Zoologica Scripta最新文献

{"title":"A renaissance of microRNAs as taxonomic and phylogenetic markers in animals","authors":"Bastian Fromm","doi":"10.1111/zsc.12684","DOIUrl":"https://doi.org/10.1111/zsc.12684","url":null,"abstract":"Molecular markers for tracing animal sample origins and compositions are critical for applications such as parasite detection, contamination screening, and sample authentication. Among these, microRNAs have emerged as promising candidates due to their deep conservation, near‐hierarchical evolution, and stability. I here review the suitability of microRNAs as taxonomic and also phylogenetic markers and show how careful annotation efforts and the establishment of the curated microRNA gene database MirGeneDB and tools like MirMachine have revitalized microRNA research. These advancements enable accurate phylogenetic and taxonomic studies, highlighting microRNAs' potential in resolving long‐standing questions in animal relationships and extending to applications in ancient DNA and environmental RNA analysis. Future research must focus on expanding microRNA complements across all Metazoa and further improving annotation methodologies.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":"37 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141503198","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":"Integrative taxonomy of the featherback fish genus Chitala (Osteoglossomorpha: Notopteridae) in Peninsular Malaysia","authors":"Luqman Hakim Ruzman, Jamsari Amirul Firdaus Jamaluddin, Abdullah Halim Muhammad‐Rasul, Tedjo Sukmono, Md. Zain Khaironizam, Sébastien Lavoué","doi":"10.1111/zsc.12678","DOIUrl":"https://doi.org/10.1111/zsc.12678","url":null,"abstract":"The taxonomy of the freshwater featherback fish genus <jats:italic>Chitala</jats:italic> (Osteoglossomorpha: Notopteridae) remains unsettled because delimiting and naming <jats:italic>Chitala</jats:italic> species based solely on morphology led to different hypotheses. In this study, we aim to determine the number and identity of <jats:italic>Chitala</jats:italic> species present in Peninsular Malaysia by employing an integrative taxonomic approach that combines morphology and two mitochondrial markers: the cytochrome c oxidase subunit I (COI) and cytochrome b genes. A total of 60 specimens of <jats:italic>Chitala</jats:italic> were collected throughout Peninsular Malaysia. Initially, all specimens were sorted into three distinct categories based on their body marking patterns. A molecular phylogenetic analysis revealed that each of these groups was monophyletic, and an automated species partition method further recognized them as distinct species. These results support the presence of three <jats:italic>Chitala</jats:italic> species in Peninsular Malaysia, even though a multivariate morphometric analysis failed to fully differentiate each of these three species. Comparison with original species descriptions and genetic data from an additional 70 <jats:italic>Chitala</jats:italic> specimens from neighbouring regions allowed us to name these species as <jats:italic>Chitala lopis</jats:italic>, <jats:italic>Chitala borneensis</jats:italic>, and <jats:italic>Chitala ornata</jats:italic>. We also showed the presence of two undescribed species in Indonesia.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":"49 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141503199","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":"Deep genetic divergence among bluefish (Pomatomus saltatrix) of the Southwestern Atlantic","authors":"Livia Bonetti Villela, Pedro Hollanda Carvalho, Anderson de Vilasboa, Ghennie Tatiana Rodríguez‐Rey, Frederico Henning, Thomas Grothues, Antonio Mateo Solé‐Cava","doi":"10.1111/zsc.12662","DOIUrl":"https://doi.org/10.1111/zsc.12662","url":null,"abstract":"Neglected cryptic diversity can lead to the permanent loss of locally adapted alleles, which can reduce resilience to rapid environmental change. It can also result in overestimation of fisheries stock sizes that can result from treating different species as if they belonged to one. Bluefish (<jats:italic>Pomatomus saltatrix</jats:italic>) is considered a circumtropical and subtropical species and an important fishery resource all over the world. Differences in ecologically relevant traits are observed among isolated populations. Also, in the Southwestern Atlantic, molecular data suggest multiple populations, but these are treated as a single fish stock by regulatory agencies due to a lack of definitive information. We used whole mitogenome sequences, nuclear (<jats:italic>rho</jats:italic>) and mitochondrial (<jats:italic>coxI</jats:italic> and <jats:italic>cytb</jats:italic>) genes, as well as microsatellites to investigate historical and current genetic population structure and parameters of bluefish in the Western Atlantic. A total of 263 samples were collected along the Brazilian coast and in the USA (New Jersey, Northwest Atlantic). Data revealed the existence of two evolutionarily significant units (ESU) of bluefish along the South American coast, later confirmed by whole mitogenome sequencing of both haplogroups. These two ESUs have a mostly parapatric distribution, with some areas of overlap, which vary along the year. We also conducted seasonal sampling in Brazil to investigate migration patterns. ESUs occur mostly north and south of parallel 23° 40′ S, with an overlap area that varied seasonally. The level of differentiation between those two ESUs in the SW Atlantic, even in sympatry, is as high as that found between them and those from the NW Atlantic and Europe. Parapatric distribution and restricted gene flow suggest the existence of ecological barriers and local adaptation. The splitting of an ancient population from the Southwestern Atlantic into two putative species is important to understand bluefish evolutionary diversification and has implications for fishery regulatory measures in Brazil.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":"29 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140927403","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":"Hidden diversity in eastern North America: The genus Ligidium (Oniscidea, Ligiidae) in the southern Appalachian Mountains","authors":"Ernesto Recuero, Michael S. Caterino","doi":"10.1111/zsc.12661","DOIUrl":"https://doi.org/10.1111/zsc.12661","url":null,"abstract":"The terrestrial isopod genus <jats:italic>Ligidium</jats:italic> includes 58 species from Europe, Asia, and North America. In Eastern North America four species are recognized: <jats:italic>L. floridanum</jats:italic> and <jats:italic>L. mucronatum</jats:italic>, known just from their type localities in Florida and Louisiana respectively, <jats:italic>L. blueridgensis</jats:italic>, endemic to the southern Appalachians, and <jats:italic>L. elrodii</jats:italic>, widespread from Georgia to Ontario. The genus shows a marked morphological conservatism, and species are differentiated mostly by small morphological differences; it is not always easy to determine if such variability represents inter‐ or intraspecific variation. Here, we explore the diversity of <jats:italic>Ligidium</jats:italic> from the southern Appalachian Mountains, exploring the congruence of morphologically defined groups with multilocus phylogenetic reconstructions and molecular species delimitation methods. We have studied a total of 130 specimens from 37 localities, mostly from the southern Appalachians, and analysed mtDNA (Cox1) and nuclear (28S, NaK) sequences. Morphologically, we recognized eight morphotypes, most of them assignable to current concepts of <jats:italic>L</jats:italic>. <jats:italic>elrodii</jats:italic> and <jats:italic>L</jats:italic>. <jats:italic>blueridgensis</jats:italic>. Phylogenetic analyses supported the evolutionary independence of all morphotypes, and suggest the existence of 8–9 species, including limited cryptic diversity. Single‐locus delimitation analyses based on mtDNA data suggest the existence of a much higher number of species than the multilocus analyses. The estimated age of the ancestors of sampled lineages indicates a long presence of the genus in eastern North America and old speciation events through the Miocene. Our results indicate a higher diversity than previously thought among the <jats:italic>Ligidium</jats:italic> populations present in the southern Appalachian Mountains, with several species to be described.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140927402","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":"Multilocus genetic and morphological phylogenetic analysis: Unveiling a new genus and species in the Tribe Nannenini of jumping spiders (Araneae, Salticidae)","authors":"Abira Satkunanathan, Suresh P. Benjamin","doi":"10.1111/zsc.12660","DOIUrl":"https://doi.org/10.1111/zsc.12660","url":null,"abstract":"Jumping spiders (Salticidae) are a diverse group of non-web-building predators and the most species-rich spider family. The Salticidae Tribe Nannenini consists of a small group of Oriental jumping spiders that are very poorly known. The use of explicit phylogenetic analyses to establish its affinities has so far remained limited. The Nannenini genus <i>Epidelaxia</i> has a peculiar morphology, making its systematic position uncertain. In this study, we present a comprehensive dataset combining molecular and morphological data for Nannenini, including exemplars from all genera. This dataset comprises DNA sequences of approximately 2400 bp, including nuclear genes (<i>18S</i>, <i>28S</i> and <i>H3</i>) and the mitochondrial gene <i>CO1</i>, sequenced for 40 taxa (20 ingroups and 20 outgroups), along with 61 morphological characters. Notably, both DNA sequences and morphological traits were analysed separately and concurrently for the first time. The Nannenini clade is recovered with high support. Further, <i>Epidelaxia</i> is monophyletic and sister to <i>Tubalaxia</i> gen. n. This is the first hypothesis on the internal phylogenetic structure of <i>Epidelaxia</i> and its placement within the Tribe Nannenini. A new genus <i>Tubalaxia</i> gen. n. and the following new species are described: <i>E. bharathi</i> sp. n., <i>E. somasundaram</i> sp. n., <i>T. castanea</i> sp. n., <i>T. aurea</i> sp. n. The following new combination is proposed: <i>Tubalaxia minuta</i> (Prószyński, 1992) <b>comb. n</b>. <i>Epidelaxia albostellata</i>, <i>E. albocruciata</i> and <i>E. obscura</i> are redescribed. It is worth noting that the newly described species face endangerment due to their limited distribution and small population sizes.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":"16 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140569304","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":"Taxonomic revision and dissolution of the genus Monachoides (Gastropoda, Stylommatophora)","authors":"Tereza Adamcová, Lucie Juřičková, Małgorzata Proćków, Eike Neubert, Adam Petrusek, Ondřej Korábek","doi":"10.1111/zsc.12658","DOIUrl":"https://doi.org/10.1111/zsc.12658","url":null,"abstract":"<jats:italic>Monachoides</jats:italic> is a genus of medium‐sized European land snails in the family Hygromiidae. Systematics of this family was until recently based on traits of the genital system that were shown to be uninformative, resulting in revisions of classifications at the genus and family levels. Up to six species were recognized in <jats:italic>Monachoides</jats:italic> lately, but the inclusion of three of these species was questionable. Our phylogenetic analysis and morphological examinations show that the genus includes species previously classified in two different Hygromiidae subfamilies. After transferring three Balkan species to the unrelated genus <jats:italic>Xerocampylaea</jats:italic>, <jats:italic>Monachoides</jats:italic> emerged as a group that diversified relatively northerly, at the boundary between the Balkans and Central Europe. One species, <jats:italic>Monachoides bacescui</jats:italic>, is synonymized here and a previously overlooked one is redescribed, leaving only three valid species in <jats:italic>Monachoides</jats:italic> as currently understood: <jats:italic>M</jats:italic>. <jats:italic>incarnatus</jats:italic>, <jats:italic>M</jats:italic>. <jats:italic>vicinu</jats:italic>s and <jats:italic>M</jats:italic>. <jats:italic>welebitanus</jats:italic>. These can be distinguished from other hygromiid species by their distinctive microsculpture of the shell surface, which also allows for identification of juveniles or fragmented fossil material. However, the clade comprising the three above species was found to also include the two species currently classified in <jats:italic>Perforatella</jats:italic>. As a result, the two genera are synonymized, with <jats:italic>Perforatella</jats:italic> having priority.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":"29 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140568734","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":"Untangling deep‐sea corals systematics: Description of a new family, Stephanocyathidae (Anthozoa, Scleractinia), through a genomic approach","authors":"Claudia Francesca Vaga, Isabela Galvao de Lossio e Seiblitz, Katia Cristina Cruz Capel, Andrea M. Quattrini, Jaroslaw Stolarski, Stephen D. Cairns, Marcelo Visentini Kitahara","doi":"10.1111/zsc.12657","DOIUrl":"https://doi.org/10.1111/zsc.12657","url":null,"abstract":"Once considered the most speciose mostly azooxanthellate scleractinian group, the family Caryophylliidae is found to be highly polyphyletic based on molecular data and is undergoing a process of systematic revision. High‐throughput sequencing methods coupled with morphological analyses have facilitated revision of several scleractinian lineages, including the aforementioned family. In previous studies that relied on few mitochondrial and nuclear markers, the caryophylliid genera <jats:italic>Stephanocyathus</jats:italic> and <jats:italic>Vaughanella</jats:italic> were phylogenetically recovered in separate clades from the lineage that includes the type genus of the family, <jats:italic>Caryophyllia</jats:italic>, which is considered the ‘true’ Caryophylliidae. To help untangle the relationship among taxa of this family, here a new deep‐sea scleractinian family (Stephanocyathidae Vaga, Cairns &amp; Kitahara fam. nov.) is proposed based on phylogenomic reconstructions coupled with molecular features, specifically gene order, of the complete mitochondrial genome. Evolutionary reconstructions were based on both mitochondrial and nuclear ultraconserved elements (UCEs) and exon loci data sets and confirmed the divergent position of the genera <jats:italic>Stephanocyathus</jats:italic> and <jats:italic>Vaughanella</jats:italic>. The new family shows a specific gene transposition in the mitochondrial genome, not present in the ‘true’ caryophylliid lineage, but instead already observed for the species <jats:italic>Paraconotrochus antarcticus</jats:italic>, recovered as sister taxon of the here proposed new family. Although its phylogenetic position is unknown, the genus <jats:italic>Ericiocyathus</jats:italic> is also added to the new family, based on macromorphological similarities. This study represents a step forward in our understanding of deep‐sea corals relationships and provide further information (e.g., mitochondrial gene order) that will aid in future efforts of assessing the systematic of caryophylliid lineages.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":"29 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140568884","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":"Biogeography, speciation and niche evolution of doraditos (Aves: Pseudocolopteryx)","authors":"Emilio A. Jordan, Juan I. Areta","doi":"10.1111/zsc.12655","DOIUrl":"https://doi.org/10.1111/zsc.12655","url":null,"abstract":"Ecological and geographical factors shape the current distribution of species. Analysing their interplay in a phylogenetic framework is key to understand the historical processes that have shaped the evolution of a group. Here, we modelled the ecological niches and geographic distributions of the five species of doraditos (<jats:italic>Pseudocolopteryx</jats:italic> spp.) to study their biogeographic histories, niche evolution and speciation process in a phylogenetic framework. Our potential distribution models uncovered novel range‐wide distributional patterns and seasonal movements in the doraditos, where four species are migratory with distinct breeding and non‐breeding distributions, and one (<jats:italic>P. sclateri</jats:italic>) exhibits a complex spatiotemporal distribution indicating nomadism. Ecological niche pairwise comparisons showed that none of the doraditos have equivalent niches and that niche differences are due to species‐specific habitat preferences. Phylogenetically weighted geographical and ecological analyses showed patterns of allopatric speciation and niche lability in the evolution of doraditos. The divergence of <jats:italic>P. sclateri</jats:italic> seems tied to its tropical‐to‐temperate wetland specialization. The montane <jats:italic>P. acutipennis</jats:italic> expanded to human‐modified lowlands following speciation, highlighting the need to control for post‐speciational changes in ecological niche comparisons as done here. In turn, <jats:italic>P. dinelliana</jats:italic>, <jats:italic>P. citreola</jats:italic> and <jats:italic>P. flaviventris</jats:italic> showed essentially allopatric breeding distributions, as a product of environmentally mediated divergence during their speciation processes. The distribution and migration data of the recently diverged cryptic sister species <jats:italic>P. citreola</jats:italic> and <jats:italic>P. flaviventris</jats:italic> are consistent with two possible speciation scenarios: peripatric speciation and migration dosing speciation.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":"22 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140017206","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":"Zooming in on amphibians: Which is the smallest vertebrate in the world?","authors":"Wendy H. Bolaños, Iuri Ribeiro Dias, Mirco Solé","doi":"10.1111/zsc.12654","DOIUrl":"https://doi.org/10.1111/zsc.12654","url":null,"abstract":"During the last decades several miniaturized frogs have been described from different parts of the world. Those frogs, measuring less than 25 mm, show similar miniaturization features as the loss of phalanges in both the anterior and posterior limbs and the reduction of bone elements. However, there seems to be a limit regarding the minimum size of frogs and here we wanted to find an answer to the question: which is the smallest amphibian in the world? In 2019, an endemic species of toad known only from two localities in southern Bahia, Brazil, was studied. When we compared the size of adult representatives of this species with those of other species discovered in various parts of the world in the last decade, we observed that individuals of <i>Brachycephalus pulex</i> are the amphibians with the smallest total length recorded, thus qualifying them to bear the title of the tiniest anuran amphibian, and also tiniest vertebrate in the world.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":"22 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139754567","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":"Capitella (Annelida: Capitellidae) species in the Gulf of Mexico: Delimitation, phylogeography and phylogeny","authors":"Justin Hilliard, Marissa Hajduk, Nuria Méndez, Anja Schulze","doi":"10.1111/zsc.12651","DOIUrl":"https://doi.org/10.1111/zsc.12651","url":null,"abstract":"<i>Capitella</i> spp. are found in marine and estuarine benthos world-wide. They are often treated as environmental sentinels because they occur in high densities in areas of anthropogenic disturbance and organic pollution. However, there are many cryptic species around the world, often grouped into the <i>Capitella capitata</i> complex. Historically, these have been differentiated using allozymes and developmental studies. Recently, single-gene sequencing, especially cytochrome <i>c</i> oxidase subunit I, and phylogenetic methods have been used to characterise populations around the world. We present molecular support and provide descriptions for five new <i>Capitella</i> spp. from the Gulf of Mexico: <i>Capitella gomexa</i> sp. n., <i>Capitella mandingensis</i> sp. n., <i>Capitella tampe</i> sp. n., <i>Capitella maculosa</i> sp. n. and <i>Capitella loucindae</i> sp. n. Two were recently differentiated on the basis of larval development and morphology. Additionally, we present an updated look at global <i>Capitella</i> phylogeny. While no apparent patterns of phylogeography were recovered, we did find support for a single origin of thoracic acicular spines.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":"77 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139755040","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}