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Derkarabetian S, Benavides LR, Giribet G. Reassessing the phylogeny of Cyphophthalmi with phylogenomics: A UCE-based phylogeny of mite harvesters (Opiliones). Mol Phylogenet Evol 2024; 199:108143. [PMID: 38977042 DOI: 10.1016/j.ympev.2024.108143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/23/2024] [Accepted: 07/01/2024] [Indexed: 07/10/2024]
Abstract
Cyphophthalmi (the mite harvesters) are a group of Opiliones with broad interest due to their species being classic examples of short-range endemics and displaying model biogeographical patterns for poor dispersers. Cyphophthalmi phylogeny has received attention using morphology, Sanger-based sequencing data, or transcriptomics. Here we turn to a new type of data, ultraconserved elements (UCEs) and provide a first phylogeny for the entire suborder Cyphophthalmi using such data and including representatives from 36 of the 46 currently recognized genera. Phylogenetic analysis of four occupancy matrices (50%, 75%, 90% and 95%), for a total of 840, 567, 129, and 23 loci, respectively, yielded a well resolved phylogeny with monophyly of Pettalidae, Parasironidae, Stylocellidae and Troglosironidae. However, Neogoveidae appeared paraphyletic with respect to Ogoveidae in all datasets and to Troglosironidae in some, and the traditional Sironidae, which was monophyletic, now appeared paraphyletic with respect to the recently erected family Parasironidae. Our phylogenomic results using UCE data resolve the position of several problematic genera (e.g., Pettalus) and add support to other parts of the tree that received low support in Sanger-based phylogenies. Our work also stresses the possibility to add museum samples to phylogenies although methods for optimizing DNA yield from such small-bodied specimens need further improvement. Finally, this backbone phylogeny demonstrates the feasibility of an all-species phylogeny using UCEs for Cyphophthalmi, and by extension, for all Opiliones.
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Affiliation(s)
- Shahan Derkarabetian
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; San Diego Natural History Museum, Department of Entomology, San Diego, CA, USA
| | - Ligia R Benavides
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
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2
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Azevedo GHF, Hedin M, Maddison WP. Phylogeny and biogeography of harmochirine jumping spiders (Araneae: Salticidae). Mol Phylogenet Evol 2024; 197:108109. [PMID: 38768874 DOI: 10.1016/j.ympev.2024.108109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 05/02/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
We use ultraconserved elements (UCE) and Sanger data to study the phylogeny, age, and biogeographical history of harmochirine jumping spiders, a group that includes the species-rich genus Habronattus, whose remarkable courtship has made it the focus of studies of behaviour, sexual selection, and diversification. We recovered 1947 UCE loci from 43 harmochirine taxa and 4 outgroups, yielding a core dataset of 193 UCEs with at least 50 % occupancy. Concatenated likelihood and ASTRAL analyses confirmed the separation of harmochirines into two major clades, here designated the infratribes Harmochirita and Pellenita. Most are African or Eurasian with the notable exception of a clade of pellenites containing Habronattus and Pellenattus of the Americas and Havaika and Hivanua of the Pacific Islands. Biogeographical analysis using the DEC model favours a dispersal of the clade's ancestor from Eurasia to the Americas, from which Havaika's ancestor dispersed to Hawaii and Hivanua's ancestor to the Marquesas Islands. Divergence time analysis on 32 loci with 85 % occupancy, calibrated by fossils and island age, dates the dispersal to the Americas at approximately 4 to 6 million years ago. The explosive radiation of Habronattus perhaps began only about 4 mya. The phylogeny clarifies both the evolution of sexual traits (e.g., the terminal apophyses was enlarged in Pellenes and not subsequently lost) and the taxonomy. Habronattus is confirmed as monophyletic. Pellenattus is raised to the status of genus, and 13 species moved into it as new combinations. Bianor stepposus Logunov, 1991 is transferred to Sibianor, and Pellenes bulawayoensis Wesołowska, 1999 is transferred to Neaetha. A molecular clock rate estimate for spider UCEs is presented and its utility to inform prior distributions is discussed.
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Affiliation(s)
| | - Marshal Hedin
- Dept of Biology, San Diego State University, San Diego, CA 92182, United States
| | - Wayne P Maddison
- Departments of Zoology and Botany and Beaty Biodiversity Museum, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
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3
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Monjaraz-Ruedas R, Starrett J, Leavitt D, Hedin M. Broken Ring Speciation in California Mygalomorph Spiders (Nemesiidae, Calisoga). Am Nat 2024; 204:55-72. [PMID: 38857341 DOI: 10.1086/730262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
AbstractIdealized ring species, with approximately continuous gene flow around a geographic barrier but singular reproductive isolation at a ring terminus, are rare in nature. A broken ring species model preserves the geographic setting and fundamental features of an idealized model but accommodates varying degrees of gene flow restriction over complex landscapes through evolutionary time. Here we examine broken ring species dynamics in Calisoga spiders, which, like the classic ring species Ensatina salamanders, are distributed around the Central Valley of California. Using nuclear and mitogenomic data, we test key predictions of common ancestry, ringlike biogeography, biogeographic timing, population connectivity, and terminal overlap. We show that a ring complex of populations shares a single common ancestor, and from an ancestral area in the Sierra Nevada mountains, two distributional and phylogenomic arms encircle the Central Valley. Isolation by distance occurs along these distributional arms, although gene flow restriction is also evident. Where divergent lineages meet in the South Coast Ranges, we find rare lineage sympatry, without evidence for nuclear gene flow and with clear evidence for morphological and ecological divergence. We discuss general insights provided by broken ring species and how such a model could be explored and extended in other systems and future studies.
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4
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Heine HLA, Derkarabetian S, Morisawa R, Fu PA, Moyes NHW, Boyer SL. Machine learning approaches delimit cryptic taxa in a previously intractable species complex. Mol Phylogenet Evol 2024; 195:108061. [PMID: 38485107 DOI: 10.1016/j.ympev.2024.108061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 04/20/2024]
Abstract
Cryptic species are not diagnosable via morphological criteria, but can be detected through analysis of DNA sequences. A number of methods have been developed for identifying species based on genetic data; however, these methods are prone to over-splitting taxa with extreme population structure, such as dispersal-limited organisms. Machine learning methodologies have the potential to overcome this challenge. Here, we apply such approaches, using a large dataset generated through hybrid target enrichment of ultraconserved elements (UCEs). Our study taxon is the Aoraki denticulata species complex, a lineage of extremely low-dispersal arachnids endemic to the South Island of Aotearoa New Zealand. This group of mite harvesters has been the subject of previous species delimitation studies using smaller datasets generated through Sanger sequencing and analytical approaches that rely on multispecies coalescent models and barcoding gap discovery. Those analyses yielded a number of putative cryptic species that seems unrealistic and extreme, based on what we know about species' geographic ranges and genetic diversity in non-cryptic mite harvesters. We find that machine learning approaches, on the other hand, identify cryptic species with geographic ranges that are similar to those seen in other morphologically diagnosable mite harvesters in Aotearoa New Zealand's South Island. We performed both unsupervised and supervised machine learning analyses, the latter with training data drawn either from animals broadly (vagile and non-vagile) or from a custom training dataset from dispersal-limited harvesters. We conclude that applying machine learning approaches to the analysis of UCE-derived genetic data is an effective method for delimiting species in complexes of low-vagility cryptic species, and that the incorporation of training data from biologically relevant analogues can be critically informative.
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Affiliation(s)
- Haley L A Heine
- Biology Department, Macalester College, 1600 Grand Ave., St. Paul, MN 55105, USA.
| | - Shahan Derkarabetian
- Museum of Comparative Zoology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA.
| | - Rina Morisawa
- Biology Department, Macalester College, 1600 Grand Ave., St. Paul, MN 55105, USA.
| | - Phoebe A Fu
- Biology Department, Macalester College, 1600 Grand Ave., St. Paul, MN 55105, USA.
| | - Nathaniel H W Moyes
- Biology Department, Macalester College, 1600 Grand Ave., St. Paul, MN 55105, USA.
| | - Sarah L Boyer
- Biology Department, Macalester College, 1600 Grand Ave., St. Paul, MN 55105, USA.
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5
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Maddison WP. Hivanua, a new genus of harmochirine jumping spiders from the Marquesas Islands (Araneae, Salticidae, Harmochirina). Zookeys 2024; 1200:215-230. [PMID: 38766409 PMCID: PMC11099472 DOI: 10.3897/zookeys.1200.120868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/02/2024] [Indexed: 05/22/2024] Open
Abstract
The genus Hivanuagen. nov. is established for the harmochirine jumping spiders of the Marquesas Islands, formerly placed in Habronattus F.O. Pickard-Cambridge, 1901 and Havaika Prószyński, 2002. The type species, Hivanuatekaosp. nov. is described, and five species described by Berland are re-illustrated and moved into the genus: Hivanuaflavipes (Berland, 1933), comb. nov., Hivanuanigrescens (Berland, 1933), comb. nov., Hivanuanigrolineata (Berland, 1933), comb. nov., Hivanuarufescens (Berland, 1934), comb. nov., and Hivanuatriangulifera (Berland, 1933), comb. nov. The female epigyne is much like that of Habronattus, Bianor Peckham & Peckham, 1896, and other harmochirines, with a centrally placed coupling pocket and two atria with crescent-shaped edges. The terminal apophysis of the male palp, which is variable throughout the pellenine subgroup of the Harmochirina, is absent in H.rufescens but present in H.tekaosp. nov., in which it is elbowed much as in Habronattus. These Pacific Island harmochirines, like the Havaika of Hawaii, appear to be largely foliage dwellers, unlike most of their continental relatives.
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Affiliation(s)
- Wayne P. Maddison
- Departments of Zoology and Botany and Beaty Biodiversity Museum, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, CanadaUniversity of British ColumbiaVancouverCanada
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Gajski D, Wolff JO, Melcher A, Weber S, Prost S, Krehenwinkel H, Kennedy SR. Facilitating taxonomy and phylogenetics: An informative and cost-effective protocol integrating long amplicon PCRs and third-generation sequencing. Mol Phylogenet Evol 2024; 192:107988. [PMID: 38072140 DOI: 10.1016/j.ympev.2023.107988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/22/2023] [Accepted: 12/07/2023] [Indexed: 12/31/2023]
Abstract
Phylogenetic inference has become a standard technique in integrative taxonomy and systematics, as well as in biogeography and ecology. DNA barcodes are often used for phylogenetic inference, despite being strongly limited due to their low number of informative sites. Also, because current DNA barcodes are based on a fraction of a single, fast-evolving gene, they are highly unsuitable for resolving deeper phylogenetic relationships due to saturation. In recent years, methods that analyse hundreds and thousands of loci at once have improved the resolution of the Tree of Life, but these methods require resources, experience and molecular laboratories that most taxonomists do not have. This paper introduces a PCR-based protocol that produces long amplicons of both slow- and fast-evolving unlinked mitochondrial and nuclear gene regions, which can be sequenced by the affordable and portable ONT MinION platform with low infrastructure or funding requirements. As a proof of concept, we inferred a phylogeny of a sample of 63 spider species from 20 families using our proposed protocol. The results were overall consistent with the results from approaches based on hundreds and thousands of loci, while requiring just a fraction of the cost and labour of such approaches, making our protocol accessible to taxonomists worldwide.
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Affiliation(s)
- Domagoj Gajski
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno 611 37, Czech Republic
| | - Jonas O Wolff
- Evolutionary Biomechanics, Zoological Institute and Museum, University of Greifswald, Loitzer Str. 26, Greifswald 17489, Germany; School of Natural Sciences, Macquarie University, NSW 2109, Sydney, Australia
| | - Anja Melcher
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Sven Weber
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Stefan Prost
- Ecology and Genetics Research Unit, University of Oulu, Pentti Kaiteran katu 1, Linnanmaa, Finland
| | - Henrik Krehenwinkel
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Susan R Kennedy
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany.
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7
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Kulkarni SS, Yamasaki T, Thi Hong Phung L, Karuaera N, Daniels SR, Gavish-Regev E, Sharma PP. Phylogenomic data reveal three new families of poorly studied Solifugae (camel spiders). Mol Phylogenet Evol 2024; 191:107989. [PMID: 38072141 DOI: 10.1016/j.ympev.2023.107989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/16/2023] [Accepted: 12/07/2023] [Indexed: 12/18/2023]
Abstract
The systematics of the arachnid order Solifugae have been an enigma, owing to challenges in interpreting morphology, a paucity of molecular phylogenetic studies sampling across the group, and a dearth of taxonomic attention for many lineages. Recent work has suggested that solifuge families largely exhibit contiguous distributions and reflect patterns of vicariance, with the exception of three families: Melanoblossidae, Daesiidae and Gylippidae. Morphological studies have cast doubt on their existing circumscriptions and the present composition of these taxa renders their distributions as disjunct. We leveraged ultraconserved elements (UCEs) to test the phylogenetic placement of three key lineages of Solifugae that cause these anomalous distributions: Dinorhax rostrumpsittaci (putative melanoblossid), Namibesia (putative daesiid), and Trichotoma (putative gylippid). Phylogenetic placement of these three genera based on UCEs rendered the families that harbor them as para- or polyphyletic, recovering instead relationships that better accord with a biogeographic history driven by vicariance. Toward a stable and phylogenetically informed classification of Solifugae, we establish three new families, Dinorhaxidae new rank, Namibesiidae new rank and Lipophagidae new rank.
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Affiliation(s)
- Siddharth S Kulkarni
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Takeshi Yamasaki
- Institute of Natural and Environmental Sciences, University of Hyogo, Yayoigaoka 6, Sanda-shi, Hyogo 669-1546, Japan; Museum of Nature and Human Activities, Hyogo, Yayoigaoka 6, Sanda-shi, Hyogo 669-1546, Japan
| | - Luong Thi Hong Phung
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay District, Hanoi, Viet Nam
| | - Nanguei Karuaera
- Department of Arachnology & Myriapodology & Ichthyology Natural Science, The National Museum of Namibia, 59 Robert Mugabe Ave, Windhoek, Namibia
| | - Savel R Daniels
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - Efrat Gavish-Regev
- The National Natural History Collections, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Giv'at Ram, Jerusalem 9190401, Israel
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA; Zoology Museum, University of Wisconsin-Madison, Madison, WI 53706, USA
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8
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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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9
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Santibáñez-López CE, Ojanguren-Affilastro AA, Graham MR, Sharma PP. Congruence between ultraconserved element-based matrices and phylotranscriptomic datasets in the scorpion Tree of Life. Cladistics 2023; 39:533-547. [PMID: 37401727 DOI: 10.1111/cla.12551] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2023] [Indexed: 07/05/2023] Open
Abstract
Scorpions are ancient and historically renowned for their potent venom. Traditionally, the systematics of this group of arthropods was supported by morphological characters, until recent phylogenomic analyses (using RNAseq data) revealed most of the higher-level taxa to be non-monophyletic. While these phylogenomic hypotheses are stable for almost all lineages, some nodes have been hard to resolve due to minimal taxonomic sampling (e.g. family Chactidae). In the same line, it has been shown that some nodes in the Arachnid Tree of Life show disagreement between hypotheses generated using transcritptomes and other genomic sources such as the ultraconserved elements (UCEs). Here, we compared the phylogenetic signal of transcriptomes vs. UCEs by retrieving UCEs from new and previously published scorpion transcriptomes and genomes, and reconstructed phylogenies using both datasets independently. We reexamined the monophyly and phylogenetic placement of Chactidae, sampling an additional chactid species using both datasets. Our results showed that both sets of genome-scale datasets recovered highly similar topologies, with Chactidae rendered paraphyletic owing to the placement of Nullibrotheas allenii. As a first step toward redressing the systematics of Chactidae, we establish the family Anuroctonidae (new family) to accommodate the genus Anuroctonus.
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Affiliation(s)
| | | | - Matthew R Graham
- Department of Biology, Eastern Connecticut State University, Willimantic, CT, 06226, USA
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
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10
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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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11
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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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12
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Kelly MBJ, Khan MK, Wierucka K, Jones BR, Shofner R, Derkarabetian S, Wolff JO. Dynamic evolution of locomotor performance independent of changes in extended phenotype use in spiders. Proc Biol Sci 2023; 290:20232035. [PMID: 37876190 PMCID: PMC10598421 DOI: 10.1098/rspb.2023.2035] [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: 05/03/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023] Open
Abstract
Many animals use self-built structures (extended phenotypes) to enhance body functions, such as thermoregulation, prey capture or defence. Yet, it is unclear whether the evolution of animal constructions supplements or substitutes body functions-with disparate feedbacks on trait evolution. Here, using brown spiders (Araneae: marronoid clade), we explored if the evolutionary loss and gain of silken webs as extended prey capture devices correlates with alterations in traits known to play an important role in predatory strikes-locomotor performance (sprint speed) and leg spination (expression of capture spines on front legs). We found that in this group high locomotor performance, with running speeds of over 100 body lengths per second, evolved repeatedly-both in web-building and cursorial spiders. There was no correlation with running speed, and leg spination only poorly correlated, relative to the use of extended phenotypes, indicating that web use does not reduce selective pressures on body functions involved in prey capture and defence per se. Consequently, extended prey capture devices serve as supplements rather than substitutions to body traits and may only be beneficial in conjunction with certain life-history traits, possibly explaining the rare evolution and repeated loss of trapping strategies in predatory animals.
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Affiliation(s)
- Michael B. J. Kelly
- Evolutionary Biomechanics, Zoological Institute and Museum, University of Greifswald, Loitzer Strasse 26, 17489 Greifswald, Germany
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Md Kawsar Khan
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- Institute of Biology, Freie Universität Berlin, Königin-Luise-Straße 1-3, 14195 Berlin, Germany
| | - Kaja Wierucka
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- Behavioural Ecology and Sociobiology Unit, German Primate Center - Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Braxton R. Jones
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- School of Biological Sciences, University of Sydney, Camperdown, New South Wales 2006, Australia
| | - Ryan Shofner
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences E26, University of New South Wales, Sydney 2052, Australia
| | - Shahan Derkarabetian
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Jonas O. Wolff
- Evolutionary Biomechanics, Zoological Institute and Museum, University of Greifswald, Loitzer Strasse 26, 17489 Greifswald, Germany
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
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13
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Derkarabetian S, Lord A, Angier K, Frigyik E, Giribet G. An Opiliones-specific ultraconserved element probe set with a near-complete family-level phylogeny. Mol Phylogenet Evol 2023; 187:107887. [PMID: 37479049 DOI: 10.1016/j.ympev.2023.107887] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/23/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023]
Abstract
Sequence capture of ultraconserved elements (UCEs) has transformed molecular systematics across many taxa, with arachnids being no exception. The probe set available for Arachnida has been repeatedly used across multiple arachnid lineages and taxonomic levels, however more specific probe sets for spiders have demonstrated that more UCEs can be recovered with higher probe specificity. In this study, we develop an Opiliones-specific UCE probe set targeting 1915 UCEs using a combination of probes designed from genomes and transcriptomes, as well as the most useful probes from the Arachnida probe set. We demonstrate the effectiveness of this probe set across Opiliones with the most complete family-level phylogeny made to date, including representatives from 61 of 63 currently described families. We also test UCE recovery from historical specimens with degraded DNA, examine population-level data sets, and assess "backwards compatibility" with samples hybridized with the Arachnida probe set. The resulting phylogenies - which include specimens hybridized using both the Opiliones and Arachnida probe sets, historical specimens, and transcriptomes - are largely congruent with previous multi-locus and phylogenomic analyses. The probe set is also "backwards compatible", increasing the number of loci obtained in samples previously hybridized with the Arachnida probe set, and shows high utility down to shallow population-level divergences. This probe set has the potential to further transform Opiliones molecular systematics, resolving many long-standing taxonomic issues plaguing this lineage.
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Affiliation(s)
- Shahan Derkarabetian
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Arianna Lord
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Katherine Angier
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Ella Frigyik
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
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14
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Ojanguren-Affilastro AA, Pizarro-Araya J, Santibáñez-López CE. Old and cold: Diverse phylogenomic datasets support an ancient transantarctic dispersive route on the scorpion family Bothriuridae in temperate Gondwana. Mol Phylogenet Evol 2023; 187:107886. [PMID: 37474014 DOI: 10.1016/j.ympev.2023.107886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/22/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023]
Abstract
In this contribution we try to unveil the diversification process of Bothriuridae in temperate Gondwana through dated phylogenomic analyses using UCE and transcriptomics, and including in the analyses species of genera Urophonius and Cercophonius, the most closely related genera of Bothriuridae from South America and Australia respectively. Additionally we explored the hypothesis that the winter activity period of some species of Urophonius, as well as the cold environmental preferences of this genus, could be related to the climatic conditions of the time frame and area in which it evolved. Genus Urophonius was recovered as sister group to Cercophonius using amino acids and UCE. The time frame obtained for the split between South American and Australian bothriurids is 94 Ma., which suggests a dispersal event through temperate Gondwana, before the final breakup of the land bridge of South America-Antarctica-Australia ca. 35 Ma. The split between summer and winter species of Urophonius, taking place at 64 Ma, is considered representative to the turnover time from the summer activity period to the winter activity period in some species of the genus. This time frame is compatible with a period of global warming of the late Cretaceous greenhouse episode that could have triggered this change.
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Affiliation(s)
| | - Jaime Pizarro-Araya
- Laboratorio de Entomología Ecológica (LEULS), Departamento de Biología, Facultad de Ciencias, Universidad de La Serena, La Serena, Chile; Grupo de Artrópodos, Sistema Integrado de Monitoreo y Evaluación de Ecosistemas Forestales Nativos (SIMEF), Santiago, Chile; Instituto de Ecología y Biodiversidad (IEB), La Serena, Chile
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15
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Kulkarni SS, Steiner HG, Garcia EL, Iuri H, Jones RR, Ballesteros JA, Gainett G, Graham MR, Harms D, Lyle R, Ojanguren-Affilastro AA, Santibañez-López CE, Silva de Miranda G, Cushing PE, Gavish-Regev E, Sharma PP. Neglected no longer: Phylogenomic resolution of higher-level relationships in Solifugae. iScience 2023; 26:107684. [PMID: 37694155 PMCID: PMC10484990 DOI: 10.1016/j.isci.2023.107684] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/26/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023] Open
Abstract
Advanced sequencing technologies have expedited resolution of higher-level arthropod relationships. Yet, dark branches persist, principally among groups occurring in cryptic habitats. Among chelicerates, Solifugae ("camel spiders") is the last order lacking a higher-level phylogeny and have thus been historically characterized as "neglected [arachnid] cousins". Though renowned for aggression, remarkable running speed, and xeric adaptation, inferring solifuge relationships has been hindered by inaccessibility of diagnostic morphological characters, whereas molecular investigations have been limited to one of 12 recognized families. Our phylogenomic dataset via capture of ultraconserved elements sampling all extant families recovered a well-resolved phylogeny, with two distinct groups of New World taxa nested within a broader Paleotropical radiation. Divergence times using fossil calibrations inferred that Solifugae radiated by the Permian, and most families diverged prior to the Paleogene-Cretaceous extinction, likely driven by continental breakup. We establish Boreosolifugae new suborder uniting five Laurasian families, and Australosolifugae new suborder uniting seven Gondwanan families using morphological and biogeographic signal.
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Affiliation(s)
- Siddharth S. Kulkarni
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Hugh G. Steiner
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Erika L. Garcia
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO 80205, USA
| | - Hernán Iuri
- División de Aracnología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Buenos Aires 1405DJR, Argentina
| | - R. Ryan Jones
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO 80205, USA
| | | | - Guilherme Gainett
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Matthew R. Graham
- Department of Biology, Eastern Connecticut State University, Willimantic, CT 06226, USA
| | - Danilo Harms
- Museum of Nature Hamburg - Zoology, Department of Invertebrates, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg, Germany
| | - Robin Lyle
- Biosystematics: Arachnology, ARC—Plant Health and Protection, Pretoria, South Africa
| | | | | | - Gustavo Silva de Miranda
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Paula E. Cushing
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO 80205, USA
| | - Efrat Gavish-Regev
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Prashant P. Sharma
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI 53706, USA
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16
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Kuntner M, Čandek K, Gregorič M, Turk E, Hamilton CA, Chamberland L, Starrett J, Cheng RC, Coddington JA, Agnarsson I, Bond JE. Increasing Information Content and Diagnosability in Family-Level Classifications. Syst Biol 2023; 72:964-971. [PMID: 37161751 PMCID: PMC10405354 DOI: 10.1093/sysbio/syad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 03/03/2023] [Accepted: 04/13/2023] [Indexed: 05/11/2023] Open
Abstract
Higher-level classifications often must account for monotypic taxa representing depauperate evolutionary lineages and lacking synapomorphies of their better-known, well-defined sister clades. In a ranked (Linnean) or unranked (phylogenetic) classification system, discovering such a depauperate taxon does not necessarily invalidate the rank classification of sister clades. Named higher taxa must be monophyletic to be phylogenetically valid. Ranked taxa above the species level should also maximize information content, diagnosability, and utility (e.g., in biodiversity conservation). In spider classification, families are the highest rank that is systematically catalogued, and incertae sedis is not allowed. Consequently, it is important that family-level taxa be well defined and informative. We revisit the classification problem of Orbipurae, an unranked suprafamilial clade containing the spider families Nephilidae, Phonognathidae, and Araneidae sensu stricto. We argue that, to maximize diagnosability, information content, conservation utility, and practical taxonomic considerations, this "splitting" scheme is superior to its recently proposed alternative, which lumps these families together as Araneidae sensu lato. We propose to redefine Araneidae and recognize a monogeneric spider family, Paraplectanoididae fam. nov. to accommodate the depauperate lineage Paraplectanoides. We present new subgenomic data to stabilize Orbipurae topology which also supports our proposed family-level classification. Our example from spiders demonstrates why classifications must be able to accommodate depauperate evolutionary lineages, for example, Paraplectanoides. Finally, although clade age should not be a criterion to determine rank, other things being equal, comparable ages of similarly ranked taxa do benefit comparative biology. [Classification, family rank, phylogenomics, systematics, monophyly, spider phylogeny.].
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Affiliation(s)
- Matjaž Kuntner
- Department of Organisms and Ecosystems Research, National Institute of Biology, Večna pot 111, SI-1000, Ljubljana, Slovenia
- Jovan Hadži Institute of Biology, Research Centre of the Slovenian Academy of Sciences and Arts, Novi trg 2, SI-1001, Ljubljana, Slovenia
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution, NW, Washington, DC 20560-0105, USA
- University of Ljubljana, National Institute of Biology, Večna pot 111, SI-1000, Ljubljana, Slovenia
- State Key Laboratory of Biocatalysis and Enzyme Engineering and Centre for Behavioural Ecology and Evolution, School of Life Sciences, Hubei University, Wuhan 430062 Hubei, China
| | - Klemen Čandek
- Department of Organisms and Ecosystems Research, National Institute of Biology, Večna pot 111, SI-1000, Ljubljana, Slovenia
- University of Ljubljana, National Institute of Biology, Večna pot 111, SI-1000, Ljubljana, Slovenia
| | - Matjaž Gregorič
- Jovan Hadži Institute of Biology, Research Centre of the Slovenian Academy of Sciences and Arts, Novi trg 2, SI-1001, Ljubljana, Slovenia
| | - Eva Turk
- University of Ljubljana, National Institute of Biology, Večna pot 111, SI-1000, Ljubljana, Slovenia
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, SI-1000, Ljubljana, Slovenia
| | - Chris A Hamilton
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, 875 Perimeter Dr. MS 2329, Moscow, ID 83844-2329, USA
| | - Lisa Chamberland
- Department of Entomology and Nematology, University of California Davis, 1 Shields Ave., Davis, CA 95616, USA
| | - James Starrett
- Department of Entomology and Nematology, University of California Davis, 1 Shields Ave., Davis, CA 95616, USA
| | - Ren-Chung Cheng
- Department of Life Sciences, National Chung Hsing University, No.145 Xingda Rd., South Dist., Taichung City 402, Taiwan
| | - Jonathan A Coddington
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution, NW, Washington, DC 20560-0105, USA
| | - Ingi Agnarsson
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution, NW, Washington, DC 20560-0105, USA
- State Key Laboratory of Biocatalysis and Enzyme Engineering and Centre for Behavioural Ecology and Evolution, School of Life Sciences, Hubei University, Wuhan 430062 Hubei, China
- Faculty of Life- and Environmental Sciences, University of Iceland, Sturlugata 7, 102 Reykjavik, Iceland
| | - Jason E Bond
- Department of Entomology and Nematology, University of California Davis, 1 Shields Ave., Davis, CA 95616, USA
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17
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Monjaraz-Ruedas R, Mendez RW, Hedin M. Species delimitation, biogeography, and natural history of dwarf funnel web spiders (Mygalomorphae, Hexurellidae, Hexurella) from the United States / Mexico borderlands. Zookeys 2023; 1167:109-157. [PMID: 37363739 PMCID: PMC10285686 DOI: 10.3897/zookeys.1167.103463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/29/2023] [Indexed: 06/28/2023] Open
Abstract
The rarely encountered spider genus Hexurella Gertsch & Platnick, 1979 includes some of the smallest mygalomorph spiders in the world, with four poorly known taxa from central and southeastern montane Arizona, southern California, and northern Baja California Norte. At time of description the genus was known from fewer than 20 individuals, with sparse natural history information suggesting a vagrant, web-building, litter-dwelling natural history. Here the first published taxonomic and natural history information for this taxon is provided in more than 50 years, working from extensive new geographic sampling, consideration of male and female morphology, and sequence capture-based nuclear phylogenomics and mitogenomics. Several new species are easily diagnosed based on distinctive male morphologies, while a complex of populations from central and northern Arizona required an integrative combination of genomic algorithmic species delimitation analyses and morphological study. Four new species are described, including H.ephedrasp. nov., H.uwiiltilsp. nov., H.xericasp. nov., and H.zassp. nov. Females of H.encina Gertsch & Platnick, 1979 are also described for the first time. It is predicted that additional new species will ultimately be found in the mountains of central and northwestern Arizona, northern mainland Mexico, and the Mojave Desert of California.
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Affiliation(s)
- Rodrigo Monjaraz-Ruedas
- Department of Biology, San Diego State University, San Diego, California 92182–4614, USASan Diego State UniversitySan DiegoUnited States of America
| | | | - Marshal Hedin
- Department of Biology, San Diego State University, San Diego, California 92182–4614, USASan Diego State UniversitySan DiegoUnited States of America
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18
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Kulkarni S, Wood HM, Hormiga G. Phylogenomics illuminates the evolution of orb webs, respiratory systems and the biogeographic history of the world's smallest orb-weaving spiders (Araneae, Araneoidea, Symphytognathoids). Mol Phylogenet Evol 2023:107855. [PMID: 37311493 DOI: 10.1016/j.ympev.2023.107855] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/01/2023] [Accepted: 06/07/2023] [Indexed: 06/15/2023]
Abstract
The miniature orb weaving spiders (symphytognathoids) are a group of small spiders (< 2 mm), including the smallest adult spider Patu digua (0.37 mm in body length), that have been classified into five families. The species of one of its constituent lineages, the family Anapidae, build a remarkable diversity of webs (ranging from orbs to sheet webs and irregular tangles) and even include a webless kleptoparasitic species. Anapids are also exceptional because of the extraordinary diversity of their respiratory systems. The phylogenetic relationships of symphytognathoid families have been recalcitrant with different classes of data, such as, monophyletic with morphology and its concatenation with Sanger-based six markers, paraphyletic (including a paraphyletic Anapidae) with solely Sanger-based six markers, and polyphyletic with transcriptomes. In this study, we capitalized on a large taxonomic sampling of symphytognathoids, focusing on Anapidae, and using de novo sequenced ultraconserved elements (UCEs) combined with UCEs recovered from available transcriptomes and genomes. We evaluated the conflicting relationships using a variety of support metrics and topology tests. We found support for the phylogenetic hypothesis proposed using morphology to obtain the "symphytognathoids'' clade, Anterior Tracheal System (ANTS) Clade and monophyly of the family Anapidae. Anapidae can be divided into three major lineages, the Vichitra Clade (including Teutoniella, Holarchaea, Sofanapis and Acrobleps), the subfamily Micropholcommatinae and the Orb-weaving anapids (Owa) Clade. Biogeographic analyses reconstructed a hypothesis of multiple long-distance transoceanic dispersal events, potentially influenced by the Antarctic Circumpolar Current and West Wind Drift. In symphytognathoids, the ancestral anterior tracheal system transformed to book lungs four times and reduced book lungs five times. The posterior tracheal system was lost six times. The orb web structure was lost four times independently and transformed into sheet web once.
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Affiliation(s)
- Siddharth Kulkarni
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, D.C. 20052, USA; Department of Entomology, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Avenue NW, Washington, DC, 20560, USA; (currently) Department of Integrative Biology, University of Wisconsin-Madison, Madison, 53706, 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, D.C. 20052, USA.
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19
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Zhang J, Li Z, Lai J, Zhang Z, Zhang F. A novel probe set for the phylogenomics and evolution of RTA spiders. Cladistics 2023; 39:116-128. [PMID: 36719825 DOI: 10.1111/cla.12523] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/10/2022] [Accepted: 12/21/2022] [Indexed: 02/01/2023] Open
Abstract
Spiders are important models for evolutionary studies of web building, sexual selection and adaptive radiation. The recent development of probes for UCE (ultra-conserved element)-based phylogenomic studies has shed light on the phylogeny and evolution of spiders. However, the two available UCE probe sets for spider phylogenomics (Spider and Arachnida probe sets) have relatively low capture efficiency within spiders, and are not optimized for the retrolateral tibial apophysis (RTA) clade, a hyperdiverse lineage that is key to understanding the evolution and diversification of spiders. In this study, we sequenced 15 genomes of species in the RTA clade, and using eight reference genomes, we developed a new UCE probe set (41 845 probes targeting 3802 loci, labelled as the RTA probe set). The performance of the RTA probes in resolving the phylogeny of the RTA clade was compared with the Spider and Arachnida probes through an in-silico test on 19 genomes. We also tested the new probe set empirically on 28 spider species of major spider lineages. The results showed that the RTA probes recovered twice and four times as many loci as the other two probe sets, and the phylogeny from the RTA UCEs provided higher support for certain relationships. This newly developed UCE probe set shows higher capture efficiency empirically and is particularly advantageous for phylogenomic and evolutionary studies of RTA clade and jumping spiders.
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Affiliation(s)
- Junxia Zhang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Zhaoyi Li
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Jiaxing Lai
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Zhisheng Zhang
- School of Life Sciences, Southwest University, Chongqing, 400700, China
| | - Feng Zhang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
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20
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Ortiz-Sepulveda CM, Genete M, Blassiau C, Godé C, Albrecht C, Vekemans X, Van Bocxlaer B. Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms. Mol Ecol Resour 2023; 23:659-679. [PMID: 36349833 DOI: 10.1111/1755-0998.13735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 10/09/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022]
Abstract
Despite the increasing accessibility of high-throughput sequencing, obtaining high-quality genomic data on non-model organisms without proximate well-assembled and annotated genomes remains challenging. Here, we describe a workflow that takes advantage of distant genomic resources and ingroup transcriptomes to select and jointly enrich long open reading frames (ORFs) and ultraconserved elements (UCEs) from genomic samples for integrative studies of microevolutionary and macroevolutionary dynamics. This workflow is applied to samples of the African unionid bivalve tribe Coelaturini (Parreysiinae) at basin and continent-wide scales. Our results indicate that ORFs are efficiently captured without prior identification of intron-exon boundaries. The enrichment of UCEs was less successful, but nevertheless produced substantial data sets. Exploratory continent-wide phylogenetic analyses with ORF supercontigs (>515,000 parsimony informative sites) resulted in a fully resolved phylogeny, the backbone of which was also retrieved with UCEs (>11,000 informative sites). Variant calling on ORFs and UCEs of Coelaturini from the Malawi Basin produced ~2000 SNPs per population pair. Estimates of nucleotide diversity and population differentiation were similar for ORFs and UCEs. They were low compared to previous estimates in molluscs, but comparable to those in recently diversifying Malawi cichlids and other taxa at an early stage of speciation. Skimming off-target sequence data from the same enriched libraries of Coelaturini from the Malawi Basin, we reconstructed the maternally-inherited mitogenome, which displays the gene order inferred for the most recent common ancestor of Unionidae. Overall, our workflow and results provide exciting perspectives for integrative genomic studies of microevolutionary and macroevolutionary dynamics in non-model organisms.
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Affiliation(s)
| | - Mathieu Genete
- CNRS, Univ. Lille, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | | | - Cécile Godé
- CNRS, Univ. Lille, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Christian Albrecht
- Department of Animal Ecology and Systematics, Justus Liebig University, D-35392 Giessen, Germany.,Department of Biology, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Xavier Vekemans
- CNRS, Univ. Lille, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
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21
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Hedin M, Milne MA. New species in old mountains: integrative taxonomy reveals ten new species and extensive short-range endemism in Nesticus spiders (Araneae, Nesticidae) from the southern Appalachian Mountains. Zookeys 2023; 1145:1-130. [DOI: 10.3897/zookeys.1145.96724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/28/2022] [Indexed: 02/05/2023] Open
Abstract
This revision is based on sampling efforts over the past three decades in the southern Appalachian Mountains which have provided Nesticus (Araneae, Nesticidae) collections of approximately 2100 adult specimens from more than 475 unique collecting events. Using a “morphology first” framework we examined recently collected specimens plus museum material to formulate morphology-based species hypotheses for putative new taxa (discovery phase). Using sequence capture of nuclear ultraconserved elements (UCEs) we analyzed 801 nuclear loci to validate new (and prior) morphology-based species hypotheses (validation phase) and reconstructed a robust backbone phylogeny including all described and new species. Sanger sequencing and UCE-bycatch were also used to gather mitochondrial data for more than 240 specimens. Based on our integrative taxonomic framework ten new Nesticus species are herein described, including N. binfordaesp. nov., N. bondisp. nov., N. caneisp. nov., N. cherokeensissp. nov., N. dellingerisp. nov., N. dykemanaesp. nov., N. jemisinaesp. nov., N. lowderisp. nov., N. roanensissp. nov., and N. templetonisp. nov. Previously unknown males are also described for N. bishopi Gertsch, 1984, N. crosbyi Gertsch, 1984, and N. silvanus Gertsch, 1984, as well as the previously unknown female for N. mimus Gertsch, 1984. Based on combined evidence N. cooperi Gertsch, 1984 is placed in synonymy with N. reclusus Gertsch, 1984. Overall, the montane radiation of Appalachian Nesticus reveals a general lack of species sympatry and compelling biogeographic patterns. Several regional Nesticus taxa are rare, microendemic habitat specialists that deserve conservation attention and detailed future monitoring as conservation sentinels.
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22
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Wang S, Lu Y, Li Y, Li S, Lin Y. Systematic notes on three troglobitic Anapistula (Araneae, Symphytognathidae) spiders from China, with the descriptions of two new species. Zookeys 2022; 1130:167-189. [PMID: 36761017 PMCID: PMC9836665 DOI: 10.3897/zookeys.1130.91467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022] Open
Abstract
Three cave-dwelling spider species belonging to the family Symphytognathidae Hickman, 1931, i.e., Anapistulasanjiao sp. nov. (♂♀), A.walayaku sp. nov. (♂♀), and A.panensis Lin, Tao & Li, 2013 (♂♀), are reported from southwest China. DNA sequences and detailed illustrations of the habitus, male palps and epigynes are provided, and their distributions are mapped. Their phylogenetic position within symphytognathids and relationships were tested and assessed using previously published phylogenetic analyses on symphytognathoids. The results showed that they form a clade with A.choojaiae Rivera-Quiroz, Petcharad & Miller, 2021 from Thailand.
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Affiliation(s)
- Shuqiao Wang
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Ying Lu
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Sichuan University, Chengdu, Sichuan 610064, China
| | - Ya Li
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Shuqiang Li
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yucheng Lin
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, China
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Chamberland L, Agnarsson I, Quayle IL, Ruddy T, Starrett J, Bond JE. Biogeography and eye size evolution of the ogre-faced spiders. Sci Rep 2022; 12:17769. [PMID: 36273015 PMCID: PMC9588044 DOI: 10.1038/s41598-022-22157-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 10/10/2022] [Indexed: 01/19/2023] Open
Abstract
Net-casting spiders (Deinopidae) comprise a charismatic family with an enigmatic evolutionary history. There are 67 described species of deinopids, placed among three genera, Deinopis, Menneus, and Asianopis, that are distributed globally throughout the tropics and subtropics. Deinopis and Asianopis, the ogre-faced spiders, are best known for their giant light-capturing posterior median eyes (PME), whereas Menneus does not have enlarged PMEs. Molecular phylogenetic studies have revealed discordance between morphology and molecular data. We employed a character-rich ultra-conserved element (UCE) dataset and a taxon-rich cytochrome-oxidase I (COI) dataset to reconstruct a genus-level phylogeny of Deinopidae, aiming to investigate the group's historical biogeography, and examine PME size evolution. Although the phylogenetic results support the monophyly of Menneus and the single reduction of PME size in deinopids, these data also show that Deinopis is not monophyletic. Consequently, we formally transfer 24 Deinopis species to Asianopis; the transfers comprise all of the African, Australian, South Pacific, and a subset of Central American and Mexican species. Following the divergence of Eastern and Western deinopids in the Cretaceous, Deinopis/Asianopis dispersed from Africa, through Asia and into Australia with its biogeographic history reflecting separation of Western Gondwana as well as long-distance dispersal events.
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Affiliation(s)
- Lisa Chamberland
- grid.27860.3b0000 0004 1936 9684Department of Entomology and Nematology, University of California Davis, Davis, CA 95616 USA
| | - Ingi Agnarsson
- grid.14013.370000 0004 0640 0021Faculty of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 102 Reykjavik, Iceland
| | - Iris L. Quayle
- grid.27860.3b0000 0004 1936 9684Department of Entomology and Nematology, University of California Davis, Davis, CA 95616 USA
| | - Tess Ruddy
- grid.267778.b0000 0001 2290 5183Vassar College, Poughkeepsie, NY 12604 USA
| | - James Starrett
- grid.27860.3b0000 0004 1936 9684Department of Entomology and Nematology, University of California Davis, Davis, CA 95616 USA
| | - Jason E. Bond
- grid.27860.3b0000 0004 1936 9684Department of Entomology and Nematology, University of California Davis, Davis, CA 95616 USA
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24
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Magalhaes ILF, Ramírez MJ. Phylogeny and biogeography of the ancient spider family Filistatidae (Araneae) is consistent both with long-distance dispersal and vicariance following continental drift. Cladistics 2022; 38:538-562. [PMID: 35475520 DOI: 10.1111/cla.12505] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2022] [Indexed: 01/31/2023] Open
Abstract
Filistatids, the crevice weavers, are an ancient family of cribellate spiders without extant close relatives. As one of the first lineages of araneomorph spiders, they present a complicated mixture of primitive and derived characters that make them a key taxon to elucidate the phylogeny of spiders, as well as the evolution of phenotypic characters in this group. Their moderate diversity (187 species in 19 genera) is distributed mainly in arid and semi-arid subtropical zones of all continents, except Antarctica. The objective of this paper is to generate a comprehensive phylogenetic hypothesis for this family to advance the understanding of its morphological evolution and biogeography, as well as lay the basis for a natural classification scheme. By studying the morphology using optical and electronic microscopy techniques, we produced a matrix of 302 morphological characters coded for a sample of 103 species of filistatids chosen to represent the phylogenetic diversity of the family. In addition, we included sequences of four molecular markers (COI, 16S, H3 and 28S; 3787 aligned positions) of 70 filistatid species. The analysis of the data (morphological, molecular, and combined) consistently indicates the separation of the Filistatidae into two subfamilies, Prithinae and Filistatinae, in addition to supporting several groups of genera: Filistata, Zaitunia and an undescribed genus from Madagascar; Sahastata and Kukulcania; all Prithinae except Filistatinella and Microfilistata; Antilloides and Filistatoides; a large Old World group including Pritha, Tricalamus, Afrofilistata, Labahitha, Yardiella, Wandella and putative new genera; and a South American group formed by Lihuelistata, Pikelinia and Misionella. Pholcoides is transferred to Filistatinae and Microfilistata is transferred to Prithinae, and each represents the sister group to the remaining genera of its own subfamily. Most genera are valid, although Pikelinia is paraphyletic with respect to Misionella, so we consider the two genera as synonyms and propose a few new generic combinations. Considering the new phylogenetic hypothesis, we discuss the evolution of some morphological character systems and the biogeography of the family. The ages of divergence between clades were estimated using a total-evidence tip-dating approach by including fossils of Filistatidae and early spider clades; this approach resulted in younger age estimates than those obtained with traditional node-dating. Filistatidae is an ancient family that started diversifying in the Mesozoic and most genera date to the Cretaceous. Clades displaying transcontinental distributions were most likely affected by continental drift, but at least one clade shows unequivocal signs of transoceanic long-distance dispersal.
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Affiliation(s)
- Ivan L F Magalhaes
- División Aracnología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" - CONICET, Av. Ángel Gallardo 470, Buenos Aires, C1405DJR, Argentina
| | - Martín J Ramírez
- División Aracnología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" - CONICET, Av. Ángel Gallardo 470, Buenos Aires, C1405DJR, Argentina
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25
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Lopardo L, Michalik P, Hormiga G. Take a deep breath… The evolution of the respiratory system of symphytognathoid spiders (Araneae, Araneoidea). ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00524-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
AbstractSpiders are unique in having a dual respiratory system with book lungs and tracheae, and most araneomorph spiders breathe simultaneously via book lungs and tracheae, or tracheae alone. The respiratory organs of spiders are diverse but relatively conserved within families. The small araneoid spiders of the symphytognathoid clade exhibit a remarkably high diversity of respiratory organs and arrangements, unparalleled by any other group of ecribellate orb weavers. In the present study, we explore and review the diversity of symphytognathoid respiratory organs. Using a phylogenetic comparative approach, we reconstruct the evolution of the respiratory system of symphytognathoids based on the most comprehensive phylogenetic frameworks to date. There are no less than 22 different respiratory system configurations in symphytognathoids. The phylogenetic reconstructions suggest that the anterior tracheal system evolved from fully developed book lungs and, conversely, reduced book lungs have originated independently at least twice from its homologous tracheal conformation. Our hypothesis suggests that structurally similar book lungs might have originated through different processes of tracheal transformation in different families. In symphytognathoids, the posterior tracheal system has either evolved into a highly branched and complex system or it is completely lost. No evident morphological or behavioral features satisfactorily explains the exceptional variation of the symphytognathoid respiratory organs.
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26
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Azevedo GHF, Bougie T, Carboni M, Hedin M, Ramírez MJ. Combining genomic, phenotypic and Sanger sequencing data to elucidate the phylogeny of the two-clawed spiders (Dionycha). Mol Phylogenet Evol 2021; 166:107327. [PMID: 34666169 DOI: 10.1016/j.ympev.2021.107327] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/03/2021] [Accepted: 10/12/2021] [Indexed: 10/20/2022]
Abstract
The importance of morphology in the phylogenomic era has recently gained attention, but relatively few studies have combined both types of information when inferring phylogenetic relationships. Sanger sequencing legacy data can also be important for understanding evolutionary relationships. The possibility of combining genomic, morphological and Sanger data in one analysis seems compelling, permitting a more complete sampling and yielding a comprehensive view of the evolution of a group. Here we used these three data types to elucidate the systematics and evolution of the Dionycha, a highly diverse group of spiders relatively underrepresented in phylogenetic studies. The datasets were analyzed separately and combined under different inference methods, including a novel approach for analyzing morphological matrices with commonly used evolutionary models. We tested alternative hypotheses of relationships and performed simulations to investigate the accuracy of our findings. We provide a comprehensive and thorough phylogenetic hypothesis for Dionycha that can serve as a robust framework to test hypotheses about the evolution of key characters. We also show that morphological data might have a phylogenetic impact, even when massively outweighed by molecular data. Our approach to analyze morphological data may serve as an alternative to the proposed practice of arbitrarily partitioning, weighting, and choosing between parsimony and stochastic models. As a result of our findings, we propose Trachycosmidae new rank for a group of Australian genera formerly included in Trochanteriidae and Gallieniellidae, and consider Ammoxenidae as a junior synonym of Gnaphosidae. We restore the family rank for Prodidomidae, but transfer the subfamily Molycriinae to Gnaphosidae. Drassinella is transferred to Liocranidae, Donuea to Corinnidae, and Mahafalytenus to Viridasiidae.
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Affiliation(s)
- Guilherme H F Azevedo
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"- CONICET, Av. Ángel Gallardo 470, Buenos Aires C1405DJR, Argentina; Dept of Biology, San Diego State University, San Diego, CA 92182, United States.
| | - Tierney Bougie
- Dept of Biology, San Diego State University, San Diego, CA 92182, United States; Evolution, Ecology, and Organismal Biology Department, University of California, Riverside, Riverside, CA 92521, United States
| | - Martin Carboni
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"- CONICET, Av. Ángel Gallardo 470, Buenos Aires C1405DJR, Argentina
| | - Marshal Hedin
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"- CONICET, Av. Ángel Gallardo 470, Buenos Aires C1405DJR, Argentina
| | - Martín J Ramírez
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"- CONICET, Av. Ángel Gallardo 470, Buenos Aires C1405DJR, Argentina
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27
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Kallal RJ, Elias DO, Wood HM. Not So Fast: Strike Kinematics of the Araneoid Trap-Jaw Spider Pararchaea alba (Malkaridae: Pararchaeinae). Integr Org Biol 2021; 3:obab027. [PMID: 34661063 PMCID: PMC8514421 DOI: 10.1093/iob/obab027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/02/2021] [Accepted: 09/20/2021] [Indexed: 02/05/2023] Open
Abstract
To capture prey otherwise unattainable by muscle function alone, some animal lineages have evolved movements that are driven by stored elastic energy, producing movements of remarkable speed and force. One such example that has evolved multiple times is a trap-jaw mechanism, in which the mouthparts of an animal are loaded with energy as they open to a wide gape and then, when triggered to close, produce a terrific force. Within the spiders (Araneae), this type of attack has thus far solely been documented in the palpimanoid family Mecysmaucheniidae but a similar morphology has also been observed in the distantly related araneoid subfamily Pararchaeinae, leading to speculation of a trap-jaw attack in that lineage as well. Here, using high-speed videography, we test whether cheliceral strike power output suggests elastic-driven movements in the pararchaeine Pararchaea alba. The strike speed attained places P. alba as a moderately fast striker exceeding the slowest mecysmaucheniids, but failing to the reach the most extreme high-speed strikers that have elastic-driven mechanisms. Using microcomputed tomography, we compare the morphology of P. alba chelicerae in the resting and open positions, and their related musculature, and based on results propose a mechanism for cheliceral strike function that includes a torque reversal latching mechanism. Similar to the distantly related trap-jaw mecysmaucheniid spiders, the unusual prosoma morphology in P. alba seemingly allows for highly maneuverable chelicerae with a much wider gape than typical spiders, suggesting that increasingly maneuverable joints coupled with a latching mechanism may serve as a precursor to elastic-driven movements.
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Affiliation(s)
- Robert J Kallal
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Damian O Elias
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Hannah M Wood
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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28
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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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29
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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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30
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Souza LHB, Silva BC, Costa CC, Brescovit AD, Rincão MP, Dias AL, Araujo D. First chromosomal analysis in Deinopidae (Araneae) reveals Sex Chromosome System X 1X 2X 3X 4, B chromosomes and polymorphism for centric fusion. ZOOLOGY 2021; 146:125906. [PMID: 33636668 DOI: 10.1016/j.zool.2021.125906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 01/23/2021] [Accepted: 02/07/2021] [Indexed: 10/22/2022]
Abstract
Here we present the first cytogentic study concerning Deinopidae and their controversial phylogenetic position. This study karyologically analyzed one population of Deinopis biaculeata Simon, 1906 and five populations of Deinopis plurituberculata Mello-Leitão, 1925. The majority of specimens of D. plurituberculata exhibited 2n♂ = 40 and 2n♀ = 44 telocentric chromosomes (however some of them showed B chromosomes, belongs to Aquidauana and Botucatu population). The Deinopis biaculeata and D. plurituberculata meiosis of males showed 18 autosomal bivalents + X1X2X3X4, n = 22 and n = 18, a rare sex chromosome system (SCS) in spiders. Some individuals of D. plurituberculata from the Campo Grande population exhibited 2n♂ = 39 and 2n♀ = 43, with a metacentric chromosome (heterozygotes for centric fusion). The D. plurituberculata males with the rearrangement exhibit diplotenes with 16 autosomal bivalents + 1 autosomal trivalent + X1X2X3X4 and metaphases II with n = 22 (18 telocentric autosomes + X1X2X3X4), n = 21 (16 telocentric autosomes + a metacentric autosome + X1X2X3X4), n = 18 (18 telocentric autosomes) and n = 17 (16 telocentric autosomes + a metacentric autosome). The Ag-NORs (silver impregnation) are terminally located in a pair, coinciding with secondary constriction, which is the most common configuration for Araneae. The relatively high diploid number in Deinopis corroborates phylogenies that place it in a basal position among Entelegynes, in the UDOH grade (Uloboridae, Deinopidae, Oecobiidae and Hersiliidae). Centric fusion in only one population of D. plurituberculata suggests low dispersion capacity of this species and an absence of homozygotes for fusion suggests their low viability or a need to increase the population sampling of D. plurituberculata exhibiting the rearrangement. B chromosomes were detected in D. plurituberculata, with interpopulacional, intrapopulacional and intraindividual numerical variation, with cells presenting 0 - 3 and 0 - 6 B chromosomes in populations of Aquidauana and Botucatu, respectively.
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Affiliation(s)
- Lucas Henrique Bonfim Souza
- Laboratório de Citotaxonomia e Evolução Cromossômica Animal, Universidade Federal de Mato Grosso do Sul, UFMS, Instituto de Biociências, Cidade Universitária, Caixa Postal 549, CEP 79070-900, Campo Grande, Brazil.
| | - Bruno Cansanção Silva
- Laboratório de Citotaxonomia e Evolução Cromossômica Animal, Universidade Federal de Mato Grosso do Sul, UFMS, Instituto de Biociências, Cidade Universitária, Caixa Postal 549, CEP 79070-900, Campo Grande, Brazil
| | - Caroline Correia Costa
- Laboratório de Citotaxonomia e Evolução Cromossômica Animal, Universidade Federal de Mato Grosso do Sul, UFMS, Instituto de Biociências, Cidade Universitária, Caixa Postal 549, CEP 79070-900, Campo Grande, Brazil
| | - Antonio Domingos Brescovit
- Laboratório de Coleções Zoológicas, Instituto Butantan, Av. Vital Brasil, 1500, CEP 05503-900, São Paulo, Brazil
| | - Matheus Pires Rincão
- Laboratório de Citogenética Animal, Universidade Estadual de Londrina, Centro de Ciências Biológicas, Departamento de Biologia Geral. Rodovia Celso Garcia Cid, PR 445 Km 380, Campus Universitário, CEP 86055-900, Paraná, Brazil
| | - Ana Lúcia Dias
- Laboratório de Citogenética Animal, Universidade Estadual de Londrina, Centro de Ciências Biológicas, Departamento de Biologia Geral. Rodovia Celso Garcia Cid, PR 445 Km 380, Campus Universitário, CEP 86055-900, Paraná, Brazil
| | - Douglas Araujo
- Laboratório de Citotaxonomia e Evolução Cromossômica Animal, Universidade Federal de Mato Grosso do Sul, UFMS, Instituto de Biociências, Cidade Universitária, Caixa Postal 549, CEP 79070-900, Campo Grande, Brazil
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31
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Girard MB, Elias DO, Azevedo G, Bi K, Kasumovic MM, Waldock JM, Rosenblum EB, Hedin M. Phylogenomics of peacock spiders and their kin (Salticidae: Maratus), with implications for the evolution of male courtship displays. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Understanding diversity has been a pursuit in evolutionary biology since its inception. A challenge arises when sexual selection has played a role in diversification. Questions of what constitutes a ‘species’, homoplasy vs. synapomorphy, and whether sexually selected traits show phylogenetic signal have hampered work on many systems. Peacock spiders are famous for sexually selected male courtship dances and peacock-like abdominal ornamentation. This lineage of jumping spiders currently includes over 90 species classified into two genera, Maratus and Saratus. Most Maratus species have been placed into groups based on secondary sexual characters, but evolutionary relationships remain unresolved. Here we assess relationships in peacock spiders using phylogenomic data (ultraconserved elements and RAD-sequencing). Analyses reveal that Maratus and the related genus Saitis are paraphyletic. Many, but not all, morphological groups within a ‘core Maratus’ clade are recovered as genetic clades but we find evidence for undocumented speciation. Based on original observations of male courtship, our comparative analyses suggest that courtship behaviour and peacock-like abdominal ornamentation have evolved sequentially, with some traits inherited from ancestors and others evolving repeatedly and independently from ‘simple’ forms. Our results have important implications for the taxonomy of these spiders, and provide a much-needed evolutionary framework for comparative studies of the evolution of sexual signal characters.
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Affiliation(s)
- Madeline B Girard
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Damian O Elias
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Guilherme Azevedo
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Ke Bi
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, USA
| | - Michael M Kasumovic
- Ecology & Evolution Research Centre, School of Biological, Earth & Environmental Sciences, UNSW, Sydney, NSW, Australia
| | - Julianne M Waldock
- Collections and Research, Western Australian Museum, Welshpool, Western Australia, Australia
| | - Erica Bree Rosenblum
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Marshal Hedin
- Department of Biology, San Diego State University, San Diego, CA, USA
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32
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Rivera-Quiroz FA, Petcharad B, Miller JA. First records and three new species of the family Symphytognathidae (Arachnida, Araneae) from Thailand, and the circumscription of the genus Crassignatha Wunderlich, 1995. Zookeys 2021; 1012:21-53. [PMID: 33584107 PMCID: PMC7854560 DOI: 10.3897/zookeys.1012.57047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/30/2020] [Indexed: 12/05/2022] Open
Abstract
The family Symphytognathidae is reported from Thailand for the first time. Three new species: Anapistula choojaiae sp. nov., Crassignatha seeliam sp. nov., and Crassignatha seedam sp. nov. are described and illustrated. Distribution is expanded and additional morphological data are reported for Patu shiluensis Lin & Li, 2009. Specimens were collected in Thailand between July and August 2018. The newly described species were found in the north mountainous region of Chiang Mai, and Patu shiluensis was collected in the coastal region of Phuket. DNA sequences are provided for all the species here studied. The relations of these symphytognathid species were tested using previously published phylogenetic analyses on micro orb-weavers. Also, we used micro CT analysis to build 3D models of the male genitalia and somatic characters of two species of Crassignatha Wunderlich, 1995. The molecular phylogeny and 3D models were used to discuss the taxonomy and circumscription of the currently valid symphytognathid genera, with focus on Crassignatha and Patu Marples, 1951. Based on this, three new combinations are suggested: Crassignatha bicorniventris (Lin & Li, 2009), comb. nov., Crassignatha quadriventris (Lin & Li, 2009), comb. nov., and Crassignatha spinathoraxi (Lin & Li, 2009), comb. nov. A new record of Crassignatha danaugirangensisMiller et al. 2014 is reported from Brunei.
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Affiliation(s)
- Francisco Andres Rivera-Quiroz
- Department of Terrestrial Zoology, Understanding Evolution group, Naturalis Biodiversity Center, Darwinweg 2, 2333CR Leiden, the NetherlandsNaturalis Biodiversity CenterLeidenNetherlands
- Institute for Biology Leiden (IBL), Leiden University, Sylviusweg 72, 2333BE Leiden, the NetherlandsLeiden UniversityLeidenNetherlands
| | - Booppa Petcharad
- Institute for Biology Leiden (IBL), Leiden University, Sylviusweg 72, 2333BE Leiden, the NetherlandsLeiden UniversityLeidenNetherlands
| | - Jeremy A. Miller
- Department of Terrestrial Zoology, Understanding Evolution group, Naturalis Biodiversity Center, Darwinweg 2, 2333CR Leiden, the NetherlandsNaturalis Biodiversity CenterLeidenNetherlands
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Ballesteros JA, Setton EVW, Santibáñez-López CE, Arango CP, Brenneis G, Brix S, Corbett KF, Cano-Sánchez E, Dandouch M, Dilly GF, Eleaume MP, Gainett G, Gallut C, McAtee S, McIntyre L, Moran AL, Moran R, López-González PJ, Scholtz G, Williamson C, Woods HA, Zehms JT, Wheeler WC, Sharma PP. Phylogenomic Resolution of Sea Spider Diversification through Integration of Multiple Data Classes. Mol Biol Evol 2021; 38:686-701. [PMID: 32915961 PMCID: PMC7826184 DOI: 10.1093/molbev/msaa228] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Despite significant advances in invertebrate phylogenomics over the past decade, the higher-level phylogeny of Pycnogonida (sea spiders) remains elusive. Due to the inaccessibility of some small-bodied lineages, few phylogenetic studies have sampled all sea spider families. Previous efforts based on a handful of genes have yielded unstable tree topologies. Here, we inferred the relationships of 89 sea spider species using targeted capture of the mitochondrial genome, 56 conserved exons, 101 ultraconserved elements, and 3 nuclear ribosomal genes. We inferred molecular divergence times by integrating morphological data for fossil species to calibrate 15 nodes in the arthropod tree of life. This integration of data classes resolved the basal topology of sea spiders with high support. The enigmatic family Austrodecidae was resolved as the sister group to the remaining Pycnogonida and the small-bodied family Rhynchothoracidae as the sister group of the robust-bodied family Pycnogonidae. Molecular divergence time estimation recovered a basal divergence of crown group sea spiders in the Ordovician. Comparison of diversification dynamics with other marine invertebrate taxa that originated in the Paleozoic suggests that sea spiders and some crustacean groups exhibit resilience to mass extinction episodes, relative to mollusk and echinoderm lineages.
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Affiliation(s)
- Jesús A Ballesteros
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI
| | - Emily V W Setton
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI
| | | | - Claudia P Arango
- Queensland Museum, Biodiversity Program, Brisbane, QLD, Australia
| | - Georg Brenneis
- Zoologisches Institut und Museum, Cytologie und Evolutionsbiologie, Universität Greifswald, Greifswald, Germany
| | - Saskia Brix
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), c/o Biocenter Grindel (CeNak), Martin-Luther-King-Platz 3, Hamburg, Germany
| | - Kevin F Corbett
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI
| | - Esperanza Cano-Sánchez
- Biodiversidad y Ecología Acuática, Departamento de Zoología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Merai Dandouch
- Department of Biology, California State University-Channel Islands, Camarillo, CA
| | - Geoffrey F Dilly
- Department of Biology, California State University-Channel Islands, Camarillo, CA
| | - Marc P Eleaume
- Départment Milieux et Peuplements Aquatiques, Muséum National d’Histoire Naturelle, Paris, France
| | - Guilherme Gainett
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI
| | - Cyril Gallut
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Concarneau, France
| | - Sean McAtee
- Department of Biology, California State University-Channel Islands, Camarillo, CA
| | - Lauren McIntyre
- Department of Biology, California State University-Channel Islands, Camarillo, CA
| | - Amy L Moran
- Department of Biology, University of Hawai’I at Mānoa, Honolulu, HI
| | - Randy Moran
- Department of Biology, California State University-Channel Islands, Camarillo, CA
| | - Pablo J López-González
- Biodiversidad y Ecología Acuática, Departamento de Zoología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Gerhard Scholtz
- Institut für Biologie, Vergleichende Zoologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Clay Williamson
- Department of Biology, California State University-Channel Islands, Camarillo, CA
| | - H Arthur Woods
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Jakob T Zehms
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI
| | - Ward C Wheeler
- Division of Invertebrate Zoology, American Museum of Natural History, New York City, NY
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI
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Abstract
Spiders (Araneae) make up a remarkably diverse lineage of predators that have successfully colonized most terrestrial ecosystems. All spiders produce silk, and many species use it to build capture webs with an extraordinary diversity of forms. Spider diversity is distributed in a highly uneven fashion across lineages. This strong imbalance in species richness has led to several causal hypotheses, such as codiversification with insects, key innovations in silk structure and web architecture, and loss of foraging webs. Recent advances in spider phylogenetics have allowed testing of some of these hypotheses, but results are often contradictory, highlighting the need to consider additional drivers of spider diversification. The spatial and historical patterns of diversity and diversification remain contentious. Comparative analyses of spider diversification will advance only if we continue to make progress with studies of species diversity, distribution, and phenotypic traits, together with finer-scale phylogenies and genomic data.
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Affiliation(s)
- Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, 5020 Bergen, Norway;
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA;
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35
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Maddison WP, Beattie I, Marathe K, Ng PYC, Kanesharatnam N, Benjamin SP, Kunte K. A phylogenetic and taxonomic review of baviine jumping spiders (Araneae, Salticidae, Baviini). Zookeys 2021; 1004:27-97. [PMID: 33384565 PMCID: PMC7758311 DOI: 10.3897/zookeys.1004.57526] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/26/2020] [Indexed: 12/02/2022] Open
Abstract
The systematics and taxonomy of the tropical Asian jumping spiders of the tribe Baviini is reviewed, with a molecular phylogenetic study (UCE sequence capture, traditional Sanger sequencing) guiding a reclassification of the group’s genera. The well-studied members of the group are placed into six genera: Bavia Simon, 1877, Indopadilla Caleb & Sankaran, 2019, Padillothorax Simon, 1901, Piranthus Thorell, 1895, Stagetillus Simon, 1885, and one new genus, Maripanthus Maddison, gen. nov. The identity of Padillothorax is clarified, and Bavirecta Kanesharatnam & Benjamin, 2018 synonymized with it. Hyctiota Strand, 1911 is synonymized with Stagetillus. The molecular phylogeny divides the baviines into three clades, the Piranthus clade with a long embolus (Piranthus, Maripanthus), the genus Padillothorax with a flat body and short embolus, and the Bavia clade with a higher body and (usually) short embolus (remaining genera). In general, morphological synapomorphies support or extend the molecularly delimited groups. Eighteen new species are described: Bavianessagyna, Indopadillabamilin, I.kodagura, I.nesinor, I.redunca, I.redynis, I.sabivia, I.vimedaba, Maripanthusdraconis (type species of Maripanthus), M.jubatus, M.reinholdae, Padillothoraxbadut, P.mulu, Piranthusapi, P.bakau, P.kohi, P.mandai, and Stagetillusirri, all sp. nov., with taxonomic authority W. Maddison. The distinctions between baviines and the astioid Nungia Żabka, 1985 are reviewed, leading to four species being moved into Nungia from Bavia and other genera. Fifteen new combinations are established: Baviamaurerae (Freudenschuss & Seiter, 2016), Indopadillaannamita (Simon, 1903), I.kahariana (Prószyński & Deeleman-Reinhold, 2013), I.sonsorol (Berry, Beatty & Prószyński, 1997), I.suhartoi (Prószyński & Deeleman-Reinhold, 2013), Maripanthusmenghaiensis (Cao & Li, 2016), M.smedleyi (Reimoser, 1929), Nungiahatamensis (Thorell, 1881), N.modesta (Keyserling, 1883), N.papakula (Strand, 1911), N.xiaolonghaensis (Cao & Li, 2016), Padillothoraxcasteti (Simon, 1900), P.exilis (Cao & Li, 2016), P.flavopunctus (Kanesharatnam & Benjamin, 2018), Stagetillusbanda (Strand, 1911), all comb. nov. One combination is restored, Baviacapistrata (C. L. Koch, 1846). Five of these new or restored combinations correct previous errors of placing species in genera that have superficially similar palps but extremely different body forms, in fact belonging in distantly related tribes, emphasizing that the general shape of male palps should be used with caution in determining relationships. A little-studied genus, Padillothorus Prószyński, 2018, is tentatively assigned to the Baviini. Ligdus Thorell, 1895 is assigned to the Ballini.
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Affiliation(s)
- Wayne P Maddison
- Departments of Zoology and Botany and Beaty Biodiversity Museum, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Imara Beattie
- Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Kiran Marathe
- Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada.,National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bengaluru 560065, India
| | - Paul Y C Ng
- 205 River Valley Road, #16-53, Singapore 238274, Republic of Singapore
| | - Nilani Kanesharatnam
- National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka.,Department of Zoology, Faculty of Science, Eastern University, Vantharumoolai, Sri Lanka
| | - Suresh P Benjamin
- National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka
| | - Krushnamegh Kunte
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bengaluru 560065, India
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36
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Ballesteros JA, Hormiga G. Molecular phylogeny of the orb-weaving spider genus Leucauge and the intergeneric relationships of Leucauginae (Araneae, Tetragnathidae). INVERTEBR SYST 2021. [DOI: 10.1071/is21029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The tetragnathid genus Leucauge includes some of the most common orb-weaving spiders in the tropics. Although some species in this genus have attained relevance as model systems for several aspects of spider biology, our understanding of the generic diversity and evolutionary relationships among the species is poor. In this study we present the first attempt to determine the phylogenetic structure within Leucauge and the relationship of this genus with other genera of Leucauginae. This is based on DNA sequences from the five loci commonly used and Histone H4, used for the first time in spider phylogenetics. We also assess the informativeness of the standard markers and test for base composition biases in the dataset. Our results suggest that Leucauge is not monophyletic since species of the genera Opas, Opadometa, Mecynometa and Alcimosphenus are included within the current circumscription of the genus. Based on a phylogenetic re-circumscription of the genus to fulfil the requirement for monophyly of taxa, Leucauge White, 1841 is deemed to be a senior synonym of the genera Opas Pickard-Cambridge, 1896 revalidated synonymy, Mecynometa Simon, 1894 revalidated synonymy, Opadometa Archer, 1951 new synonymy and Alcimosphenus Simon, 1895 new synonymy. We identify groups of taxa critical for resolving relationships within Leucauginae and describe the limitations of the standard loci for accomplishing these resolutions.
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37
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Kulkarni S, Hormiga G. Hooroo mates! Phylogenomic data suggest that the closest relatives of the iconic Tasmanian cave spider Hickmania troglodytes are in Australia and New Zealand, not in South America. INVERTEBR SYST 2021. [DOI: 10.1071/is21030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Hickmania troglodytes is an emblematic cave spider representing a monotypic cribellate spider genus. This is the only Australian lineage of Austrochilidae while the other members of the family are found in southern South America. In addition to being the largest spider in Tasmania, Hickmania is an oddity in Austrochilidae because this is the only lineage in the family bearing posterior book lungs, tarsal spines and an embolar process on male pedipalps. Six-gene Sanger sequences and genome scale data such as ultraconserved elements (UCEs) and transcriptomes have suggested that Hickmania troglodytes is not nested with the family of current classification, Austrochilidae. We studied the phylogenetic placement of Hickmania troglodytes using an increased taxon sample by combining publicly available UCE and UCEs recovered from transcriptomic data in a parsimony and maximum likelihood framework. Based on our phylogenetic results we formally transfer Hickmania troglodytes from Austrochilidae to the family Gradungulidae. The cladistic placement of Hickmania in the family Gradungulidae fits the geographic distribution of both gradungulids (restricted to Australia and New Zealand) and austrochilids (restricted to southern South America) more appropriately.
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38
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Xu X, Su YC, Ho SYW, Kuntner M, Ono H, Liu F, Chang CC, Warrit N, Sivayyapram V, Aung KPP, Pham DS, Norma-Rashid Y, Li D. Phylogenomic Analysis of Ultraconserved Elements Resolves the Evolutionary and Biogeographic History of Segmented Trapdoor Spiders. Syst Biol 2020; 70:1110-1122. [PMID: 33367903 DOI: 10.1093/sysbio/syaa098] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 01/24/2023] Open
Abstract
The segmented trapdoor spiders (Liphistiidae) are the sole surviving family of the suborder Mesothelae, which forms the sister lineage to all other living spiders. Liphistiids have retained a number of plesiomorphic traits and their present-day distribution is limited to East and Southeast Asia. Studying this group has the potential to shed light on the deep evolutionary history of spiders, but the phylogeny and divergence times of the family have not been resolved with confidence. We performed phylogenomic and molecular dating analyses of 2,765 ultraconserved element loci from 185 liphistiid taxa. Our analyses show that the crown group of Liphistiidae appeared in the mid-Cretaceous at 102 Ma (95% credibility interval 92-113 Ma), but it was not until the Neogene that much of the diversification within the family occurred in mainland Southeast and East Asia. This diversification was coincident with tectonic events such as the extension of the East Asian continental margin, as well as geological upheavals in Indochina induced by the collision between India and Asia. Our study highlights the important role of major tectonic events in shaping the evolutionary history, present-day diversity, and geographical distribution of mesothele and liphistiid spiders.
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Affiliation(s)
- Xin Xu
- College of Life Sciences, Hunan Normal University, Changsha, Hunan, China.,State Key Laboratory of Biocatalysis and Enzyme Engineering, and Centre for Behavioural Ecology and Evolution, School of Life Sciences, Hubei University, 368 Youyi Road, Wuhan, Hubei Province, China.,School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Yong-Chao Su
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore.,Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung City, Taiwan
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Matjaž Kuntner
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and Centre for Behavioural Ecology and Evolution, School of Life Sciences, Hubei University, 368 Youyi Road, Wuhan, Hubei Province, China.,Department of Organisms and Ecosystems Research, National Institute of Biology, Ljubljana, Slovenia.,Jovan Hadži Institute of Biology, Scientific Research Centre of the Slovenian Academy of Sciences and Arts, Ljubljana, Slovenia.,Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., USA
| | - Hirotsugu Ono
- Department of Zoology, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba-shi, Ibaraki-ken, Japan
| | - Fengxiang Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and Centre for Behavioural Ecology and Evolution, School of Life Sciences, Hubei University, 368 Youyi Road, Wuhan, Hubei Province, China
| | - Chia-Chen Chang
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore
| | - Natapot Warrit
- Center of Excellence in Entomology and Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Varat Sivayyapram
- Center of Excellence in Entomology and Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Khin Pyae Pyae Aung
- Department of Zoology, University of Yangon, Kamayut Township, Pyay Road, Yangon, Myanmar.,Department of Biology, Taungoo Education College, Taungoo, Myanmar
| | - Dinh Sac Pham
- Department of Experimental Taxonomy and Genetic Diversity, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Y Norma-Rashid
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Daiqin Li
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore
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39
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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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40
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Kennedy SR, Prost S, Overcast I, Rominger AJ, Gillespie RG, Krehenwinkel H. High-throughput sequencing for community analysis: the promise of DNA barcoding to uncover diversity, relatedness, abundances and interactions in spider communities. Dev Genes Evol 2020; 230:185-201. [PMID: 32040713 PMCID: PMC7127999 DOI: 10.1007/s00427-020-00652-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 01/29/2020] [Indexed: 12/19/2022]
Abstract
Large-scale studies on community ecology are highly desirable but often difficult to accomplish due to the considerable investment of time, labor and, money required to characterize richness, abundance, relatedness, and interactions. Nonetheless, such large-scale perspectives are necessary for understanding the composition, dynamics, and resilience of biological communities. Small invertebrates play a central role in ecosystems, occupying critical positions in the food web and performing a broad variety of ecological functions. However, it has been particularly difficult to adequately characterize communities of these animals because of their exceptionally high diversity and abundance. Spiders in particular fulfill key roles as both predator and prey in terrestrial food webs and are hence an important focus of ecological studies. In recent years, large-scale community analyses have benefitted tremendously from advances in DNA barcoding technology. High-throughput sequencing (HTS), particularly DNA metabarcoding, enables community-wide analyses of diversity and interactions at unprecedented scales and at a fraction of the cost that was previously possible. Here, we review the current state of the application of these technologies to the analysis of spider communities. We discuss amplicon-based DNA barcoding and metabarcoding for the analysis of community diversity and molecular gut content analysis for assessing predator-prey relationships. We also highlight applications of the third generation sequencing technology for long read and portable DNA barcoding. We then address the development of theoretical frameworks for community-level studies, and finally highlight critical gaps and future directions for DNA analysis of spider communities.
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Affiliation(s)
- Susan R Kennedy
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
| | - Stefan Prost
- LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg Museum, Frankfurt, Germany
- National Zoological Garden, South African National Biodiversity Institute, Pretoria, South Africa
| | - Isaac Overcast
- Graduate Center of the City University New York, New York, NY, USA
- Ecole Normale Supérieure, Paris, France
| | | | - Rosemary G Gillespie
- Environmental Sciences Policy and Management, University of California Berkeley, Berkeley, CA, USA
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41
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Hormiga G, Scharff N. The malkarid spiders of New Zealand (Araneae : Malkaridae). INVERTEBR SYST 2020. [DOI: 10.1071/is19073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This paper addresses the systematics of the New Zealand spiders of the family Malkaridae. Malkarids are small araneoid spiders that live primarily in the leaf litter and mosses of temperate and tropical wet forests in Australia and New Zealand, with the exception of a single species in southern South America and another in New Caledonia. We treat the New Zealand species of Malkaridae that are not members of the subfamily Pararchaeinae, a monophyletic group of 11 new species that we classify in 2 new genera (Tingotingo, gen. nov. and Whakamoke, gen. nov.) and a new subfamily (Tingotinginae, subfam. nov.). We describe, diagnose, illustrate and map the distribution of specimen records of these 11 new species of New Zealand Malkaridae: Tingotingo porotiti, sp. nov., T. pouaru, sp. nov., T. tokorera, sp. nov., T. aho, sp. nov., Whakamoke orongorongo, sp. nov.; W. tarakina, sp. nov.; W. guacamole, sp. nov.; W. hunahuna, sp. nov.; W. paoka, sp. nov.; W. heru, sp. nov.; and W. rakiura, sp. nov. We also treat the phylogenetic relationships of Malkaridae and use the results of our previous work on the molecular phylogeny of Araneoidea as the bases for the classification of the family. Tingotingo, gen. nov. and Whakamoke, gen. nov. are sister clades. Tingotinginae, subfam. nov. is the sister group of the Malkarinae plus Pararchaeinae clade. We further hypothesise and discuss the morphological synapomorphies of Malkaridae, Tingotinginae, subfam. nov. and the two new genera.
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