BMC ecology and evolution最新文献

{"title":"Diverging impacts of precipitation change on aboveground and belowground ecosystem functioning in a desert steppe.","authors":"Liu Bai, Yuanyuan Cui, Zhongwu Wang, Yahong Liu","doi":"10.1186/s12862-026-02537-5","DOIUrl":"10.1186/s12862-026-02537-5","url":null,"abstract":"<p><strong>Background: </strong>Precipitation is a limiting factor for various system functions in desert steppe ecosystems, and its impacts on aboveground and belowground processes may diverge. To evaluate these differences, for five years, we conducted field experiments to examine the effects of four different precipitation treatments [natural precipitation (W_CK), as well as a 50% decrease (W_- 50%), 50% increase (W_+ 50%), and 100% increase (W_+ 100%) in natural precipitation] on the functioning of a desert steppe.</p><p><strong>Results: </strong>The results showed that W_- 50% significantly reduced aboveground ecosystem multifunctionality (AEMF), while W_+ 50% and W_+ 100% significantly increased AEMF and ecosystem multifunctionality (EMF). There was no significant difference in belowground ecosystem multifunctionality (BEMF) between these treatments. Furthermore, precipitation alterations significantly modified soil water content and pH, while also influencing vegetation coverage and species richness. Partial Least Squares Path Modeling (PLS-PM) revealed that precipitation primarily drove changes in AEMF through a direct cascading pathway by significantly regulating the soil microenvironment, rather than directly through shifts in vegetation characteristics. Additionally, the model demonstrated a lack of explanatory power for BEMF.</p><p><strong>Conclusions: </strong>The asymmetric precipitation response of desert steppes highlights the critical need to determine belowground stability thresholds for sustainable ecosystem management under climate extremes.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13450519/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148152555","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":"Long-term monitoring reveals climate-driven seasonal dynamics of Zeugodacus cucurbitae (Coquillett) in Tanzania and prospects for pest control.","authors":"Maulid W Mwatawala, Marc De Meyer, Jackline Bakengesa, Mwajuma K Zinga, Joseph O Ruboha","doi":"10.1186/s12862-026-02536-6","DOIUrl":"10.1186/s12862-026-02536-6","url":null,"abstract":"<p><p>Zeugodacus cucurbitae (Coquillett) is a major and economically important pest of cucurbit crops, causing substantial losses to farmers across the tropics and subtropics. We analyzed a long-term trapping dataset (October 2004 - February 2012), collected from various agro-ecological settings in the Morogoro Region of Tanzania. This included a warm lowland orchard at Sokoine University of Agriculture (SUA) (526 m.a.s.l.) and a cooler highland orchard at Nyandira (1580 m.a.s.l.), as well as five additional locations along the same altitudinal gradient. Adult male Z. cucurbitae were monitored using cue-lure-baited modified McPhail traps. The abundance data was standardised as Flies per Trap per Day (FTD). Climatic-driven data were compiled from multiple sources. Results revealed significant spatial variation in Z. cucurbitae abundance along the altitudinal gradient (p < 0.0001), with sustained high densities at SUA, Kibundi and Mlali, intermediate levels at Langali, and chronically low abundance at Nyandira and Visada. Inter-annual variation was significant (p < 0.0001), with marked regional amplification in 2011-2012, whereas month-of-year effects were not significant (p = 0.7925). Directional increases occurred at Kibundi and Langali, while SUA and Mlali showed episodic dynamics and Nyandira remained stable at low levels. Abundance was negatively associated with elevation and positively associated with temperature (both p < 0.0001). Management should therefore continue in low-altitude areas, while regular monitoring, especially in high-altitude areas, is necessary to detect any steady increase in Z. cucurbitae abundance.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13449795/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148145527","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":"Human pressure and protection gradients reshape diel activity patterns of terrestrial mammals.","authors":"Dol Raj Thanet, Saneer Lamichhane, Peggy A Bevan, Guilherme Braga Ferreira, Santosh Rayamajhi, Thakur Silwal, Kate E Jones","doi":"10.1186/s12862-026-02538-4","DOIUrl":"10.1186/s12862-026-02538-4","url":null,"abstract":"<p><strong>Background: </strong>Human activities increasingly reshape wildlife diel activity patterns, yet species-specific adjustments across land-use gradients with varying levels of human pressure and protection remain poorly understood. Nepal's 2020 COVID-19 lockdown created a quasi-experimental reduction in human mobility, allowing clearer attribution of temporal responses to human pressure.</p><p><strong>Methods: </strong>Using camera trap data from matched 30-day windows (March 24-April 24) in 2019 (pre-lockdown) and 2020 (lockdown) across the Bardia complex, representing a mosaic of human pressure and protection gradients, including Bardia National Park (NP), its buffer zone (BZ), and adjacent human-dominated areas outside of buffer zone (OBZ). NP-2020 treated as the baseline and quantified species-specific activity patterns with kernel densities, coefficients of overlap (Δ, 95% CIs), circular mean peak-time shifts (hours, 95% CIs), and a nocturnality index (% detections between 19:00-05:00 h, 95% bootstrap CIs). We analyzed four contrasts and reported overlap and peak-time shifts within species, contrasting NP-2020 with the same species in BZ and OBZ during survey periods 2019 and 2020.</p><p><strong>Results: </strong>Relative to the NP-2020, herbivores -especially chital, barking deer, hog deer, and wild boar shifted activity peaks by ~ 6-11 h toward night and showed reduced overlap within-species in BZ and OBZ, with several near anti-phase schedules in OBZ. Sambar remained comparatively stable and crepuscular, while tigers exhibited low NP-BZ overlap and near 12 h offsets in their activity peaks. Lockdown conditions increased overlap and attenuated nocturnal displacement for several species (notably chital and sambar), evidencing rapid behavioral relaxation.</p><p><strong>Conclusion: </strong>The dominant pattern is a gradient of increasing nocturnality and declining overlap in activity patterns as human pressure increases from NP to BZ to OBZ, with persistent nocturnality in hog deer and wild boar indicating chronic constraints. We emphasize integrating temporal refugia into management by limiting high-intensity human activities during crepuscular periods and reducing nighttime noise and lighting at forest-agriculture interfaces, so wildlife need not rely on extreme nocturnality to coexist with humans. Long-term monitoring that couples activity metrics (overlap, peak-time shifts) with environmental factors and physiological indicators is needed to evaluate demographic and fitness consequences and to inform temporal ecology in multi-use landscapes.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13449679/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148102461","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":"Non-additive transcriptional regulation underpins an additive survival trait in populations of Drosophila selected for increased post infection survival.","authors":"Tsering Choton, Nidhi Krishna Shrivastava, Harisankar Durga, Aindrila Das, Nagaraj Guru Prasad","doi":"10.1186/s12862-026-02534-8","DOIUrl":"10.1186/s12862-026-02534-8","url":null,"abstract":"<p><strong>Background: </strong>Understanding how immunity evolves requires integrating organismal resistance with the underlying genetic and regulatory mechanisms. However, evolutionary gains in survival may arise from distinct genetic architectures and sex-specific regulatory strategies. Bridging this gap requires integrating phenotypic measures of resistance with mechanistic insights into gene regulation and immune deployment, allowing evolutionary responses to be interpreted in terms of their underlying biological processes. Using Drosophila melanogaster populations experimentally selected for increased survival post infection with Enterococcus faecalis, we dissected the quantitative genetic basis of post-infection survival and the transcriptional architecture associated with it.</p><p><strong>Results: </strong>F1 hybrid analyses revealed an additive genetic basis for survivorship in both sexes, consistent with a polygenic response to selection. In contrast, gene expression showed extensive sex-specific regulation and hybrid misexpression. Males strongly upregulated antimicrobial peptides yet suffered greater mortality, suggesting a costly or inefficient immune strategy. Females relied on distinct effector pathways and exhibited superior survivorship. Notably, transcriptional induction of the melanization precursor PPO1 did not correspond to increased phenoloxidase enzyme activity, revealing a post-transcriptional constraint on immune deployment.</p><p><strong>Conclusion: </strong>Together, these results show that while the genetic basis of survivorship is additive, the evolved immune phenotype is shaped by sex-specific regulatory divergence, hybrid incompatibilities, and functional bottlenecks. This emphasizes the need to integrate quantitative genetic, transcriptomic, and functional assays to understand the evolution of immune defense.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13449500/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148145536","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 squirrel barrier concept and its bearing on the evolution of aerial mammals.","authors":"Norberto P Giannini, Alan Cannell","doi":"10.1186/s12862-026-02532-w","DOIUrl":"10.1186/s12862-026-02532-w","url":null,"abstract":"<p><p>Three vertebrate lineages conquered powered fight in different epochs of the Phanerozoic: pterosaurs, dinosaurs (birds) and mammals (bats). The evolutionary mechanisms proposed for the demanding transition to powered flight have been contentious. For mammals, recent evidence suggests that the Darwinian hypothesis of a gliding transition is supported, based on aerodynamic and paleo-atmosphere reconstructions. However, it is surprising that the many (at least 12) confirmed, independent lineages of gliding mammals that existed since the Jurassic to the present never evolved powered flight. To explain this, Pennycuick in 2008 advanced the theoretical concept of the squirrel barrier: gliding mammals face a tradeoff between the cost of abandoning their agile arboreal lifestyle, and the potential gains of powered flight, thereby limiting the evolution of the higher-aspect-ratio wings required for achieving the latter. This concept was seldom discussed, used or tested. Here we examine critically the squirrel barrier concept and its implicit components, contrasting its predictions with available evidence, specifically from morphology, aerodynamics, and fossils. We found the concept highly relevant, and more complex than originally stated. A more nuanced approach to the probable conditions that must be met to transition from the locomotor style of ancestors to flying descendants reveals several intermediate such barriers, of which the squirrel barrier is one requiring profound evolutionary changes. Glide distance is a measure of glide efficiency, because the longer the glide the better the use of the large amount of energy invested in climbing up to the launch point in the canopy. Based on observational data and aerodynamics, we hypothesize that colugos (Dermoptera: Cynocephalidae) are able to maximize glide distance and glide ratio beyond average performance and thus might be beyond the squirrel barrier as proposed by Pennycuick, but still falling too short of reaching sustained powered flight, which constitute an additional, \"hard\" flight barrier.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13430832/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148058720","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":"Functional diversity patterns of urban and forest breeding birds across four city-forest pairs in China.","authors":"Sidan Lin, Wei Liang","doi":"10.1186/s12862-026-02535-7","DOIUrl":"10.1186/s12862-026-02535-7","url":null,"abstract":"<p><p>Urbanisation has led to rapid declines in species richness, contributing to urban biotic homogenisation. Nonetheless, our understanding of the effects of urbanisation on functional community structures remains limited. During the 2023 breeding season, we employed a standardised point-count method to survey bird communities across four cities and their corresponding forest habitats in China, and compared the functional structural characteristics of urban and forest avian communities. Our results revealed that urban birds showed greater functional trait differences, which partially compensated for reduced species richness. While forest bird communities showed declines in species and functional richness with increasing latitude, urban communities displayed a weaker latitudinal trend, which we tentatively interpreted as a possible, but unconfirmed, buffering effect on the urban environment. However, we observed a decrease in functional redundancy and an imbalance within urban avian communities along the latitudinal gradient, suggesting potential shifts in the abundance-based community structure that merit further investigation. We caution that all latitudinal inferences are exploratory, as they are based on only four city-forest pairs, which severely limits statistical power and generalisability. Therefore, our findings should be viewed as hypothesis-generating rather than confirmatory. They provide preliminary evidence that the functional structure of urban avian communities may differ from that of forest communities; however, broader sampling across more cities and latitudes is needed to validate these patterns and draw firm conclusions about their stability.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13217865/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148038389","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":"How toothed whales divide up the world: phylogeny and ecology shape life-history strategies of odontocetes.","authors":"Steven H Ferguson, Laura J Feyrer, Evelien de Greef, Jeff W Higdon","doi":"10.1186/s12862-026-02530-y","DOIUrl":"10.1186/s12862-026-02530-y","url":null,"abstract":"<p><strong>Background: </strong>Understanding the evolution of life-history strategies within a taxonomic guild offers critical insights into how species allocate energy toward growth, reproduction, and survival in response to environmental pressures. We examined 42 odontocete whale species using six key life-history traits and three major environmental variables- latitude, bathymetry, and sea ice -to identify broad patterns in ecological and evolutionary strategies.</p><p><strong>Results: </strong>While controlling for body size and phylogenetic relatedness, we used archetypal clustering analysis to identify three groups of species according to shared life-history characteristics: bet-hedging, slow, and fast. We then assessed environmental associations among these three life-history strategies. Ancestral state reconstruction was used to disentangle the roles of phylogenetic constraint and ecological adaptation in shaping these strategies. Our results reveal convergence in life-history traits among distantly related species occupying deep, offshore habitats, suggesting that environmental similarity can drive parallel evolutionary outcomes. In contrast, species inhabiting more ephemeral, high-latitude environments with seasonal sea ice exhibit lineage-specific adaptations, reflecting a stronger influence of evolutionary history.</p><p><strong>Conclusions: </strong>These findings offer a framework for tailoring conservation strategies to the distinct ecological profiles of odontocete groups, accounting for factors such as exposure to anthropogenic stressors, reliance on specialized habitats, and inherently slow recovery rates following human exploitation.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13244838/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147990410","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 City Nature Challenge as an urban BioBlitz: evaluating Citizen Science contributions to biodiversity monitoring in Berlin.","authors":"Julia Flister, Alexis Tinker-Tsavalas, Silke Voigt-Heucke, Boris Schröder, Frederic Griesbaum","doi":"10.1186/s12862-026-02524-w","DOIUrl":"10.1186/s12862-026-02524-w","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;The human-induced loss of biodiversity demands innovative, resource efficient monitoring approaches, such as Citizen Science, to complement traditional biodiversity monitoring methods. BioBlitz events are an established Citizen Science format for biodiversity monitoring that generates as many species observations as possible in a short period of time and within a limited area through collaboration between scientists, the public and nature enthusiasts. The most prominent example of a large-scale worldwide urban BioBlitz event is the City Nature Challenge (CNC). This study investigates whether and how BioBlitz events, specifically the CNC Berlin, can complement existing biodiversity monitoring by addressing three key questions: (1) how species composition compares to existing datasets, (2) how data quality varies across taxonomic groups and participants, and (3) how participant engagement shapes data generation. We further assess taxonomic biases in the CNC Berlin 2023 and 2024 datasets to evaluate their contribution to urban biodiversity monitoring. For a better understanding, the CNC Berlin data is compared with a reference dataset from GBIF (Global Biodiversity Information Facility), an international open-access database compiling biodiversity records from multiple observation platforms. The reference dataset is limited to Berlin, covers a comparable time period and includes biodiversity data from a number of Citizen Science observation platforms.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Participation in CNC Berlin has increased substantially, with the number of contributors rising from 184 in 2023 to 361 in 2024, reflecting growing involvement. Analysis of the uploaded observations during CNC 2023 and 2024 in Berlin revealed clear differences in participant activity levels: while highly active individuals were few, they contributed a substantial portion of the total observations. The comparison of the observed species in taxonomic groups from CNC Berlin 2023 and 2024 with the GBIF reference dataset revealed the impact of highly active species experts participating in BioBlitz events on particular species groups like fungi and lichens. This highlights the influence of species experts on BioBlitz datasets. In total birds, reptiles, fish, and mammals were more likely to reach \"Research Grade\" status on iNaturalist, whereas arachnids, protozoans, insects, and chromista had substantially lower Research-Grade rates. Of the 2,440 species listed in the GBIF reference dataset, 1,027 species (42%) were also recorded during CNC Berlin 2023 and 2024. Observations included threatened amphibians, such as the Spadefoot Toad (Pelobates fuscus) and the Great Crested Newt (Triturus cristatus), rare birds like the Whinchat (Saxicola rubetra), and several invasive species, including crayfish (Procambarus spp.) and Giant Hogweed (Heracleum mantegazzianum). Notably, the potentially invasive mysid Hemimysis anomala was recorded in Berlin for th","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":"26 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13188247/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147984656","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":"Integrating morphology, nuclear SSR, and chloroplast genomes to investigate hybrid origin and species delimitation in the Lycium barbarum L. and its varieties in China.","authors":"Lei Zhang, Jinju Zhao, Chaopan Zhang, Xiulian Liao, Guoqi Zheng, Yuqing Wei","doi":"10.1186/s12862-026-02533-9","DOIUrl":"10.1186/s12862-026-02533-9","url":null,"abstract":"<p><p>The genus Lycium L. has a considerable economic and ecological value, yet species delimitation has long posed taxonomic challenges. The two varieties, L. barbarum var. auranticarpum K. F. Ching and L. barbarum var. implicatum T. Y. Chen & Xu L. Jiang, exhibit intermediate or overlapping morphological characteristics and are therefore speculated to be of hybrid origin involving L. barbarum var. barbarum L. and L. ruthenicum Murray. To test this hypothesis, we assessed their phylogenetic relationships using morphological traits, nuclear simple sequence repeat (SSR) markers, and chloroplast genomic data. Morphological examination confirmed that the individuals of both varieties exhibited intermediate traits between L. barbarum var. barbarum and L. ruthenicum or overlapping L. barbarum var. barbarum. Analysis of nuclear SSR data further indicated that all assessed individuals possessed a mixed genetic composition derived from the two putative parental species, supporting their hybrid status. Chloroplast phylogeny reconstructed using both the maximum likelihood (ML) and Bayesian inference (BI) methods yielded highly consistent topologies. These analyses strongly support (BS = 100%; PP = 1) a monophyletic clade containing L. barbarum var. auranticarpum, L. barbarum var. implicatum, and L. ruthenicum. Collectively, evidence from morphology, SSR markers, and chloroplast genome data indicate that L. barbarum var. auranticarpum and L. barbarum var. implicatum were hybrids derived from crosses between L. ruthenicum and L. barbarum var. barbarum. This study highlighted the value of integrating multiple data types to resolve complex taxonomic issues and provides a practical framework for future species delimitation studies. It also offers molecular tools and genetic insights that may facilitate the breeding of improved Lycium varieties with desirable agronomic traits.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13217809/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147977700","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":"Revised taxonomy reveals sustained introgression and secondary contact in ancient lake ricefishes.","authors":"Yuki Yashima, Andy B Nofrianto, Handung Nuryadi, Ryo Kakioka, Hirozumi Kobayashi, Satoshi Ansai, Ixchel F Mandagi, Kawilarang W A Masengi, Sjamsu A Lawelle, Atsushi J Nagano, Junko Kusumi, Kazunori Yamahira","doi":"10.1186/s12862-026-02529-5","DOIUrl":"10.1186/s12862-026-02529-5","url":null,"abstract":"<p><strong>Background: </strong>Biotic diversification in ancient lakes is shaped by complex geological histories and genetic exchange among populations. The Malili Lake system on Sulawesi Island represents a classic natural laboratory for studying freshwater fish evolution and harbors multiple endemic Oryzias species that diversified under repeated hydrological reorganizations. Previous genomic analyses inferred that two sympatric species in Lake Towuti (O. profundicola and O. loxolepis) experienced a single ancient introgression event from a \"ghost lineage\" derived from O. marmoratus inhabiting another lake. However, recent taxonomic re-evaluation has revealed the presence of an extant O. marmoratus population within Lake Towuti itself. This finding suggests that the putative ghost lineage may in fact represent a living population co-occurring in the lake, calling for a re-examination of the introgression history and speciation mode in Lake Towuti.</p><p><strong>Results: </strong>By incorporating newly generated ddRAD-seq data from the true O. marmoratus in Lake Towuti, we reanalyzed phylogenetic relationships and population genetic structure among Malili Lake Oryzias. Previously reported major phylogenetic relationships and inter-lake introgression patterns were largely reproduced. In contrast, TreeMix and f₄-statistic analyses revealed that introgression signals previously attributed to a \"ghost lineage\" into O. profundicola and O. loxolepis instead originated from the extant O. marmoratus population coexisting within Lake Towuti. Demographic model comparisons explicitly incorporating within-lake gene flow further supported a scenario in which O. profundicola and O. loxolepis diverged in allopatry, subsequently came into secondary contact within Lake Towuti, and later experienced additional gene flow following secondary contact with O. marmoratus that entered the lake.</p><p><strong>Conclusion: </strong>Our results demonstrate that introgression from the O. marmoratus lineage into O. profundicola and O. loxolepis was not a single ancient event, but rather a more sustained process. This finding highlights the critical importance of taxonomic resolution for accurately inferring introgression and divergence history. Comparative studies across other ancient lakes on Sulawesi will be valuable for understanding how the timing and nature of gene flow from third lineages influence patterns of population divergence and the strength of reproductive isolation.</p>","PeriodicalId":93910,"journal":{"name":"BMC ecology and evolution","volume":"26 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13169800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147936335","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}