Systematic Biology最新文献

{"title":"Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards.","authors":"Anthony J Barley, Adrián Nieto-Montes de Oca, Norma L Manríquez-Morán, Robert C Thomson","doi":"10.1093/sysbio/syae040","DOIUrl":"10.1093/sysbio/syae040","url":null,"abstract":"<p><p>-Gene flow between diverging lineages challenges the resolution of species boundaries and the understanding of evolutionary history in recent radiations. Here, we integrate phylogenetic and coalescent tools to resolve reticulate patterns of diversification and use a perspective focused on evolutionary mechanisms to distinguish interspecific and intraspecific taxonomic variation. We use this approach to resolve the systematics for one of the most intensively studied but difficult to understand groups of reptiles: the spotted whiptail lizards of the genus Aspidoscelis (A. gularis complex). Whiptails contain the largest number of unisexual species known within any vertebrate group and the spotted whiptail complex has played a key role in the generation of this diversity through hybrid speciation. Understanding lineage boundaries and the evolutionary history of divergence and reticulation within this group is therefore key to understanding the generation of unisexual diversity in whiptails. Despite this importance, long-standing confusion about their systematics has impeded understanding of which gonochoristic species have contributed to the formation of unisexual lineages. Using reduced representation genomic data, we resolve patterns of divergence and gene flow within the spotted whiptails and clarify patterns of hybrid speciation. We find evidence that biogeographically structured ecological and environmental variation has been important in morphological and genetic diversification, as well as the maintenance of species boundaries in this system. Our study elucidates how gene flow among lineages and the continuous nature of speciation can bias the practice of species delimitation and lead taxonomists operating under different frameworks to different conclusions (here we propose that a 2 species arrangement best reflects our current understanding). In doing so, this study provides conceptual and methodological insights into approaches to resolving diversification patterns and species boundaries in rapid radiations with complex histories, as well as long-standing taxonomic challenges in the field of systematic biology.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"901-919"},"PeriodicalIF":6.1,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141634644","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":"PhyloJunction: A Computational Framework for Simulating, Developing, and Teaching Evolutionary Models.","authors":"Fábio K Mendes, Michael J Landis","doi":"10.1093/sysbio/syae048","DOIUrl":"10.1093/sysbio/syae048","url":null,"abstract":"<p><p>We introduce PhyloJunction, a computational framework designed to facilitate the prototyping, testing, and characterization of evolutionary models. PhyloJunction is distributed as an open-source Python library that can be used to implement a variety of models, thanks to its flexible graphical modeling architecture and dedicated model specification language. Model design and use are exposed to users via command-line and graphical interfaces, which integrate the steps of simulating, summarizing, and visualizing data. This article describes the features of PhyloJunction-which include, but are not limited to, a general implementation of a popular family of phylogenetic diversification models-and, moving forward, how it may be expanded to not only include new models, but to also become a platform for conducting and teaching statistical learning.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"1051-1060"},"PeriodicalIF":6.1,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141902966","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":"Phylogenetic Biogeography Inference Using Dynamic Paleogeography Models and Explicit Geographic Ranges.","authors":"J Salvador Arias","doi":"10.1093/sysbio/syae051","DOIUrl":"10.1093/sysbio/syae051","url":null,"abstract":"<p><p>To model distribution ranges, the most popular methods of phylogenetic biogeography divide Earth into a handful of predefined areas. Other methods use explicit geographic ranges, but unfortunately, these methods assume a static Earth, ignoring the effects of plate tectonics and the changes in the landscape. To address this limitation, I propose a method that uses explicit geographic ranges and incorporates a plate motion model and a paleolandscape model directly derived from the models used by geologists in their tectonic and paleogeographic reconstructions. The underlying geographic model is a high-resolution pixelation of a spherical Earth. Biogeographic inference is based on diffusion, approximates the effects of the landscape, uses a time-stratified model to take into account the geographic changes, and directly integrates over all probable histories. By using a simplified stochastic mapping algorithm, it is possible to infer the ancestral locations as well as the distance traveled by the ancestral lineages. For illustration, I applied the method to an empirical phylogeny of the Sapindaceae plants. This example shows that methods based on explicit geographic data, coupled with high-resolution paleogeographic models, can provide detailed reconstructions of the ancestral areas but also include inferences about the probable dispersal paths and diffusion speed across the taxon history. The method is implemented in the program PhyGeo.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"995-1014"},"PeriodicalIF":6.1,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142037036","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":"Biased Gene Introgression and Adaptation in the Face of Chloroplast Capture in Aquilegia amurensis.","authors":"Huaying Wang, Wei Zhang, Yanan Yu, Xiaoxue Fang, Tengjiao Zhang, Luyuan Xu, Lei Gong, Hongxing Xiao","doi":"10.1093/sysbio/syae039","DOIUrl":"10.1093/sysbio/syae039","url":null,"abstract":"<p><p>-Chloroplast capture, a phenomenon that can occur through interspecific hybridization and introgression, is frequently invoked to explain cytonuclear discordance in plants. However, relatively few studies have documented the mechanisms of cytonuclear coevolution and its potential for driving species differentiation and possible functional differences in the context of chloroplast capture. To address this crucial question, we chose the Aquilegia genus, which is known for having minimal sterility among species, and inferred that A. amurensis captured the plastome of A. parviflora based on cytonuclear discordance and gene flow between the 2 species. We focused on the introgression region and its differentiation from corresponding regions in closely related species, especially its composition in a chloroplast capture scenario. We found that nuclear genes encoding cytonuclear enzyme complexes (CECs; i.e., organelle-targeted genes) of chloroplast donor species were selectively retained and displaced the original CEC genes in chloroplast-receiving species due to cytonuclear interactions during introgression. Notably, the intrinsic correlation of CEC introgression was a greater degree of evolutionary distance for these CECs between A. amurensis and A. parviflora. Terpene synthase activity genes (GO: 0010333) were overrepresented among the introgressed genes, and more than 30% of these genes were CEC genes. These findings support our observations that floral terpene release pattern is similar between A. amurensis and A. parviflora compared with A. japonica. Our study clarifies the mechanisms of cytonuclear coevolution, species differentiation, and functional differences in the context of chloroplast capture and highlights the potential role of chloroplast capture in adaptation.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"886-900"},"PeriodicalIF":6.1,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141601838","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":"Bayesian Inference Under the Multispecies Coalescent with Ancient DNA Sequences.","authors":"Anna A Nagel, Tomáš Flouri, Ziheng Yang, Bruce Rannala","doi":"10.1093/sysbio/syae047","DOIUrl":"10.1093/sysbio/syae047","url":null,"abstract":"<p><p>Ancient DNA (aDNA) is increasingly being used to investigate questions such as the phylogenetic relationships and divergence times of extant and extinct species. If aDNA samples are sufficiently old, expected branch lengths (in units of nucleotide substitutions) are reduced relative to contemporary samples. This can be accounted for by incorporating sample ages into phylogenetic analyses. Existing methods that use tip (sample) dates infer gene trees rather than species trees, which can lead to incorrect or biased inferences of the species tree. Methods using a multispecies coalescent (MSC) model overcome these issues. We developed an MSC model with tip dates and implemented it in the program BPP. The method performed well for a range of biologically realistic scenarios, estimating calibrated divergence times and mutation rates precisely. Simulations suggest that estimation precision can be best improved by prioritizing sampling of many loci and more ancient samples. Incorrectly treating ancient samples as contemporary in analyzing simulated data, mimicking a common practice of empirical analyses, led to large systematic biases in model parameters, including divergence times. Two genomic datasets of mammoths and elephants were analyzed, demonstrating the method's empirical utility.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"964-978"},"PeriodicalIF":6.1,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11637557/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141793571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Double-edged Sword: Evolutionary Novelty along Deep-time Diversity Oscillation in An Iconic Group of Predatory Insects (Neuroptera: Mantispoidea)","authors":"Hongyu Li, De Zhuo, Bo Wang, Hiroshi Nakamine, Shûhei Yamamoto, Weiwei Zhang, James E Jepson, Michael Ohl, Ulrike Aspöck, Horst Aspöck, Thet Tin Nyunt, Michael S Engel, Michael J Benton, Philip Donoghue, Xingyue Liu","doi":"10.1093/sysbio/syae068","DOIUrl":"https://doi.org/10.1093/sysbio/syae068","url":null,"abstract":"Evolutionary novelties are commonly identified as drivers of lineage diversification, with key innovations potentially triggering adaptive radiation. Nevertheless, testing hypotheses on the role of evolutionary novelties in promoting diversification through deep time has proven challenging. Here we unravel the role of the raptorial appendages, with evolutionary novelties for predation, in the macroevolution of a predatory insect lineage, the Superfamily Mantispoidea (mantidflies, beaded lacewings, thorny lacewings, and dipteromantispids), based on a new dated phylogeny and quantitative evolutionary analyses on modern and fossil species. We demonstrate a single origin of the raptorial foreleg and its associated novelties as key innovations triggering an early radiation of raptorial mantispoids from the Late Triassic to the Early Jurassic. Subsequently, the evolution of the raptorial foreleg influenced the diversification in different modes among lineages. At times, it might have limited the morphological diversity of other body parts and lead to lineage constraint by intensifying competition and lowering environmental resilience, e.g., in thorny lacewings, whose extant diversity is meagre. Conversely, in mantidflies, reduced emphasis on foreleg novelties and increased plasticity in other body parts may lead to better adaptation to predator-prey interactions and environmental shifts, thus maintaining a stable or accelerated level of diversification. We also reveal how major environmental change and lineage interactions interplayed with raptorial novelties in shaping the significant oscillations of mantispoid diversification over deep time, especially the abrupt shift near the mid-Cretaceous. However, by excluding a substantial portion of samples from the mid-Cretaceous of Myanmar, these shifts of some evolutionary parameters, such as morphological disparity, body size, and diversification rates, became inconspicuous and might be overestimated due to sampling bias. Our results uncover the intricate evolutionary patterns and profound significance of raptorial specializations, providing new insights into the role of novelties in forming evolutionary trajectories, both for the better and worse. [evolutionary novelty; macroevolution; diversification; raptorial foreleg; fossil; insect; Mantispoidea]","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"5 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142694243","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":"Are Modern Cryptic Species Detectable in the Fossil Record? A Case Study on Agamid Lizards.","authors":"Till Ramm, Jaimi A Gray, Christy A Hipsley, Scott Hocknull, Jane Melville, Johannes Müller","doi":"10.1093/sysbio/syae067","DOIUrl":"https://doi.org/10.1093/sysbio/syae067","url":null,"abstract":"<p><p>Comparisons of extant and extinct biodiversity are often dependent on objective morphology-based identifications of fossils and assume a well-established and comparable taxonomy for both fossil and modern taxa. However, since many modern (cryptic) species are delimitated mainly via external morphology and / or molecular data, it is often unclear to what degree fossilized (osteological) remains allow classification to a similar level. When intraspecific morphological variation in extant taxa is poorly known, the definition of extinct species as well as the referral of fossils to extant species can be heavily biased, particularly if fossils are represented by incomplete isolated skeletal elements. This problem is especially pronounced in squamates (lizards and snakes) owing to a lack of osteological comparative knowledge for many lower taxonomic groups, concomitant with a recent increase of molecular studies revealing great cryptic diversity. Here, we apply a quantitative approach using 3D geometric morphometrics on 238 individuals of 14 genera of extant Australian and Papua New Guinean agamid lizards to test the value of two isolated skull bones (frontals and maxillae) for inferring taxonomic and ecological affinities. We further test for the consistency of intra- and interspecific morphological variability of these elements as a proxy for extinct taxonomic richness. We show that both bones are diagnostic at the generic level, and both can infer microhabitat and are of palaeoecological utility. However, species-level diversity is likely underestimated by both elements, with ~30-40% of species pairs showing no significant differences in shape. Mean intraspecific morphological variability is largely consistent across species and bones and thus a useful proxy for extinct species diversity. Reducing sample size and landmark completeness to approximate fossil specimens led to decreased classification accuracy and increased variance of morphological disparity, raising further doubts on the transferability of modern species borders to the fossil record of agamids. Our results highlight the need to establish appropriate levels of morphology-based taxonomic or ecological groupings prior to comparing extant and extinct biodiversity.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":""},"PeriodicalIF":6.1,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142688897","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":"Testing relationships between multiple regional features and biogeographic processes of speciation, extinction, and dispersal","authors":"Sarah K Swiston, Michael J Landis","doi":"10.1093/sysbio/syae062","DOIUrl":"https://doi.org/10.1093/sysbio/syae062","url":null,"abstract":"The spatial and environmental features of regions where clades are evolving are expected to impact biogeographic processes such as speciation, extinction, and dispersal. Any number of regional features (such as elevation, distance, area, etc.) may be directly or indirectly related to these processes. For example, it may be that distances or differences in elevation or both may limit dispersal rates. However, it is difficult to disentangle which features are most strongly related to rates of different processes. Here, we present an extensible Multi-feature Feature-Informed GeoSSE (MultiFIG) model that allows for the simultaneous investigation of any number of regional features. MultiFIG provides a conceptual framework for incorporating large numbers of features of different types, including categorical, quantitative, within-region, and between-region features, along with a mathematical framework for translating those features into biogeographic rates for statistical hypothesis testing. Using traditional Bayesian parameter estimation and reversible-jump Markov chain Monte Carlo, MultiFIG allows for the exploration of models with different numbers and combinations of feature-effect parameters, and generates estimates for the strengths of relationships between each regional feature and core process. We validate this model with a simulation study covering a range of scenarios with different numbers of regions, tree sizes, and feature values. We also demonstrate the application of MultiFIG with an empirical case study of the South American lizard genus Liolaemus, investigating sixteen regional features related to area, distance, and elevation. Our results show two important feature-process relationships: a negative distance/dispersal relationship, and a negative area/extinction relationship. Interestingly, although speciation rates were found to be higher in Andean versus non-Andean regions, the model did not assign significance to Andean- or elevation-related parameters. These results highlight the need to consider multiple regional features in biogeographic hypothesis testing.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"191 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142678579","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":"Robustness of Divergence Time Estimation Despite Gene Tree Estimation Error: A Case Study of Fireflies (Coleoptera: Lampyridae)","authors":"Sebastian Höhna, Sarah E Lower, Pablo Duchen, Ana Catalán","doi":"10.1093/sysbio/syae065","DOIUrl":"https://doi.org/10.1093/sysbio/syae065","url":null,"abstract":"Genomic data has become ubiquitous in phylogenomic studies, including divergence time estimation, but provide new challenges. These challenges include, amongst others, biological gene tree discordance, methodological gene tree estimation error, and computational limitations on performing full Bayesian inference under complex models. In this study, we use a recently published firefly (Coleoptera: Lampyridae) anchored hybrid enrichment dataset (AHE; 436 loci for 88 Lampyridae species and 10 outgroup species) as a case study to explore gene tree estimation error and the robustness of divergence time estimation. First, we explored the amount of model violation using posterior predictive simulations because model violations are likely to bias phylogenetic inferences and produce gene tree estimation error. We specifically focused on missing data (either uniformly distributed or systematically) and the distribution of highly variable and conserved sites (either uniformly distributed or clustered). Our assessment of model adequacy showed that standard phylogenetic substitution models are not adequate for any of the 436 AHE loci. We tested if the model violations and alignment errors resulted indeed in gene tree estimation error by comparing the observed gene tree discordance to simulated gene tree discordance under the multispecies coalescent model. Thus, we show that the inferred gene tree discordance is not only due to biological mechanism but primarily due to inference errors. Lastly, we explored if divergence time estimation is robust despite the observed gene tree estimation error. We selected four subsets of the full AHE dataset, concatenated each subset and performed a Bayesian relaxed clock divergence estimation in RevBayes. The estimated divergence times overlapped for all nodes that are shared between the topologies. Thus, divergence time estimation is robust using any well selected data subset as long as the topology inference is robust.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"20 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142610475","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":"Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama.","authors":"Benjamin M Titus, H Lisle Gibbs, Nuno Simões, Marymegan Daly","doi":"10.1093/sysbio/syae045","DOIUrl":"10.1093/sysbio/syae045","url":null,"abstract":"<p><p>Recent genomic analyses have highlighted the prevalence of speciation with gene flow in many taxa and have underscored the importance of accounting for these reticulate evolutionary processes when constructing species trees and generating parameter estimates. This is especially important for deepening our understanding of speciation in the sea where fast-moving ocean currents, expanses of deep water, and periodic episodes of sea level rise and fall act as soft and temporary allopatric barriers that facilitate both divergence and secondary contact. Under these conditions, gene flow is not expected to cease completely while contemporary distributions are expected to differ from historical ones. Here, we conduct range-wide sampling for Pederson's cleaner shrimp (Ancylomenes pedersoni), a species complex from the Greater Caribbean that contains three clearly delimited mitochondrial lineages with both allopatric and sympatric distributions. Using mtDNA barcodes and a genomic ddRADseq approach, we combine classic phylogenetic analyses with extensive topology testing and demographic modeling (10 site frequency replicates × 45 evolutionary models × 50 model simulations/replicate = 22,500 simulations) to test species boundaries and reconstruct the evolutionary history of what was expected to be a simple case study. Instead, our results indicate a history of allopatric divergence, secondary contact, introgression, and endemic hybrid speciation that we hypothesize was driven by the final closure of the Isthmus of Panama and the strengthening of the Gulf Stream Current ~3.5 Ma. The history of this species complex recovered by model-based methods that allow reticulation differs from that recovered by standard phylogenetic analyses and is unexpected given contemporary distributions. The geologically and biologically meaningful insights gained by our model selection analyses illuminate what is likely a novel pathway of species formation not previously documented that resulted from one of the most biogeographically significant events in Earth's history.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"758-768"},"PeriodicalIF":6.1,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141749074","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}