Distribution and Phylogeography of Caryopteris incana (Lamiaceae) Based on Chloroplast DNA Sequences in West Kyushu, Japan

Caryopteris incana is a continental plant, transferred to Japan from continental Asia via a land bridge between the Korean Peninsula and Tsushima Islands during a glacial period. It currently grows wild in West Kyushu, Japan. In a previous study, we investigated the distribution of C. incana in the Tsushima Islands and confirmed the genetic structure of populations by using chloroplast DNA sequence analysis, suggesting that different haplotypes were distributed in the same area. Thus, it seemed that populations of C. incana throughout the Tsushima Islands colonized at different times;each haplotype had remained within its population without mixing. In this study, we conducted fieldwork to construct a detailed distribution map in West Kyushu excluding the Tsushima Islands. Additionally, we confirmed genetic structure of the C. incana population in these areas by using chloroplast DNA sequence analysis to study the intraspecific phylogenetic relationship of C. incana in Japan. We confirmed 37 natural populations in 257 locations throughout West Kyushu excluding the 72 natural populations in the Tsushima Islands. We also confirmed a recent decreasing trend in the number of natural populations in the Nagasaki Mainland. Using the leaves of individuals cultivated from seeds collected from each natural population, we analyzed the chloroplast DNA sequence variations. Among the investigated populations, sequence variations were confirmed in six regions of chloroplast DNA, and those haplotypes were mainly classified into two groups distributed in different areas on the phylogenetic tree. This finding revealed that the common ancestor of C. incana in Japan diverged early into two groups, followed by a fragmentation in population distribution for each area. The haplotype network almost reflected the geographical distribution on haplotypes. However, several haplotypes that were distributed in other areas were confirmed in the Nagasaki Mainland, suggesting a complicated distribution formation in the past.

Landscape genetic analyses reveal host association of mitochondrial haplotypes in the Asian corn borer,Ostrinia furnacalis

Crop expansion often leads to high pest pressure.These pests may have fitness trade-offs related to host use,and some host-associated genotypes may benefit and increase in frequency.However,evidence concerning the effect of host availability on spatial distribution and frequency of mitochondrial haplotypes is scarce.We studied genetic variation of the Asian corn borer,Ostrinia furnacalis(Guenée),across a large area during 2 years(2016 and 2017).Mitochondrial sequence data were obtained from 530 individuals collected from 79 locations in Shandong Province,China.In total,155 haplotypes were found based on the combined cytochrome oxidase subunit 1(COI)and COII genes.Three haplotypes(H2,H12,and H23)were dominant,whereas most of the other haplotypes occurred in low frequency.A haplotype network showed that the 155 haplotypes can be grouped into three clusters.Haplotype clusters seemed to be randomly distributed.The frequency of H12(in Cluster 1)was positively correlated with maize crop proportion,but negatively correlated with other crops(primarily vegetables,oilseed crops,and cotton)at all spatial scales(1-,3-,and 5-km radius).Cluster 2 had haplotype H23,and this cluster was negatively correlated with semi-natural habitats.Cluster 3 had no dominant haplotype and was not affected by landscape factors.We conclude that H12 may be a maize-associated haplotype.Further study is needed to verify the possibility that the carriers of this haplotype may possess some fitness trade-offs.Our study highlights the importance of host availability in O.furnacalis haplotype distribution and frequency.

Insights into the divergent evolution of the oceanic squid Sthenoteuthis oualaniensis(Cephalopoda:Ommastrephidae)from the Indian Ocean

Sthenoteuthis oualaniensis is known for its complex population structure with three major transoceanic forms(viz.middle-sized,dwarf,and giant forms)whose taxonomic status has been disputed for decades.This integrated taxonomic study examines these prevenient morphotypes gathered on cruises in the Indian Ocean to ascertain their status in the evolutionary history of the species.Molecular analyses employing mitochondrial(COI,ND2)and nuclear(H3)markers revealed four genetically distinct and novel lineages of the species in the Indian Ocean,representing three morphotypes from the Arabian Sea and one from the Southern Indian Ocean.The mitochondrial-based phylograms revealed two distinct clades in the species:“dwarf forms+giant form”and“middle-sized forms,”which further branch into geographically structured evolutionary units.Species delimitation analyses recovered five distinct clades,namely,the Arabian Sea giant and dwarf forms,Equatorial,Eastern Typical,and Other Middle-sized forms,representing the consensus molecular operational taxonomic units.H3 being heterozygous could not resolve the phylogeny.Haplotype network and AMOVA analysis of mtDNA genes indicated explicit phylogeographic structuring of haplotypes,whereas these outputs and PCA results were incongruent with the morphological grouping.Phenetic features distinguishing the morphotypes were sometimes plastic and mismatched with the genotypes.The giant form was genetically close to the dwarf forms,contradicting the earlier notion that it descended from the middle-sized form.It may be assumed that the dwarf form evolved following sympatric speciation and adaptation to warm equatorial waters,while the focal features of the Western Arabian Sea guide toward allopatric speciation of the giant form.

Genomic Epidemiology of SARS-CoV-2 in Pakistan

COVID-19 has swept globally and Pakistan is no exception.To investigate the initial introductions and transmissions of the SARS-CoV-2 in Pakistan,we performed the largest genomic epidemiology study of COVID-19 in Pakistan and generated 150 complete SARS-CoV-2 genome sequences from samples collected from March 16 to June 1,2020.We identified a total of 347 mutated positions,31 of which were over-represented in Pakistan.Meanwhile,we found over 1000 intra-host single-nucleotide variants(iSNVs).Several of them occurred concurrently,indicating possible interactions among them or coevolution.Some of the high-frequency iSNVs in Pakistan were not observed in the global population,suggesting strong purifying selections.The genomic epidemiology revealed five distinctive spreading clusters.The largest cluster consisted of 74 viruses which were derived from different geographic locations of Pakistan and formed a deep hierarchical structure,indicating an extensive and persistent nation-wide transmission of the virus that was probably attributed to a signature mutation(G8371T in ORF1ab)of this cluster.Furthermore,28 putative international introductions were identified,several of which are consistent with the epidemiological investigations.In all,this study has inferred the possible pathways of introductions and transmissions of SARS-CoV-2 in Pakistan,which could aid ongoing and future viral surveillance and COVID-19 control.