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Jason E. Bond - One of the best experts on this subject based on the ideXlab platform.
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Phylogenetic Systematics and Evolution of the Spider Infraorder Mygalomorphae Using Genomic Scale Data
Systematic biology, 2019Co-Authors: Vera Opatova, Chris A Hamilton, Marshal Hedin, Laura Montes De Oca, Jiří Král, Jason E. BondAbstract:The infraorder Mygalomorphae is one of the three main lineages of spiders comprising over 3000 nominal species. This ancient group has a worldwide distribution that includes among its ranks large and charismatic taxa such as tarantulas, trapdoor spiders, and highly venomous funnel-web spiders. Based on past molecular studies using Sanger-sequencing approaches, numerous mygalomorph families (e.g., Hexathelidae, Ctenizidae, Cyrtaucheniidae, Dipluridae, and Nemesiidae) have been identified as non-monophyletic. However, these data were unable to sufficiently resolve the higher-level (intra- and interfamilial) relationships such that the necessary changes in classification could be made with confidence. Here, we present a comprehensive phylogenomic treatment of the spider infraorder Mygalomorphae. We employ 472 loci obtained through anchored hybrid enrichment to reconstruct relationships among all the mygalomorph spider families and estimate the timeframe of their diversification. We sampled nearly all currently recognized families, which has allowed us to assess their status, and as a result, propose a new classification scheme. Our generic-level sampling has also provided an evolutionary framework for revisiting questions regarding silk use in mygalomorph spiders. The first such analysis for the group within a strict phylogenetic framework shows that a sheet web is likely the plesiomorphic condition for mygalomorphs, as well as providing insights to the ancestral foraging behavior for all spiders. Our divergence time estimates, concomitant with detailed biogeographic analysis, suggest that both ancient continental-level vicariance and more recent dispersal events have played an important role in shaping modern day distributional patterns. Based on our results, we relimit the generic composition of the Ctenizidae, Cyrtaucheniidae, Dipluridae, and Nemesiidae. We also elevate five subfamilies to family rank: Anamidae (NEW RANK), Euagridae (NEW RANK), Ischnothelidae (NEW RANK), Pycnothelidae (NEW RANK), and Bemmeridae (NEW RANK). Three families Entypesidae (NEW FAMILY), Microhexuridae (NEW FAMILY), and Stasimopidae (NEW FAMILY), and one subfamily Australothelinae (NEW SUBFAMILY) are newly proposed. Such a major rearrangement in classification, recognizing nine newly established family-level rank taxa, is the largest the group has seen in over three decades. [Biogeography; molecular clocks; phylogenomics; spider web foraging; taxonomy.].
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A new species of Pionothele from Gobabeb, Namibia (Araneae, Mygalomorphae, Nemesiidae).
ZooKeys, 2019Co-Authors: Jason E. Bond, Trip LambAbstract:The mygalomorph spider genus Pionothele Purcell, 1902 comprises two nominal species known only from South Africa. We describe here a new species, Pionothelegobabeb sp. n., from Namibia. This new species is currently only known from a very restricted area in the Namib Desert of western Namibia.
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Phylogenetic systematics and evolution of the spider infraorder Mygalomorphae using genomic scale data
2019Co-Authors: Vera Opatova, Chris A Hamilton, Marshal Hedin, Laura Montes De Oca, Jiří Král, Jason E. BondAbstract:Abstract The Infraorder Mygalomorphae is one of the three main lineages of spiders comprising over 3,000 nominal species. This ancient group has a world-wide distribution that includes among its ranks large and charismatic taxa such as tarantulas, trapdoor spiders, and highly venomous funnel web spiders. Based on past molecular studies using Sanger-sequencing approaches, numerous mygalomorph families (e.g., Hexathelidae, Ctenizidae, Cyrtaucheniidae, Dipluridae and Nemesiidae) have been identified as non-monophyletic. However, these data were unable to sufficiently resolve the higher-level (intra- and interfamilial) relationships such that the necessary changes in classification could be made with confidence. Here we present the most comprehensive phylogenomic treatment of the spider infraorder Mygalomorphae conducted to date. We employ 472 loci obtained through Anchored Hybrid Enrichment to reconstruct relationships among all the mygalomorph spider families and estimate the timeframe of their diversification. We performed an extensive generic sampling of all currently recognized families, which has allowed us to assess their status, and as a result, propose a new classification scheme. Our generic-level sampling has also provided an evolutionary framework for revisiting questions regarding silk use in mygalomorph spiders. The first such analysis for the group within a strict phylogenetic framework shows that a sheet web is likely the plesiomorphic condition for mygalomorphs, as well as providing hints to the ancestral foraging behavior for all spiders. Our divergence time estimates, concomitant with detailed biogeographic analysis, suggest that both ancient continental-level vicariance and more recent dispersal events have played an important role in shaping modern day distributional patterns. Based on our results, we relimit the generic composition of the Ctenizidae, Cyrtaucheniidae, Dipluridae and Nemesiidae. We also elevate five subfamilies to family rank: Anamidae (NEW RANK), Euagridae (NEW RANK), Ischnothelidae (NEW RANK), Pycnothelidae (NEW RANK), and Bemmeridae (NEW RANK). The three families Hermachidae (NEW FAMILY), Microhexuridae (NEW FAMILY), and Stasimopidae (NEW FAMILY) are newly proposed. Such a major rearrangement in classification, recognizing eight newly established family-level rank taxa, is the largest the group has seen in over three decades since Raven’s (1985) taxonomic treatment.
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Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life
BMC Evolutionary Biology, 2016Co-Authors: Chris A Hamilton, Alan R. Lemmon, Emily Moriarty Lemmon, Jason E. BondAbstract:Background Despite considerable effort, progress in spider molecular systematics has lagged behind many other comparable arthropod groups, thereby hindering family-level resolution, classification, and testing of important macroevolutionary hypotheses. Recently, alternative targeted sequence capture techniques have provided molecular systematics a powerful tool for resolving relationships across the Tree of Life. One of these approaches, Anchored Hybrid Enrichment (AHE), is designed to recover hundreds of unique orthologous loci from across the genome, for resolving both shallow and deep-scale evolutionary relationships within non-model systems. Herein we present a modification of the AHE approach that expands its use for application in spiders, with a particular emphasis on the infraorder Mygalomorphae. Results Our aim was to design a set of probes that effectively capture loci informative at a diversity of phylogenetic timescales. Following identification of putative arthropod-wide loci, we utilized homologous transcriptome sequences from 17 species across all spiders to identify exon boundaries. Conserved regions with variable flanking regions were then sought across the tick genome, three published araneomorph spider genomes, and raw genomic reads of two mygalomorph taxa. Following development of the 585 target loci in the Spider Probe Kit, we applied AHE across three taxonomic depths to evaluate performance: deep-level spider family relationships (33 taxa, 327 loci); family and generic relationships within the mygalomorph family Euctenizidae (25 taxa, 403 loci); and species relationships in the North American tarantula genus Aphonopelma (83 taxa, 581 loci). At the deepest level, all three major spider lineages (the Mesothelae, Mygalomorphae, and Araneomorphae) were supported with high bootstrap support. Strong support was also found throughout the Euctenizidae, including generic relationships within the family and species relationships within the genus Aptostichus . As in the Euctenizidae, virtually identical topologies were inferred with high support throughout Aphonopelma . Conclusions The Spider Probe Kit, the first implementation of AHE methodology in Class Arachnida, holds great promise for gathering the types and quantities of molecular data needed to accelerate an understanding of the spider Tree of Life by providing a mechanism whereby different researchers can confidently and effectively use the same loci for independent projects, yet allowing synthesis of data across independent research groups.
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Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life
BMC evolutionary biology, 2016Co-Authors: Chris A Hamilton, Alan R. Lemmon, Emily Moriarty Lemmon, Jason E. BondAbstract:Despite considerable effort, progress in spider molecular systematics has lagged behind many other comparable arthropod groups, thereby hindering family-level resolution, classification, and testing of important macroevolutionary hypotheses. Recently, alternative targeted sequence capture techniques have provided molecular systematics a powerful tool for resolving relationships across the Tree of Life. One of these approaches, Anchored Hybrid Enrichment (AHE), is designed to recover hundreds of unique orthologous loci from across the genome, for resolving both shallow and deep-scale evolutionary relationships within non-model systems. Herein we present a modification of the AHE approach that expands its use for application in spiders, with a particular emphasis on the infraorder Mygalomorphae. Our aim was to design a set of probes that effectively capture loci informative at a diversity of phylogenetic timescales. Following identification of putative arthropod-wide loci, we utilized homologous transcriptome sequences from 17 species across all spiders to identify exon boundaries. Conserved regions with variable flanking regions were then sought across the tick genome, three published araneomorph spider genomes, and raw genomic reads of two mygalomorph taxa. Following development of the 585 target loci in the Spider Probe Kit, we applied AHE across three taxonomic depths to evaluate performance: deep-level spider family relationships (33 taxa, 327 loci); family and generic relationships within the mygalomorph family Euctenizidae (25 taxa, 403 loci); and species relationships in the North American tarantula genus Aphonopelma (83 taxa, 581 loci). At the deepest level, all three major spider lineages (the Mesothelae, Mygalomorphae, and Araneomorphae) were supported with high bootstrap support. Strong support was also found throughout the Euctenizidae, including generic relationships within the family and species relationships within the genus Aptostichus. As in the Euctenizidae, virtually identical topologies were inferred with high support throughout Aphonopelma. The Spider Probe Kit, the first implementation of AHE methodology in Class Arachnida, holds great promise for gathering the types and quantities of molecular data needed to accelerate an understanding of the spider Tree of Life by providing a mechanism whereby different researchers can confidently and effectively use the same loci for independent projects, yet allowing synthesis of data across independent research groups.
Fernando Pérez-miles - One of the best experts on this subject based on the ideXlab platform.
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The first Paratropididae (Araneae, Mygalomorphae) from Colombia: new genus, species and records.
ZooKeys, 2019Co-Authors: Carlos Perafán, William Galvis, Fernando Pérez-milesAbstract:The family of mygalomorph spiders Paratropididae Simon, 1889 is here reported for the first time for Colombia, where it is represented by three genera (Anisaspis, Paratropis, Stormtropisgen. n.) and eight species. One genus, Stormtropis, and six species constitute new taxa that are here diagnosed, described and illustrated. The geographical distribution of Paratropispapilligera FO Pickard-Cambridge, 1896 and Paratropiselicioi Duperre, 2015 are also redescribed and expanded on the basis of new material examined. The diagnosis of the subfamily Paratropidinae, Paratropis Simon, 1889 and Anisaspis Simon, 1892 are emended including the variations of the new species. Likewise, a geographic distribution map for the entire family and a taxonomic key for the males of Paratropidinae are included. Other biogeographic, morphological, and taxonomic aspects are discussed.
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Behavior and Biology of Mygalomorphae
Behaviour and Ecology of Spiders, 2017Co-Authors: Fernando Pérez-miles, Carlos PerafánAbstract:The infraorder Mygalomorphae comprises almost 3000 species. It is widely distributed all over the world, and about one third of the species included in this infraorder is represented in the Neotropics. The knowledge on several aspects of the biology of Mygalomorphae is relatively scarce in comparison with the Araneomorphae. However, recent studies developed all over the world, but especially in the Neotropical region, are continuously contributing to add information on foraging strategies, communication, reproductive biology, habitat selection, and defenses against natural enemies, minimizing the differences in the status of knowledge between these groups. In this chapter, we review some the main topics on Mygalomorphae biology, including behavior and ecology.
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A comparative morphological study of the epiandrous apparatus in mygalomorph spiders (Araneae, Mygalomorphae)
Micron (Oxford England : 1993), 2016Co-Authors: Nelson Ferretti, Sofía Copperi, Gabriel Pompozzi, Alda González, A. Wehitt, E. Galíndez, Fernando Pérez-milesAbstract:Many adult male spiders have silk glands which are not associated with the spinnerets. They occur on the anterior margin of the genital furrow and are used during the building of the sperm web and sperm droplet induction. These epiandrous glands exit the body through ducts which lead to specialized spigots. In the taxon Mygalomorphae, the presence of epiandrous spigots is just reported for a couple of species but their morphology has not been investigated. In this paper we provide a detailed study of the ultrastructure morphology of eighteen species belonging to eight families using light and scanning electron microscopy (SEM). We describe and present images of the epiandrous spigots above the genital opening. Also, we compare the morphology of spigots between families and describe the epiandrous glands through histology.
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On Munduruku, a new Theraphosid genus from Oriental Amazonia (Araneae, Mygalomorphae)
Iheringia. Série Zoologia, 2013Co-Authors: Laura T. Miglio, Alexandre B. Bonaldo, Fernando Pérez-milesAbstract:Munduruku gen. nov. is proposed for the type species Munduruku bicoloratum sp. nov., from Juruti and Santarem, Para, Brazil. The main diagnostic character of Munduruku gen. nov. is the presence of a subapical, lanceolate keel on the male palpal bulb, which is unique among the basal taxa of Theraphosinae with type III-IV urticating setae. The female spermathecae consist of two spheroid receptacles with funnel-shaped necks, each of which bears a sclerotized area. In both sexes, the abdomen is remarkably patterned, an uncommon feature in adults of New World theraphosids. Both the bulbus lanceolate keel and the abdominal color pattern are hypothesized as synapomorphies of the genus.
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Historical biogeography of mygalomorph spiders from the peripampasic orogenic arc based on track analysis and PAE as a panbiogeographical tool
Systematics and Biodiversity, 2012Co-Authors: Nelson Ferretti, Alda González, Fernando Pérez-milesAbstract:A panbiogeographical analysis of Mygalomorphae spiders was undertaken in order to determine generalized tracks and biogeographical nodes in the peripampasic orogenic arc. This arc comprises mountainous systems that harbour a high number of endemic species, while they exhibit biotic connections that have become fragmented probably during Tertiary tectonics. They are considered relevant areas for biodiversity conservation. A total of 1078 records of 51 Mygalomorphae species were analysed and ten areas were delimited based on geological data. We used track analysis and parsimony analysis of endemicity as a panbiogeographical tool. Five generalized tracks and three nodes were recovered. The tracks recovered in Argentina could be explained as a consequence of two events: (i) Atlantic marine transgressions during the Middle and Late Miocene; and (ii) changes in the climate of southern South America from the Miocene to Pliocene, caused by the gradual raising of the Andean chain and also, the additional uplift of...
Nelson Ferretti - One of the best experts on this subject based on the ideXlab platform.
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A comparative morphological study of the epiandrous apparatus in mygalomorph spiders (Araneae, Mygalomorphae)
Micron (Oxford England : 1993), 2016Co-Authors: Nelson Ferretti, Sofía Copperi, Gabriel Pompozzi, Alda González, A. Wehitt, E. Galíndez, Fernando Pérez-milesAbstract:Many adult male spiders have silk glands which are not associated with the spinnerets. They occur on the anterior margin of the genital furrow and are used during the building of the sperm web and sperm droplet induction. These epiandrous glands exit the body through ducts which lead to specialized spigots. In the taxon Mygalomorphae, the presence of epiandrous spigots is just reported for a couple of species but their morphology has not been investigated. In this paper we provide a detailed study of the ultrastructure morphology of eighteen species belonging to eight families using light and scanning electron microscopy (SEM). We describe and present images of the epiandrous spigots above the genital opening. Also, we compare the morphology of spigots between families and describe the epiandrous glands through histology.
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Turkish Journal of Zoology Turk J Zool
2016Co-Authors: Nelson Ferretti, Sofía Copperi, Gabriel PompozziAbstract:doi:10.3906/zoo-1304-47 Fight or flight: agonistic interactions between females of Acanthogonatus centralis Goloboff 1995 (Araneae, Mygalomorphae
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la comunidad de aranas Mygalomorphae araneae de la reserva natural sierra del tigre tandilia buenos aires argentina
Revista Mexicana De Biodiversidad, 2014Co-Authors: Nelson Ferretti, Sofía Copperi, Gabriel Pompozzi, Alda González, Leonela Schwerdt, Fernando PerezmilesAbstract:We documented the specific richness, abundance and activity of the Mygalomorph spider community in the Natural Reserve Sierra del Tigre, Buenos Aires, Argentina. This hilly ecosystem is home for many endemic species and rich in native fauna and flora. Spider abundance was sampled monthly from May 2011 - May 2012 by hand capture and pitfall traps. The species recorded in the study area were Actinopus sp. 1 (Actinopodidae), Grammostola vachoni Schiapelli y Gerschman, 1960; Plesiopelma longisternale Schiapelli y Gerschman, 1942 and Catumiri argentinense (Mello-Leitao, 1941) (Theraphosidae). Grammostola vachoni was the dominant species in hand capture and Actinopus sp. 1 in pitfall traps. The seasonal variation, diversity, and abundance of the mygalomorph community are analyzed and discussed here. The Mygalomorphae of the Tandilia system comprises an important group of sedentary and cryptozoic spiders that seem to be dependent on habitat type and environmental factors.
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Fight or flight: agonistic interactions between females of Acanthogonatus centralis Goloboff 1995 (Araneae, Mygalomorphae)
TURKISH JOURNAL OF ZOOLOGY, 2014Co-Authors: Nelson Ferretti, Sofía Copperi, Gabriel PompozziAbstract:doi:10.3906/zoo-1304-47 Fight or flight: agonistic interactions between females of Acanthogonatus centralis Goloboff 1995 (Araneae, Mygalomorphae
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Historical biogeography of mygalomorph spiders from the peripampasic orogenic arc based on track analysis and PAE as a panbiogeographical tool
Systematics and Biodiversity, 2012Co-Authors: Nelson Ferretti, Alda González, Fernando Pérez-milesAbstract:A panbiogeographical analysis of Mygalomorphae spiders was undertaken in order to determine generalized tracks and biogeographical nodes in the peripampasic orogenic arc. This arc comprises mountainous systems that harbour a high number of endemic species, while they exhibit biotic connections that have become fragmented probably during Tertiary tectonics. They are considered relevant areas for biodiversity conservation. A total of 1078 records of 51 Mygalomorphae species were analysed and ten areas were delimited based on geological data. We used track analysis and parsimony analysis of endemicity as a panbiogeographical tool. Five generalized tracks and three nodes were recovered. The tracks recovered in Argentina could be explained as a consequence of two events: (i) Atlantic marine transgressions during the Middle and Late Miocene; and (ii) changes in the climate of southern South America from the Miocene to Pliocene, caused by the gradual raising of the Andean chain and also, the additional uplift of...
Chris A Hamilton - One of the best experts on this subject based on the ideXlab platform.
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Phylogenetic Systematics and Evolution of the Spider Infraorder Mygalomorphae Using Genomic Scale Data
Systematic biology, 2019Co-Authors: Vera Opatova, Chris A Hamilton, Marshal Hedin, Laura Montes De Oca, Jiří Král, Jason E. BondAbstract:The infraorder Mygalomorphae is one of the three main lineages of spiders comprising over 3000 nominal species. This ancient group has a worldwide distribution that includes among its ranks large and charismatic taxa such as tarantulas, trapdoor spiders, and highly venomous funnel-web spiders. Based on past molecular studies using Sanger-sequencing approaches, numerous mygalomorph families (e.g., Hexathelidae, Ctenizidae, Cyrtaucheniidae, Dipluridae, and Nemesiidae) have been identified as non-monophyletic. However, these data were unable to sufficiently resolve the higher-level (intra- and interfamilial) relationships such that the necessary changes in classification could be made with confidence. Here, we present a comprehensive phylogenomic treatment of the spider infraorder Mygalomorphae. We employ 472 loci obtained through anchored hybrid enrichment to reconstruct relationships among all the mygalomorph spider families and estimate the timeframe of their diversification. We sampled nearly all currently recognized families, which has allowed us to assess their status, and as a result, propose a new classification scheme. Our generic-level sampling has also provided an evolutionary framework for revisiting questions regarding silk use in mygalomorph spiders. The first such analysis for the group within a strict phylogenetic framework shows that a sheet web is likely the plesiomorphic condition for mygalomorphs, as well as providing insights to the ancestral foraging behavior for all spiders. Our divergence time estimates, concomitant with detailed biogeographic analysis, suggest that both ancient continental-level vicariance and more recent dispersal events have played an important role in shaping modern day distributional patterns. Based on our results, we relimit the generic composition of the Ctenizidae, Cyrtaucheniidae, Dipluridae, and Nemesiidae. We also elevate five subfamilies to family rank: Anamidae (NEW RANK), Euagridae (NEW RANK), Ischnothelidae (NEW RANK), Pycnothelidae (NEW RANK), and Bemmeridae (NEW RANK). Three families Entypesidae (NEW FAMILY), Microhexuridae (NEW FAMILY), and Stasimopidae (NEW FAMILY), and one subfamily Australothelinae (NEW SUBFAMILY) are newly proposed. Such a major rearrangement in classification, recognizing nine newly established family-level rank taxa, is the largest the group has seen in over three decades. [Biogeography; molecular clocks; phylogenomics; spider web foraging; taxonomy.].
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Phylogenetic systematics and evolution of the spider infraorder Mygalomorphae using genomic scale data
2019Co-Authors: Vera Opatova, Chris A Hamilton, Marshal Hedin, Laura Montes De Oca, Jiří Král, Jason E. BondAbstract:Abstract The Infraorder Mygalomorphae is one of the three main lineages of spiders comprising over 3,000 nominal species. This ancient group has a world-wide distribution that includes among its ranks large and charismatic taxa such as tarantulas, trapdoor spiders, and highly venomous funnel web spiders. Based on past molecular studies using Sanger-sequencing approaches, numerous mygalomorph families (e.g., Hexathelidae, Ctenizidae, Cyrtaucheniidae, Dipluridae and Nemesiidae) have been identified as non-monophyletic. However, these data were unable to sufficiently resolve the higher-level (intra- and interfamilial) relationships such that the necessary changes in classification could be made with confidence. Here we present the most comprehensive phylogenomic treatment of the spider infraorder Mygalomorphae conducted to date. We employ 472 loci obtained through Anchored Hybrid Enrichment to reconstruct relationships among all the mygalomorph spider families and estimate the timeframe of their diversification. We performed an extensive generic sampling of all currently recognized families, which has allowed us to assess their status, and as a result, propose a new classification scheme. Our generic-level sampling has also provided an evolutionary framework for revisiting questions regarding silk use in mygalomorph spiders. The first such analysis for the group within a strict phylogenetic framework shows that a sheet web is likely the plesiomorphic condition for mygalomorphs, as well as providing hints to the ancestral foraging behavior for all spiders. Our divergence time estimates, concomitant with detailed biogeographic analysis, suggest that both ancient continental-level vicariance and more recent dispersal events have played an important role in shaping modern day distributional patterns. Based on our results, we relimit the generic composition of the Ctenizidae, Cyrtaucheniidae, Dipluridae and Nemesiidae. We also elevate five subfamilies to family rank: Anamidae (NEW RANK), Euagridae (NEW RANK), Ischnothelidae (NEW RANK), Pycnothelidae (NEW RANK), and Bemmeridae (NEW RANK). The three families Hermachidae (NEW FAMILY), Microhexuridae (NEW FAMILY), and Stasimopidae (NEW FAMILY) are newly proposed. Such a major rearrangement in classification, recognizing eight newly established family-level rank taxa, is the largest the group has seen in over three decades since Raven’s (1985) taxonomic treatment.
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re evaluating conservation priorities of new world tarantulas araneae theraphosidae in a molecular framework indicates non monophyly of the genera aphonopelma and brachypelma
Systematics and Biodiversity, 2018Co-Authors: Steven P Turner, Ray Gabriel, Stuart J Longhorn, Chris A Hamilton, Fernando Perezmiles, Alfried P VoglerAbstract:We present a mtDNA gene tree of tarantula spiders (Araneae: Mygalomorphae: Theraphosidae) based on the mitochondrial 16S-tRNA (leu)-ND1 gene region as a promising initial molecular hypothesis to clarify the taxonomy of the largest subfamily, Theraphosinae. Many species of this New World subfamily are traded widely as exotic pets, yet few scientific studies on them exist, and the robustness of many supposed taxonomic groupings is debatable. Yet the validity of taxon names and knowledge of their distinctiveness is vital for trade regulation, most notably for the Neotropical genus Brachypelma Simon 1891, which is listed under CITES (Appendix II, see online supplemental material, which is available from the article's Taylor & Francis Online page at https://doi.org/10.1080/14772000.2017.1346719). The use of molecular markers for tarantula taxonomy has been limited until recently, with most previous studies relying on morphological methods. Our findings, from newly collected molecular data, have several nomencl...
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Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life
BMC Evolutionary Biology, 2016Co-Authors: Chris A Hamilton, Alan R. Lemmon, Emily Moriarty Lemmon, Jason E. BondAbstract:Background Despite considerable effort, progress in spider molecular systematics has lagged behind many other comparable arthropod groups, thereby hindering family-level resolution, classification, and testing of important macroevolutionary hypotheses. Recently, alternative targeted sequence capture techniques have provided molecular systematics a powerful tool for resolving relationships across the Tree of Life. One of these approaches, Anchored Hybrid Enrichment (AHE), is designed to recover hundreds of unique orthologous loci from across the genome, for resolving both shallow and deep-scale evolutionary relationships within non-model systems. Herein we present a modification of the AHE approach that expands its use for application in spiders, with a particular emphasis on the infraorder Mygalomorphae. Results Our aim was to design a set of probes that effectively capture loci informative at a diversity of phylogenetic timescales. Following identification of putative arthropod-wide loci, we utilized homologous transcriptome sequences from 17 species across all spiders to identify exon boundaries. Conserved regions with variable flanking regions were then sought across the tick genome, three published araneomorph spider genomes, and raw genomic reads of two mygalomorph taxa. Following development of the 585 target loci in the Spider Probe Kit, we applied AHE across three taxonomic depths to evaluate performance: deep-level spider family relationships (33 taxa, 327 loci); family and generic relationships within the mygalomorph family Euctenizidae (25 taxa, 403 loci); and species relationships in the North American tarantula genus Aphonopelma (83 taxa, 581 loci). At the deepest level, all three major spider lineages (the Mesothelae, Mygalomorphae, and Araneomorphae) were supported with high bootstrap support. Strong support was also found throughout the Euctenizidae, including generic relationships within the family and species relationships within the genus Aptostichus . As in the Euctenizidae, virtually identical topologies were inferred with high support throughout Aphonopelma . Conclusions The Spider Probe Kit, the first implementation of AHE methodology in Class Arachnida, holds great promise for gathering the types and quantities of molecular data needed to accelerate an understanding of the spider Tree of Life by providing a mechanism whereby different researchers can confidently and effectively use the same loci for independent projects, yet allowing synthesis of data across independent research groups.
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Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life
BMC evolutionary biology, 2016Co-Authors: Chris A Hamilton, Alan R. Lemmon, Emily Moriarty Lemmon, Jason E. BondAbstract:Despite considerable effort, progress in spider molecular systematics has lagged behind many other comparable arthropod groups, thereby hindering family-level resolution, classification, and testing of important macroevolutionary hypotheses. Recently, alternative targeted sequence capture techniques have provided molecular systematics a powerful tool for resolving relationships across the Tree of Life. One of these approaches, Anchored Hybrid Enrichment (AHE), is designed to recover hundreds of unique orthologous loci from across the genome, for resolving both shallow and deep-scale evolutionary relationships within non-model systems. Herein we present a modification of the AHE approach that expands its use for application in spiders, with a particular emphasis on the infraorder Mygalomorphae. Our aim was to design a set of probes that effectively capture loci informative at a diversity of phylogenetic timescales. Following identification of putative arthropod-wide loci, we utilized homologous transcriptome sequences from 17 species across all spiders to identify exon boundaries. Conserved regions with variable flanking regions were then sought across the tick genome, three published araneomorph spider genomes, and raw genomic reads of two mygalomorph taxa. Following development of the 585 target loci in the Spider Probe Kit, we applied AHE across three taxonomic depths to evaluate performance: deep-level spider family relationships (33 taxa, 327 loci); family and generic relationships within the mygalomorph family Euctenizidae (25 taxa, 403 loci); and species relationships in the North American tarantula genus Aphonopelma (83 taxa, 581 loci). At the deepest level, all three major spider lineages (the Mesothelae, Mygalomorphae, and Araneomorphae) were supported with high bootstrap support. Strong support was also found throughout the Euctenizidae, including generic relationships within the family and species relationships within the genus Aptostichus. As in the Euctenizidae, virtually identical topologies were inferred with high support throughout Aphonopelma. The Spider Probe Kit, the first implementation of AHE methodology in Class Arachnida, holds great promise for gathering the types and quantities of molecular data needed to accelerate an understanding of the spider Tree of Life by providing a mechanism whereby different researchers can confidently and effectively use the same loci for independent projects, yet allowing synthesis of data across independent research groups.
Kailash Chandra - One of the best experts on this subject based on the ideXlab platform.
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the complete mitochondrial genome of endemic giant tarantula lyrognathus crotalus araneae theraphosidae and comparative analysis
Scientific Reports, 2020Co-Authors: Vikas Kumar, Kaomud Tyagi, Rajasree Chakraborty, Priya Prasad, Shantanu Kundu, Inderjeet Tyagi, Kailash ChandraAbstract:The complete mitochondrial genome of Lyrognathus crotalus is sequenced, annotated and compared with other spider mitogenomes. It is 13,865 bp long and featured by 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and a control region (CR). Most of the PCGs used ATN start codon except cox3, and nad4 with TTG. Comparative studies indicated the use of TTG, TTA, TTT, GTG, CTG, CTA as start codons by few PCGs. Most of the tRNAs were truncated and do not fold into the typical cloverleaf structure. Further, the motif (CATATA) was detected in CR of nine species including L. crotalus. The gene arrangement of L. crotalus compared with ancestral arthropod showed the transposition of five tRNAs and one tandem duplication random loss (TDRL) event. Five plesiomophic gene blocks (A-E) were identified, of which, four (A, B, D, E) retained in all taxa except family Salticidae. However, block C was retained in Mygalomorphae and two families of Araneomorphae (Hypochilidae and Pholcidae). Out of 146 derived gene boundaries in all taxa, 15 synapomorphic gene boundaries were identified. TreeREx analysis also revealed the transposition of trnI, which makes three derived boundaries and congruent with the result of the gene boundary mapping. Maximum likelihood and Bayesian inference showed similar topologies and congruent with morphology, and previously reported multi-gene phylogeny. However, the Gene-Order based phylogeny showed sister relationship of L. crotalus with two Araneomorphae family members (Hypochilidae and Pholcidae) and other Mygalomorphae species.
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The Complete Mitochondrial Genome of endemic giant tarantula, Lyrognathus crotalus (Araneae: Theraphosidae) and comparative analysis.
Scientific reports, 2020Co-Authors: Vikas Kumar, Kaomud Tyagi, Rajasree Chakraborty, Priya Prasad, Shantanu Kundu, Inderjeet Tyagi, Kailash ChandraAbstract:The complete mitochondrial genome of Lyrognathus crotalus is sequenced, annotated and compared with other spider mitogenomes. It is 13,865 bp long and featured by 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and a control region (CR). Most of the PCGs used ATN start codon except cox3, and nad4 with TTG. Comparative studies indicated the use of TTG, TTA, TTT, GTG, CTG, CTA as start codons by few PCGs. Most of the tRNAs were truncated and do not fold into the typical cloverleaf structure. Further, the motif (CATATA) was detected in CR of nine species including L. crotalus. The gene arrangement of L. crotalus compared with ancestral arthropod showed the transposition of five tRNAs and one tandem duplication random loss (TDRL) event. Five plesiomophic gene blocks (A-E) were identified, of which, four (A, B, D, E) retained in all taxa except family Salticidae. However, block C was retained in Mygalomorphae and two families of Araneomorphae (Hypochilidae and Pholcidae). Out of 146 derived gene boundaries in all taxa, 15 synapomorphic gene boundaries were identified. TreeREx analysis also revealed the transposition of trnI, which makes three derived boundaries and congruent with the result of the gene boundary mapping. Maximum likelihood and Bayesian inference showed similar topologies and congruent with morphology, and previously reported multi-gene phylogeny. However, the Gene-Order based phylogeny showed sister relationship of L. crotalus with two Araneomorphae family members (Hypochilidae and Pholcidae) and other Mygalomorphae species.
