Systematic Biology最新文献

{"title":"Punctuated versus gradual shifts in the multivariate evolutionary process: a test with paired radiations of scincid lizards","authors":"Natasha Stepanova, James D Boyko, Jada Lin, Alison R Davis Rabosky, Daniel L Rabosky","doi":"10.1093/sysbio/syaf002","DOIUrl":"https://doi.org/10.1093/sysbio/syaf002","url":null,"abstract":"As lineages become separated in time, they are expected to accumulate mutational (or developmental-genetic) differences that influence the macroevolutionary trajectories of those lineages even under similar environmental conditions. Here, we compare the dynamics of phenotypic evolution in radiations of scincid lizards from Australia and Madagascar that are separated by more than 100 million years of independent evolution and show rampant phenotypic parallelism. We collected linear measurements of the skull, limbs, and limb girdles from micro-CT scans of 94 Australian and 29 Malagasy species. Using multivariate comparative methods, we tested whether the underlying evolutionary covariance structure for this superficial parallelism was conserved and whether these patterns were consistent across distinct functional modules. Malagasy and most Australian skinks have similar covariance matrices for skull evolution. Results are ambiguous for limbs and limb girdles, as some trait subsets support different evolutionary processes and for other subsets, a shared covariance matrix could not be rejected. However, across most trait sets, the extremely speciose Australian genus Ctenotus exhibits a radically different covariance structure from all other lizards in these groups, including several closely related genera. The shift in Ctenotus demonstrates that the architecture of trait correlations can change at relatively shallow timescales and may explain the unique position of this clade in morphospace relative to other scincid lizards from both geographic regions. More generally, our results demonstrate that the multivariate evolutionary process can change dramatically in a relatively short period of time.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"49 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142987311","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":"Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants","authors":"Marek L Borowiec, Y Miles Zhang, Karen Neves, Manuela O Ramalho, Brian L Fisher, Andrea Lucky, Corrie S Moreau","doi":"10.1093/sysbio/syaf001","DOIUrl":"https://doi.org/10.1093/sysbio/syaf001","url":null,"abstract":"While some relationships in phylogenomic studies have remained stable since the Sanger sequencing era, many challenging nodes remain, even with genome-scale data. Incongruence or lack of resolution in the phylogenomic era is frequently attributed to inadequate data modeling and analytical issues that lead to systematic biases. However, few studies investigate the potential for random error or establish expectations for the level of resolution achievable with a given empirical dataset and integrate uncertainties across methods when faced with conflicting results. Ants are the most species-rich lineage of social insects and one of the most ecologically important terrestrial animals. Consequently, ants have garnered significant research attention, including their systematics. Despite this, there has been no comprehensive genus-level phylogeny of the ants inferred using genomic data that thoroughly evaluates both signal strength and incongruence. In this study, we provide insight into and quantify uncertainty across the ant tree of life by utilizing the most taxonomically comprehensive Ultraconserved Elements dataset of ants to date, including 277 (81%) of recognized ant genera from all 16 extant subfamilies, and representing over 98% of described species. We use simulations to establish expectations for resolution, identify branches with less-than-expected concordance, and dissect the effects of data and model selection on recalcitrant nodes. Simulations show that hundreds of loci are needed to resolve recalcitrant nodes on our genus-level ant phylogeny. This demonstrates the continued role of random error in phylogenomic studies. Our analyses provide a comprehensive picture of support and incongruence across the ant phylogeny, while offering a more nuanced depiction of uncertainty and significantly expanding generic sampling. We use a consensus approach to integrate uncertainty across different analyses and find that assumptions about root age exert substantial influence on divergence dating. Our results suggest that advancing the understanding of ant phylogeny will require not only more data but also more refined phylogenetic models. We also provide a workflow for identifying under-supported nodes in concatenation analyses, outline a pragmatic way to reconcile conflicting results in phylogenomics, and introduce a user-friendly locus selection tool for divergence dating.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"1 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142936914","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":"Phylogenomic Insights into the Evolution and Origin of Nematoda","authors":"Xue Qing, Y Miles Zhang, Sidi Sun, Mohammed Ahmed, Wen-Sui Lo, Wim Bert, Oleksandr Holovachov, Hongmei Li","doi":"10.1093/sysbio/syae073","DOIUrl":"https://doi.org/10.1093/sysbio/syae073","url":null,"abstract":"The phylum Nematoda represents one of the most cosmopolitan and abundant metazoan groups on Earth. In this study, we reconstructed the phylogenomic tree for phylum Nematoda. A total of 60 genomes, belonging to eight nematode orders, were newly sequenced, providing the first low-coverage genomes for the orders Dorylaimida, Mononchida, Monhysterida, Chromadorida, Triplonchida, and Enoplida. The resulting phylogeny is well-resolved across most clades, with topologies remaining consistent across various reconstruction parameters. The subclass Enoplia is placed as a sister group to the rest of Nematoda, agreeing with previous published phylogenies. While the order Triplonchida is monophyletic, it is not well-supported, and the order Enoplida is paraphyletic. Taxa possessing a stomatostylet form a monophyletic group; however, the superfamily Aphelenchoidea does not constitute a monophyletic clade. The genera Trichinella and Trichuris are inferred to have shared a common ancestor approximately 202 millions of years ago (Ma), a considerably later period than previously suggested. All stomatostylet-bearing nematodes are proposed to have originated ~305 Ma, corresponding to the transition from the Devonian to the Permian period. The genus Thornia is placed outside of Dorylaimina and Nygolaimina, disagreeing with its position in previous studies. Additionally, we tested the whole genome amplification method and demonstrated that it is a promising strategy for obtaining sufficient DNA for phylogenomic studies of microscopic eukaryotes. This study significantly expanded the current nematode genome dataset, and the well-resolved phylogeny enhances our understanding of the evolution of Nematoda.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"65 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142905028","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 timelines help explain the evolution of parental care strategies","authors":"Zackary A Graham, Zachary J Loughman, Alexandre V Palaoro","doi":"10.1093/sysbio/syae069","DOIUrl":"https://doi.org/10.1093/sysbio/syae069","url":null,"abstract":"Comparative research on the evolution of parental care has followed a general trend in recent years, with researchers gathering data on clutch size or egg size and correlating these traits with ecological variables across a phylogeny. The goal of these studies is to shed light on how and why certain strategies evolve. However, results vary across studies, and we rarely have results explaining why the observed pattern occurred, leaving us with further hypotheses to test. By using a combination of comparative methods, we provide an explanation of how such patterns emerge based on the evolutionary timeline of constructing burrows and the energy invested into egg size and egg number; this combination also allowed us to pinpoint why the pattern occurred. We do so with data on freshwater crayfish, which are ideal for such investigations because they vary in their reliance on burrows, their body size, and their investment into their offspring. Specifically, we tested whether a strong dependence on burrows is related to investment in eggs (i.e., larger eggs or more eggs) given the body size of the species. Surprisingly, we found no correlation between burrowing and the size or number of eggs crayfish lay; instead, body size was the best predictor of the number of eggs (but not the size of eggs) that each species lays. Interestingly, our analysis suggests that crayfish ancestors had a small clutch size, relatively large eggs, and a weak connection to burrows. Thus, the shift to heavily relying on burrows appeared after this lineage was already investing in large eggs, which gives insights into the colonization of freshwater by an ancestral astacidean ancestor. While other studies show that the evolution of parental care strategies is not straightforward, our study provides a clear evolutionary timeline of the interplay between the evolution of burrowing behavior and shifts in the evolution of egg investment. Furthermore, our work showcases how merging multiple phylogenetically informed approaches can disentangle the origin and evolution of life history traits.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"28 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142809649","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":"Discordance Down Under: Combining phylogenomics & fungal symbioses to detangle difficult nodes in a diverse tribe of Australian terrestrial orchids","authors":"Ryan P O’Donnell, Darren C J Wong, Ryan D Phillips, Rod Peakall, Celeste C Linde","doi":"10.1093/sysbio/syae070","DOIUrl":"https://doi.org/10.1093/sysbio/syae070","url":null,"abstract":"Orchid mycorrhizal fungi (OMF) associations in the Orchidaceae are thought to have been a major driver of diversification in the family. In the terrestrial orchid tribe Diurideae, it has long been hypothesised that OMF symbiont associations may reflect evolutionary relationships among orchid hosts. Given that recent phylogenomic efforts have been unable to fully resolve relationships among subtribes in the Diurideae, we sought to ascertain whether orchid OMF preferences may lend support to certain phylogenetic hypotheses. First, we used phylogenomic methods and Bayesian divergence time estimation to produce a genus-level tree for the Diurideae. Next, we synthesised decades of published fungal sequences and morphological/germination data to identify dominant fungal partners at the genus scale and perform ancestral state reconstruction to estimate the evolutionary trajectory of fungal symbiont shifts. Across the tribe, we found phylogenomic discordance stemming from incomplete lineage sorting. However, our results also revealed unprecedented phylogenetic niche conservatism of fungal symbionts within the tribe: entire genera, subtribes, and even groups of related subtribes associate with only a single fungal family, suggesting that fungal symbiont preferences in the Diurideae do indeed reflect phylogenetic relationships among orchid hosts. Moreover, we show that these relationships have evolved directionally from generalist associations with multiple fungal families towards more specific partnerships with only one fungal family. Orchid symbiont preferences here provide new insights into the placement of several groups with longstanding phylogenetic uncertainty. In spite of complex evolutionary histories, host-symbiont relationships can be used to help detangle alternative phylogenetic hypotheses.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"1 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142805468","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":"Persistent Gene Flow Suggests an Absence of Reproductive Isolation in an African Antelope Speciation Model.","authors":"Xi Wang, Casper-Emil Tingskov Pedersen, Georgios Athanasiadis, Genís Garcia-Erill, Kristian Hanghøj, Laura D Bertola, Malthe Sebro Rasmussen, Mikkel Schubert, Xiaodong Liu, Zilong Li, Long Lin, Renzo F Balboa, Emil Jørsboe, Casia Nursyifa, Shanlin Liu, Vincent Muwanika, Charles Masembe, Lei Chen, Wen Wang, Ida Moltke, Hans R Siegismund, Anders Albrechtsen, Rasmus Heller","doi":"10.1093/sysbio/syae037","DOIUrl":"10.1093/sysbio/syae037","url":null,"abstract":"<p><p>African antelope diversity is a globally unique vestige of a much richer world-wide Pleistocene megafauna. Despite this, the evolutionary processes leading to the prolific radiation of African antelopes are not well understood. Here, we sequenced 145 whole genomes from both subspecies of the waterbuck (Kobus ellipsiprymnus), an African antelope believed to be in the process of speciation. We investigated genetic structure and population divergence and found evidence of a mid-Pleistocene separation on either side of the eastern Great Rift Valley, consistent with vicariance caused by a rain shadow along the so-called \"Kingdon's Line.\" However, we also found pervasive evidence of both recent and widespread historical gene flow across the Rift Valley barrier. By inferring the genome-wide landscape of variation among subspecies, we found 14 genomic regions of elevated differentiation, including a locus that may be related to each subspecies' distinctive coat pigmentation pattern. We investigated these regions as candidate speciation islands. However, we observed no significant reduction in gene flow in these regions, nor any indications of selection against hybrids. Altogether, these results suggest a pattern whereby climatically driven vicariance is the most important process driving the African antelope radiation and suggest that reproductive isolation may not set in until very late in the divergence process. This has a significant impact on taxonomic inference, as many taxa will be in a gray area of ambiguous systematic status, possibly explaining why it has been hard to achieve consensus regarding the species status of many African antelopes. Our analyses demonstrate how population genetics based on low-depth whole genome sequencing can provide new insights that can help resolve how far lineages have gone along the path to speciation.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"979-994"},"PeriodicalIF":6.1,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11637686/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141976713","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":"Phylogenomics and Pervasive Genome-Wide Phylogenetic Discordance Among Fin Whales (Balaenoptera physalus).","authors":"Fabricio Furni, Eduardo R Secchi, Camilla Speller, Daniel DenDanto, Christian Ramp, Finn Larsen, Sally Mizroch, Jooke Robbins, Richard Sears, Jorge Urbán R, Martine Bérubé, Per J Palsbøll","doi":"10.1093/sysbio/syae049","DOIUrl":"10.1093/sysbio/syae049","url":null,"abstract":"<p><p>Phylogenomics has the power to uncover complex phylogenetic scenarios across the genome. In most cases, no single topology is reflected across the entire genome as the phylogenetic signal differs among genomic regions due to processes, such as introgression and incomplete lineage sorting. Baleen whales are among the largest vertebrates on Earth with a high dispersal potential in a relatively unrestricted habitat, the oceans. The fin whale (Balaenoptera physalus) is one of the most enigmatic baleen whale species, currently divided into four subspecies. It has been a matter of debate whether phylogeographic patterns explain taxonomic variation in fin whales. Here we present a chromosome-level whole genome analysis of the phylogenetic relationships among fin whales from multiple ocean basins. First, we estimated concatenated and consensus phylogenies for both the mitochondrial and nuclear genomes. The consensus phylogenies based upon the autosomal genome uncovered monophyletic clades associated with each ocean basin, aligning with the current understanding of subspecies division. Nevertheless, discordances were detected in the phylogenies based on the Y chromosome, mitochondrial genome, autosomal genome and X chromosome. Furthermore, we detected signs of introgression and pervasive phylogenetic discordance across the autosomal genome. This complex phylogenetic scenario could be explained by a puzzle of introgressive events, not yet documented in fin whales. Similarly, incomplete lineage sorting and low phylogenetic signal could lead to such phylogenetic discordances. Our study reinforces the pitfalls of relying on concatenated or single locus phylogenies to determine taxonomic relationships below the species level by illustrating the underlying nuances that some phylogenetic approaches may fail to capture. We emphasize the significance of accurate taxonomic delineation in fin whales by exploring crucial information revealed through genome-wide assessments.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"873-885"},"PeriodicalIF":6.1,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11637684/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142000709","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":"Blouch: Bayesian Linear Ornstein-Uhlenbeck Models for Comparative Hypotheses.","authors":"Mark Grabowski","doi":"10.1093/sysbio/syae044","DOIUrl":"10.1093/sysbio/syae044","url":null,"abstract":"<p><p>Relationships among species in the tree of life can complicate comparative methods and testing adaptive hypotheses. Models based on the Ornstein-Uhlenbeck process permit hypotheses about adaptation to be tested by allowing traits to either evolve toward fixed adaptive optima (e.g., regimes or niches) or track continuously changing optima that can be influenced by other traits. These models allow estimation of the effects of both adaptation and phylogenetic inertia-resistance to adaptation due to any source-on trait evolution, an approach known as the \"adaptation-inertia\" framework. However, previous applications of this framework, and most approaches suggested to deal with the issue of species non-independence, are based on a maximum likelihood approach, and thus it is difficult to include information based on prior biological knowledge in the analysis, which can affect resulting inferences. Here, I present Blouch, (Bayesian Linear Ornstein-Uhlenbeck Models for Comparative Hypotheses), which fits allometric and adaptive models of continuous trait evolution in a Bayesian framework based on fixed or continuous predictors and incorporates measurement error. I first briefly discuss the models implemented in Blouch, and then the new applications for these models provided by a Bayesian framework. This includes the advantages of assigning biologically meaningful priors when compared to non-Bayesian approaches, allowing for varying effects (intercepts and slopes), and multilevel modeling. Validations on simulated data show good performance in recovering the true evolutionary parameters for all models. To demonstrate the workflow of Blouch on an empirical dataset, I test the hypothesis that the relatively larger antlers of larger-bodied deer are the result of more intense sexual selection that comes along with their tendency to live in larger breeding groups. While results show that larger-bodied deer that live in larger breeding groups have relatively larger antlers, deer living in the smallest groups appear to have a different and steeper scaling pattern of antler size to body size than other groups. These results are contrary to previous findings and may argue that a different type of sexual selection or other selective pressures govern optimum antler size in the smallest breeding groups.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"1038-1050"},"PeriodicalIF":6.1,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11637605/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141752780","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":"Inferring Taxonomic Affinities and Genetic Distances Using Morphological Features Extracted from Specimen Images: A Case Study with a Bivalve Data Set.","authors":"Martin Hofmann, Steffen Kiel, Lara M Kösters, Jana Wäldchen, Patrick Mäder","doi":"10.1093/sysbio/syae042","DOIUrl":"10.1093/sysbio/syae042","url":null,"abstract":"<p><p>Reconstructing the tree of life and understanding the relationships of taxa are core questions in evolutionary and systematic biology. The main advances in this field in the last decades were derived from molecular phylogenetics; however, for most species, molecular data are not available. Here, we explore the applicability of 2 deep learning methods-supervised classification approaches and unsupervised similarity learning-to infer organism relationships from specimen images. As a basis, we assembled an image data set covering 4144 bivalve species belonging to 74 families across all orders and subclasses of the extant Bivalvia, with molecular phylogenetic data being available for all families and a complete taxonomic hierarchy for all species. The suitability of this data set for deep learning experiments was evidenced by an ablation study resulting in almost 80% accuracy for identifications on the species level. Three sets of experiments were performed using our data set. First, we included taxonomic hierarchy and genetic distances in a supervised learning approach to obtain predictions on several taxonomic levels simultaneously. Here, we stimulated the model to consider features shared between closely related taxa to be more critical for their classification than features shared with distantly related taxa, imprinting phylogenetic and taxonomic affinities into the architecture and training procedure. Second, we used transfer learning and similarity learning approaches for zero-shot experiments to identify the higher-level taxonomic affinities of test species that the models had not been trained on. The models assigned the unknown species to their respective genera with approximately 48% and 67% accuracy. Lastly, we used unsupervised similarity learning to infer the relatedness of the images without prior knowledge of their taxonomic or phylogenetic affinities. The results clearly showed similarities between visual appearance and genetic relationships at the higher taxonomic levels. The correlation was 0.6 for the most species-rich subclass (Imparidentia), ranging from 0.5 to 0.7 for the orders with the most images. Overall, the correlation between visual similarity and genetic distances at the family level was 0.78. However, fine-grained reconstructions based on these observed correlations, such as sister-taxa relationships, require further work. Overall, our results broaden the applicability of automated taxon identification systems and provide a new avenue for estimating phylogenetic relationships from specimen images.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"920-940"},"PeriodicalIF":6.1,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141752782","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":"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}