Systematic Biology最新文献

{"title":"Data Fusion for Integrative Species Identification Using Deep Learning","authors":"Lara M Ko¨sters, Kevin Karbstein, Martin Hofmann, Ladislav Hodaˇc, Patrick Ma¨der, Jana Wa¨ldchen","doi":"10.1093/sysbio/syaf026","DOIUrl":"https://doi.org/10.1093/sysbio/syaf026","url":null,"abstract":"DNA analyses have revolutionized species identification and taxonomic work. Yet, persistent challenges arise from little differentiation among and considerable variation within species, particularly among closely related groups. While images are commonly used as an alternative modality for automated identification tasks, their usability is limited by the same concerns. An integrative strategy, fusing molecular and image data through machine learning, holds significant promise for fine-grained species identification. However, a systematic overview and rigorous statistical testing concerning molecular and image preprocessing and fusion techniques, including practical advice for biologists, are missing so far. We introduce a machine learning scheme that integrates both molecular and image data for species identification. Initially, we systematically assess and compare three different DNA arrangements (aligned, unaligned, SNP-reduced) and two encoding methods (fractional, ordinal). Additionally, artificial neural networks are used to extract visual and molecular features, and we propose strategies for fusing this information. Specifically, we investigate three strategies: I) fusing directly after feature extraction, II) fusing features that passed through a fully connected layer after feature extraction, and III) fusing the output scores of both unimodal models. We systematically and statistically evaluate these strategies for four eukaryotic datasets, including two plant (Asteraceae, Poaceae) and two animal families (Lycaenidae, Coccinellidae) using Leave-One-Out Cross-Validation (LOOCV). In addition, we developed an approach to understand molecular- and image-specific identification failure. Aligned sequences with nucleotides encoded as decimal number vectors achieved the highest identification accuracy among DNA data preprocessing techniques in all four datasets. Fusing molecular and visual features directly after feature extraction yielded the best results for three out of four datasets (52-99%).Overall, combining DNA with image data significantly increased accuracy in three out of four datasets, with plant datasets showing the most substantial improvement (Asteraceae: +19%, Poaceae: +13.6%). Even for Lycaenidae with high identification accuracy based on molecular data (>96%), a statistically significant improvement (+2.1%) was observed.Detailed analysis of confusion rates between and within genera shows that DNA alone tends to identify the genus correctly, but often fails to recognize the species. The failure to resolve species is alleviated by including image data in the training. This increase in resolution hints at a hierarchical role of modalities in which molecular data coarsely groups the specimens to then be guided towards a more fine-grained identification by the connected image. We systematically showed and explained, for the first time, that optimizing the preprocessing and integration of molecular and image data offers signific","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"8 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144288200","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":"Species Richness and Speciation Rates for all Terrestrial Animals Emerge from a Synthesis of Ecological Theories.","authors":"Lucas D Fernandes, Rogier E Hintzen, Samuel E D Thompson, Tatsiana Barychka, Derek Tittensor, Michael Harfoot, Tim Newbold, James Rosindell","doi":"10.1093/sysbio/syaf006","DOIUrl":"10.1093/sysbio/syaf006","url":null,"abstract":"<p><p>The total number of species on earth and the rate at which new species are created are fundamental questions for ecology, evolution and conservation. These questions have typically been approached separately, despite their obvious interconnection. In this study, we approach both questions in conjunction, for all terrestrial animals. To do this, we combine two previously unconnected bodies of theory: general ecosystem models and individual-based ecological neutral theory. General ecosystem models provide us with estimated numbers of individual organisms, separated by functional group and body size. Neutral theory, applied within a guild of functionally similar individuals, connects species richness, speciation rate, and number of individual organisms. In combination, for terrestrial endotherms where species numbers are known, they provide us with estimates for speciation rates as a function of body size and diet class. Extrapolating the same rates to guilds of ectotherms enables us to estimate the species richness of those groups, including species yet to be described. We find that speciation rates per species per million years decrease with increasing body size. Rates are also higher for carnivores compared to omnivores or herbivores of the same body size. Our estimate for the total number of terrestrial species of animals is in the range 1.03-2.92 million species, a value consistent with estimates from previous studies, despite having used a fundamentally new approach. Perhaps what is most remarkable about these results is that they have been obtained using only limited data from larger endotherms and their speciation rates, with the predictive process being based on mechanistic theory. This work illustrates the potential of a new approach to classic eco-evolutionary questions, while also adding weight to existing predictions. As we now face an era of dramatic biological change, new methods will be needed to mechanistically model global biodiversity at the species and individual organism level. This will be a huge challenge but the combination of general ecosystem models and neutral theory that we introduce here is a way to tractably achieve it.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"469-482"},"PeriodicalIF":6.1,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143743968","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":"Repeated Evolution of Storage Root and Invasions of Alpine Biome Drove Replicated Radiations of the Megadiverse Corydalis (Papaveraceae) in the Qinghai-Tibet Plateau.","authors":"Huan-Wen Peng, Yuan-Yuan Ling, Kun-Li Xiang, Andrey S Erst, Xiao-Qian Li, Lian Lian, Bing Liu, Tatyana V Erst, Rosa Del C Ortiz, Florian Jabbour, Wei Wang","doi":"10.1093/sysbio/syaf014","DOIUrl":"10.1093/sysbio/syaf014","url":null,"abstract":"<p><p>-The interplay of key innovation and ecological opportunity is commonly recognized to be the catalyst for rapid radiation. Underground storage organs (USOs), as a vital ecological trait, are advantageous for the adaptation of plants to extreme environments, but receive less attention compared to aboveground organs. Repeated evolution of various USOs has occurred across the plant tree of life. However, whether repeated occurrences of a USO in different clades of a group can promote its replicated radiations in combination with the invasion of similar environments remains poorly known. Corydalis is a megadiverse genus in Papaveraceae and exhibits remarkable variations in USO morphology and biome occupancy. Here, we first generated a robust phylogeny for Corydalis with wide taxonomic and genomic coverage based on plastome and nuclear ribosomal DNA sequence data. By dating the branching events, reconstructing ancestral ranges, evaluating diversification dynamics, and inferring evolutionary patterns of USOs and biomes and their correlations, we then tested whether the interplay of USO evolution and biome shifts has driven rapid diversification of some Corydalis lineages. Our results indicate that Corydalis began to diversify in the Qinghai-Tibet Plateau (QTP) at ca. 41 Ma, and 88% of dispersals happened through forests, suggesting that forests served as important dispersal corridors for range expansion of the genus. The storage root has originated independently at least 6 times in Corydalis since the Miocene, and its acquisition could have operated as a key innovation toward the adaptation to the alpine biome in the QTP. Repeated evolution of this game-changing trait and invasions of alpine biome, in combination with geoclimatic changes, could have jointly driven independent radiations of the 2 clades of Corydalis in the QTP at ca. 6 Ma. Our study provides new insights into the joint contribution of USO repeated evolution and biome shifts to replicated radiations, hence increasing our ability to predict evolutionary trajectories in plants facing similar environmental pressures.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"359-372"},"PeriodicalIF":6.1,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143459507","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":"Correction to: Phylogenomic Discordance is Driven by Wide-Spread Introgression and Incomplete Lineage Sorting During Rapid Species Diversification Within Rattlesnakes (Viperidae: Crotalus and Sistrurus).","authors":"","doi":"10.1093/sysbio/syaf008","DOIUrl":"10.1093/sysbio/syaf008","url":null,"abstract":"","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"511"},"PeriodicalIF":6.1,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12162145/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625970","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":"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":"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 2 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 paleoecological 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":"373-394"},"PeriodicalIF":6.1,"publicationDate":"2025-06-12","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":"Link between the Birth-Death process and the Kingman Coalescent - Applications to Phylogenetic Epidemiology.","authors":"Josselin Cornuault, Fabio Pardi, Celine Scornavacca","doi":"10.1093/sysbio/syaf024","DOIUrl":"https://doi.org/10.1093/sysbio/syaf024","url":null,"abstract":"<p><p>The two most popular tree models used in phylogenetics are the birth-death process (BD) and the Kingman coalescent (KC). These two models differ in several respects, notably: (i) the curve of the population size through time is a stochastic process in the BD, versus a parametrized curve in the KC, (ii) the BD makes assumptions about the way samples are collected, while the KC conditions on the number of samples and the collection times, thus bypassing the need to describe the sampling procedure. These two models have been applied to different contexts: the BD in macroevolutionary studies of clades of species, and the KC for populations. The exception is the field of phylogenetic epidemiology which uses both models. This then asks the question of how such different models can be used in the same context. In this paper, we study large-population limits of the BD, in a search for a mathematical link between the BD and the KC. We show that the KC is the large-population limit of a BD conditioned on a given population trajectory, and we provide the formula for the parameter θ of the limiting KC. This formula appears in earlier studies, but the present article is the first to show formally how the correspondence arises as a large-population limit, and that the BD needs to be conditioned for the KC to arise. Besides these fundamentally mathematical results, we demonstrate how our findings can be used practically in phylogenetic inference. In particular, we propose a new method for phylogenetic epidemiology, called CalicoBird, ensuing from our results. We conjecture that this new method, used in conjunction with auxiliary data (e.g. prevalence or incidence data), should allow estimating important epidemiological parameters (e.g. the prevalence and the effective reproduction number), in a way that is robust to the data-generating model and the sampling procedure. Future studies will be needed to put our claims to the test.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":""},"PeriodicalIF":6.1,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144258976","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":"Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to Evade (Over-)optimization","authors":"Anastasis Togkousidis, Alexandros Stamatakis, Olivier Gascuel","doi":"10.1093/sysbio/syaf043","DOIUrl":"https://doi.org/10.1093/sysbio/syaf043","url":null,"abstract":"Maximum Likelihood (ML) based phylogenetic inference constitutes a challenging optimization problem. Given a set of aligned input sequences, phylogenetic inference tools strive to determine the tree topology, the branch-lengths, and the evolutionary model parameters that maximize the phylogenetic likelihood function. However, there exist compelling reasons to not push optimization to its limits, by means of early, yet adequate stopping criteria. Since input sequences are typically subject to stochastic and systematic noise, caution is warranted to prevent over-optimization and the risk of overfitting the model to noisy data. To address this, we integrate the Kishino-Hasegawa (KH) test into RAxML-NG as a reliable and fast-to-compute Early Stopping criterion to effectively limit excessive and compute-intensive over-optimization. Initially, we introduce a simplified heuristic tree search strategy in RAxML-NG (sRAxML-NG) as an underlying method for Early Stopping. Subsequently, we use the KH test in combination with sRAxML-NG, to statistically assess the significance of differences between intermediate trees prior to and after major optimization steps. The tree search terminates early when improvements are statistically insignificant. We also propose an extension to the standard KH test that allows to correct for multiple testing, which maintains accuracy while achieving even higher speedups. For benchmarking we use 300 large representative empirical datasets from TreeBASE. For 98% of the DNA datasets, all Early Stopping methods we introduce infer trees that are statistically equivalent to those inferred from RAxML-NG v1.2. For AA datasets, the fraction of datasets where sRAxML-NG, KH, and the KH-multiple testing versions infer statistically equivalent trees is 96%, 95%, and 92%, respectively. In conjuction with sRAxML-NG, the average speedup achieved by the KH-multiple testing version is 5x for DNA and 3.9x for protein datasets compared to RAxML-NG v1.2. We implemented our stopping criteria in RAxML-NG, which is available under GNU GPL at https://github.com/togkousa/raxml-ng/tree/stopping-criteria.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"12 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144183773","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 Estimation of Branch-specific Shifts in the Tempo of Origination","authors":"Bjørn T Kopperud, Sebastian Höhna","doi":"10.1093/sysbio/syaf041","DOIUrl":"https://doi.org/10.1093/sysbio/syaf041","url":null,"abstract":"Studying rates of species diversification is one of the key themes in macroevolution. In particular, we are interested in if some clades in a phylogeny diversify more rapidly/slowly than others due to branch-specific diversification rates. A common approach in neontological studies is to use a phylogenetic birth-death process to model species diversification. Specifically, the birth-death-shift process is used to model branch-specific shifts in the tempo of diversification. Here, we present Pesto, a new method and software that estimates branch-specific diversification rates using an empirical Bayes approach. Pesto does not rely on Markov chain Monte Carlo simulations and instead deterministically computes the posterior mean branch-specific diversification rates using only two traversals of the tree. This method is blazingly fast: the birth-death-shift model can be fitted to large phylogenies (&amp;gt;20k taxa) in minutes on a personal computer while also providing branch-specific inference of diversification rate shift events. Thus, we can robustly infer branch-specific diversification rates and the number of diversification rate shift events for large-scale phylogenies, as well as exploring the characteristics of the birth-death-shift model through complex and large-scale simulations. Here, we first describe the method and the software implementation Pesto and explore its behavior using trees simulated under the birth-death-shift model. Then, we explore the behavior of inferring significant branch-specific diversification rate shifts using both Bayes factors and effect sizes. We find few to no false positive inferences of diversification rate shift events but many false negatives (reduced power). The most difficult parameter to estimate is the rate at which diversification rate shifts occur. Despite this, branch-specific diversification rate estimates are precise and nearly unbiased.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"146 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144176808","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 Cross-Species Gene Flow Using Genomic Data Depends on the Methods: Case Study of Gene Flow in Drosophila.","authors":"Jiayi Ji,Thomas Roberts,Tomáš Flouri,Ziheng Yang","doi":"10.1093/sysbio/syaf019","DOIUrl":"https://doi.org/10.1093/sysbio/syaf019","url":null,"abstract":"Analysis of genomic data in the past two decades has highlighted the prevalence of introgression as an important evolutionary force in both plants and animals. The genus Drosophila has received much attention recently, with an analysis of genomic sequence data revealing widespread introgression across the species phylogeny for the genus. However, the methods used in the study are based on data summaries for species triplets and are unable to infer gene flow between sister lineages or to identify the direction of gene flow. Hence, we reanalyze a subset of the data using the Bayesian program bpp, which is a full-likelihood implementation of the multispecies coalescent model and can provide more powerful inference of gene flow between species, including its direction, timing, and strength. While our analysis supports the presence of gene flow in the species group, the results differ from the previous study: we infer gene flow between sister lineages undetected previously whereas most gene-flow events inferred in the previous study are rejected in our tests. To verify our conclusions, we performed simulations to examine the properties of Bayesian and summary methods. Bpp was found to have high power to detect gene flow, high accuracy in estimated rates of gene flow, and robustness under misspecification of the mode of gene flow. In contrast, summary methods had low power and produced biased estimates of introgression probability. Our results highlight an urgent need for improving the statistical properties of summary methods and the computational efficiency of likelihood methods for inferring gene flow using genomic sequence data.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"12 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144146188","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":"Type genomics: a Framework for integrating Genomic Data into Biodiversity and Taxonomic research.","authors":"Harald Letsch,Carola Greve,Anna K Hundsdoerfer,Iker Irisarri,Jenna M Moore,Marianne Espeland,Stefan Wanke,Umilaela Arifin,Mozes P K Blom,Carolina Corrales,Alexander Donath,Uwe Fritz,Gunther Köhler,Patrick Kück,Sarah Lemer,Ximo Mengual,Nancy Mercado Salas,Karen Meusemann,Anja Palandačić,Christian Printzen,Julia D Sigwart,Karina L Silva-Brandão,Marianna Simões,Madlen Stange,Alexander Suh,Nikolaus Szucsich,Ekin Tilic,Till Töpfer,Astrid Böhne,Axel Janke,Steffen Pauls","doi":"10.1093/sysbio/syaf040","DOIUrl":"https://doi.org/10.1093/sysbio/syaf040","url":null,"abstract":"Name-bearing type specimens have a fundamental role in characterising biodiversity, as these objects represent the physical link between a scientific name and the biological organism. Type specimens are usually deposited in natural history collections, which provide key infrastructure for research on essential biological structures and processes, while preserving records of biodiversity for future generations. Modern systematics increasingly depends on genetic and genomic data to differentiate and characterise species. While the results of genome sequencing are often connected to a physical voucher specimen, they are rarely derived from the ultimate taxonomic reference for a species, i.e., the name-bearing type specimens. This is a known but under-appreciated problem for ensuring the replicability of findings, especially those that affect the interpretation of biodiversity distributions and phylogenetic relationships. Destructive sampling of museum specimens, particularly of type material, often carries a high risk of sequencing failure, and thus the cost of damage to the specimen may outweigh the resulting benefit. Both taxonomic work and genome sequencing require specialist skills and there are often communication gaps between the respective experts. A new, harmonised approach, maximising information extraction while minimising risk to type specimens, is a critical step forward toward linking disciplines across biodiversity research and promoting a better taxonomic and systematic understanding of eukaryotic diversity. The genetic make-up of a type specimen is a fundamental part of its biological information, which can and should be made freely and digitally available through type genomics. Here we describe guidelines for the use of nomenclatural types in genome sequencing approaches considering different kinds of types in different stages of preservation and different data types.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"55 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144103601","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}