Assessing the origin, genetic structure and demographic history of the common pheasant (Phasianus colchicus) in the introduced European range

The common pheasant, a game species widely introduced throughout the world, can be considered as an ideal model to study the effects of introduction events on local adaptations, biogeographic patterns, and genetic divergence processes. We aimed to assess the origin, spatial patterns of genetic variation, and demographic history of the introduced populations in the contact zone of Central and Southeast Europe, using mitochondrial DNA control region sequences and microsatellite loci. Both types of molecular markers indicated relatively low to moderate levels of genetic variation. The mtDNA analyses revealed that common pheasants across the study area are divided into two distinct clades: B (mongolicus group) and F (colchicus group). Analyses of the microsatellite data consistently suggested a differentiation between Hungary and Serbia, with the pheasant population in Hungary being much more genetically homogeneous, while that of Serbia has much more genetic mixture and admixture. This cryptic differentiation was not detected using a non-spatial Bayesian clustering model. The analyses also provided strong evidence for a recent population expansion. This fundamental information is essential for adequate and effective conservation management of populations of a game species of great economic and ecological importance in the studied geographical region.

Impact of Host Resistance to Tomato Spotted Wilt Orthotospovirus in Peanut Cultivars on Virus Population Genetics and Thrips Fitness

Thrips-transmitted tomato spotted wilt orthotospovirus (TSWV) is a major constraint to peanut production in the southeastern United States. Peanut cultivars with resistance to TSWV have been widely used for over twenty years. Intensive usage of resistant cultivars has raised concerns about possible selection pressure against TSWV and a likelihood of resistance breakdown. Population genetics of TSWV isolates collected from cultivars with varying levels of TSWV resistance was investigated using five TSWV genes. Phylogenetic trees of genes did not indicate host resistance-based clustering of TSWV isolates. Genetic variation in TSWV isolates and neutrality tests suggested recent population expansion. Mutation and purifying selection seem to be the major forces driving TSWV evolution. Positive selection was found in N and RdRp genes but was not influenced by TSWV resistance. Population differentiation occurred between isolates collected from 1998 and 2010 and from 2016 to 2019 but not between isolates from susceptible and resistant cultivars. Evaluated TSWV-resistant cultivars differed, albeit not substantially, in their susceptibility to thrips. Thrips oviposition was reduced, and development was delayed in some cultivars. Overall, no evidence was found to support exertion of selection pressure on TSWV by host resistance in peanut cultivars, and some cultivars differentially affected thrips fitness than others.

Population Genetics of the Black Citrus Aphid Aphis aurantii (Hemiptera, Aphididae) in China

The black citrus aphid, Aphis aurantiiBoyer de Fonscolombe, 1841, is one of the most destructive pests in commercial tea plantations and gardens in China. In this study, we investigated the population genetic structure of A. aurantii based on the concatenated sequences of two mitochondrial genes, cytochrome c oxidase I (cox1) and cytochrome b (cytb). A total of 166 haplotypes were identified from 177 individuals collected at 11 locations in China. The whole Chinese A. aurantii population showed a low nucleotide diversity (0.00968) and a high population diversity (haplotype diversity; 0.9991). The haplotypes of the 11 local populations were widely distributed in the neighbor-joining phylogenetic tree and haplotype network diagram, whereas no apparent lineages were detected. Gene flow analysis showed gene exchanges among local populations. The pairwise Fst values revealed a certain amount of genetic difference among local populations. Analysis of molecular variance (AMOVA) reflected genetic differences both within and among populations. The isolation by distance (IBD) analysis revealed a high positive correlation between the geographic distance and genetic distance of the different populations. Neutral test and mismatch distribution suggested that A. aurantii may have experienced recent population expansion events.

Genetic Structure and Diversity of Banana Bunchy Top Virus (BBTV) in the Philippines

Banana bunchy top virus (BBTV) is an important disease of banana in the Philippines and in other banana-producing countries. This study was conducted to investigate the genetic structure and diversity of Philippine BBTV isolates which remain unexplored in the country. BBTV-infected plant tissues were sampled from banana-growing provinces (i.e., Cagayan, Isabela, Quirino, Batangas, Laguna, Rizal, Quezon, Palawan, Cebu, Leyte, and Davao del Sur) and the partial DNA-R gene of BBTV was sequenced. Analysis of all local BBTV isolates showed a nucleotide diversity (π) of 0.00721, average number of nucleotide differences (k) of 5.51984, and haplotype diversity (hd) of 0.971. Neutrality tests using Fu′s Fs and Tajima′s D showed significant and highly negative values which suggest an excess number of rare alleles due to recent population expansion or from genetic hitchhiking. Haplotype network and phylogenetic analyses revealed that the local BBTV isolates were closely related to Southeast Asian (SEA) group and exhibited a monophyletic clade with distinct haplotype grouping from other SEA sequences. However, some Indonesian and Indian reference sequences were also clustered within the Philippine BBTV group suggesting sequence homology. Results also showed that the local BBTV isolates may be categorized into three major haplotype groups (HA, HB, and HC) but only the HC group remained distinct upon comparison with other Philippine and SEA reference sequences. BBTV isolates from Quezon were the most diverse while isolates from Palawan displayed low genetic diversity indices and belonged only in the HC group. The assessment of the degree of variability among Philippine BBTV isolates will provide a reference towards the development of high-throughput BBTV detection systems as well as enable to devise plant breeding strategies to manage the current BBTV spread and variations.

Genetic Diversity and Demographic History of the Shaggy Soft-Haired Mouse Abrothrix hirta (Cricetidae; Abrotrichini)

Genetic information on species can inform decision making regarding conservation of biodiversity since the response of organisms to changing environments depend, in part, on their genetic makeup. Territories of central-southern Chile and Argentina have undergone a varying degree of impact during the Quaternary, where the response of local fauna and flora was rather species-specific. Here, we focus on the sigmodontine rodent Abrothrix hirta, distributed from 35° S in Chile and Argentina to northern Tierra del Fuego. Based on 119,226 transcriptome-derived SNP loci from 46 individuals of A. hirta, we described the geographic distribution of the genetic diversity of this species using a maximum likelihood tree, principal component and admixture analyses. We also addressed the demographic history of the main intraspecific lineages of A. hirta using GADMA. We found that A. hirta exhibited four allopatric intraspecific lineages. Three main genetic groups were identified by a Principal Component Analysis and by Ancestry analysis. The demographic history of A. hirta was characterized by recent population stability for populations at the northernmost part of the range, while southern populations experienced a recent population expansion.

Chromoblastomycosis in an Endemic Area of Brazil: A Clinical-Epidemiological Analysis and a Worldwide Haplotype Network

Chromoblastomycosis (CBM) is a neglected implantation mycosis prevalent in tropical climate zones, considered an occupational disease that affects impoverished rural populations. This retrospective study described clinical aspects of CBM in a hyperendemic area in Brazil and constructed a worldwide haplotype network of Fonsecaea spp. strains. The variables were collected from medical records using a standard report form, reporting 191 patients with CBM from Maranhão, Brazil. The mean age was 56.1 years, 168 (88%) patients were male and predominantly farmers (85.8%). The mean time of evolution of the disease until diagnosis was 9.4 years. Lower limbs (81.2%) and upper limbs (14.2%) were the main sites affected. Most patients exhibited verrucous (55%) and infiltrative plaque (48.2%). Fonsecaea spp. were identified in 136 cases and a haplotype network constructed with ITS sequences of 185 global strains revealed a total of 59 haplotypes exhibiting high haplotypic and low nucleotide diversities. No correlation was observed between the different haplotypes of Fonsecaea species and dermatological patterns, severity of disease or geographic distribution inside Maranhão. Data from this area contributed to better understanding the epidemiology of CBM. For the first time, a robust haplotype network with Fonsecaea strains reveals an evolutionary history with a recent population expansion.

Invasive and Quarantine Risks of Cacopsylla chinensis (Hemiptera: Psyllidae) in East Asia: Hybridization or Gene Flow Between Differentiated Lineages

Pear psyllids are major pests and the causal agents of pear decline disease in orchards. In the past two decades, their outbreaks have raised issues pertaining to invasions and taxonomic identification of the dimorphic Cacopsylla chinensis (Yang and Li) in East Asia. The present study elucidated, as an aid to quarantine management, the invasive origins, differentiation history, and putative gene flow and hybridization between C. chinensis and its sibling species Cacopsylla jukyungi (Kwon). Analyses revealed that the ancestors of C. jukyungi might have diverged from C. chinensis approximately 3.5 million yr ago (Mya) and that differentiation between C. chinensis lineages I and II probably occurred 1.5 Mya. The known overlapping distribution of C. chinensis and C. jukyungi in northeastern China and the two C. chinensis lineages in the Bohai Rim region and Taiwan could be attributed to recent population expansion after the Last Glacial Maximum and/or anthropogenic activities. Analyses of the nuclear gene demonstrated that frequent gene flow between the two C. chinensis lineages and the paraphyletic relationship between C. chinensis and C. jukyungi might be caused by incomplete lineage sorting or hybridization events. On the basis of the current distribution, it is evident that C. jukyungi is not present in middle-southern China, whereas C. chinensis is not distributed in Japan and Korea. Preventing new invasions of Cacopsylla psyllids among geographic regions through the transportation of pear scions is thus pivotal in East Asia, particularly for the possible genetic exchanges among differentiated lineages after secondary invasion events.

Comparative genetic diversity of Cryptosporidium species causing human infections

Parasites sometimes expand their host range and cause new disease aetiologies. Genetic changes can then occur due to host-specific adaptive alterations, particularly when parasites cross between evolutionarily distant hosts. Characterizing genetic variation in Cryptosporidium from humans and other animals may have important implications for understanding disease dynamics and transmission. We analyse sequences from four loci (gp60, HSP-70, COWP and actin) representing multiple Cryptosporidium species reported in humans. We predicted low genetic diversity in species that present unusual human infections due to founder events and bottlenecks. High genetic diversity was observed in isolates from humans of Cryptosporidium meleagridis, Cryptosporidium cuniculus, Cryptosporidium hominis and Cryptosporidium parvum. A deviation of expected values of neutrality using Tajima's D was observed in C. cuniculus and C. meleagridis. The high genetic diversity in C. meleagridis and C. cuniculus did not match our expectations but deviations from neutrality indicate a recent decrease in genetic variability through a population bottleneck after an expansion event. Cryptosporidium hominis was also found with a significant Tajima's D positive value likely caused by recent population expansion of unusual genotypes in humans. These insights indicate that changes in genetic diversity can help us to understand host-parasite adaptation and evolution.