BMC ecology and evolution最新文献

{"title":"Environmental specificity of karst cave habitats evidenced by diverse symbiotic bacteria in Opiliones.","authors":"Likun Zhao, Ruoyi Xiao, Shanfeng Zhang, Chao Zhang, Feng Zhang","doi":"10.1186/s12862-024-02248-9","DOIUrl":"10.1186/s12862-024-02248-9","url":null,"abstract":"<p><strong>Background: </strong>Karst caves serve as natural laboratories, providing organisms with extreme and constant conditions that promote isolation, resulting in a genetic relationship and living environment that is significantly different from those outside the cave. However, research on cave creatures, especially Opiliones, remains scarce, with most studies focused on water, soil, and cave sediments.</p><p><strong>Results: </strong>The structure of symbiotic bacteria in different caves were compared, revealing significant differences. Based on the alpha and beta diversity, symbiotic bacteria abundance and diversity in the cave were similar, but the structure of symbiotic bacteria differed inside and outside the cave. Microorganisms in the cave play an important role in material cycling and energy flow, particularly in the nitrogen cycle. Although microbial diversity varies inside and outside the cave, Opiliones in Beijing caves and Hainan Island exhibited a strong similarity, indicating that the two environments share commonalities.</p><p><strong>Conclusions: </strong>The karst cave environment possesses high microbial diversity and there are noticeable differences among different caves. Different habitats lead to significant differences in the symbiotic bacteria in Opiliones inside and outside the cave, and cave microorganisms have made efforts to adapt to extreme environments. The similarity in symbiotic bacteria community structure suggests a potential similarity in host environments, providing an explanation for the appearance of Sinonychia martensi in caves in the north.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":"24 1","pages":"58"},"PeriodicalIF":0.0,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11080181/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140892906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of Neowestiellopsis persica A1387 (Hapalosiphonaceae) based on the cpcA, psbA, rpoC1, nifH and nifD gene sequences.","authors":"Bahareh Nowruzi, Lenka Hutarova, Dominika Vešelenyiova, James S Metcalf","doi":"10.1186/s12862-024-02244-z","DOIUrl":"10.1186/s12862-024-02244-z","url":null,"abstract":"<p><strong>Background: </strong>Complex descriptions of new strains of cyanobacteria appear very frequently. The main importance of these descriptions concerns potential new substances that they could synthesise, as well as their different properties as a result of their different ecological niches. The main gene used for these descriptions is 16 S with ITS or whole genome sequencing. Neowestiellopsis persica represents a unique example of the influence of ecology on morphological changes, with almost identical 16 S identity. Although our previously described Neowestiellopsis persica strain A1387 was characterized by 16 S analysis, we used different molecular markers to provide a way to separate strains of this genus that are closely related at the genetic level.</p><p><strong>Materials and methods: </strong>In order to conduct an in-depth study, several molecular markers, namely psbA, rpoC1, nifD, nifH and cpcA were sequenced and studied in Neowestiellopsis persica strain A1387.</p><p><strong>Results: </strong>The results of the phylogenetic analysis, based on cpcA, showed that the studied strain A 1387 falls into a separate clade than N. persica, indicating that this signature sequence could be a useful molecular marker for phylogenetic separation of similar strains isolated in the future.</p><p><strong>Conclusions: </strong>Analysis of strain A1387 based on gene differences confirmed that it is a Neowestiellopsis strain. The morphological changes observed in the previous study could be due to different ecological and cultivation conditions compared to the type species. At the same time, the sequences obtained have increased our understanding of this species and will help in the future to better identify strains belonging to the genus Neowestiellopsis.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":"24 1","pages":"57"},"PeriodicalIF":0.0,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11075313/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140872481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The nature and distribution of putative non-functional alleles suggest only two independent events at the origins of Astyanax mexicanus cavefish populations.","authors":"Maxime Policarpo, Laurent Legendre, Isabelle Germon, Philippe Lafargeas, Luis Espinasa, Sylvie Rétaux, Didier Casane","doi":"10.1186/s12862-024-02226-1","DOIUrl":"10.1186/s12862-024-02226-1","url":null,"abstract":"<p><strong>Background: </strong>Several studies suggested that cavefish populations of Astyanax mexicanus settled during the Late Pleistocene. This implies that the cavefish's most conspicuous phenotypic changes, blindness and depigmentation, and more cryptic characters important for cave life, evolved rapidly.</p><p><strong>Results: </strong>Using the published genomes of 47 Astyanax cavefish from la Cueva de El Pachón, El Sótano de la Tinaja, La Cueva Chica and El Sótano de Molino, we searched for putative loss-of-function mutations in previously defined sets of genes, i.e., vision, circadian clock and pigmentation genes. Putative non-functional alleles for four vision genes were identified. Then, we searched genome-wide for putative non-functional alleles in these four cave populations. Among 512 genes with segregating putative non-functional alleles in cavefish that are absent in surface fish, we found an enrichment in visual perception genes. Among cavefish populations, different levels of shared putative non-functional alleles were found. Using a subset of 12 genes for which putative loss-of-function mutations were found, we extend the analysis of shared pseudogenes to 11 cave populations. Using a subset of six genes for which putative loss-of-function mutations were found in the El Sótano del Toro population, where extensive hybridization with surface fish occurs, we found a correlation between the level of eye regression and the amount of putative non-functional alleles.</p><p><strong>Conclusions: </strong>We confirm that very few putative non-functional alleles are present in a large set of vision genes, in accordance with the recent origin of Astyanax mexicanus cavefish. Furthermore, the genome-wide analysis indicates an enrichment of putative loss-of-function alleles in genes with vision-related GO-terms, suggesting that visual perception may be the function chiefly impacted by gene losses related to the shift from a surface to a cave environment. The geographic distribution of putative loss-of-function alleles newly suggests that cave populations from Sierra de Guatemala and Sierra de El Abra share a common origin, albeit followed by independent evolution for a long period. It also supports that populations from the Micos area have an independent origin. In El Sótano del Toro, the troglomorphic phenotype is maintained despite massive introgression of the surface genome.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":"24 1","pages":"41"},"PeriodicalIF":0.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10983663/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140332289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Species and structural diversity of trees at the structural type level.","authors":"Yuanfa Li, Liting Wei","doi":"10.1186/s12862-024-02229-y","DOIUrl":"10.1186/s12862-024-02229-y","url":null,"abstract":"<p><strong>Background: </strong>Species and structural diversity are important for understanding the formation of forest communities, key ecological processes, and improving forest ecological functions and services, but their spatial characteristics have received little attention. Based on the spatial relationships among neighbouring trees, we proposed to divide trees within a structural unit into 15 structural types, and used the univariate distributions of the uniform angle index (W), mingling (M), and dominance (U), along with four common species diversity indices, to analyse the diversity of structural types in natural forests near the Tropic of Cancer.</p><p><strong>Results: </strong>Only a portion of clumped class maintained aggregation, most exhibited a random pattern. Species mixture increased exponentially across distribution classes, and abundance and richness exhibited an initial increase followed by a slight decrease. The distribution patterns of mixture classes varied from highly clustered to random, and M distributions gradually shifted from an inverted J-shaped curve to a J-shaped curve. Abundance and richness exhibited an exponential distribution, whereas the Shannon-Wiener index increased linearly. The W distribution of differentiation classes approximated a normal distribution, whereas M distributions exhibited a J shape. The U distribution of each structure type was approximately 0.2.</p><p><strong>Conclusions: </strong>These results reveal the species and structural diversity characteristics of trees at the structural type level and expand our knowledge of forest biodiversity. The new method proposed here should significantly contribute to biodiversity monitoring efforts in terrestrial ecosystems, and suggests that higher standards for the simulation and reconstruction of stand structure, as well as thinning in near-natural forests, is warranted.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":"24 1","pages":"40"},"PeriodicalIF":0.0,"publicationDate":"2024-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10976781/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140320063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"eDNA metabarcoding reveals biodiversity and depth stratification patterns of dinoflagellate assemblages within the epipelagic zone of the western Coral Sea.","authors":"Megan Carve, Tahnee Manning, Aidyn Mouradov, Jeff Shimeta","doi":"10.1186/s12862-024-02220-7","DOIUrl":"10.1186/s12862-024-02220-7","url":null,"abstract":"<p><strong>Background: </strong>Dinoflagellates play critical roles in the functioning of marine ecosystems but also may pose a hazard to human and ecosystem health by causing harmful algal blooms (HABs). The Coral Sea is a biodiversity hotspot, but its dinoflagellate assemblages in pelagic waters have not been studied by modern sequencing methods. We used metabarcoding of the 18 S rRNA V4 amplicon to assess the diversity and structure of dinoflagellate assemblages throughout the water column to a depth of 150 m at three stations in the Western Coral Sea. Additionally, at one station we compared metabarcoding with morphological methods to optimise identification and detection of dinoflagellates.</p><p><strong>Results: </strong>Stratification of dinoflagellate assemblages was evident in depth-specific relative abundances of taxonomic groups; the greatest difference was between the 5-30 m assemblages and the 130-150 m assemblages. The relative abundance of Dinophyceae (photosynthetic and heterotrophic) decreased with increasing depth, whereas that of Syndiniales (parasitic) increased with increasing depth. The composition of major taxonomic groups was similar among stations. Taxonomic richness and diversity of amplicon sequence variants (ASVs) were similar among depths and stations; however, the abundance of dominant taxa was highest within 0-30 m, and the abundance of rare taxa was highest within 130-150 m, indicating adaptations to specific depth strata. The number of unclassified ASVs at the family and species levels was very high, particularly for Syndinian representatives.</p><p><strong>Conclusions: </strong>Dinoflagellate assemblages in open water of the Coral Sea are highly diverse and taxonomically stratified by depth; patterns of relative abundance along the depth gradient reflect environmental factors and ecological processes. Metabarcoding detects more species richness than does traditional microscopical methods of sample analysis, yet the methods are complementary, with morphological analysis revealing additional richness. The large number of unclassified dinoflagellate-ASVs indicates a need for improved taxonomic reference databases and suggests presence of dinoflagellate-crypto and-morphospecies.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":"24 1","pages":"38"},"PeriodicalIF":0.0,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10964515/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140289942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fitness difference between two synonymous mutations of Phytophthora infestans ATP6 gene.","authors":"Oswald Nkurikiyimfura, Abdul Waheed, Hanmei Fang, Xiaoxian Yuan, Lixia Chen, Yan-Ping Wang, Guodong Lu, Jiasui Zhan, Lina Yang","doi":"10.1186/s12862-024-02223-4","DOIUrl":"10.1186/s12862-024-02223-4","url":null,"abstract":"<p><strong>Background: </strong>Sequence variation produced by mutation provides the ultimate source of natural selection for species adaptation. Unlike nonsynonymous mutation, synonymous mutations are generally considered to be selectively neutral but accumulating evidence suggests they also contribute to species adaptation by regulating the flow of genetic information and the development of functional traits. In this study, we analysed sequence characteristics of ATP6, a housekeeping gene from 139 Phytophthora infestans isolates, and compared the fitness components including metabolic rate, temperature sensitivity, aggressiveness, and fungicide tolerance among synonymous mutations.</p><p><strong>Results: </strong>We found that the housekeeping gene exhibited low genetic variation and was represented by two major synonymous mutants at similar frequency (0.496 and 0.468, respectively). The two synonymous mutants were generated by a single nucleotide substitution but differed significantly in fitness as well as temperature-mediated spatial distribution and expression. The synonymous mutant ending in AT was more common in cold regions and was more expressed at lower experimental temperature than the synonymous mutant ending in GC and vice versa.</p><p><strong>Conclusion: </strong>Our results are consistent with the argument that synonymous mutations can modulate the adaptive evolution of species including pathogens and have important implications for sustainable disease management, especially under climate change.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":"24 1","pages":"36"},"PeriodicalIF":0.0,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10946160/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140144769","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A large new Middle Jurassic ichthyosaur shows the importance of body size evolution in the origin of the Ophthalmosauria.","authors":"Feiko Miedema, Dylan Bastiaans, Torsten M Scheyer, Christian Klug, Erin E Maxwell","doi":"10.1186/s12862-024-02208-3","DOIUrl":"10.1186/s12862-024-02208-3","url":null,"abstract":"<p><p>The Middle Jurassic is an important time period for the evolutionary history of marine reptiles as it represented a transitional phase for many clades. Notably, in ichthyosaurs, many early parvipelvian taxa went extinct. The Middle Jurassic saw the emergence of the derived Ophthalmosauria, ultimately becoming the dominant ichthyosaurian clade by the end of the epoch. Even though this is an important period in the evolutionary history of Ophthalmosauria, our understanding remains limited in terms of morphology and taxonomy due to the scarcity of vertebrate-bearing strata. Here we present a large new ichthyosaur from the Bajocian of Switzerland, represented by an almost complete skull with 3D-preserved bones, the (inter)clavicles and a large portion of the postcranial skeleton. After CT- and surface scanning, we reconstructed the 3D in vivo morphology. Our morphological observations and phylogenetic analyses show that the new taxon named Argovisaurus martafernandezi is nested at the base of the Ophthalmosauria. The holotype and only known specimen of Argovisaurus likely represents an adult individual. Bajocian members of the Ophthalmosauria (Mollesaurus and Argovisaurus) were large-bodied animals, a trait typically associated with the more derived Platypterygiinae. This hints at the importance of a large body size early in ophthalmosaurian evolution.LSID: urn:lsid:zoobank.org:act:C3312628-1544-4B87-BBE3-B12346A30BE3LSID: urn:lsid:zoobank.org:act:23C2BD71-8CF0-4D99-848A-0D631518415B.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":"24 1","pages":"34"},"PeriodicalIF":0.0,"publicationDate":"2024-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10944604/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140141236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new sphenodontian (Diapsida: Lepidosauria) from the Upper Triassic (Norian) of Germany and its implications for the mode of sphenodontian evolution.","authors":"Lisa S Freisem, Johannes Müller, Hans-Dieter Sues, Gabriela Sobral","doi":"10.1186/s12862-024-02218-1","DOIUrl":"10.1186/s12862-024-02218-1","url":null,"abstract":"<p><p>The Arnstadt Formation of Saxony-Anhalt, Germany has yielded some of Germany's most substantial finds of Late Triassic tetrapods, including the sauropodomorph Plateosaurus and the stem-turtle Proganochelys quenstedti. Here, we describe an almost complete skull of a new sphenodontian taxon from this formation (Norian, 227-208 Ma), making it the oldest known articulated sphenodontian skull from Europe and one of the oldest in the world. The material is represented by the dermal skull roof and by the complete maxilla and temporal region, as well as parts of the palate, braincase, and lower jaw. A phylogenetic assessment recovers it as a basal sphenodontian closely related to Planocephalosaurus robinsonae and to Eusphenodontia, making it the earliest-diverging sphenodontian known with an articulated skull. Its cranial anatomy is generally similar to the well-known Diphydontosaurus avonis from the Rhaetian of England, showing that this successful phenotype was already established in the clade around 10 myr earlier than assumed. An analysis of evolutionary change rates recovers high rates of evolution in basal sphenodontians, with decreasing rates throughout the evolution of the group. However, contrary to previous studies, reversals in this trend were identified, indicating additional peaks of evolutionary change. These results improve our understanding of the early sphenodontian diversity in Europe, providing critical information on evolutionary trends throughout the history of the clade and sparking renewed interest in its evolution.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":"24 1","pages":"35"},"PeriodicalIF":0.0,"publicationDate":"2024-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10944618/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140141237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: A juvenile bird with possible crown-group affinities from a dinosaur-rich Cretaceous ecosystem in North America.","authors":"Chase Doran Brownstein","doi":"10.1186/s12862-024-02216-3","DOIUrl":"10.1186/s12862-024-02216-3","url":null,"abstract":"","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":"24 1","pages":"32"},"PeriodicalIF":0.0,"publicationDate":"2024-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10938709/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140121796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Intra-population variability of the saccular, utricular and lagenar otoliths of the garfish Belone belone (Linnaeus, 1760) from South-Western Ionian Sea (Central Mediterranean Sea).","authors":"Claudio D'Iglio, Marco Albano, Sergio Famulari, Alex Carnevale, Serena Savoca, Nunziacarla Spanò, Gioele Capillo","doi":"10.1186/s12862-024-02219-0","DOIUrl":"10.1186/s12862-024-02219-0","url":null,"abstract":"<p><p>The garfish Belone belone represents the only valid endemic Belone species for the Mediterranean Sea and the eastern Atlantic Ocean. It shows a wide global distribution range, with a high commercial value and ecological relevance in the pelagic domain. Despite this, there needs to be more knowledge regarding the otoliths of this species, with the total absence of descriptions regarding asterisci and lapilli from Mediterranean populations and a lack of studies on the reliability of shape analysis on its sagittae. The present paper aims to provide the first main contours description of the three otoliths pairs from a Mediterranean population, providing an accurate investigation of morphology, morphometry, and intra-specific variability of sagittae, lapilli, and asterisci. Results showed (i) the absence of directional bilateral asymmetry and sexual asymmetry for the three otoliths pairs, (ii) a different morphology and morphometry of sagittae, lapilli and asterisci than those described in the literature, and (iii) an enhanced variability between sagittae morphometry and shape between the three investigated size classes. All these data confirmed the reliability of the studied species of shape analysis, showing a geographical and size-related variability of otoliths features probably related to genetics, environmental conditions, and life habits variations.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":"24 1","pages":"31"},"PeriodicalIF":0.0,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10926657/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140095329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}