Systematic Biology最新文献

{"title":"A phylogenetic approach to delimitate species in a probabilistic way","authors":"Xia Hua, Craig Moritz","doi":"10.1093/sysbio/syaf004","DOIUrl":"https://doi.org/10.1093/sysbio/syaf004","url":null,"abstract":"Different species concepts and their associated criteria have been used to delimit species boundaries, such as the absence of gene flow for the biological species concept and the presence of morphological distinction for the morphological species concept. The need for different delimitation criteria largely reflects the fact that species are generated under various speciation mechanisms. A key question is how to make species delimitation consistent in a species group, especially when we want to delimit the species boundaries over many newly discovered evolutionary lineages and add these new lineages into a comparative analysis. Instead of forcing a single definition of ‘species’, we can acknowledge different delimitation criteria by modelling how fast lineages in a species group evolve to meet these criteria along a phylogenetic tree. This study presents such a new model and a new delimitation approach that calculates the probability of each possible species identity of a lineage. We use simulations to show that our likelihood function gives accurate estimates of parameters in the model and our approach have high power to correctly identify species identities. We apply the approach to lineages in two real species groups that already have genomic and morphological evidence for their species identities. Our approach gives consistent inference of species identities with these existing pieces of evidence. We also demonstrate how to use our model to test a popular hypothesis about speciation process across all lineages in a species group and discuss further extension of the model to study speciation.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"4 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143044198","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":"Dating the bacterial tree of life based on ancient symbiosis.","authors":"Sishuo Wang, Haiwei Luo","doi":"10.1093/sysbio/syae071","DOIUrl":"https://doi.org/10.1093/sysbio/syae071","url":null,"abstract":"<p><p>Obtaining a timescale for bacterial evolution is crucial to understand early life evolution but is difficult owing to the scarcity of bacterial fossils. Here, we introduce multiple new time constraints to calibrate bacterial evolution based on ancient symbiosis. This idea is implemented using a bacterial tree constructed with genes found in the mitochondrial lineages phylogenetically embedded within Proteobacteria. The expanded mitochondria-bacterial tree allows the node age constraints of eukaryotes established by their abundant fossils to be propagated to ancient co-evolving bacterial symbionts and across the bacterial tree of life. Importantly, we formulate a new probabilistic framework that considers uncertainty in inference of the ancestral lifestyle of modern symbionts to apply 19 relative time constraints (RTC) each informed by host-symbiont association to constrain bacterial symbionts no older than their eukaryotic host. Moreover, we develop an approach to incorporating substitution mixture models that better accommodate substitutional saturation and compositional heterogeneity for dating deep phylogenies. Our analysis estimates that the last bacterial common ancestor (LBCA) occurred approximately 4.0-3.5 billion years ago (Ga), followed by rapid divergence of major bacterial clades. It is generally robust to alternative root ages, root positions, tree topologies, fossil ages, ancestral lifestyle reconstruction, gene sets, among other factors. The obtained timetree serves as a foundation for testing hypotheses regarding bacterial diversification and its correlation with geobiological events across different timescales.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":""},"PeriodicalIF":6.1,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143024894","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":"Integrating Deep Learning Derived Morphological Traits and Molecular Data for Total-Evidence Phylogenetics: Lessons from Digitized Collections.","authors":"Roberta Hunt,José L Reyes-Hernández,Josh Jenkins Shaw,Alexey Solodovnikov,Kim Steenstrup Pedersen","doi":"10.1093/sysbio/syae072","DOIUrl":"https://doi.org/10.1093/sysbio/syae072","url":null,"abstract":"Deep learning has previously shown success in automatically generating morphological traits which carry a phylogenetic signal. In this paper we explore combining molecular data with deep learning derived morphological traits from images of pinned insects to generate total-evidence phylogenies and we reveal challenges. Deep learning derived morphological traits, while informative, underperform when used in isolation compared to molecular analyses. However, they can improve molecular results in total evidence settings. We use a dataset of rove beetle images to compare the effect of different dataset splits and deep metric loss functions on morphological and total evidence results. We find a slight preference for the cladistic dataset split and contrastive loss function. Additionally, we explore the effect of varying the number of genes used in inference and find that different gene combinations provide the best results when used on their own vs in total evidence analysis. Despite the promising nature of integrating deep learning techniques with molecular data, challenges remain regarding the strength of the phylogenetic signal and the resource demands of data acquisition. We suggest that future work focus on improved trait extraction and the development of disentangled networks to better interpret the derived traits, thus expanding the applicability of these methods in phylogenetic studies.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"107 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142991741","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":"Inference of multiple mergers while dating a pathogen phylogeny","authors":"David Helekal, Jere Koskela, Xavier Didelot","doi":"10.1093/sysbio/syaf003","DOIUrl":"https://doi.org/10.1093/sysbio/syaf003","url":null,"abstract":"The vast majority of pathogen phylogenetic studies do not consider the possibility of multiple merger events being present, where a single node of the tree leads to more than two descendent branches. These events are however likely to occur when studying a relatively small population or if there is high variability in the reproductive chances. Here we consider the problem of detecting the presence of multiple mergers in the context of dating a phylogeny, that is determining the date of each of the nodes. We use the Lambda-coalescent theory as a modelling framework and show how Bayesian inference can be efficiently performed using a Billera-Holmes- Vogtmann space embedding and a customised Markov Chain Monte Carlo sampling scheme. We applied this new analysis methodology to a large number of simulated datasets to show that it is possible to infer if and when multiple merger events occurred, and that the phylogenetic dating is improved as a result of taking this information into account. We also analysed real datasets of Vibrio cholerae and Mycobacterium tuberculosis to demonstrate the relevance of our approach to real pathogen evolutionary epidemiology. We have implemented our new methodology in a R package which is freely available at https://github.com/dhelekal/MMCTime.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"28 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142989247","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":"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}