Lars Dietz,Jonas Eberle,Sandra Kukowka,Lars Podsiadlowski,Erika Bazzato,Madlen Stange,Rachel C M Warnock,Oliver Niehuis,Christoph Mayer,Dirk Ahrens
{"title":"Cryptic species can be phylogenetically old despite strong sex-biased dispersal.","authors":"Lars Dietz,Jonas Eberle,Sandra Kukowka,Lars Podsiadlowski,Erika Bazzato,Madlen Stange,Rachel C M Warnock,Oliver Niehuis,Christoph Mayer,Dirk Ahrens","doi":"10.1093/sysbio/syaf072","DOIUrl":"https://doi.org/10.1093/sysbio/syaf072","url":null,"abstract":"The impact of strongly differentiated populations on species delimitation due to limited or sex-biased dispersal remains challenging and under-explored in the framework of integrative taxonomy. The Mediterranean chafer beetle genus Pachypus is remarkable for its extreme female philopatry, with entirely wingless and subterranean females. This makes Pachypus an interesting case study. Based on a dataset of over 900 protein-coding genes (metazoan universal single-copy orthologs; mzl-USCOs), we investigated phylogeny, species delimitation, gene flow, and population differentiation to provide an integrative assessment of species boundaries. Integrative consideration of all results led to the recognition of 14 mostly morphologically cryptic species, including several new taxa. Most inferred speciation events occurred in the time between the end of the Messinian salinity crisis (about 5.3 million years ago) and the early Pleistocene. Phylogenetically old species and lack of recent speciation was unexpected because of the extreme philopatry, the morphological similarity of the species, and the high degree of differentiation observed among populations of the same species. Speciation was partly associated with the disruption of previously more connected ranges after the Messinian salinity crisis (MSC). This also helps clarify the extent to which the Mediterranean dried out during the MSC, since land connections in the circum-Tyrrhenian region must have persisted long enough for flightless Pachypus females to disperse across drifting land areas connecting the Apennine Peninsula and Africa. We found evidence for historical gene flow between species, while more recent gene flow between populations is low, which is potentially the cause of considerable over-splitting found in the Bayesian Phylogenetics & Phylogeography (BPP) species delimitation analysis. We showed that integrating the outcome of the BPP species delimitation with genealogical divergence index (gdi) values proved to be helpful in some cases but was inconclusive in many others. Generalized Mixed Yule Coalescent (GMYC) and Poisson Tree Processes (PTP) analyses were less prone to over-splitting. This illustrates how species delimitation analyses of cases with restricted or sex-biased dispersal and highly differentiated populations can serve as empirical tests of the utility and robustness of delimitation approaches.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"122 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145277386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Guanliang Meng,Lars Podsiadlowski,Dimitar Dimitrov,Bernhard A Huber
{"title":"The Complex Interplay between Evolutionary Flexibility and Diversification in a Family of Spiders.","authors":"Guanliang Meng,Lars Podsiadlowski,Dimitar Dimitrov,Bernhard A Huber","doi":"10.1093/sysbio/syaf070","DOIUrl":"https://doi.org/10.1093/sysbio/syaf070","url":null,"abstract":"Understanding the mechanisms of how morphological traits drive speciation and contribute to species richness is pivotal in evolutionary biology. In this context, the evolutionary flexibility of morphological traits may play a significant role. Using the diverse daddy long-legs spiders, Pholcidae, which currently includes some 2,000 described species, we explored the interplay between speciation rate, trait evolution rate, microhabitat shift rate, species richness, interspecific variability of body size, leg length, relative leg length, and leg proportions. We applied a combination of large-scale genomic and taxonomic sampling, and phylogenetic and comparative analyses to assess the dynamics of diversification and evolutionary flexibility (measured as either the standard variance or disparity of traits), as well as their interactions. We found that increased evolutionary flexibility is accompanied with accelerated rates in speciation and trait evolution, and with higher species richness. We also observed near-isometry of leg length and body size in the species-rich lineages, suggesting stabilizing selection, while positive allometry in the species-poor lineages indicates directional selection. Additionally, we found a positive correlation between trait evolution rates and microhabitat shifts. We argue that environmental heterogeneity and frequent microhabitat shifts may contribute to the origin and maintenance of evolutionary flexibility, which in turn influences the organisms' ability to exploit new resources and habitats. On the other hand, our study suggests that a lack of evolutionary flexibility, e.g. due to dwarfism or gigantism, could be an evolutionary dead end. This study enhances our understanding of the mechanisms of diversification, demonstrating that evolutionary flexibility of morphological traits may vary among closely related taxa and is likely to have contributed to the uneven distribution of biodiversity across the tree of life.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"79 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145277387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Craig F Barrett,John V Freudenstein,Samuel V Skibicki,Cameron W Corbett,Brandon T Sinn,Hana L Thixton-Nolan,William J Baker,Vincent S F T Merckx,Oscar Alejandro Pérez-Escobar,Matthew C Pace,Paul M Peterson,Kenji Suetsugu,Tomohisa Yukawa
{"title":"Nuclear Phylogenomic Insights into Relationships, Support, and Conflict Among the Early Diverging Lineages of the Megadiverse Epidendroid Orchids.","authors":"Craig F Barrett,John V Freudenstein,Samuel V Skibicki,Cameron W Corbett,Brandon T Sinn,Hana L Thixton-Nolan,William J Baker,Vincent S F T Merckx,Oscar Alejandro Pérez-Escobar,Matthew C Pace,Paul M Peterson,Kenji Suetsugu,Tomohisa Yukawa","doi":"10.1093/sysbio/syaf069","DOIUrl":"https://doi.org/10.1093/sysbio/syaf069","url":null,"abstract":"Parasites present fascinating examples of evolutionary modification that simultaneously pose challenges for systematics. This is exemplified by fully mycoheterotrophic orchids, which are completely dependent on fungi, constituting nearly half of all fully mycoheterotrophic plant species. A large concentration of mycoheterotrophic lineages is found among the eight tribes comprising the base of the megadiverse orchid subfamily Epidendroideae, here referred to as the Early Diverging Epidendroideae (EDE). To date, relationships among the EDE have been problematic. Previous analyses have suffered from sparse taxon sampling, weak support from limited loci, or long branch attraction in plastid-based analyses. We conducted the most comprehensive nuclear phylogenomic analysis of the EDE to date, using Angiosperms353 loci, coalescent analyses, and deep exploration of support, conflict, saturation, and introgression. Our study is the first to include phylogenomic data from all eight EDE tribes, with 22 of 26 EDE genera represented. We took a novel approach selecting best-fit mixture model configurations at the individual locus level, which provided significantly better fit overall and required fewer parameters than all other models, with implications for clades characterized by lineage-specific rate heterogeneity. We recovered strong support for monophyly of all EDE tribes except for Neottieae, which were inferred to be paraphyletic. Based on quartet sampling analysis, information content was generally rich for deep relationships among the EDE tribes, but overall support was weak. We found evidence of saturation and putative introgression, with two inferred reticulation events. We conclude that short internal branches associated with rapid diversification, incomplete lineage sorting, and putative introgression resulted in low concordant signal among EDE tribes, underscoring the continued difficulty in resolving their relationships. Nonetheless, we provide the first strongly supported phylogenetic hypothesis for the five genera of Gastrodieae, representing the largest known diversification of fully mycoheterotrophic plants. We discuss our findings considering recent phylogenomic studies, taxonomy, morphology, and biogeographic implications.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"22 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145229214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gina M Calabrese,Kira E Delmore,Jochen B W Wolf,Rebecca Safran,Daniel L Rabosky
{"title":"No Consistent Effect of Migration on Speciation Rates in Two Avian Superfamilies: A Check on the Robustness of Trait-Dependent Diversification Methods.","authors":"Gina M Calabrese,Kira E Delmore,Jochen B W Wolf,Rebecca Safran,Daniel L Rabosky","doi":"10.1093/sysbio/syaf068","DOIUrl":"https://doi.org/10.1093/sysbio/syaf068","url":null,"abstract":"Seasonal migration is performed by taxonomically diverse groups across the planet's oceans and continents. Migration has been hypothesized to promote speciation through a variety of mechanisms that may initiate reproductive isolation and population divergence, such as temporal or spatial migratory divides, migration 'falloffs', or the colonization of new, geographically isolated breeding areas. Migration has also been implicated in recent population divergence within a handful of bird species; however, it is unknown whether migration is generally associated with higher speciation rates. We sought to test this question in two large clades of new world birds with diverse migratory phenotypes, the suboscines and the Emberizoidea, employing three state-of-the-art comparative methods of trait-based diversification: estimates of tip speciation rates using 1) BAMM and 2) ClaDS; and 3) hidden-state speciation extinction models. Our results differed across methods and across taxonomic scales, suggesting an acute need to corroborate inferences across different frameworks and datasets prior to concluding that a given trait has, in fact, promoted diversification. Overall, and based upon the majority of results across different methods, we conclude that there is no methodologically-consistent evidence of faster speciation in migratory lineages in these groups. We discuss the biological implications of this finding, as well as the challenges of inference posed by current trait-based diversification methods.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"23 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145209293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Evolutionary rate incongruences in squamates reveal contrasting patterns of evolutionary novelties and innovation.","authors":"Tiago R Simões,Arthur S Brum,Stephanie E Pierce","doi":"10.1093/sysbio/syaf067","DOIUrl":"https://doi.org/10.1093/sysbio/syaf067","url":null,"abstract":"Understanding the rate of phenotypic evolution can reveal fundamental aspects of organismal evolutionary trajectories. Hence, several studies have attempted to detect the tempo of evolution for multiple organisms, although based on different datatypes (e.g., discrete and morphometric) and methods (phylodynamic vs comparative methods). Here, we ask whether these competing approaches provide comparable estimates of rate trajectories using an expanded squamate phylogenetic dataset that is matched (to the species-level) with new geometric morphometric data, while also assessing method robustness to fossil sampling. Our new squamate total-evidence time-tree suggests a new placement for several putative stem pleurodontan iguanians (Temujinidae) as stem acrodontans, while matching divergence time estimates of recent phylogenomic studies. We show that low fossil sampling inadvertently removes entire regions of the morphospace and leads to contraction of crown clade phenotypic diversity, as morphospace boundaries are frequently delimited by transitional fossils. Critically, different datatypes produce incongruent rate patterns, which are further exacerbated by methodological differences. We suggest that phylogenetic discrete data (i.e., characters) are strongly influenced by neomorphisms and reveal phenotypic novelties, while morphometric data (i.e., shape) reflects changes in phenotypic refinement leading to phenotypic innovation. This conceptual distinction conciliates discrepant macroevolution trajectories across squamates, which we expect to be generalizable to other systems across the Tree of Life.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"28 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145153406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Brian Tilston Smith,Agusto Luzuriaga-Neira,David Alvarez-Ponce,Kaiya L Provost,Gregory Thom,Leo Joseph
{"title":"Introgressed variants obscure phylogenetic relationships but are not subject to positive selection in Australasian long-tailed parrots.","authors":"Brian Tilston Smith,Agusto Luzuriaga-Neira,David Alvarez-Ponce,Kaiya L Provost,Gregory Thom,Leo Joseph","doi":"10.1093/sysbio/syaf066","DOIUrl":"https://doi.org/10.1093/sysbio/syaf066","url":null,"abstract":"Gene flow often obscures phylogenetic relationships but the evolutionary significance of introgressed variants is unclear. Here we examine the Australasian long-tailed parrots (Psittaculinae: Polytelini) in which an unexpected sister relationship between Polytelis alexandrae and the genus Aprosmictus, and not the other Polytelis species, has been observed. We tested whether this relationship was due to ancient introgression in whole genomes. We found that the majority of gene trees had Ap. erythropterus and P. alexandrae as sister taxa, whereas network analysis indicated monophyly of Polytelis, 48% of gene trees being in phylogenetic conflict due to introgression from Ap. erythropterus into P. alexandrae. Further analyses confidently confirmed that 4-8% of the genome of P. alexandrae was introgressed from Ap. erythropterus with signals of gene flow occurring throughout the genome. These findings indicate that topologies with P. alexandrae and the genus Ap. erythropterus as sister taxa were biased by gene flow and affirm that Polytelis is monophyletic. Next, we assessed the evolutionary outcomes for introgressed variants and found that, among introgressed protein-coding genes, only two (0.8%) were under positive selection, in comparison to 99 (1.7%) of non-introgressed genes. Our results indicate that, despite the ubiquity of detectable introgression in phylogenies, many genetic variants flowing between species may play a minor role in molecular adaptations.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"102 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145153407","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Carlos J Pavón-Vázquez,Alison J Fitch,Paul Doughty,Stephen C Donnellan,J Scott Keogh
{"title":"Integrating Genomics, Collections, and Community Science to Delimit Species Clarifies the Taxonomy of a Variable Monitor Lizard (Varanus tristis).","authors":"Carlos J Pavón-Vázquez,Alison J Fitch,Paul Doughty,Stephen C Donnellan,J Scott Keogh","doi":"10.1093/sysbio/syaf064","DOIUrl":"https://doi.org/10.1093/sysbio/syaf064","url":null,"abstract":"The accurate characterization of species diversity is a vital prerequisite for ecological and evolutionary research, as well as conservation. Thus, it is necessary to generate robust hypotheses of species limits based on the inference of evolutionary processes. Integrative species delimitation, the inference of species limits based on multiple sources of evidence, can provide unique insight into species diversity and the processes behind it. Here, we show how community observations can be integrated with standard molecular and phenotypic datasets under an integrative framework to identify the processes generating genetic and phenotypic variation. We implement this approach in Varanus tristis, a widespread and variable complex of Australian monitor lizards. Using genomic, phenotypic (linear and geometric morphometrics, coloration), spatial, and environmental data, we show that disparity in this complex is inconsistent with intraspecific variation and instead suggests that speciation has occurred. Based on our results, we provide an updated taxonomy for this complex and identify the processes that may have been responsible for the geographic sorting of variation. Our workflow provides a guideline for the integrative analysis of several types of data to identify the occurrence and causes of speciation. Furthermore, our study highlights the benefits and caveats associated with community science and machine learning-two tools used here-in taxonomic research.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"37 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145133916","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Hybridization and Polyploidy shaped the Evolutionary History of a Complex of Cryptic Species in European Woodrushes (Luzula sect. Luzula).","authors":"Valentin Heimer,Pau Carnicero,Carolina Carrizo García,Andreas Hilpold,Jasna Dolenc Koce,J Luis Leal,Mingai Li,Claudio Varotto,Peter Schönswetter,Božo Frajman","doi":"10.1093/sysbio/syaf065","DOIUrl":"https://doi.org/10.1093/sysbio/syaf065","url":null,"abstract":"Polyploidization has played a central role in the evolutionary history of most plant lineages, yet it poses significant challenges for phylogenetic inference, particularly in allopolyploid complexes with reticulate species relationships. Luzula sect. Luzula (Juncaceae) is a taxonomically intricate group characterized by widespread polyploidy, agmatoploidy, and high morphological uniformity. Focusing on the Eastern Alps, a key center of its diversity, we collected 1,002 samples of nine species and applied an integrative framework combining ddRADseq, plastid sequencing, relative genome size estimation, and chromosome counting to disentangle its evolutionary history. We extended previously inferred phylogenetic relationships and assessed gene flow among diploids, establishing a baseline for investigating the origin of polyploids. By analyzing patterns of genotype frequencies and genetic affinities to diploids, we inferred the most likely parental species of polyploids and identified key hybridization events shaping the current taxonomic and karyotypic diversity within this group. Our results reveal weak genetic differentiation among some diploid lineages, likely reflecting gene flow and incomplete lineage sorting. We propose a common allopolyploid origin of two tetraploids, which subsequently gave rise to a third tetraploid and a hexaploid species through interploidy hybridization. Although the parental species of some polyploids remain obscure, our genomic data highlight polyploidy and hybridization as major drivers of speciation in this poorly understood lineage. This study underscores the value of integrative approaches in resolving reticulate plant phylogenies and advances our understanding of polyploid speciation.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"85 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145133918","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nicola S Heckeberg,Alessio Capobianco,Basanta Khakurel,Gustavo Darlim,Sebastian Höhna
{"title":"Practical Guide and Review of Fossil Tip-Dating in Phylogenetics.","authors":"Nicola S Heckeberg,Alessio Capobianco,Basanta Khakurel,Gustavo Darlim,Sebastian Höhna","doi":"10.1093/sysbio/syaf050","DOIUrl":"https://doi.org/10.1093/sysbio/syaf050","url":null,"abstract":"Phylogenetic tip-dating has been and still is revolutionizing evolutionary biology in several ways. Fossil tip-dating, where fossils are placed into a phylogeny as tips based on morphological and/or molecular character information, provides a more principled approach to infer time-calibrated phylogenies compared with node-dating. Additionally, phylogenetic trees with fossils as tips become more and more important to elucidate evolutionary processes in macroevolutionary studies, e.g., deciphering diversification patterns and directional phenotypic evolution. Fossil tip-dating is slowly gathering popularity in empirical applications and has progressed substantially since its first demonstration in 2011, with respect to improved statistical models, software and datasets. Nevertheless, executing a phylogenetic fossil tip-dating analysis is complicated and comes with many challenges. Here, we provide an extensive review and overview of methods and models for phylogenetic tip-dating analyses with fossils. We focus both on data collection and preparation as well as on modeling choices. We start with a survey of all published phylogenetic tip-dating studies to date, showing common data and modeling choices as well as trends towards new approaches. Then, we walk readers through sections of molecular evolution, morphological evolution (both for discrete and continuous data), and lineage evolution (the fossilized-birth-death process). In each section, we describe the data and standard models with their underlying assumptions, and provide an outlook and practical recommendations.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"40 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145127098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Mechanisms of Community Assembly through the lens of Phylogenetic Diversity: a Critical Reappraisal","authors":"Thibault Kasprzyk, Gilles Dauby, Alain Vanderpoorten, Olivier J Hardy","doi":"10.1093/sysbio/syaf062","DOIUrl":"https://doi.org/10.1093/sysbio/syaf062","url":null,"abstract":"Darwin was one of the first to hypothesize a connection between niche differentiation and competition and species relatedness, offering an appealing framework to disentangle community assembly processes based on phylogenetic diversity patterns. Community assembly is, however, the result of several processes including potentially confounding factors associated with dispersal limitations and spatial effects, casting doubt about the application of phylogenetic diversity metrics to infer community assembly processes. We implemented a spatially-explicit model involving limited dispersal, drift, trait-based selection and competition to simulate community composition under competing assembly processes in a landscape with contrasted habitat connectivity. The phylogenetic structure of communities globally varied depending on assembly processes and the combination thereof, validating the assumption, made by a large number of studies but seldom tested in a spatially-explicit context, that different assembly processes indeed lead to significantly different patterns of community phylogenetic structure. All the investigated alpha metrics exhibited a poor ability to detect overdispersion under stabilizing processes, and some even unduly recovered a signal of clustering. Some of the most widely used metrics, such as UniFrac, carry a redundant signal with non-phylogenetic metrics, and hence, poorly capture the phylogenetic signal in the data. We identified three metrics, namely Bst or Pst for abundance data and PIst for occurrence data, which best retrieved the correct signal of phylogenetic structure under different assembly processes. Spatial effects may blur the phylogenetic structure of communities and decrease our ability to infer underlying processes. However, meaningful results may be obtained when the appropriate comparisons are made. In particular, phylogenetic clustering under equalizing processes must be tested on inter-habitat comparisons because it is the differential filtering of species between habitats that reveals the impact of equalizing processes. Our simulations further suggest that a significant phylogenetic structure of communities can be retrieved even in species-poor communities, except when the communities being compared are dominated by a single, most abundant species. We therefore conclude with best practices to adequately infer assembly processes with useful phylogenetic diversity metrics.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"54 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145089415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}