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An integrative taxonomy approach evaluates the limits of the widespread tarantula Plesiopelma longisternale (Araneae: Mygalomorphae: Theraphosidae) and reveals a new species from Argentina
... Yamamoto et al. (2007) transferred Plesiopelma physopus (Mello-Leitão, 1926) and Plesiopelma minensis (Mello-Leitão 1943) from Tmesiphantes Simon 1892 and Yamamoto et al. (2012) Studying the material of Plesiopelma from several sites of Uruguay deposited in the arachnological collection of the Facultad de Ciencias (FCE-My), we found some individuals from Lavalleja and Maldonado that fit with the diagnosis of the genus but differs from all known species. We collected additional material from the same sites, performed a molecular study, and included it in the phylogeny recently published by Ferretti et al. (2024). Both morphological and molecular results congruently support the presence of a new species, consequently we propose Plesiopelma arevaloae sp. ...
... Studied individuals were deposited in the arachnological collection of the Facultad de Ciencias, Montevideo, Uruguay (Curator: Dr. Miguel Simó). Description style, terms and morphological characters examined are the usually used in the standards of Theraphosidae taxonomy (Pérez-Miles, 2020) and specially used in last Plesiopelma studies (Ferretti & Barneche, 2013;Ferretti et al., 2024). All measurements are given in millimeters and were taken with an ocular micrometer and digital caliper. ...
... The PCR was performed using NZYtech Green Master Mix following their standard protocol. The PCR was performed in the SimpliAmp thermocycler (appliedbiosystems by thermo fisher scientific) and Ferretti et al. (2024) cycling conditions were followed. The PCR products were sent for purification and subsequent sequencing to the company Macrogen (South Korea), where both strands were sequenced. ...
We describe and illustrate a new tarantula species of the genus Plesiopelma from Lavalleja and Maldonado, Uruguay. Plesiopelma arevaloae sp. nov. is distinguished from other known species by morphological characters and molecular evidence.
... Compared to most mygalomorph families, theraphosid diversity is widespread with a near global, largely pan-tropical distribution. As such, tarantula systematics and taxonomy is a global endeavor with research being undertaken on species from all continents (except Antarctica): North America (Hendrixson et al., 2015;Ortiz and Francke, 2015, 2016Turner et al., 2018;Graham et al., 2020;Mendoza and Francke, 2020); South America (Peŕez-Miles and Locht, 2003;Bertani and Fukushima, 2009;Guadanucci, 2011Guadanucci, , 2014Perafań et al., 2015;Cifuentes et al., 2016;Ferretti et al., 2018;Hüsser, 2018;Nicoletta et al., 2020;Candia-Ramıŕez and Francke, 2021;Cifuentes and Bertani, 2022;Gabriel et al., 2023;Galleti-Lima et al., 2023;Kaderka et al., 2023;Sherwood et al., 2023;Ferretti et al., 2024;Peñaherrera-R et al., 2024); Europe (Korba et al., 2022); Africa , Midgley and Engelbrecht, 2019; Asia (Schmidt and von Wirth, 1996;West et al., 2012;Prasanth and Jose, 2014;Sanap & Mizra 2014;Nunn et al., 2016;Montemor et al., 2020;Sivayyapram et al., 2020;Yu et al., 2021;Songsangchote et al., 2022;Chomphuphuang et al., 2023); and Australia (Raven, 2005;Briggs et al., 2023). ...
... This trend of incorporating DNA quickly diminishes, with no new species described using DNA from 2020 to 2022. There are only a handful of studies that have incorporated molecular data into their species delimitation studies and generic revisions including: Aphonopelma (Hendrixson et al., 2013;Hamilton et al., 2011Hamilton et al., , 2014Hamilton et al., , 2016, the Australian species (Briggs et al., 2023), Bonnetina (Ortiz and Franke 2015;2016, 2017, Brachypelma Simon, 1891 (Mendoza and, Davus O.Pickard-Cambridge, 1892 (Candia-Ramí rez and Francke, 2021), Grammostola Simon, 1892(Montes de Oca et al., 2016, Ischnocolus Ausserer, 1871(Korba et al., 2022, Pamphobeteus Pocock, 1901(Cifuentes et al., 2016, Plesiopelma Pocock, 1901(Ferretti et al., 2024, Tliltocatl Mendoza and Francke, 2020 (Mendoza and Francke, 2020), Lasiocyano, Parvicarina, Tekoapora (Galleti-Lima et al., 2023), and Urupelma (Kaderka et al., 2023). ...
Systematics provides the foundational knowledge about the units of biodiversity, i.e., species, and how we classify them. The results of this discipline extend across Biology and can have important impacts on conservation. Here we review the systematic and taxonomic practices within Theraphosidae over the last 260 years. We examine the rate of newly described species and investigate the contemporary practices being used in the description of new genera and species. There have been two large waves of theraphosid taxonomy, with an explosive growth of newly described species and author combinations in the last 60 years. We look back and find that during 2010–2024 contemporary practices in theraphosid systematics and taxonomy have remained largely static, being dominated by morphology-based approaches. Over this period, only 10% of newly described species incorporated DNA data or explicitly stated the species concept used. Similarly for genera, only five of the 37 newly described genera over that time were supported as distinct and monophyletic by DNA. We highlight the taxonomic movement of species among Theraphosidae, Barychelidae, and Paratropididae; however, given the limited molecular sampling for the two latter families, the boundaries of these families remain a significant area of needed research. To promote inclusivity, we provide a copy of this paper in Spanish as supplementary material.
... The infraorder Mygalomorphae includes animals commonly known as tarantulas, trapdoor spiders, funnel-web and sheet-web weaving spiders and forms 31 families (World Spider Catalog 2024). The definition of species boundaries in mygalomorph spiders is historically based on morphological characters (Raven 1985), which can be an issue due to the homogeneous morphology and continuous variation across species; the advent of molecular analysis integrated into Mygalomorphae systematics has enabled the identification of cryptic species (Hamilton et al. 2011;Ortiz and Francke 2017;Candia-Ramírez and Francke 2021;Ferretti et al. 2024). The taxonomic placement of mygalomorph species, and even genera, turns out to be quite challenging with the use of morphological characters, due to the fact that they are often revealed as rather restrictive or subjective. ...
Spiders of the genus Aname L. Koch, 1873, commonly referred to as wishbone spiders, are a ubiquitous and extremely diverse component of the Australian mygalomorph fauna. Distributed across most of mainland Australia, and with an estimated endemic fauna in excess of 300 species, it is perhaps the world’s most diverse mygalomorph spider genus. Unsurprisingly, this group presents an enormous taxonomic challenge, with 80% or more of the fauna still undescribed, and a large proportion of species occurring in arid, semi-arid or otherwise remote parts of inland Australia. To address these shortfalls, this study represents the first in a planned series of major revisions to rapidly advance our knowledge of the Australian wishbone spiders. Here, we revise the Aname fauna of subtropical and tropical eastern Australia, applying an integrative approach of unprecedented monographic scope for a taxonomic study on Australian Mygalomorphae, bringing together morphological monography, live habitus information, burrowing biology and molecular phylogenetics resulting from extensive field work. Our expanded molecular phylogeny is augmented with 131 new barcode (COI) sequences from eastern Australian Aname species, and we provide descriptions, natural history observations and distributional data for a total of 68 eastern species. Of these, 10 represent redescriptions of previously described and valid species: A. barrema Raven, 1985, A. blackdownensis Raven, 1985, A. camara Raven, 1985, A. carina Raven, 1985, A. distincta (Rainbow, 1914), A. longitheca Raven, 1985, A. inimica Raven, 1985, A. pallida L. Koch, 1873, A. robertsorum Raven, 1985, and A. warialda Raven, 1985. Three represent species previously considered junior synonyms that have now been revalidated: A. attenuata (Rainbow & Pulleine, 1918) stat. rev., A. giraulti (Rainbow, 1914) stat. rev., and A. villosa Rainbow & Pulleine, 1918 stat. rev. One species (Aname collinsorum Raven, 1985) is now considered a junior synonym of Aname giraulti (Rainbow, 1914) syn. nov. Finally, 55 species are newly described: Aname albicula sp. nov., A. ammolithica sp. nov., A. aurantella sp. nov., A. aurensis sp. nov., A. barakula sp. nov., A. bifaceta sp. nov., A. boreovillosa sp. nov., A. braemar sp. nov., A. briggsi sp. nov., A. broadwater sp. nov., A. calida sp. nov., A. callitra sp. nov., A. cassowariensis sp. nov., A. consuelo sp. nov., A. convoluta sp. nov., A. corundaria sp. nov., A. cudmore sp. nov., A. dingo sp. nov., A. distorta sp. nov., A. eddieorum sp. nov., A. ethabuka sp. nov., A. ferruginea sp. nov., A. flexicaudula sp. nov., A. fossoria sp. nov., A. fuscochelicera sp. nov., A. gilbertensis sp. nov., A. harmoniosa sp. nov., A. hughenden sp. nov., A. inglewood sp. nov., A. insolita sp. nov., A. intermedia sp. nov., A. lambkinae sp. nov., A. lawrenceae sp. nov., A. litoralis sp. nov., A. magnifica sp. nov., A. mariala sp. nov., A. mulgana sp. nov., A. namoi sp. nov., A. nigrochelicera sp. nov., A. nigrotarsa sp. nov., A. occivillosa sp. nov., A. olkola sp. nov., A. platensis sp. nov., A. pyroensis sp. nov., A. rubrochelicera sp. nov., A. rupicola sp. nov., A. savannella sp. nov., A. savannensis sp. nov., A. scutitheca sp. nov., A. serpentina sp. nov., A. tropicana sp. nov., A. truncata sp. nov., A. vigilata sp. nov., A. viridiensis sp. nov., and A. warrego sp. nov.
Las arañas migalomorfas (infraorden Mygalomorphae) constituyen un grupo con una rica historia evolutiva, amplia variedad de modos de vida y adaptaciones ecológicas singulares, lo que las convierte en excelentes modelos de estudio. Desde 2006, hemos abordado el estudio de las migalomorfas en diferentes áreas como la taxonomía, sistemática, biogeografía, comportamiento, ecología e historia natural. Este ensayo reúne las metodologías empleadas en nuestras investigaciones, que incluyen la obtención de especímenes, trabajos de campo y la implementación de análisis cladísticos basados en caracteres morfológicos, complementados con herramientas moleculares para esclarecer relaciones evolutivas complejas. También abordamos estudios sobre biología reproductiva, comportamiento y ecología, los cuales han permitido una comprensión más profunda e integral de la relación de las migalomorfas con el entorno. Estos avances no sólo enriquecen el conocimiento sobre la biodiversidad del grupo, sino que también contribuyen a su conservación y al desarrollo de proyecciones sobre las especies conocidas y aún por descubrir. Palabras claves: metodología, araña, estudios integrativos, modelos de estudio. ABSTRACT Mygalomorph spiders (infraorder Mygalomorphae) are a group with a rich evolutionary history, a wide variety of life strategies and unique ecological adaptations, making them excellent study models. Since 2006, we have been studying mygalomorphs from different approaches, such as taxon-omy, systematic, biogeography, behavior, ecology and Weaving stories: the science behind the study of the mygalomorphs of Argentina. natural history. This essay gathers the methodologies used in our researches, including specimens collection, field work, and the implementation of cladistic analysis based on morphological features, together with molecular tools for clarifying complex evolutionary relationships. We also studied reproductive biology, behavior and ecology, for a deeper and integrative understanding of the relationship between the mygalomorph and their environment. These advances not only enrich the knowledge about the group's biodiversity but also contribute to its conservation and the development of projections of known and unknown species.
Herein, we describe three new species of the spider genus Naphrys Edwards, 2003 from Mexico: Naphrys echeri sp. nov., Naphrys tecoxquin sp. nov., and Naphrys tuuca sp. nov. An integrative taxonomic approach was applied, utilizing data from morphology, ultra-morphology, the mitochondrial gene COI, and distribution records. Four molecular methods for species delimitation were implemented under the corrected p-distance Neighbor-Joining (NJ) criteria: (1) Assemble Species by Automatic Partitioning (ASAP); (2) general mixed Yule coalescent (GMYC); (3) Bayesian Poisson tree process (bPTP); and (4) multi-rate Poisson tree process (mPTP). Both morphological and molecular data supported the delimitation and recognition of the three new species. The average interspecific genetic distance (p-distance) within the genus Naphrys is 14%, while the intraspecific genetic distances (p-distance) is <2% for most species. We demonstrate that the natural distribution of Naphrys is not restricted to the Nearctic region. Furthermore, the reported localities herein represent the first with precise locations in the country for Naphrys acerba. In addition, a taxonomic identification key is provided for the species in the genus.
The Mediterranean recluse spider, Loxosceles rufescens, has been discovered for the first time inhabiting human dwellings in Bangkok, Thailand. Expeditions across 39 localities revealed five establishments with L. rufescens populations. The highest density was recorded in a storage house on Yaowarat Road, located in the heart of Bangkok's Chinatown, where 315 individuals were found, including adults, juveniles, and spiderlings. This medically significant spider's presence in such a densely populated urban area raises concerns about potential envenomation risks. Thirteen specimens of L. rufescens were extracted for DNA and sequenced for molecular phylogenetic analyses. COI and ITS2 markers were used to investigate relationships within L. rufescens and across available Loxosceles species sequences. Results indicate COI is superior for resolving species-level genetic clusters compared to ITS2. Surprisingly, L. rufescens individuals from the same house were found in significantly distant COI lineages, suggesting mtDNA may not be suitable for studying intra-specific phylogeography in this case. Species delimitation methods ABGD and ASAP demonstrated promising results for both COI and ITS2, while bPTP and GMYC tended to overestimate species numbers. ITS2 exhibited high sequence similarity in L. rufescens, suggesting potential utility as a barcoding marker for identification of this globally distributed species. Genetic distance analyses revealed a potential barcoding gap (K2P) of 8–9 % for COI and <2 % for ITS2 in Loxosceles. This study contributes valuable sequence data for the medically important genus Loxosceles and highlights the need for integrative approaches in understanding its evolution and spread. The findings have important implications for pest management strategies and public health in urban environments.
The monophyly of Theraphosinae is supported by both morphological and molecular phylogenies. However, intergeneric relationships often show polytomies and branches with low support. A previous phylogenetic study proposed an intergeneric relationship for the subfamily based on molecular data and divided it into three tribes: Grammostolini, Hapalopini and Theraphosini. However, not all genera of Theraphosinae were sampled, and some relationships were inferred based on morphological similarities. Regarding the Hapalopini from Brazil, the relationships of some genera are still uncertain, such as Kochiana, Catanduba, and Munduruku. In this paper, we describe four new species of Hapalopini from Brazil: Cyriocosmus paresi sp. nov., Hapalopus akroa sp. nov., H. guidonae sp. nov., and K. fukushimae sp. nov. In addition, we propose an updated diagnosis for these three genera and for the species K. brunnipes and M. bicoloratum.
Theraphosinae is the most diverse subfamily of Theraphosidae spiders, but their evolutionary history remains unresolved to date. This problem is common in taxonomic groups with phylogenetic hypotheses that have often been based only on qualitative morphological characters and, rarely, on molecular analyses. Phylogenomics has significantly contributed to the understanding of the evolution of many non-model groups, such as spiders. Herein, we employed ultraconserved elements (UCEs) phylogenomics to propose a new hypothesis for a group of Theraphosinae genera, namely Lasiodoriforms: Vitalius, Lasiodora, Eupalaestrus, Pterinopelma, Proshapalopus, and Nhandu. We propose three genera and their respective morphological diagnoses are provided. Our phylogeny supports the transfer of species from the genus Vitalius to Pterinopelma and Proshapalopus and from Proshapalopus to Eupalaestrus. Finally, we describe a new species of Vitalius from Southern Brazil. Based on these three new generic descriptions and transferred species, the Lasiodoriform tarantulas comprise nine genera from Argentina, Brazil, Paraguay, and Uruguay, and the genus Vitalius now includes seven species.
Theraphosidae is the most diversified family of mygalomorph spiders, commonly known as tarantulas. Two genera inhabit the Mediterranean region: Chaetopelma in the east and Ischnocolus mostly in the western part of the Basin. Their phylogenetic position and the validity of some Ischnocolus species remain unclear. We implemented a multilocus target approach to shed new light on the position of both genera and further integrated molecular data with additional lines of evidence (morphology and ecology) to explore species boundaries in western Mediterranean Ischnocolus. Our results reveal that Ischnocolus and Chaetopelma are not closely related. Chaetopelma formed a clade with the African subfamily Eumenophorinae and Ischnocolus was recovered in a clade comprising all remaining theraphosids. The western Mediterranean Ischnocolus comprises two deeply divergent clades that separated during the Early Miocene and differ in both morphology and lifestyle. We found molecular, morphological and ecological evidence to restore the name Ischnocolus mogadorensis and revalidate this species. We also uncovered distinct allopatric lineages in Ischnocolus elongatus. However, the lack of males, the uniform morphology of females and low within-clade support hampered the assessment of their status and boundaries. Finally, our data support that I. elongatus should be considered a senior synonym of Ischnocolus hancocki and Harpactirella insidiosa.
The holotype of Hapalotremus albipes Simon, 1903 is redescribed. Four new species of the genus Hapalotremus Simon, 1903 are described: Hapalotremus apasanka sp. nov., Hapalotremus hananqheswa sp. nov., and Hapalotremus kaderkai sp. nov. from Peru, and Hapalotremus yuraqchanka sp. nov. from Bolivia. Discussion on palpal bulb morphology, ontogenetic spermathecal morphology, and biogeography is presented. Historical information about collectors and comments on the accession numbers and other label information of historical specimens is also presented.
Integrative taxonomy is relevant for the discovery and delimitation of cryptic species by incorporating different sources of evidence to construct rigorous species hypotheses. The genus Davus was recently revised and it was found that Davus pentaloris presents high morphological variation across its widespread distribution. However, tarantulas usually present low dispersal capabilities that occasionally result in local endemism. In order to evaluate species boundaries within this taxon, we examine the morphological variation and, additionally, employ four strategies based on mtDNA data (COI): two distance-based [automatic barcode gap discovery (ABGD) and Neighbor-Joining (NJ)] and two tree-based methods [general mixed Yule coalescent (GMYC) and Bayesian Poisson tree process (bPTP)]. Available morphological evidence recovers 13 putative morphospecies, but the different methods based on molecular data recover a variable number of candidate species (16–18). Based on the congruence across all analyses and the available morphological data, we recognize 13 clearly diagnosable species, 12 of them new to science. We conclude that the underestimation of the diversity in D. pentaloris was mainly caused by deficient practices in taxonomy, rather than by the presence of cryptic diversity. Although COI is a functional barcoding marker and it gives reliable results in our study, we recommend combining multiple sources of evidence and strategies to construct better species delimitation hypotheses.
The tarantula genus Brachypelma includes colourful species that are highly sought after in the commercial pet trade. They are all included in CITES appendix II. We present phylogenetic analyses using molecular and morphological characters to revise Brachypelma, in which we include all currently known species. Our results agree with a previous study that shows the non-monophyly of Brachypelma. Both phylogenies strongly favour the division of Brachypelma into two smaller genera. The first clade (Brachypelma s.s.) is formed by B.albiceps, B. auratum, B. baumgarteni, B. boehmei, B. emilia, B. hamorii, B. klaasi and B. smithi. The species included in the second clade are transferred to the new genus Tliltocatl and is formed by T. albopilosum comb. nov., T. epicureanum comb. nov., T. kahlenbergi comb. nov., T. sabulosum comb. nov., T. schroederi comb. nov., T. vagans comb. nov. and T. verdezi comb. nov. Both genera can be differentiated by their coloration and the shape of the genitalia. We transfer to Tliltocatl: T. alvarezi, T. andrewi and T. aureoceps, but should be considered as nomina dubia. In addition, we transfer B. fossorium to Stichoplastoris. We discuss the implications of these taxonomical changes for CITES and for the Mexican Laws for wildlife protection.
The tropical and subtropical rainforests of Australia’s eastern mesic zone have given rise to a complex and highly diverse biota. Numerous old endemic, niche-conserved groups persist in the montane rainforests south of Cooktown, where concepts of serial allopatric speciation resulting from the formation of xeric interzones have largely driven our biogeographic understanding of the region. Among invertebrate taxa, studies on less vagile arachnid lineages now complement extensive research on vertebrate taxa, and phylogenetic studies on mygalomorph spiders in particular are revealing significant insights about the biogeographic history of the Australian continent since the Eocene. One mygalomorph lineage entirely endemic to Australia’s tropical and subtropical eastern rainforests is the open-holed trapdoor spider genus Namea Raven, 1984 (family Anamidae). We explore, for the first time, the phylogenetic diversity and systematics of this group of spiders, with the aims of understanding patterns of rainforest diversity in Namea, of exploring the relative roles of lineage overlap versus in situ speciation in driving predicted high levels of congeneric sympatry, and of broadly reconciling morphology with evolutionary history. Original and legacy sequences were obtained for three mtDNA and four nuDNA markers from 151 specimens, including 82 specimens of Namea. We recovered a monophyletic genus Namea sister to the genus Teyl Main, 1975, and monophyletic species clades corresponding to 30 morphospecies OTUs, including 22 OTUs nested within three main species-complex lineages. Remarkable levels of sympatry for a single genus of mygalomorph spiders were revealed in rainforest habitats, with upland subtropical rainforests in south-eastern Queensland often home to multiple (up to six) congeners of usually disparate phylogenetic affinity living in direct sympatry or close parapatry, likely the result of simultaneous allopatric speciation in already co-occurring lineages, and more recent dispersal in a minority of taxa. In situ speciation, in contrast, appears to have played a relatively minor role in generating sympatric diversity within rainforest ‘islands’. At the population level, changes in the shape and spination of the male first leg relative to evolutionary history reveal subtle but consistent interspecific morphological shifts in the context of otherwise intraspecific variation, and understanding this morphological variance provides a useful framework for future taxonomic monography. Based on the phylogenetic results, we further provide a detailed taxonomic synopsis of the genus Namea, formally diagnosing three main species-complexes (the brisbanensis-complex, the dahmsi-complex and the jimna-complex), re-illustrating males of all 15 described species, and providing images of live spiders and burrows where available. In doing so, we reveal a huge undescribed diversity of Namea species from tropical and subtropical rainforest habitats, and an old endemic fauna that is beginning to shed light on more complex patterns of rainforest biogeography.
We present the latest version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which contains many sophisticated
methods and tools for phylogenomics and phylomedicine. In this major upgrade, MEGA has been optimized for use on 64-bit computing
systems for analyzing bigger datasets. Researchers can now explore and analyze tens of thousands of sequences in MEGA. The
new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict
gene duplication events in gene family trees. The 64-bit MEGA is made available in two interfaces: graphical and command line.
The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OSX. The command
line MEGA is available as native applications for Windows, Linux, and Mac OSX. They are intended for use in high-throughput
and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
The tarantula genus Tmesiphantes Simon, 1892 (Theraphosinae) includes nine valid species, with records for the states of Bahia (T. nubilus, T. caymmii, T. amadoi, T. bethaniae, T. hypogeus, and T. mirim), Minas Gerais (T. perp and T. riopretano), and Pará (T. aridai), all in Brazil. In the present study, we reviewed the taxonomy of the Tmesiphantes species and performed a phylogenetic analysis using morphological characters. Four new species are described: T. amazonicus sp. nov., T. guayarus sp. nov., T. nordestinus sp. nov., and T. raulseixasi sp. nov., which expand the geographic distribution for the following states in Brazil: Goiás, Mato Grosso, Piauí, Paraíba, and Pernambuco, occurring in the Caatinga shrublands Cerrado savannas, Atlantic rain forest, and Brazilian Amazon. Phylogenetic analysis included 30 terminal taxa and 37 characters, including representatives of nine genera of Theraphosinae. The Tmesiphantes species formed a monophyletic group with the species hitherto included in Melloleitaoina and Magulla, with the latter being paraphyletic, which led us to propose the synonymy of these three genera. An updated diagnosis is proposed for the genus Tmesiphantes, which now comprises 19 species, occurring in major Brazilian biomes and in Argentina. A distribution map that includes all Tmesiphantes species and notes on their distributions are provided.
The potentials and limitations of different approaches to revealing species boundaries and describing cryptic species are discussed. Both the traditional methods of species delimitation, mostly based on morphological analysis, and the approaches using molecular markers are considered. Besides, the prospects of species identification using digital image recognition and machine learning are briefly considered. It is concluded that molecular markers provide very important material for species delimitation; the value of these data increases manifold if they can be compared with information on morphology, geographic distribution, and ecological preferences of the studied taxa. In many cases, only a practicing taxonomist who knows his or her group thoroughly can correctly interpret the molecular data and incorporate them into the existing knowledge system in order to make a taxonomic decision.
The mygalomorph trapdoor spider family Migidae displays a quintessential Gondwanan distribution, including species in Australia, Africa, Madagascar, New Zealand, New Caledonia, and the southern cone of South America. The Argentinean fauna consists of a single species, Calathotarsus simoni Schiapelli & Gerschman, 1975 Schiapelli, R., & Gerschman, B. S. (1975). Calathotarsus simoni sp. nov. (Araneae, Migidae). Physis (Revista de la Sociedad Argentina de Ciencias Naturales), 34, 17–21. [Google Scholar], with a highly localized distribution range restricted to two mountain ranges in the southern Buenos Aires province, central Argentina. The recent discovery of specimens from new localities including adult males and females revealed morphological differences. Similarly, a molecular phylogenetic analysis using mitochondrial and nuclear markers distinguished two main lineages within C. simoni, showing genetic divergence in the levels reported for other species within the family. The two lineages corresponded to each of the two main ranges inhabited by the species and matched the morphological differences observed. Finally, an ecological niche modelling analysis revealed significant ecological differences between the lineages inhabiting the two mountain ranges. Based on integration of all the evidence, the new species Calathotarsus fangioi sp. nov. is described. The new species is circumscribed to the easternmost mountain range of Tandilia, while the distribution C. simoni is re-delimited to include only the western range of Ventania. Both species are diagnosed, described, and illustrated. This new species description and the conservation status for these remarkable spiders are further discussed.
Based on molecular and morphological phylogenetic analyses a new genus of Theraphosidae is described, Pseudoclamorisgen. n.Tapinaucheniusgigas and Tapinaucheniuselenae are transferred to Pseudoclamoris and a new species of Pseudoclamoris from the Amazon Region is described: P.burgessisp. n. Two new species of Tapinauchenius from the Caribbean are described: T.rastisp. n. and T.polybotessp. n.Tapinaucheniussubcaeruleus is considered a nomen dubium . Psalmopoeinae subfamily is diagnosed based on molecular and morphological phylogenies, and Pseudoclamorisgen. n. and Ephebopus Simon, 1892 are included. A taxonomic key for Psalmopoeinae genera Tapinauchenius , Pseudoclamoris , Psalmopoeus , and Ephebopus is provided.
Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) (Drummond et al., 2002; Mau et al., 1999; Rannala and Yang, 1996) flourishes as a popular approach to uncover the evolutionary relationships among taxa, such as genes, genomes, individuals or species. MCMC approaches generate samples of model parameter values - including the phylogenetic tree -drawn from their posterior distribution given molecular sequence data and a selection of evolutionary models. Visualising, tabulating and marginalising these samples is critical for approximating the posterior quantities of interest that one reports as the outcome of a Bayesian phylogenetic analysis. To facilitate this task, we have developed the Tracer (version 1.7) software package to process MCMC trace files containing parameter samples and to interactively explore the high-dimensional posterior distribution. Tracer works automatically with sample output from BEAST (Drummond et al., 2012), BEAST2 (Bouckaert et al., 2014), LAMARC (Kuhner, 2006), Migrate (Beerli, 2006), MrBayes (Ronquist et al., 2012), RevBayes (Höhna et al., 2016) and possibly other MCMC programs from other domains.
Species are fundamental units in biological research and can be defined on the basis of various operational criteria. There has been growing use of molecular approaches for species delimitation. Among the most widely used methods, the generalized mixed Yule-coalescent (GMYC) and Poisson tree processes (PTP) were designed for the analysis of single-locus data but are often applied to concatenations of multilocus data. In contrast, the Bayesian multispecies coalescent approach in the software BPP explicitly models the evolution of multilocus data. In this study, we compare the performance of GMYC, PTP, and BPP using synthetic data generated by simulation under various speciation scenarios. We show that in the absence of gene flow, the main factor influencing the performance of these methods is the ratio of population size to divergence time, while number of loci and sample size per species have smaller effects. Given appropriate priors and correct guide trees, BPP shows lower rates of species overestimation and underestimation, and is generally robust to various potential confounding factors except high levels of gene flow. The single-threshold GMYC and the best strategy that we identified in PTP generally perform well for scenarios involving more than a single putative species when gene flow is absent, but PTP outperforms GMYC when fewer species are involved. Both methods are more sensitive than BPP to the effects of gene flow and potential confounding factors. Case studies of bears and bees further validate some of the findings from our simulation study, and reveal the importance of using an informed starting point for molecular species delimitation. Our results highlight the key factors affecting the performance of molecular species delimitation, with potential benefits for using these methods within an integrative taxonomic framework.
The mygalomorph spiders in the family Theraphosidae, also known as "tarantulas", are one of the most famous and diverse groups of arachnids, but their evolutionary history remains poorly understood since morphological analysis have only provided mostly controversial results, and a broad molecular perspective has been lacking until now. In this study we provide a preliminary molecular phylogenetic hypothesis of relationships among theraphosid subfamilies, based on 3.5 kbp of three nuclear and three mitochondrial markers, for 52 taxa representing 10 of the 11 commonly accepted subfamilies. Our analysis confirms the monophyly of Theraphosidae and for most recognized theraphosid subfamilies, supports the validity of the Stromatopelminae and Poecilotheriinae, and indicates paraphyly of the Schismatothelinae. The placement of representatives of Schismatothelinae also indicates possible non-monophyly of Aviculariinae and supports the distinction of a previously contentious subfamily Psalmopoeinae. Major clades typically corresponded to taxa occurring in the same biogeographic region, with two of them each occurring in Africa, South America and Asia. Because relationships among these major clades were poorly supported, more extensive molecular data sets are required to test the hypothesis of independent colonization and multiple dispersal events among these continents.
The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches.
Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested datasets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
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 nomenclatural implications, suggesting a need for a rigorous overhaul of Theraphosinae classification at multiple hierarchical levels. Here, we take steps toward a revised classification, favouring division of Theraphosinae into three tribes: the Theraphosini trib. nov., the Hapalopini trib. nov., and the Grammostolini trib. nov. We also make conservation recommendations for two non-monophyletic genera. Firstly, we recover Aphonopelma Pocock 1901 as polyphyletic, finding that the large radiation into the USA and Mexico is taxonomically distinct from at least three other lineages distributed throughout Central America, one of which includes the type species of the genus. Secondly, and importantly for conservation, we find diphyly in the CITES listed genus Brachypelma Simon 1891, where our data strongly favour a division into two distinct smaller genera. We consider only the lineage with endemics in the Pacific coastal zone of Mexico to be of conservation concern. Finally, we also make suggestions on the future direction of revisionary research for the Theraphosidae as a whole.
http://zoobank.org/urn:lsid:zoobank.org:pub:B37F7795-3F92-4334-A0C7-65C8026EE1FB
Systematics has been formally implemented for about 250 years. In the last decades it has suffered great intellectual change, with the embrace of phylogenetic theory and the availability of molecular information. Here we conduct a systematic revision of Bonnetina, a group of tarantulas endemic to Mexico. Species delimitation is mainly conducted from the integration of morphological and molecular information. The mitochondrial cytochrome c oxidase subunit I (COI) marker is used as molecular barcode, and two formal molecular delimitation methods are employed: Hard-Gap barcoding and Poisson Tree Process. In a few cases, we used geographic distribution modelling for predicting the potential distribution of species. We also make a deeper than usual integration of the molecular information in the taxonomy of the group, by providing combined morphological and molecular diagnoses of the species. From our data, we provide a new diagnosis of Bonnetina and recognize the existence of 17 solidly supported species in the genus, 10 of which are newly described. We provide a COI reference alignment to ease future molecular identifications of Bonnetina species. Our work highlights the importance of using several sources of evidence to the species delimitation problem, because any single view is prone to give biased results.
Mexican red-kneed tarantulas of the genus Brachypelma are regarded as some of the most desirable invertebrate pets, and although bred in captivity, they continue to be smuggled out of the wild in large numbers. Species are often difficult to identify based solely on morphology, therefore prompt and accurate identification is required for adequate protection. Thus, we explored the applicability of using COI-based DNA barcoding as a complementary identification tool. Brachypelma smithi (F. O. Pickard-Cambridge, 1897) and Brachypelma hamorii Tesmongt, Cleton & Verdez, 1997 are redescribed, and their morphological differences defined. Brachypelma annitha is proposed as a new synonym of B. smithi. The current distribution of red-kneed tarantulas shows that the Balsas River basin may act as a geographical barrier. Morphological and molecular evidence are concordant and together provide robust hypotheses for delimiting Mexican red-kneed tarantula species. DNA barcoding of these tarantulas is further shown to be useful for species-level identification and for potentially preventing black market trade in these spiders. As a Convention on International Trade in Endangered Species (CITES) listing does not protect habitat, or control wildlife management or human interactions with organisms, it is important to support environmental conservation activities to provide an alternative income for local communities and to avoid damage to wildlife populations.
Motivation:
In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced "Poisson Tree Processes" (PTP) method is a phylogeny-aware approach that does not rely on such thresholds. Yet, two weaknesses of PTP impact its accuracy and practicality when applied to large datasets; it does not account for divergent intraspecific variation and is slow for a large number of sequences.
Results:
We introduce the multi-rate PTP (mPTP), an improved method that alleviates the theoretical and technical shortcomings of PTP. It incorporates different levels of intraspecific genetic diversity deriving from differences in either the evolutionary history or sampling of each species. Results on empirical data suggest that mPTP is superior to PTP and popular distance-based methods as it, consistently yields more accurate delimitations with respect to the taxonomy (i.e., identifies more taxonomic species, infers species numbers closer to the taxonomy). Moreover, mPTP does not require any similarity threshold as input. The novel dynamic programming algorithm attains a speedup of at least five orders of magnitude compared to PTP, allowing it to delimit species in large (meta-) barcoding data. In addition, Markov Chain Monte Carlo sampling provides a comprehensive evaluation of the inferred delimitation in just a few seconds for millions of steps, independently of tree size.
Availability and implementation:
mPTP is implemented in C and is available for download at http://github.com/Pas-Kapli/mptp under the GNU Affero 3 license. A web-service is available at http://mptp.h-its.org .
Contact:
: paschalia.kapli@h-its.org or alexandros.stamatakis@h-its.org or tomas.flouri@h-its.org.
Supplementary information:
Supplementary data are available at Bioinformatics online.
This systematic study documents the taxonomy, diversity, and distribution of the tarantula spider genus Aphonopelma Pocock, 1901 within the United States. By employing phylogenomic, morphological, and geospatial data, we evaluated all 55 nominal species in the United States to examine the evolutionary history of Aphonopelma and the group's taxonomy by implementing an integrative approach to species delimitation. Based on our analyses, we now recognize only 29 distinct species in the United States. We propose 33 new synonymies (A. apacheum, A. minchi, A. rothi, A. schmidti, A. stahnkei = A. chalcodes; A. arnoldi = A. armada; A. behlei, A. vogelae = A. marxi; A. breenei = A. anax; A. chambersi, A. clarum, A. cryptethum, A. sandersoni, A. sullivani = A. eutylenum; A. clarki, A. coloradanum, A. echinum, A. gurleyi, A. harlingenum, A. odelli, A. waconum, A. wichitanum = A. hentzi; A. heterops = A. moderatum; A. jungi, A. punzoi = A. vorhiesi; A. brunnius, A. chamberlini, A. iviei, A. lithodomum, A. smithi, A. zionis - = A. iodius; A. phanum, A. reversum = A. steindachneri), 14 new species (A. atomicum sp. n., A. catalina sp. n., A. chiricahua sp. n., A. icenoglei sp. n., A. johnnycashi sp. n., A. madera sp. n., A. mareki sp. n., A. moellendorfi sp. n., A. parvum sp. n., A. peloncillo sp. n., A. prenticei sp. n., A. saguaro sp. n., A. superstitionense sp. n., and A. xwalxwal sp. n.), and seven nomina dubia (A. baergi, A. cratium, A. hollyi, A. mordax, A. radinum, A. rusticum, A. texense). Our proposed species tree based on Anchored Enrichment data delimits five major lineages: a monotypic group confined to California, a western group, an eastern group, a group primarily distributed in high- elevation areas, and a group that comprises several miniaturized species. Multiple species are distributed throughout two biodiversity hotspots in the United States (i.e., California Floristic Province and Madrean Pine-Oak Woodlands). Keys are provided for identification of both males and females. By conducting the most comprehensive sampling of a single theraphosid genus to date, this research significantly broadens the scope of prior molecular and morphological investigations, finally bringing a modern understanding of species delimitation in this dynamic and charismatic group of spiders.
The mygalomorph genus Grammostola (family Theraphosidae) is endemic to South America. The species Grammostola anthracina is one of the largest spiders in Uruguay and reputed to be the longest lived tarantula in the world. This nominal species has two distinct colour morphs comprising black and reddish-brown forms with controversial taxonomic status. Here, we present a phylogenetic study based on molecular characters (cytochrome c oxidase subunit I) of haplotypes of G. anthracina and closely related species. Our analysis together with new morphological data and biogeographical information indicates that the two morphs of G. anthracina constitute different species that are not sister to each other. Consequently, a new species, Grammostola quirogai is described, diagnosed and illustrated to encompass the black morph. Phylogenetic relationships and new taxonomic characters for Grammostola species included in this study are discussed.
Aim
Phylogeographical studies in the Mojave and Sonoran deserts often find genetic discontinuities that pre‐date the Pleistocene. A recent synthesis of phylogeographical data, called the Mojave Assembly Model, provides a hypothesis for the historical assembly of these desert biotas but does not adequately capture the complexity of pre‐Pleistocene vicariance events. We tested this model and assessed pre‐Pleistocene divergences by exploring the phylogeography of the Aphonopelma mojave group, which is composed of turret‐building tarantula species from the Mojave and Sonoran deserts.
Location
Mojave and Sonoran deserts, south‐western USA .
Methods
We augmented the sampling from a previous study by sequencing mitochondrial DNA ( COI ) from new material of the A. mojave group. We used phylogenetic and network analyses to identify clades and a molecular clock and lineages‐through‐time plots ( LTT plots) to explore the timing and tempo of diversification. We tested for demographic expansion using neutrality tests and mismatch distributions. Species distribution models ( SDM s) were constructed to compare current suitable habitat to that at the Last Glacial Maximum ( LGM ).
Results
Phylogenetic, network and molecular‐clock analyses identified six major clades that probably diverged during the late Miocene. The rate of diversification appears to have slowed during the Pliocene. Most clades exhibit signals of recent demographic expansion. SDM s predicted that suitable habitat shifted south and to lower elevations during the LGM .
Main conclusions
Phylogeographical analyses suggest that the A. mojave group experienced a burst of diversification in the late Miocene, followed by population expansions during the Pleistocene. Six major clades with origins in the late Miocene cannot be adequately explained by the Mojave Assembly Model. We propose the novel hypothesis that Miocene extensional tectonics caused populations to diverge in allopatry by producing low‐elevation habitat barriers. Geological models, such as kinematic reconstructions, provide an ideal but underutilized framework for testing biogeographical hypotheses in these deserts and the wider Basin and Range Province.
Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast
programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus,
there is need for additional approaches that employ different search strategies to find ML trees and that are at the same
time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation
method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found
higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use
the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein
alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3–97.1%. IQ-TREE
is freely available at http://www.cibiv.at/software/iqtree.
The Madrean Sky Islands of northern Mexico and the south‐western United States are located in the Madrean pine–oak woodlands ‘biodiversity hotspot’. This area is renowned for its exceptional flora and fauna, but comparatively little is known about arthropod diversity in this region. We obtained specimens of the tarantula genus Aphonopelma from five different mountain ranges (Huachucas, Pajaritos, Peloncillos, Santa Catalinas, and Santa Ritas) to assess patterns of diversity within the group.
Species delimitation in tarantulas is difficult because they possess few informative morphological features. We implemented a rigorous methodological framework for delimiting species that incorporated multiple lines of evidence (molecules, distributional information, morphology, and breeding period) in an explicitly hypothesis‐driven manner.
Our integrative taxonomic approach delimited three species (all undescribed): one endemic to the Peloncillos, one endemic to the Santa Catalinas, and one that is more widely distributed in the Huachucas, Santa Ritas, and Pajaritos. These patterns of diversity and endemicity are comparable to other arachnids in the region and suggest that species‐level diversity of stenotypic/dispersal‐limited arthropods throughout the Madrean Sky Island Region may be underestimated.
Ecological data are not widely available for Madrean Sky Island tarantulas and it is difficult to evaluate their conservation status. Several intrinsic (patterns of endemicity, limited vagility, and life history) and extrinsic (habitat degradation, commercial exploitation, and climate change) factors, however, suggest that these spiders may be of conservation concern. The approach taken in this study highlights the importance of considering multiple lines of evidence when species delimitation has direct implications on conservation.
The California floristic province is home to several threatened or endangered species and has been the focus of numerous conservation efforts. These conservation efforts have largely ignored the diverse and distinctive arthropod fauna found in this region.
We investigate the species boundaries of the four tarantula (Araneae: Theraphosidae) species endemic to California's Southern Coast Ranges through molecular phylogenetic analysis using a 680 bp region of the mitochondrial gene cytochrome oxidase subunit 1 from 51 individuals.
Our analysis resulted in a well‐supported phylogeny showing three distinct clades. As a result, we recognise only one species in the Southern Coast Ranges ( Aphonopelma brunnius , with A. chamberlini and A. smithi treated as junior synonyms; if the holotype of A. rileyi is located it will likely be a synonym as well). Two additional species were found in the foothills of the Sierra Nevada.
Although the tarantulas in California's Southern Coast Ranges are not as endemic as was previously thought, their position as top arthropod predators make them ideal sentinel species, suggesting they should be targeted by conservationists. Furthermore, our analyses illustrate the importance in using molecular tools to investigate biodiversity.
Two new species of tarantulas from Mexico are described and illustrated: Bonnetina tenuiverpis and Bonnetina juxtantricola, from the states of Mexico and Guerrero, respectively. Male palpal bulbs, tibial apophyses and spermatheca are among the most taxonomically informative characters. Male bulb microstructure is revealed from scanning electron microscopy; both new and homologous structures to other
Theraphosinae genera are identified and described. Nomenclatural changes for male tibial apophyses are also proposed. The holotype male and allotype female of one of the species are molecularly characterized and matched from CO1 partial sequence
Two new species of Plesiopelma Pocock, 1901 from northern Argentina are described and diagnosed based on males and habitat descriptions are presented. Males of Plesiopelma paganoi sp. nov. differ from most of species by the absence of spiniform setae on the retrolateral face of cymbium, aspect of the palpal bulb. Plesiopelma aspidosperma sp. nov. differs from most species of the genus by the presence of spiniform setae on the retrolateral face of cymbium and it can be distinguished from P. myodes Pocock, 1901, P. longisternale (Schiapelli & Gerschman, 1942) and P. rectimanum (Mello-Leitão, 1923) by the separated palpal bulb keels and basal nodule of metatarsus I very developed. It differs from P. minense (Mello-Leitão, 1943) by the shape of the palpal bulb and basal nodule on metatarsus I well developed. Specimens were captured in Salta province, Argentina, inhabiting high cloud forests of Yungas eco-region. RESUMEN. Descripción de dos nuevas especies de Plesiopelma (Araneae, Theraphosidae, Theraphosinae) de Argentina. Dos nuevas especies de Plesiopelma Pocock, 1901 del norte de Argentina son diferenciadas y se describen en base a ejemplares machos y se presentan distingue de P. myodes Pocock, 1901, P. longisternale (Schiapelli & Gerschman, 1942) y P. rectimanum (Mello-Leitão, 1923) por las quillas del bulbo separadas y el nódulo basal del metatarso I muy desarrollado. Se diferencia de P. minense (Mello-Leitão, 1943) por la forma del órgano palpar y el nódulo basal del metatarso I desarrollado. Los especímenes se capturaron en la provincia de Salta, Argentina, habitando nuboselvas de altura en la eco-región de Yungas.
En el presente trabajo se ofrece una clave para la identificación de las especies de arañas pertenecientes al infraorden Mygalomorphae conocidas en la provincia de Buenos Aires, Argentina. Además, se presenta una breve descripción de algunos aspectos de su biología y distribución. Abstract In this contribution we provide a key for the recognition of the species of the spider infraorder Mygalomorphae known in Buenos Aires province, Argentina. We also provide a brief description of some aspects on their biology and distribution.
Contemporary species concepts are diverse. Nonetheless, all share the fundamental idea that species are segments of Uneages at the population level of biological organ- ization. They differ in the secondary properties (e.g., intrinsic reproductive isolation, monophyly, diagnosability) that are treated as necessary for considering lineages to be species. A unified species concept can be achieved by interpreting the common fundamental idea of being a separately evolving lineage segment as the only neces- sary property of species and viewing the various secondary properties either as lines of evidence relevant to assessing lineage separation or as properties that define dif- ferent subcategories of the species category (e.g., reproductively isolated species, monophyletic species, diagnosable species). This unified species concept has a num- ber of consequences for taxonomy, including the need to acknowledge that undiffer- entiated and undiagnosable lineages are species, that species can fuse, that species can be nested within other species, that the species category is not a taxonomic rank, and that new taxonomic practices and conventions are needed to accommodate these conclusions. Although acceptance of a unified species concept has some radical con- sequences for taxonomy, it also reflects a change in the general conceptuaUzation of the species category that has been underway for more than a half-centurya shift from viewing the species category as one member of the hierarchy of taxonomic ranks to viewing it as a natural kind whose members are the units at one of the lev- els of biological organization. This change is related to a more general shift in the pri- mary concern of the discipline of systematics (including taxonomy), from the utiU- tarian activity of classifying organisms to the scientific activity of testing hypotheses about lineage boundaries and phylogenetic relationships. The unified species concept is a natural outcome of this conceptual shift and represents the more complete acceptance of the idea that species are one of the fundamental units of biology. As such, the unified species concept is central to the future of taxonomy.
DNA barcoding-type studies assemble single-locus data from large samples of individuals and species, and have provided new kinds of data for evolutionary surveys of diversity. An important goal of many such studies is to delimit evolutionarily significant species units, especially in biodiversity surveys from environmental DNA samples. The Generalized Mixed Yule Coalescent (GMYC) method is a likelihood method for delimiting species by fitting within- and between-species branching models to reconstructed gene trees. Although the method has been widely used, it has not previously been described in detail or evaluated fully against simulations of alternative scenarios of true patterns of population variation and divergence between species. Here, we present important reformulations to the GMYC method as originally specified, and demonstrate its robustness to a range of departures from its simplifying assumptions. The main factor affecting the accuracy of delimitation is the mean population size of species relative to divergence times between them. Other departures from the model assumptions, such as varying population sizes among species, alternative scenarios for speciation and extinction, and population growth or subdivision within species, have relatively smaller effects. Our simulations demonstrate that support measures derived from the likelihood function provide a robust indication of when the model performs well and when it leads to inaccurate delimitations. Finally, the so-called single threshold version of the method outperforms the multiple threshold version of the method on simulated data: we argue that this might represent a fundamental limit due to the nature of evidence used to delimit species in this approach. Together with other studies comparing its performance relative to other methods, our findings support the robustness of GMYC as a tool for delimiting species when only single-locus information is available.
This systematic study documents the taxonomy, diversity, and distribution of 40 species of the predominately Californian trapdoor spider genus Aptostichus Simon, 1891. Thirty-three of these species are newly described: Aptostichus dantrippi, Aptostichus cabrillo, Aptostichus pennjillettei, Aptostichus asmodaeus, Aptostichus nateevansi, Aptostichus chiricahua, Aptostichus icenoglei, Aptostichus isabella, Aptostichus muiri, Aptostichus barackobamai, Aptostichus sinnombre, Aptostichus hedinorum, Aptostichus aguacaliente, Aptostichus chemehuevi, Aptostichus sarlacc, Aptostichus derhamgiulianii, Aptostichus anzaborrego, Aptostichus serrano, Aptostichus mikeradtkei, Aptostichus edwardabbeyi, Aptostichus killerdana, Aptostichus cahuilla, Aptostichus satleri, Aptostichus elisabethae, Aptostichus fornax, Aptostichus lucerne, Aptostichus fisheri, Aptostichus bonoi, Aptostichus cajalco, Aptostichus sierra, Aptostichus huntington, Aptostichus dorothealangeae, and Aptostichus chavezi. Most of these species are restricted to the California Floristic Province, a known biodiversity hotspot. Of the 40 recognized species, over half are considered to be imperiled or vulnerable and two have likely gone extinct over the past half-century; the conservation status of only 11 species is considered to be secure. Using 73 quantitative and qualitative morphological characters I propose a preliminary phylogeny for the genus that recognizes four major lineages: the Atomarius, Simus, Hesperus, and Sierra species groups. Additionally, the phylogenetic analysis indicates that adaptations favoring the invasion of the arid desert habitats of southern California have evolved multiple times across the group. The existence of both desert and non - desert species in three of the four species groups makes this genus an ideal candidate for the study of the evolutionary ecology of desert arthropods. A set of molecular characters based on the contiguous mitochondrial DNA genes 16S-tRNA valine-12S is used in an independent analysis to assist in placement of specimens into species. The taxonomy section explicitly identifies the concept employed in species delimitation. Niche based distribution models are constructed to predict the ranges of species for which an adequate number of sampling sites were known.
Chinchaysuyu gen. nov. is described as a new monotypic Theraphosidae genus from northern Peru, with distinct genitalic morphology. Males of Chinchaysuyu gen. nov. differ from all known species by having a palpal bulb organ with many conspicuous keels extending towards the subtegulum. Females differ by having two pairs of short and hyper-sclerotized receptacles. This new genus is described and illustrated on the basis of the type species Chinchaysuyu spinosa sp. nov. and their morphological affinities and its phylogenetic position are analyzed and discussed.
Aim
Comparative phylogeography aims to unravel similarities in the population structure and evolutionary processes undergone by co‐distributed taxa, under the assumption that they will have experienced the same geoclimatic events. However, small differences in functional traits, particularly those related to dispersal abilities, may translate into incongruent evolutionary histories. Here, we used a sequence target multi‐locus approach to infer and compare the phylogeographical patterns of three sympatric mygalomorph spiders in the Argentinean Peripampasic orogenic arc.
Location
The mountainous systems of central and northern Argentina.
Taxon
Acanthogonatus centralis , Grammostola vachoni and Plesiopelma longisternale (Araneae: Mygalomorphae).
Methods
We inferred mitochondrial gene trees ( 16 S + L1 + nad1) and nuclear (ITS2) networks of three species of mygalomorph spiders from 159 individuals using Bayesian and Maximum likelihood approaches, and estimated divergence times in a Bayesian framework. Based on our time‐stamped gene trees, we reconstructed ancestral areas using the Bayesian Binary MCMC method.
Results
Deeply divergent and highly geographically structured populations, isolated since the Late Miocene to mid Pliocene, were obtained in the pycnothelid Acanthogonatus centralis . Conversely, the theraphosids Plesiopelma longisternale and Grammostola vachoni showed slightly divergent and poorly geographically structured populations, tracing back to the Late Pliocene to Early Pleistocene.
Main conclusions
We propose that differences in dispersion rates and time of colonization between the theraphosids and the pycnothelid species led to divergent lineage history despite common environmental conditions. We corroborate the key role played by the Plio‐Pleistocene geoclimatic events in shaping the present‐day diversity of mygalomorph spiders along the Peripampasic orogenic arc. Additionally, we uncovered potentially overlooked species diversity within G . vachoni .
Spiders are perfect model for developmental stage and growth studies because the juvenile period is broken into instars. Theraphosidae family, are largest and longest-lived spiders and females continue to grow and molt over the sexually mature stage is reached. However, their development and growth are still unknown. Thus, our objective was describe in detail the development of the juveniles of Grammostola vachoni until reaching the adulthood, estimate the growth of somatic and spermathecae dimensions, and analyze any possible allometric relation between the spermathecae and body size during the development. The mortality of individuals was 10.7% per year; and both sexes molted between once and twice by a year with a peak in the molt frequency in the third year of life. The intermolt interval was similar between sexes and tended to increase during development. The spermathecae appeared in the immature females more frequently in the 8th molt (4.03 years) and males reached adulthood frequently at the 11th molt (7.03 years). Both sexes had similar growth percentage (38%) and its was constant throughout their whole development. In contrast, the spermathecae growth percentage was 98% and always was higher than the percentage of body growth. The somatic characters did not show any differences between females and males. The spermathecae measurements showed positive allometric growth related to the body size. The results of our study completes the baseline biology information about the development, growth and its relationship, aspects mostly unknown in tarantulas.
Theraphosinae is the most diverse subfamily of tarantulas in the world, with more than 500 known species. The group is endemic to the New World and its geographic distribution ranges from Southern North America to temperate zones of South America. The largest and most long-lived spiders in the world belong to this subfamily. They inhabit almost all terrestrial environments from sea level up to 4500 m altitude. Beyond the morphological diagnostic characters of the subfamily, this group is also characterized by a singular mechanism of defense, employing abdominal urticating setae that they can release to the air when they are disturbed. For over a century, this subfamily remained poorly known from both biological and taxonomical aspects. In fact, most genera were established during the last few decades and several papers on behavior, ecology, and reproduction were published. Due to their size, longevity, sex dimorphism, relatively easy conditions for breeding, and other biological characteristics, this group constitutes an interesting model for studies on metabolism, thermoregulation, biomechanics, communication, reproduction, and development. This chapter will present an updated overview of the taxonomy and phylogeny of the group as well as a revision of recent scientific contributions in different fields of general biology.
Determining species boundaries forms an important foundation for biological research. However, the results of molecular species delimitation can vary with the data sets and methods that are used. Here we use a two-step approach to delimit species in the genus Heptathela, a group of primitively segmented trapdoor spiders that are endemic to Japanese islands. Morphological evidence suggests the existence of 19 species in the genus. We tested this initial species hypothesis by using six molecular species-delimitation methods to analyse 180 mitochondrial COI sequences of Heptathela sampled from across the known range of the genus. We then conducted a set of more focused analyses by sampling additional genetic markers from the subset of taxa that were inconsistently delimited by the single-locus analyses of mitochondrial DNA. Multilocus species delimitation was performed using two Bayesian approaches based on the multispecies coalescent. Our approach identified 20 putative species among the 180 sampled individuals of Heptathela. We suggest that our two-step approach provides an efficient strategy for delimiting species while minimizing costs and computational time.
The tarantula spider genus Aphonopelma Pocock, 1901 has received considerable attention in recent years but the group’s diversity remains poorly understood in Mexico, particularly in the pine-oak woodlands of the Sierra Madre Occidental and associated Madrean “Sky Islands”. A pair of tarantulas discovered from an unsampled region in the Sierra de Bacadéhuachi (the westernmost range of the Sierra Madre Occidental) in northeastern Sonora was found to be closely related to four species from the Madrean “Sky Islands” in Arizona and New Mexico. An integrative approach for delimiting species (incorporating data from molecular phylogenetics, morphology, distributions, and breeding periods) suggests that the specimens from Sierra de Bacadéhuachi belong to an undescribed species that is herein named Aphonopelma bacadehuachi sp. nov. This new species adds to our knowledge of an increasingly diverse assemblage of Aphonopelma from the Madrean Pine-Oak Woodlands Hotspot. Collaborations between Mexican and American researchers are needed to accelerate discovery and description of the group’s remaining diversity, particularly in light of the many threats facing the ecoregion including habitat degradation and climate change.
Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
Determining species boundaries is a central debate in biology. Several recently developed molecular delimitation methods have highlighted extensive inconsistency in classical morphological taxonomy. However, choosing between them is contentious. Molecular studies on theraphosid spiders have found considerable cryptic diversity and many species redundantly described. Most of these studies have relied only on COI, a mitochondrial marker that has proven its efficacy in animal studies, but which also might lead to an over-estimation of diversity. Here we present an integrative approach to species delimitation in Bonnetina, a poorly known group of tarantulas endemic to Mexico. We employed morphological evidence, as well as different setups with distance-based (Hard-Gap barcoding and ABGD) and tree-based (GMYC, PTP and BPP) molecular barcod- ing approaches, using one mitochondrial (COI) and one nuclear (ITS1) rapidly evolving loci. BPP is also used as a multi-locus method. We also explored the influence of ambiguous alignment choice and of cod- ing gaps as characters in phylogenetic inference and in species delimitation with that marker. Different delimitation methods with COI gave moderately variable results and this gene exhibited a universal barcode gap. The ITS1 gene tree was well supported and robust to alignment choice; with this locus, coding gaps improved branch support and species delimitation with PTP. No universal barcode gap was found with ITS1, and single locus delimitations returned disparate results. However, this locus helped to highlight cases of under- and overestimations by COI. BPP gave solutions with many lineages, in single locus and combined analyses, especially with the recently implemented unguided methodology. We recognize 12 robustly supported species in our data set, of which seven remain undescribed, and three are morphologically cryptic. For COI Bonnetina species identification, we propose intra- and inter-specific thresholds of 2% and 6% sequence divergence, respectively. We conclude that morphological signal for species delimitation in Bonnetina is higher than for other studied tarantulas, but it fails to recognize several lineages in the genus. COI is a functional barcoding marker, and the most reliable source of evidence that we used, but it may also lead to inaccurate delimitations. ITS1 is a highly informative locus for species delimitation and species-level phylogeny, but it performs poorly as a barcoding marker. Due to variability between delimitation methods, we suggest combining evidence from multiple approaches to get better-supported results.
Species delimitation is the act of identifying species-level biological diversity. In recent years, the field has witnessed a dramatic increase in the number of methods available for delimiting species. However, most recent investigations only utilize a handful (i.e. 2-3) of the available methods, often for unstated reasons. Because the parameter space that is potentially relevant to species delimitation far exceeds the parameterization of any existing method, a given method necessarily makes a number of simplifying assumptions, any one of which could be violated in a particular system. We suggest that researchers should apply a wide range of species delimitation analyses to their data and place their trust in delimitations that are congruent across methods. Incongruence across the results from different methods is evidence of either a difference in the power to detect cryptic lineages across one or more of the approaches used to delimit species and could indicate that assumptions of one or more of the methods have been violated. In either case, the inferences drawn from species delimitation studies should be conservative, for in most contexts it is better to fail to delimit species than it is to falsely delimit entities that do not represent actual evolutionary lineages.
Species are a fundamental unit for biological studies, yet no uniform guidelines exist for determining species limits in an objective manner. Given the large number of species concepts available, defining species can be both highly subjective and biased. Although morphology has been commonly used to determine species boundaries, the availability and prevalence of genetic data has allowed researchers to use such data to make inferences regarding species limits. Genetic data also have been used in the detection of cryptic species, where other lines of evidence (morphology in particular) may underestimate species diversity. In this study, we investigate species limits in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus) from California. Multiple approaches were used to determine species boundaries in this highly genetically fragmented group, including both multilocus discovery and validation approaches (plus a chimeric approach). Additionally, we introduce a novel tree-based discovery approach using species trees. Results suggest that this complex includes multiple cryptic species, with two groupings consistently recovered across analyses. Due to incongruence across analyses for the remaining samples, we take a conservative approach and recognize a three species complex, and formally describe two new species (Aliatypus roxxiae, sp. nov. and Aliatypus starretti, sp. nov.). This study helps to clarify species limits in a genetically fragmented group and provides a framework for identifying and defining the cryptic lineage diversity that prevails in many organismal groups.