Mitochondrial Phylogenomics Of Spiders(Arthropoda: Araneae)

Spiders are one of the most species-rich natural enemies in terrestrial ecosystems.They exist widely in various habitats such as farmlands,orchards and grasslands,and play an important role in the biological control of insect pests.At present,many studies have been carried out on systematic evolution of spiders based on morphological data,several molecular markers and transcriptomic data,but the phylogenetic relationships among some spider taxa remains controversial.Mitochondrial genomes(mitogenomes)have been widely used in studies of arthropod phylogeny,but currently the number of sequenced spider mitogenomes are limited.Here,mitogenomes of 23 spider species from 16 families were sequenced,assembled,and annotated,by combining with 55 previously published spider mitogenomes retrieved from the Gen Bank,to analyze the characteristics of mitogenomes of spider species.In addition,the potential of mitogenome data in spider phylogenetic research was evaluated,the evolutionary characteristics of spider mitochondrial gene rearrangement,truncated t RNAs,and web traits were explored,and divergence time of different spider groups was estimated.This thesis aims to understand the phylogenetic evolution of spiders from a mitogenomic perspective.The main results are as follows:1.In this study,mitogenomes of 23 spider species from 16 families were newly sequenced,of which eight families were reported for the first time.The sequenced mitogenomes of all spiders were typically circular double-stranded molecules.All spider species encoded 37 mitochondrial genes except for Pirata subpiraticus which lacked trn G.Most spider species contained only one control region which conservatively located between trn Q and trn M.But the second putative control regions were found,i.e.between trn T and nad1 in one Titanoecidae species,between trn L2 and trn N in six Dysderidae species.2.The lengths of 77 spider mitochondrial t RNA genes were extremely truncated(57 ± 3 bp),resulting in the lack of DHU arms or T?C arms in most t RNAs,and only seven t RNAs exhibited the typical clover secondary structure in all spider species.There were three kinds of anticodons in the spider mitochondrial trn S1 gene,namely the typical anticodon GCT,and the two atypical anticodons CCT and TCT.Both evolutionary rates and length of all t RNA genes were significantly correlated with that of two r RNA genes(P < 0.01,r=0.538;P < 0.05,r = 0.286),demonstrating co-evolution between t RNA and r RNA genes.3.Phylogenetic relationships of spiders were reconstructed using four mitogenomic datasets and two analytical methods,involving a total of 78 species in 29 families.Seven different phylogenetic relationships were obtained,and tree topology tests supported the phylogenetic tree based on the 13P123 AA dataset using Bayesian inference as the best topology.The phylogenetic results supported the monophyly of suborder,infraorder,retrolateral tibial apophysis clade,and families(except for Pisauridae).Araneomorphae was composed of the family Hypochilidae,Synspermiata and Entelegynae,of which Hypochilidae and Synspermiata grouped together.Within Entelegynae,Eresidae and Araneoidea were clustered together,which was a sister group of the RTA clade plus Titanoecidae,along with Oecobiidae at the base position of Entelegynae.Within Araneoidea,Linyphiidae and Tetragnathidae were first grouped together,and then group with Araneidae.The results supported the non-monophy of Eresoidea,and determined the phylogenetic positions of Eresidae,Oecobiidae and Titanoecidae4.Mitochondrial gene arrangements were analyzed 77 spider mitogenomes implementing two independent methods(CREx and q MGR)and 13 gene arrangement modes were found.Mesothelae retained the same gene arrangement as the arthropod ancestor(Limulus polyphemus),while Opisthothelae showed extensive gene rearrangement.The 12 gene rearrangement modes involved t RNAs and control region,but not protein-coding genes(PCGs),and were divided into four types: transposition,inversion,inverse transposition,and random loss of tandem repeats.The rearrangement frequency of the control region was the highest,followed by nine t RNAs.The gene segment trn A-trn R-trn N-trn S1 and the gene segment near the control region were two rearrangement hotspots.The evolutionary rates of four PCGs,ten t RNA genes and rrn S were significantly correlated with the three kinds of rearrangement distances(reversal distance,breakpoints and rearrangement frequency)(P<0.05),and the evolutionary rate of combined two r RNAs was significantly correlated with the reversal distance(P<0.05).These observations suggested that mitochondrial gene rearrangement was significantly assocated with the evolutionary rate.5.The divergence time estimation of spiders based on fossil calibrations showed that spiders originated in the Carboniferous period(?329 Myr,million years ago)and Opisthothelae originated in the Permian period(?258 Myr);divergence time of Araneoidea and the RTA clade was estimated to be diverged during the Jurassic period,and the divergence time of Lycosoidea was estimated to be the Cretaceous period(?107Myr).Two methods(Phytools and Past ML)were used to reconstruct the ancestral state of spider web traits based on 12 kinds of web types.The results indicated that the common ancestor of spiders had the ability to spin forage webs and likely foraged depending on a silk-lined burrow.The ancestors of some groups,such as Araneomorphae,Araneoidea,the RTA clade,and Synspermiata,have lost webs.Hunting spiders,such as species from Lycosidae and Oxyopidae,do not build forage webs,indicating that a trade-off between hunting and forage web-building might be an important life-history strategy for spiders.