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Adrián-Serrano S, Pavlek M, Arnedo MA. A targeted gene phylogenetic framework to investigate diversification in the highly diverse yet geographically restricted red devil spiders (Araneae, Dysderidae). Cladistics 2024. [PMID: 39105704 DOI: 10.1111/cla.12595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/12/2024] [Accepted: 07/10/2024] [Indexed: 08/07/2024] Open
Abstract
The family Dysderidae is a highly diverse group of nocturnal ground-dwelling and active-hunter spiders. Dysderids are mostly restricted to the Western Palearctic, and particularly rich and abundant around the Mediterranean region. Interestingly, the distribution of species richness among its 24 genera and three subfamilies is highly biased-80% of its 644 documented species belong to just two genera, Dysdera (326) and Harpactea (211). Dysderidae provides an excellent study case for evolutionary and ecological research. It includes cases of trophic specialization, which are uncommon among spiders, and exhibit other remarkable biological (e.g. holocentric chromosomes), behavioural (e.g. cryptic female choice), evolutionary (e.g. adaptive radiation) and ecological features (e.g. recurrent colonization of the subterranean environment). The lack of a quantitative hypothesis on its phylogenetic structure has hampered its potential as a testing ground for evolutionary, biogeographical and ecological hypotheses. Here, we present the results of a target, multi-locus phylogenetic analysis, using mitochondrial (cox1, 16s and 12s) and nuclear genes (h3, 28s and 18s), of the most exhaustive taxonomic sample within Dysderidae (104 spp.) to date and across related families (Synspermiata) (83 spp.). We estimate divergence times using a combination of fossil and biogeographic node calibrations and use this timeline to identify shifts in diversification rates. Our results support the monophyly of the Dysderidae subfamilies Rhodinae and Dysderinae but reject Harpacteinae as currently defined. Moreover, the clades recovered within Harpacteinae do not support its current taxonomy. The origin of the family most likely post-dated the break-up of Pangea, and cave colonization may be older than previously considered. After correcting for the taxonomic artefacts, we identified a significant shift in diversification rates at the base of the genus Dysdera. Although the unique coexistence of specialist and generalist diets within the lineage could be suggested as the potential driver for the rate acceleration, further quantitative analyses would be necessary to test this hypothesis.
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Affiliation(s)
- Silvia Adrián-Serrano
- Departament Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Av. Diagonal 645, E-08028, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Diagonal 645, E-08028, Barcelona, Spain
| | - Martina Pavlek
- Departament Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Av. Diagonal 645, E-08028, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Diagonal 645, E-08028, Barcelona, Spain
- Ruđer Bošković Institute, Bijenička cesta 54, Zagreb, Croatia
- Croatian Biospeleological Society, Roosveltov trg 6, Zagreb, Croatia
| | - Miquel A Arnedo
- Departament Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Av. Diagonal 645, E-08028, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Diagonal 645, E-08028, Barcelona, Spain
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2
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Wood HM, Wunderlich J. Burma Terrane Amber Fauna Shows Connections to Gondwana and Transported Gondwanan Lineages to the Northern Hemisphere (Araneae: Palpimanoidea). Syst Biol 2023; 72:1233-1246. [PMID: 37527553 DOI: 10.1093/sysbio/syad047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/24/2023] [Accepted: 07/31/2023] [Indexed: 08/03/2023] Open
Abstract
Burmese amber is a significant source of fossils that documents the mid-Cretaceous biota. This deposit was formed around 99 Ma on the Burma Terrane, which broke away from Gondwana and later collided with Asia, although the timing is disputed. Palpimanoidea is a dispersal-limited group that was a dominant element of the Mesozoic spider fauna, and has an extensive fossil record, particularly from Burmese amber. Using morphological and molecular data, evolutionary relationships of living and fossil Palpimanoidea are examined. Divergence dating with fossils as terminal tips shows timing of diversification is contemporaneous with continental breakup.Ancestral range estimations show widespread ancestral ranges that divide into lineages that inherit different Pangean fragments, consistent with vicariance. Our results suggest that the Burmese amber fauna has ties to Gondwana due to a historical connection in the Early Cretaceous, and that the Burma Terrane facilitated biotic exchange by transporting lineages from Gondwana into the Holarctic in the Cretaceous.
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Affiliation(s)
- Hannah M Wood
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC 20560, USA
| | - Jörg Wunderlich
- Oberer Häuselbergweg 24, 69493 Hirschberg an der Bergstraße, Germany
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Kulkarni S, Wood HM, Hormiga G. Advances in the reconstruction of the spider tree of life: A roadmap for spider systematics and comparative studies. Cladistics 2023; 39:479-532. [PMID: 37787157 DOI: 10.1111/cla.12557] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 07/27/2023] [Accepted: 08/17/2023] [Indexed: 10/04/2023] Open
Abstract
In the last decade and a half, advances in genetic sequencing technologies have revolutionized systematics, transforming the field from studying morphological characters or a few genetic markers, to genomic datasets in the phylogenomic era. A plethora of molecular phylogenetic studies on many taxonomic groups have come about, converging on, or refuting prevailing morphology or legacy-marker-based hypotheses about evolutionary affinities. Spider systematics has been no exception to this transformation and the inter-relationships of several groups have now been studied using genomic data. About 51 500 extant spider species have been described, all with a conservative body plan, but innumerable morphological and behavioural peculiarities. Inferring the spider tree of life using morphological data has been a challenging task. Molecular data have corroborated many hypotheses of higher-level relationships, but also resulted in new groups that refute previous hypotheses. In this review, we discuss recent advances in the reconstruction of the spider tree of life and highlight areas where additional effort is needed with potential solutions. We base this review on the most comprehensive spider phylogeny to date, representing 131 of the 132 spider families. To achieve this sampling, we combined six Sanger-based markers with newly generated and publicly available genome-scale datasets. We find that some inferred relationships between major lineages of spiders (such as Austrochiloidea, Palpimanoidea and Synspermiata) are robust across different classes of data. However, several new hypotheses have emerged with different classes of molecular data. We identify and discuss the robust and controversial hypotheses and compile this blueprint to design future studies targeting systematic revisions of these problematic groups. We offer an evolutionary framework to explore comparative questions such as evolution of venoms, silk, webs, morphological traits and reproductive strategies.
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Affiliation(s)
- Siddharth Kulkarni
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Avenue NW, Washington, DC, 20560, USA
| | - Hannah M Wood
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Avenue NW, Washington, DC, 20560, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA
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Bellvert A, Adrián-Serrano S, Macías-Hernández N, Toft S, Kaliontzopoulou A, Arnedo MA. The Non-Dereliction in Evolution: Trophic Specialisation Drives Convergence in the Radiation of Red Devil Spiders (Araneae: Dysderidae) in the Canary Islands. Syst Biol 2023; 72:998-1012. [PMID: 37474131 DOI: 10.1093/sysbio/syad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/22/2023] Open
Abstract
Natural selection plays a key role in deterministic evolution, as clearly illustrated by the multiple cases of repeated evolution of ecomorphological characters observed in adaptive radiations. Unlike most spiders, Dysdera species display a high variability of cheliceral morphologies, which has been suggested to reflect different levels of specialization to feed on isopods. In this study, we integrate geometric morphometrics and experimental trials with a fully resolved phylogeny of the highly diverse endemic species from the Canary Islands to 1) quantitatively delimit the different cheliceral morphotypes present in the archipelago, 2) test their association with trophic specialization, as reported for continental species, 3) reconstruct the evolution of these ecomorphs throughout the diversification of the group, 4) test the hypothesis of convergent evolution of the different morphotypes, and 5) examine whether specialization constitutes a case of evolutionary irreversibility in this group. We show the existence of 9 cheliceral morphotypes and uncovered their significance for trophic ecology. Further, we demonstrate that similar ecomorphs evolved multiple times in the archipelago, providing a novel study system to explain how convergent evolution and irreversibility due to specialization may be combined to shape phenotypic diversification in adaptive radiations.
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Affiliation(s)
- Adrià Bellvert
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona (UB), Av. Diagonal, 643, 08028 Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Silvia Adrián-Serrano
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona (UB), Av. Diagonal, 643, 08028 Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Nuria Macías-Hernández
- Department of Animal Biology, Edaphology and Geology, Universidad de La Laguna, Tenerife, Canary Islands, Spain
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History, University of Helsinki, Finland
| | - Søren Toft
- Department of Biology, Aarhus University, Ny Munkegade 116, DK-8000 Århus C, Denmark
| | - Antigoni Kaliontzopoulou
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona (UB), Av. Diagonal, 643, 08028 Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Miquel A Arnedo
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona (UB), Av. Diagonal, 643, 08028 Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
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Caetano C, Griswold CE, Michalik P, Labarque FM. Evolution and comparative morphology of raptorial feet in spiders. ARTHROPOD STRUCTURE & DEVELOPMENT 2023; 74:101255. [PMID: 37011488 DOI: 10.1016/j.asd.2023.101255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 06/02/2023]
Abstract
Spiders are among the most diverse animals, which developed different morphological and behavioral traits for capturing prey. We studied the anatomy and functionality of the rare and apomorphic raptorial spider feet using 3D reconstruction modeling, among other imaging techniques. The evolutionary reconstruction of the raptorial feet (tarsus plus pretarsus) features using a composite tree of spiders, indicating that similar traits emerged three times independently in Trogloraptoridae, Gradungulinae, and Doryonychus raptor (Tetragnathidae). The characteristics defining the raptorial feet are an interlocked complex merging of the base of the elongated prolateral claw with the pretarsal sclerotized ring, with the former clasping against the tarsus. Raptorial feet even flex over robust raptorial macrosetae forming a reduced tarsal version of a catching basket to encase prey during hunting. Our results show that Celaeniini (Araneidae) and Heterogriffus berlandi (Thomisidae), taxa previously compared with raptorial spiders, lack the raptorial feet key characteristics and the tarsal-catching basket. We make predictions about the possible behavior of the abovementioned taxa that will need to be tested by observing living specimens. We conclude that multiple morphological tarsal and pretarsal micro-structures define the raptorial foot functional unit and recommend a comprehensive evaluation before assigning this configuration to any spider taxa.
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Affiliation(s)
- Carolina Caetano
- Departamento de Ecologia e Biologia Evolutiva (DEBE), Universidade Federal de São Carlos (UFSCar), campus São Carlos, Rodovia Washington Luís, Km 235, CEP, 13565-905, São Carlos, SP, Brazil; Departamento de Hidrobiologia (DHb), Universidade Federal de São Carlos (UFSCar), campus São Carlos, Rodovia Washington Luís, Km 235, CEP, 13565-905, São Carlos, SP, Brazil.
| | - Charles E Griswold
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA.
| | - Peter Michalik
- Zoologisches Institut und Museum, Universität Greifswald, Greifswald, Germany.
| | - Facundo M Labarque
- Departamento de Ecologia e Biologia Evolutiva (DEBE), Universidade Federal de São Carlos (UFSCar), campus São Carlos, Rodovia Washington Luís, Km 235, CEP, 13565-905, São Carlos, SP, Brazil.
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Rix MG, Wood HM, Harvey MS, Michalik P. Micro-Computed Tomography Reveals a Remarkable Twin Intromittent Organ in Spiders – A Novelty for Arachnids With Direct Sperm Transfer. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.794708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The modification of male pedipalps into secondary sexual intromittent organs is one of the hallmark characteristics of spiders, yet understanding the development and evolution of male genitalia across the order remains a challenging prospect. The embolus – the sclerite bearing the efferent spermatic duct or spermophor, and used to deliver sperm directly to the female genitalia during copulation – has always been considered the single unambiguously homologous palpal sclerite shared by all spider species, fundamental to the bauplan of the order and to the evolution and functional morphology of spider reproductive systems. Indeed, after two centuries of comparative research on spider reproduction, the presence of a single spermophor and embolus on each of a male spider’s two pedipalps remains a central tenet of evolutionary arachnology. Our findings challenge this premise, and reveal a remarkable twin intromittent organ sperm transfer system in a lineage of Australian palpimanoid spiders, characterized by a bifurcate spermophor and the presence of two efferent ducts leading to a pair of embolic sclerites on each pedipalp. This is the first time such a remarkable conformation has been observed in any group of arachnids with direct sperm transfer, complicating our understanding of palpal sclerite homologies, and challenging ideas about the evolution of spider genitalia.
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Kallal RJ, Kulkarni SS, Dimitrov D, Benavides LR, Arnedo MA, Giribet G, Hormiga G. Converging on the orb: denser taxon sampling elucidates spider phylogeny and new analytical methods support repeated evolution of the orb web. Cladistics 2021; 37:298-316. [PMID: 34478199 DOI: 10.1111/cla.12439] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2020] [Indexed: 12/20/2022] Open
Abstract
High throughput sequencing and phylogenomic analyses focusing on relationships among spiders have both reinforced and upturned long-standing hypotheses. Likewise, the evolution of spider webs-perhaps their most emblematic attribute-is being understood in new ways. With a matrix including 272 spider species and close arachnid relatives, we analyze and evaluate the relationships among these lineages using a variety of orthology assessment methods, occupancy thresholds, tree inference methods and support metrics. Our analyses include families not previously sampled in transcriptomic analyses, such as Symphytognathidae, the only araneoid family absent in such prior works. We find support for the major established spider lineages, including Mygalomorphae, Araneomorphae, Synspermiata, Palpimanoidea, Araneoidea and the Retrolateral Tibial Apophysis Clade, as well as the uloborids, deinopids, oecobiids and hersiliids Grade. Resulting trees are evaluated using bootstrapping, Shimodaira-Hasegawa approximate likelihood ratio test, local posterior probabilities and concordance factors. Using structured Markov models to assess the evolution of spider webs while accounting for hierarchically nested traits, we find multiple convergent occurrences of the orb web across the spider tree-of-life. Overall, we provide the most comprehensive spider tree-of-life to date using transcriptomic data and use new methods to explore controversial issues of web evolution, including the origins and multiple losses of the orb web.
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Affiliation(s)
- Robert J Kallal
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA.,Department of Entomology, National Museum of Natural History, 10th & Constitution Ave. NW, Washington, DC, 20560, USA
| | - Siddharth S Kulkarni
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA.,Department of Entomology, National Museum of Natural History, 10th & Constitution Ave. NW, Washington, DC, 20560, USA
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, P.O. Box 7800, Bergen, 5020, Norway
| | - Ligia R Benavides
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Miquel A Arnedo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biodiversity Research Institute (IRBio), Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, Spain
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA
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Bennett R, Copley C, Copley D. Cybaeus (Araneae: Cybaeidae) in the Nearctic: the devius and tardatus species groups of the Californian clade. Zootaxa 2021; 5026:451-479. [PMID: 34810921 DOI: 10.11646/zootaxa.5026.4.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Indexed: 11/04/2022]
Abstract
Species of North American Cybaeus L. Koch (Araneae: RTA clade: Cybaeidae) are moist-forest spiders classified in Holarctic and Californian clades. Here, in the fourth paper in a planned series reviewing the six Californian clade species groups, we review the species of the devius and tardatus groups. We recognize five species in the devius group (Cybaeus bilectus Bennett spec. nov., C. bryoncavus Bennett spec. nov., C. devius Chamberlin Ivie, C. echo Bennett spec. nov., and C. wilsonia Bennett spec. nov.) and four in the tardatus group (C. orarius Bennett spec. nov., C. piazzai Bennett spec. nov., C. tardatus Chamberlin, and C. topanga Bennett spec. nov.). All of these species are rarely encountered and have restricted distributions either in the central and southern Sierra Nevada Mountains of eastern California, U.S.A (devius group) or the southern coast of western California (tardatus group). Some of these species are likely endangered or already extinct; most have not been seen in many decades and none have been collected more recently than 1995. Descriptions, illustrations, distribution maps, and identification keys are provided as well as a discussion of conservation issues of relevance to the group.
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Affiliation(s)
- Robb Bennett
- Department of Entomology, Natural History Section, Royal British Columbia Museum, 675 Belleville Street, Victoria, British Columbia, Canada V8W 9W2. .
| | - Claudia Copley
- Department of Entomology, Natural History Section, Royal British Columbia Museum, 675 Belleville Street, Victoria, British Columbia, Canada V8W 9W2. .
| | - Darren Copley
- Department of Entomology, Natural History Section, Royal British Columbia Museum, 675 Belleville Street, Victoria, British Columbia, Canada V8W 9W2. .
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Guo X, Selden PA, Ren D. New specimens from Mid-Cretaceous Myanmar amber illuminate the phylogenetic placement of Lagonomegopidae (Arachnida: Araneae). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
New lagonomegopid spiders are described from Mid-Cretaceous Myanmar (Burmese) amber. Two new genera and species based on single specimens, Scopomegops fax gen. & sp. nov. and Hiatomegops spinalis gen. & sp. nov. are described. Two specimens belonging to Lineaburmops beigeli are further described. Additionally, after re-examining the holotype of Odontomegops titan, a detailed description of its basal ventral abdomen is added here. A phylogenetic analysis was performed to investigate the phylogenetic placement of Lagonomegopidae. A matrix of 79 morphological characters, scored for six lagonomegopid taxa and 26 non-lagonomegopid taxa, was analysed through parsimony and Bayesian phylogenetic inference. Our results recover extant Palpimanoidea as a monophyletic group and partly suggest that Lagonomegopidae is the sister-group to extant Palpimanoidea. The external sexual organs, retrolateral tibial apophysis on the male palp and tracheal spiracle in lagonomegopids are discussed.
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Affiliation(s)
- Xiangbo Guo
- College of Life Sciences and Academy for Multidisciplinary Studies, Capital Normal University , Xisanhuanbeilu, Haidian District, Beijing , China
| | - Paul A Selden
- College of Life Sciences and Academy for Multidisciplinary Studies, Capital Normal University , Xisanhuanbeilu, Haidian District, Beijing , China
- Department of Geology, University of Kansas , Jayhawk Boulevard, Lawrence KS , USA
- Natural History Museum , London , UK
| | - Dong Ren
- College of Life Sciences and Academy for Multidisciplinary Studies, Capital Normal University , Xisanhuanbeilu, Haidian District, Beijing , China
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Ávila Herrera IM, Král J, Pastuchová M, Forman M, Musilová J, Kořínková T, Šťáhlavský F, Zrzavá M, Nguyen P, Just P, Haddad CR, Hiřman M, Koubová M, Sadílek D, Huber BA. Evolutionary pattern of karyotypes and meiosis in pholcid spiders (Araneae: Pholcidae): implications for reconstructing chromosome evolution of araneomorph spiders. BMC Ecol Evol 2021; 21:75. [PMID: 33941079 PMCID: PMC8091558 DOI: 10.1186/s12862-021-01750-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 01/25/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Despite progress in genomic analysis of spiders, their chromosome evolution is not satisfactorily understood. Most information on spider chromosomes concerns the most diversified clade, entelegyne araneomorphs. Other clades are far less studied. Our study focused on haplogyne araneomorphs, which are remarkable for their unusual sex chromosome systems and for the co-evolution of sex chromosomes and nucleolus organizer regions (NORs); some haplogynes exhibit holokinetic chromosomes. To trace the karyotype evolution of haplogynes on the family level, we analysed the number and morphology of chromosomes, sex chromosomes, NORs, and meiosis in pholcids, which are among the most diverse haplogyne families. The evolution of spider NORs is largely unknown. RESULTS Our study is based on an extensive set of species representing all major pholcid clades. Pholcids exhibit a low 2n and predominance of biarmed chromosomes, which are typical haplogyne features. Sex chromosomes and NOR patterns of pholcids are diversified. We revealed six sex chromosome systems in pholcids (X0, XY, X1X20, X1X2X30, X1X2Y, and X1X2X3X4Y). The number of NOR loci ranges from one to nine. In some clades, NORs are also found on sex chromosomes. CONCLUSIONS The evolution of cytogenetic characters was largely derived from character mapping on a recently published molecular phylogeny of the family. Based on an extensive set of species and mapping of their characters, numerous conclusions regarding the karyotype evolution of pholcids and spiders can be drawn. Our results suggest frequent autosome-autosome and autosome-sex chromosome rearrangements during pholcid evolution. Such events have previously been attributed to the reproductive isolation of species. The peculiar X1X2Y system is probably ancestral for haplogynes. Chromosomes of the X1X2Y system differ considerably in their pattern of evolution. In some pholcid clades, the X1X2Y system has transformed into the X1X20 or XY systems, and subsequently into the X0 system. The X1X2X30 system of Smeringopus pallidus probably arose from the X1X20 system by an X chromosome fission. The X1X2X3X4Y system of Kambiwa probably evolved from the X1X2Y system by integration of a chromosome pair. Nucleolus organizer regions have frequently expanded on sex chromosomes, most probably by ectopic recombination. Our data suggest the involvement of sex chromosome-linked NORs in achiasmatic pairing.
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Affiliation(s)
- Ivalú M. Ávila Herrera
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
| | - Jiří Král
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
| | - Markéta Pastuchová
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
| | - Martin Forman
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
| | - Jana Musilová
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
- Research Team of Plant Stress Biology and Biotechnology, Division of Crop Genetics and Breeding, Crop Research Institute, Drnovská 507/73, 161 00 Prague 6, Czech Republic
| | - Tereza Kořínková
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
- Prague 1, Czech Republic
| | - František Šťáhlavský
- Invertebrate Zoology Unit, Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague 2, Czech Republic
| | - Magda Zrzavá
- Laboratory of Molecular Cytogenetics, Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Laboratory of Molecular Cytogenetics, Department of Molecular Biology and Genetics, Institute of Entomology, Biology Centre CAS, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Petr Nguyen
- Laboratory of Molecular Cytogenetics, Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Laboratory of Molecular Cytogenetics, Department of Molecular Biology and Genetics, Institute of Entomology, Biology Centre CAS, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Pavel Just
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
- Invertebrate Zoology Unit, Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague 2, Czech Republic
| | - Charles R. Haddad
- Research Group of Arachnid Systematics and Ecology, Department of Zoology and Entomology, Faculty of Natural and Agricultural Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300 Republic of South Africa
| | - Matyáš Hiřman
- Invertebrate Zoology Unit, Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague 2, Czech Republic
| | - Martina Koubová
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
| | - David Sadílek
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
- Invertebrate Zoology Unit, Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague 2, Czech Republic
| | - Bernhard A. Huber
- Arachnida Section, Alexander Koenig Zoological Research Museum, Adenauerallee 160, 53113 Bonn, Germany
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Kulkarni S, Kallal RJ, Wood H, Dimitrov D, Giribet G, Hormiga G. Interrogating Genomic-Scale Data to Resolve Recalcitrant Nodes in the Spider Tree of Life. Mol Biol Evol 2021; 38:891-903. [PMID: 32986823 PMCID: PMC7947752 DOI: 10.1093/molbev/msaa251] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genome-scale data sets are converging on robust, stable phylogenetic hypotheses for many lineages; however, some nodes have shown disagreement across classes of data. We use spiders (Araneae) as a system to identify the causes of incongruence in phylogenetic signal between three classes of data: exons (as in phylotranscriptomics), noncoding regions (included in ultraconserved elements [UCE] analyses), and a combination of both (as in UCE analyses). Gene orthologs, coded as amino acids and nucleotides (with and without third codon positions), were generated by querying published transcriptomes for UCEs, recovering 1,931 UCE loci (codingUCEs). We expected that congeners represented in the codingUCE and UCEs data would form clades in the presence of phylogenetic signal. Noncoding regions derived from UCE sequences were recovered to test the stability of relationships. Phylogenetic relationships resulting from all analyses were largely congruent. All nucleotide data sets from transcriptomes, UCEs, or a combination of both recovered similar topologies in contrast with results from transcriptomes analyzed as amino acids. Most relationships inferred from low-occupancy data sets, containing several hundreds of loci, were congruent across Araneae, as opposed to high occupancy data matrices with fewer loci, which showed more variation. Furthermore, we found that low-occupancy data sets analyzed as nucleotides (as is typical of UCE data sets) can result in more congruent relationships than high occupancy data sets analyzed as amino acids (as in phylotranscriptomics). Thus, omitting data, through amino acid translation or via retention of only high occupancy loci, may have a deleterious effect in phylogenetic reconstruction.
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Affiliation(s)
- Siddharth Kulkarni
- Department of Biological Sciences, The George Washington University, Washington, DC
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC
| | - Robert J Kallal
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC
| | - Hannah Wood
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, Washington, DC
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Ramírez MJ, Magalhaes ILF, Derkarabetian S, Ledford J, Griswold CE, Wood HM, Hedin M. Sequence Capture Phylogenomics of True Spiders Reveals Convergent Evolution of Respiratory Systems. Syst Biol 2020; 70:14-20. [PMID: 32497195 DOI: 10.1093/sysbio/syaa043] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 05/16/2020] [Accepted: 05/27/2020] [Indexed: 12/25/2022] Open
Abstract
The common ancestor of spiders likely used silk to line burrows or make simple webs, with specialized spinning organs and aerial webs originating with the evolution of the megadiverse "true spiders" (Araneomorphae). The base of the araneomorph tree also concentrates the greatest number of changes in respiratory structures, a character system whose evolution is still poorly understood, and that might be related to the evolution of silk glands. Emphasizing a dense sampling of multiple araneomorph lineages where tracheal systems likely originated, we gathered genomic-scale data and reconstructed a phylogeny of true spiders. This robust phylogenomic framework was used to conduct maximum likelihood and Bayesian character evolution analyses for respiratory systems, silk glands, and aerial webs, based on a combination of original and published data. Our results indicate that in true spiders, posterior book lungs were transformed into morphologically similar tracheal systems six times independently, after the evolution of novel silk gland systems and the origin of aerial webs. From these comparative data, we put forth a novel hypothesis that early-diverging web-building spiders were faced with new energetic demands for spinning, which prompted the evolution of similar tracheal systems via convergence; we also propose tests of predictions derived from this hypothesis.[Book lungs; discrete character evolution; respiratory systems; silk; spider web evolution; ultraconserved elements.].
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Affiliation(s)
- Martín J Ramírez
- Division of Arachnology, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Buenos Aires, Argentina
| | - Ivan L F Magalhaes
- Division of Arachnology, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Buenos Aires, Argentina
| | - Shahan Derkarabetian
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joel Ledford
- Department of Plant Biology, University of California, Davis, CA 95616 USA
| | - Charles E Griswold
- Entomology, California Academy of Sciences, San Francisco, CA, 94118, USA
| | - Hannah M Wood
- National Museum of Natural History, Smithsonian Institution, Washington DC 20560-0188, USA
| | - Marshal Hedin
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
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