Molecular Phylogenetics and Evolution最新文献

{"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}

{"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}