Molecular Phylogenetics and Evolution最新文献

{"title":"Peering through the hedge: Multiple datasets yield insights into the phylogenetic relationships and incongruences in the tribe Lilieae (Liliaceae)","authors":"Deng-Feng Xie ,&nbsp;Juan Li ,&nbsp;Jia-Hui Sun ,&nbsp;Rui-Yu Cheng ,&nbsp;Yuan Wang ,&nbsp;Bo-Ni Song ,&nbsp;Xing-Jin He ,&nbsp;Song-Dong Zhou","doi":"10.1016/j.ympev.2024.108182","DOIUrl":"10.1016/j.ympev.2024.108182","url":null,"abstract":"<div><p>The increasing use of genome-scale data has significantly facilitated phylogenetic analyses, contributing to the dissection of the underlying evolutionary mechanisms that shape phylogenetic incongruences, such as incomplete lineage sorting (ILS) and hybridization. Lilieae, a prominent member of the Liliaceae family, comprises four genera and approximately 260 species, representing 43% of all species within Liliaceae. They possess high ornamental, medicinal and edible values. Yet, no study has explored the validity of various genome-scale data in phylogenetic analyses within this tribe, nor have potential evolutionary mechanisms underlying its phylogenetic incongruences been investigated. Here, transcriptome, Angiosperms353, plastid and mitochondrial data, were collected from 50 to 93 samples of Lilieae, covering all four recognized genera. Multiple datasets were created and used for phylogenetic analyses based on concatenated and coalescent-based methods. Evolutionary rates of different datasets were calculated, and divergence times were estimated. Various approaches, including coalescence simulation, Quartet Sampling (QS), calculation of concordance factors (gCF and sCF), as well as MSCquartets and reticulate network inference, were carried out to infer the phylogenetic discordances and analyze their underlying mechanisms using a reduced 33-taxon dataset. Despite extensive phylogenetic discordances among gene trees, robust phylogenies were inferred from nuclear and plastid data compared to mitochondrial data, with lower synonymous substitution detected in mitochondrial genes than in nuclear and plastid genes. Significant ILS was detected across the phylogeny of Lilieae, with clear evidence of reticulate evolution identified. Divergence time estimation indicated that most of lineages in Lilieae diverged during a narrow time frame (ranging from 5.0 Ma to 10.0 Ma), consistent with the notion of rapid radiation evolution. Our results suggest that integrating transcriptomic and plastid data can serve as cost-effective and efficient tools for phylogenetic inference and evolutionary analysis within Lilieae, and Angiosperms353 data is also a favorable choice. Mitochondrial data are more suitable for phylogenetic analyses at higher taxonomic levels due to their stronger conservation and lower synonymous substitution rates. Significant phylogenetic incongruences detected in Lilieae were caused by both incomplete lineage sorting (ILS) and reticulate evolution, with hybridization and “ghost introgression” likely prevalent in the evolution of Lilieae species. Our findings provide new insights into the phylogeny of Lilieae, enhancing our understanding of the evolution of species in this tribe.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"200 ","pages":"Article 108182"},"PeriodicalIF":3.6,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142121251","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":"A molecular phylogeny of the Petaluridae (Odonata: Anisoptera): A 160-Million-Year-Old story of drift and extinction","authors":"Ethan R. Tolman ,&nbsp;Christopher D. Beatty ,&nbsp;Manpreet K. Kohli ,&nbsp;John Abbott ,&nbsp;Seth M. Bybee ,&nbsp;Paul B. Frandsen ,&nbsp;J. Stephen Gosnell ,&nbsp;Robert Guralnick ,&nbsp;V.J. Kalkman ,&nbsp;Lacie G. Newton ,&nbsp;Anton Suvorov ,&nbsp;Jessica L. Ware","doi":"10.1016/j.ympev.2024.108185","DOIUrl":"10.1016/j.ympev.2024.108185","url":null,"abstract":"<div><p>Petaluridae (Odonata: Anisoptera) is a relict dragonfly family, having diverged from its sister family in the Jurassic, of eleven species that are notable among odonates (dragonflies and damselflies) for their exclusive use of fen and bog habitats, their burrowing behavior as nymphs, large body size as adults, and extended lifespans. To date, several nodes within this family remain unresolved, limiting the study of the evolution of this peculiar family. Using an anchored hybrid enrichment dataset of over 900 loci we reconstructed the species tree of Petaluridae. To estimate the temporal origin of the genera within this family, we used a set of well-vetted fossils and a relaxed molecular clock model in a divergence time estimation analysis. We estimate that Petaluridae originated in the early Cretaceous and confirm the existence of monophyletic Gondwanan and Laurasian clades within the family. Our relaxed molecular clock analysis estimated that these clades diverged from their MRCA approximately 160 mya. Extant lineages within this family were identified to have persisted from 6 (<em>Uropetala</em>) to 120 million years (<em>Phenes</em>). Our biogeographical analyses focusing on a set of key regions suggest that divergence within Petaluridae is largely correlated with continental drift, the exposure of land bridges, and the development of mountain ranges. Our results support the hypothesis that species within Petaluridae have persisted for tens of millions of years, with little fossil evidence to suggest widespread extinction in the family, despite optimal conditions for the fossilization of nymphs. Petaluridae appear to be a rare example of habitat specialists that have persisted for tens of millions of years.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"200 ","pages":"Article 108185"},"PeriodicalIF":3.6,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142115159","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":"Phylogenomics resolves the backbone of Poales and identifies signals of hybridization and polyploidy","authors":"Huijun Wang ,&nbsp;Zhigang Wu ,&nbsp;Tao Li ,&nbsp;Jindong Zhao","doi":"10.1016/j.ympev.2024.108184","DOIUrl":"10.1016/j.ympev.2024.108184","url":null,"abstract":"<div><p>Poales, as one of the largest orders of angiosperm, holds crucial economic and ecological importance. Nevertheless, achieving a consensus topology has been challenging in previous studies due to limited molecular data and sparse taxon sampling. The uneven distribution of species diversity among families and the factors leading to elevated species richness in certain lineages have also been subjects of ongoing discussion and investigation. In this study, we conducted a comprehensive sampling, including representatives from all 14 families and 85 taxa of Poales, along with five additional outgroups. To reconstruct the phylogeny of Poales, we employed a combination of coalescent and concatenation methods on three nuclear gene sets (1093, 491, 143) and one plastid gene set (53), which were inferenced from genomic data. We also conducted phylogenetic hypothesis analyses to evaluate two major conflicting nodes detected in phylogenetic analyses. As a result, we successfully resolved the backbone of Poales and provided a timeline for its evolutionary history. We recovered the sister relationship between Typhaceae and Bromeliaceae as the earliest diverging families within Poales. The clade consisting of Ecdeiocoleaceae and Joinvilleaceae was recovered as the sister group of Poaceae. Within the xyrid clade, Mayacaceae and Erioaculaceae + Xyridaceae successively diverged along the backbone of Poales. The topology of [Aristidoideae, ((Micrairoideae, Panicoideae), (Arundinoideae, (Chloridoideae, Danthonioideae)))] within the PACMAD clade has received strong support from multiple findings. We also delved into the underlying biological factors that contributed to the conflicting nodes observed in the phylogenetic analysis. Apart from the uncertainty regarding the sister group of Poaceae caused by cytonuclear discordance, frequent hybridization and polyploidy may have contributed to other conflicting nodes. We identified 26 putative whole-genome duplication (WGD) events within Poales. However, apart from the σ-WGD and the ρ-WGD, we did not observe any potential polyploid events that could be directly linked to the species diversification in specific lineages. Furthermore, there was a significant increase in the net diversification rate of Poales following the K-Pg boundary.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"200 ","pages":"Article 108184"},"PeriodicalIF":3.6,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001763/pdfft?md5=d3663215683c6c8c75044949ae96866d&pid=1-s2.0-S1055790324001763-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142115160","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":"Machine learning can be as good as maximum likelihood when reconstructing phylogenetic trees and determining the best evolutionary model on four taxon alignments","authors":"Nikita Kulikov ,&nbsp;Fatemeh Derakhshandeh ,&nbsp;Christoph Mayer","doi":"10.1016/j.ympev.2024.108181","DOIUrl":"10.1016/j.ympev.2024.108181","url":null,"abstract":"<div><p>Phylogenetic tree reconstruction with molecular data is important in many fields of life science research. The gold standard in this discipline is the phylogenetic tree reconstruction based on the Maximum Likelihood method. In this study, we present neural networks to predict the best model of sequence evolution and the correct topology for four sequence alignments of nucleotide or amino acid sequence data. We trained neural networks with different architectures using simulated alignments for a wide range of evolutionary models, model parameters and branch lengths. By comparing the accuracy of model and topology prediction of the trained neural networks with Maximum Likelihood and Neighbour Joining methods, we show that for quartet trees, the neural network classifier outperforms the Neighbour Joining method and is in most cases as good as the Maximum Likelihood method to infer the best model of sequence evolution and the best tree topology. These results are consistent for nucleotide and amino acid sequence data. We also show that our method is superior for model selection than previously published methods based on convolutionary networks. Furthermore, we found that neural network classifiers are much faster than the IQ-TREE implementation of the Maximum Likelihood method. Our results show that neural networks could become a true competitor for the Maximum Likelihood method in phylogenetic reconstructions.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"200 ","pages":"Article 108181"},"PeriodicalIF":3.6,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001738/pdfft?md5=036b68ef8f10032070e9c004f3188ff9&pid=1-s2.0-S1055790324001738-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142098994","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":"Phylogenomic analyses of Blattodea combining traditional methods, incremental tree-building, and quality-aware support","authors":"Dominic A. Evangelista ,&nbsp;Dvorah Nelson ,&nbsp;Zuzana Kotyková Varadínová ,&nbsp;Michael Kotyk ,&nbsp;Nicolas Rousseaux ,&nbsp;Tristan Shanahan ,&nbsp;Phillippe Grandcolas ,&nbsp;Frédéric Legendre","doi":"10.1016/j.ympev.2024.108177","DOIUrl":"10.1016/j.ympev.2024.108177","url":null,"abstract":"<div><p>Despite the many advances of the genomic era, there is a persistent problem in assessing the uncertainty of phylogenomic hypotheses. We see this in the recent history of phylogenetics for cockroaches and termites (Blattodea), where huge advances have been made, but there are still major inconsistencies between studies. To address this, we present a phylogenetic analysis of Blattodea that emphasizes identification and quantification of uncertainty. We analyze 1183 gene domains using three methods (multi-species coalescent inference, concatenation, and a supermatrix-supertree hybrid approach) and assess support for controversial relationships while considering data quality. The hybrid approach—here dubbed “tiered phylogenetic inference”—incorporates information about data quality into an incremental tree building framework. Leveraging this method, we are able to identify cases of low or misleading support that would not be possible otherwise, and explore them more thoroughly with follow-up tests. In particular, quality annotations pointed towards nodes with high bootstrap support that later turned out to have large ambiguities, sometimes resulting from low-quality data. We also clarify issues related to some recalcitrant nodes: Anaplectidae’s placement lacks unbiased signal, Ectobiidae s.s. and Anaplectoideini need greater taxon sampling, the deepest relationships among most Blaberidae lack signal. As a result, several previous phylogenetic uncertainties are now closer to being resolved (e.g., African and Malagasy “<em>Rhabdoblatta”</em> spp. are the sister to all other Blaberidae, and Oxyhaloinae is sister to the remaining Blaberidae). Overall, we argue for more approaches to quantifying support that take data quality into account to uncover the nature of recalcitrant nodes.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"200 ","pages":"Article 108177"},"PeriodicalIF":3.6,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001696/pdfft?md5=73a7050cb65428d10be88be9dfb52c1a&pid=1-s2.0-S1055790324001696-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141984018","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":"Phylogenetic relationships and historical biogeography of silkmoths (Lepidoptera: Bombycidae) suggest an origin in Southern Gondwana","authors":"Rung-Juen Lin ,&nbsp;Yu-Chi Lin ,&nbsp;Michael F. Braby ,&nbsp;Andreas Zwick ,&nbsp;Yu-Feng Hsu","doi":"10.1016/j.ympev.2024.108176","DOIUrl":"10.1016/j.ympev.2024.108176","url":null,"abstract":"<div><p>Silkmoths (Bombycidae) have a disjunct distribution predominantly in the Southern Hemisphere and Asia. Here we reconstruct the phylogenetic history of the family to test competing hypotheses on their origin and assess how vicariance and long-distance dispersal shaped their current distribution. We sequenced up to 5,074 base pairs from six loci (COI, EF1-α, wgl, CAD, GAPDH, and RpS5) to infer the historical biogeography of Bombycidae. The multilocus dataset covering 20 genera (80 %) of the family, including 17 genera (94 %) of Bombycinae and 3 genera (43 %) of Epiinae, was used to estimate phylogenetic patterns, divergence times and biogeographic reconstruction. Dating estimates extrapolated from secondary calibration sources indicate the Bombycidae stem-group originated approximately 64 Mya. The subfamilies Epiinae (South America) and Bombycinae (Australia, Asia, East Palaearctic, and Africa) were reciprocally monophyletic, diverging at c. 56 Mya (95 % credibility interval: 66–46 Mya). The ‘basal’ lineage of Bombycinae — <em>Gastridiota</em> + <em>Elachyophtalma</em> — split from the rest of Bombycinae c. 53 Mya (95 % credibility interval: 63–43 Mya). <em>Gastridiota</em> is a monobasic genus with a relictual distribution in subtropical forests of eastern Australia. The Oriental and African genera comprised a monophyletic group: the Oriental region was inferred to have been colonized from a long-distance dispersal event from Australia to South-East Asia c. 53 Mya or possibly later (c. 36–26 Mya); Africa was subsequently colonized by dispersal from Asia c. 16 Mya (95 % credibility interval: 21–12 Mya). Based on the strongly supported phylogenetic relationships and estimates of divergence times, we conclude that Bombycidae had its origin in the fragment of Southern Gondwana consisting of Australia, Antarctica and South America during the Paleocene. The disjunction between South America (Epiinae) and Australia (Bombycinae) is best explained by vicariance in the Eocene, whereas the disjunct distribution in Asia and Africa is best explained by more recent dispersal events.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"200 ","pages":"Article 108176"},"PeriodicalIF":3.6,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141918161","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":"The last of their kind: Is the genus Scutiger (Anura: Megophryidae) a relict element of the paleo-Transhimalaya biota?","authors":"Sylvia Hofmann ,&nbsp;Lars Podsiadlowski ,&nbsp;Tobias Andermann ,&nbsp;Michael Matschiner ,&nbsp;Chitra B. Baniya ,&nbsp;Spartak N. Litvinchuk ,&nbsp;Sebastian Martin ,&nbsp;Rafaqat Masroor ,&nbsp;Jianhuan Yang ,&nbsp;Yuchi Zheng ,&nbsp;Daniel Jablonski ,&nbsp;Joachim Schmidt","doi":"10.1016/j.ympev.2024.108166","DOIUrl":"10.1016/j.ympev.2024.108166","url":null,"abstract":"<div><p>The orographic evolution of the Himalaya-Tibet Mountain system continues to be a subject of controversy, leading to considerable uncertainty regarding the environment and surface elevation of the Tibetan Plateau during the Cenozoic era. As many geoscientific (but not paleontological) studies suggest, elevations close to modern heights exist in vast areas of Tibet since at least the late Paleogene, implicating the presence of large-scale alpine environments for more than 30 million years. To explore a recently proposed alternative model that assumes a warm temperate environment across paleo-Tibet, we carried out a phylogeographic survey using genomic analyses of samples covering the range of endemic lazy toads (<em>Scutiger</em>) across the Himalaya-Tibet orogen. We identified two main clades, with several, geographically distinct subclades. The long temporal gap between the stem and crown age of <em>Scutiger</em> may suggest high extinction rates. Diversification within the crown group, depending on the calibration, occurred either from the Mid-Miocene or Late-Miocene and continued until the Holocene. The present-day Himalayan <em>Scutiger</em> fauna could have evolved from lineages that existed on the southern edges of the paleo-Tibetan area (the Transhimalaya = Gangdese Shan), while extant species living on the eastern edge of the Plateau originated probably from the eastern edges of northern parts of the ancestral Tibetan area (Hoh Xil, Tanggula Shan). Based on the Mid-Miocene divergence time estimation and ancestral area reconstruction, we propose that uplift-associated aridification of a warm temperate Miocene-Tibet, coupled with high extirpation rates of ancestral populations, and species range shifts along drainage systems and epigenetic transverse valleys of the rising mountains, is a plausible scenario explaining the phylogenetic structure of <em>Scutiger</em>. This hypothesis aligns with the fossil record but conflicts with geoscientific concepts of high elevated Tibetan Plateau since the late Paleogene. Considering a Late-Miocene/Pliocene divergence time, an alternative scenario of dispersal from SE Asia into the East, Central, and West Himalaya cannot be excluded, although essential evolutionary and biogeographic aspects remain unresolved within this model.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108166"},"PeriodicalIF":3.6,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141914686","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":"Whole-genome-based phylogenetic analyses provide new insights into the evolution of springtails (Hexapoda: Collembola)","authors":"Daoyuan YU ,&nbsp;Shiyu DU ,&nbsp;Xiping WEI ,&nbsp;Jie ZHU ,&nbsp;Yinhuan DING ,&nbsp;Feng HU ,&nbsp;Manqiang LIU ,&nbsp;Feng ZHANG","doi":"10.1016/j.ympev.2024.108169","DOIUrl":"10.1016/j.ympev.2024.108169","url":null,"abstract":"<div><p>Springtails (Collembola) stand as one of the most abundant, widespread, and ancient terrestrial arthropods on earth. However, their evolutionary history and deep phylogenetic relationships remain elusive. In this study, we employed phylogenomic approaches to elucidate the basal relationships among Collembola. We sampled whole-genome data representing all major collembolan lineages in proportion to their known diversity. To account for potential phylogenomic biases, we implemented various data extraction, locus sampling, and signal filtering strategies to generate matrices. Subsequently, we applied a diverse array of tree-searching and rate-modelling methods to reconstruct the phylogeny. Our analyses, utilizing different matrices and methods, converged on the same unrooted relationships among collembolan ingroups, supporting the current ordinal classification and challenging the monophyly of Arthropleona and Symphypleona <em>s.l.</em> However, discrepancies across analyses existed in the root of Collembola. Among various root positions, those based on more informative matrices and biologically realistic models, favoring a basal topology of Entomobryomorpha + (Symphypleona <em>s.s.</em> + (Neelipleona + Poduromorpha)), were supported by subsequent methodological assessment, topology tests, and rooting analyses. This optimal topology suggests multiple independent reduction of the pronotum in non-poduromorph orders and aligns with the plesiomorphic status of neuroendocrine organs and epicuticular structure of Entomobryomorpha. Fossil-calibrated dating analyses based on the optimal topology indicated late-Paleozoic to mid-Mesozoic origins of the crown Collembola and four orders. In addition, our results questioned the monophyly of Isotomidae and Neanuridae, underscoring the need for further attention to the systematics of these families. Overall, this study provides novel insights into the phylogenetic backbone of Collembola, which will inform future studies on the systematics, ecology, and evolution of this significant arthropod lineage.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"200 ","pages":"Article 108169"},"PeriodicalIF":3.6,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141914687","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 tree statistics: A systematic overview using the new R package ‘treestats’","authors":"Thijs Janzen,&nbsp;Rampal S. Etienne","doi":"10.1016/j.ympev.2024.108168","DOIUrl":"10.1016/j.ympev.2024.108168","url":null,"abstract":"<div><p>Phylogenetic trees are believed to contain a wealth of information on diversification processes. However, comparing phylogenetic trees is not straightforward due to their high dimensionality. Researchers have therefore defined a wide range of low-dimensional summary statistics. Currently, it remains unexplored to what extent these summary statistics cover the same underlying information and what summary statistics best explain observed variation across phylogenies. Furthermore, a large subset of available summary statistics focusses on measuring the topological features of a phylogenetic tree, but are often only explored at the extreme edge cases of the fully balanced or imbalanced tree and not for trees of intermediate balance.</p><p>Here, we introduce a new R package called ‘treestats’, that provides speed optimized code to compute 70 summary statistics. We study correlations between summary statistics on empirical trees and on trees simulated using several diversification models. Furthermore, we introduce an algorithm to create intermediately balanced trees in a well-defined manner, in order to explore variation in summary statistics across a balance gradient.</p><p>We find that almost all summary statistics are correlated with tree size, and find that it is difficult, if not impossible, to correct for tree size, unless the tree generating model is known. Furthermore, we find that across empirical and simulated trees, at least three large clusters of correlated summary statistics can be found, where statistics group together based on information used (topology or branching times). However, the finer grained correlation structure appears to depend strongly on either the taxonomic group studied (in empirical studies) or the tree generating model (in simulation studies).</p><p>Amongst statistics describing the (im)balance of a tree, we find that almost all statistics vary non-linearly, and sometimes even non-monotonically, with our generated balance gradient. This indicates that balance is perhaps a more complex property of a tree than previously thought. Furthermore, using our new imbalancing algorithm, we devise a numerical test to identify balance statistics, and identify several statistics as balance statistics that were not previously considered as such. Lastly, our results lead to several recommendations on which statistics to select when analyzing and comparing phylogenetic trees.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"200 ","pages":"Article 108168"},"PeriodicalIF":3.6,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S105579032400160X/pdfft?md5=32adcc7509fbad416d837e8d108cca1d&pid=1-s2.0-S105579032400160X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141908494","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":"Phylotranscriptomic relationships of the Oophila clade of green algae associated to amphibian egg masses","authors":"Miguel Vences ,&nbsp;Maria Sachs ,&nbsp;Iker Irisarri ,&nbsp;Fabian Bartels ,&nbsp;Pontus F. Eriksson ,&nbsp;Sven Künzel ,&nbsp;Atsushi Kurabayashi ,&nbsp;Ane T. Laugen ,&nbsp;Zachary T. Vegso ,&nbsp;Cory D. Bishop ,&nbsp;Ryan Kerney ,&nbsp;Hartmut Arndt","doi":"10.1016/j.ympev.2024.108165","DOIUrl":"10.1016/j.ympev.2024.108165","url":null,"abstract":"<div><p>Green algae usually assigned to the genus <em>Oophila</em> are known to colonize egg capsules of amphibian egg masses across the Nearctic and Palearctic regions. We study the phylogenetic relationships of these algae using a phylotranscriptomic data set of 76 protein-coding single-copy nuclear genes. Our data set includes novel RNAseq data for six amphibian-associated and five free-living green algae, and draft genomes of two of the latter. Within the <em>Oophila</em> clade (nested within Moewusinia), we find samples from two European frogs (<em>Rana dalmatina</em> and <em>R. temporaria</em>) closely related to those of the North American frog <em>R. aurora</em> (<em>Oophila</em> subclade III). An isolate from the North American <em>R. sylvatica</em> (subclade IV) appears to be sister to the Japanese isolate from the salamander <em>Hynobius nigrescens</em> (subclade J1), and subclade I algae from <em>Ambystoma maculatum</em> are sister to all other lineages in the <em>Oophila</em> clade. Two free-living algae (<em>Chlamydomonas nasuta</em> and <em>Cd. pseudogloeogama</em>) are nested within the <em>Oophila</em> clade, and a strain of the type species of <em>Chlorococcum</em> (<em>Cc. infusionum</em>) is related to this assemblage. Our phylotranscriptomic tree suggests that recognition of different species within the <em>Oophila</em> clade (“clade B” of earlier studies) is warranted, and calls for a comprehensive taxonomic revision of Moewusinia.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"200 ","pages":"Article 108165"},"PeriodicalIF":3.6,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S105579032400157X/pdfft?md5=05342644f755243808914b1a33f83602&pid=1-s2.0-S105579032400157X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141908495","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}