The North Pacific distribution of coastal aleocharines has been explained as the result of either dispersal or vicariance. The rove beetle genus Psammostiba is a marine littoral group that occurs on the Pacific coasts of the Northern Hemisphere. We performed phylogenetic analysis of Psammostiba using molecular characters (4685 bp) to investigate their biogeographic patterns. The data were analysed using parsimony, Bayesian and maximum likelihood methods. Model‐based analyses showed the same pattern of Psammostiba species relationships, but parsimony analysis yielded different species relationships for the unresolved clade of Psammostiba. According to the reconstruction of the ancestral areas, both vicariance (two events) and dispersal (one event) have played roles in shaping its current distribution. Biogeographical analyses suggest that the common ancestor of Psammostiba occurred widely along the Pacific coasts of the Northern Hemisphere and underwent vicariance events.
{"title":"Rove beetles occurred widely along the Pacific coasts of the Northern Hemisphere: Phylogeny and biogeography of the marine littoral Psammostiba (Coleoptera, Staphylinidae)","authors":"Jeong‐Hun Song, Jong‐Keun Jung, Kee‐Jeong Ahn","doi":"10.1111/zsc.12688","DOIUrl":"https://doi.org/10.1111/zsc.12688","url":null,"abstract":"The North Pacific distribution of coastal aleocharines has been explained as the result of either dispersal or vicariance. The rove beetle genus <jats:italic>Psammostiba</jats:italic> is a marine littoral group that occurs on the Pacific coasts of the Northern Hemisphere. We performed phylogenetic analysis of <jats:italic>Psammostiba</jats:italic> using molecular characters (4685 bp) to investigate their biogeographic patterns. The data were analysed using parsimony, Bayesian and maximum likelihood methods. Model‐based analyses showed the same pattern of <jats:italic>Psammostiba</jats:italic> species relationships, but parsimony analysis yielded different species relationships for the unresolved clade of <jats:italic>Psammostiba</jats:italic>. According to the reconstruction of the ancestral areas, both vicariance (two events) and dispersal (one event) have played roles in shaping its current distribution. Biogeographical analyses suggest that the common ancestor of <jats:italic>Psammostiba</jats:italic> occurred widely along the Pacific coasts of the Northern Hemisphere and underwent vicariance events.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141547553","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}
Thayse Cristine Melo Benathar, Leonardo Carreira Trevelin, Jeferson Costa Carneiro, Luis Reginaldo Ribeiro Rodrigues, Iracilda Sampaio, Patricia Caroline O'Brien, Malcolm Andrew Ferguson‐Smith, Fengtang Yangg, Cleusa Yoshiko Nagamachi, Julio César Pieczarka
Integrating different lines of evidence is currently recognized as the most robust approach to investigating taxonomic questions, particularly those concerning cryptic diversity. In recent years, different sources of evidence have pointed to new cryptic taxa for bats, with the genus Hsunycteris being an excellent study group because of its large karyotypic variability and high genetic divergence revealed by the latest taxonomic and systematic reviews. This study tests the cryptic diversity hypothesis for the Hsunycteris thomasi complex through an integrative approach using species delimitation, phylogenetic analysis, chromosome painting, and linear morphometry. Our results suggest the existence of three lineages for H. thomasi that are morphologically indistinguishable, confirming the two previously described lineages in the literature and adding a third. We argue that the paraphyly in H. thomasi, as reported by previous studies, should be treated as independent species since they have unique evolutionary histories. Finally, we demonstrate that chromosomal and molecular methods are indispensable for recognizing and confirming groups that include cryptic species or species with confusing and controversial taxonomy.
整合不同的证据目前被认为是研究分类学问题，特别是有关隐性多样性问题的最有力的方法。近年来，不同来源的证据都指出了蝙蝠的新隐性类群，其中蝙蝠属（Hsunycteris）是一个极好的研究类群，因为最新的分类学和系统学综述揭示了该类群较大的核型变异性和较高的遗传分化。本研究通过物种划分、系统进化分析、染色体绘制和线性形态测量等综合方法，检验了Hsunycteris thomasi复合体的隐性多样性假说。我们的研究结果表明，H. thomasi 存在三个形态上无法区分的品系，证实了之前文献中描述的两个品系，并增加了第三个品系。我们认为，由于 H. thomasi 具有独特的进化历史，因此应将其视为独立的物种。最后，我们证明了染色体和分子方法对于识别和确认包括隐蔽物种或分类混乱且有争议的物种的类群是不可或缺的。
{"title":"A case of cryptic diversity in the bat Hsunycteris thomasi (Lonchophyllinae, Chiroptera): New insights into unrecognized species","authors":"Thayse Cristine Melo Benathar, Leonardo Carreira Trevelin, Jeferson Costa Carneiro, Luis Reginaldo Ribeiro Rodrigues, Iracilda Sampaio, Patricia Caroline O'Brien, Malcolm Andrew Ferguson‐Smith, Fengtang Yangg, Cleusa Yoshiko Nagamachi, Julio César Pieczarka","doi":"10.1111/zsc.12682","DOIUrl":"https://doi.org/10.1111/zsc.12682","url":null,"abstract":"Integrating different lines of evidence is currently recognized as the most robust approach to investigating taxonomic questions, particularly those concerning cryptic diversity. In recent years, different sources of evidence have pointed to new cryptic taxa for bats, with the genus <jats:italic>Hsunycteris</jats:italic> being an excellent study group because of its large karyotypic variability and high genetic divergence revealed by the latest taxonomic and systematic reviews. This study tests the cryptic diversity hypothesis for the <jats:italic>Hsunycteris thomasi</jats:italic> complex through an integrative approach using species delimitation, phylogenetic analysis, chromosome painting, and linear morphometry. Our results suggest the existence of three lineages for <jats:italic>H. thomasi</jats:italic> that are morphologically indistinguishable, confirming the two previously described lineages in the literature and adding a third. We argue that the paraphyly in <jats:italic>H. thomasi</jats:italic>, as reported by previous studies, should be treated as independent species since they have unique evolutionary histories. Finally, we demonstrate that chromosomal and molecular methods are indispensable for recognizing and confirming groups that include cryptic species or species with confusing and controversial taxonomy.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141516848","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}
Victor H. S. Mollmann, Marlise L. Bartholomei‐Santos, Gracieli Fernandes, Gislaine Puli, Emerson C. Mossolin, Marcelo M. Dalosto, Sandro Santos
Aegla is a genus of freshwater anomuran crabs encompassing 94 described species occurring in meridional South America. Brazil harbours the greatest diversity of species, mainly in its southern region, which becomes a priority area for Aegla conservation due to high species richness and phylogenetic diversity, elevated endemism and threats to the Atlantic Forest. Here, we assessed Aegla richness and distribution in this priority area and tested the hypothesis of crypticism in the region's species. Sampling sites were distributed inside and in the surroundings of five protected areas, covering the major distribution range of several species described for southern Brazil. We applied three species delimitation methods to COI mitochondrial gene data, coupled with phylogenetic and morphological analyses. By integrating species delimitation based on the COI data and traditional taxonomy, we uncovered a high proportion of hidden diversity among Aegla in our study area and identified ten known species besides impressive 17 new putative species. Of these, eight are possible new taxonomic units that do not conform to any known species, and nine are divided into three cryptic groups: Aegla jarai complex, Aegla franciscana complex and Aegla camargoi complex. Most of these species have a narrow spatial distribution, making them highly vulnerable to habitat degradation. Despite the real richness of the genus still being largely unknown, the high diversity revealed here makes our study area the richest known region regarding the number of Aegla species within its distribution, making this area even more worthy for conservation efforts.
Aegla是淡水无尾类蟹属，共有94个已描述的物种，分布于南美洲中部。巴西拥有最丰富的物种多样性，主要分布在其南部地区，由于物种丰富度和系统发育多样性高、地方特有性高以及大西洋森林面临的威胁，该地区成为保护Aegla的重点地区。在此，我们评估了这一重点地区的Aegla物种丰富度和分布情况，并检验了该地区物种隐匿性的假设。取样点分布在五个保护区内部和周边地区，涵盖了巴西南部多个物种的主要分布范围。我们对 COI 线粒体基因数据采用了三种物种划分方法，并进行了系统发育和形态分析。通过将基于 COI 数据的物种划分与传统分类学相结合，我们发现了研究区域内 Aegla 的高比例隐藏多样性，并确定了 10 个已知物种以及令人印象深刻的 17 个推定新物种。其中，8 个可能是新的分类单元，与任何已知物种都不一致，9 个分为 3 个隐性类群：Aegla jarai复合群、Aegla franciscana复合群和Aegla camargoi复合群。这些物种大多空间分布狭窄，极易受到栖息地退化的影响。尽管该属物种的真正丰富程度在很大程度上仍不为人所知，但这里揭示的高度多样性使我们的研究区域成为目前已知Aegla物种分布最丰富的地区，使该地区更值得保护。
{"title":"Hidden diversity of Aegla (Decapoda, Anomura) in a priority area for conservation","authors":"Victor H. S. Mollmann, Marlise L. Bartholomei‐Santos, Gracieli Fernandes, Gislaine Puli, Emerson C. Mossolin, Marcelo M. Dalosto, Sandro Santos","doi":"10.1111/zsc.12686","DOIUrl":"https://doi.org/10.1111/zsc.12686","url":null,"abstract":"<jats:italic>Aegla</jats:italic> is a genus of freshwater anomuran crabs encompassing 94 described species occurring in meridional South America. Brazil harbours the greatest diversity of species, mainly in its southern region, which becomes a priority area for <jats:italic>Aegla</jats:italic> conservation due to high species richness and phylogenetic diversity, elevated endemism and threats to the Atlantic Forest. Here, we assessed <jats:italic>Aegla</jats:italic> richness and distribution in this priority area and tested the hypothesis of crypticism in the region's species. Sampling sites were distributed inside and in the surroundings of five protected areas, covering the major distribution range of several species described for southern Brazil. <jats:italic>We applied three species</jats:italic> delimitation methods to <jats:italic>COI</jats:italic> mitochondrial gene data, coupled with phylogenetic and morphological analyses. By integrating species delimitation based on the <jats:italic>COI</jats:italic> data and traditional taxonomy, we uncovered a high proportion of hidden diversity among <jats:italic>Aegla</jats:italic> in our study area and identified ten known species besides impressive 17 new putative species. Of these, eight are possible new taxonomic units that do not conform to any known species, and nine are divided into three cryptic groups: <jats:italic>Aegla jarai</jats:italic> complex, <jats:italic>Aegla franciscana</jats:italic> complex and <jats:italic>Aegla camargoi</jats:italic> complex. Most of these species have a narrow spatial distribution, making them highly vulnerable to habitat degradation. Despite the real richness of the genus still being largely unknown, the high diversity revealed here makes our study area the richest known region regarding the number of <jats:italic>Aegla</jats:italic> species within its distribution, making this area even more worthy for conservation efforts.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141516847","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}
Alexandra Saranchina, Andrei Mutin, Ekaterina Govorukhina, Yaroslav Rzhechitskiy, Anton Gurkov, Maxim Timofeyev, Polina Drozdova
Baikal amphipods are one of the most unique freshwater species flocks of over 350 morphological species and subspecies playing multiple ecological roles in this ancient lake. However, molecular phylogeny studies accumulate evidence that this number is underestimated. Previously, we showed that an abundant littoral species Eulimnogammarus verrucosus comprised at least three genetic lineages: southern (S), western (W), and eastern (E), inhabiting corresponding parts of Baikal shore. The Angara River is the only outflow of the lake and is inhabited by amphipods originating from Baikal, which were previously analysed only morphologically. The river has parts with strong current or closed bays as opposed to sea‐like conditions of Lake Baikal, which raises the question of which species were able to adapt here. Here we studied the phylogeny of E. verrucosus from the Angara River, which could be reached by two lineages, S and W. We analysed 17 sites from 0.6 to 650 km from the outflow. Cytochrome c oxidase subunit I (COI) and 18S rRNA analysis showed that the sites closest to Baikal were inhabited by the S and W lineages sympatrically. The other sites were inhabited by the S lineage at both banks and also by the novel A (Angara) lineage. The A lineage was the first to split up from the last common ancestor of all E. verrucosus. Our data confirm the importance of considering cryptic diversity in ecological monitoring, and in order to simplify the identification of the genetic lineage, we developed a web‐app speCOIdent.
贝加尔湖片脚类动物是最独特的淡水物种群之一，有 350 多个形态物种和亚种，在这个古老的湖泊中发挥着多种生态作用。然而，分子系统学研究积累的证据表明，这一数字被低估了。此前，我们研究发现，贝加尔湖畔丰富的沿岸物种Eulimnogammarus verrucosus至少包括三个遗传系：南部（S）、西部（W）和东部（E），栖息在贝加尔湖畔的相应区域。安加拉河是贝加尔湖唯一的外流河，河中栖息着来自贝加尔湖的片脚类动物，以前只对其进行过形态分析。与贝加尔湖类似大海的条件不同，安加拉河有部分河段水流湍急或河湾封闭，这就提出了哪些物种能够适应这里的问题。在此，我们研究了安加拉河中蚯蚓的系统发育情况，安加拉河可由 S 和 W 两条支系到达。细胞色素 c 氧化酶亚单位 I（COI）和 18S rRNA 分析表明，最靠近贝加尔湖的地点由 S 和 W 两系共栖。其他地点由两岸的 S 系和新的 A（安加拉）系居住。A 系是第一个从所有 E. verrucosus 的最后一个共同祖先分裂出来的。我们的数据证实了在生态监测中考虑隐性多样性的重要性，为了简化遗传系的识别，我们开发了一个网络应用程序 speCOIdent。
{"title":"Genetic diversity in a Baikal species complex Eulimnogammarus verrucosus (Amphipoda: Gammaroidea) in the Angara River, the only outflow of Lake Baikal","authors":"Alexandra Saranchina, Andrei Mutin, Ekaterina Govorukhina, Yaroslav Rzhechitskiy, Anton Gurkov, Maxim Timofeyev, Polina Drozdova","doi":"10.1111/zsc.12681","DOIUrl":"https://doi.org/10.1111/zsc.12681","url":null,"abstract":"Baikal amphipods are one of the most unique freshwater species flocks of over 350 morphological species and subspecies playing multiple ecological roles in this ancient lake. However, molecular phylogeny studies accumulate evidence that this number is underestimated. Previously, we showed that an abundant littoral species <jats:italic>Eulimnogammarus verrucosus</jats:italic> comprised at least three genetic lineages: southern (S), western (W), and eastern (E), inhabiting corresponding parts of Baikal shore. The Angara River is the only outflow of the lake and is inhabited by amphipods originating from Baikal, which were previously analysed only morphologically. The river has parts with strong current or closed bays as opposed to sea‐like conditions of Lake Baikal, which raises the question of which species were able to adapt here. Here we studied the phylogeny of <jats:italic>E. verrucosus</jats:italic> from the Angara River, which could be reached by two lineages, S and W. We analysed 17 sites from 0.6 to 650 km from the outflow. Cytochrome c oxidase subunit I (COI) and 18S rRNA analysis showed that the sites closest to Baikal were inhabited by the S and W lineages sympatrically. The other sites were inhabited by the S lineage at both banks and also by the novel A (Angara) lineage. The A lineage was the first to split up from the last common ancestor of all <jats:italic>E. verrucosus</jats:italic>. Our data confirm the importance of considering cryptic diversity in ecological monitoring, and in order to simplify the identification of the genetic lineage, we developed a web‐app speCOIdent.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141503197","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}
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.
{"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":null,"pages":null},"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}
Luqman Hakim Ruzman, Jamsari Amirul Firdaus Jamaluddin, Abdullah Halim Muhammad‐Rasul, Tedjo Sukmono, Md. Zain Khaironizam, Sébastien Lavoué
The taxonomy of the freshwater featherback fish genus Chitala (Osteoglossomorpha: Notopteridae) remains unsettled because delimiting and naming Chitala species based solely on morphology led to different hypotheses. In this study, we aim to determine the number and identity of Chitala 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 Chitala 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 Chitala 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 Chitala specimens from neighbouring regions allowed us to name these species as Chitala lopis, Chitala borneensis, and Chitala ornata. We also showed the presence of two undescribed species in Indonesia.
{"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":null,"pages":null},"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}
Viktoria E. Bogantes, Karin Meiβner, D. S. Waits, K. Kocot, K. M. Halanych
Most efforts at improving accuracy in phylogenomic reconstructions have focused on improving tree‐building methods or orthology determination. Even though the use of whole genome sequence or transcriptome data is increasing, the degree to which accurate genome assembly and annotation influence phylogenetic inference has not been well explored. Here, we use low‐coverage whole genome sequencing of spionid annelids to explore the impact of different assemblers and annotation strategies on tree reconstruction. We also produce a phylogenetic hypothesis that spans the breadth of Spionidae, examining the current systematics of the group, which is based on morphological parsimony analyses and classical taxonomy. Our results show that both assembly and annotation can have important consequences for the pool of loci that may be available for tree reconstruction. When an identical phylogenomic pipeline is used, differences in assembly and annotation can account for variation in reconstructed topologies. Interestingly, the completeness and depth of the data used for training annotation software (i.e. data from model systems) appear to be more important, by some measures, than the degree of phylogenetic relatedness of the organism from which training data are drawn. Despite variation in recovered topologies, the recognised subfamily Spioninae is nested within Nerininae, suggesting that diagnostic characters of Nerininae (e.g. thick egg membrane, short‐headed sperm) are symplesiomorphies of Spionidae rather than apomorphies of a particular subclade. With the increased use of genomic data, our results advocate for a broader consideration of how assembly and annotation may impact data matrices used in phylogenomic analyses.
{"title":"Phylogenomic reconstruction influenced by assembly and annotation parameters: Using whole genome data to unravel the relationships of Spionidae (Annelida)","authors":"Viktoria E. Bogantes, Karin Meiβner, D. S. Waits, K. Kocot, K. M. Halanych","doi":"10.1111/zsc.12676","DOIUrl":"https://doi.org/10.1111/zsc.12676","url":null,"abstract":"Most efforts at improving accuracy in phylogenomic reconstructions have focused on improving tree‐building methods or orthology determination. Even though the use of whole genome sequence or transcriptome data is increasing, the degree to which accurate genome assembly and annotation influence phylogenetic inference has not been well explored. Here, we use low‐coverage whole genome sequencing of spionid annelids to explore the impact of different assemblers and annotation strategies on tree reconstruction. We also produce a phylogenetic hypothesis that spans the breadth of Spionidae, examining the current systematics of the group, which is based on morphological parsimony analyses and classical taxonomy. Our results show that both assembly and annotation can have important consequences for the pool of loci that may be available for tree reconstruction. When an identical phylogenomic pipeline is used, differences in assembly and annotation can account for variation in reconstructed topologies. Interestingly, the completeness and depth of the data used for training annotation software (i.e. data from model systems) appear to be more important, by some measures, than the degree of phylogenetic relatedness of the organism from which training data are drawn. Despite variation in recovered topologies, the recognised subfamily Spioninae is nested within Nerininae, suggesting that diagnostic characters of Nerininae (e.g. thick egg membrane, short‐headed sperm) are symplesiomorphies of Spionidae rather than apomorphies of a particular subclade. With the increased use of genomic data, our results advocate for a broader consideration of how assembly and annotation may impact data matrices used in phylogenomic analyses.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141341144","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}
Michal Rindos, Roman V. Yakovlev, Karen McLachlan Hamilton, Zdenek Faltynek Fric, S. Knyazev, Reza Zahiri
The phylogeography of economically important forest pests is important for understanding their demographic and evolutionary history. Linking the genetic data obtained with the bioclimatic models helps reveal future demographic trends of the pest species studied. Lymantria monacha is a polyphagous species that feeds on numerous coniferous and deciduous trees throughout the Palaearctic and is known to cause catastrophic defoliation, particularly in Europe. In addition, data from various mapping programmes over the last decade have revealed changes in the distribution of L. monacha. Therefore, in this study, we decided to clarify the evolutionary and demographic history of this important forest species using genetic data complemented by bioclimatic modelling. Our results confirmed the systematic status and monophyly of L. monacha. However, the lack of a geographical pattern between the studied regions suggests that the current genetic structure may be the result of recent dispersal events. Moreover, we found that the areas of high genetic diversity are consistent with potential past range shifts and survival of changes in climate and host plant availability. These two main variables also seem to determine the future range of L. monacha. Also, our modelling confirmed a poleward shift in its range and with a significant retraction from its current southern edge of distribution.
具有重要经济意义的森林害虫的系统地理学对于了解其人口和进化历史非常重要。将获得的遗传数据与生物气候模型联系起来，有助于揭示所研究害虫物种的未来种群趋势。Lymantria monacha 是一种多食性害虫，在整个古北欧地区以众多针叶树和落叶树为食，已知会造成灾难性的落叶，尤其是在欧洲。此外，过去十年间各种测绘计划的数据显示，L. monacha 的分布发生了变化。因此，在这项研究中，我们决定利用遗传数据并辅以生物气候模型，来阐明这一重要森林物种的进化和人口历史。我们的研究结果证实了 L. monacha 的系统地位和单系性。然而，研究区域之间缺乏地理模式，这表明目前的遗传结构可能是近期扩散事件的结果。此外，我们还发现，遗传多样性较高的地区与过去可能发生的分布区转移以及气候和寄主植物可用性变化的存活情况相一致。这两个主要变量似乎也决定了 L. monacha 未来的分布范围。此外，我们的建模证实了其分布范围的极地转移，并从目前的南部分布边缘显著后撤。
{"title":"Phylogeography and bioclimatic models revealed a complicated genetic structure and future range shifts of Lymantria monacha L.","authors":"Michal Rindos, Roman V. Yakovlev, Karen McLachlan Hamilton, Zdenek Faltynek Fric, S. Knyazev, Reza Zahiri","doi":"10.1111/zsc.12679","DOIUrl":"https://doi.org/10.1111/zsc.12679","url":null,"abstract":"The phylogeography of economically important forest pests is important for understanding their demographic and evolutionary history. Linking the genetic data obtained with the bioclimatic models helps reveal future demographic trends of the pest species studied. Lymantria monacha is a polyphagous species that feeds on numerous coniferous and deciduous trees throughout the Palaearctic and is known to cause catastrophic defoliation, particularly in Europe. In addition, data from various mapping programmes over the last decade have revealed changes in the distribution of L. monacha. Therefore, in this study, we decided to clarify the evolutionary and demographic history of this important forest species using genetic data complemented by bioclimatic modelling. Our results confirmed the systematic status and monophyly of L. monacha. However, the lack of a geographical pattern between the studied regions suggests that the current genetic structure may be the result of recent dispersal events. Moreover, we found that the areas of high genetic diversity are consistent with potential past range shifts and survival of changes in climate and host plant availability. These two main variables also seem to determine the future range of L. monacha. Also, our modelling confirmed a poleward shift in its range and with a significant retraction from its current southern edge of distribution.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141342924","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}
Freshwater bivalves (Bivalvia, Unionida) are one of the most threatened groups of animals in the world. Defining species boundaries and understanding the phylogeny and genetic diversity of these species is key to guiding their conservation and management. However, the presence of significant phenotypic plasticity and convergence within this group complicates species delimitation. This includes the freshwater mussel genus Nodularia, endemic to East Asia, for which a comprehensive understanding of species diversity and phylogenetic relationships remains elusive due to inadequate sampling in previous studies, particularly in China, a widely recognized biodiversity hotspot for freshwater mussels. Here, we conduct comprehensive taxonomic and phylogenetic analyses of Nodularia species based on extensive sampling across 23 provinces in China and multiple data sources, including shell morphology, soft body anatomy, six‐gene (COI + ND1 + 16S + 18S + 28S + histone H3) and mitogenome datasets. The integrative systematics approach used here reveals 10 distinct species in this genus, four of which are new to science, i.e. Nodularia hanensis sp. nov., Nodularia huana sp. nov., Nodularia fusiformans sp. nov., Nodularia dualobtusus sp. nov. and two of which are new records for China, i.e. Nodularia dorri (Wattebled [Journal de Conchyliologie, 34, 1886, 54]) and Nodularia micheloti (Morlet [Journal de Conchyliologie, 34, 1886, 75]). We also propose that the nominal species Nodularia jourdyi (Morlet [Journal de Conchyliologie, 34, 1886, 75]) syn. nov. is a new synonym for Nodularia douglasiae (Griffith & Pidgeon, 1833) based on molecular data. BI, ML, and BEAST analyses based on the six‐gene dataset and mitochondrial phylogenomics consistently support the following phylogenetic relationships: (N. dorri + (N. hanensis sp. nov. + N. micheloti)) + (N. breviconcha + (N. huana sp. nov. + (N. fusiformans sp. nov. + ((N. nuxpersicae + N. nipponensis) + (N. dualobtusus sp. nov. + N. douglasiae))))). The molecular clock with fossil calibration indicates that Nodularia originated in the Late Cretaceous period (ca. 73.78 Mya). It then diverged into two independent clades during the Middle Paleogene (ca. 45.01 Mya), followed by a rapid burst of extant speciation during the Neogene (mean age 28.28 to 4.79 Mya). Nodularia breviconcha is the earliest differentiated taxon among the 10 Nodularia taxa, appearing during the Paleogene‐Neogene transition (28.28 Mya; 95% HPD = 14.35–48.44 Mya). Taken together, we provide a robust systematic framework for Nodularia species, addressing phylogenetic relationships, taxonomy, and evolutionary history of this group.
{"title":"Diversity, morphology, and phylogeny of freshwater mussels of the genus Nodularia (Bivalvia: Unionidae) from China, with descriptions of four new species","authors":"Ruiwen Wu, Lili Liu, Liping Zhang, Xiongjun Liu, Zhengkun Hu, Dandong Jin, Zepeng Zhang, Xiaoping Wu, Zhicai Xie, Zhengfei Li, M. Lopes‐Lima","doi":"10.1111/zsc.12677","DOIUrl":"https://doi.org/10.1111/zsc.12677","url":null,"abstract":"Freshwater bivalves (Bivalvia, Unionida) are one of the most threatened groups of animals in the world. Defining species boundaries and understanding the phylogeny and genetic diversity of these species is key to guiding their conservation and management. However, the presence of significant phenotypic plasticity and convergence within this group complicates species delimitation. This includes the freshwater mussel genus Nodularia, endemic to East Asia, for which a comprehensive understanding of species diversity and phylogenetic relationships remains elusive due to inadequate sampling in previous studies, particularly in China, a widely recognized biodiversity hotspot for freshwater mussels. Here, we conduct comprehensive taxonomic and phylogenetic analyses of Nodularia species based on extensive sampling across 23 provinces in China and multiple data sources, including shell morphology, soft body anatomy, six‐gene (COI + ND1 + 16S + 18S + 28S + histone H3) and mitogenome datasets. The integrative systematics approach used here reveals 10 distinct species in this genus, four of which are new to science, i.e. Nodularia hanensis sp. nov., Nodularia huana sp. nov., Nodularia fusiformans sp. nov., Nodularia dualobtusus sp. nov. and two of which are new records for China, i.e. Nodularia dorri (Wattebled [Journal de Conchyliologie, 34, 1886, 54]) and Nodularia micheloti (Morlet [Journal de Conchyliologie, 34, 1886, 75]). We also propose that the nominal species Nodularia jourdyi (Morlet [Journal de Conchyliologie, 34, 1886, 75]) syn. nov. is a new synonym for Nodularia douglasiae (Griffith & Pidgeon, 1833) based on molecular data. BI, ML, and BEAST analyses based on the six‐gene dataset and mitochondrial phylogenomics consistently support the following phylogenetic relationships: (N. dorri + (N. hanensis sp. nov. + N. micheloti)) + (N. breviconcha + (N. huana sp. nov. + (N. fusiformans sp. nov. + ((N. nuxpersicae + N. nipponensis) + (N. dualobtusus sp. nov. + N. douglasiae))))). The molecular clock with fossil calibration indicates that Nodularia originated in the Late Cretaceous period (ca. 73.78 Mya). It then diverged into two independent clades during the Middle Paleogene (ca. 45.01 Mya), followed by a rapid burst of extant speciation during the Neogene (mean age 28.28 to 4.79 Mya). Nodularia breviconcha is the earliest differentiated taxon among the 10 Nodularia taxa, appearing during the Paleogene‐Neogene transition (28.28 Mya; 95% HPD = 14.35–48.44 Mya). Taken together, we provide a robust systematic framework for Nodularia species, addressing phylogenetic relationships, taxonomy, and evolutionary history of this group.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141350257","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}
Gabriel S. C. Silva, Marcelo S. Rocha, B. F. Melo, Lais Reia, F. F. Roxo, M. Sabaj, Claudio Oliveira
Pimelodidae is a family of large‐sized catfishes consisting of 116 valid species divided into 30 genera distributed in the Neotropical region. Despite recent advancements in understanding the pimelodid phylogeny, several internal relationships have remained unclear and have received limited support from various phylogenetic analyses. We provide a new genomic dataset comprising 55 species representing 25 genera of Pimelodidae and related siluriform families Aspredinidae, Auchenipteridae, Cetopsidae, Doradidae, Diplomystidae, Heptapteridae, Loricariidae, and Pseudopimelodidae. Our phylogenetic analyses support the monophyly of Pimelodidae, as well as the existence of four major lineages: the Steindachneridion clade, the Leiarius + Phractocephalus clade, and two major subclades herein classified as Sorubiminae and Pimelodinae. Our topology resolves Phractocephalus sister to Leiarius differing from previous phylogenies. In Sorubiminae, Zungaro is sister to two large clades: one with Sorubim, Sorubimichthys, and Pseudoplatystoma, and the other with Hemisorubim, Platysilurus, Platystomatichthys, Brachyplatystoma, and Hypophthalmus. In Pimelodinae, we found the Pimelodus ornatus clade, the calophysines, and the clade with Exallodontus, Propimelodus, and Pimelodus altissimus closer to the Pimelodus group. Parapimelodus, Duopalatinus, Iheringichthys, and Bergiaria are included within the Pimelodus group. The Pimelodus group contains four main components: (1) Duopalatinus peruanus, (2) the trans‐Andean Pimelodus grosskopfii; (3) Pimelodus maculatus clade with species from the Brazilian Shield in southeastern Brazil; and (4) Pimelodus blochii clade composed by species from the Amazon, Orinoco, Paraná‐Paraguay, Parnaíba, São Francisco and coastal drainages of the Guiana Shield. The P. maculatus clade is composed by phenotypically diverse species, and the P. blochii clade houses species morphologically similar that appear nested within the widely distributed P. blochii.
{"title":"Phylogenomics of the catfish family Pimelodidae with focus on the genus Pimelodus support the recognition of Sorubiminae and Pimelodinae (Teleostei, Siluriformes)","authors":"Gabriel S. C. Silva, Marcelo S. Rocha, B. F. Melo, Lais Reia, F. F. Roxo, M. Sabaj, Claudio Oliveira","doi":"10.1111/zsc.12671","DOIUrl":"https://doi.org/10.1111/zsc.12671","url":null,"abstract":"Pimelodidae is a family of large‐sized catfishes consisting of 116 valid species divided into 30 genera distributed in the Neotropical region. Despite recent advancements in understanding the pimelodid phylogeny, several internal relationships have remained unclear and have received limited support from various phylogenetic analyses. We provide a new genomic dataset comprising 55 species representing 25 genera of Pimelodidae and related siluriform families Aspredinidae, Auchenipteridae, Cetopsidae, Doradidae, Diplomystidae, Heptapteridae, Loricariidae, and Pseudopimelodidae. Our phylogenetic analyses support the monophyly of Pimelodidae, as well as the existence of four major lineages: the Steindachneridion clade, the Leiarius + Phractocephalus clade, and two major subclades herein classified as Sorubiminae and Pimelodinae. Our topology resolves Phractocephalus sister to Leiarius differing from previous phylogenies. In Sorubiminae, Zungaro is sister to two large clades: one with Sorubim, Sorubimichthys, and Pseudoplatystoma, and the other with Hemisorubim, Platysilurus, Platystomatichthys, Brachyplatystoma, and Hypophthalmus. In Pimelodinae, we found the Pimelodus ornatus clade, the calophysines, and the clade with Exallodontus, Propimelodus, and Pimelodus altissimus closer to the Pimelodus group. Parapimelodus, Duopalatinus, Iheringichthys, and Bergiaria are included within the Pimelodus group. The Pimelodus group contains four main components: (1) Duopalatinus peruanus, (2) the trans‐Andean Pimelodus grosskopfii; (3) Pimelodus maculatus clade with species from the Brazilian Shield in southeastern Brazil; and (4) Pimelodus blochii clade composed by species from the Amazon, Orinoco, Paraná‐Paraguay, Parnaíba, São Francisco and coastal drainages of the Guiana Shield. The P. maculatus clade is composed by phenotypically diverse species, and the P. blochii clade houses species morphologically similar that appear nested within the widely distributed P. blochii.","PeriodicalId":49334,"journal":{"name":"Zoologica Scripta","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141369353","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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