Zhumei Ren

Complete Chloroplast Genome Sequence of Holoparasite Cistanche deserticola (Orobanchaceae) Reveals Gene Loss and Horizontal Gene Transfer from Its Host Haloxylon ammodendron (Chenopodiaceae)

Background The central function of chloroplasts is to carry out photosynthesis, and its gene content and structure are highly conserved across land plants. Parasitic plants, which have reduced photosynthetic ability, suffer gene losses from the chloroplast (cp) genome accompanied by the relaxation of selective constraints. Compared with the rapid rise in the number of cp genome sequences of photosynthetic organisms, there are limited data sets from parasitic plants. Principal Findings/Significance Here we report the complete sequence of the cp genome of Cistanche deserticola, a holoparasitic desert species belonging to the family Orobanchaceae. The cp genome of C. deserticola is greatly reduced both in size (102,657 bp) and in gene content, indicating that all genes required for photosynthesis suffer from gene loss and pseudogenization, except for psbM. The striking difference from other holoparasitic plants is that it retains almost a full set of tRNA genes, and it has lower dN/dS for most genes than another close holoparasitic plant, E. virginiana, suggesting that Cistanche deserticola has undergone fewer losses, either due to a reduced level of holoparasitism, or to a recent switch to this life history. We also found that the rpoC2 gene was present in two copies within C. deserticola. Its own copy has much shortened and turned out to be a pseudogene. Another copy, which was not located in its cp genome, was a homolog of the host plant, Haloxylon ammodendron (Chenopodiaceae), suggesting that it was acquired from its host via a horizontal gene transfer.

Complete nucleotide sequence and gene arrangement of the mitochondrial genome of the crab-eating frog Fejervarya cancrivora and evolutionary implications

The complete nucleotide sequence of the mitochondrial (mt) genome of the crab-eating frog, Fejervarya cancrivora Gravenhorst (Amphibia: Anura: Ranidae), was determined. The mt genome is 17,843 bp long and contains 13 protein-coding (ATP6, ATP8, COI-III, ND1-6 and 4L, and Cyt b) and two ribosomal RNA (12S and 16SrRNA) genes. Although metazoan mt genomes typically encode 22 transfer RNA genes (tRNAs), the F. cancrivora mtDNA contains 23 tRNAs due to the presence of an extra copy of tRNA(Met). A major noncoding region and a prominent intergenic spacer corresponding to the control region and light-strand replication origin were also found. To confirm the phylogenetic position of F. cancrivora, we compared the gene arrangement with that of other anurans and performed phylogenetic analyses based on mt genomic data. The genome organization of F. cancrivora mtDNA differs from that of typical vertebrates and neobatrachian frogs but is identical with that of F. limnocharis, suggesting that the unique gene arrangement occurred in the common ancestor of the genus. Phylogenetic analyses supported the monophyly of the Fejervarya species used here as well as the dicroglossini clade. Although the family Ranidae as previously recognized (= Ranidae, Discoglossidae, and some other natatanuran families; sensu Frost et al., 2006) is shown as a clade in the maximum parsimony analysis, the maximum likelihood and the Bayesian analyses suggest the paraphyly of the Ranidae with respect to the families, Mantellidae and Rhacophoridae. Three-tandem duplications of gene regions followed by subsequent deletions of supernumerary genes were proposed to explain the evolution of the extra tRNA(Met) and translocation of ND5 from the original neobatrachian gene order.

Historical biogeography of Eastern Asian–Eastern North American disjunct Melaphidina aphids (Hemiptera: Aphididae: Eriosomatinae) on Rhus hosts (Anacardiaceae)

Intercontinental biotic disjunctions have been documented and analyzed in numerous Holarctic taxa. Patterns previously synthesized for animals compared to plants suggest that the timing of animal disjunctions are mostly Early Tertiary and were generated by migration and vicariance events occurring in the North Atlantic, while plant disjunctions are mostly Mid-Late Tertiary and imply migration and vicariance over Beringia. Melaphidina aphids (Hemiptera: Aphididae: Fordini) exhibit host-alternating life cycles comprising an obligate seasonal shift between Rhus subgenus Rhus species (Anacardiaceae) and mosses (Bryophyta). Similar to their Rhus hosts, melaphidines are distributed disjunctly between Eastern Asia and Eastern North America. We examined evolutionary relationships within Melaphidina to determine the position of the North American lineage, date its divergence from Asian relatives, and compare these results to a previous historical biogeographic study of Rhus. We sampled nine species and three subspecies representing all six genera of Melaphidina. Data included sequences of mitochondrial cytochrome c oxidase subunits I and II+leucine tRNA, cytochrome b, and nuclear elongation factor 1α genes. Phylogenetic analyses (Bayesian, maximum-likelihood, parsimony) of the combined data (3282 bp) supported the monophyly of all genera except Nurudea and Schlechtendalia, due to the position of N. ibofushi. While the exact position of the North American Melaphis was not well resolved, there was high support for a derived position within Asian taxa. The divergence of Melaphis from Asian relatives centered on the Eocene-Oligocene boundary (~33-35Ma), which coincides with closure of Beringian Land Bridge I. This also corresponded to the Asian-North American disjunction previously estimated for subgenus Rhus spp. We suggest the late-Eocene Bering Land Bridge as the most likely migration route for Melaphis ancestors, as was also hypothesized for North American Rhus ancestors. Results for the Melaphidina disjunction depart from the modal pattern in animal lineages, and present a case where insect and host-plant taxa apparently responded similarly to Tertiary climate change.

Population genetic structure and phylogeographical pattern of rice grasshopper, Oxya hyla intricata, across Southeast Asia

The rice grasshopper, Oxya hyla intricata, is a rice pest in Southeast Asia. In this study, population genetic diversity and structure of this Oxya species was examined using both DNA sequences and AFLP technology. The samples of 12 populations were collected from four Southeast Asian countries, among which 175 individuals were analysed using mitochondrial DNA cytochrome c oxidase subunit I (COI) sequences, and 232 individuals were examined using amplified fragment length polymorphisms (AFLP) to test whether the phylogeographical pattern and population genetics of this species are related to past geological events and/or climatic oscillations. No obvious trend of genetic diversity was found along a latitude/longitude gradient among different geographical groups. Phylogenetic analysis indicated three deep monophyletic clades that approximately correspond to three geographical regions separated by high mountains and a deep strait, and TCS analysis also revealed three disconnected networks, suggesting that spatial and temporal separations by vicariance, which were also supported by AMOVA as a source of the molecular variance presented among groups. Gene flow analysis showed that there had been frequent historical gene flow among local populations in different regions, but the networks exhibited no shared haplotype among populations. In conclusion, the past geological events and climatic fluctuations are the most important factor on the phylogeographical structure and genetic patterns of O. hyla intricata in Southeast Asia. Habitat, vegetation, and anthropogenic effect may also contribute to gene flow and introgression of this species. Moreover, temperature, abundant rainfall and a diversity of graminaceous species are beneficial for the migration of O. hyla intricata. High haplotype diversity, deep phylogenetic division, negative Fu’s Fs values and unimodal and multimodal distribution shapes all suggest a complicated demographic expansion pattern of these O. hyla intricata populations, which might have been caused by climatic oscillations during glacial periods in the Quaternary.

Molecular Phylogenetic Analysis of the Main Lineages of Nymphalinae (Nymphalidae: Lepidoptera) Based on the Partial Mitochondrial COI Gene

The phylogenetic relationships of the subfamily Nymphalinae (sensu Chou 1994) were analyzed based on 1 488 bp of mtDNA cytochrome oxidase subunit I (COI) gene sequence data obtained from 24 individuals, along with those of eight species obtained from GenBank. The base compositions of this COI fragment varied among the individuals as follows: T 39.9%, C 14.6%, A 32.2%, and G 13.4%, with a strong AT bias (72.1%), as usually found in insect mitochondrial genomes. The A + T contents of the third, second, and first codon positions of the COI fragments in this study was 92.4, 62.2, and 61.4%, respectively. The phylogenetic trees were reconstructed by neighbor-joining (NJ), maximum likelihood (ML), and Bayesian methods by using Byblia anvatara as outgroup. Phylogenetic analyses based on the COI gene sequence data created very similar topologies, which were producing trees with two main clades A and B, and five subclades. The data indicated that the tribes Nymphalini and Hypolimni (sensu Chou 1994) are not monophyletic groups, and the genus Junonia should be removed from Nymphalini to Hypolimni (= Junoniini). On the basis of the data, the Symbrenthia and Araschnia had a relative distant relationship with the rest of Nymphalini. The relationships of species in the Nymphalini were confirmed via the NJ, ML, and Bayesian methods, namely ((((Nymphalis + Kaniska) + Polygonia) + Aglais) + Vanessa) + (Symbrenthia + Araschnia). This investigation provides a little novel information for Chinese researches of butterflies.

Nurudea zhengii Ren and Qiao, A New Species of the Rhus Gall Aphids (Aphididae: Eriosomatinae: Fordini) from Eastern China

Zhu-Mei Ren1,*, Xu Su2, Carol D von Dohlen3 and Jun Wen4,1,* 1School of Life Science, Shanxi University, Taiyuan 030006, Shanxi, China 2Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibetan Plateau in Qinghai Province, School of Life Science, Qinghai Normal University, Xining 810008, Qinghai, China 3Department of Biology, Utah State University, Utah 84322, U.S.A 4Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington DC 20013, U.S.A Article Information Received 19 December 2017 Revised 18 February 2018 Accepted 28 March 2018 Available online 31 August 2018

Another look at the phylogenetic relationships and intercontinental biogeography of eastern Asian – North American Rhus gall aphids (Hemiptera: Aphididae: Eriosomatinae): Evidence from mitogenome sequences via genome skimming

The Rhus gall aphids are sometimes referred to as subtribe Melaphidina (Aphididae: Eriosomatinae: Fordini) and comprise a unique group that forms galls on the primary host plants, Rhus. We examined the evolutionary relationships within the Melaphidina aphids using sequences of the complete mitochondrial genome and with samples of 11 of the 12 recognized species representing all six genera. Bayesian, maximum likelihood and parsimony analyses of the mitochondrial genome data support five well-supported clades within Melaphidina: (1) Nurudea (except N. ibofushi), (2) Schlechtendalia-Nurudea ibofushi, (3) Meitanaphis-Kaburagia, (4) Floraphis, and (5) Melaphis. Nurudea shiraii and N. yanoniella are sister to each other, but N. ibofushi is nested within Schlechtendalia. The Nurudea shiraii-N. yanoniella clade is sister to the large clade of the remaining taxa of Melaphidina aphids. The Bayesian and maximum likelihood analyses support the North American Melaphis rhois as sister to the clade of Floraphis-Kaburagia-Meitanaphis-Schlechtendalia from eastern Asia, whereas the parsimony analysis suggests Melaphis sister to Floraphis with low support (bootstrap support 38%), and the amino acid data weakly place it sister to Schlechtendalia-Nurudea ibofushi. The Melaphis position needs to be further tested with nuclear data. Meitanaphis flavogallis is sister to Kaburagia species instead of grouping with Meitanaphis elongallis. Using the Bayesian method, the North American Melaphis was estimated to have diverged from its closest Asian relatives around 64.6 (95% HPD 59.4-69.8) Ma, which is in the early Paleocene near the Cretaceous and Paleogene boundary (K/Pg boundary). At the K/Pg boundary, mass extinctions caused many types of insect-plant associations to disappear, and these extinctions may explain some of the difficulties in the phylogenetic placement of Melaphis within the analyses.