Marek Uvizl, Zuzana Kotyková Varadínová, Petr Benda
The horseshoe bats of the Rhinolophus ferrumequinum group form a well-defined lineage within the Afro-Palaearctic clade of the genus Rhinolophus. The group currently comprises four species widely distributed across the Palaearctic and Afrotropic regions: R. bocharicus (Central Asia), R. clivosus (from northern Africa and the Levant through Arabian Peninsula and eastern Africa to southern Africa), R. ferrumequinum (from western Europe and northern Africa through the Balkans and Middle East to Central Asia and India) and R. nippon (southern and central China, Korea, and Japan). The broad ranges and geographical variations within these species have led to the proposal of numerous subspecies. The phylogenetic relationships and intraspecific variation of the R. ferrumequinum group were investigated using a genetic approach. One mitochondrial marker and five nuclear markers were sequenced and supplemented with available sequences for all four species of the group. Our study revealed five major lineages within the R. ferrumequinum group, resulting in the recognition of four currently known species and identification of a new species. The prior name available for this lineage/species is R. acrotis. The relationships between the lineages varied depending on the chosen marker, leaving the interspecific relations within the ferrumequinum group unresolved. In addition, the results indicated that R. clivosus experienced historic introgression from northern Africa and the Levant, resulting in replacement of its mtDNA by that of R. ferrumequinum. Together, this study introduces a new Rhinolophus species, which increases the number of species in the ferrumequinum group to five.
Rhinolophus ferrumequinum 马蹄蝠群是 Rhinolophus 属非洲-古北支系中一个明确的支系。该类目前包括四个物种，广泛分布于古北和非洲热带地区：R. bocharicus（中亚）、R. clivosus（从非洲北部和黎凡特经阿拉伯半岛和非洲东部到非洲南部）、R. ferrumequinum（从欧洲西部和非洲北部经巴尔干半岛和中东到中亚和印度）和 R. nippon（中国南部和中部、韩国和日本）。这些物种的分布范围广，地理差异大，因此被提出了许多亚种。我们采用遗传学方法研究了 R. ferrumequinum 组的系统发育关系和种内变异。对一个线粒体标记和五个核标记进行了测序，并补充了该类群所有四个物种的现有序列。我们的研究揭示了 R. ferrumequinum 群体中的五个主要世系，从而确认了目前已知的四个物种，并鉴定出一个新物种。该品系/物种的现有名称为 R. acrotis。各品系之间的关系因所选标记的不同而各异，因此 ferrumequinum 群内的种间关系尚未确定。此外，研究结果表明，R. clivosus 经历了从非洲北部和黎凡特的历史性引入，导致其 mtDNA 被 R. ferrumequinum 的 mtDNA 所取代。总之，这项研究引入了一个新的犀牛物种，使 ferrumequinum 群的物种数量增加到五个。
{"title":"Phylogenetic relationships among horseshoe bats within the Rhinolophus ferrumequinum group (Mammalia, Chiroptera)","authors":"Marek Uvizl, Zuzana Kotyková Varadínová, Petr Benda","doi":"10.1111/zsc.12650","DOIUrl":"https://doi.org/10.1111/zsc.12650","url":null,"abstract":"The horseshoe bats of the <i>Rhinolophus ferrumequinum</i> group form a well-defined lineage within the Afro-Palaearctic clade of the genus <i>Rhinolophus</i>. The group currently comprises four species widely distributed across the Palaearctic and Afrotropic regions: <i>R. bocharicus</i> (Central Asia), <i>R. clivosus</i> (from northern Africa and the Levant through Arabian Peninsula and eastern Africa to southern Africa), <i>R. ferrumequinum</i> (from western Europe and northern Africa through the Balkans and Middle East to Central Asia and India) and <i>R. nippon</i> (southern and central China, Korea, and Japan). The broad ranges and geographical variations within these species have led to the proposal of numerous subspecies. The phylogenetic relationships and intraspecific variation of the <i>R. ferrumequinum</i> group were investigated using a genetic approach. One mitochondrial marker and five nuclear markers were sequenced and supplemented with available sequences for all four species of the group. Our study revealed five major lineages within the <i>R. ferrumequinum</i> group, resulting in the recognition of four currently known species and identification of a new species. The prior name available for this lineage/species is <i>R. acrotis</i>. The relationships between the lineages varied depending on the chosen marker, leaving the interspecific relations within the <i>ferrumequinum</i> group unresolved. In addition, the results indicated that <i>R. clivosus</i> experienced historic introgression from northern Africa and the Levant, resulting in replacement of its mtDNA by that of <i>R. ferrumequinum</i>. Together, this study introduces a new <i>Rhinolophus</i> species, which increases the number of species in the <i>ferrumequinum</i> group to five.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139561382","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}
Species diversity can be underestimated due to a lack of regional studies and limitations in research methods. China is widely recognized as one of the primary hotspots for the biodiversity of freshwater mussels as it harbours a wealth of endemic species. Pseudocuneopsis was recently established to belong to the Unioninae subfamily within Unionidae and is endemic to China. Recent research has expanded the diversity and range of distribution of this genus. However, sufficient data is required to precisely determine the phylogenetic relationships within Pseudocuneopsis. This study conducted an integrative taxonomy using morphological, COI barcode, and complete maternal mitogenome data to clarify the taxonomy of Pseudocuneopsis. Both morphological and COI barcode data supported the validity of all Pseudocuneopsis species. Furthermore, a new species, Pseudocuneopsis yemaoi sp. n. was described from a tributary of the Man River in Hubei, China. Mitochondrial phylogenomic analyses showed that P. yemaoi was closely related to P. sichuanensis and resolved phylogenetic relationship as (P. capitata + (P. yangshuoensis + (P. sichuanensis + P. yemaoi))). Our results highlight the significance of utilizing integrative classification methods. Moreover, we propose enhancing the research and preservation measures of minor streams in China, as these streams may house distinctive species.
由于缺乏区域研究和研究方法的局限性，物种多样性可能被低估。中国被公认为淡水贻贝生物多样性的主要热点地区之一，因为这里有丰富的特有物种。假楔贻贝（Pseudocuneopsis）最近被确定为属于贻贝科（Unionidae）中的Unioninae亚科，是中国特有的物种。最近的研究扩大了该属的多样性和分布范围。然而，要精确地确定假楔蛾属的系统发育关系还需要足够的数据。本研究利用形态学、COI条形码和完整的母体有丝分裂基因组数据进行了综合分类，以明确假楔蛾属的分类。形态学和 COI 条形码数据都支持所有 Pseudocuneopsis 物种的有效性。此外，还描述了产自中国湖北漫江支流的一个新物种 Pseudocuneopsis yemaoi sp.线粒体系统发生组分析表明，P. yemaoi与P. sichuanensis亲缘关系密切，其系统发生关系为（P. capitata + (P. yangshuoensis + (P. sichuanensis + P. yemaoi)）。我们的结果凸显了利用综合分类方法的意义。此外，我们建议加强对中国小溪流的研究和保护措施，因为这些溪流可能蕴藏着独特的物种。
{"title":"Revisiting the genus Pseudocuneopsis (Bivalvia, Unionidae): Morphology, mitochondrial phylogenomics, and the description of a new species","authors":"Yu-Ting Dai, Zhong-Guang Chen, Ke-Jia Peng, Shan Ouyang, Xiao-Chen Huang, Xiao-Ping Wu","doi":"10.1111/zsc.12647","DOIUrl":"https://doi.org/10.1111/zsc.12647","url":null,"abstract":"Species diversity can be underestimated due to a lack of regional studies and limitations in research methods. China is widely recognized as one of the primary hotspots for the biodiversity of freshwater mussels as it harbours a wealth of endemic species. <i>Pseudocuneopsis</i> was recently established to belong to the Unioninae subfamily within Unionidae and is endemic to China. Recent research has expanded the diversity and range of distribution of this genus. However, sufficient data is required to precisely determine the phylogenetic relationships within <i>Pseudocuneopsis</i>. This study conducted an integrative taxonomy using morphological, <i>COI</i> barcode, and complete maternal mitogenome data to clarify the taxonomy of <i>Pseudocuneopsis</i>. Both morphological and <i>COI</i> barcode data supported the validity of all <i>Pseudocuneopsis</i> species. Furthermore, a new species, <i>Pseudocuneopsis yemaoi</i> sp. n. was described from a tributary of the Man River in Hubei, China. Mitochondrial phylogenomic analyses showed that <i>P. yemaoi</i> was closely related to <i>P. sichuanensis</i> and resolved phylogenetic relationship as (<i>P. capitata</i> + (<i>P. yangshuoensis</i> + (<i>P. sichuanensis</i> + <i>P. yemaoi</i>))). Our results highlight the significance of utilizing integrative classification methods. Moreover, we propose enhancing the research and preservation measures of minor streams in China, as these streams may house distinctive species.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139422227","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}
Lívia Estéfane Fernandes Frateles, Nelson Jorge da Silva, L. C. Terribile, J. Diniz‐Filho
The magnitude of life on Earth and human limitations hinder the understanding of even the most basic aspects of biodiversity, such as the identity of species inhabiting the Earth, the so‐called Linnean shortfall. Evaluating patterns in species description dates and their relationship with macroecological variables can help guide where taxonomic efforts should be focused. Therefore, we aim to assess the Linnean shortfall in the knowledge of New World coralsnake biodiversity. We modelled species description dates and estimated that approximately one‐third of the coralsnake diversity remains unknown. The undescribed species are evolutionarily closely related to the already described species. Moreover, recently described species in the group have more restricted geographic ranges and tend to be small‐bodied. The western Amazon and the dry diagonal (i.e. Caatinga, Cerrado, and Chaco) are the areas with the oldest description dates. However, assemblages in these areas have the largest average geographic distances to the type locality of their species, suggesting that little taxonomic effort has been dedicated intrinsically to these regions. We suggest that allocating taxonomic efforts to the dry diagonal and the use of integrative taxonomic techniques for better species delimitation are imperative to fill the Linnean shortfall for the New World coralsnakes.
{"title":"Linnean shortfall and space‐time patterns in species description of New World coralsnakes (Serpentes: Elapidae)","authors":"Lívia Estéfane Fernandes Frateles, Nelson Jorge da Silva, L. C. Terribile, J. Diniz‐Filho","doi":"10.1111/zsc.12644","DOIUrl":"https://doi.org/10.1111/zsc.12644","url":null,"abstract":"The magnitude of life on Earth and human limitations hinder the understanding of even the most basic aspects of biodiversity, such as the identity of species inhabiting the Earth, the so‐called Linnean shortfall. Evaluating patterns in species description dates and their relationship with macroecological variables can help guide where taxonomic efforts should be focused. Therefore, we aim to assess the Linnean shortfall in the knowledge of New World coralsnake biodiversity. We modelled species description dates and estimated that approximately one‐third of the coralsnake diversity remains unknown. The undescribed species are evolutionarily closely related to the already described species. Moreover, recently described species in the group have more restricted geographic ranges and tend to be small‐bodied. The western Amazon and the dry diagonal (i.e. Caatinga, Cerrado, and Chaco) are the areas with the oldest description dates. However, assemblages in these areas have the largest average geographic distances to the type locality of their species, suggesting that little taxonomic effort has been dedicated intrinsically to these regions. We suggest that allocating taxonomic efforts to the dry diagonal and the use of integrative taxonomic techniques for better species delimitation are imperative to fill the Linnean shortfall for the New World coralsnakes.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139382822","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}
The taxonomic status and interspecies relationships of hares (genus Lepus) in Xinjiang, China, remain ambiguous owing to extremely similar external morphologies, introgressive hybridization between species and a lack of molecular genetic records. In this study, a total of 154 hare specimens were used to clarify their taxonomic status. Based on multiple lines of evidence, including observations and comparisons of external morphological characteristics, skull morphometrics and genome-wide single nucleotide polymorphism (SNP) datasets, four hare species were recognised. Lepus yarkandensis and Lepus timidus, which have obvious morphological characteristics, were identified as two distinct species, as previously reported. Combining the integrated morphological and molecular datasets with the relevant literature, we proposed suggestions on the classification of the more controversial hares. Due to molecular and morphological similarities, hares in northern and central Xinjiang were divided into two subspecies of Lepus tolai, namely, Lepus tolai lehmanni and Lepus tolai centrasiaticus. Despite similar external morphological characters, hares in the southwest Pamir Plateau and its surroundings can be distinguished from L. tolai by differences in skull morphology and genetic divergence and were, therefore, considered a subspecies of Lepus tibetanus, Lepus tibetanus pamirensis. Furthermore, we found that hybridization and introgression occurred between sympatric or parapatric hares, especially between L. yarkandensis and L. tibetanus pamirensis, L. yarkandensis and L. tolai centrasiaticus, and L. tolai lehmanni and L. timidus.
{"title":"Taxonomic status of hares (Lepus spp.) in Xinjiang, China (Lagomorpha: Leporidae): An integrative approach","authors":"Wen-Juan Shan, Zu-Rui Li, Hui-Ying Dai, Peng-Cheng Dong, Yu-Cong Zhang","doi":"10.1111/zsc.12645","DOIUrl":"https://doi.org/10.1111/zsc.12645","url":null,"abstract":"The taxonomic status and interspecies relationships of hares (genus <i>Lepus</i>) in Xinjiang, China, remain ambiguous owing to extremely similar external morphologies, introgressive hybridization between species and a lack of molecular genetic records. In this study, a total of 154 hare specimens were used to clarify their taxonomic status. Based on multiple lines of evidence, including observations and comparisons of external morphological characteristics, skull morphometrics and genome-wide single nucleotide polymorphism (SNP) datasets, four hare species were recognised. <i>Lepus yarkandensis</i> and <i>Lepus timidus</i>, which have obvious morphological characteristics, were identified as two distinct species, as previously reported. Combining the integrated morphological and molecular datasets with the relevant literature, we proposed suggestions on the classification of the more controversial hares. Due to molecular and morphological similarities, hares in northern and central Xinjiang were divided into two subspecies of <i>Lepus tolai</i>, namely, <i>Lepus tolai lehmanni</i> and <i>Lepus tolai centrasiaticus</i>. Despite similar external morphological characters, hares in the southwest Pamir Plateau and its surroundings can be distinguished from <i>L. tolai</i> by differences in skull morphology and genetic divergence and were, therefore, considered a subspecies of <i>Lepus tibetanus</i>, <i>Lepus tibetanus pamirensis</i>. Furthermore, we found that hybridization and introgression occurred between sympatric or parapatric hares, especially between <i>L. yarkandensis</i> and <i>L. tibetanus pamirensis</i>, <i>L. yarkandensis</i> and <i>L. tolai centrasiaticus</i>, and <i>L. tolai lehmanni</i> and <i>L. timidus</i>.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139373395","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}
Sofia Marques Silva, Ana Carolina Pavan, Samara Alves Barroso de Souza, Gilmax Gonçalves Ferreira, José de Sousa e Silva, Leonardo C. Trevelin
The Neotropical realm is vastly known for its richness, being the Amazon one of the main cradles of taxonomic diversity in the region. In the last decades, molecular analyses have been further increasing the number of Amazonian vertebrate species, hidden under traditional taxonomy due to morphological convergence. Bats represent an interesting example, as the number of recognized bat species is continuously expanding with the identification of numerous cryptic taxa. Studies combining different lines of evidence, such as morphometric and molecular approaches, have been playing an important role in addressing knowledge gaps on Neotropical bat diversity. Within the Phyllostomidae family, the dwarf little fruit bat Rhinophylla pumilio is a forest-dependent species, with a disjunct distribution in the Amazonian and Atlantic forests. Moreover, different karyotypes have been recovered across the species distribution, suggesting this might be one more example of cryptic diversity. Here, we test this assumption by identifying geographic patterns of morphological and molecular variation within the species' entire range of distribution. Our results point to an overall morphological and morphometric homogeneity, except between Atlantic Forest and Amazonian specimens, with significant dissimilarity among some cranial characters. Furthermore, genetic data suggest a rapid and recent diversification, with these two lineages most likely corresponding to speciating taxa. Within the Amazonian forest, our molecular analyses also recovered four additional lineages, likely encompassing intraspecific diversity. Furthermore, studies are required to confirm the need for a taxonomic rearrangement.
{"title":"Morphological and genetic diversity in a South American forest-dependent bat","authors":"Sofia Marques Silva, Ana Carolina Pavan, Samara Alves Barroso de Souza, Gilmax Gonçalves Ferreira, José de Sousa e Silva, Leonardo C. Trevelin","doi":"10.1111/zsc.12646","DOIUrl":"https://doi.org/10.1111/zsc.12646","url":null,"abstract":"The Neotropical realm is vastly known for its richness, being the Amazon one of the main cradles of taxonomic diversity in the region. In the last decades, molecular analyses have been further increasing the number of Amazonian vertebrate species, hidden under traditional taxonomy due to morphological convergence. Bats represent an interesting example, as the number of recognized bat species is continuously expanding with the identification of numerous cryptic taxa. Studies combining different lines of evidence, such as morphometric and molecular approaches, have been playing an important role in addressing knowledge gaps on Neotropical bat diversity. Within the Phyllostomidae family, the dwarf little fruit bat <i>Rhinophylla pumilio</i> is a forest-dependent species, with a disjunct distribution in the Amazonian and Atlantic forests. Moreover, different karyotypes have been recovered across the species distribution, suggesting this might be one more example of cryptic diversity. Here, we test this assumption by identifying geographic patterns of morphological and molecular variation within the species' entire range of distribution. Our results point to an overall morphological and morphometric homogeneity, except between Atlantic Forest and Amazonian specimens, with significant dissimilarity among some cranial characters. Furthermore, genetic data suggest a rapid and recent diversification, with these two lineages most likely corresponding to speciating taxa. Within the Amazonian forest, our molecular analyses also recovered four additional lineages, likely encompassing intraspecific diversity. Furthermore, studies are required to confirm the need for a taxonomic rearrangement.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2023-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139066983","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}
Modern genomic techniques have enabled the generation of phylogenetic datasets of unprecedented scale. However, there are also troves of molecular data accumulated from past studies using Sanger sequencing, often at fine taxonomic scales. Combining both sources of data is an obviously appealing possibility, but it can also lead to inconsistency due to high levels of missing data, disparities in the scale of Sanger versus genomic datasets, and little overlap in sequences across terminals. To provide an empirical investigation of the potential of such ‘hybrid’ datasets, we combined data from ultraconserved elements (UCEs) for 183 species of Cryptini (Ichneumonidae, Hymenoptera) with a previously existing dataset of 7 loci and morphological data including 308 species plus outgroup taxa. Bioinformatics pipelines allowed recovery of ‘legacy’ markers from the bycatch of UCE sequencing, reducing the problem of limited character overlap. The resulting tree combining Sanger and UCE data is highly supported and includes dense taxon sampling of the group, allowing for a better understanding of the global radiation of Cryptini. The Neotropical region had the highest phylogenetic diversity but the lowest level of phylogenetic dispersion when corrected for standardized effect size, while the Oriental fauna showed the highest level of phylogenetic dispersion. Our results highlight the potential of hybrid datasets to produce a more complete picture of the Tree of Life combining affordability, robust support and deep taxonomic sampling.
{"title":"Leveraging museum specimens, genomics and legacy datasets to unravel the phylogeny and biogeography of cryptin wasps (Hymenoptera, Ichneumonidae, Cryptini)","authors":"Bernardo F. Santos, Seán G. Brady","doi":"10.1111/zsc.12639","DOIUrl":"https://doi.org/10.1111/zsc.12639","url":null,"abstract":"Modern genomic techniques have enabled the generation of phylogenetic datasets of unprecedented scale. However, there are also troves of molecular data accumulated from past studies using Sanger sequencing, often at fine taxonomic scales. Combining both sources of data is an obviously appealing possibility, but it can also lead to inconsistency due to high levels of missing data, disparities in the scale of Sanger versus genomic datasets, and little overlap in sequences across terminals. To provide an empirical investigation of the potential of such ‘hybrid’ datasets, we combined data from ultraconserved elements (UCEs) for 183 species of Cryptini (Ichneumonidae, Hymenoptera) with a previously existing dataset of 7 loci and morphological data including 308 species plus outgroup taxa. Bioinformatics pipelines allowed recovery of ‘legacy’ markers from the bycatch of UCE sequencing, reducing the problem of limited character overlap. The resulting tree combining Sanger and UCE data is highly supported and includes dense taxon sampling of the group, allowing for a better understanding of the global radiation of Cryptini. The Neotropical region had the highest phylogenetic diversity but the lowest level of phylogenetic dispersion when corrected for standardized effect size, while the Oriental fauna showed the highest level of phylogenetic dispersion. Our results highlight the potential of hybrid datasets to produce a more complete picture of the Tree of Life combining affordability, robust support and deep taxonomic sampling.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2023-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139020397","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}
Didier Aurelle, Anne Haguenauer, Chloé Blaise, Lauric Reynes, Sophie Arnaud-Haond, Joana Boavida, Cédric Cabau, Christophe Klopp, Tomas Lundalv, Camille Noûs, Stéphane Sartoretto, Claudia Wienberg, Carlos E. Jiménez, Covadonga Orejas
The deep-sea corals Dendrophyllia ramea and Dendrophyllia cornigera occur in Mediterranean and Atlantic waters. Both species are found in different environmental conditions, and they can colonize hard and soft substrates. These species then display an important ecological plasticity along with morphological plasticity. Nevertheless, there is a large knowledge gap on the genetic characteristics of the two species, including on the relationships between them and the possibility of cryptic species along their range. The recent discovery of Dendrophyllia populations off Cyprus in the eastern Mediterranean Sea raised new questions in this context. These corals were related to D. ramea but had some morphological differences with other known populations of this species. Here, we study the specific status of Dendrophyllia corals from Cyprus on the basis of morphology and genetics. The genetic data are interpreted by comparison with the same analysis performed on two Caryophyllia species. Both morphological and genetic data confirm that corals found off Cyprus belong to the D. ramea species. We further tested the speciation scenario using transcriptome data: the results indicate an absence of current gene flow between D. ramea and D. cornigera and that the divergence occurred more than 3 million years ago. We discuss the possible historical and ecological factors which may have shaped speciation in these species.
深海珊瑚 Dendrophyllia ramea 和 Dendrophyllia cornigera 出现在地中海和大西洋水域。这两个物种生活在不同的环境条件下，它们可以在硬基质和软基质上定居。因此，这些物种在具有形态可塑性的同时，还具有重要的生态可塑性。然而，关于这两个物种的遗传特征，包括它们之间的关系以及在其分布范围内可能存在的隐生物种，还存在很大的知识空白。最近在地中海东部的塞浦路斯附近发现的 Dendrophyllia 种群提出了这方面的新问题。这些珊瑚与 D. ramea 有亲缘关系，但与该物种的其他已知种群在形态上存在一些差异。在此，我们根据形态学和遗传学研究了塞浦路斯 Dendrophyllia 珊瑚的具体状况。通过与对两个 Caryophyllia 种类进行的相同分析进行比较，对遗传数据进行了解释。形态学和遗传学数据都证实，在塞浦路斯近海发现的珊瑚属于 D. ramea 种。我们利用转录组数据进一步检验了物种分化的设想：结果表明，D. ramea 和 D. cornigera 之间目前没有基因流，其分化发生在 300 多万年前。我们讨论了可能影响这些物种分化的历史和生态因素。
{"title":"On the specific status of eastern Mediterranean Dendrophyllia corals (Cnidaria, Anthozoa): Genetic characterization and speciation scenarios","authors":"Didier Aurelle, Anne Haguenauer, Chloé Blaise, Lauric Reynes, Sophie Arnaud-Haond, Joana Boavida, Cédric Cabau, Christophe Klopp, Tomas Lundalv, Camille Noûs, Stéphane Sartoretto, Claudia Wienberg, Carlos E. Jiménez, Covadonga Orejas","doi":"10.1111/zsc.12643","DOIUrl":"https://doi.org/10.1111/zsc.12643","url":null,"abstract":"The deep-sea corals <i>Dendrophyllia ramea</i> and <i>Dendrophyllia cornigera</i> occur in Mediterranean and Atlantic waters. Both species are found in different environmental conditions, and they can colonize hard and soft substrates. These species then display an important ecological plasticity along with morphological plasticity. Nevertheless, there is a large knowledge gap on the genetic characteristics of the two species, including on the relationships between them and the possibility of cryptic species along their range. The recent discovery of <i>Dendrophyllia</i> populations off Cyprus in the eastern Mediterranean Sea raised new questions in this context. These corals were related to <i>D. ramea</i> but had some morphological differences with other known populations of this species. Here, we study the specific status of <i>Dendrophyllia</i> corals from Cyprus on the basis of morphology and genetics. The genetic data are interpreted by comparison with the same analysis performed on two <i>Caryophyllia</i> species. Both morphological and genetic data confirm that corals found off Cyprus belong to the <i>D. ramea</i> species. We further tested the speciation scenario using transcriptome data: the results indicate an absence of current gene flow between <i>D. ramea</i> and <i>D. cornigera</i> and that the divergence occurred more than 3 million years ago. We discuss the possible historical and ecological factors which may have shaped speciation in these species.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2023-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138823849","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}
Francesco Belluardo, Daniele Pellitteri-Rosa, Walter Cocca, Cristiano Liuzzi, Catarina Rato, Angelica Crottini, Adriana Bellati
Geckos of clade III of the Tarentola mauritanica species complex are widespread throughout southern Europe and northern Africa. We investigated the genetic variability of the Italian populations by performing a widespread sampling throughout the mainland and the two main islands of Sicily and Sardinia. We analysed 199 newly generated sequences of the mitochondrial 16S rRNA gene and 269 nuclear genotypes inferred from nine microsatellite loci from 307 individuals. We found 13 new mitochondrial haplotypes in Italy, whereas previous findings reported a single haplotype widespread throughout the country and in the rest of Europe, which currently make Italy the centre of genetic diversity of this taxon. There was no evidence of mitochondrial DNA structuring with geographic correlation. At the population genetic level, our multilocus approach based on nuclear markers returned a shallow genetic structure. Nonetheless, we disclosed the presence of at least four distinct genetic clusters (namely the Adriatic, two Tyrrhenian and the Calabrian clusters). Our findings do not support the two hypotheses proposed to explain the low level of mitochondrial polymorphism in this taxon, namely the genetic hitch-hiking due to selective sweep and the historical human-mediated colonization hypotheses. Based on the fossil record, the presence in Italy of this taxon since the Pleistocene Epoch is plausible. Given the discordance in genetic structure between mitochondrial and nuclear DNA, the exact role of the Italian Peninsula in shaping the observed patterns of genetic diversity during the Pleistocenic climatic oscillations needs further investigation.
Tarentola mauritanica物种群第三支系的壁虎广泛分布于欧洲南部和非洲北部。我们在意大利本土以及西西里岛和撒丁岛这两个主要岛屿上广泛取样，研究了意大利种群的遗传变异性。我们分析了从 307 个个体中新产生的 199 个线粒体 16S rRNA 基因序列和从 9 个微卫星位点推断出的 269 个核基因型。我们在意大利发现了 13 个新的线粒体单倍型，而之前的研究结果只报告了一个单倍型，该单倍型广泛分布于意大利和欧洲其他地区，因此意大利目前是该类群的遗传多样性中心。没有证据表明线粒体 DNA 结构与地域相关。在种群遗传水平上，我们基于核标记的多焦点方法得出的遗传结构较浅。不过，我们发现至少存在四个不同的遗传群（即亚得里亚海群、两个第勒尼安海群和卡拉布里亚海群）。我们的研究结果并不支持为解释该类群线粒体多态性水平较低而提出的两种假说，即选择性扫荡导致的基因搭便车假说和历史上人类促成的殖民假说。根据化石记录，该类群自更新世以来就存在于意大利是可信的。鉴于线粒体 DNA 和核 DNA 在遗传结构上的不一致性，意大利半岛在形成所观察到的更新世气候振荡期间遗传多样性模式方面的确切作用需要进一步研究。
{"title":"Multilocus phylogeography of Italian Moorish geckos adds insights into the evolutionary history of European populations","authors":"Francesco Belluardo, Daniele Pellitteri-Rosa, Walter Cocca, Cristiano Liuzzi, Catarina Rato, Angelica Crottini, Adriana Bellati","doi":"10.1111/zsc.12642","DOIUrl":"https://doi.org/10.1111/zsc.12642","url":null,"abstract":"Geckos of clade III of the <i>Tarentola mauritanica</i> species complex are widespread throughout southern Europe and northern Africa. We investigated the genetic variability of the Italian populations by performing a widespread sampling throughout the mainland and the two main islands of Sicily and Sardinia. We analysed 199 newly generated sequences of the mitochondrial 16S rRNA gene and 269 nuclear genotypes inferred from nine microsatellite loci from 307 individuals. We found 13 new mitochondrial haplotypes in Italy, whereas previous findings reported a single haplotype widespread throughout the country and in the rest of Europe, which currently make Italy the centre of genetic diversity of this taxon. There was no evidence of mitochondrial DNA structuring with geographic correlation. At the population genetic level, our multilocus approach based on nuclear markers returned a shallow genetic structure. Nonetheless, we disclosed the presence of at least four distinct genetic clusters (namely the Adriatic, two Tyrrhenian and the Calabrian clusters). Our findings do not support the two hypotheses proposed to explain the low level of mitochondrial polymorphism in this taxon, namely the genetic hitch-hiking due to selective sweep and the historical human-mediated colonization hypotheses. Based on the fossil record, the presence in Italy of this taxon since the Pleistocene Epoch is plausible. Given the discordance in genetic structure between mitochondrial and nuclear DNA, the exact role of the Italian Peninsula in shaping the observed patterns of genetic diversity during the Pleistocenic climatic oscillations needs further investigation.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2023-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138715074","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}
Mesodesma donacium is a surf clam endemic to the southeast Pacific coast, and it is an important resource species of the sandy beach artisanal fishery in Peru and Chile. Over time, the species has shown high variability in population dynamics (presence and abundance), which has been attributed to overfishing and environmental events. In this study, we assess the phylogeography of seven natural beds of M. donacium (17 to 42° S), to reveal the geographic distribution of the genetic diversity through the analysis of 278 sequences of the mitochondrial gene COI. Sequences of the nuclear genes 18S and 28S were used to evaluate the divergence of COI haplogroups. Two divergent parapatric mitochondrial haplogroups were found, which lacked divergence at nuclear markers (18S and 28S); this mito-nuclear discordance allows inferring that there is no reproductive isolation of mitochondrial haplogroups. The North haplogroup is the only one present at the northernmost site, while only the South haplogroup was present in Cucao in the south. Between 28° and 32° S, coincident with a coastal biogeographic break at 30° S, both haplogroups are in sympatry. Haplogroups differed in their genetic structure, with the North haplogroup representing a single, highly diverse population and the South haplogroup with genetic differentiation and more restricted genetic diversity and gene flow. The divergence in mitochondrial haplogroups without nuclear divergence suggests a past scenario of geographic isolation in the northern and southern areas, without developing reproductive isolation, followed by secondary contact. Given the phylogeography, genetic information should be considered in restocking and management activities.
{"title":"Mito-nuclear discordance and phylogeography of the surf clam Mesodesma donacium along the Southeast Pacific coast","authors":"Carmen R. Liza, Wolfgang B. Stotz, Pilar A. Haye","doi":"10.1111/zsc.12641","DOIUrl":"https://doi.org/10.1111/zsc.12641","url":null,"abstract":"<i>Mesodesma donacium</i> is a surf clam endemic to the southeast Pacific coast, and it is an important resource species of the sandy beach artisanal fishery in Peru and Chile. Over time, the species has shown high variability in population dynamics (presence and abundance), which has been attributed to overfishing and environmental events. In this study, we assess the phylogeography of seven natural beds of <i>M. donacium</i> (17 to 42° S), to reveal the geographic distribution of the genetic diversity through the analysis of 278 sequences of the mitochondrial gene COI. Sequences of the nuclear genes 18S and 28S were used to evaluate the divergence of COI haplogroups. Two divergent parapatric mitochondrial haplogroups were found, which lacked divergence at nuclear markers (18S and 28S); this mito-nuclear discordance allows inferring that there is no reproductive isolation of mitochondrial haplogroups. The North haplogroup is the only one present at the northernmost site, while only the South haplogroup was present in Cucao in the south. Between 28° and 32° S, coincident with a coastal biogeographic break at 30° S, both haplogroups are in sympatry. Haplogroups differed in their genetic structure, with the North haplogroup representing a single, highly diverse population and the South haplogroup with genetic differentiation and more restricted genetic diversity and gene flow. The divergence in mitochondrial haplogroups without nuclear divergence suggests a past scenario of geographic isolation in the northern and southern areas, without developing reproductive isolation, followed by secondary contact. Given the phylogeography, genetic information should be considered in restocking and management activities.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2023-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138685488","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}
Siti Zafirah Ghazali, Sébastien Lavoué, Norli Fauzani Mohd Abu Hassan Alshari, Danial Hariz Zainal Abidin, Jamsari Amirul Firdaus Jamaluddin, Min Pau Tan, Siti Azizah Mohd Nor
Glass-perchlets of the genus Ambassis (Teleostei; Ambassidae) form an important component of the brackish and marine coastal fish communities of tropical Asia. However, their species-level diversity is still poorly documented because of the absence of recent taxonomic revisions in this region and the limited availability of specimens for research. In addition, long-standing taxonomic and nomenclatural issues complicate the studies of this genus. Herein, we examine the diversity of Ambassis in Peninsular Malaysia using an integrative taxonomic approach and a large set of recently collected specimens from this region. Our initial morphological observations of 260 specimens revealed the presence of eight species, identified as Ambassis dussumieri, Ambassis interrupta, Ambassis kopsii, Ambassis macracanthus, Ambassis nalua, Ambassis octava, Ambassis urotaenia and Ambassis vachellii. We then sequenced the barcode fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene for 122 of our specimens, representing all eight morpho-species. Automatic species delimitation methods recovered nine Molecular Operational Taxonomic Units (MOTUs) because A. interrupta is made of two MOTUs. Morphological re-examination within A. interrupta detected variation at one character, congruent with molecular delimitation. Overall, our integrative approach unveiled rich species-level diversity within the genus Ambassis in Peninsular Malaysia, with the presence of nine species. Further comparisons between our COI dataset and the COI sequences archived in the Barcode of Life Data System (BOLD) from specimens of Ambassis broadly collected in tropical Asian regions, indicated regional-scale hidden diversity and identification conflicts, triggering the need for a complete taxonomic revision of this genus.
玻璃鲈属（Teleostei; Ambassidae）是亚洲热带咸水和海水沿岸鱼类群落的重要组成部分。然而，由于该地区近期缺乏分类学修订，而且可供研究的标本有限，因此对其物种多样性的记录仍然很少。此外，长期存在的分类和命名问题也使该属的研究复杂化。在本文中，我们使用综合分类方法和最近从该地区采集的大量标本，研究了马来西亚半岛安巴丝的多样性。我们对 260 份标本进行了初步形态学观察，发现了 8 个物种，分别为 Ambassis dussumieri、Ambassis interrupta、Ambassis kopsii、Ambassis macracanthus、Ambassis nalua、Ambassis octava、Ambassis urotaenia 和 Ambassis vachellii。然后，我们对 122 个标本的线粒体细胞色素 c 氧化酶亚单位 I（COI）基因条形码片段进行了测序，这些标本代表了所有 8 个形态种。自动物种划分方法恢复了九个分子操作分类单元（MOTU），因为 A. interrupta 是由两个分子操作分类单元组成的。在 A. interrupta 中，形态学再研究发现了一个特征的变异，与分子定界一致。总之，我们的综合方法揭示了马来西亚半岛 Ambassis 属中丰富的物种多样性，共存在 9 个物种。我们的 COI 数据集与存档于生命条形码数据系统（BOLD）的 COI 序列之间的进一步比较表明，在亚洲热带地区广泛收集的 Ambassis 标本具有区域范围的隐藏多样性和识别冲突，因此有必要对该属进行全面的分类修订。
{"title":"Cracking the glass-perchlet code: Integrative taxonomy uncovers high species-level diversity within the glass-perchlet genus Ambassis (Ambassidae) in tropical Asia","authors":"Siti Zafirah Ghazali, Sébastien Lavoué, Norli Fauzani Mohd Abu Hassan Alshari, Danial Hariz Zainal Abidin, Jamsari Amirul Firdaus Jamaluddin, Min Pau Tan, Siti Azizah Mohd Nor","doi":"10.1111/zsc.12640","DOIUrl":"https://doi.org/10.1111/zsc.12640","url":null,"abstract":"Glass-perchlets of the genus <i>Ambassis</i> (Teleostei; Ambassidae) form an important component of the brackish and marine coastal fish communities of tropical Asia. However, their species-level diversity is still poorly documented because of the absence of recent taxonomic revisions in this region and the limited availability of specimens for research. In addition, long-standing taxonomic and nomenclatural issues complicate the studies of this genus. Herein, we examine the diversity of <i>Ambassis</i> in Peninsular Malaysia using an integrative taxonomic approach and a large set of recently collected specimens from this region. Our initial morphological observations of 260 specimens revealed the presence of eight species, identified as <i>Ambassis dussumieri</i>, <i>Ambassis interrupta</i>, <i>Ambassis kopsii</i>, <i>Ambassis macracanthus</i>, <i>Ambassis nalua</i>, <i>Ambassis octava</i>, <i>Ambassis urotaenia</i> and <i>Ambassis vachellii</i>. We then sequenced the barcode fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene for 122 of our specimens, representing all eight morpho-species. Automatic species delimitation methods recovered nine Molecular Operational Taxonomic Units (MOTUs) because <i>A. interrupta</i> is made of two MOTUs. Morphological re-examination within <i>A. interrupta</i> detected variation at one character, congruent with molecular delimitation. Overall, our integrative approach unveiled rich species-level diversity within the genus <i>Ambassis</i> in Peninsular Malaysia, with the presence of nine species. Further comparisons between our COI dataset and the COI sequences archived in the Barcode of Life Data System (BOLD) from specimens of <i>Ambassis</i> broadly collected in tropical Asian regions, indicated regional-scale hidden diversity and identification conflicts, triggering the need for a complete taxonomic revision of this genus.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2023-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138575663","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}
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