Molecular Phylogenetics and Evolution最新文献

{"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}

{"title":"Historical biogeography and the evolution of habitat preference in the North American camel spider family, Eremobatidae (Arachnida:Solifugae)","authors":"Erika L. Garcia ,&nbsp;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}

{"title":"The small and inconspicuous majority: Revealing the megadiversity and historical biogeography of the Pristimantis unistrigatus species group (Anura, Strabomantidae)","authors":"Alexander Tamanini Mônico ,&nbsp;Esteban Diego Koch ,&nbsp;Miquéias Ferrão ,&nbsp;Igor Yuri Fernandes ,&nbsp;Giselle Moura Guimarães Marques ,&nbsp;Juan Carlos Chaparro ,&nbsp;Miguel Trefaut Rodrigues ,&nbsp;Albertina Pimentel Lima ,&nbsp;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}

{"title":"A global blueberry phylogeny: Evolution, diversification, and biogeography of Vaccinieae (Ericaceae)","authors":"Anna L. Becker ,&nbsp;Andrew A. Crowl ,&nbsp;James L. Luteyn ,&nbsp;Andre S. Chanderbali ,&nbsp;Walter S. Judd ,&nbsp;Paul S. Manos ,&nbsp;Douglas E. Soltis ,&nbsp;Stephen A. Smith ,&nbsp;Deise J.P. Goncalves ,&nbsp;Christopher W. Dick ,&nbsp;William N. Weaver ,&nbsp;Pamela S. Soltis ,&nbsp;Nico Cellinese ,&nbsp;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}

{"title":"Deciphering the evolution and biogeography of ant-ferns Lecanopteris s.s","authors":"Li-Ju Jiang ,&nbsp;Jing Zhao ,&nbsp;Jia-Guan Wang ,&nbsp;Sven Landrein ,&nbsp;Ji-Pu Shi ,&nbsp;Chuan-Jie Huang ,&nbsp;Miao Luo ,&nbsp;Xin-Mao Zhou ,&nbsp;Hong-Bin Niu ,&nbsp;Zhao-Rong He","doi":"10.1016/j.ympev.2024.108199","DOIUrl":"10.1016/j.ympev.2024.108199","url":null,"abstract":"<div><p>Southeast Asia is a biodiversity hotspot characterized by a complex paleogeography, and its Polypodiopsida flora is particularly diverse. While hybridization is recognized as common in ferns, further research is needed to investigate the relationship between hybridization events and fern diversity. <em>Lecanopteris</em> s.s., an ant-associated fern, has been subject to debate regarding species delimitations primarily due to limited DNA markers and species sampling. Our study integrates 22 newly generated plastomes, 22 transcriptomes, and flow cytometry of all native species along with two cultivated hybrids. Our objective is to elucidate the reticulate evolutionary history within <em>Lecanopteris</em> s.s. through the integration of phylobiogeographic reconstruction, gene flow inference, and genome size estimation. Key findings of our study include: (1) An enlarged plastome size (178–187 Kb) in <em>Lecanopteris</em> s.s., attributed to extreme expansion of the Inverted Repeat (IR) regions; (2) The traditional ‘pumila’ and ‘crustacea’ groups are paraphyletic; (3) Significant cytonuclear discordance attributed to gene flow; (4) Natural hybridization and introgression in the ‘pumila’ and ‘darnaedii’ groups; (5) <em>L. luzonensis</em> is the maternal parent of <em>L</em>. ‘Yellow Tip’, with <em>L. pumila</em> suggested as a possible paternal parent; (6) <em>L</em>. ‘Tatsuta’ is a hybrid between <em>L. luzonensis</em> and <em>L. crustacea</em>; (7) <em>Lecanopteris</em> s.s. first diverged during the Neogene and then during the middle Miocene climatic optimum in the Indochina and Sundaic regions. In conclusion, the biogeographic history and speciation of <em>Lecanopteris</em> have been profoundly shaped by past climate changes and geodynamics of Southeast Asia. Dispersals, hybridization and introgression between species act as pivotal factors in the evolutionary trajectory of <em>Lecanopteris</em> s.s.. This research provides a robust framework for further exploration and understanding of the complex dynamics driving the diversification and distribution patterns within Polypodiaceae subfamily Microsoroideae.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108199"},"PeriodicalIF":3.6,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142270805","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":"Shining new light on naupliar eyes: A novel molecular phylogeny for Pleuromamma (Family: Metridinidae) and the characterization of luciferase and opsin expression","authors":"Tom Iwanicki ,&nbsp;Jessica W. Chen ,&nbsp;Junya Hirai ,&nbsp;Hunter DeTurk ,&nbsp;Mireille Steck ,&nbsp;Erica Goetze ,&nbsp;Megan L. Porter","doi":"10.1016/j.ympev.2024.108200","DOIUrl":"10.1016/j.ympev.2024.108200","url":null,"abstract":"<div><div><em>Pleuromamma</em> (Giesbrecht, 1898) is a cosmopolitan genus of metridinid copepods, with species that perform remarkable diel vertical migrations (DVM) and emit a bioluminescent secretion when disturbed that varies both spectrally and kinetically. Copepod bioluminescence is autogenic and uses luciferase enzymes that catalyze a luciferin, coelenterazine, to produce light. <em>Pleuromamma</em> possess naupliar eyes, relatively simple photosensitive structures used for many visually-guided behaviors. Yet the fundamental molecular unit for vision, the opsin protein, has not been previously described for the family. The light producers and detectors are important to study because DVM is a behavior that mediates significant active elemental fluxes between the upper ocean and midwaters across vast stretches of oceanic habitat, and DVM is guided by visual behaviors, with animals tracking an isolume. Here we provide the first fully resolved molecular phylogeny for <em>Pleuromamma</em> (Family: Metridinidae) and describe the luciferase and opsin gene diversity and expression using de novo assembled transcriptomes. We successfully sequenced and assembled transcriptomes for 10 of 11 described species of <em>Pleuromamma</em> as well as two other metridinid species: <em>Metridia longa</em> and <em>Gaussia princeps</em>. In all species, we obtained coding sequences of one putative rhabdomeric middle wavelength sensitive visual opsin gene, as well as several non-visual opsins – a c-type pteropsin and a tetra-opsin type peropsin. Furthermore, <em>Pleuromamma</em> express luciferases from each of two main evolutionary clades (Luc1 and Luc2), and a single paralog (Luc2a) dominates expression throughout the group. The variation in luciferase number, sequence, and expression among species could lead to different spectral and kinetic properties of bioluminescence and aid in congener recognition.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108200"},"PeriodicalIF":3.6,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301882","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":"Phylogenomics resolves a 100-year-old debate regarding the evolutionary history of caddisflies (Insecta: Trichoptera)","authors":"Xinyu Ge ,&nbsp;Lang Peng ,&nbsp;John C. Morse ,&nbsp;Jingyuan Wang ,&nbsp;Haoming Zang ,&nbsp;Lianfang Yang ,&nbsp;Changhai Sun ,&nbsp;Beixin Wang","doi":"10.1016/j.ympev.2024.108196","DOIUrl":"10.1016/j.ympev.2024.108196","url":null,"abstract":"<div><p>Trichoptera (caddisfly) phylogeny provides an interesting example of aquatic insect evolution, with rich ecological diversification, especially for underwater architecture. Trichoptera provide numerous critical ecosystem services and are also one of the most important groups of aquatic insects for assessing water quality. The phylogenetic relationships of Trichoptera have been debated for nearly a century. In particular, the phylogenetic position of the “cocoon-makers” within Trichoptera has long been contested. Here, we designed a universal single-copy orthologue and sets of ultraconserved element markers specific for Trichoptera for the first time. Simultaneously, we reconstructed the phylogenetic relationship of Trichoptera based on genome data from 111 species, representing 29 families and 71 genera. Our phylogenetic inference clarifies the probable phylogenetic relationships of “cocoon-makers” within Integripalpia. Hydroptilidae is considered as the basal lineage within Integripalpia, and the families Glossosomatidae, Hydrobiosidae, and Rhyacophilidae formed a monophyletic clade, sister to the integripalpian subterorder Phryganides. The resulting divergence time and ancestral state reconstruction suggest that the most recent common ancestor of Trichoptera appeared in the early Permian and that diversification was strongly correlated with habitat change.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108196"},"PeriodicalIF":3.6,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142263920","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":"Phylogenomic analysis of brachyuran crabs using transcriptome data reveals possible sources of conflicting phylogenetic relationships within the group","authors":"Da Pan ,&nbsp;Yunlong Sun ,&nbsp;Boyang Shi ,&nbsp;Ruxiao Wang ,&nbsp;Peter K.L. Ng ,&nbsp;Danièle Guinot ,&nbsp;Neil Cumberlidge ,&nbsp;Hongying Sun","doi":"10.1016/j.ympev.2024.108201","DOIUrl":"10.1016/j.ympev.2024.108201","url":null,"abstract":"<div><p>Despite extensive morphological and molecular studies, the phylogenetic interrelationships within the infraorder Brachyura and the phylogenetic positions of many taxa remain uncertain. Studies that used a limited number of molecular markers have often failed to provide sufficient resolution, and may be susceptible to stochastic errors and incomplete lineage sorting (ILS). Here we reconstructed the phylogenetic relationships within the Brachyura using transcriptome data of 56 brachyuran species, including 14 newly sequenced taxa. Five supermatrices were constructed in order to exclude different sources of systematic error. The results of the phylogenetic analyses indicate that Heterotremata is non-monophyletic, and that the two Old World primary freshwater crabs (Potamidae and Gecarcinucidae) and the Hymenosomatoidea form a clade that is sister to the Thoracotremata, and outside the Heterotremata. We also found that ILS is the main cause of the gene-tree discordance of these freshwater crabs. Divergence time estimations indicate that the Brachyura has an ancient origin, probably either in the Triassic or Jurassic, and that the majority of extant families and superfamilies first appeared during the Cretaceous, with a constant increase of diversity in Post-Cretaceous-Palaeogene times. The results support the hypothesis that the two Old World freshwater crab families included in this study (Potamidae and Gecarcinucidae) diverged from their marine ancestors around 120 Ma, in the Cretaceous. In addition, this work provides new insights that may aid in the reclassification of some of the more problematic brachyuran groups.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108201"},"PeriodicalIF":3.6,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142239072","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}