Molecular Phylogenetics and Evolution最新文献

{"title":"Population genomics of the southern giraffe","authors":"David Prochotta ,&nbsp;Sven Winter ,&nbsp;Julian Fennessy ,&nbsp;Axel Janke","doi":"10.1016/j.ympev.2024.108198","DOIUrl":"10.1016/j.ympev.2024.108198","url":null,"abstract":"<div><p>Studying wildlife taxonomic diversity and identifying distinct populations has traditionally been largely based on morphology and geographic origin. More recently, this method has been supplemented by genetic data from the mitochondrial genome. However, this is limited as only maternally inherited and may not reflect the true nature of a population’s genetics. Within the giraffe (<em>Giraffa</em> spp.), subspecies and unique populations were successfully characterized using both mitochondrial and genomic DNA studies, which led to new insights and, in some cases, unexpected results that required further verification. Here, we sequenced the genomes of 85 southern giraffe (<em>G. giraffa</em>) individuals from ten populations across southern Africa for a detailed investigation into the genetic diversity and history of its two subspecies, the Angolan (<em>G. g. angolensis</em>) and the South African (<em>G. g. giraffa</em>) giraffe. While the overall genotypes show low levels of runs of homozygosity compared to other mammals, the degree of heterozygosity is limited despite the large population size of South African giraffe. The nuclear genotype is largely congruent with the mitochondrial genotype. However, we have identified that the distribution of the Angolan giraffe is not as far east as indicated in an earlier mitochondrial DNA study. Botswana’s Central Kalahari Game Reserve giraffe are unique, with a clear admixture of Angolan and South African giraffe populations. However, the enigmatic desert-dwelling giraffe of northwest Namibia is locally distinct from other Angolan giraffe yet exhibits intra-subspecies signs of admixture resulting from a recent introduction of individuals from Namibia’s Etosha National Park. Whole genome sequencing is an invaluable and nearly indispensable tool for wildlife management to uncover genetic diversity that is undetectable through mitogenomic, geographical, and morphological means.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108198"},"PeriodicalIF":3.6,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001908/pdfft?md5=917747e305057c1149b9c1ff8191073f&pid=1-s2.0-S1055790324001908-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142270806","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":"Molecular phylogeny and species diversity of the genus Dichaetophora Duda and related taxa (Diptera: Drosophilidae)","authors":"Takehiro K. Katoh ,&nbsp;Ji-Min Chen ,&nbsp;Jin-Hua Yang ,&nbsp;Guang Zhang ,&nbsp;Lu Wang ,&nbsp;Awit Suwito ,&nbsp;Paulus Ak Meleng ,&nbsp;Masanori J. Toda ,&nbsp;Ya-Ping Zhang ,&nbsp;Jian-Jun Gao","doi":"10.1016/j.ympev.2024.108194","DOIUrl":"10.1016/j.ympev.2024.108194","url":null,"abstract":"<div><p>Our intensive surveys of wild drosophilids in East and Southeast Asia discovered a great species diversity (more than 100 putatively new species) of the genus <em>Dichaetophora</em>, which is currently comprised of 67 formally described species assigned into five species groups, i.e., <em>agbo</em>, <em>tenuicauda</em>, <em>acutissima</em>, <em>sinensis</em> and <em>trilobita</em>. In the present study, we delimited species from a huge amount of samples of <em>Dichaetophora</em> and allied taxa (the genus <em>Mulgravea</em> and the subgenus <em>Dudaica</em> of <em>Drosophila</em>) collected from a wide range of the Oriental and east Palearctic regions. We first sorted all specimens into morpho-species, and representative specimen(s) selected from each morpho-species were subjected to barcoding of <em>COI</em> (the cytochrome <em>c</em> oxidase subunit I gene) sequences. The applied ASAP (Assemble Species by Automatic Partitioning) analysis estimated a total of 166 to 168 MOTUs (molecular operational taxonomic units). Integrating this result with morphological evidence from re-examined, detailed structures of male terminalia, we recognized a total of 144 (109 new and 35 known) species in our sample. Out of them, 83 species representing the supraspecific taxa of <em>Dichaetophora</em>, <em>Mulgravea</em> and <em>Dudaica</em> were selected, along with 33 species from major genera and subgenera of <em>Drosophila</em> in the tribe Drosophilini, as in-group and four species from the tribe Colocasiomyini as out-group for phylogenetic reconstruction based on 12 nuclear gene markers. In the trees constructed by the maximum likelihood and Bayesian inference methods, the three focal taxa (i.e., <em>Dichaetophora</em>, <em>Mulgravea</em> and <em>Dudaica</em>) formed a clade provisionally called the “pan-<em>Dichaetophora</em>”. Within this large clade, the <em>agbo</em>, <em>tenuicauda</em>, <em>sinensis</em> and <em>trilobita</em> groups of <em>Dichaetophora</em>, <em>Mulgravea</em> and <em>Dudaica</em> were recovered as monophyletic groups, but <em>Dichaetophora</em> and its <em>acutissima</em> group were regarded as paraphyletic. In addition, two clusters were recognized among ungrouped species of <em>Dichaetophora</em>. Thus, the present study has uncovered some issues concerning the taxonomy of the pan-<em>Dichaetophora</em>. Such issues will be addressed elsewhere in the phylogenetic reclassification of the pan-<em>Dichaetophora</em>, along with descriptions/redescriptions of a large number of new/known species delimited in the present study.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108194"},"PeriodicalIF":3.6,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142239073","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":"Reticulate evolution: Detection and utility in the phylogenomics era","authors":"Saelin Bjornson ,&nbsp;Heroen Verbruggen ,&nbsp;Nathan S. Upham ,&nbsp;Jacob L. Steenwyk","doi":"10.1016/j.ympev.2024.108197","DOIUrl":"10.1016/j.ympev.2024.108197","url":null,"abstract":"<div><p>Phylogenomics has enriched our understanding that the Tree of Life can have network-like or reticulate structures among some taxa and genes. Two non-vertical modes of evolution – hybridization/introgression and horizontal gene transfer – deviate from a strictly bifurcating tree model, causing non-treelike patterns. However, these reticulate processes can produce similar patterns to incomplete lineage sorting or recombination, potentially leading to ambiguity. Here, we present a brief overview of a phylogenomic workflow for inferring organismal histories and compare methods for distinguishing modes of reticulate evolution. We discuss how the timing of coalescent events can help disentangle introgression from incomplete lineage sorting and how horizontal gene transfer events can help determine the relative timing of speciation events. In doing so, we identify pitfalls of certain methods and discuss how to extend their utility across the Tree of Life. Workflows, methods, and future directions discussed herein underscore the need to embrace reticulate evolutionary patterns for understanding the timing and rates of evolutionary events, providing a clearer view of life’s history.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108197"},"PeriodicalIF":3.6,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001891/pdfft?md5=2bec56b2fab35b10bc8cc62f1367f71c&pid=1-s2.0-S1055790324001891-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142228977","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":"A land plant phylogenetic framework for GLABROUS INFLORESCENCE STEMS (GIS), SUPERMAN, JAGGED and allies plus their TOPLESS co-repressor","authors":"Clemens Roessner ,&nbsp;Sven Griep ,&nbsp;Annette Becker","doi":"10.1016/j.ympev.2024.108195","DOIUrl":"10.1016/j.ympev.2024.108195","url":null,"abstract":"<div><p>Members of the plant specific family of C1-1i zinc<!--> <!-->finger transcription<!--> <!-->factors (ZF-TFs), such as SUPERMAN, JAGGED, KNUCKLES or GIS,<!--> <!-->regulate<!--> <!-->diverse<!--> <!-->developmental processes including sexual reproduction. C1-1is consist of one zinc-finger and one to two EAR domains, connected by large intrinsically disordered regions (IDR). While the role of C1-i1 ZF-TFs in development processes is well known for some genes in Arabidopsis, rice or tomato<!--> <!-->a comprehensive and broad<!--> <!-->phylogenetic background is lacking, yet knowledge of orthology is a requirement for a better understanding of C1-1i-Zf-TFs diverse roles in plants. Here, we provide a fine-grained and land plant wide classification of C1-1i sub-families and their known co-repressors TOPLESS and TOPLESS RELATED. Our work combines the identification of orthologous groups with Maximum-Likelihood phylogeny reconstructions and digital gene expression analyses mining high quality land plant genomes and transcriptomes to generate a comprehensive framework of C1-1i ZF-TF evolution. We show that C1-1i’s are low to moderate copy genes<!--> <!-->and that orthologous genes<!--> <!-->only partially<!--> <!-->have<!--> <!-->conserved sub-family and life cycle stage dependent expression pattern across land plants while others are highly diverged. Our work<!--> <!-->provides the phylogenetic framework for C1-1i ZF-TFs, s and strengthen C1-1 ZF-TFs as a potential model for IDR-research in plants.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108195"},"PeriodicalIF":3.6,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001878/pdfft?md5=6cc9b54fef4912cae6d55d5a777d4ce3&pid=1-s2.0-S1055790324001878-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142183391","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":"Evolution of chitin-synthase in molluscs and their response to ocean acidification","authors":"Maoxiao Peng ,&nbsp;João C.R. Cardoso ,&nbsp;Deborah M. Power","doi":"10.1016/j.ympev.2024.108192","DOIUrl":"10.1016/j.ympev.2024.108192","url":null,"abstract":"<div><p>Chitin-synthase (CHS) is found in most eukaryotes and has a complex evolutionary history. Research into CHS has mainly been in the context of biomineralization of mollusc shells an area of high interest due to the consequences of ocean acidification. Exploration of <em>CHS</em> at the genomic level in molluscs, the evolution of isoforms, their tissue distribution, and response to environmental challenges are largely unknown. Exploiting the extensive molecular resources for mollusc species it is revealed that bivalves possess the largest number of <em>CHS</em> genes (12–22) reported to date in eukaryotes. The evolutionary tree constructed at the class level of molluscs indicates four <em>CHS</em> Type II isoforms (A-D) probably existed in the most recent common ancestor, and Type II-A (Type II-A-1/Type II-A-2) and Type II-C (Type II-C-1/Type II-C-2) underwent further differentiation. Non-specific loss of <em>CHS</em> isoforms occurred at the class level, and in some Type II (B-D groups) isoforms the myosin head domain, which is associated with shell formation, was not preserved and highly species-specific tissue expression of <em>CHS</em> isoforms occurred. These observations strongly support the idea of CHS functional diversification with shell biomineralization being one of several important functions. Analysis of transcriptome data uncovered the species-specific potential of <em>CHS</em> isoforms in shell formation and a species-specific response to ocean acidification (OA). The impact of OA was not <em>CHS</em> isoform-dependent although in <em>Mytilus</em>, Type I-B and Type II-D gene expression was down-regulated in both <em>M. galloprovincialis</em> and <em>M. coruscus</em>. In summary, during <em>CHS</em> evolution the gene family expanded in bivalves generating a large diversity of isoforms with different structures and with a ubiquitous tissue distribution suggesting that chitin is involved in many biological functions. These findings provide insight into <em>CHS</em> evolution in molluscs and lay the foundation for research into their function and response to environmental changes.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108192"},"PeriodicalIF":3.6,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001842/pdfft?md5=07fdc475a8de4990d8d6b1f4b16b4b70&pid=1-s2.0-S1055790324001842-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142173208","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":"Between sea angels and butterflies: A global phylogeny of pelagic pteropod molluscs","authors":"Jose Vidal-Miralles ,&nbsp;Peter Kohnert ,&nbsp;Marina Monte ,&nbsp;Xavier Salvador ,&nbsp;Michael Schrödl ,&nbsp;Juan Moles","doi":"10.1016/j.ympev.2024.108183","DOIUrl":"10.1016/j.ympev.2024.108183","url":null,"abstract":"<div><div>Pteropods, holoplanktonic gastropods, play pivotal roles in marine ecosystems as integral components of food webs and carbon cycling. With global change threatening pelagic ecosystem equilibrium, conserving pteropod biodiversity is paramount. Here, we present the most extensive phylogenetic study of the order Pteropoda to date, utilizing a complete mitogenome phylogeny to support the suppression of Thecosomata, thus demonstrating the lack of relationship between Pseudothecosomata and Euthecosomata. Through multilocus Sanger-based taxon sampling with 411 specimens (92 newly sequenced), representing nearly 100 species (out of 163 valid) from various oceans, we elucidate robust support for higher taxonomic rankings. Despite strong support, relationships between the major groups Gymnosomata, Pseudothecosomata, and Euthecosomata remain contentious. Our study addresses unresolved taxonomic questions, identifying cryptic species complexes across vast biogeographic areas, and offering unprecedented insights into pteropod diversity. We shed light on several open questions in pteropod systematics, proposing the reclassification of <em>L. antarctica</em> stat. rest. and elucidating the position of <em>Thliptodon</em>, Heliconoididae, and Thieleidae. This systematic review enhances our understanding of pteropod diversity and underscores the urgency of conservation efforts in the face of changing oceanic conditions.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108183"},"PeriodicalIF":3.6,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142141831","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":"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}