Evolutionary Trends in the Spider Tree of Life with Appraisal of the Miniature Orbweaving Spiders (Araneae, Araneoidea, “symphytognathoids”)
Open AccessSpiders (Araneae) are an ancient group with the oldest fossils dating to the Carboniferous era, with diversification events of major clades in the Mesozoic and of their suborders extending well into the Palaeozoic. The studies about the evolutionary relationships among the diversity of about 50,000 known species has been a Herculean task. Despite years of research about reconstructing the evolutionary history of spiders using morphology, there has been difficulty in interpreting limited and challenging morphological and behavioural characters, resulting in failure to resolve and converge on a single topology at many important nodes. Phylogenomic data such as transcriptomes have proven useful for resolving deep nodes and recalcitrant groups in the spider tree of life. In the first chapter of this work, I assess whether a genomic-scale data set of a different data class corroborates the phylogenetic relationships recovered using transcriptomes. Because spiders are an ancient group, I chose to use target-capture method to sequence ultraconserved elements (UCEs) in spider genomes. UCEs can be sequenced from dried, formalin-preserved, old museum specimens, are cost-effective, and some UCEs have known functions and are conserved among distantly related taxonomic groups. To maximize the yield of UCEs, I developed a specialized target-capture probe set for spiders using three spider genomes, namely Loxosceles reclusa (Sicariidae), Parasteatoda tepidariorum (Theridiidae) and Stegodyphus mimosarum (Eresidae), that targets over 2,000 ultraconserved elements (UCEs), and then demonstrate the utility of this probe set through sequencing and phylogenetic analysis. I recovered UCE-based molecular sequences from 84 taxa belonging to 48 spider families using the previously available Arachnida probe set and compared them with UCE sequences recovered from our “spider-specific” probe set. These two probe-sets recovered a maximum of 710 and 1,547 UCE loci, respectively, from the same taxon, showing that the “spider specific” probe set doubled the available loci to be used for phylogenetic inference. Phylogenetic analyses using maximum likelihood and coalescent methods corroborated most nodes resolved by recent transcriptomic analyses, but not all. Our preferred hypothesis based on topology tests, suggests monophyly of the ‘symphytognathoids’ (the miniature orb weavers), (albeit with very small taxon sample), which in previous studies has only been supported by a combination of morphological, behavioural characters and targeted sequencing of six genetic markers. Exploring the causes of incongruence in relationships between transcriptome and UCE-based phylogenies and the monophyly of symphytognathoids formed the basis for the next two chapters of this dissertation. In the second chapter, I aimed 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). I hypothesize that transcriptomes contain ultraconserved regions and that analyzing data as amino acids versus nucleotides can influence the inferred phylogenetic relationships. To test this, I reconstructed and compared phylogenies using nucleotide and amino acid data sets from sequences derived from both transcriptomes and ultraconserved regions of the genome. On recovering UCEs from transcriptomes, I reconstructed phylogenies using sequences from transcriptomes, UCEs, and a combination of data sources, at both the amino acid and nucleotide levels at different levels of missing data. All nucleotide data sets from transcriptomes, UCEs, or a combination of both, recovered similar topologies in contrast with the results from the amino acid data set of transcriptomes. 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. I concluded that omitting data, through amino acid translation or via retention of only high occupancy loci, may have a negative impact effect in phylogenetic reconstruction. In the third chapter, I explored the phylogenetic relationships between the symphytognathoid families- Anapidae, Mysmenidae, Symphytognathidae, Synaphridae and Theridiosomatidae using a large sample of UCE data. On recovering that their monophyly is robust, I studied the transformations among the diverse configurations of the respiratory systems of Anapidae (anterior book lungs, reduced book lungs, tracheae; posterior tracheae present or absent). Further, I also investigated the evolutionary history of the diverse web architectures seen in extant symphytognathoids (various modification of orb web, sheet web, cob web, kleptoparasitic symphytognathoids with no web). Finally, in this chapter, I also study the biogeographic history of Anapidae to find what historical events shaped the distribution of extant lineages of Anapidae. Biogeographic analyses reconstructed a Gondwanan ancestral area for Anapidae and the divergence of its lineages coincide with the period of Gondwana breakup. I found an extensive geographical structure within three well-supported clades which is a result of primarily vicariance followed by multiple dispersal events. 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 and secondarily gained six times. The orb web structure was lost four times independently and transformed into sheet web once. The fourth chapter deals with constructing the most comprehensive reconstruction of the spider tree of life representing 125 of the currently described 128 (97.7%) spider families. To achieve this sampling, I combined a legacy data set of Sanger-sequence based six markers with newly generated and publicly available genome-scale data sets. I find that the relationships between major lineages of spiders (such as Austrochiloidea, Palpimanoidea, Synspermiata, etc.) are robust across different classes of data. However, several surprising new hypotheses have emerged with different classes of molecular data. For example, the diphyly of the family Hahniidae of which one group forms a sister group to the most speciose clade of spiders- the Tibial Apophysis Clade. I identify and discuss the controversial hypotheses and compile this manual to design future studies targeting systematic revisions of these problematic groups. This dissertation chapter provides an evolutionary framework to exploring questions such as evolution of venom, silk, webs, eye arrangements, behaviors, etc. In the fifth and final chapter, I conducted a taxonomic revision of the genus Orsinome. It belongs to the family Tetragnathidae, commonly known as “long-jawed spiders”, and is distributed in Asia and Oceania. I conducted a phylogenetic analysis using six standardly used Sanger-sequenced markers to determine the monophyly and suggest putative morphological synapomorphies of Orsinome. I propose a new placement for a misplaced species in Orsinome- Metleucauge armata (Pocock, 1901) comb.nov. (first record of this genus from India), demonstrate that Orsinome cavernicola (Thorell, 1878) (Indonesia), and Orsinome phrygiana Simon, 1901 (Malaysia, Indonesia) are misplaced in the genus. I describe three new Orsinome species- Orsinome n.sp. 1 (Solomon Islands), Orsinome n.sp. 2 (Indonesia, Sulawesi) and Orsinome n.sp. 3 (Indonesia, Ambon Islands) respectively. All these three species in addition to Orsinome pilatrix (Thorell, 1878) (Ambon Islands) and Orsinome megaloverpa Hormiga & Kallal, 2018 (Philippines) represent extremely long and coiled embolus and conductor which is grouped as the megaloverpa species group. The paraphyly of Tylorida (a closely related group of Orsinome) resulted in description of a new genus- n. gen.1 to accommodate Tylorida marmorea (Pocock, 1901), the spider with unique behavior of escaping into water on perceiving predator or disturbance and N.gen.1 n.sp.1. from Madagascar, suggesting that this genus could be a Gondwanan relictual group.
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