Cladistics最新文献

{"title":"A targeted gene phylogenetic framework to investigate diversification in the highly diverse yet geographically restricted red devil spiders (Araneae, Dysderidae)","authors":"Silvia Adrián-Serrano,&nbsp;Martina Pavlek,&nbsp;Miquel A. Arnedo","doi":"10.1111/cla.12595","DOIUrl":"10.1111/cla.12595","url":null,"abstract":"<p>The family Dysderidae is a highly diverse group of nocturnal ground-dwelling and active-hunter spiders. Dysderids are mostly restricted to the Western Palearctic, and particularly rich and abundant around the Mediterranean region. Interestingly, the distribution of species richness among its 24 genera and three subfamilies is highly biased—80% of its 644 documented species belong to just two genera, <i>Dysdera</i> (326) and <i>Harpactea</i> (211). Dysderidae provides an excellent study case for evolutionary and ecological research. It includes cases of trophic specialization, which are uncommon among spiders, and exhibit other remarkable biological (e.g. holocentric chromosomes), behavioural (e.g. cryptic female choice), evolutionary (e.g. adaptive radiation) and ecological features (e.g. recurrent colonization of the subterranean environment). The lack of a quantitative hypothesis on its phylogenetic structure has hampered its potential as a testing ground for evolutionary, biogeographical and ecological hypotheses. Here, we present the results of a target, multi-locus phylogenetic analysis, using mitochondrial (cox1, 16s and 12s) and nuclear genes (h3, 28s and 18s), of the most exhaustive taxonomic sample within Dysderidae (104 spp.) to date and across related families (Synspermiata) (83 spp.). We estimate divergence times using a combination of fossil and biogeographic node calibrations and use this timeline to identify shifts in diversification rates. Our results support the monophyly of the Dysderidae subfamilies Rhodinae and Dysderinae but reject Harpacteinae as currently defined. Moreover, the clades recovered within Harpacteinae do not support its current taxonomy. The origin of the family most likely post-dated the break-up of Pangea, and cave colonization may be older than previously considered. After correcting for the taxonomic artefacts, we identified a significant shift in diversification rates at the base of the genus <i>Dysdera</i>. Although the unique coexistence of specialist and generalist diets within the lineage could be suggested as the potential driver for the rate acceleration, further quantitative analyses would be necessary to test this hypothesis.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 6","pages":"577-597"},"PeriodicalIF":3.9,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12595","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141894743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Insights from the first phylogenomic analysis of flat wasps (Hymenoptera, Bethylidae) reveal two new subfamilies","authors":"Bernardo F. Santos,&nbsp;Wesley D. Colombo,&nbsp;Elizabeth A. Murray,&nbsp;Seán G. Brady,&nbsp;Celso O. Azevedo","doi":"10.1111/cla.12594","DOIUrl":"10.1111/cla.12594","url":null,"abstract":"<p>Despite significant advances in alpha level taxonomy in the past few decades, the higher-level phylogeny of flat wasps (Hymenoptera, Bethylidae) remains poorly explored. Herein we provide the first phylogenomic assessment of the family based on data from ultraconserved elements for 96 species in 61 genera of the family, with material from 29 countries and all biogeographic regions. Dataset cutoffs including ultraconserved element loci recovered for 50 and 70% of terminals resulted in matrices with 1513 and 451 loci, which were analysed in both parsimony and maximum likelihood frameworks. We also provide the first analyses of divergence dating for the family based on the calibration of 12 nodes. All analyses recovered the Bethylidae as a monophyletic group and estimated the origin of the family at around 143 Ma. The results suggest that all extant subfamilies had already diversified by the Late Cretaceous. All topologies suggest that <i>Glenosema</i> and <i>Chilepyris</i> form a clade separate from other Scleroderminae; owing to the morphological distinctiveness of each genus, we propose that they are accommodated in two new subfamilies, Glenoseminae subf. nov. and Chilepyrinae subf. nov. The monotypic sclerodermine genus <i>Galodoxa</i> was consistently recovered within Epyrinae and is transferred to the latter subfamily.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 5","pages":"510-525"},"PeriodicalIF":3.9,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12594","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141762352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 new Urbacodon (Theropoda, Troodontidae) from the Upper Cretaceous Iren Dabasu Formation, China: Implications for troodontid phylogeny and tooth biology","authors":"Shuo Wang,&nbsp;Nuo Ding,&nbsp;Qingwei Tan,&nbsp;Rui Yang,&nbsp;Qiyue Zhang,&nbsp;Lin Tan","doi":"10.1111/cla.12592","DOIUrl":"10.1111/cla.12592","url":null,"abstract":"<p>Tooth attachment and replacement play significant roles in the feeding ecology of polyphyodont vertebrates, yet these aspects have remained largely unexplored in non-avialan paravians including troodontids. Here, we describe a new troodontid species, <i>Urbacodon norelli</i> <b>sp.n.</b>, recovered from the Upper Cretaceous Iren Dabasu Formation of Inner Mongolia, China, based on an incomplete right dentary and 12 associated replacement teeth. <i>Urbacodon norelli</i> is distinguished from all other known troodontids, including its relative <i>U. itemirensis</i> from Uzbekistan, by several features: the presence of paired dentary symphyseal foramina, the presence of a relatively steep anterior margin of the dentary, the absence of a dentary chin, the presence of a common groove hosting the anterior 12 dentary teeth, and the presence of relatively larger dentary teeth. Phylogenetic analysis places both species of <i>Urbacodon</i> as sister taxa to <i>Zanabazar junior</i>, confirming their status as later-diverging troodontids. Radiographs revealed an alternating tooth replacement pattern in <i>U. norelli</i>, with a maximum Zahnreihen-spacing estimated to be 3. During tooth replacement, the anteriorly inclined interdental septa, which wedge between anterior dentary teeth, underwent frequent remodelling as the developing tooth moved upwards, particularly anterolabially. This rapid turnover left insufficient time for an interdental plate to form, resulting in the absence of such structures in this specimen. The frequent remodelling of periodontal tissues accompanying tooth replacement is likely to account for the absence of interdental plates. The discovery of this new troodontid expands our understanding of paravian theropods from the Upper Cretaceous Iren Dabasu Formation and provides valuable insights into troodontid tooth biology.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"41 1","pages":"104-134"},"PeriodicalIF":3.9,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141629243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Measuring homoplasy I: comprehensive measures of maximum and minimum cost under parsimony across discrete cost matrix character types","authors":"Jennifer F. Hoyal Cuthill,&nbsp;Graeme T. Lloyd","doi":"10.1111/cla.12582","DOIUrl":"10.1111/cla.12582","url":null,"abstract":"<p>Here, we propose, prove mathematically and discuss maximum and minimum measures of maximum parsimony evolution across 12 discrete phylogenetic character types, classified across 4467 morphological and molecular datasets. Covered character types are: constant, binary symmetric, multistate unordered (non-additive) symmetric, multistate linear ordered symmetric, multistate non-linear ordered symmetric, binary irreversible, multistate irreversible, binary Dollo, multistate Dollo, multistate custom symmetric, binary custom asymmetric and multistate custom asymmetric characters. We summarize published solutions and provide and prove a range of new formulae for the algebraic calculation of minimum (<i>m</i>), maximum (<i>g</i>) and maximum possible (<i>g</i>_max) character cost for applicable character types. Algorithms for exhaustive calculation of <i>m</i>, <i>g</i> and <i>g</i>_max applicable to all classified character types (within computational limits on the numbers of taxa and states) are also provided. The general algorithmic solution for minimum steps (<i>m</i>) is identical to a minimum spanning tree on the state graph or minimum weight spanning arborescence on the state digraph. Algorithmic solutions for character <i>g</i> and <i>g</i>_max are based on matrix mathematics equivalent to optimization on the star tree, respectively for given state frequencies and all possible state frequencies meeting specified numbers of taxa and states. We show that maximizing possible cost (<i>g</i>_max) with given transition costs can be equivalent to maximizing, across all possible state frequency combinations, the lowest implied cost of state transitions if any one state is ancestral on the star tree, via the solution of systems of linear equations. The methods we present, implemented in the Claddis R package, extend to a comprehensive range, the fundamental character types for which homoplasy may be measured under parsimony using <i>m</i>, <i>g</i> and <i>g</i>_max, including extra cost (<i>h</i>), consistency index (<i>ci</i>), retention index (<i>ri</i>) or indices based thereon.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"41 1","pages":"1-27"},"PeriodicalIF":3.9,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12582","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141460508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete phylogeny of Micrathena spiders suggests multiple dispersal events among Neotropical rainforests, islands and landmasses, and indicates that Andean orogeny promotes speciation","authors":"Ivan L. F. Magalhaes,&nbsp;Pedro H. Martins,&nbsp;Bárbara T. Faleiro,&nbsp;Teofânia H. D. A. Vidigal,&nbsp;Fabrício R. Santos,&nbsp;Leonardo S. Carvalho,&nbsp;Adalberto J. Santos","doi":"10.1111/cla.12593","DOIUrl":"10.1111/cla.12593","url":null,"abstract":"<p>The Neotropical region is the most diverse on the planet, largely owing to its mosaic of tropical rainforests. Multiple tectonic and climatic processes have been hypothesized to contribute to generating this diversity, including Andean orogeny, the closure of the Isthmus of Panama, the GAARlandia land bridge and historical connections among currently isolated forests. <i>Micrathena</i> spiders are diverse and widespread in the region, and thus a complete phylogeny of this genus allows the testing of hypotheses at multiple scales. We estimated a complete, dated phylogeny using morphological data for 117 <i>Micrathena</i> species and molecular data of up to five genes for a subset of 79 species. Employing event-based approaches and biogeographic stochastic mapping while considering phylogenetic uncertainty, we estimated ancestral distributions, the timing and direction of dispersal events and diversification rates among areas. The phylogeny is generally robust, with uncertainty in the position of some of the species lacking sequences. <i>Micrathena</i> started diversifying around 25 Ma. Andean cloud forests show the highest <i>in-situ</i> speciation, while the Amazon is the major dispersal source for adjacent areas. The Dry Diagonal generated few species and is a sink of diversity. Species exchange between Central and South America involved approximately 23 dispersal events and started ~20 Ma, which is consistent with a Miocene age for the Isthmus of Panama closure. We inferred four dispersal events from Central America to the Antilles in the last 20 Myr, indicating the spiders did not reach the islands through the GAARlandia land bridge. We identified important species exchange routes among the Amazon, Andean cloud forests and Atlantic forests during the Plio-Pleistocene. Sampling all species of the genus was fundamental to the conclusions above, especially in identifying the Andean forests as the area that generated the majority of species. This highlights the importance of complete taxonomic sampling in biogeographic studies.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 5","pages":"552-575"},"PeriodicalIF":3.9,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141302072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ultraconserved elements from transcriptome and genome data provide insight into the phylogenomics of Sternorrhyncha (Insecta: Hemiptera)","authors":"Dajun Liu,&nbsp;Jinyu Cui,&nbsp;Yubo Liu,&nbsp;Minmin Niu,&nbsp;Fang Wang,&nbsp;Qing Zhao,&nbsp;Bo Cai,&nbsp;Hufang Zhang,&nbsp;Jiufeng Wei","doi":"10.1111/cla.12585","DOIUrl":"10.1111/cla.12585","url":null,"abstract":"<p>Sternorrhyncha, one of the four major suborders of Hemiptera, is a phytophagous taxon inclusive of nearly 18 000 described species. The phylogenetic relationships within the taxon and the earliest-branching lineage of its infraorders remain incompletely understood. This study attempted to illuminate the phylogenetic relationships within Sternorrhyncha through the use of maximum likelihood, Bayesian inference and maximum parsimony analyses, employing ultraconserved element (UCE) data from 39 genomic and 62 transcriptomic datasets and thereby representing most families within the taxon. The probe set Hemiptera 2.7Kv1 was used to recover a total of 2731 UCE loci: from 547 to 1699 (with an average of 1084) across all genomic datasets and from 108 to 849 (with an average of 329) across all transcriptomic datasets. All three types of phylogenetic analyses employed in this study produced robust statistical support for Sternorrhyncha being a monophyletic group. The different methods of phylogenetic analysis produced inconsistent descriptions of topological structure at the infraorder level: while maximum likelihood and Bayesian inference analyses produced strong statistical evidence (100%) indicating the clade Psylloidea + Aleyrodoidea to be a sister of the clade Aphidoidea (Aphidomorpha) + Coccoidea (Coccomorpha), the maximum parsimony analysis failed to recover a similar result. Our results also provide detail on the phylogenetic relationships within each infraorder. This study presents the first use of UCE data to investigate the phylogeny of Sternorrhyncha. It also shows the viability of amalgamating genomic and transcriptomic data in studies of phylogenetic relationships, potentially highlighting a resource-efficient approach for future inquiries into diverse taxa through the integration of varied data sources.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 5","pages":"496-509"},"PeriodicalIF":3.9,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141161311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new abelisaurid dinosaur from the end Cretaceous of Patagonia and evolutionary rates among the Ceratosauria","authors":"Diego Pol,&nbsp;Mattia Antonio Baiano,&nbsp;David Černý,&nbsp;Fernando E. Novas,&nbsp;Ignacio A. Cerda,&nbsp;Michael Pittman","doi":"10.1111/cla.12583","DOIUrl":"10.1111/cla.12583","url":null,"abstract":"<p>Gondwanan dinosaur faunae during the 20 Myr preceding the Cretaceous–Palaeogene (K/Pg) extinction included several lineages that were absent or poorly represented in Laurasian landmasses. Among these, the South American fossil record contains diverse abelisaurids, arguably the most successful groups of carnivorous dinosaurs from Gondwana in the Cretaceous, reaching their highest diversity towards the end of this period. Here we describe <i>Koleken inakayali</i> gen. et sp. n., a new abelisaurid from the La Colonia Formation (Maastrichtian, Upper Cretaceous) of Patagonia. <i>Koleken inakayali</i> is known from several skull bones, an almost complete dorsal series, complete sacrum, several caudal vertebrae, pelvic girdle and almost complete hind limbs. The new abelisaurid shows a unique set of features in the skull and several anatomical differences from <i>Carnotaurus sastrei</i> (the only other abelisaurid known from the La Colonia Formation). <i>Koleken inakayali</i> is retrieved as a brachyrostran abelisaurid, clustered with other South American abelisaurids from the latest Cretaceous (Campanian–Maastrichtian), such as <i>Aucasaurus</i>, <i>Niebla</i> and <i>Carnotaurus</i>. Leveraging our phylogeny estimates, we explore rates of morphological evolution across ceratosaurian lineages, finding them to be particularly high for elaphrosaurine noasaurids and around the base of Abelisauridae, before the Early Cretaceous radiation of the latter clade. The Noasauridae and their sister clade show contrasting patterns of morphological evolution, with noasaurids undergoing an early phase of accelerated evolution of the axial and hind limb skeleton in the Jurassic, and the abelisaurids exhibiting sustained high rates of cranial evolution during the Early Cretaceous. These results provide much needed context for the evolutionary dynamics of ceratosaurian theropods, contributing to broader understanding of macroevolutionary patterns across dinosaurs.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 3","pages":"307-356"},"PeriodicalIF":3.6,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12583","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141071175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"On the importance of sequence alignment inspections in plastid phylogenomics – an example from revisiting the relationships of the water-lilies","authors":"Jessica A. Roestel,&nbsp;John H. Wiersema,&nbsp;Robert K. Jansen,&nbsp;Thomas Borsch,&nbsp;Michael Gruenstaeudl","doi":"10.1111/cla.12584","DOIUrl":"10.1111/cla.12584","url":null,"abstract":"<p>The water-lily clade represents the second earliest-diverging branch of angiosperms. Most of its species belong to Nymphaeaceae, of which the “core Nymphaeaceae”—comprising the genera <i>Euryale</i>, <i>Nymphaea</i> and <i>Victoria</i>—is the most diverse clade. Despite previous molecular phylogenetic studies on the core Nymphaeaceae, various aspects of their evolutionary relationships have remained unresolved. The length-variable introns and intergenic spacers are known to contain most of the sequence variability within the water-lily plastomes. Despite the challenges with multiple sequence alignment, any new molecular phylogenetic investigation on the core Nymphaeaceae should focus on these noncoding plastome regions. For example, a new plastid phylogenomic study on the core Nymphaeaceae should generate DNA sequence alignments of all plastid introns and intergenic spacers based on the principle of conserved sequence motifs. In this investigation, we revisit the phylogenetic history of the core Nymphaeaceae by employing such an approach. Specifically, we use a plastid phylogenomic analysis strategy in which all coding and noncoding partitions are separated and then undergo software-driven DNA sequence alignment, followed by a motif-based alignment inspection and adjustment. This approach allows us to increase the reliability of the character base compared to the default practice of aligning complete plastomes through software algorithms alone. Our approach produces significantly different phylogenetic tree reconstructions for several of the plastome regions under study. The results of these reconstructions underscore that <i>Nymphaea</i> is paraphyletic in its current circumscription, that each of the five subgenera of <i>Nymphaea</i> is monophyletic, and that the subgenus <i>Nymphaea</i> is sister to all other subgenera of <i>Nymphaea</i>. Our results also clarify many evolutionary relationships within the <i>Nymphaea</i> subgenera <i>Brachyceras</i>, <i>Hydrocallis</i> and <i>Nymphaea</i>. In closing, we discuss whether the phylogenetic reconstructions obtained through our motif-based alignment adjustments are in line with morphological evidence on water-lily evolution.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 5","pages":"469-495"},"PeriodicalIF":3.9,"publicationDate":"2024-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12584","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140959871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the effects of weighting against homoplasy in genealogies of palaeontological phylogenetic matrices","authors":"Martín D. Ezcurra","doi":"10.1111/cla.12581","DOIUrl":"10.1111/cla.12581","url":null,"abstract":"<p>Although simulations have shown that implied weighting (IW) outperforms equal weighting (EW) in phylogenetic parsimony analyses, weighting against homoplasy lacks extensive usage in palaeontology. Iterative modifications of several phylogenetic matrices in the last decades resulted in extensive genealogies of datasets that allow the evaluation of differences in the stability of results for alternative character weighting methods directly on empirical data. Each generation was compared against the most recent generation in each genealogy because it is assumed that it is the most comprehensive (higher sampling), revised (fewer misscorings) and complete (lower amount of missing data) matrix of the genealogy. The analyses were conducted on six different genealogies under EW and IW and extended implied weighting (EIW) with a range of concavity constant values (<i>k</i>) between 3 and 30. Pairwise comparisons between trees were conducted using Robinson–Foulds distances normalized by the total number of groups, distortion coefficient, subtree pruning and regrafting moves, and the proportional sum of group dissimilarities. The results consistently show that IW and EIW produce results more similar to those of the last dataset than EW in the vast majority of genealogies and for all comparative measures. This is significant because almost all of these matrices were originally analysed only under EW. Implied weighting and EIW do not outperform each other unambiguously. Euclidean distances based on a principal components analysis of the comparative measures show that different ranges of <i>k-</i>values retrieve the most similar results to the last generation in different genealogies. There is a significant positive linear correlation between the optimal <i>k-</i>values and the number of terminals of the last generations. This could be employed to inform about the range of <i>k-</i>values to be used in phylogenetic analyses based on matrix size but with the caveat that this emergent relationship still relies on a low sample size of genealogies.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 3","pages":"242-281"},"PeriodicalIF":3.6,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12581","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140904560","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PSA: an effective method for predicting horizontal gene transfers through parsimonious phylogenetic networks","authors":"Yuan Zhang,&nbsp;Juan Wang,&nbsp;Jing Yu","doi":"10.1111/cla.12578","DOIUrl":"10.1111/cla.12578","url":null,"abstract":"<p>Horizontal gene transfer (HGT) from one organism to another, according to some researchers, can be abundant in the evolution of species. A phylogenetic network is a network structure that describes the HGTs among species. Several studies have proposed methods to construct phylogenetic networks to predict HGTs based on parsimony values. Existing definitions of parsimony values for a phylogenetic network are based on the assumption that each gene site or segment evolves independently along different trees in the network. However, in the current study, we define a novel parsimony value, denoted the <i>p</i> definition, for phylogenetic networks, considering that a gene as a whole typically evolves along a tree. Using Simulated Annealing, a new method called the Phylogeny with Simulated Annealing (PSA) algorithm is proposed to search for an optimal network based on the <i>p</i> definition. The PSA method is tested on the simulated data. The results reveal that the parsimonious networks constructed using PSA can better represent the evolutionary relationships of species involving HGTs. Additionally, the HGTs predicted using PSA are more accurate than those predicted using other methods. The PSA algorithm is publicly accessible at http://github.com/imustu/sap.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 4","pages":"443-455"},"PeriodicalIF":3.9,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140877851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}