Molecular Phylogenetics and Evolution最新文献

{"title":"A consequential one-night stand: Episodic historical hybridization leads to mitochondrial takeover in sympatric desert ant-eating spiders","authors":"David Ortiz ,&nbsp;Stano Pekár ,&nbsp;Malahat Dianat","doi":"10.1016/j.ympev.2024.108167","DOIUrl":"10.1016/j.ympev.2024.108167","url":null,"abstract":"<div><p>Disentangling the genomic intricacies underlying speciation and the causes of discordance between sources of evidence can offer remarkable insights into evolutionary dynamics. The ant-eating spider <em>Zodarion nitidum</em>, found across the Middle East and Egypt, displays yellowish and blackish morphs that co-occur sympatrically. These morphs additionally differ in behavioral and physiological features and show complete pre-mating reproductive isolation. In contrast, they possess similar sexual features and lack distinct differences in their mitochondrial DNA. We analyzed both <em>Z. nitidum</em> morphs and outgroups using genome-wide and additional mitochondrial DNA data. The genomic evidence indicated that <em>Yellow</em> and <em>Black</em> are reciprocally independent lineages without signs of recent admixture. Interestingly, the sister group of <em>Yellow</em> is not <em>Black</em> but <em>Z. luctuosum</em>, a morphologically distinct species. Genomic gene flow analyses pinpointed an asymmetric nuclear introgression event, with <em>Yellow</em> contributing nearly 5 % of its genome to <em>Black</em> roughly 320,000 years ago, intriguingly aligning with the independently estimated origin of the mitochondrial DNA of <em>Black</em>. We conclude that the blackish and yellowish morphs of <em>Z. nitidum</em> are long-diverged distinct species, and that the ancient and modest genomic introgression event registered resulted in a complete mitochondrial takeover of <em>Black</em> by <em>Yellow</em>. This investigation underscores the profound long-term effects that even modest hybridization events can have on the genome of organisms. It also exemplifies the utility of phylogenetic networks for estimating historical events and how integrating independent lines of evidence can increase the reliability of such estimations.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"199 ","pages":"Article 108167"},"PeriodicalIF":3.6,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141894977","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 including new sequence data of phytoplankton-infecting chytrids reveals multiple independent lifestyle transitions across the phylum.","authors":"Pauline C Thomé, Justyna Wolinska, Silke Van Den Wyngaert, Albert Reñé, Doris Ilicic, Ramsy Agha, Hans-Peter Grossart, Esther Garcés, Michael T Monaghan, Jürgen F H Strassert","doi":"10.1016/j.ympev.2024.108103","DOIUrl":"10.1016/j.ympev.2024.108103","url":null,"abstract":"<p><p>Parasitism is the most common lifestyle on Earth and has emerged many times independently across the eukaryotic tree of life. It is frequently found among chytrids (Chytridiomycota), which are early-branching unicellular fungi that feed osmotrophically via rhizoids as saprotrophs or parasites. Chytrids are abundant in most aquatic and terrestrial environments and fulfil important ecosystem functions. As parasites, they can have significant impacts on host populations. They cause global amphibian declines and influence the Earth's carbon cycle by terminating algal blooms. To date, the evolution of parasitism within the chytrid phylum remains unclear due to the low phylogenetic resolution of rRNA genes for the early diversification of fungi, and because few parasitic lineages have been cultured and genomic data for parasites is scarce. Here, we combine transcriptomics, culture-independent single-cell genomics and a phylogenomic approach to overcome these limitations. We newly sequenced 29 parasitic taxa and combined these with existing data to provide a robust backbone topology for the diversification of Chytridiomycota. Our analyses reveal multiple independent lifestyle transitions between parasitism and saprotrophy among chytrids and multiple host shifts by parasites. Based on these results and the parasitic lifestyle of other early-branching holomycotan lineages, we hypothesise that the chytrid last common ancestor was a parasite of phytoplankton.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"108103"},"PeriodicalIF":4.1,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140961154","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":"Exploring the phylogeny and depth evolution of cusk eels and their relatives (Ophidiiformes: Ophidioidei)","authors":"Man-Kwan Wong,&nbsp;Wei-Jen Chen","doi":"10.1016/j.ympev.2024.108164","DOIUrl":"10.1016/j.ympev.2024.108164","url":null,"abstract":"<div><p>With 289 known species in 51 genera, the ophidiiform family Ophidiidae together with their relatives from the Carapidae (36 species in eight genera) of the same suborder Ophidioidei dominate the deep sea, but some occur also in shallow water habitats. Despite their high species diversity in the deep sea and wide bathymetric distributions, their phylogenetic relationships and evolution remain unexplored due in part to sampling difficulties. Thanks to the biodiversity exploratory program entitled “<em>Tropical Deep-Sea Benthos</em>” and joint efforts between Taiwan and French teams for sampling from different localities across the Indo-West Pacific over the last two decades, we are able to compile comprehensive datasets for investigations. In this study, 59 samples representing 36 of 59 known ophidioid genera are selected and used to construct a multi-gene dataset to infer the phylogenetic relationships of ophidioid fishes and their relatives. Our results reveal that the Ophidiidae forms a paraphyletic group with respect to the Carapidae. The four main clades of Ophidioidei resolved are the (1) clade comprising species from the subfamily Brotulinae; (2) clade that includes species in the genera <em>Acanthonus</em> and <em>Xyelacyba</em>; (3) clade grouping <em>Hypopleuron caninum</em> with species from the family Carapidae; and (4) clade containing the species in the subfamily Brotulotaenilinae, Neobythitinae (in part), and Ophidiinae. Accordingly, we suggest the following new revisions based on our results and proposed morphological diagnoses. The subfamily Brotulinae should be elevated to the family level. The genera <em>Xyelacyba</em> and probably <em>Tauredophidium</em> (unsampled in this study) should be included in the newly established family Acanthonidae with <em>Acanthonus</em>. The families Carapidae and Ophidiidae are re-defined. Our time-calibrated phylogenetic and ancestral depth reconstructions enable us to clarify the evolutionary history of ophidiiform fishes and infer past patterns of species distributions at different depths. While Ophidiiformes is inferred to have originated in shallow waters around 96.25 million years ago (Mya), the common ancestor to the Ophidioidei is inferred to have invaded the deep sea around 90.22 Mya, the dates coinciding with the global anoxic event of the OAE2. The observed bathymetric distribution patterns in Ophidioidei most likely point to the mesopelagic zone as the center of origin and diversification. This was followed by multiple events of depth transitions or range expansions towards either shallower waters or greater depth zones, which were likely triggered by past climate changes during the Paleogene-Neogene.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"199 ","pages":"Article 108164"},"PeriodicalIF":3.6,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141861811","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":"Underground speciation: Unraveling the systematics and evolution of the highly diverse tuco-tucos (genus Ctenomys) with genomic data","authors":"Ivanna H. Tomasco ,&nbsp;Santiago G. Ceballos ,&nbsp;Ailin Austrich ,&nbsp;Federico Brook ,&nbsp;Diego A. Caraballo ,&nbsp;Gabriela P. Fernández ,&nbsp;Cecilia Lanzone ,&nbsp;Matías S. Mora ,&nbsp;Andrés Parada ,&nbsp;R. Tatiana Sánchez ,&nbsp;Enrique P. Lessa","doi":"10.1016/j.ympev.2024.108163","DOIUrl":"10.1016/j.ympev.2024.108163","url":null,"abstract":"<div><p>Subterranean rodents of the genus <em>Ctenomys</em> (tuco-tucos) are endemic to South America and have experienced relatively recent radiation. There are about 67 recognized species that originated in approximately 1–2 MY. They stand out for their species richness, extraordinary chromosomal diversity, and wide range of habitat they occupy in the continent. Phylogenetic relationships among species of tuco-tucos have been challenging to resolve. Groups of closely-related species have been suggested, but their relationships must be resolved. This study estimates the phylogeny of the genus using massive sequencing, generating thousands of independent molecular markers obtained by RADseq, with a taxonomic sampling that includes 66% of the recognized species. The sequences obtained were mapped against the <em>C. sociabilis</em> genome, recovering up to 1,215 widely shared RAD loci with more than 19,000 polymorphic sites. Our new phylogenetic hypothesis corroborated the species groups previously proposed with cytochrome <em>b</em> gene sequences and provided a much greater resolution of the relationships among species groups. The <em>frater</em> group is sister to all other tuco-tucos, whereas some of the earlierliest proposals placed the <em>sociabilis</em> group as sister to all other tuco-tucos. <em>Ctenomys leucodon</em>, previously proposed as an independent lineage, is associated with the <em>frater</em> group with moderate statistical support. The <em>magellanicus</em> and <em>mendocinus</em> are sister groups in a major clade formed by the <em>boliviensis</em>, <em>talarum</em>, <em>tucumanus</em>, <em>torquatus</em>, and <em>opimus</em> groups. <em>Ctenomys viperinus</em>, included in the phylogeny for the first time, belongs to the <em>tucumanus</em> group. This multi-locus phylogenetic hypothesis provides insights into the historical biogeography of understanding this highly diverse genus.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"199 ","pages":"Article 108163"},"PeriodicalIF":3.6,"publicationDate":"2024-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141850032","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 insights into the Salicaceae: The evolution of willows and beyond","authors":"Ezgi Ogutcen ,&nbsp;Paola de Lima Ferreira ,&nbsp;Natascha D. Wagner ,&nbsp;Pia Marinček ,&nbsp;Jing Vir Leong ,&nbsp;Gibson Aubona ,&nbsp;Jeannine Cavender-Bares ,&nbsp;Jan Michálek ,&nbsp;Lucy Schroeder ,&nbsp;Brian E. Sedio ,&nbsp;Radim J. Vašut ,&nbsp;Martin Volf","doi":"10.1016/j.ympev.2024.108161","DOIUrl":"10.1016/j.ympev.2024.108161","url":null,"abstract":"<div><p>The Salicaceae includes approximately 54 genera and over 1,400 species with a cosmopolitan distribution. Members of the family are well-known for their diverse secondary plant metabolites, and they play crucial roles in tropical and temperate forest ecosystems. Phylogenetic reconstruction of the Salicaceae has been historically challenging due to the limitations of molecular markers and the extensive history of hybridization and polyploidy within the family. Our study employs whole-genome sequencing of 74 species to generate an extensive phylogeny of the Salicaceae. We generated two RAD-Seq enriched whole-genome sequence datasets and extracted two additional gene sets corresponding to the universal Angiosperms353 and Salicaceae-specific targeted-capture arrays. We reconstructed maximum likelihood-based molecular phylogenies using supermatrix and coalescent-based supertree approaches. Our fossil-calibrated phylogeny estimates that the Salicaceae originated around 128 million years ago and unravels the complex taxonomic relationships within the family. Our findings confirm the non-monophyly of the subgenus <em>Salix</em> s.l. and further support the merging of subgenera <em>Chamaetia</em> and <em>Vetrix</em>, both of which exhibit intricate patterns within and among different sections. Overall, our study not only enhances our understanding of the evolution of the Salicaceae, but also provides valuable insights into the complex relationships within the family.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"199 ","pages":"Article 108161"},"PeriodicalIF":3.6,"publicationDate":"2024-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001532/pdfft?md5=ef314acf1a28b68faf600b4943e9537b&pid=1-s2.0-S1055790324001532-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141847521","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 analysis reveals the evolutionary history of Paleartic needle-leaved junipers","authors":"David Gutiérrez-Larruscain ,&nbsp;Pablo Vargas ,&nbsp;Mario Fernández-Mazuecos ,&nbsp;Juli G. Pausas","doi":"10.1016/j.ympev.2024.108162","DOIUrl":"10.1016/j.ympev.2024.108162","url":null,"abstract":"<div><p>Needle-leaved junipers (<em>Juniperus</em> sect. <em>Juniperus</em>, Cupressaceae) are coniferous trees and shrubs with red or blue fleshy cones. They are distributed across Asia, Macaronesia and the Mediterranean Basin, with one species (<em>J. communis</em>) having a circumboreal distribution. Here we aim to resolve the phylogeny of this clade to infer its intricate evolutionary history. To do so, we built a comprehensive, time-calibrated phylogeny using genotyping-by-sequencing (GBS) and combine it with species occurrence using phylogeographic tools. Our results provide solid phylogenetic resolution to propose a new taxonomic classification and a biogeographical history of the section. Specifically, we confirm the monophyly of two groups within <em>J.</em> sect. <em>Juniperus</em>: the Asian (blue-cone) species including the circumboreal <em>J. communis,</em> and the Mediterranean-Macaronesian (red-cone) species. In addition, we provide strong phylogenetic evidence for three distinct species (<em>J. badia</em>, <em>J. conferta</em>, <em>J. lutchuensis</em>) previously considered subspecies or varieties, as well as for the differentiation between the eastern and western Mediterranean lineages of <em>J. macrocarpa</em>. Our findings suggest that the Mediterranean basin was the primary center of diversification for <em>Juniperus</em> sect. <em>Juniperus</em>, followed by an East Asian-Tethyan disjunction resulting from uplifts of the Qinghai-Tibetan Plateau and climatic shifts. The colonization history of Macaronesia by red-cone junipers from the western Mediterranean appears to have taken place independently in two different geological periods: the Miocene (Azores) and the Pliocene (Madeira-Canary Islands). Overall, genomic data and phylogenetic analysis are key to consider a new taxonomic proposal and reconstruct the biogeographical history of the iconic needle-leaved junipers across the Paleartic.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"199 ","pages":"Article 108162"},"PeriodicalIF":3.6,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001544/pdfft?md5=83a30aec3b772a2ca4dddfc1a54e67d2&pid=1-s2.0-S1055790324001544-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141790077","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":"Evolutionary relationships and fine-scale geographic structuring in the temperate percichthyid genus Gadopsis (blackfishes) to support fisheries and conservation management","authors":"Matthew A. Campbell ,&nbsp;Michael P. Hammer ,&nbsp;Mark Adams ,&nbsp;Tarmo A. Raadik ,&nbsp;Peter J. Unmack","doi":"10.1016/j.ympev.2024.108159","DOIUrl":"10.1016/j.ympev.2024.108159","url":null,"abstract":"<div><p><em>Gadopsis</em> (Percichthyidae) is a freshwater genus distributed in south-eastern Australia, including Tasmania, and comprises two recognized species. Previous molecular phylogenetic investigations of the genus, mostly conducted in the pre-genomics era and reflecting a range of geographic and molecular sampling intensities, have supported the recognition of up to seven candidate species. Here we analyze a genome-wide SNP dataset that provides comprehensive geographic and genomic coverage of <em>Gadopsis</em> to produce a robust hypothesis of species boundaries and evolutionary relationships. We then leverage the SNP dataset to characterize relationships within candidate species that lack clear intraspecific phylogenetic relationships. We find further support for the seven previously identified candidate species of <em>Gadopsis</em> and evidence that the Bass Strait centered candidate species (SBA) originated from ancient hybridization. The SNP dataset permits a high degree of intraspecific resolution, providing improvements over previous studies, with numerous candidate species showing intraspecific divisions in phylogenetic analysis. Further population genetic analysis of the Murray-Darling candidate species (NMD) and SBA finds support for <em>K</em> = 6 and <em>K</em> = 7 genetic clusters, respectively. The SNP data generated for this study have diverse applications in natural resource management for these fishes of conservation concern.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"199 ","pages":"Article 108159"},"PeriodicalIF":3.6,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001519/pdfft?md5=8fd7fb08ffaa63b55a66e3434e4abf7d&pid=1-s2.0-S1055790324001519-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141728382","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":"Whole genome phylogenomics helps to resolve the phylogenetic position of the Zygothrica genus group (Diptera, Drosophilidae) and the causes of previous incongruences","authors":"Maiara Hartwig Bessa ,&nbsp;Marco Silva Gottschalk ,&nbsp;Lizandra Jaqueline Robe","doi":"10.1016/j.ympev.2024.108158","DOIUrl":"10.1016/j.ympev.2024.108158","url":null,"abstract":"<div><p>Incomplete Lineage Sorting (ILS) and introgression are among the two main factors causing incongruence between gene and species trees. Advances in phylogenomic studies have allowed us to overcome most of these issues, providing reliable phylogenetic hypotheses while revealing the underlying evolutionary scenario. Across the last century, many incongruent phylogenetic reconstructions were recovered for Drosophilidae, employing a limited sampling of genetic markers or species. In these studies, the monophyly and the phylogenetic positioning of the <em>Zygothrica</em> genus group stood out as one of the most controversial questions. Thus, here, we addressed these issues using a phylogenomic approach, while accessing the influence of ILS and introgressions on the diversification of these species and addressing the spatio-temporal scenario associated with their evolution. For this task, the genomes of nine specimens from six Neotropical species belonging to the <em>Zygothrica</em> genus group were sequenced and evaluated in a phylogenetic framework encompassing other 39 species of Drosophilidae. Nucleotide and amino acid sequences recovered for a set of 2,534 single-copy genes by BUSCO were employed to reconstruct maximum likelihood (ML) concatenated and multi-species coalescent (MSC) trees. Likelihood mapping, quartet sampling, and reticulation tests were employed to infer the level and causes of incongruence. Lastly, a penalized-likelihood molecular clock strategy with fossil calibrations was performed to infer divergence times. Taken together, our results recovered the subdivision of <em>Drosophila</em> into six different lineages, one of which clusters species of the <em>Zygothrica</em> genus group (except for <em>H. duncani</em>). The divergence of this lineage was dated to Oligocene ∼ 31 Mya and seems to have occurred in the same timeframe as other key diversification within <em>Drosophila</em>. According to the concatenated and MSC strategies, this lineage is sister to the clade joining <em>Drosophila</em> (<em>Siphlodora</em>) with the Hawaiian <em>Drosophila</em> and <em>Scaptomyza</em>. Likelihood mapping, quartet sampling, reticulation reconstructions as well as introgression tests revealed that this lineage was the target of several hybridization events involving the ancestors of different <em>Drosophila</em> lineages. Thus, our results generally show introgression as a major source of previous incongruence. Nevertheless, the similar diversification times recovered for several of the Neotropical <em>Drosophila</em> lineages also support the scenario of multiple and simultaneous diversifications taking place at the base of Drosophilidae phylogeny, at least in the Neotropics.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"199 ","pages":"Article 108158"},"PeriodicalIF":3.6,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141725150","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":"Genetic diversity of the largest African mole-rat genus, Bathyergus. one, two or four species?","authors":"R. Šumbera ,&nbsp;M. Uhrová ,&nbsp;G. Montoya-Sanhueza ,&nbsp;A. Bryjová ,&nbsp;N.C. Bennett ,&nbsp;O. Mikula","doi":"10.1016/j.ympev.2024.108157","DOIUrl":"10.1016/j.ympev.2024.108157","url":null,"abstract":"<div><p>Recent advances in sequencing technology and phylogenetic methods allow us to solve puzzling taxonomic questions using detailed analyses of genetic diversity of populations and gene flow between them. The genus of solitary-living dune mole-rat, <em>Bathyergus</em>, is quite unique among six genera of African mole-rats. The animals are by far the largest and the only scratch digging mole-rat genus possessing a skull less adapted to digging, grooved upper incisors, and more surface locomotor activity. Most authors recognize two species of dune mole-rats, <em>B. suillus</em> and <em>B. janetta</em>, but according to others, the genus is monotypic. In addition, recent molecular studies have revealed cryptic genetic diversity and suggested the existence of up to four species. In our study, we used mitochondrial and genome-wide nuclear data collected throughout the distribution of the genus to investigate the number of species. In agreement with previous studies, we found <em>Bathyergus</em> to be differentiated into several distinct lineages, but we also found evidence for a degree of gene flow between some of them. Furthermore, we confirmed that <em>B. janetta</em> is nested within <em>B. suillus</em>, making the latter paraphyletic and we documented an instance of local mitochondrial introgression between these two nominal species. Phylogeographic structure of the genus was found to be very shallow. Although traditionally dated to the Miocene, we found the first split within the genus to be much younger estimated to 0.82 Ma before present. Genealogical distinctiveness of some lineages was very low, and the coancestry matrix showed extensive sharing of closely related haplotypes throughout the genus. Accordingly, Infomap clustering on the matrix showed all populations to form a single cluster. Overall, our study tends to support the existence of only one species of <em>Bathyergus</em> namely, <em>B. suillus</em>. Environmental niche modelling confirmed its dependence on sandy soils and the preference for soils with relatively high carbon content. Bayesian skyline plots indicate recent population decline in the <em>janetta</em> lineage, probably related to global environmental change.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"199 ","pages":"Article 108157"},"PeriodicalIF":3.6,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141728332","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":"Inferring phylogenetic networks from multifurcating trees via cherry picking and machine learning","authors":"Giulia Bernardini ,&nbsp;Leo van Iersel ,&nbsp;Esther Julien ,&nbsp;Leen Stougie","doi":"10.1016/j.ympev.2024.108137","DOIUrl":"10.1016/j.ympev.2024.108137","url":null,"abstract":"<div><p>The Hybridization problem asks to reconcile a set of conflicting phylogenetic trees into a single phylogenetic network with the smallest possible number of reticulation nodes. This problem is computationally hard and previous solutions are limited to small and/or severely restricted data sets, for example, a set of binary trees with the same taxon set or only two non-binary trees with non-equal taxon sets. Building on our previous work on binary trees, we present <span>FHyNCH</span>, the first algorithmic framework to heuristically solve the Hybridization problem for large sets of multifurcating trees whose sets of taxa may differ. Our heuristics combine the cherry-picking technique, recently proposed to solve the same problem for binary trees, with two carefully designed machine-learning models. We demonstrate that our methods are practical and produce qualitatively good solutions through experiments on both synthetic and real data sets.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"199 ","pages":"Article 108137"},"PeriodicalIF":3.6,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001295/pdfft?md5=aededa43382f7fa94b9e3b6e72546061&pid=1-s2.0-S1055790324001295-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141728333","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}