Histone H3 and U2 snRNA DNA sequences and arthropod molecular evolution

Colgan, Donald J.; McLauchlan, A; Wilson, George; Livingston, S. P.; Edgecombe, Gregory D.; Macaranas, Julie M.; Cassis, Gerasimos; Gray, Michael R.

doi:10.1071/zo98048

Cited by 852 publications

(402 citation statements)

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“…Primer sets for the PCR and cycle sequencing (CS) reactions used in this study were as follows: for 28S rRNA (28S), 28F and 28R (PCR and CS) (Hou et al 2007) with 28SF and 28SR (CS) (Tomikawa et al 2012) as internal primers; for histone H3 (H3), H3aF and H3bR (PCR and CS) (Colgan et al 1998); for cytochrome c oxidase subunit I (COI), LCO1490 and HCO2198 (PCR and CS) (Folmer et al 1994), or jgL-CO1490 and jgHCO2198 (Geller et al 2013), respectively, with M13F and M13R tails (Messing 1983), used for PCR, and then M13F and M13R used as primers for CS, followed Raupach et al (2015); for 16S rRNA (16S), 16STf (Macdonald III et al 2005) and 16Sbr (Palumbi 1996; modified to correspond with "Fruit Fly") (PCR and CS).…”

Section: Pcr and Dna Sequencingmentioning

confidence: 99%

A molecular phylogeny of Pseudocrangonyx from Japan, including a new subterranean species (Crustacea, Amphipoda, Pseudocrangonyctidae)

Tomikawa¹,

Nakano²,

Sato³

et al. 2016

ZSE

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A subterranean species of pseudocrangonyctid amphipod, Pseudocrangonyx gudariensis Tomikawa & Sato, sp. n., is described from the spring-fed stream Gudari-numa in Hakkoda Mountains, Aomori Prefecture, northern Japan. Pseudocrangonyx gudariensis is morphologically similar to P. coreanus Uéno, 1966 and P. febras Sidorov, 2009 based on its relatively small body size, small number of articles of rami of pleopods, and urosomite 1 without basal setae. However, P. gudariensis is distinguished from those species based on the following characteristics: from P. coreanus, antenna 2 of female without calceoli, palmar margins of gnathopods 1 and 2 with distally notched robust setae, inner margin of inner ramus of uropod 2 with 4 robust setae, and basal part of inner ramus of uropod 2 without slender seta; and from P. febras, carpus of gnathopod 2 without serrate robust setae on posterodistal corners, peduncle of pleopods 1 and 2 with setae, and longer article 2 of uropod 3. Phylogenetic analyses using nuclear 28S rRNA and histone H3, and mitochondrial cytochrome c oxidase subunit I and 16S rRNA markers showed that P. gudariensis is placed among known Pseudocrangonyx Akatsuka and Komai, 1922 species. However, its exact phylogenetic position within the genus could not be determined. The polyphyly of the Japanese Pseudocrangonyx species indicates that multiple colonization events of Pseudocrangonyx ancestors to the Japanese Archipelago could have occurred. The reliability of the past Pseudocrangonyx records from Japan is briefly discussed.

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Section: Pcr and Dna Sequencingmentioning

confidence: 99%

A molecular phylogeny of Pseudocrangonyx from Japan, including a new subterranean species (Crustacea, Amphipoda, Pseudocrangonyctidae)

Tomikawa¹,

Nakano²,

Sato³

et al. 2016

ZSE

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“…The PCR temperature profile was 94C for 3 min, followed by 29 cycles of 94 1C for 30 s, 68 1C for 30 s, 72 1C for 45 s, followed by 72 1C for 10 min. All negative results were checked for DNA quality using either primers ef1-aF139 (5 0 -TTGCCACACCGCTCATATCGCTTG-3 0 ) and ef1-aR321 (5 0 -CGCTTTTCACGCTCTTCGGATTTT-3 0 ) for the host nuclear gene ef1-a or H3aF (5 0 -ATGGCTCG TACCAAGCAGACVGC-3 0 ) and H3bR (5 0 -ATATCCTT RGGCATRATRGTGAC-3) for histone H3 (Colgan et al, 1998).…”

Section: Fitness Assaysmentioning

confidence: 99%

Endosymbiont costs and benefits in a parasitoid infected with both Wolbachia and Cardinium

et al. 2010

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Theory suggests that maternally inherited endosymbionts can promote their spread and persistence in host populations by enhancing the production of daughters by infected hosts, either by improving overall host fitness, or through reproductive manipulation. In the doubly infected parasitoid wasp Encarsia inaron, Wolbachia manipulates host reproduction through cytoplasmic incompatibility (CI), but Cardinium does not. We investigated the fitness costs and/or benefits of infection by each bacterium in differentially cured E. inaron as a potential explanation for persistence of Cardinium in this population. We introgressed lines infected with Wolbachia, Cardinium or both with the cured line to create a similar genetic background, and evaluated several parasitoid fitness parameters. We found that symbiont infection resulted in both fitness costs and benefits for E. inaron. The cost was lower initial egg load for all infected wasps. The benefit was increased survivorship, which in turn increased male production for wasps infected with only Cardinium. Female production was unaffected by symbiont infection; we therefore have not yet identified a causal fitness effect that can explain the persistence of Cardinium in the population. Interestingly, the Cardinium survivorship benefit was not evident when Wolbachia was also present in the host, and the reproduction of doubly infected individuals did not differ significantly from uninfected wasps. Therefore, the results of our study show that even when multiple infections seem to have no effect on a host, there may be a complex interaction of costs and benefits among symbionts.

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“…Compared with the null model that assumes uniform branching rate for all lineages, both single-and multiple-threshold GMYC analyses provided significantly better fits to the ultrametric tree (likelihood ratio test, p , 0.05). Single-and multiple-threshold models delimited 22 (confidence interval ¼ 18-24) and 24 (16)(17)(18)(19)(20)(21)(22)(23)(24) entities, respectively. Because the multiple-threshold model did not provide a significant improvement for the data (likelihood ratio test, p ¼ 0.88), a single exemplar representing each independent entity delimited from the single-threshold model was selected for estimation of divergence times ( figure 3).…”

Section: (C) Divergence Timesmentioning

confidence: 99%

“…An approximately 410-bp portion of mitochondrial 16S was amplified with primers Y16F (5 0 -GGTAATTT GACCGTGCTAAG-3 0 ) and Y16R (5 0 -CCGRTTTGAACTCARATC ATGT-3 0 ). A 327-bp histone H3 region was amplified with primers H3F and H3R [23], and an approximately 1340-bp nuclear 28S fragment was amplified with primer pair 28S-3311F and 28S-4434R [22]. DNA sequencing was carried out using BigDye technology on an ABI 3730 automated sequencer (Applied Biosystems, Foster City, CA, USA).…”

Section: (B) Laboratory Protocolsmentioning

confidence: 99%

Marine incursion into East Asia: a forgotten driving force of biodiversity

Yang

Hou

2013

Proc. R. Soc. B.

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Episodic marine incursion has been a major driving force in the formation of present-day diversity. Marine incursion is considered to be one of the most productive 'species pumps' particularly because of its division and coalescence effects. Marine incursion events and their impacts on diversity are well documented from South America, North America and Africa; however, their history and impacts in continental East Asia largely remain unknown. Here, we propose a marine incursion scenario occurring in East Asia during the Miocene epoch, 10-17 Ma. Our molecular phylogenetic analysis of Platorchestia talitrids revealed that continental terrestrial populations (Platorchestia japonica) form a monophyletic group that is the sister group to the Northwest Pacific coastal species Platorchestia pacifica. The divergence time between the two species coincides with Middle Miocene high global sea levels. We suggest that the inland form arose as a consequence of a marine incursion event. This is the first solid case documenting the impact of marine incursion on extant biodiversity in continental East Asia. We believe that such incursion event has had major impacts on other organisms and has played an important role in the formation of biodiversity patterns in the region.

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Histone H3 and U2 snRNA DNA sequences and arthropod molecular evolution

Cited by 852 publications

References 0 publications

A molecular phylogeny of Pseudocrangonyx from Japan, including a new subterranean species (Crustacea, Amphipoda, Pseudocrangonyctidae)

A molecular phylogeny of Pseudocrangonyx from Japan, including a new subterranean species (Crustacea, Amphipoda, Pseudocrangonyctidae)

Endosymbiont costs and benefits in a parasitoid infected with both Wolbachia and Cardinium

Marine incursion into East Asia: a forgotten driving force of biodiversity

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