{"title":"Reviewers for Insect Systematics and Diversity (November 2022–October 2023)","authors":"","doi":"10.1093/isd/ixad025","DOIUrl":"https://doi.org/10.1093/isd/ixad025","url":null,"abstract":"","PeriodicalId":48498,"journal":{"name":"Insect Systematics and Diversity","volume":" 16","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139392317","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kathryn A Sullivan, Erika M Tucker, N. J. Dowdy, Julie M Allen, Vijay Barve, James H Boone, Sarah E Bush, Neal L Evenhuis, Michael Hastriter, Jessica E Light, Teresa Mayfield-Meyer, Barry M OConnor, J. Poelen, Gabor R Racz, Katja C. Seltmann, J. Zaspel
Classification of the biological diversity on Earth is foundational to all areas of research within the natural sciences. Reliable biological nomenclatural and taxonomic systems facilitate efficient access to information about organisms and their names over time. However, broadly sharing, accessing, delivering, and updating these resources remains a persistent problem. This barrier has been acknowledged by the biodiversity data sharing community, yet concrete efforts to standardize and continually update taxonomic names in a sustainable way remain limited. High diversity groups such as arthropods are especially challenging as available specimen data per number of species is substantially lower than vertebrate or plant groups. The Terrestrial Parasite Tracker Thematic Collections Network project developed a workflow for gathering expert-verified taxonomic names across all available sources, aligning those sources, and publishing a single resource that provides a model for future endeavors to standardize digital specimen identification data. The process involved gathering expert-verified nomenclature lists representing the full taxonomic scope of terrestrial arthropod parasites, documenting issues experienced, and finding potential solutions for reconciliation of taxonomic resources against large data publishers. Although discordance between our expert resources and the Global Biodiversity Information Facility are relatively low, the impact across all taxa affects thousands of names that correspond to hundreds of thousands of specimen records. Here, we demonstrate a mechanism for the delivery and continued maintenance of these taxonomic resources, while highlighting the current state of taxon name curation for biodiversity data sharing.
{"title":"Building a community-based taxonomic resource for digitization of parasites and their hosts","authors":"Kathryn A Sullivan, Erika M Tucker, N. J. Dowdy, Julie M Allen, Vijay Barve, James H Boone, Sarah E Bush, Neal L Evenhuis, Michael Hastriter, Jessica E Light, Teresa Mayfield-Meyer, Barry M OConnor, J. Poelen, Gabor R Racz, Katja C. Seltmann, J. Zaspel","doi":"10.1093/isd/ixad023","DOIUrl":"https://doi.org/10.1093/isd/ixad023","url":null,"abstract":"Classification of the biological diversity on Earth is foundational to all areas of research within the natural sciences. Reliable biological nomenclatural and taxonomic systems facilitate efficient access to information about organisms and their names over time. However, broadly sharing, accessing, delivering, and updating these resources remains a persistent problem. This barrier has been acknowledged by the biodiversity data sharing community, yet concrete efforts to standardize and continually update taxonomic names in a sustainable way remain limited. High diversity groups such as arthropods are especially challenging as available specimen data per number of species is substantially lower than vertebrate or plant groups. The Terrestrial Parasite Tracker Thematic Collections Network project developed a workflow for gathering expert-verified taxonomic names across all available sources, aligning those sources, and publishing a single resource that provides a model for future endeavors to standardize digital specimen identification data. The process involved gathering expert-verified nomenclature lists representing the full taxonomic scope of terrestrial arthropod parasites, documenting issues experienced, and finding potential solutions for reconciliation of taxonomic resources against large data publishers. Although discordance between our expert resources and the Global Biodiversity Information Facility are relatively low, the impact across all taxa affects thousands of names that correspond to hundreds of thousands of specimen records. Here, we demonstrate a mechanism for the delivery and continued maintenance of these taxonomic resources, while highlighting the current state of taxon name curation for biodiversity data sharing.","PeriodicalId":48498,"journal":{"name":"Insect Systematics and Diversity","volume":"57 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139294825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Vladislav Ivanov, Gergin Blagoev, Samuel Danflous, Peter Gajdoš, Toke Thomas Høye, Kyung Min Lee, Yuri Marusik, Cecilie Lohse Mielec, Christoph Muster, Julien Pétillon, Jörg Spelda, Marko Mutanen
Abstract Holarctic species offer great opportunities to study biogeography, phylogenetics, taxonomy, and local adaptation. Species that are considered conspecific between the Palearctic and the Nearctic realms are often split into 2 or more species when denser sampling and molecular markers are applied. Similar in complexity but at a finer geographical scale are species groups having Arctic-Alpine distributions where lineages have complicated demographic histories due to glacial dynamics. In both cases, allopatric speciation might not result in fast differentiation of morphological characters if environmental conditions in isolated areas are similar and the main driver of variability is genetic drift. Here, we study the Holarctic Pardosa hyperborea (Thorell, 1872) and its closest European relatives to assess their taxonomic status and patterns of genetic variability. Based on DNA barcodes and genomic data from double-digest restriction site associated sequencing, we propose that the North American populations should be regarded as a distinct species (P. luteola Emerton,1894, stat. resurr.), possibly consisting of several independent lineages. With the help of D-statistics, population genetic simulations and phylogenetic networks analysis, we demonstrate historical introgression among European species of the group and a likely explanation for shared DNA barcodes among allopatric and fully differentiated species. Our study exposes a promising model for studying speciation processes and demographic history in parallel on both sides of the Atlantic Ocean and demonstrates the usefulness of genomic tools in elucidating the taxonomy and biogeography of taxa across broad geographic scales.
{"title":"Across mountains and ocean: species delimitation and historical connectivity in Holarctic and Arctic-Alpine wolf spiders (Lycosidae, <i>Pardosa</i>)","authors":"Vladislav Ivanov, Gergin Blagoev, Samuel Danflous, Peter Gajdoš, Toke Thomas Høye, Kyung Min Lee, Yuri Marusik, Cecilie Lohse Mielec, Christoph Muster, Julien Pétillon, Jörg Spelda, Marko Mutanen","doi":"10.1093/isd/ixad018","DOIUrl":"https://doi.org/10.1093/isd/ixad018","url":null,"abstract":"Abstract Holarctic species offer great opportunities to study biogeography, phylogenetics, taxonomy, and local adaptation. Species that are considered conspecific between the Palearctic and the Nearctic realms are often split into 2 or more species when denser sampling and molecular markers are applied. Similar in complexity but at a finer geographical scale are species groups having Arctic-Alpine distributions where lineages have complicated demographic histories due to glacial dynamics. In both cases, allopatric speciation might not result in fast differentiation of morphological characters if environmental conditions in isolated areas are similar and the main driver of variability is genetic drift. Here, we study the Holarctic Pardosa hyperborea (Thorell, 1872) and its closest European relatives to assess their taxonomic status and patterns of genetic variability. Based on DNA barcodes and genomic data from double-digest restriction site associated sequencing, we propose that the North American populations should be regarded as a distinct species (P. luteola Emerton,1894, stat. resurr.), possibly consisting of several independent lineages. With the help of D-statistics, population genetic simulations and phylogenetic networks analysis, we demonstrate historical introgression among European species of the group and a likely explanation for shared DNA barcodes among allopatric and fully differentiated species. Our study exposes a promising model for studying speciation processes and demographic history in parallel on both sides of the Atlantic Ocean and demonstrates the usefulness of genomic tools in elucidating the taxonomy and biogeography of taxa across broad geographic scales.","PeriodicalId":48498,"journal":{"name":"Insect Systematics and Diversity","volume":"56 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135254876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tomasz W Pyrcz, Keith R Willmott, Dorota Lachowska-Cierlik, Artur Mrozek, Klaudia Florczyk, Oscar Mahecha-J, Marianne Espeland
Abstract Analysis of a target enrichment molecular dataset confirms the monophyly of the Neotropical montane butterfly group known as the Pronophila Westwood clade, 1 of 2 major lineages of the satyrine subtribe Pronophilina. The Pronophila clade comprises 18–20 recognized genera and some 125 species. Within this group, the genus Pseudomaniola Röber appears as paraphyletic, and is split here into 3 genera, Pseudomaniola sensu novum with 6 species, including 4 previously considered as subspecies of P. phaselis (Hewitson), the monobasic Fahraeusia Pyrcz n. gen. for Catargynnis asuba Thieme, n. comb., and Boyeriana Pyrcz, Espeland & Willmott n. gen., with 9 species. The adults of all 3 genera can be recognized by their wing color patterns, but the strongest synapomorphies are found in the genitalia, especially those of the male, supporting the above systematic decisions. Notable differences are also found in scale organization and morphology. A divergence time analysis suggests that Fahraeusia diverged from Pseudomaniola + Boyeriana in the mid-Miocene, around 12 Mya, and the subsequent separation of the last 2 genera occurred at the start of the Pliocene at around 5 Mya.
摘要对目标富集分子数据集的分析证实了新热带山地蝴蝶类群proophila Westwood分支的单一性，该分支是satyrine亚部落proophilina的2个主要谱系之一。原蝇分支包括18-20个公认的属和大约125种。在这一类群中，假omaniola Röber属以副葡萄球菌的形式出现，在这里分为3属，假omaniola sensu novum有6种，包括4个以前被认为是P. phaselis (Hewitson)的亚种，单基faraeusia Pyrcz n. gen为Catargynnis asuba Thieme, n. comb。波耶里亚娜·派尔茨，西班牙;Willmott n. gen.，有9种。3属成虫均可通过翅膀的颜色模式来识别，但突触性最强的是生殖器，尤其是雄性的生殖器，这支持了上述系统决策。在鳞片组织和形态上也存在显著差异。分化时间分析表明，faraeusia与Pseudomaniola + Boyeriana的分化发生在中新世中期，约12亿年前，最后2个属的分离发生在上新世初期，约5亿年前。
{"title":"Phylogeny and systematics of the “<i>Pronophila</i> clade,” with 2 new genera to resolve the formerly polyphyletic genus <i>Pseudomaniola</i> (Lepidoptera: Nymphalidae: Satyrinae)","authors":"Tomasz W Pyrcz, Keith R Willmott, Dorota Lachowska-Cierlik, Artur Mrozek, Klaudia Florczyk, Oscar Mahecha-J, Marianne Espeland","doi":"10.1093/isd/ixad020","DOIUrl":"https://doi.org/10.1093/isd/ixad020","url":null,"abstract":"Abstract Analysis of a target enrichment molecular dataset confirms the monophyly of the Neotropical montane butterfly group known as the Pronophila Westwood clade, 1 of 2 major lineages of the satyrine subtribe Pronophilina. The Pronophila clade comprises 18–20 recognized genera and some 125 species. Within this group, the genus Pseudomaniola Röber appears as paraphyletic, and is split here into 3 genera, Pseudomaniola sensu novum with 6 species, including 4 previously considered as subspecies of P. phaselis (Hewitson), the monobasic Fahraeusia Pyrcz n. gen. for Catargynnis asuba Thieme, n. comb., and Boyeriana Pyrcz, Espeland & Willmott n. gen., with 9 species. The adults of all 3 genera can be recognized by their wing color patterns, but the strongest synapomorphies are found in the genitalia, especially those of the male, supporting the above systematic decisions. Notable differences are also found in scale organization and morphology. A divergence time analysis suggests that Fahraeusia diverged from Pseudomaniola + Boyeriana in the mid-Miocene, around 12 Mya, and the subsequent separation of the last 2 genera occurred at the start of the Pliocene at around 5 Mya.","PeriodicalId":48498,"journal":{"name":"Insect Systematics and Diversity","volume":"52 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135736991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract Flea beetles (Alticini) represent one of the most diverse groups within the family Chrysomelidae and are associated with more than 100 different plant families. Conspicuously, only 10 genera account for about a quarter of flea beetle diversity, whereas about 380 genera each comprise less than 10 species, indicating different rates of diversification within the Alticini. Here, we reconstructed the phylogenetic relationships of 608 species in 101 Alticini genera using mitogenomes and cytochrome oxidase I, and applied several frameworks of clade-specific diversification rate analyses. Increased diversification rates were consistently detected in the cosmopolitan genera Altica Goffroy, Longitarsus Berthold, and Phyllotreta Chevrolat, and in neotropical taxa of the subtribe Oedionychina. In addition, we tested whether the evolution of specialized interactions with plants of the order Brassicales influenced the diversification of Phyllotreta and Psylliodes Berthold flea beetles. Specialization on Brassicales was only associated with increased diversification rates in Phyllotreta but not in Psylliodes. Our results indicate that host associations per se do not explain different diversification rates and lay the groundwork for investigating the evolutionary drivers of rapid radiations in Alticini.
{"title":"Jumping to new hosts: the diversification of flea beetles (Coleoptera: Chrysomelidae: Alticini) in the context of their host plant associations","authors":"Harald Letsch, Franziska Beran","doi":"10.1093/isd/ixad019","DOIUrl":"https://doi.org/10.1093/isd/ixad019","url":null,"abstract":"Abstract Flea beetles (Alticini) represent one of the most diverse groups within the family Chrysomelidae and are associated with more than 100 different plant families. Conspicuously, only 10 genera account for about a quarter of flea beetle diversity, whereas about 380 genera each comprise less than 10 species, indicating different rates of diversification within the Alticini. Here, we reconstructed the phylogenetic relationships of 608 species in 101 Alticini genera using mitogenomes and cytochrome oxidase I, and applied several frameworks of clade-specific diversification rate analyses. Increased diversification rates were consistently detected in the cosmopolitan genera Altica Goffroy, Longitarsus Berthold, and Phyllotreta Chevrolat, and in neotropical taxa of the subtribe Oedionychina. In addition, we tested whether the evolution of specialized interactions with plants of the order Brassicales influenced the diversification of Phyllotreta and Psylliodes Berthold flea beetles. Specialization on Brassicales was only associated with increased diversification rates in Phyllotreta but not in Psylliodes. Our results indicate that host associations per se do not explain different diversification rates and lay the groundwork for investigating the evolutionary drivers of rapid radiations in Alticini.","PeriodicalId":48498,"journal":{"name":"Insect Systematics and Diversity","volume":"91 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135346621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jacob A Gorneau, Sarah C Crews, Franklyn Cala-Riquelme, Katherine O Montana, Joseph C Spagna, Francesco Ballarin, Lina M Almeida-Silva, Lauren A Esposito
Abstract Relationships among spider families that lack support through other lines of evidence (e.g., morphology) have recently been uncovered through molecular phylogenetics. One such group is the “marronoid” clade, which contains about 3,400 described species in 9 families. Marronoids run the gamut of life history strategies, with social species, species producing a variety of silk types, and species occurring in a range of extreme environments. Despite recognition of the ecological variability in the group, there remains uncertainty about family- level relationships, leaving diverse ecologies without an evolutionary context. The phylogenies produced to date have relatively low nodal support, there are few defined morphological synapomorphies, and the internal relationships of many families remain unclear. We use 93 exemplars from all marronoid families and ultraconserved element loci captured in silico from a combination of 48 novel low-coverage whole genomes and genomic data from the Sequence Read Archive (SRA) to produce a 50% occupancy matrix of 1,277 loci from a set of ultraconserved element probes. These loci were used to infer a phylogeny of the marronoid clade and to evaluate the familial relationships within the clade, and were combined with single-locus (Sanger) legacy data to further increase taxonomic sampling. Our results indicate a clearly defined and well-supported marronoid clade and provide evidence for both monophyly and paraphyly within the currently defined families of the clade. We propose taxonomic changes in accordance with the resulting phylogenetic hypothesis, including elevating Cicurinidae (restored status) and Macrobunidae (new rank).
{"title":"Webs of intrigue: museum genomics elucidate relationships of the marronoid spider clade (Araneae)","authors":"Jacob A Gorneau, Sarah C Crews, Franklyn Cala-Riquelme, Katherine O Montana, Joseph C Spagna, Francesco Ballarin, Lina M Almeida-Silva, Lauren A Esposito","doi":"10.1093/isd/ixad021","DOIUrl":"https://doi.org/10.1093/isd/ixad021","url":null,"abstract":"Abstract Relationships among spider families that lack support through other lines of evidence (e.g., morphology) have recently been uncovered through molecular phylogenetics. One such group is the “marronoid” clade, which contains about 3,400 described species in 9 families. Marronoids run the gamut of life history strategies, with social species, species producing a variety of silk types, and species occurring in a range of extreme environments. Despite recognition of the ecological variability in the group, there remains uncertainty about family- level relationships, leaving diverse ecologies without an evolutionary context. The phylogenies produced to date have relatively low nodal support, there are few defined morphological synapomorphies, and the internal relationships of many families remain unclear. We use 93 exemplars from all marronoid families and ultraconserved element loci captured in silico from a combination of 48 novel low-coverage whole genomes and genomic data from the Sequence Read Archive (SRA) to produce a 50% occupancy matrix of 1,277 loci from a set of ultraconserved element probes. These loci were used to infer a phylogeny of the marronoid clade and to evaluate the familial relationships within the clade, and were combined with single-locus (Sanger) legacy data to further increase taxonomic sampling. Our results indicate a clearly defined and well-supported marronoid clade and provide evidence for both monophyly and paraphyly within the currently defined families of the clade. We propose taxonomic changes in accordance with the resulting phylogenetic hypothesis, including elevating Cicurinidae (restored status) and Macrobunidae (new rank).","PeriodicalId":48498,"journal":{"name":"Insect Systematics and Diversity","volume":"24 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135736989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Antoine Guiguet, John F Tooker, Andrew R Deans, István Mikó, Gang Ning, Szabina Schwéger, Heather M Hines
Abstract Many herbivorous insect species are capable of hijacking plant development to induce novel plant organs called galls. In most groups of galling insects, the insect organs and molecular signals involved in gall induction are poorly understood. We focused on gall wasps (Hymenoptera:Cynipidae), the second largest clade of gall inducers (~1,400 spp.), for which the developmental stages and organs responsible for gall development are unclear. We investigated the female metasomal anatomy of 69 gall-inducing and 29 non-gall-inducing species across each of the major lineages of Cynipoidea, to test relationships between this lifestyle and the relative size of secretory organs. We confirmed that the venom apparatus in gall-inducing species is greatly expanded, although gall-inducing lineages vary in the relative size of these glands. Among these gallers, we measured the largest venom gland apparatus relative to body size ever recorded in insects. Non-galling inquiline species are accompanied by a reduction of this apparatus. Comparative microscopic analysis of venom glands suggests varying venom gland content across the lineages. Some oak gallers also had enlarged accessory glands, a lipid-rich organ whose function remains unclear, and which has not been previously studied in relation to gall formation. Together, the massive expansion of secretory organs specifically in gall-inducing species suggests a role of these secretions in the process of gall formation, and the variance in size of venom glands, accessory glands, and the contents of these glands among gallers, suggests that gall formation across this clade is likely to employ a diversity of molecular strategies.
{"title":"Comparative anatomy of venom glands suggests a role of maternal secretions in gall induction by cynipid wasps (Hymenoptera: Cynipidae)","authors":"Antoine Guiguet, John F Tooker, Andrew R Deans, István Mikó, Gang Ning, Szabina Schwéger, Heather M Hines","doi":"10.1093/isd/ixad022","DOIUrl":"https://doi.org/10.1093/isd/ixad022","url":null,"abstract":"Abstract Many herbivorous insect species are capable of hijacking plant development to induce novel plant organs called galls. In most groups of galling insects, the insect organs and molecular signals involved in gall induction are poorly understood. We focused on gall wasps (Hymenoptera:Cynipidae), the second largest clade of gall inducers (~1,400 spp.), for which the developmental stages and organs responsible for gall development are unclear. We investigated the female metasomal anatomy of 69 gall-inducing and 29 non-gall-inducing species across each of the major lineages of Cynipoidea, to test relationships between this lifestyle and the relative size of secretory organs. We confirmed that the venom apparatus in gall-inducing species is greatly expanded, although gall-inducing lineages vary in the relative size of these glands. Among these gallers, we measured the largest venom gland apparatus relative to body size ever recorded in insects. Non-galling inquiline species are accompanied by a reduction of this apparatus. Comparative microscopic analysis of venom glands suggests varying venom gland content across the lineages. Some oak gallers also had enlarged accessory glands, a lipid-rich organ whose function remains unclear, and which has not been previously studied in relation to gall formation. Together, the massive expansion of secretory organs specifically in gall-inducing species suggests a role of these secretions in the process of gall formation, and the variance in size of venom glands, accessory glands, and the contents of these glands among gallers, suggests that gall formation across this clade is likely to employ a diversity of molecular strategies.","PeriodicalId":48498,"journal":{"name":"Insect Systematics and Diversity","volume":"7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135688623","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Grey T Gustafson, Rachel D Glynn, Andrew E Z Short, Sergei Tarasov, Nicole L Gunter
Abstract Tailoring ultraconserved element (UCE) probe set design to focal taxa has been demonstrated to improve locus recovery and phylogenomic inference. However, beyond conducting expensive in vitro testing, it remains unclear how best to determine whether an existing UCE probe set is likely to suffice for phylogenomic inference or whether tailored probe design will be desirable. Here we investigate the utility of 8 different UCE probe sets for the in silico phylogenomic inference of scarabaeoid beetles. Probe sets tested differed in terms of (i) how phylogenetically distant from Scarabaeoidea taxa those used during probe design are, (ii) breadth of phylogenetic inference probe set was designed for, and (iii) method of probe design. As part of this study, 2 new UCE probe sets are produced for the beetle family Scarabaeidae and superfamily Hydrophiloidea. We confirm that probe set utility decreases with increasing phylogenetic distance from target taxa. In addition, narrowing the phylogenetic breadth of probe design decreases the phylogenetic capture range. We also confirm previous findings regarding ways to optimize UCE probe design. Finally, we make suggestions regarding assessment of need for de novo probe design.
{"title":"To design, or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe design","authors":"Grey T Gustafson, Rachel D Glynn, Andrew E Z Short, Sergei Tarasov, Nicole L Gunter","doi":"10.1093/isd/ixad014","DOIUrl":"https://doi.org/10.1093/isd/ixad014","url":null,"abstract":"Abstract Tailoring ultraconserved element (UCE) probe set design to focal taxa has been demonstrated to improve locus recovery and phylogenomic inference. However, beyond conducting expensive in vitro testing, it remains unclear how best to determine whether an existing UCE probe set is likely to suffice for phylogenomic inference or whether tailored probe design will be desirable. Here we investigate the utility of 8 different UCE probe sets for the in silico phylogenomic inference of scarabaeoid beetles. Probe sets tested differed in terms of (i) how phylogenetically distant from Scarabaeoidea taxa those used during probe design are, (ii) breadth of phylogenetic inference probe set was designed for, and (iii) method of probe design. As part of this study, 2 new UCE probe sets are produced for the beetle family Scarabaeidae and superfamily Hydrophiloidea. We confirm that probe set utility decreases with increasing phylogenetic distance from target taxa. In addition, narrowing the phylogenetic breadth of probe design decreases the phylogenetic capture range. We also confirm previous findings regarding ways to optimize UCE probe design. Finally, we make suggestions regarding assessment of need for de novo probe design.","PeriodicalId":48498,"journal":{"name":"Insect Systematics and Diversity","volume":"10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136184761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kali Swichtenberg, M. Kamiński, Olivia M. Gearner, R. Lumen, K. Kanda, A. Smith
The darkling beetle tribe Adesmiini (Tenebrionidae: Pimeliinae) is a prominent part of African and western Palearctic desert faunas, with most species being day-active fast-running detritivores. Taxonomic diversity within the tribe is highest in the southern Afrotropical realm (where all genera are present); only 1 genus, the species-rich Adesmia, occurs north of the Sahara. Despite notable species, such as the fog-basking beetle Onymacris unguicularis (a focal taxon in desert ecological research), Adesmiini has undergone few modern taxonomic or phylogenetic studies. Hence, generic concepts and pronounced diurnal activity, rare in the primarily nocturnal family Tenebrionidae, remain poorly explored. To investigate evolutionary relationships and diurnal origins within the tribe, we generated a genomic dataset of 529 protein-coding genes across 43 species spanning 10 of 11 Adesmiini genera. Our resulting phylogeny for the tribe rejects the monophyly of 5 currently recognized Adesmiini genera (i.e., Adesmia, Metriopus, Onymacris, Physadesmia, and Stenocara). Ancestral state reconstruction of diurnal activity using eye shape as a proxy supports the hypothesis that Adesmiini were primitively diurnal, followed by at least 4 shifts to nocturnal or crepuscular activity.
{"title":"Preliminary phylogenomic analyses reveal multiple reversions to nocturnal behavior and morphology within the primarily diurnal tribe Adesmiini (Coleoptera: Tenebrionidae)","authors":"Kali Swichtenberg, M. Kamiński, Olivia M. Gearner, R. Lumen, K. Kanda, A. Smith","doi":"10.1093/isd/ixad013","DOIUrl":"https://doi.org/10.1093/isd/ixad013","url":null,"abstract":"\u0000 The darkling beetle tribe Adesmiini (Tenebrionidae: Pimeliinae) is a prominent part of African and western Palearctic desert faunas, with most species being day-active fast-running detritivores. Taxonomic diversity within the tribe is highest in the southern Afrotropical realm (where all genera are present); only 1 genus, the species-rich Adesmia, occurs north of the Sahara. Despite notable species, such as the fog-basking beetle Onymacris unguicularis (a focal taxon in desert ecological research), Adesmiini has undergone few modern taxonomic or phylogenetic studies. Hence, generic concepts and pronounced diurnal activity, rare in the primarily nocturnal family Tenebrionidae, remain poorly explored. To investigate evolutionary relationships and diurnal origins within the tribe, we generated a genomic dataset of 529 protein-coding genes across 43 species spanning 10 of 11 Adesmiini genera. Our resulting phylogeny for the tribe rejects the monophyly of 5 currently recognized Adesmiini genera (i.e., Adesmia, Metriopus, Onymacris, Physadesmia, and Stenocara). Ancestral state reconstruction of diurnal activity using eye shape as a proxy supports the hypothesis that Adesmiini were primitively diurnal, followed by at least 4 shifts to nocturnal or crepuscular activity.","PeriodicalId":48498,"journal":{"name":"Insect Systematics and Diversity","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48260656","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lan-Wei Yeh, Hsin-Ping Ko, P. Yang, Kwok-Ching Wong, T. Sota, Chung‐Ping Lin
The endangered endemic ground beetle, Carabus nankotaizanus Kano, 1932 (Coleoptera: Carabidae), consists of 4 subspecies distributed across the lowlands to mountain forests of Taiwan. However, continuous morphological variation among the subspecies and large altitudinal range gaps between lowland and mountain populations of C. nankotaizanus raise questions concerning its species boundaries. We assessed the species boundaries between lowland and mountain populations of C. nankotaizanus using an integrative approach combining morphological, molecular, life-history, and ecological traits. Future suitable habitats were predicted using ecological niche models to evaluate the effect of range shifts driven by climate warming. The analyses of morphological and ecological traits indicate that the lowland and mountain populations of C. nankotaizanus are 2 distinct phenetic and ecological species. The molecular phylogeny further supported 4 divergent groups (paraphyletic C. nankotaizanus sp. 1 of the northern lowland + monophyletic C. nankotaizanus sp. 2 of the northern mountain, paraphyletic C. nankotaizanus sp. 3 of the southeastern lowland + monophyletic C. nankotaizanus sp. 4 of the mountain groups). We recommend the designation of the 4 cryptic C. nankotaizanus as candidate species and officially protected evolutionary lineages. Future range shifts of C. nankotaizanus sp. 1 to higher latitudinal lowlands of northern Taiwan may pose significant challenges to its conservation due to urban development and island boundary. By contrast, upcoming range shifts of the mountain C. nankotaizanus species to higher altitudes of protected national parks and forest reserves in the Central Mountain Range may not represent a major threat to its survival.
{"title":"Integrative systematics and conservation of endangered Carabus nankotaizanus (Coleoptera: Carabidae) in Taiwan","authors":"Lan-Wei Yeh, Hsin-Ping Ko, P. Yang, Kwok-Ching Wong, T. Sota, Chung‐Ping Lin","doi":"10.1093/isd/ixad016","DOIUrl":"https://doi.org/10.1093/isd/ixad016","url":null,"abstract":"\u0000 The endangered endemic ground beetle, Carabus nankotaizanus Kano, 1932 (Coleoptera: Carabidae), consists of 4 subspecies distributed across the lowlands to mountain forests of Taiwan. However, continuous morphological variation among the subspecies and large altitudinal range gaps between lowland and mountain populations of C. nankotaizanus raise questions concerning its species boundaries. We assessed the species boundaries between lowland and mountain populations of C. nankotaizanus using an integrative approach combining morphological, molecular, life-history, and ecological traits. Future suitable habitats were predicted using ecological niche models to evaluate the effect of range shifts driven by climate warming. The analyses of morphological and ecological traits indicate that the lowland and mountain populations of C. nankotaizanus are 2 distinct phenetic and ecological species. The molecular phylogeny further supported 4 divergent groups (paraphyletic C. nankotaizanus sp. 1 of the northern lowland + monophyletic C. nankotaizanus sp. 2 of the northern mountain, paraphyletic C. nankotaizanus sp. 3 of the southeastern lowland + monophyletic C. nankotaizanus sp. 4 of the mountain groups). We recommend the designation of the 4 cryptic C. nankotaizanus as candidate species and officially protected evolutionary lineages. Future range shifts of C. nankotaizanus sp. 1 to higher latitudinal lowlands of northern Taiwan may pose significant challenges to its conservation due to urban development and island boundary. By contrast, upcoming range shifts of the mountain C. nankotaizanus species to higher altitudes of protected national parks and forest reserves in the Central Mountain Range may not represent a major threat to its survival.","PeriodicalId":48498,"journal":{"name":"Insect Systematics and Diversity","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45456719","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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