Anna Wróbel, Ewelina Klichowska, Arkadiusz Nowak, Marcin Nobis
Diversification and demographic responses are key processes shaping species evolutionary history. Yet we still lack a full understanding of ecological mechanisms that shape genetic diversity at different spatial scales upon rapid environmental changes. In this study, we examined genetic differentiation in an extremophilic grass Puccinellia pamirica and factors affecting its population dynamics among the occupied hypersaline alpine wetlands on the arid Pamir Plateau in Central Asia. Using genomic data, we found evidence of fine-scale population structure and gene flow among the localities established across the high-elevation plateau as well as fingerprints of historical demographic expansion. We showed that an increase in the effective population size could coincide with the Last Glacial Period, which was followed by the species demographic decline during the Holocene. Geographic distance plays a vital role in shaping the spatial genetic structure of P. pamirica alongside with isolation-by-environment and habitat fragmentation. Our results highlight a complex history of divergence and gene flow in this species-poor alpine region during the Late Quaternary. We demonstrate that regional climate specificity and a shortage of nonclimate data largely impede predictions of future range changes of the alpine extremophile using ecological niche modeling. This study emphasizes the importance of fine-scale environmental heterogeneity for population dynamics and species distribution shifts.
多样性和人口反应是影响物种进化史的关键过程。然而,我们对环境快速变化时在不同空间尺度上形成遗传多样性的生态机制仍缺乏全面了解。在这项研究中,我们考察了中亚干旱的帕米尔高原上一种嗜极端水草 Puccinellia pamirica 的遗传分化以及影响其种群动态的因素。利用基因组数据,我们发现了在高海拔高原各地建立的精细种群结构和基因流动的证据,以及历史上人口扩张的痕迹。我们的研究表明,有效种群数量的增加可能与末次冰川期相吻合,而在全新世期间,种群数量随之减少。除了环境隔离和栖息地破碎化之外,地理距离对 P. pamirica 的空间遗传结构的形成也起着至关重要的作用。我们的研究结果突显了第四纪晚期这一物种贫乏的高山地区复杂的分化和基因流动历史。我们的研究结果表明,地区气候的特殊性和非气候数据的缺乏在很大程度上阻碍了利用生态位建模预测这种高山极端物种未来分布范围的变化。这项研究强调了细尺度环境异质性对种群动态和物种分布变化的重要性。
{"title":"Alpine Extremophytes in Evolutionary Turmoil: Complex Diversification Patterns and Demographic Responses of a Halophilic Grass in a Central Asian Biodiversity Hotspot.","authors":"Anna Wróbel, Ewelina Klichowska, Arkadiusz Nowak, Marcin Nobis","doi":"10.1093/sysbio/syad073","DOIUrl":"10.1093/sysbio/syad073","url":null,"abstract":"<p><p>Diversification and demographic responses are key processes shaping species evolutionary history. Yet we still lack a full understanding of ecological mechanisms that shape genetic diversity at different spatial scales upon rapid environmental changes. In this study, we examined genetic differentiation in an extremophilic grass Puccinellia pamirica and factors affecting its population dynamics among the occupied hypersaline alpine wetlands on the arid Pamir Plateau in Central Asia. Using genomic data, we found evidence of fine-scale population structure and gene flow among the localities established across the high-elevation plateau as well as fingerprints of historical demographic expansion. We showed that an increase in the effective population size could coincide with the Last Glacial Period, which was followed by the species demographic decline during the Holocene. Geographic distance plays a vital role in shaping the spatial genetic structure of P. pamirica alongside with isolation-by-environment and habitat fragmentation. Our results highlight a complex history of divergence and gene flow in this species-poor alpine region during the Late Quaternary. We demonstrate that regional climate specificity and a shortage of nonclimate data largely impede predictions of future range changes of the alpine extremophile using ecological niche modeling. This study emphasizes the importance of fine-scale environmental heterogeneity for population dynamics and species distribution shifts.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11282368/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139032576","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}
Killian Smith, Daniel Ayres, René Neumaier, Gert Wörheide, Sebastian Höhna
Phylogenies are central to many research areas in biology and commonly estimated using likelihood-based methods. Unfortunately, any likelihood-based method, including Bayesian inference, can be restrictively slow for large datasets-with many taxa and/or many sites in the sequence alignment-or complex substitutions models. The primary limiting factor when using large datasets and/or complex models in probabilistic phylogenetic analyses is the likelihood calculation, which dominates the total computation time. To address this bottleneck, we incorporated the high-performance phylogenetic library BEAGLE into RevBayes, which enables multi-threading on multi-core CPUs and GPUs, as well as hardware specific vectorized instructions for faster likelihood calculations. Our new implementation of RevBayes+BEAGLE retains the flexibility and dynamic nature that users expect from vanilla RevBayes. In addition, we implemented native parallelization within RevBayes without an external library using the message passing interface (MPI); RevBayes+MPI. We evaluated our new implementation of RevBayes+BEAGLE using multi-threading on CPUs and 2 different powerful GPUs (NVidia Titan V and NVIDIA A100) against our native implementation of RevBayes+MPI. We found good improvements in speedup when multiple cores were used, with up to 20-fold speedup when using multiple CPU cores and over 90-fold speedup when using multiple GPU cores. The improvement depended on the data type used, DNA or amino acids, and the size of the alignment, but less on the size of the tree. We additionally investigated the cost of rescaling partial likelihoods to avoid numerical underflow and showed that unnecessarily frequent and inefficient rescaling can increase runtimes up to 4-fold. Finally, we presented and compared a new approach to store partial likelihoods on branches instead of nodes that can speed up computations up to 1.7 times but comes at twice the memory requirements.
{"title":"Bayesian Phylogenetic Analysis on Multi-Core Compute Architectures: Implementation and Evaluation of BEAGLE in RevBayes With MPI.","authors":"Killian Smith, Daniel Ayres, René Neumaier, Gert Wörheide, Sebastian Höhna","doi":"10.1093/sysbio/syae005","DOIUrl":"10.1093/sysbio/syae005","url":null,"abstract":"<p><p>Phylogenies are central to many research areas in biology and commonly estimated using likelihood-based methods. Unfortunately, any likelihood-based method, including Bayesian inference, can be restrictively slow for large datasets-with many taxa and/or many sites in the sequence alignment-or complex substitutions models. The primary limiting factor when using large datasets and/or complex models in probabilistic phylogenetic analyses is the likelihood calculation, which dominates the total computation time. To address this bottleneck, we incorporated the high-performance phylogenetic library BEAGLE into RevBayes, which enables multi-threading on multi-core CPUs and GPUs, as well as hardware specific vectorized instructions for faster likelihood calculations. Our new implementation of RevBayes+BEAGLE retains the flexibility and dynamic nature that users expect from vanilla RevBayes. In addition, we implemented native parallelization within RevBayes without an external library using the message passing interface (MPI); RevBayes+MPI. We evaluated our new implementation of RevBayes+BEAGLE using multi-threading on CPUs and 2 different powerful GPUs (NVidia Titan V and NVIDIA A100) against our native implementation of RevBayes+MPI. We found good improvements in speedup when multiple cores were used, with up to 20-fold speedup when using multiple CPU cores and over 90-fold speedup when using multiple GPU cores. The improvement depended on the data type used, DNA or amino acids, and the size of the alignment, but less on the size of the tree. We additionally investigated the cost of rescaling partial likelihoods to avoid numerical underflow and showed that unnecessarily frequent and inefficient rescaling can increase runtimes up to 4-fold. Finally, we presented and compared a new approach to store partial likelihoods on branches instead of nodes that can speed up computations up to 1.7 times but comes at twice the memory requirements.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139571417","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}
Joanna M Wolfe, Lauren Ballou, Javier Luque, Victoria M Watson-Zink, Shane T Ahyong, Joëlle Barido-Sottani, Tin-Yam Chan, Ka Hou Chu, Keith A Crandall, Savel R Daniels, Darryl L Felder, Harrison Mancke, Joel W Martin, Peter K L Ng, Javier Ortega-Hernández, Emma Palacios Theil, N Dean Pentcheff, Rafael Robles, Brent P Thoma, Ling Ming Tsang, Regina Wetzer, Amanda M Windsor, Heather D Bracken-Grissom
For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7600 species representing a striking diversity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 tips spanning 88 of 109 brachyuran families. Using 36 newly vetted fossil calibrations, we infer that brachyurans most likely diverged in the Triassic, with family-level splits in the late Cretaceous and early Paleogene. By contrast, the root age is underestimated with automated sampling of 328 fossil occurrences explicitly incorporated into the tree prior, suggesting such models are a poor fit under heterogeneous fossil preservation. We apply recently defined trait-by-environment associations to classify a gradient of transitions from marine to terrestrial lifestyles. We estimate that crabs left the marine environment at least 7 and up to 17 times convergently, and returned to the sea from non-marine environments at least twice. Although the most highly terrestrial- and many freshwater-adapted crabs are concentrated in Thoracotremata, Bayesian threshold models of ancestral state reconstruction fail to identify shifts to higher terrestrial grades due to the degree of underlying change required. Lineages throughout our tree inhabit intertidal and marginal marine environments, corroborating the inference that the early stages of terrestrial adaptation have a lower threshold to evolve. Our framework and extensive new fossil and natural history datasets will enable future comparisons of non-marine adaptation at the morphological and molecular level. Crabs provide an important window into the early processes of adaptation to novel environments, and different degrees of evolutionary constraint that might help predict these pathways. [Brachyura; convergent evolution; crustaceans; divergence times; fossil calibration; molecular phylogeny; terrestrialization; threshold model.].
{"title":"Convergent Adaptation of True Crabs (Decapoda: Brachyura) to a Gradient of Terrestrial Environments.","authors":"Joanna M Wolfe, Lauren Ballou, Javier Luque, Victoria M Watson-Zink, Shane T Ahyong, Joëlle Barido-Sottani, Tin-Yam Chan, Ka Hou Chu, Keith A Crandall, Savel R Daniels, Darryl L Felder, Harrison Mancke, Joel W Martin, Peter K L Ng, Javier Ortega-Hernández, Emma Palacios Theil, N Dean Pentcheff, Rafael Robles, Brent P Thoma, Ling Ming Tsang, Regina Wetzer, Amanda M Windsor, Heather D Bracken-Grissom","doi":"10.1093/sysbio/syad066","DOIUrl":"10.1093/sysbio/syad066","url":null,"abstract":"<p><p>For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7600 species representing a striking diversity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 tips spanning 88 of 109 brachyuran families. Using 36 newly vetted fossil calibrations, we infer that brachyurans most likely diverged in the Triassic, with family-level splits in the late Cretaceous and early Paleogene. By contrast, the root age is underestimated with automated sampling of 328 fossil occurrences explicitly incorporated into the tree prior, suggesting such models are a poor fit under heterogeneous fossil preservation. We apply recently defined trait-by-environment associations to classify a gradient of transitions from marine to terrestrial lifestyles. We estimate that crabs left the marine environment at least 7 and up to 17 times convergently, and returned to the sea from non-marine environments at least twice. Although the most highly terrestrial- and many freshwater-adapted crabs are concentrated in Thoracotremata, Bayesian threshold models of ancestral state reconstruction fail to identify shifts to higher terrestrial grades due to the degree of underlying change required. Lineages throughout our tree inhabit intertidal and marginal marine environments, corroborating the inference that the early stages of terrestrial adaptation have a lower threshold to evolve. Our framework and extensive new fossil and natural history datasets will enable future comparisons of non-marine adaptation at the morphological and molecular level. Crabs provide an important window into the early processes of adaptation to novel environments, and different degrees of evolutionary constraint that might help predict these pathways. [Brachyura; convergent evolution; crustaceans; divergence times; fossil calibration; molecular phylogeny; terrestrialization; threshold model.].</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11282366/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71522557","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}
The Andes mountains of western South America are a globally important biodiversity hotspot, yet there is a paucity of resolved phylogenies for plant clades from this region. Filling an important gap in our understanding of the World's richest flora, we present the first phylogeny of Freziera (Pentaphylacaceae), an Andean-centered, cloud forest radiation. Our dataset was obtained via hybrid-enriched target sequence capture of Angiosperms353 universal loci for 50 of the ca. 75 spp., obtained almost entirely from herbarium specimens. We identify high phylogenomic complexity in Freziera, including the presence of data artifacts. Via by-eye observation of gene trees, detailed examination of warnings from recently improved assembly pipelines, and gene tree filtering, we identified that artifactual orthologs (i.e., the presence of only one copy of a multicopy gene due to differential assembly) were an important source of gene tree heterogeneity that had a negative impact on phylogenetic inference and support. These artifactual orthologs may be common in plant phylogenomic datasets, where multiple instances of genome duplication are common. After accounting for artifactual orthologs as source of gene tree error, we identified a significant, but nonspecific signal of introgression using Patterson's D and f4 statistics. Despite phylogenomic complexity, we were able to resolve Freziera into 9 well-supported subclades whose evolution has been shaped by multiple evolutionary processes, including incomplete lineage sorting, historical gene flow, and gene duplication. Our results highlight the complexities of plant phylogenomics, which are heightened in Andean radiations, and show the impact of filtering data processing artifacts and standard filtering approaches on phylogenetic inference.
南美洲西部的安第斯山脉是全球重要的生物多样性热点地区,但该地区植物支系的系统发生却很少。我们首次提出了以安第斯山脉为中心的云林辐射植物--Freziera(五枫香科)的系统发生,填补了我们对世界上最丰富植物区系了解的一个重要空白。我们的数据集是通过rid-enriched target sequence capture of Angiosperms获得的。这些数据几乎全部来自标本馆标本。我们在 Freziera 中发现了高度的系统发生复杂性,包括数据伪造的存在。通过亲眼观察基因树、详细检查最近改进的组装管道发出的警告以及基因树过滤,我们发现伪造的直系同源物(即由于差异组装导致多拷贝基因只有一个拷贝)是基因树异质性的一个重要来源,对系统发生推断和支持有负面影响。在植物系统发生组数据集中,这些人为的直向同源物可能很常见,因为在植物系统发生组数据集中,多个基因组重复的情况很普遍。在考虑了作为基因树误差来源的伪造直系同源物之后,我们利用 Patterson's D 和 f4 统计发现了一个显著但非特异性的引种信号。尽管系统发生组十分复杂,但我们仍能将 Freziera 分解为 9 个支持度较高的亚支系,其进化受多种进化过程的影响,包括不完全的世系分类、历史基因流和基因复制。我们的研究结果凸显了植物系统发生组学的复杂性,而安第斯地区的辐射则使这种复杂性更加突出,同时也显示了过滤数据处理人工痕迹和标准过滤方法对系统发生推断的影响。
{"title":"Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora.","authors":"Laura A Frost, Ana M Bedoya, Laura P Lagomarsino","doi":"10.1093/sysbio/syad076","DOIUrl":"10.1093/sysbio/syad076","url":null,"abstract":"<p><p>The Andes mountains of western South America are a globally important biodiversity hotspot, yet there is a paucity of resolved phylogenies for plant clades from this region. Filling an important gap in our understanding of the World's richest flora, we present the first phylogeny of Freziera (Pentaphylacaceae), an Andean-centered, cloud forest radiation. Our dataset was obtained via hybrid-enriched target sequence capture of Angiosperms353 universal loci for 50 of the ca. 75 spp., obtained almost entirely from herbarium specimens. We identify high phylogenomic complexity in Freziera, including the presence of data artifacts. Via by-eye observation of gene trees, detailed examination of warnings from recently improved assembly pipelines, and gene tree filtering, we identified that artifactual orthologs (i.e., the presence of only one copy of a multicopy gene due to differential assembly) were an important source of gene tree heterogeneity that had a negative impact on phylogenetic inference and support. These artifactual orthologs may be common in plant phylogenomic datasets, where multiple instances of genome duplication are common. After accounting for artifactual orthologs as source of gene tree error, we identified a significant, but nonspecific signal of introgression using Patterson's D and f4 statistics. Despite phylogenomic complexity, we were able to resolve Freziera into 9 well-supported subclades whose evolution has been shaped by multiple evolutionary processes, including incomplete lineage sorting, historical gene flow, and gene duplication. Our results highlight the complexities of plant phylogenomics, which are heightened in Andean radiations, and show the impact of filtering data processing artifacts and standard filtering approaches on phylogenetic inference.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139088586","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}
Luna L Sánchez Reyes, Emily Jane McTavish, Brian O'Meara
Chronograms-phylogenies with branch lengths proportional to time-represent key data on timing of evolutionary events, allowing us to study natural processes in many areas of biological research. Chronograms also provide valuable information that can be used for education, science communication, and conservation policy decisions. Yet, achieving a high-quality reconstruction of a chronogram is a difficult and resource-consuming task. Here we present DateLife, a phylogenetic software implemented as an R package and an R Shiny web application available at www.datelife.org, that provides services for efficient and easy discovery, summary, reuse, and reanalysis of node age data mined from a curated database of expert, peer-reviewed, and openly available chronograms. The main DateLife workflow starts with one or more scientific taxon names provided by a user. Names are processed and standardized to a unified taxonomy, allowing DateLife to run a name match across its local chronogram database that is curated from Open Tree of Life's phylogenetic repository, and extract all chronograms that contain at least two queried taxon names, along with their metadata. Finally, node ages from matching chronograms are mapped using the congruification algorithm to corresponding nodes on a tree topology, either extracted from Open Tree of Life's synthetic phylogeny or one provided by the user. Congruified node ages are used as secondary calibrations to date the chosen topology, with or without initial branch lengths, using different phylogenetic dating methods such as BLADJ, treePL, PATHd8, and MrBayes. We performed a cross-validation test to compare node ages resulting from a DateLife analysis (i.e, phylogenetic dating using secondary calibrations) to those from the original chronograms (i.e, obtained with primary calibrations), and found that DateLife's node age estimates are consistent with the age estimates from the original chronograms, with the largest variation in ages occurring around topologically deeper nodes. Because the results from any software for scientific analysis can only be as good as the data used as input, we highlight the importance of considering the results of a DateLife analysis in the context of the input chronograms. DateLife can help to increase awareness of the existing disparities among alternative hypotheses of dates for the same diversification events, and to support exploration of the effect of alternative chronogram hypotheses on downstream analyses, providing a framework for a more informed interpretation of evolutionary results.
{"title":"DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life.","authors":"Luna L Sánchez Reyes, Emily Jane McTavish, Brian O'Meara","doi":"10.1093/sysbio/syae015","DOIUrl":"10.1093/sysbio/syae015","url":null,"abstract":"<p><p>Chronograms-phylogenies with branch lengths proportional to time-represent key data on timing of evolutionary events, allowing us to study natural processes in many areas of biological research. Chronograms also provide valuable information that can be used for education, science communication, and conservation policy decisions. Yet, achieving a high-quality reconstruction of a chronogram is a difficult and resource-consuming task. Here we present DateLife, a phylogenetic software implemented as an R package and an R Shiny web application available at www.datelife.org, that provides services for efficient and easy discovery, summary, reuse, and reanalysis of node age data mined from a curated database of expert, peer-reviewed, and openly available chronograms. The main DateLife workflow starts with one or more scientific taxon names provided by a user. Names are processed and standardized to a unified taxonomy, allowing DateLife to run a name match across its local chronogram database that is curated from Open Tree of Life's phylogenetic repository, and extract all chronograms that contain at least two queried taxon names, along with their metadata. Finally, node ages from matching chronograms are mapped using the congruification algorithm to corresponding nodes on a tree topology, either extracted from Open Tree of Life's synthetic phylogeny or one provided by the user. Congruified node ages are used as secondary calibrations to date the chosen topology, with or without initial branch lengths, using different phylogenetic dating methods such as BLADJ, treePL, PATHd8, and MrBayes. We performed a cross-validation test to compare node ages resulting from a DateLife analysis (i.e, phylogenetic dating using secondary calibrations) to those from the original chronograms (i.e, obtained with primary calibrations), and found that DateLife's node age estimates are consistent with the age estimates from the original chronograms, with the largest variation in ages occurring around topologically deeper nodes. Because the results from any software for scientific analysis can only be as good as the data used as input, we highlight the importance of considering the results of a DateLife analysis in the context of the input chronograms. DateLife can help to increase awareness of the existing disparities among alternative hypotheses of dates for the same diversification events, and to support exploration of the effect of alternative chronogram hypotheses on downstream analyses, providing a framework for a more informed interpretation of evolutionary results.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11282365/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140176511","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}
The processes responsible for the formation of Earth's most conspicuous diversity pattern, the latitudinal diversity gradient (LDG), remain unexplored for many clades in the Tree of Life. Here, we present a densely sampled and dated molecular phylogeny for the most speciose clade of damselflies worldwide (Odonata: Coenagrionoidea) and investigate the role of time, macroevolutionary processes, and biome-shift dynamics in shaping the LDG in this ancient insect superfamily. We used process-based biogeographic models to jointly infer ancestral ranges and speciation times and to characterize within-biome dispersal and biome-shift dynamics across the cosmopolitan distribution of Coenagrionoidea. We also investigated temporal and biome-dependent variation in diversification rates. Our results uncover a tropical origin of pond damselflies and featherlegs ~105 Ma, while highlighting the uncertainty of ancestral ranges within the tropics in deep time. Even though diversification rates have declined since the origin of this clade, global climate change and biome-shifts have slowly increased diversity in warm- and cold-temperate areas, where lineage turnover rates have been relatively higher. This study underscores the importance of biogeographic origin and time to diversify as important drivers of the LDG in pond damselflies and their relatives, while diversification dynamics have instead resulted in the formation of ephemeral species in temperate regions. Biome-shifts, although limited by tropical niche conservatism, have been the main factor reducing the steepness of the LDG in the last 30 Myr. With ongoing climate change and increasing northward range expansions of many damselfly taxa, the LDG may become less pronounced. Our results support recent calls to unify biogeographic and macroevolutionary approaches to improve our understanding of how latitudinal diversity gradients are formed and why they vary across time and among taxa.
对于生命之树上的许多支系来说,地球上最明显的多样性模式--纬度多样性梯度(LDG)的形成过程仍有待探索。在本文中,我们展示了一个取样密集且年代久远的分子系统发育,该系统发育针对的是世界上种类最多的豆娘科(Odonata: Coenagrionoidea),并研究了时间、宏观进化过程和生物迁移动力学在形成这一古老昆虫超科的纬度多样性梯度中的作用。我们利用基于过程的生物地理学模型来共同推断祖先的分布范围和物种形成时间,并描述 Coenagrionoidea 在世界性分布中的生物群内扩散和生物群转移动态。我们还研究了多样化率随时间和生物群的变化。我们的研究结果揭示了池袋豆娘和羽腿豆娘在距今约 105 Ma 时起源于热带,同时强调了热带祖先分布范围在深部时间的不确定性。尽管自该支系起源以来其分化率有所下降,但全球气候变化和生物迁移缓慢地增加了暖温带和寒温带地区的多样性,这些地区的种系更替率相对较高。这项研究强调了生物地理起源和分化时间的重要性,它们是池塘豆娘及其近缘种的 LDG 的重要驱动因素,而分化动态反而导致了温带地区短暂物种的形成。尽管生物迁移受到热带生态位保守性的限制,但在过去的30 Myr中,生物迁移是降低LDG陡度的主要因素。随着气候变化的持续和许多豆娘类群向北扩展,LDG可能会变得不那么明显。我们的研究结果支持了最近的呼吁,即统一生物地理学和宏观进化方法,以加深我们对纬度多样性梯度如何形成及其为何在不同时期和不同类群之间变化的理解。
{"title":"Tropical Origin, Global Diversification, and Dispersal in the Pond Damselflies (Coenagrionoidea) Revealed by a New Molecular Phylogeny.","authors":"Beatriz Willink, Jessica L Ware, Erik I Svensson","doi":"10.1093/sysbio/syae004","DOIUrl":"10.1093/sysbio/syae004","url":null,"abstract":"<p><p>The processes responsible for the formation of Earth's most conspicuous diversity pattern, the latitudinal diversity gradient (LDG), remain unexplored for many clades in the Tree of Life. Here, we present a densely sampled and dated molecular phylogeny for the most speciose clade of damselflies worldwide (Odonata: Coenagrionoidea) and investigate the role of time, macroevolutionary processes, and biome-shift dynamics in shaping the LDG in this ancient insect superfamily. We used process-based biogeographic models to jointly infer ancestral ranges and speciation times and to characterize within-biome dispersal and biome-shift dynamics across the cosmopolitan distribution of Coenagrionoidea. We also investigated temporal and biome-dependent variation in diversification rates. Our results uncover a tropical origin of pond damselflies and featherlegs ~105 Ma, while highlighting the uncertainty of ancestral ranges within the tropics in deep time. Even though diversification rates have declined since the origin of this clade, global climate change and biome-shifts have slowly increased diversity in warm- and cold-temperate areas, where lineage turnover rates have been relatively higher. This study underscores the importance of biogeographic origin and time to diversify as important drivers of the LDG in pond damselflies and their relatives, while diversification dynamics have instead resulted in the formation of ephemeral species in temperate regions. Biome-shifts, although limited by tropical niche conservatism, have been the main factor reducing the steepness of the LDG in the last 30 Myr. With ongoing climate change and increasing northward range expansions of many damselfly taxa, the LDG may become less pronounced. Our results support recent calls to unify biogeographic and macroevolutionary approaches to improve our understanding of how latitudinal diversity gradients are formed and why they vary across time and among taxa.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11282367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139542962","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}
Michaël P J Nicolaï, Bert Van Hecke, Svana Rogalla, Gerben Debruyn, Rauri C K Bowie, Nicholas J Matzke, Shannon J Hackett, Liliana D'Alba, Matthew D Shawkey
How and why certain groups become speciose is a key question in evolutionary biology. Novel traits that enable diversification by opening new ecological niches are likely important mechanisms. However, ornamental traits can also promote diversification by opening up novel sensory niches and thereby creating novel inter-specific interactions. More specifically, ornamental colors may enable more precise and/or easier species recognition and may act as key innovations by increasing the number of species-specific patterns and promoting diversification. While the influence of coloration on diversification is well-studied, the influence of the mechanisms that produce those colors (e.g., pigmentary, nanostructural) is less so, even though the ontogeny and evolution of these mechanisms differ. We estimated a new phylogenetic tree for 121 sunbird species and combined color data of 106 species with a range of phylogenetic tools to test the hypothesis that the evolution of novel color mechanisms increases diversification in sunbirds, one of the most colorful bird clades. Results suggest that: (1) the evolution of novel color mechanisms expands the visual sensory niche, increasing the number of achievable colors, (2) structural coloration diverges more readily across the body than pigment-based coloration, enabling an increase in color complexity, (3) novel color mechanisms might minimize trade-offs between natural and sexual selection such that color can function both as camouflage and conspicuous signal, and (4) despite structural colors being more colorful and mobile, only melanin-based coloration is positively correlated with net diversification. Together, these findings explain why color distances increase with an increasing number of sympatric species, even though packing of color space predicts otherwise.
{"title":"The Evolution of Multiple Color Mechanisms Is Correlated with Diversification in Sunbirds (Nectariniidae).","authors":"Michaël P J Nicolaï, Bert Van Hecke, Svana Rogalla, Gerben Debruyn, Rauri C K Bowie, Nicholas J Matzke, Shannon J Hackett, Liliana D'Alba, Matthew D Shawkey","doi":"10.1093/sysbio/syae006","DOIUrl":"10.1093/sysbio/syae006","url":null,"abstract":"<p><p>How and why certain groups become speciose is a key question in evolutionary biology. Novel traits that enable diversification by opening new ecological niches are likely important mechanisms. However, ornamental traits can also promote diversification by opening up novel sensory niches and thereby creating novel inter-specific interactions. More specifically, ornamental colors may enable more precise and/or easier species recognition and may act as key innovations by increasing the number of species-specific patterns and promoting diversification. While the influence of coloration on diversification is well-studied, the influence of the mechanisms that produce those colors (e.g., pigmentary, nanostructural) is less so, even though the ontogeny and evolution of these mechanisms differ. We estimated a new phylogenetic tree for 121 sunbird species and combined color data of 106 species with a range of phylogenetic tools to test the hypothesis that the evolution of novel color mechanisms increases diversification in sunbirds, one of the most colorful bird clades. Results suggest that: (1) the evolution of novel color mechanisms expands the visual sensory niche, increasing the number of achievable colors, (2) structural coloration diverges more readily across the body than pigment-based coloration, enabling an increase in color complexity, (3) novel color mechanisms might minimize trade-offs between natural and sexual selection such that color can function both as camouflage and conspicuous signal, and (4) despite structural colors being more colorful and mobile, only melanin-based coloration is positively correlated with net diversification. Together, these findings explain why color distances increase with an increasing number of sympatric species, even though packing of color space predicts otherwise.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139642990","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}
Konstantinos Giannakis, Luke Richards, Iain G Johnston
Comparative analysis of variables across phylogenetically linked observations can reveal mechanisms and insights in evolutionary biology. As the taxonomic breadth of the sample of interest increases, challenges of data sparsity, poor phylogenetic resolution, and complicated evolutionary dynamics emerge. Here, we investigate a cross-eukaryotic question where all these problems exist: which organismal ecology features are correlated with gene retention in mitochondrial and chloroplast DNA (organelle DNA or oDNA). Through a wide palette of synthetic control studies, we first characterize the specificity and sensitivity of a collection of parametric and non-parametric phylogenetic comparative approaches to identify relationships in the face of such sparse and awkward datasets. This analysis is not directly focused on oDNA, and so provides generalizable insights into comparative approaches with challenging data. We then combine and curate ecological data coupled to oDNA genome information across eukaryotes, including a new semi-automated approach for gathering data on organismal traits from less systematized open-access resources including encyclopedia articles on species and taxa. The curation process also involved resolving several issues with existing datasets, including enforcing the clade-specificity of several ecological features and fixing incorrect annotations. Combining this unique dataset with our benchmarked comparative approaches, we confirm support for several known links between organismal ecology and organelle gene retention, identify several previously unidentified relationships constituting possible ecological contributors to oDNA genome evolution, and provide support for a recently hypothesized link between environmental demand and oDNA retention. We, with caution, discuss the implications of these findings for organelle evolution and of this pipeline for broad comparative analyses in other fields.
{"title":"Ecological Predictors of Organelle Genome Evolution: Phylogenetic Correlations with Taxonomically Broad, Sparse, Unsystematized Data.","authors":"Konstantinos Giannakis, Luke Richards, Iain G Johnston","doi":"10.1093/sysbio/syae009","DOIUrl":"10.1093/sysbio/syae009","url":null,"abstract":"<p><p>Comparative analysis of variables across phylogenetically linked observations can reveal mechanisms and insights in evolutionary biology. As the taxonomic breadth of the sample of interest increases, challenges of data sparsity, poor phylogenetic resolution, and complicated evolutionary dynamics emerge. Here, we investigate a cross-eukaryotic question where all these problems exist: which organismal ecology features are correlated with gene retention in mitochondrial and chloroplast DNA (organelle DNA or oDNA). Through a wide palette of synthetic control studies, we first characterize the specificity and sensitivity of a collection of parametric and non-parametric phylogenetic comparative approaches to identify relationships in the face of such sparse and awkward datasets. This analysis is not directly focused on oDNA, and so provides generalizable insights into comparative approaches with challenging data. We then combine and curate ecological data coupled to oDNA genome information across eukaryotes, including a new semi-automated approach for gathering data on organismal traits from less systematized open-access resources including encyclopedia articles on species and taxa. The curation process also involved resolving several issues with existing datasets, including enforcing the clade-specificity of several ecological features and fixing incorrect annotations. Combining this unique dataset with our benchmarked comparative approaches, we confirm support for several known links between organismal ecology and organelle gene retention, identify several previously unidentified relationships constituting possible ecological contributors to oDNA genome evolution, and provide support for a recently hypothesized link between environmental demand and oDNA retention. We, with caution, discuss the implications of these findings for organelle evolution and of this pipeline for broad comparative analyses in other fields.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11282362/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140068682","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}
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 towards 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.
{"title":"Blouch: Bayesian Linear Ornstein-Uhlenbeck Models for Comparative Hypotheses.","authors":"Mark Grabowski","doi":"10.1093/sysbio/syae044","DOIUrl":"https://doi.org/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 towards 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":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Martin Hofmann, Steffen Kiel, Lara M Kösters, Jana Wäldchen, Patrick Mäder
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 two deep learning methods - supervised classification approaches and unsupervised similarity learning - to infer organism relationships from specimen images. As a basis, we assembled an image dataset 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 dataset 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 dataset. 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.
{"title":"Inferring Taxonomic Affinities and Genetic Distances Using Morphological Features Extracted from Specimen Images: a Case Study with a Bivalve dataset.","authors":"Martin Hofmann, Steffen Kiel, Lara M Kösters, Jana Wäldchen, Patrick Mäder","doi":"10.1093/sysbio/syae042","DOIUrl":"https://doi.org/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 two deep learning methods - supervised classification approaches and unsupervised similarity learning - to infer organism relationships from specimen images. As a basis, we assembled an image dataset 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 dataset 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 dataset. 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":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-24","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}