scholarly journals Spiders did not repeatedly gain, but repeatedly lost, foraging webs

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6703 ◽  
Author(s):  
Jonathan A. Coddington ◽  
Ingi Agnarsson ◽  
Chris A. Hamilton ◽  
Jason E. Bond

Much genomic-scale, especially transcriptomic, data on spider phylogeny has accumulated in the last few years. These data have recently been used to investigate the diverse architectures and the origin of spider webs, concluding that the ancestral spider spun no foraging web, that spider webs evolvedde novo10–14 times, and that the orb web evolved at least three times. These findings in fact result from a particular phylogenetic character coding strategy, specifically coding theabsenceof webs as logically equivalent, and homologous to, 10 other observable (i.e., not absent) web architectures. “Absence” of webs should be regarded as inapplicable data. To be analyzed properly by character optimization algorithms, it should be coded as “?” because these codes—or their equivalent—are handled differently by such algorithms. Additional problems include critical misspellings of taxon names from one analysis to the next (misspellings cause some optimization algorithms to drop terminals, which affects taxon sampling and results), and mistakes in spider natural history. In sum, the method causes character optimization algorithms to produce counter-intuitive results, and does not distinguish absence from secondary loss. Proper treatment of missing entries and corrected data instead imply that foraging webs are primitive for spiders and that webs have been lost ∼5–7 times, not gained 10–14 times. The orb web, specifically, may be homologous (originated only once) although lost 2–6 times.

2018 ◽  
Author(s):  
Jonathan A Coddington ◽  
Ingi Agnarsson ◽  
Chris Hamilton ◽  
Jason E Bond

Much genomic-scale, especially transcriptomic, data on spider phylogeny has accumulated in the last few years. These data have recently been used to investigate the diverse architectures and the origin of spider webs, concluding that the ancestral spider spun no foraging web, that spider webs evolved de novo 10-14 times, and that the orb web evolved at least three times. In fact, these findings principally result from inappropriate phylogenetic methodology, specifically coding the absence of webs as logically equivalent, and homologous to, 10 other observable (i.e. not absent) web architectures. “Absence” of webs is simply inapplicable data. To be analyzed properly by character optimization algorithms, it must be coded as “?” or “-” because these codes, and these alone, are handled differently by such algorithms. Additional problems include critical misspellings of taxon names from one analysis to the next (dropping even one taxon affects taxon sampling and results), and mistakes in spider natural history. In sum, methodological error: 1) causes character optimization algorithms to produce illogical results, and 2) does not distinguish absence from secondary loss. Proper methodology and corrected data instead imply that foraging webs are primitive for spiders and that webs have been lost ~5-7 times, not gained 10-14 times. The orb web, specifically, may be homologous (originated only once) although lost 2-6 times.


2018 ◽  
Author(s):  
Jonathan A Coddington ◽  
Ingi Agnarsson ◽  
Chris Hamilton ◽  
Jason E Bond

Much genomic-scale, especially transcriptomic, data on spider phylogeny has accumulated in the last few years. These data have recently been used to investigate the diverse architectures and the origin of spider webs, concluding that the ancestral spider spun no foraging web, that spider webs evolved de novo 10-14 times, and that the orb web evolved at least three times. In fact, these findings principally result from inappropriate phylogenetic methodology, specifically coding the absence of webs as logically equivalent, and homologous to, 10 other observable (i.e. not absent) web architectures. “Absence” of webs is simply inapplicable data. To be analyzed properly by character optimization algorithms, it must be coded as “?” or “-” because these codes, and these alone, are handled differently by such algorithms. Additional problems include critical misspellings of taxon names from one analysis to the next (dropping even one taxon affects taxon sampling and results), and mistakes in spider natural history. In sum, methodological error: 1) causes character optimization algorithms to produce illogical results, and 2) does not distinguish absence from secondary loss. Proper methodology and corrected data instead imply that foraging webs are primitive for spiders and that webs have been lost ~5-7 times, not gained 10-14 times. The orb web, specifically, may be homologous (originated only once) although lost 2-6 times.


2019 ◽  
Author(s):  
Joseph L. DeRisi ◽  
Greg Huber ◽  
Amy Kistler ◽  
Hanna Retallack ◽  
Michael Wilkinson ◽  
...  

ABSTRACTNarnaviruses have been described as positive-sense RNA viruses with a remarkably simple genome of ∼ 3 kb, encoding only a highly conserved RNA-dependent RNA polymerase (RdRp). Many narnaviruses, however, are ‘ambigrammatic’ and harbour an additional uninterrupted open reading frame (ORF) covering almost the entire length of the reverse complement strand. No function has been described for this ORF, yet the absence of stops is conserved across diverse narnaviruses, and in every case the codons in the reverse ORF and the RdRp are aligned. The > 3 kb ORF overlap on opposite strands, unprecedented among RNA viruses, motivates an exploration of the constraints imposed or alleviated by the codon alignment. Here, we show that only when the codon frames are aligned can all stop codons be eliminated from the reverse strand by synonymous single-nucleotide substitutions in the RdRp gene, suggesting a mechanism for de novo gene creation within a strongly conserved amino-acid sequence. It will be fascinating to explore what implications this coding strategy has for other aspects of narnavirus biology. Beyond narnaviruses, our rapidly expanding catalogue of viral diversity may yet reveal additional examples of this broadly-extensible principle for ambigrammatic-sequence development.


Data in Brief ◽  
2021 ◽  
pp. 107536
Author(s):  
Anita Mann ◽  
Naresh Kumar ◽  
Ashwani Kumar ◽  
Charu Lata ◽  
Arvind Kumar ◽  
...  

2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Sergio Gonzalez ◽  
Bernardo Clavijo ◽  
Máximo Rivarola ◽  
Patricio Moreno ◽  
Paula Fernandez ◽  
...  

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Joseph L. DeRisi ◽  
Greg Huber ◽  
Amy Kistler ◽  
Hanna Retallack ◽  
Michael Wilkinson ◽  
...  

AbstractNarnaviruses have been described as positive-sense RNA viruses with a remarkably simple genome of ~3 kb, encoding only a highly conserved RNA-dependent RNA polymerase (RdRp). Many narnaviruses, however, are ‘ambigrammatic’ and harbour an additional uninterrupted open reading frame (ORF) covering almost the entire length of the reverse complement strand. No function has been described for this ORF, yet the absence of stops is conserved across diverse narnaviruses, and in every case the codons in the reverse ORF and the RdRp are aligned. The >3 kb ORF overlap on opposite strands, unprecedented among RNA viruses, motivates an exploration of the constraints imposed or alleviated by the codon alignment. Here, we show that only when the codon frames are aligned can all stop codons be eliminated from the reverse strand by synonymous single-nucleotide substitutions in the RdRp gene, suggesting a mechanism for de novo gene creation within a strongly conserved amino-acid sequence. It will be fascinating to explore what implications this coding strategy has for other aspects of narnavirus biology. Beyond narnaviruses, our rapidly expanding catalogue of viral diversity may yet reveal additional examples of this broadly-extensible principle for ambigrammatic-sequence development.


2019 ◽  
Vol 286 (1896) ◽  
pp. 20182684 ◽  
Author(s):  
Sarah Lemer ◽  
Rüdiger Bieler ◽  
Gonzalo Giribet

Bivalvia has been the subject of extensive recent phylogenetic work to attempt resolving either the backbone of the bivalve tree using transcriptomic data, or the tips using morpho-anatomical data and up to five genetic markers. Yet the first approach lacked decisive taxon sampling and the second failed to resolve many interfamilial relationships, especially within the diverse clade Imparidentia. Here we combine dense taxon sampling with 108 deep-sequenced Illumina-based transcriptomes to provide resolution in nodes that required additional study. We designed specific data matrices to address the poorly resolved relationships within Imparidentia. Our results support the overall backbone of the bivalve tree, the monophyly of Bivalvia and all its main nodes, although the monophyly of Protobranchia remains less clear. Likewise, the inter-relationships of the six main bivalve clades were fully supported. Within Imparidentia, resolution increases when analysing Imparidentia-specific matrices. Lucinidae, Thyasiridae and Gastrochaenida represent three early branches. Gastrochaenida is sister group to all remaining imparidentians, which divide into six orders. Neoheterodontei is always fully supported, and consists of Sphaeriida, Myida and Venerida, with the latter now also containing Mactroidea, Ungulinoidea and Chamidae, a family particularly difficult to place in earlier work. Overall, our study, by using densely sampled transcriptomes, provides the best-resolved bivalve phylogeny to date.


Cladistics ◽  
2020 ◽  
Author(s):  
Robert J. Kallal ◽  
Siddharth S. Kulkarni ◽  
Dimitar Dimitrov ◽  
Ligia R. Benavides ◽  
Miquel A. Arnedo ◽  
...  

2007 ◽  
Vol 55 (1) ◽  
pp. 9 ◽  
Author(s):  
Dinesh Rao ◽  
Ken Cheng ◽  
Marie E. Herberstein

A long-running debate in the spider literature concerns the function of the extra silk decorations in some spider webs. These decorations are appended to the web and constitute a highly visible signal, which is inconsistent with the trend towards web invisibility. Despite the sustained attention of researchers, the exact function of these decorations is yet to be understood. While most studies have focussed on testing particular hypotheses, there has been a dearth of natural history data regarding web decorations in field conditions. In this study we present baseline data regarding the influence of seasonality, microhabitat characteristics and ecology on the presence of web decorations in an Australian orb web spider, Argiope keyserlingi. In particular, we show that there is preference among spiders to build their webs between bushes and to face the south-east, but this preference does not influence decoration building.


2010 ◽  
Vol 8 (57) ◽  
pp. 457-471 ◽  
Author(s):  
Aaron M. T. Harmer ◽  
Todd A. Blackledge ◽  
Joshua S. Madin ◽  
Marie E. Herberstein

Spider silks exhibit remarkable properties, surpassing most natural and synthetic materials in both strength and toughness. Orb-web spider dragline silk is the focus of intense research by material scientists attempting to mimic these naturally produced fibres. However, biomechanical research on spider silks is often removed from the context of web ecology and spider foraging behaviour. Similarly, evolutionary and ecological research on spiders rarely considers the significance of silk properties. Here, we highlight the critical need to integrate biomechanical and ecological perspectives on spider silks to generate a better understanding of (i) how silk biomechanics and web architectures interacted to influence spider web evolution along different structural pathways, and (ii) how silks function in an ecological context, which may identify novel silk applications. An integrative, mechanistic approach to understanding silk and web function, as well as the selective pressures driving their evolution, will help uncover the potential impacts of environmental change and species invasions (of both spiders and prey) on spider success. Integrating these fields will also allow us to take advantage of the remarkable properties of spider silks, expanding the range of possible silk applications from single threads to two- and three-dimensional thread networks.


Sign in / Sign up

Export Citation Format

Share Document