BMC ecology and evolution最新文献

{"title":"Greater risk-taking by non-native than native shrimp: an advantage in a human-disturbed environment?","authors":"Alfredo Escanciano Gómez, Charlotte Ipenburg, Ulrika Candolin","doi":"10.1186/s12862-024-02330-2","DOIUrl":"10.1186/s12862-024-02330-2","url":null,"abstract":"<p><strong>Background: </strong>The invasion of non-native species into ecosystems is a growing human-induced problem. To control their spread and population growth, knowledge is needed on the factors that facilitate or impede their invasions. In animals, traits often associated with invasion success are high activity, boldness, and aggression. However, these traits also make individuals susceptible to predation, which could curb population growth. We investigated if a recent invader into the Baltic Sea, the shrimp Palaemon elegans, differs in risk-taking from a native shrimp, P. adspersus. We recorded activity, habitat choice, and response to perceived predation threat of both species.</p><p><strong>Results: </strong>We found the invading shrimp to take greater risks than the native one; while the native shrimp adjusted its behaviour to habitat structure and exposure to a perceived predator, the non-native shrimp did not, and it resumed normal activity sooner after a perceived predation threat. Despite the greater risk taking by the non-native shrimp, its population has grown rapidly during the last two decades in the investigated area and is now larger than that of the native shrimp.</p><p><strong>Conclusions: </strong>We discuss plausible explanations for the population growth of the invader, including the recent decline in predatory fishes that could have reduced the cost of risk-taking, and anthropogenic eutrophication that has increased food abundance could have allowed the population growth. These results stress the need to assess the optimality of the behaviours of both native and non-native species when investigating the factors that influence invasion success in human-disturbed environments.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":"24 1","pages":"143"},"PeriodicalIF":2.3,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11574993/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142670108","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":"Survival cost sharing among altruistic full siblings in Mendelian population.","authors":"József Garay, Inmaculada López, Zoltán Varga, Villő Csiszár, Tamás F Móri","doi":"10.1186/s12862-024-02317-z","DOIUrl":"10.1186/s12862-024-02317-z","url":null,"abstract":"<p><strong>Background: </strong>We focus on Haldane's familial selection in monogamous families in a diploid population, where the survival probability of each sibling is determined by altruistic food sharing with its siblings during starvation. An autosomal recessive-dominant or intermediate allele pair uniquely determines the altruistic or selfish behavior, which are coded by homozygotes. We focus on the case when additive cost and benefit functions determine the survival probability of each full sibling.</p><p><strong>Results: </strong>We provide conditions for the existence of the altruistic and selfish homozygote. We show that the condition of evolutionary stability of altruism depends on the genotype-phenotype mapping. Furthermore, if the offspring size increases then the condition of evolutionary stability of altruism becomes stricter. Contrary to that, for the evolutionary stability of selfish behavior it is enough if the classical Hamilton's rule does not hold. Moreover, when the classical Hamilton's rule holds and the condition of evolutionary stability of altruism does not hold, then the selfish and altruistic phenotypes coexist.</p><p><strong>Conclusions: </strong>In summary, the classical Hamilton's rule is a sufficient condition for the existence of altruism, but it alone does not imply the evolutionary stability of the pure altruistic homozygote population when the altruistic siblings share the cost of altruism.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":"24 1","pages":"142"},"PeriodicalIF":2.3,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11572324/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142670109","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":"Next-generation phylogeography reveals unanticipated population history and climate and human impacts on the endangered floodplain bitterling (Acheilognathus longipinnis).","authors":"Keisuke Onuki, Ryosuke K Ito, Tappei Mishina, Yasuyuki Hashiguchi, Koki Ikeya, Kazuhiko Uehara, Masaki Nishio, Ryoichi Tabata, Seiichi Mori, Katsutoshi Watanabe","doi":"10.1186/s12862-024-02326-y","DOIUrl":"10.1186/s12862-024-02326-y","url":null,"abstract":"<p><strong>Background: </strong>Floodplains harbor highly biodiverse ecosystems, which have been strongly affected by both past climate change and by recent human activities, resulting in a high prevalence of many endangered species in these habitats. Understanding the history of floodplain species over a wide range of timescales can contribute to effective conservation planning. We reconstructed the population formation history of the Itasenpara bitterling Acheilognathus longipinnis, an endangered floodplain fish species in Japan, over a broad timescale based on phylogenetic analysis, demographic modeling, and historical demographic analysis using mitogenome and whole-genome sequences. A genome sequence was newly assembled as a reference for the resequencing analysis. This bitterling is distributed in three plains separated by high mountain ranges and exhibits ecological characteristics well adapted to floodplain environments.</p><p><strong>Results: </strong>Our analyses revealed an unexpected population branching pattern, gene flow, and timing of the differentiation that occurred within a few hundred thousand years, i.e., long after the mountain uplift that was assumed to be the primary geological cause of the population differentiation. The analyses also showed that all local populations experienced a severe decline during the last glacial and post-glacial periods.</p><p><strong>Conclusions: </strong>Our results suggest that the floodplain bitterling was able to disperse through unknown routes after mountain uplift and that its populations were strongly influenced by climatic and geographic changes in glacial-interglacial cycles and subsequent human activities, probably related to its floodplain-dependent ecology. The genomic data highlight the unanticipated distribution process of this species and the magnitude of the impact of human activities, with important implications for its conservation.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":"24 1","pages":"141"},"PeriodicalIF":2.3,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11555866/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142634237","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":"Repeated evolution on oceanic islands: comparative genomics reveals species-specific processes in birds.","authors":"María Recuerda, Julio César Hernández Montoya, Guillermo Blanco, Borja Milá","doi":"10.1186/s12862-024-02320-4","DOIUrl":"10.1186/s12862-024-02320-4","url":null,"abstract":"<p><p>Understanding the interplay between genetic drift, natural selection, gene flow, and demographic history in driving phenotypic and genomic differentiation of insular populations can help us gain insight into the speciation process. Comparing patterns across different insular taxa subjected to similar selective pressures upon colonizing oceanic islands provides the opportunity to study repeated evolution and identify shared patterns in their genomic landscapes of differentiation. We selected four species of passerine birds (Common Chaffinch Fringilla coelebs/canariensis, Red-billed Chough Pyrrhocorax pyrrhocorax, House Finch  Haemorhous mexicanus and Dark-eyed/island Junco Junco hyemalis/insularis) that have both mainland and insular populations. Changes in body size between island and mainland populations were consistent with the island rule. For each species, we sequenced whole genomes from mainland and insular individuals to infer their demographic history, characterize their genomic differentiation, and identify the factors shaping them. We estimated the relative (F_st) and absolute (d_xy) differentiation, nucleotide diversity (π), Tajima's D, gene density and recombination rate. We also searched for selective sweeps and chromosomal inversions along the genome. All species shared a marked reduction in effective population size (N_e) upon island colonization. We found diverse patterns of differentiated genomic regions relative to the genome average in all four species, suggesting the role of selection in island-mainland differentiation, yet the lack of congruence in the location of these regions indicates that each species evolved differently in insular environments. Our results suggest that the genomic mechanisms involved in the divergence upon island colonization-such as chromosomal inversions, and historical factors like recurrent selection-differ in each species, despite the highly conserved structure of avian genomes and the similar selective factors involved. These differences are likely influenced by factors such as genetic drift, the polygenic nature of fitness traits and the action of case-specific selective pressures.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":"24 1","pages":"140"},"PeriodicalIF":2.3,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11545622/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142634252","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":"Unravelling spatial scale effects on elevational diversity gradients: insights from montane small mammals in Kenya.","authors":"Kenneth Otieno Onditi, Noé U de la Sancha, Simon Musila, Esther Kioko, Xuelong Jiang","doi":"10.1186/s12862-024-02328-w","DOIUrl":"10.1186/s12862-024-02328-w","url":null,"abstract":"<p><strong>Background: </strong>Montane ecosystems play crucial roles as global biodiversity hotspots. However, climatic changes and anthropogenic pressure increasingly threaten the stability of montane community dynamics, such as diversity-elevation interactions, creating a challenge in understanding species biogeography and community ecology dynamics in these crucial conservation areas. We examined how varying sampling spatial grains influence small mammal diversity patterns within Kenya's tallest montane ecosystems.</p><p><strong>Methods: </strong>Employing a combination of multidimensional alpha diversity metrics and multisite beta diversity characteristics (species richness, phylogenetic and functional diversity and divergence, and multisite beta diversity) alongside spatial generalized additive multivariate regression analyses, we tested how spatial scaling influences elevational diversity gradient patterns and their associations with environmental and human activity variables.</p><p><strong>Results: </strong>The diversity-elevation associations were generally homogeneous across spatial grains; however, idiosyncratic patterns emerged across mountains. The total (taxonomic, phylogenetic, and functional) beta diversity, nestedness, and turnover resultant components monotonically increased or decreased with varying spatial grains. The associations between the diversity patterns and the environmental and human footprint variables increased with spatial grain size but also presented variations across mountains and indices. Species richness and phylogenetic and functional richness indices were more strongly influenced by spatial scale variations than were the divergence and community structure indices in both the diversity distribution patterns and their associations with the environmental and human variables.</p><p><strong>Conclusions: </strong>The diversity-elevation and diversity-environment (including human activity pressure) relationships across spatial grains suggest that montane small mammal diversity patterns portray subtle but systematic sensitivity to sampling spatial grain variation and underscore the importance of geographical context in shaping these elevational diversity gradients. For improved effectiveness, conservation efforts should consider these spatial effects and the unique geographical background of individual montane ecosystems.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":"24 1","pages":"139"},"PeriodicalIF":2.3,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11545329/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142634268","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":"Great ape abundance and per capita carbon storage in their habitats.","authors":"Prince Degny Vale, Ernest Dadis Bush Fotsing, Samedi Jean Pierre Mucyo, Williams Danladi Abwage, Serge Ely Dibakou, Kouame Paul N'Goran, Tenekwetche Sop, Yntze van der Hoek, Stefanie Heinicke, Lars Kulik, Inza Kone, Hjalmar Kuehl","doi":"10.1186/s12862-024-02327-x","DOIUrl":"10.1186/s12862-024-02327-x","url":null,"abstract":"<p><p>The ecological importance of great apes is widely recognised, yet few studies have highlighted the role of protecting great apes' habitats in mitigating climate change, particularly through carbon sequestration. This study used GIS tools to extract data from various sources, including the International Union for Conservation of Nature database, to examine carbon quantity and great ape abundance in African great ape habitats. Subsequently, we employed a generalised linear model to assess the relationship between locally measured great ape populations abundance and carbon storage across areas with different levels of protection. Our findings showed a positive relationship between the abundance of great apes in their habitats and carbon storage, likely since conservation efforts in great apes habitats may be strengthened with higher great ape populations. The results reveal that gorilla habitats exhibited higher carbon storage than chimpanzee habitats. Specifically, the areas inhabited by gorillas are associated with a mean increase of 27.47 t/ha in carbon storage. Additionally, we observed a positive association between highly protected areas and carbon storage within great ape habitats. Our model indicates that highly protected areas increase the mean carbon stored by 1.13 t/ha compared to medium protected areas, which show a reduction of 15.49 t/ha. This highlights the critical role that protected areas play in both species conservation and carbon sequestration, contributing significantly to climate mitigation efforts. Furthermore, our study underscores the significant contribution of great ape habitats, extending beyond protected areas, to carbon storage, highlighting the potential for synergistic conservation strategies targeting both great apes and carbon sequestration. Protecting great apes is vital for reducing carbon emissions from deforestation and boosting tropical forest carbon sinks. Since nearly 90% of great apes live outside protected areas, targeted conservation in these low-protected areas is also crucial.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":"24 1","pages":"137"},"PeriodicalIF":4.6,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11542465/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142607617","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":"Oceanic islands act as drivers for the genetic diversity of marine species: Cardita calyculata (Linnaeus, 1758) in the NE Atlantic as a case-study.","authors":"Livia Sinigaglia, L Baptista, C Alves, F Feldmann, C Sacchetti, C Rupprecht, T Vijayan, E Martín-González, S P Ávila, A M Santos, M Curto, H Meimberg","doi":"10.1186/s12862-024-02322-2","DOIUrl":"10.1186/s12862-024-02322-2","url":null,"abstract":"<p><p>Geographic distribution, as well as evolutionary and biogeographic processes and patterns of marine invertebrate benthic species are strongly shaped by dispersal ability during the life cycle. Remote oceanic islands lie at the brink of complex biotic and abiotic interactions which have significantly influenced the biodiversity patterns we see today. The interaction between geological environmental change and taxon-specific dispersal modes can influence species evolutionary patterns, eventually delimiting species-specific biogeographic regions. In this study, we compare the population genetic patterns of the marine bivalve Cardita calyculata in the northeast Atlantic, discussing the role of Macaronesian islands during past climatic cycles. The genetic structure and diversity patterns were outlined based on SSR-GBAS loci of 165 individuals and on the mitochondrial COI marker of 22 individuals from the Canary Islands, Madeira, Azores and the Mediterranean. The highly structured genetic pattern found among regions and within archipelagos suggests the central role of oceanic islands in promoting the divergence of the species in both the NE Atlantic and the Mediterranean. The high degree of divergence in the COI dataset (> 7%) suggests the existence of potential cryptic speciation that needs to be further explored with a more comprehensive sampling. Such patterns are only congruent with a scenario where C. calyculata populations were maintained during glacial/interglacial cycles, supporting the role of the studied archipelagos as drivers of diversity for marine biota. We stress the importance of developing studies for species with various life history and dispersal modes. In such a way, a more profound understanding of the biogeographic and evolutionary significance of oceanic islands can catalyse directed conservation efforts, especially in the context of the ongoing climate crisis.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":"24 1","pages":"138"},"PeriodicalIF":4.6,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11542354/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142607618","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 systematic review of poeciliid fish invasions in Africa.","authors":"Joshua Pritchard Cairns, Pedro Henrique Negreiros de Bragança, Josie South","doi":"10.1186/s12862-024-02321-3","DOIUrl":"10.1186/s12862-024-02321-3","url":null,"abstract":"<p><strong>Background: </strong>This review compiles and synthesises the existing information concerning non-native poeciliid introductions to Africa. The recent upsurge in research on invasive poeciliids has revealed their widespread occurrence in Africa.</p><p><strong>Results: </strong>Within the 87 relevant articles, 74% reported on the presence of Gambusia spp., 33% on P. reticulata, 19% on X. hellerii, 11% on X. maculatus, and 5% on other ornamental poeciliids. Overall, poeciliids have been documented as introduced to 25 different countries in Africa. With Gambusia spp. being introduced to 16 countries and P. reticulata to 19 countries. Our results are representative of the current state of research on invasive poeciliids in Africa. There was a concentration of studies in South Africa, with limited research elsewhere. Current distribution data is relatively patchy, although widespread surveys of multiple river systems in Morocco and South Africa, confirmed widespread and abundant established poeciliid populations. The ecological impacts of invasive poeciliids in Africa remain understudied but evidence indicates deleterious effects on native fish, invertebrates, and amphibians, many of which are critically endangered or endemic.</p><p><strong>Conclusion: </strong>Current research is limited in reporting from certain countries and ecological impacts. An increased effort to monitor species composition in vulnerable waterbodies, especially in the many African countries where invasive poeciliids are reported, should be completed to reveal further established populations. Future research should prioritise quantifying the ecological impacts of invasive poeciliids in the field and identifying both vulnerable and resistant native ecosystems to guide future management decisions.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":"24 1","pages":"136"},"PeriodicalIF":2.3,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11539733/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142592407","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":"Terraces in species tree inference from gene trees.","authors":"Mursalin Habib, Kowshic Roy, Saem Hasan, Atif Hasan Rahman, Md Shamsuzzoha Bayzid","doi":"10.1186/s12862-024-02309-z","DOIUrl":"10.1186/s12862-024-02309-z","url":null,"abstract":"<p><p>A terrace in a phylogenetic tree space is a region where all trees contain the same set of subtrees, due to certain patterns of missing data among the taxa sampled, resulting in an identical optimality score for a given data set. This was first investigated in the context of phylogenetic tree estimation from sequence alignments using maximum likelihood (ML) and maximum parsimony (MP). It was later extended to the species tree inference problem from a collection of gene trees, where a set of equally optimal species trees was referred to as a \"pseudo\" species tree terrace which does not consider the topological proximity of the trees in terms of the induced subtrees resulting from certain patterns of missing data. In this study, we mathematically characterize species tree terraces and investigate the mathematical properties and conditions that lead multiple species trees to induce/display an identical set of locus-specific subtrees owing to missing data. We report that species tree terraces are agnostic to gene tree heterogeneity. Therefore, we introduce and characterize a special type of gene tree topology-aware terrace which we call \"peak terrace\". Moreover, we empirically investigated various challenges and opportunities related to species tree terraces through extensive empirical studies using simulated and real biological data. We demonstrate the prevalence of species tree terraces and the resulting ambiguity created for tree search algorithms. Remarkably, our findings indicate that the identification of terraces could potentially lead to advances that enhance the accuracy of summary methods and provide reasonably accurate branch support.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":"24 1","pages":"135"},"PeriodicalIF":2.3,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533290/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142577186","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":"Comparative analysis of chloroplast genomes in ten holly (Ilex) species: insights into phylogenetics and genome evolution.","authors":"Jiaxin Hu, Daoliang Yan, Huwei Yuan, Jianhong Zhang, Bingsong Zheng","doi":"10.1186/s12862-024-02318-y","DOIUrl":"10.1186/s12862-024-02318-y","url":null,"abstract":"<p><p>In order to clarify the chloroplast genomes and structural features of ten Ilex species and provide insights into the phylogeny and genome evolution of the genus Ilex, we conducted a comparative analysis of chloroplast genomes using bioinformatics methods. The chloroplast genomes of ten Ilex species were obtained, and their structural features and variations were compared. The results indicated that all chloroplast genomes in the genus Ilex exhibit a double-stranded circular structure, with sizes ranging from 157,356 to 158,018 bp, showing minimal differences in size. The chloroplast genomes of the ten Ilex species have a relatively conservative gene count, with a total of 134 to 135 genes, including 88 or 89 protein-coding genes, and a conserved number of 8 rRNA genes. Each chloroplast genome contains 3 to 123 SSR (Simple Sequence Repeat) sites, predominantly composed of mononucleotide and trinucleotide repeats, with no detection of pentanucleotide or hexanucleotide repeats. The variation in dispersed repeat sequences among Ilex species is minimal, with a total repeat sequence number ranging from 1 to 14, concentrated in the length range of 30 to 42 base pairs. The expansion and contraction of chloroplast genome boundaries among Ilex species are relatively stable, with only minor variations observed in individual species. Variations in non-coding regions are more pronounced than those in coding regions, with the variability in the Large Single Copy region (LSC) being the highest, while the variability in the Inverted Repeat region A (IRa) is the lowest. The divergence time among Ilex species was estimated using the MCMC-tree module, revealing the evolutionary relationships among these species, their common ancestors, and their differentiation throughout the evolutionary process. The research findings provide a valuable reference for the systematic study and molecular marker development of Ilex plants.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":"24 1","pages":"133"},"PeriodicalIF":2.3,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11526546/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142549529","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}