Pub Date : 2024-10-09DOI: 10.1016/j.ympev.2024.108217
Juan F. Alzate , Favio A. González , Natalia Pabón-Mora
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.
{"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 , Favio A. González , 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}
Pub Date : 2024-10-04DOI: 10.1016/j.ympev.2024.108214
Irina A. Ekimova , Dimitry M. Schepetov , Brenna Green , Maria V. Stanovova , Tatiana I. Antokhina , Terrence Gosliner , Manuel Antonio E. Malaquias , Ángel Valdés
Nudibranch molluscs Coryphella 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 Coryphella, estimation of divergence times between species, an ancestral area reconstruction, and a population analysis of widely distributed trans-Arctic species Coryphella verrucosa 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 Coryphella, 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 Coryphella 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.
{"title":"Scaling the high latitudes: evolution, diversification, and dispersal of Coryphella nudibranchs across the Northern Hemisphere","authors":"Irina A. Ekimova , Dimitry M. Schepetov , Brenna Green , Maria V. Stanovova , Tatiana I. Antokhina , Terrence Gosliner , Manuel Antonio E. Malaquias , 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}
Pub Date : 2024-10-03DOI: 10.1016/j.ympev.2024.108211
Taichang Mu , Yongsheng Lin , Huili Pu , Nemat O. Keyhani , Yuxiao Dang , Huajun Lv , Zhiying Zhao , Zhiang Heng , Ziyi Wu , Chengjie Xiong , Longbing Lin , Yuxi Chen , Hailan Su , Xiayu Guan , Junzhi Qiu
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, Pseudoplagiostoma fafuense sp. nov., Ps. ilicis sp. nov., Ps. sanmingense sp. nov. and Ps. bambusae are described and a key of Pseudoplagiostomataceae is provided. With respect to Pyrisporaceae, we considered Pseudoplagiostoma castaneae to be a synonym of Pyrispora castaneae. In addition, a new species of Schizoparmaceae, Coniella fujianensis sp. nov. is described and illustrated.
{"title":"Molecular phylogenetic and estimation of evolutionary divergence and biogeography of the family Schizoparmaceae and allied families (Diaporthales, Ascomycota)","authors":"Taichang Mu , Yongsheng Lin , Huili Pu , Nemat O. Keyhani , Yuxiao Dang , Huajun Lv , Zhiying Zhao , Zhiang Heng , Ziyi Wu , Chengjie Xiong , Longbing Lin , Yuxi Chen , Hailan Su , Xiayu Guan , 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}
Pub Date : 2024-10-02DOI: 10.1016/j.ympev.2024.108209
Andrew W. Thompson , Amanda C. Black , Yu Huang , Qiong Shi , Andrew I. Furness , Ingo Braasch , Federico G. Hoffmann , Guillermo Ortí
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 dN/dS ratios. We show that some genes have higher dN/dS 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.
{"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 , Amanda C. Black , Yu Huang , Qiong Shi , Andrew I. Furness , Ingo Braasch , Federico G. Hoffmann , 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}
Pub Date : 2024-10-02DOI: 10.1016/j.ympev.2024.108210
Lars Dietz , Sandra Kukowka , Jonas Eberle , Christoph Mayer , Oliver Niehuis , Lars Podsiadlowski , Dirk Ahrens
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 Pleophylla (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 Pleophylla 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 Pleophylla 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 Pleophylla. 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.
在此，我们基于对950个核基因（元类动物级通用单拷贝直向同源物；mzl-USCOs）的分析，提出了一个近乎完整的物种级系统发育，其中包括25个已知物种中的23个。通过目标富集或基因组猎枪测序，从新鲜采集、乙醇保存的样本和干燥的博物馆标本中获得了 DNA 序列。与 Dietz 等人（2023a）的研究相比，本研究通过对乙醇样本进行目标 DNA 富集而新获得的 mzl-USCOs 序列的比对完整性非常不均匀且较低（29-62 %），而从干燥样本中获得的序列比对完整性更低（∼19 %）。从低覆盖率枪式测序中获得的序列的比对完整性最高（∼ 92 %），尽管平均覆盖率远低于目标富集样本。我们利用所得到的系统发生重建了该类群的历史生物地理学。为了估算时间校准树，我们将Pleophylla的mzl-USCO数据与Scarabaeoidea现有转录组数据集的核苷酸比对结合起来，并使用了两套不同的次级校准点。尽管博物馆标本的 mzl-USCO 序列捕获率存在问题，但我们仍能推断出一个清晰的 Pleophylla 属系统发生，同时还能对序列数据较少的物种的系统发生位置提供可靠的估计。我们的研究清楚地确定了南非是 Pleophylla 的地理起源地。时间和生物地理历史证实了自始新世以来森林的持续破碎化。即使在中新世期间，也只有一次从南部非洲到东非弧的长距离扩散事件，这突出表明了这些适应森林的螯足类的扩散可能性有限，在更新世期间，它们似乎并没有沿着假定的森林走廊向北扩展重要的分布区。
{"title":"Museomics reveal origins of East African Pleophylla forest chafers and Miocene forest connectivity","authors":"Lars Dietz , Sandra Kukowka , Jonas Eberle , Christoph Mayer , Oliver Niehuis , Lars Podsiadlowski , 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}
Pub Date : 2024-09-27DOI: 10.1016/j.ympev.2024.108208
Yuxin Tao , Zichao Zeng , Yuhui Deng , Menghan Zhang , Fengping Wang , Yinzhao Wang
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, dsrAB is the hallmark of sulfur-metabolizing prokaryotes. Our detailed analyses suggested that the evolution of dsrAB 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.
{"title":"Phylogeny and evolution of dissimilatory sulfite reduction in prokaryotes","authors":"Yuxin Tao , Zichao Zeng , Yuhui Deng , Menghan Zhang , Fengping Wang , 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}
Pub Date : 2024-09-26DOI: 10.1016/j.ympev.2024.108204
Natalia Tkach , Sirus Leonard Rasti , Martin Röser
The western Eurasian-Mediterranean grass genus Cynosurus, 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 (trnL–F, matK) 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 Cynosurus 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 Cynosurus s.l. but instead argue for dividing it into three monophyletic genera: Cynosurus s.s., Falona, which is reestablished here, and Ciliochloa, 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 Ciliochloa effusa, C. effusa var. obliquata, C. effusa var. fertilis, C. elegans, C. gracilis, C. turcomanica and Falona colorata.
西欧亚-地中海禾本科草属（Cynosurus）约有 11 个种，在花序外侧、背面的可育小穗远端经常出现明显的不育小穗，这在形态上很好地划分了该属。然而，我们利用核核糖体 DNA（ITS、ETS）和质体 DNA 序列（trnL-F、matK）进行的分子系统学研究表明，该属目前的划分不是单系的，而是由三个不同的系组成。研究发现，这些支系与在分类学上被归入 Parapholiinae 亚族的 6-7 个属密切相关。在我们的分析中，这些 Parapholiinae 属始终是单系的，但与 Cynosurus 的三个系的关系因所研究的 DNA 区域而异。质体和核 DNA 的情况都是如此，细胞核不一致和 "叶绿体捕获 "表明杂交较早。有趣的是，即使在核核糖体 DNA 的 18S-26S 三元组方面，杂交也被证明是最有可能的解释，因为在核核糖体 DNA 的 18S-26S 三元组中，ITS 和 ETS 之间存在特殊的进化差异。这些结果突出说明了杂交在禾本科植物进化过程中的重要作用。在分类学方面，我们的研究结果反对保留 Cynosurus s.l.这一多系属，而主张将其分为三个单系属：Cynosurus s.s.、Falona（在此重新确立）和 Ciliochloa（描述为一个新属）。此外，还建议将 Cynosurinae 和 Parapholiinae 两个亚族合并为单一的 Cynosurinae 亚族，该亚族也是单系的。讨论了不育小穗形成的可能遗传背景以及偶尔出现的具有持续可育小穗的花序。C. effusa var. obliquata、C. effusa var. fertilis、C. elegans、C. gracilis、C. turcomanica 和 Falona colorata。
{"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 , Sirus Leonard Rasti , 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}
Pub Date : 2024-09-19DOI: 10.1016/j.ympev.2024.108193
Erika L. Garcia , Paula E. Cushing
Abiotic variables can influence species distributions, often restricting taxa to an acquired climatic signature or conversely, related species are conserved in the same ecological space over millions of years. An investigation into how abiotic change has shaped geographic distributions of taxa may be key to understanding diversification of lineages, and in the absence of reliable morphological characteristics, such information may support taxonomic units at multiple scales.
Here, we examine the historical biogeography and patterns of habitat preference within the North American solifuge family, Eremobatidae. A previous study demonstrated that a major taxonomic revision of Eremobatidae is warranted, however recent studies demonstrate high levels of morphological convergence within the group, thus a re-classification of generic boundaries using additional information must be prioritized before we can formally begin solid revisionary efforts. In this study, we aimed to reconstruct a well-resolved phylogenetic hypothesis of Eremobatidae by filtering UCE loci based on informativeness, by mitigating the effect of cogenic UCE on phylogenetic estimation, and by supplementing our curated UCE loci with mitochondrial information. Using our preferred topology, in conjunction with published estimated divergence dates for Eremobatidae, we inferred a time-calibrated phylogenetic hypothesis to inform the historical biogeography and patterns of habitat preference. The two major habitat types that were observed for Eremobatidae were warm deserts for early diverging taxa and a subsequent evolution to cold deserts and Mediterranean California ecoregions for later diverging taxa. Eremobatid niche space, determined by temperature and precipitation, has been conserved for at least 25 million years in North America, supporting a warm desert origin, and thus supporting high species richness in the Sonoran and Mexican Plateau. Overall, our study provides support for new generic level designations within Eremobatidae.
{"title":"Historical biogeography and the evolution of habitat preference in the North American camel spider family, Eremobatidae (Arachnida:Solifugae)","authors":"Erika L. Garcia , Paula E. Cushing","doi":"10.1016/j.ympev.2024.108193","DOIUrl":"10.1016/j.ympev.2024.108193","url":null,"abstract":"<div><div>Abiotic variables can influence species distributions, often restricting taxa to an acquired climatic signature or conversely, related species are conserved in the same ecological space over millions of years. An investigation into how abiotic change has shaped geographic distributions of taxa may be key to understanding diversification of lineages, and in the absence of reliable morphological characteristics, such information may support taxonomic units at multiple scales.</div><div>Here, we examine the historical biogeography and patterns of habitat preference within the North American solifuge family, Eremobatidae. A previous study demonstrated that a major taxonomic revision of Eremobatidae is warranted, however recent studies demonstrate high levels of morphological convergence within the group, thus a re-classification of generic boundaries using additional information must be prioritized before we can formally begin solid revisionary efforts. In this study, we aimed to reconstruct a well-resolved phylogenetic hypothesis of Eremobatidae by filtering UCE loci based on informativeness, by mitigating the effect of cogenic UCE on phylogenetic estimation, and by supplementing our curated UCE loci with mitochondrial information. Using our preferred topology, in conjunction with published estimated divergence dates for Eremobatidae, we inferred a time-calibrated phylogenetic hypothesis to inform the historical biogeography and patterns of habitat preference. The two major habitat types that were observed for Eremobatidae were warm deserts for early diverging taxa and a subsequent evolution to cold deserts and Mediterranean California ecoregions for later diverging taxa. Eremobatid niche space, determined by temperature and precipitation, has been conserved for at least 25 million years in North America, supporting a warm desert origin, and thus supporting high species richness in the Sonoran and Mexican Plateau. Overall, our study provides support for new generic level designations within Eremobatidae.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108193"},"PeriodicalIF":3.6,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301881","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}
Pub Date : 2024-09-19DOI: 10.1016/j.ympev.2024.108203
Alexander Tamanini Mônico , Esteban Diego Koch , Miquéias Ferrão , Igor Yuri Fernandes , Giselle Moura Guimarães Marques , Juan Carlos Chaparro , Miguel Trefaut Rodrigues , Albertina Pimentel Lima , Antoine Fouquet
With more than 600 recognized species, the genus Pristimantis is already the most diverse among vertebrates, but described species only represent a fraction of the actual diversity in this clade. This genus is widely distributed throughout the Neotropics and represents an interesting model for biogeographic studies because Pristimantis spp. are direct developing and generally have narrow ecological niches and low dispersal abilities. The P. unistrigatus species group is one of the most important components in the genus (ca. 200 recognized species) and has been supported by morphological but not by molecular evidence. We assessed the species boundaries and distribution in the P. unistrigatus species group and infer spatiotemporal patterns of diversification related to historical landscape changes in the Neotropics. We gathered three mitochondrial, and two nuclear DNA loci from 416 specimens throughout the range of the group, and including 68 nominal species. We redefine the group based on the obtained phylogeny and found 151 candidate species that composes it, with 83 of these remaining undescribed. We recovered 11 major clades within the group that diverged before 13 Ma. The diversification of the group started during the early Miocene most likely in northwestern South America, currently corresponding to western Amazonia and northern Andes. The other neotropical areas subsequently acted as sinks, receiving lineages mostly during the last 10 Ma, after the demise of the Pebas System and the setup of the modern Amazonian hydrographic system.
Pristimantis 属拥有 600 多个公认的物种，已经成为脊椎动物中物种最丰富的属，但已描述的物种仅占该支系实际多样性的一小部分。该属广泛分布于整个新热带地区，是生物地理学研究的一个有趣模型，因为 Pristimantis 属是直接发育的，通常具有狭窄的生态位和较低的变异性。P. unistrigatus物种组是该属最重要的组成部分之一（约有 200 个公认的物种），已得到形态学证据的支持，但未得到分子证据的支持。我们评估了 P. unistrigatus 物种群的物种边界和分布情况，并推断了与新热带地区历史景观变化有关的物种多样化时空模式。我们从该物种群分布区的 416 个标本中收集了三个线粒体和两个核 DNA 位点，其中包括 68 个标称物种。我们根据所获得的系统发生重新定义了该类群，并发现了 151 个候选物种，其中 83 个物种仍未被描述。我们在该类群中发现了 11 个在 13 Ma 年前分化的主要支系。该类群的分化很可能始于中新世早期的南美洲西北部，目前相当于亚马孙西部和安第斯北部。其他新热带地区随后成为吸收汇，主要在最近 10 Ma 期间，即佩巴斯系统消亡和现代亚马逊水文系统建立之后接受了该类群。
{"title":"The small and inconspicuous majority: Revealing the megadiversity and historical biogeography of the Pristimantis unistrigatus species group (Anura, Strabomantidae)","authors":"Alexander Tamanini Mônico , Esteban Diego Koch , Miquéias Ferrão , Igor Yuri Fernandes , Giselle Moura Guimarães Marques , Juan Carlos Chaparro , Miguel Trefaut Rodrigues , Albertina Pimentel Lima , Antoine Fouquet","doi":"10.1016/j.ympev.2024.108203","DOIUrl":"10.1016/j.ympev.2024.108203","url":null,"abstract":"<div><div>With more than 600 recognized species, the genus <em>Pristimantis</em> is already the most diverse among vertebrates, but described species only represent a fraction of the actual diversity in this clade. This genus is widely distributed throughout the Neotropics and represents an interesting model for biogeographic studies because <em>Pristimantis</em> spp. are direct developing and generally have narrow ecological niches and low dispersal abilities. The <em>P. unistrigatus</em> species group is one of the most important components in the genus (ca. 200 recognized species) and has been supported by morphological but not by molecular evidence. We assessed the species boundaries and distribution in the <em>P. unistrigatus</em> species group and infer spatiotemporal patterns of diversification related to historical landscape changes in the Neotropics. We gathered three mitochondrial, and two nuclear DNA loci from 416 specimens throughout the range of the group, and including 68 nominal species. We redefine the group based on the obtained phylogeny and found 151 candidate species that composes it, with 83 of these remaining undescribed. We recovered 11 major clades within the group that diverged before 13 Ma. The diversification of the group started during the early Miocene most likely in northwestern South America, currently corresponding to western Amazonia and northern Andes. The other neotropical areas subsequently acted as sinks, receiving lineages mostly during the last 10 Ma, after the demise of the Pebas System and the setup of the modern Amazonian hydrographic system.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108203"},"PeriodicalIF":3.6,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301883","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}
Pub Date : 2024-09-15DOI: 10.1016/j.ympev.2024.108202
Anna L. Becker , Andrew A. Crowl , James L. Luteyn , Andre S. Chanderbali , Walter S. Judd , Paul S. Manos , Douglas E. Soltis , Stephen A. Smith , Deise J.P. Goncalves , Christopher W. Dick , William N. Weaver , Pamela S. Soltis , Nico Cellinese , Peter W. Fritsch
Vaccinieae is a morphologically diverse and species-rich (∼1430 species) tribe in Ericaceae. Although the majority of diversity is tropical, Vaccinieae are best known for temperate crops (i.e., blueberries, cranberries, and lingonberries) in Vaccinium. Vaccinium itself (∼500 species) has been previously suggested as highly polyphyletic and taxonomic boundaries among many of the other genera in the tribe remain uncertain. We assessed the evolutionary history of Vaccinieae with phylogenomic analyses based on a target-enrichment dataset containing 256 low-copy nuclear loci and 210 species representing 30 of the 35 genera in the tribe and 25 of the 29 sections of Vaccinium. We conducted time-calibrated biogeographic analyses and diversification analyses to explore the area of origin and global dispersal history of the tribe. The analysis recovered a temperate North American origin for Vaccinieae approximately 30 million years ago. Tropical diversity of Vaccinieae was inferred to result from multiple, independent movements into the tropics from north-temperate ancestors. Diversification rate increases corresponded to radiation into the Andes and SE Asia. The pseudo-10-locular ovary evolved once in the tribe from the five-locular state, coinciding with the diversification of a major clade that includes most Asian Vaccinium and the group from which commercial blueberries are derived (V. sect. Cyanococcus). A reconstruction from available chromosome counts suggests that a major polyploid event predated the evolution of nearly half the diversity of Vaccinieae. The extent of polyphyly in Vaccinium documented here supports the need for a generic reclassification of the tribe.
{"title":"A global blueberry phylogeny: Evolution, diversification, and biogeography of Vaccinieae (Ericaceae)","authors":"Anna L. Becker , Andrew A. Crowl , James L. Luteyn , Andre S. Chanderbali , Walter S. Judd , Paul S. Manos , Douglas E. Soltis , Stephen A. Smith , Deise J.P. Goncalves , Christopher W. Dick , William N. Weaver , Pamela S. Soltis , Nico Cellinese , Peter W. Fritsch","doi":"10.1016/j.ympev.2024.108202","DOIUrl":"10.1016/j.ympev.2024.108202","url":null,"abstract":"<div><div>Vaccinieae is a morphologically diverse and species-rich (∼1430 species) tribe in Ericaceae. Although the majority of diversity is tropical, Vaccinieae are best known for temperate crops (i.e., blueberries, cranberries, and lingonberries) in <em>Vaccinium</em>. <em>Vaccinium</em> itself (∼500 species) has been previously suggested as highly polyphyletic and taxonomic boundaries among many of the other genera in the tribe remain uncertain. We assessed the evolutionary history of Vaccinieae with phylogenomic analyses based on a target-enrichment dataset containing 256 low-copy nuclear loci and 210 species representing 30 of the 35 genera in the tribe and 25 of the 29 sections of <em>Vaccinium</em>. We conducted time-calibrated biogeographic analyses and diversification analyses to explore the area of origin and global dispersal history of the tribe. The analysis recovered a temperate North American origin for Vaccinieae approximately 30 million years ago. Tropical diversity of Vaccinieae was inferred to result from multiple, independent movements into the tropics from north-temperate ancestors. Diversification rate increases corresponded to radiation into the Andes and SE Asia. The pseudo-10-locular ovary evolved once in the tribe from the five-locular state, coinciding with the diversification of a major clade that includes most Asian <em>Vaccinium</em> and the group from which commercial blueberries are derived (<em>V.</em> sect. <em>Cyanococcus</em>). A reconstruction from available chromosome counts suggests that a major polyploid event predated the evolution of nearly half the diversity of Vaccinieae. The extent of polyphyly in <em>Vaccinium</em> documented here supports the need for a generic reclassification of the tribe.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108202"},"PeriodicalIF":3.6,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142263919","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}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号