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108211"},"PeriodicalIF":3.6,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142378652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic data support phylogenetic congruence and reveal genomic changes associated with the repeated evolution of annualism in aplocheiloid killifishes (Cyprinodontiformes)","authors":"Andrew W. Thompson ,&nbsp;Amanda C. Black ,&nbsp;Yu Huang ,&nbsp;Qiong Shi ,&nbsp;Andrew I. Furness ,&nbsp;Ingo Braasch ,&nbsp;Federico G. Hoffmann ,&nbsp;Guillermo Ortí","doi":"10.1016/j.ympev.2024.108209","DOIUrl":"10.1016/j.ympev.2024.108209","url":null,"abstract":"<div><div>Repeated evolution of novel life histories that are correlated with ecological variables offers opportunities to study convergence in genetic, developmental, and metabolic features. Nearly half of the 800 species of Aplocheiloid killifishes, a clade of teleost fishes with a circumtropical distribution, are “annual” or seasonal species that survive in ephemeral bodies of water that desiccate and are unfeasible for growth, reproduction, or survival for weeks to months every year. But the repeated evolution of adaptations that are key features of the annual life history among these fishes remains poorly known without a robust phylogenetic framework. We present a large-scale phylogenomic reconstruction of aplocheiloid killifishes evolution using newly sequenced transcriptomes obtained from a diversity of killifish lineages representing putative independent origins of annualism. Ancestral state estimation shows that developmental dormancy (diapause), a key trait of the killifish annual life cycle, may have originated up to seven times independently among African and South American lineages. To further explore the genetic basis of this unique trait, we measure changes in evolutionary rates among orthologous genes across the killifish tree of life by quantifying codon evolution using d<em>N</em>/d<em>S</em> ratios. We show that some genes have higher d<em>N</em>/d<em>S</em> ratios in lineages leading to species with annual life history. Many of them constitute key developmental genes or nuclear-encoded metabolic genes that control oxidative phosphorylation. Lastly, we compare these genes with higher ω to genes previously associated to developmental dormancy and metabolic shifts in killifishes and other vertebrates, and thereby identify molecular evolutionary signatures of repeated transitions to extreme environments.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108209"},"PeriodicalIF":3.6,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142376294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Museomics reveal origins of East African Pleophylla forest chafers and Miocene forest connectivity","authors":"Lars Dietz ,&nbsp;Sandra Kukowka ,&nbsp;Jonas Eberle ,&nbsp;Christoph Mayer ,&nbsp;Oliver Niehuis ,&nbsp;Lars Podsiadlowski ,&nbsp;Dirk Ahrens","doi":"10.1016/j.ympev.2024.108210","DOIUrl":"10.1016/j.ympev.2024.108210","url":null,"abstract":"<div><div>Here we present a nearly complete species-level phylogeny including 23 of the 25 known species of the forest-dwelling herbivorous scarab chafer beetle genus <em>Pleophylla</em> (Coleoptera: Scarabaeidae: Sericinae), based on the analysis of 950 nuclear genes (metazoan-level universal single-copy orthologs; mzl-USCOs). DNA sequences were obtained from freshly collected, ethanol-preserved samples and from dried museum specimens by target enrichment or genome shotgun sequencing. Alignment completeness of mzl-USCOs newly obtained here by target DNA enrichment of ethanol samples were very heterogenous and lower (29–62 %) than in Dietz et al. (2023a), while that of sequences recovered from dried samples was even lower (∼19 %). Alignment completeness of the sequences obtained from low coverage shotgun sequencing was highest (∼92 %), although the average coverage was much lower than for the target enrichment samples. We used the resulting phylogeny to reconstruct the historical biogeography of the group. To estimate a time-calibrated tree, we combined the mzl-USCO data of <em>Pleophylla</em> with a nucleotide alignment from an available transcriptomic dataset of Scarabaeoidea and used two different sets of secondary calibration points. Despite the problems associated with the capture rate of mzl-USCO sequences from museum specimens, we were able to infer a well-resolved phylogeny of the genus <em>Pleophylla</em> that also provided reliable estimates of the phylogenetic position of species for which we had little sequence data. Our study clearly identified South Africa as the geographic origin of <em>Pleophylla</em>. Timing and biogeographic history confirm a persistent fragmentation of forests since the Eocene. The occurrence of only one long-distance dispersal event from southern Africa to the Eastern African Arc even during the Miocene highlights the limited dispersal possibilities for these forest-adapted chafers, which do not seem to have had important northerly range expansions along hypothetical forest corridors during the Pleistocene.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108210"},"PeriodicalIF":3.6,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142376293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogeny and evolution of dissimilatory sulfite reduction in prokaryotes","authors":"Yuxin Tao ,&nbsp;Zichao Zeng ,&nbsp;Yuhui Deng ,&nbsp;Menghan Zhang ,&nbsp;Fengping Wang ,&nbsp;Yinzhao Wang","doi":"10.1016/j.ympev.2024.108208","DOIUrl":"10.1016/j.ympev.2024.108208","url":null,"abstract":"<div><div>Sulfate is the second most common nonmetallic ion in modern oceans, as its concentration dramatically increased alongside tectonic activity and atmospheric oxidation in the Proterozoic. Microbial sulfate/sulfite metabolism, involving organic carbon or hydrogen oxidation, is linked to sulfur and carbon biogeochemical cycles. However, the coevolution of microbial sulfate/sulfite metabolism and Earth’s history remains unclear. Here, we conducted a comprehensive phylogenetic analysis to explore the evolutionary history of the dissimilatory sulfite reduction (Dsr) pathway. The phylogenies of the Dsr-related genes presented similar branching patterns but also some incongruencies, indicating the complex origin and evolution of Dsr. Among these genes, <em>dsrAB</em> is the hallmark of sulfur-metabolizing prokaryotes. Our detailed analyses suggested that the evolution of <em>dsrAB</em> was shaped by vertical inheritance and multiple horizontal gene transfer events and that selection pressure varied across distinct lineages. Dated phylogenetic trees indicated that key evolutionary events of dissimilatory sulfur-metabolizing prokaryotes were related to the Great Oxygenation Event (2.4–2.0 Ga) and several geological events in the “Boring Billion” (1.8–0.8 Ga), including the fragmentation of the Columbia supercontinent (approximately 1.6 Ga), the rapid increase in marine sulfate (1.3–1.2 Ga), and the Neoproterozoic glaciation event (approximately 1.0 Ga). We also proposed that the voluminous iron formations (approximately 1.88 Ga) might have induced the metabolic innovation of iron reduction. In summary, our study provides new insights into Dsr evolution and a systematic view of the coevolution of dissimilatory sulfur-metabolizing prokaryotes and the Earth’s environment.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108208"},"PeriodicalIF":3.6,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142333092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Disentangling conflicting molecular phylogenetic signals in nuclear and plastid DNA of the western Eurasian-Mediterranean grass genus Cynosurus and its relatives (Poaceae subtribes Cynosurinae and Parapholiinae)","authors":"Natalia Tkach ,&nbsp;Sirus Leonard Rasti ,&nbsp;Martin Röser","doi":"10.1016/j.ympev.2024.108204","DOIUrl":"10.1016/j.ympev.2024.108204","url":null,"abstract":"<div><div>The western Eurasian-Mediterranean grass genus <em>Cynosurus</em>, comprising about 11 species, is morphologically well delimited by the regular occurrence of conspicuous sterile spikelets distal to the fertile ones on the outer, abaxial side of the inflorescences. However, our molecular phylogenetic study using nuclear ribosomal DNA (ITS, ETS) and plastid DNA sequences (<em>trnL–F</em>, <em>matK</em>) has shown that the genus is not monophyletic in its current delimitation, but consists of three distinct lineages. These lineages were found to be closely related to a group of 6–7 genera taxonomically assigned to the subtribe Parapholiinae. These Parapholiinae genera were consistently monophyletic in our analyses, but the suggested relationships to the three lineages of <em>Cynosurus</em> varied depending on the particular DNA region examined. This was the case for both plastid and nuclear DNA, with cytonuclear discordance and ‘chloroplast capture’ indicating earlier hybridization. Interestingly, hybridization also proved to be the most likely explanation even with regard to the 18S–26S cistrons of the nuclear ribosomal DNA, where an exceptional evolutionary divergence between ITS and ETS was found. The results highlight and illustrate the important role of hybridization in the evolution of grasses. In terms of taxonomy, our findings argue against maintaining a polyphyletic genus <em>Cynosurus s.l.</em> but instead argue for dividing it into three monophyletic genera: <em>Cynosurus s.s.</em>, <em>Falona</em>, which is reestablished here, and <em>Ciliochloa</em>, which is described as a new genus. In addition, it is proposed that the two subtribes Cynosurinae and Parapholiinae be combined into a single subtribe Cynosurinae, which is also monophyletic. The possible genetic background of the formation of sterile spikelets and the occasional occurrence of inflorescences with consistently fertile spikelets are discussed. New combinations are <em>Ciliochloa effusa</em>, <em>C. effusa</em> var. <em>obliquata</em>, <em>C. effusa</em> var. <em>fertilis</em>, <em>C. elegans, C. gracilis, C. turcomanica</em> and <em>Falona colorata</em>.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108204"},"PeriodicalIF":3.6,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142333165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}