Molecular Phylogenetics and Evolution最新文献

{"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}

{"title":"Population genomics of the southern giraffe","authors":"David Prochotta ,&nbsp;Sven Winter ,&nbsp;Julian Fennessy ,&nbsp;Axel Janke","doi":"10.1016/j.ympev.2024.108198","DOIUrl":"10.1016/j.ympev.2024.108198","url":null,"abstract":"<div><p>Studying wildlife taxonomic diversity and identifying distinct populations has traditionally been largely based on morphology and geographic origin. More recently, this method has been supplemented by genetic data from the mitochondrial genome. However, this is limited as only maternally inherited and may not reflect the true nature of a population’s genetics. Within the giraffe (<em>Giraffa</em> spp.), subspecies and unique populations were successfully characterized using both mitochondrial and genomic DNA studies, which led to new insights and, in some cases, unexpected results that required further verification. Here, we sequenced the genomes of 85 southern giraffe (<em>G. giraffa</em>) individuals from ten populations across southern Africa for a detailed investigation into the genetic diversity and history of its two subspecies, the Angolan (<em>G. g. angolensis</em>) and the South African (<em>G. g. giraffa</em>) giraffe. While the overall genotypes show low levels of runs of homozygosity compared to other mammals, the degree of heterozygosity is limited despite the large population size of South African giraffe. The nuclear genotype is largely congruent with the mitochondrial genotype. However, we have identified that the distribution of the Angolan giraffe is not as far east as indicated in an earlier mitochondrial DNA study. Botswana’s Central Kalahari Game Reserve giraffe are unique, with a clear admixture of Angolan and South African giraffe populations. However, the enigmatic desert-dwelling giraffe of northwest Namibia is locally distinct from other Angolan giraffe yet exhibits intra-subspecies signs of admixture resulting from a recent introduction of individuals from Namibia’s Etosha National Park. Whole genome sequencing is an invaluable and nearly indispensable tool for wildlife management to uncover genetic diversity that is undetectable through mitogenomic, geographical, and morphological means.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108198"},"PeriodicalIF":3.6,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001908/pdfft?md5=917747e305057c1149b9c1ff8191073f&pid=1-s2.0-S1055790324001908-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142270806","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":"Molecular phylogeny and species diversity of the genus Dichaetophora Duda and related taxa (Diptera: Drosophilidae)","authors":"Takehiro K. Katoh ,&nbsp;Ji-Min Chen ,&nbsp;Jin-Hua Yang ,&nbsp;Guang Zhang ,&nbsp;Lu Wang ,&nbsp;Awit Suwito ,&nbsp;Paulus Ak Meleng ,&nbsp;Masanori J. Toda ,&nbsp;Ya-Ping Zhang ,&nbsp;Jian-Jun Gao","doi":"10.1016/j.ympev.2024.108194","DOIUrl":"10.1016/j.ympev.2024.108194","url":null,"abstract":"<div><p>Our intensive surveys of wild drosophilids in East and Southeast Asia discovered a great species diversity (more than 100 putatively new species) of the genus <em>Dichaetophora</em>, which is currently comprised of 67 formally described species assigned into five species groups, i.e., <em>agbo</em>, <em>tenuicauda</em>, <em>acutissima</em>, <em>sinensis</em> and <em>trilobita</em>. In the present study, we delimited species from a huge amount of samples of <em>Dichaetophora</em> and allied taxa (the genus <em>Mulgravea</em> and the subgenus <em>Dudaica</em> of <em>Drosophila</em>) collected from a wide range of the Oriental and east Palearctic regions. We first sorted all specimens into morpho-species, and representative specimen(s) selected from each morpho-species were subjected to barcoding of <em>COI</em> (the cytochrome <em>c</em> oxidase subunit I gene) sequences. The applied ASAP (Assemble Species by Automatic Partitioning) analysis estimated a total of 166 to 168 MOTUs (molecular operational taxonomic units). Integrating this result with morphological evidence from re-examined, detailed structures of male terminalia, we recognized a total of 144 (109 new and 35 known) species in our sample. Out of them, 83 species representing the supraspecific taxa of <em>Dichaetophora</em>, <em>Mulgravea</em> and <em>Dudaica</em> were selected, along with 33 species from major genera and subgenera of <em>Drosophila</em> in the tribe Drosophilini, as in-group and four species from the tribe Colocasiomyini as out-group for phylogenetic reconstruction based on 12 nuclear gene markers. In the trees constructed by the maximum likelihood and Bayesian inference methods, the three focal taxa (i.e., <em>Dichaetophora</em>, <em>Mulgravea</em> and <em>Dudaica</em>) formed a clade provisionally called the “pan-<em>Dichaetophora</em>”. Within this large clade, the <em>agbo</em>, <em>tenuicauda</em>, <em>sinensis</em> and <em>trilobita</em> groups of <em>Dichaetophora</em>, <em>Mulgravea</em> and <em>Dudaica</em> were recovered as monophyletic groups, but <em>Dichaetophora</em> and its <em>acutissima</em> group were regarded as paraphyletic. In addition, two clusters were recognized among ungrouped species of <em>Dichaetophora</em>. Thus, the present study has uncovered some issues concerning the taxonomy of the pan-<em>Dichaetophora</em>. Such issues will be addressed elsewhere in the phylogenetic reclassification of the pan-<em>Dichaetophora</em>, along with descriptions/redescriptions of a large number of new/known species delimited in the present study.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108194"},"PeriodicalIF":3.6,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142239073","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":"Reticulate evolution: Detection and utility in the phylogenomics era","authors":"Saelin Bjornson ,&nbsp;Heroen Verbruggen ,&nbsp;Nathan S. Upham ,&nbsp;Jacob L. Steenwyk","doi":"10.1016/j.ympev.2024.108197","DOIUrl":"10.1016/j.ympev.2024.108197","url":null,"abstract":"<div><p>Phylogenomics has enriched our understanding that the Tree of Life can have network-like or reticulate structures among some taxa and genes. Two non-vertical modes of evolution – hybridization/introgression and horizontal gene transfer – deviate from a strictly bifurcating tree model, causing non-treelike patterns. However, these reticulate processes can produce similar patterns to incomplete lineage sorting or recombination, potentially leading to ambiguity. Here, we present a brief overview of a phylogenomic workflow for inferring organismal histories and compare methods for distinguishing modes of reticulate evolution. We discuss how the timing of coalescent events can help disentangle introgression from incomplete lineage sorting and how horizontal gene transfer events can help determine the relative timing of speciation events. In doing so, we identify pitfalls of certain methods and discuss how to extend their utility across the Tree of Life. Workflows, methods, and future directions discussed herein underscore the need to embrace reticulate evolutionary patterns for understanding the timing and rates of evolutionary events, providing a clearer view of life’s history.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108197"},"PeriodicalIF":3.6,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001891/pdfft?md5=2bec56b2fab35b10bc8cc62f1367f71c&pid=1-s2.0-S1055790324001891-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142228977","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":"A land plant phylogenetic framework for GLABROUS INFLORESCENCE STEMS (GIS), SUPERMAN, JAGGED and allies plus their TOPLESS co-repressor","authors":"Clemens Roessner ,&nbsp;Sven Griep ,&nbsp;Annette Becker","doi":"10.1016/j.ympev.2024.108195","DOIUrl":"10.1016/j.ympev.2024.108195","url":null,"abstract":"<div><p>Members of the plant specific family of C1-1i zinc<!--> <!-->finger transcription<!--> <!-->factors (ZF-TFs), such as SUPERMAN, JAGGED, KNUCKLES or GIS,<!--> <!-->regulate<!--> <!-->diverse<!--> <!-->developmental processes including sexual reproduction. C1-1is consist of one zinc-finger and one to two EAR domains, connected by large intrinsically disordered regions (IDR). While the role of C1-i1 ZF-TFs in development processes is well known for some genes in Arabidopsis, rice or tomato<!--> <!-->a comprehensive and broad<!--> <!-->phylogenetic background is lacking, yet knowledge of orthology is a requirement for a better understanding of C1-1i-Zf-TFs diverse roles in plants. Here, we provide a fine-grained and land plant wide classification of C1-1i sub-families and their known co-repressors TOPLESS and TOPLESS RELATED. Our work combines the identification of orthologous groups with Maximum-Likelihood phylogeny reconstructions and digital gene expression analyses mining high quality land plant genomes and transcriptomes to generate a comprehensive framework of C1-1i ZF-TF evolution. We show that C1-1i’s are low to moderate copy genes<!--> <!-->and that orthologous genes<!--> <!-->only partially<!--> <!-->have<!--> <!-->conserved sub-family and life cycle stage dependent expression pattern across land plants while others are highly diverged. Our work<!--> <!-->provides the phylogenetic framework for C1-1i ZF-TFs, s and strengthen C1-1 ZF-TFs as a potential model for IDR-research in plants.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108195"},"PeriodicalIF":3.6,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001878/pdfft?md5=6cc9b54fef4912cae6d55d5a777d4ce3&pid=1-s2.0-S1055790324001878-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142183391","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":"Evolution of chitin-synthase in molluscs and their response to ocean acidification","authors":"Maoxiao Peng ,&nbsp;João C.R. Cardoso ,&nbsp;Deborah M. Power","doi":"10.1016/j.ympev.2024.108192","DOIUrl":"10.1016/j.ympev.2024.108192","url":null,"abstract":"<div><p>Chitin-synthase (CHS) is found in most eukaryotes and has a complex evolutionary history. Research into CHS has mainly been in the context of biomineralization of mollusc shells an area of high interest due to the consequences of ocean acidification. Exploration of <em>CHS</em> at the genomic level in molluscs, the evolution of isoforms, their tissue distribution, and response to environmental challenges are largely unknown. Exploiting the extensive molecular resources for mollusc species it is revealed that bivalves possess the largest number of <em>CHS</em> genes (12–22) reported to date in eukaryotes. The evolutionary tree constructed at the class level of molluscs indicates four <em>CHS</em> Type II isoforms (A-D) probably existed in the most recent common ancestor, and Type II-A (Type II-A-1/Type II-A-2) and Type II-C (Type II-C-1/Type II-C-2) underwent further differentiation. Non-specific loss of <em>CHS</em> isoforms occurred at the class level, and in some Type II (B-D groups) isoforms the myosin head domain, which is associated with shell formation, was not preserved and highly species-specific tissue expression of <em>CHS</em> isoforms occurred. These observations strongly support the idea of CHS functional diversification with shell biomineralization being one of several important functions. Analysis of transcriptome data uncovered the species-specific potential of <em>CHS</em> isoforms in shell formation and a species-specific response to ocean acidification (OA). The impact of OA was not <em>CHS</em> isoform-dependent although in <em>Mytilus</em>, Type I-B and Type II-D gene expression was down-regulated in both <em>M. galloprovincialis</em> and <em>M. coruscus</em>. In summary, during <em>CHS</em> evolution the gene family expanded in bivalves generating a large diversity of isoforms with different structures and with a ubiquitous tissue distribution suggesting that chitin is involved in many biological functions. These findings provide insight into <em>CHS</em> evolution in molluscs and lay the foundation for research into their function and response to environmental changes.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108192"},"PeriodicalIF":3.6,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001842/pdfft?md5=07fdc475a8de4990d8d6b1f4b16b4b70&pid=1-s2.0-S1055790324001842-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142173208","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":"Between sea angels and butterflies: A global phylogeny of pelagic pteropod molluscs","authors":"Jose Vidal-Miralles ,&nbsp;Peter Kohnert ,&nbsp;Marina Monte ,&nbsp;Xavier Salvador ,&nbsp;Michael Schrödl ,&nbsp;Juan Moles","doi":"10.1016/j.ympev.2024.108183","DOIUrl":"10.1016/j.ympev.2024.108183","url":null,"abstract":"<div><div>Pteropods, holoplanktonic gastropods, play pivotal roles in marine ecosystems as integral components of food webs and carbon cycling. With global change threatening pelagic ecosystem equilibrium, conserving pteropod biodiversity is paramount. Here, we present the most extensive phylogenetic study of the order Pteropoda to date, utilizing a complete mitogenome phylogeny to support the suppression of Thecosomata, thus demonstrating the lack of relationship between Pseudothecosomata and Euthecosomata. Through multilocus Sanger-based taxon sampling with 411 specimens (92 newly sequenced), representing nearly 100 species (out of 163 valid) from various oceans, we elucidate robust support for higher taxonomic rankings. Despite strong support, relationships between the major groups Gymnosomata, Pseudothecosomata, and Euthecosomata remain contentious. Our study addresses unresolved taxonomic questions, identifying cryptic species complexes across vast biogeographic areas, and offering unprecedented insights into pteropod diversity. We shed light on several open questions in pteropod systematics, proposing the reclassification of <em>L. antarctica</em> stat. rest. and elucidating the position of <em>Thliptodon</em>, Heliconoididae, and Thieleidae. This systematic review enhances our understanding of pteropod diversity and underscores the urgency of conservation efforts in the face of changing oceanic conditions.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108183"},"PeriodicalIF":3.6,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142141831","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}