BMC Ecology and Evolution最新文献

{"title":"Genomics of hybrid parallel origin in Aquilegia ecalcarata","authors":"Fang‐Dong Geng, Miao‐Qing Liu, Xue‐Dong Zhang, Lu-Zhen Wang, Meng‐Fan Lei","doi":"10.1186/s12862-024-02266-7","DOIUrl":"https://doi.org/10.1186/s12862-024-02266-7","url":null,"abstract":"","PeriodicalId":9127,"journal":{"name":"BMC Ecology and Evolution","volume":"16 4","pages":"1-16"},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141265283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Peripatric speciation within Torreya fargesii (Taxaceae) in the Hengduan Mountains inferred from multi-loci phylogeography","authors":"Yixuan Kou, Dengmei Fan, Shanmei Cheng, Yi Yang, Meixia Wang, Yujin Wang, Zhiyong Zhang","doi":"10.1186/s12862-023-02183-1","DOIUrl":"https://doi.org/10.1186/s12862-023-02183-1","url":null,"abstract":"","PeriodicalId":9127,"journal":{"name":"BMC Ecology and Evolution","volume":"10 3‐5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138624145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines","authors":"Mustafa Raza, Edgardo M. Ortiz, Lea Schwung, Gentaro Shigita, Hanno Schaefer","doi":"10.1186/s12862-023-02185-z","DOIUrl":"https://doi.org/10.1186/s12862-023-02185-z","url":null,"abstract":"","PeriodicalId":9127,"journal":{"name":"BMC Ecology and Evolution","volume":"115 51","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138609408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ecosystem restoration, regeneration and rewilding.","authors":"Nancy Shackelford, Carmel McDougall","doi":"10.1186/s12862-023-02165-3","DOIUrl":"10.1186/s12862-023-02165-3","url":null,"abstract":"<p><p>Anthropomorphic activities have caused major damage to ecosystems worldwide. Although documenting this damage is important, implementing measures to halt and reverse ecosystem decline is critical and is now being prioritised globally. To support global goals to protect and restore nature, BMC Ecology and Evolution has launched a new article collection to encourage contributions from the multifaceted ecosystem restoration community.</p>","PeriodicalId":9127,"journal":{"name":"BMC Ecology and Evolution","volume":"23 1","pages":"52"},"PeriodicalIF":0.0,"publicationDate":"2023-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10500817/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10308153","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":"Native amphibian toxin reduces invasive crayfish feeding with potential benefits to stream biodiversity.","authors":"Gary M Bucciarelli, Sierra J Smith, Justin J Choe, Phoebe D Shin, Robert N Fisher, Lee B Kats","doi":"10.1186/s12862-023-02162-6","DOIUrl":"10.1186/s12862-023-02162-6","url":null,"abstract":"<p><strong>Background: </strong>Biodiversity is generally reduced when non-native species invade an ecosystem. Invasive crayfish, Procambarus clarkii, populate California freshwater streams, and in the Santa Monica Mountains (Los Angeles, USA), their introduction has led to trophic cascades due to omnivorous feeding behavior and a rapid rate of population growth. The native California newt, Taricha torosa, possesses a neurotoxin, tetrodotoxin (TTX), that affects freshwater animal behavior. Given P. clarkii has a limited evolutionary history with TTX, we hypothesized that TTX may affect crayfish feeding behaviors. To determine if TTX affects P. clarkii behavior, we measured cumulative movement and various feeding behaviors of P. clarkii exposed to (i) waterborne, ecologically realistic concentrations of TTX (~ 3.0 × 10^- 8 moles/L), (ii) an anuran chemical cue to account for intraguild cues, or (iii) a T. torosa chemical cue with quantitated TTX in it (~ 6.2 × 10^- 8 moles/L).</p><p><strong>Results: </strong>We found that the presence of TTX in any form significantly reduced crayfish movement and decreased the amount of food consumed over time. Crayfish responses to the anuran treatment did not significantly differ from controls.</p><p><strong>Conclusion: </strong>Our laboratory results show that naturally occurring neurotoxin from native California newts limits invasive crayfish foraging and feeding rates, which may play a role in preserving local stream ecosystems by limiting invasive crayfish behaviors that are detrimental to biodiversity.</p>","PeriodicalId":9127,"journal":{"name":"BMC Ecology and Evolution","volume":"23 1","pages":"51"},"PeriodicalIF":0.0,"publicationDate":"2023-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10498594/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10309045","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":"Detecting natural selection in trait-trait coevolution.","authors":"Daohan Jiang, Jianzhi Zhang","doi":"10.1186/s12862-023-02164-4","DOIUrl":"10.1186/s12862-023-02164-4","url":null,"abstract":"<p><p>No phenotypic trait evolves independently of all other traits, but the cause of trait-trait coevolution is poorly understood. While the coevolution could arise simply from pleiotropic mutations that simultaneously affect the traits concerned, it could also result from multivariate natural selection favoring certain trait relationships. To gain a general mechanistic understanding of trait-trait coevolution, we examine the evolution of 220 cell morphology traits across 16 natural strains of the yeast Saccharomyces cerevisiae and the evolution of 24 wing morphology traits across 110 fly species of the family Drosophilidae, along with the variations of these traits among gene deletion or mutation accumulation lines (a.k.a. mutants). For numerous trait pairs, the phenotypic correlation among evolutionary lineages differs significantly from that among mutants. Specifically, we find hundreds of cases where the evolutionary correlation between traits is strengthened or reversed relative to the mutational correlation, which, according to our population genetic simulation, is likely caused by multivariate selection. Furthermore, we detect selection for enhanced modularity of the yeast traits analyzed. Together, these results demonstrate that trait-trait coevolution is shaped by natural selection and suggest that the pleiotropic structure of mutation is not optimal. Because the morphological traits analyzed here are chosen largely because of their measurability and thereby are not expected to be biased with regard to natural selection, our conclusion is likely general.</p>","PeriodicalId":9127,"journal":{"name":"BMC Ecology and Evolution","volume":"23 1","pages":"50"},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10496359/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10309044","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":"Purifying selection leads to low protein diversity of the mitochondrial cyt b gene in avian malaria parasites.","authors":"Xinyi Wang, Staffan Bensch, Xi Huang, Lu Dong","doi":"10.1186/s12862-023-02155-5","DOIUrl":"10.1186/s12862-023-02155-5","url":null,"abstract":"<p><strong>Background: </strong>Mitochondrial respiration plays a central role in the survival of many eukaryotes, including apicomplexan parasites. A 479-bp fragment from the mitochondrial cytochrome b gene is widely used as a barcode to identify genetic lineages of avian malaria parasites Plasmodium and related haemosporidians. Here we looked for evidence of selection in the avian Plasmodium cyt b gene, using tests of selection and protein structure modeling. We also tested for the association between cyt b polymorphism and the host specificity of these parasites.</p><p><strong>Results: </strong>Based on 1,089 lineages retrieved from the Malavi database, we found that the frequency of the most conserved amino acids in most sites was more than 90%, indicating that the protein diversity of the avian Plasmodium cyt b barcode was low. The exceptions were four amino acid sites that were highly polymorphic, though the substitutions had only slight functional impacts on the encoded proteins. The selection analyses revealed that avian Plasmodium cyt b was under strong purifying selection, and no positively selected sites were detected. Besides, lineages with a wide host range tend to share cyt b protein haplotypes.</p><p><strong>Conclusions: </strong>Our research indicates that purifying selection is the dominant force in the evolution of the avian Plasmodium cyt b lineages and leads to its low diversity at the protein level. Host specificity may also play a role in shaping the low mitochondrial diversity in the evolution of avian malaria parasites. Our results highlight the importance of considering selection pressure on the cyt b barcode region and lay a foundation for further understanding the evolutionary pattern of mitochondrial genes in avian malaria.</p>","PeriodicalId":9127,"journal":{"name":"BMC Ecology and Evolution","volume":"23 1","pages":"49"},"PeriodicalIF":0.0,"publicationDate":"2023-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10494422/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10358277","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":"Ecological correlates of cranial evolution in the megaradiation of dipsadine snakes.","authors":"Gregory G Pandelis, Michael C Grundler, Daniel L Rabosky","doi":"10.1186/s12862-023-02157-3","DOIUrl":"10.1186/s12862-023-02157-3","url":null,"abstract":"<p><strong>Background: </strong>Dipsadine snakes represent one of the most spectacular vertebrate radiations that have occurred in any continental setting, with over 800 species in South and Central America. Their species richness is paralleled by stunning ecological diversity, ranging from arboreal snail-eating and aquatic eel-eating specialists to terrestrial generalists. Despite the ecological importance of this clade, little is known about the extent to which ecological specialization shapes broader patterns of phenotypic diversity within the group. Here, we test how habitat use and diet have influenced morphological diversification in skull shape across 160 dipsadine species using micro-CT and 3-D geometric morphometrics, and we use a phylogenetic comparative approach to test the contributions of habitat use and diet composition to variation in skull shape among species.</p><p><strong>Results: </strong>We demonstrate that while both habitat use and diet are significant predictors of shape in many regions of the skull, habitat use significantly predicts shape in a greater number of skull regions when compared to diet. We also find that across ecological groupings, fossorial and aquatic behaviors result in the strongest deviations in morphospace for several skull regions. We use simulations to address the robustness of our results and describe statistical anomalies that can arise from the application of phylogenetic generalized least squares to complex shape data.</p><p><strong>Conclusions: </strong>Both habitat and dietary ecology are significantly correlated with skull shape in dipsadines; the strongest relationships involved skull shape in snakes with aquatic and fossorial lifestyles. This association between skull morphology and multiple ecological axes is consistent with a classic model of adaptive radiation and suggests that ecological factors were an important component in driving morphological diversification in the dipsadine megaradiation.</p>","PeriodicalId":9127,"journal":{"name":"BMC Ecology and Evolution","volume":"23 1","pages":"48"},"PeriodicalIF":0.0,"publicationDate":"2023-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10485986/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10308594","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":"Common lizard microhabitat selection varies by sex, parity mode, and colouration.","authors":"Hans Recknagel, William T Harvey, Megan Layton, Kathryn R Elmer","doi":"10.1186/s12862-023-02158-2","DOIUrl":"10.1186/s12862-023-02158-2","url":null,"abstract":"<p><strong>Background: </strong>Animals select and interact with their environment in various ways, including to ensure their physiology is at its optimal capacity, access to prey is possible, and predators can be avoided. Often conflicting, the balance of choices made may vary depending on an individual's life-history and condition. The common lizard (Zootoca vivipara) has egg-laying and live-bearing lineages and displays a variety of dorsal patterns and colouration. How colouration and reproductive mode affect habitat selection decisions on the landscape is not known. In this study, we first tested if co-occurring male and female viviparous and oviparous common lizards differ in their microhabitat selection. Second, we tested if the dorsal colouration of an individual lizard matched its basking site choice within the microhabitat where it was encountered, which could be related to camouflage and crypsis.</p><p><strong>Results: </strong>We found that site use differed from the habitat otherwise available, suggesting lizards actively choose the composition and structure of their microhabitat. Females were found in areas with more wood and less bare ground compared to males; we speculate that this may be for better camouflage and reducing predation risk during pregnancy, when females are less mobile. Microhabitat use also differed by parity mode: viviparous lizards were found in areas with more density of flowering plants, while oviparous lizards were found in areas that were wetter and had more moss. This may relate to differing habitat preferences of viviparous vs. oviparous for clutch lay sites. We found that an individual's dorsal colouration matched that of the substrate of its basking site. This could indicate that individuals may choose their basking site to optimise camouflage within microhabitat. Further, all individuals were found basking in areas close to cover, which we expect could be used to escape predation.</p><p><strong>Conclusions: </strong>Our study suggests that common lizards may actively choose their microhabitat and basking site, balancing physiological requirements, escape response and camouflage as a tactic for predator avoidance. This varies for parity modes, sexes, and dorsal colourations, suggesting that individual optimisation strategies are influenced by inter-individual variation within populations as well as determined by evolutionary differences associated with life history.</p>","PeriodicalId":9127,"journal":{"name":"BMC Ecology and Evolution","volume":"23 1","pages":"47"},"PeriodicalIF":0.0,"publicationDate":"2023-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10478496/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10304597","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":"Holistic view of the seascape dynamics and environment impact on macro-scale genetic connectivity of marine plankton populations.","authors":"Romuald Laso-Jadart, Michael O'Malley, Adam M Sykulski, Christophe Ambroise, Mohammed-Amin Madoui","doi":"10.1186/s12862-023-02160-8","DOIUrl":"10.1186/s12862-023-02160-8","url":null,"abstract":"<p><strong>Background: </strong>Plankton seascape genomics studies have revealed different trends from large-scale weak differentiation to microscale structures. Previous studies have underlined the influence of the environment and seascape on species differentiation and adaptation. However, these studies have generally focused on a few single species, sparse molecular markers, or local scales. Here, we investigated the genomic differentiation of plankton at the macro-scale in a holistic approach using Tara Oceans metagenomic data together with a reference-free computational method.</p><p><strong>Results: </strong>We reconstructed the F_ST-based genomic differentiation of 113 marine planktonic taxa occurring in the North and South Atlantic Oceans, Southern Ocean, and Mediterranean Sea. These taxa belong to various taxonomic clades spanning Metazoa, Chromista, Chlorophyta, Bacteria, and viruses. Globally, population genetic connectivity was significantly higher within oceanic basins and lower in bacteria and unicellular eukaryotes than in zooplankton. Using mixed linear models, we tested six abiotic factors influencing connectivity, including Lagrangian travel time, as proxies of oceanic current effects. We found that oceanic currents were the main population genetic connectivity drivers, together with temperature and salinity. Finally, we classified the 113 taxa into parameter-driven groups and showed that plankton taxa belonging to the same taxonomic rank such as phylum, class or order presented genomic differentiation driven by different environmental factors.</p><p><strong>Conclusion: </strong>Our results validate the isolation-by-current hypothesis for a non-negligible proportion of taxa and highlight the role of other physicochemical parameters in large-scale plankton genetic connectivity. The reference-free approach used in this study offers a new systematic framework to analyse the population genomics of non-model and undocumented marine organisms from a large-scale and holistic point of view.</p>","PeriodicalId":9127,"journal":{"name":"BMC Ecology and Evolution","volume":"23 1","pages":"46"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10472650/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10296910","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}