Jenna M McCullough, Chad M Eliason, Shannon Hackett, Corinne E Myers, Michael J Andersen
The flora and fauna of island systems-especially those in the Indo-Pacific-are renowned for their exceptional diversification and for shaping key evolutionary theories. Yet, phylogenetic studies often undersample the full diversity of these geographic radiations. This gap stems both from the challenges of collecting single-island endemics and from the poor performance of degraded DNA when using museum specimens to infer evolutionary relationships. Advances in generating genome-wide datasets with degraded DNA from museum samples are overcoming these obstacles. Here, we leveraged whole genome resequencing (20X average coverage) and extensive sampling of all taxonomic diversity within Todiramphus kingfishers, a rapid radiation of largely island endemic 'Great Speciators.' We found that four types of molecular markers (UCEs, BUSCOs, SNPs, and mtDNA) and tree building methods did not recover a single well-supported and concordant species-level topology. Instead, we revealed pervasive incomplete lineage sorting and both ancient and contemporary gene flow, processes contribute to conflicting evolutionary histories. Complete taxonomic sampling uncovered a novel case of mitochondrial discordance between two allopatric species, consistent with a historical (but since lost) hybrid zone during successive island colonizations. Together, these results underscore how dense genomic and taxonomic sampling can reveal complex evolutionary dynamics in rapid island radiations.
{"title":"Phylogenomics of a genus of 'Great Speciators' reveals rampant incomplete lineage sorting, gene flow, and mitochondrial discordance in island systems.","authors":"Jenna M McCullough, Chad M Eliason, Shannon Hackett, Corinne E Myers, Michael J Andersen","doi":"10.1093/sysbio/syaf075","DOIUrl":"https://doi.org/10.1093/sysbio/syaf075","url":null,"abstract":"<p><p>The flora and fauna of island systems-especially those in the Indo-Pacific-are renowned for their exceptional diversification and for shaping key evolutionary theories. Yet, phylogenetic studies often undersample the full diversity of these geographic radiations. This gap stems both from the challenges of collecting single-island endemics and from the poor performance of degraded DNA when using museum specimens to infer evolutionary relationships. Advances in generating genome-wide datasets with degraded DNA from museum samples are overcoming these obstacles. Here, we leveraged whole genome resequencing (20X average coverage) and extensive sampling of all taxonomic diversity within Todiramphus kingfishers, a rapid radiation of largely island endemic 'Great Speciators.' We found that four types of molecular markers (UCEs, BUSCOs, SNPs, and mtDNA) and tree building methods did not recover a single well-supported and concordant species-level topology. Instead, we revealed pervasive incomplete lineage sorting and both ancient and contemporary gene flow, processes contribute to conflicting evolutionary histories. Complete taxonomic sampling uncovered a novel case of mitochondrial discordance between two allopatric species, consistent with a historical (but since lost) hybrid zone during successive island colonizations. Together, these results underscore how dense genomic and taxonomic sampling can reveal complex evolutionary dynamics in rapid island radiations.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145329821","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}
Samuel Martin, Niels Holtgrefe, Vincent Moulton, Richard M Leggett
A core goal of phylogenomics is to determine the evolutionary history of a set of species from biological sequence data. Phylogenetic networks are able to describe more complex evolutionary phenomena than phylogenetic trees but are more difficult to accurately reconstruct. Recently, there has been growing interest in developing methods to infer semi-directed phylogenetic networks. As computing such networks can be computationally intensive, one approach to building such networks is to puzzle together smaller networks. Thus, it is essential to have robust methods for inferring semi-directed phylogenetic networks on small numbers of taxa. In this paper, we investigate an algebraic method for performing phylogenetic network inference from nucleotide sequence data on 4-leaf semi-directed phylogenetic networks by analysing the distribution of leaf-pattern probabilities. On simulated data, we found that we can correctly identify with high accuracy the undirected phylogenetic network for sequences of length at least 10kbp. We found that identifying the semi-directed network is more challenging and requires sequences of length approaching 10Mbp. We are also able to use our approach to identify tree-like evolution and determine the underlying tree. Finally, we employ our method on a real dataset from Xiphophorus species and use the results to build a phylogenetic network.
{"title":"Algebraic Invariants for Inferring 4-leaf Semi-Directed Phylogenetic Networks","authors":"Samuel Martin, Niels Holtgrefe, Vincent Moulton, Richard M Leggett","doi":"10.1093/sysbio/syaf071","DOIUrl":"https://doi.org/10.1093/sysbio/syaf071","url":null,"abstract":"A core goal of phylogenomics is to determine the evolutionary history of a set of species from biological sequence data. Phylogenetic networks are able to describe more complex evolutionary phenomena than phylogenetic trees but are more difficult to accurately reconstruct. Recently, there has been growing interest in developing methods to infer semi-directed phylogenetic networks. As computing such networks can be computationally intensive, one approach to building such networks is to puzzle together smaller networks. Thus, it is essential to have robust methods for inferring semi-directed phylogenetic networks on small numbers of taxa. In this paper, we investigate an algebraic method for performing phylogenetic network inference from nucleotide sequence data on 4-leaf semi-directed phylogenetic networks by analysing the distribution of leaf-pattern probabilities. On simulated data, we found that we can correctly identify with high accuracy the undirected phylogenetic network for sequences of length at least 10kbp. We found that identifying the semi-directed network is more challenging and requires sequences of length approaching 10Mbp. We are also able to use our approach to identify tree-like evolution and determine the underlying tree. Finally, we employ our method on a real dataset from Xiphophorus species and use the results to build a phylogenetic network.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"19 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145295941","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}
Accurate species tree reconstruction in the presence of widespread gene duplication and loss is a challenging problem in eukaryote phylogenomics. Many phylogenomics methods have been developed over the years to address this challenge; these range from older methods based on gene tree parsimony to newer quartet-based methods. In this work, we introduce improved software for gene tree parsimony-based species tree reconstruction under gene duplication and loss. The new software, DupLoss-2, uses an improved procedure for computing gene losses and is far more accurate and much easier to use than its previous version released over a decade ago. We thoroughly evaluate DupLoss-2 and eight other existing methods, including ASTRAL-Pro, ASTRAL-Pro 2, DISCO-ASTRAL, DISCO-ASTRID, FastMulRFS, and SpeciesRax, using existing benchmarking data and find that DupLoss-2 outperforms all other methods on most of the datasets. It delivers an average of almost 30% reduction in reconstruction error compared to iGTP-Duploss, the previous version of this software, and a 10% reduction compared to the best performing existing method. DupLoss-2 is written in C++ and is freely available open-source.
{"title":"DupLoss-2: Improved Phylogenomic Species Tree Inference under Gene Duplication and Loss.","authors":"Rachel A Parsons, Mukul S Bansal","doi":"10.1093/sysbio/syaf073","DOIUrl":"https://doi.org/10.1093/sysbio/syaf073","url":null,"abstract":"<p><p>Accurate species tree reconstruction in the presence of widespread gene duplication and loss is a challenging problem in eukaryote phylogenomics. Many phylogenomics methods have been developed over the years to address this challenge; these range from older methods based on gene tree parsimony to newer quartet-based methods. In this work, we introduce improved software for gene tree parsimony-based species tree reconstruction under gene duplication and loss. The new software, DupLoss-2, uses an improved procedure for computing gene losses and is far more accurate and much easier to use than its previous version released over a decade ago. We thoroughly evaluate DupLoss-2 and eight other existing methods, including ASTRAL-Pro, ASTRAL-Pro 2, DISCO-ASTRAL, DISCO-ASTRID, FastMulRFS, and SpeciesRax, using existing benchmarking data and find that DupLoss-2 outperforms all other methods on most of the datasets. It delivers an average of almost 30% reduction in reconstruction error compared to iGTP-Duploss, the previous version of this software, and a 10% reduction compared to the best performing existing method. DupLoss-2 is written in C++ and is freely available open-source.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145281029","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}
Lars Dietz,Jonas Eberle,Sandra Kukowka,Lars Podsiadlowski,Erika Bazzato,Madlen Stange,Rachel C M Warnock,Oliver Niehuis,Christoph Mayer,Dirk Ahrens
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.
{"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
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.
{"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
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.
{"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
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.
{"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}
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.
{"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
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.
{"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
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.
{"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}
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