Low Intraspecific Genetic Diversity Research Articles

Low Genetic Variation Contrasts With Variable Morphotypes in Neoscytalidium dimidiatum From the Philippines and Their Aggressiveness to Dragon Fruit Species

ABSTRACTNeoscytalidium dimidiatum is an asexual, opportunistic and necrotrophic pathogen that causes the devastating stem canker disease of dragon fruit species (Selenicereus spp.). Despite this, information about its intraspecific diversity remains lacking. Examination of the morphological variations of 40 N. dimidiatum isolates hosted by S. megalanthus, S. monacanthus and S. undatus from eight allopatric regions in the Philippines detected three distinct morphotypes. Sequencing of three partial gene markers (ITS, ACT and TUB2) of representative isolates revealed low intraspecific genetic diversity of the pathogen from the three hosts. Phylogenetic analysis of internal transcribed spacer (ITS) sequences of the isolates in this study and worldwide collections of the phytopathogen in the GenBank database infers similar founding populations and the possible specificity of the dragon fruit‐infecting N. dimidiatum. Pathogenicity and aggressiveness assay of the isolates on detached stems of dragon fruit did not detect host specificity to S. monacanthus and S. undatus. However, some isolates (i.g., MBDF0802A, MBDF0808B, MBDF0339A and MBDF0007A) significantly had shorter latent period to the stems of S. undatus than S. monacanthus. A higher aggressiveness component of lesion size development on S. undatus stems by isolates from S. monacanthus was recorded suggesting a possible directional selection of highly aggressive N. dimidiatum in this host. This is the first population study on the phenotypic traits and the genetic structure of N. dimidiatum. Valuable inputs for further study of the pathogen are provided, which may help inform the design of management options for stem canker disease of dragon fruit.

Surveillance for Selected Pathogens and Parasites of Northern Bobwhite (Colinus virginianus) from Western Oklahoma, USA, 2018-20.

The Northern Bobwhite (Colinus virginianus) has been undergoing a range-wide population decline. Potential causes for declines across its historic range have been investigated for decades and include habitat loss and fragmentation and a variety of parasitic and infectious diseases. Although there have been studies on bobwhite ecology in Oklahoma, USA, relatively little is known about parasites and pathogens in the region. We evaluated the health of free-ranging bobwhites from nine sites in western Oklahoma. From 2018 to 2020, 206 bobwhites were evaluated for gross and microscopic lesions and tested for selected pathogens. In general, bobwhites were in good nutritional condition with ample muscle mass and fat stores. No significant gross lesions were observed in any bobwhite and no significant histologic lesions were detected in a subset. There was no evidence of infection with or exposure to reticuloendotheliosis virus, West Nile virus, respiratory Mycoplasmataceae species, Pasteurella multocida, intestinal Eimeria spp., or oral Trichomonas spp. Several pathogens of potential concern were detected, including avian adenovirus (8.6%), Toxoplasma gondii (2.3%), and haemosporidians (a Haemoproteus sp. (1.5%), Leucocytozoon schoutedeni (1.5%), and Plasmodium homopolare haplotype 2 [lineage LAIRI01; 3.6%]). Physaloptera sp. (12%) and Sarcocystis sp. (1%) were detected in the breast muscle. Low intraspecific genetic diversity was noted for Physaloptera sp., and sequences were most similar to Physaloptera sequences from bobwhites and grasshoppers (Orthoptera) in Texas. Low intensities of chewing lice, chiggers, and ticks were observed. A subset of bobwhites had evidence of exposure to selected toxicants and heavy metals; a small number had low levels of iron, manganese, zinc, molybdenum, and copper, which were not considered diagnostically relevant. In general, bobwhites from western Oklahoma appeared to be in good health with a low diversity of pathogens detected, but future work is needed to understand potentially changing disease risks for this population.

Genetic variation and phylogenetic relationships of commercial populations of Bombus ignitus (Hymenoptera, Apidae) with wild populations in Eastern Asia

The bumblebee, Bombus ignitus (Hymenoptera, Apidae), plays a vital role in pollination in Northeast Asia, including Korea, China, Japan, and Far East Russia. Understanding the genetic makeup of the population can aid in its conservation. This study explores the DNA barcode region of cytochrome C oxidase subunit I (COI) of B. ignitus in commercial populations from Korea and Japan. The results reveal low intraspecific genetic diversity among commercially reared populations, with a maximum sequence divergence of 0.3%. Analysis of a 458-bp region of the COI gene, including 384 previously reported sequences, identified 20 haplotypes with the highest sequence divergence of 2.01% in East Asia. Commercial populations show a genetic similarity primarily with the Japanese population. Cross-mating with native populations could result in competition and genetic contamination, leading to reduced fitness and sensitivity to future environmental conditions. Morphological similarities make monitoring of such effects challenging. This study provides a basis for further research on population studies, conservation, and commercialization of local populations of B. ignitus for better pollination services while minimizing risks of reducing genetic diversity and increasing competition between native and introduced populations.

Phylogeography of the economic seaweeds <italic>Chondrus</italic> (Gigartinales, Rhodophyta) in the northwest Pacific based on <italic>rbc</italic>L and COI-5P genes

The red algal genus Chondrus have long been used as raw materials for carrageenan and dietary fiber in health foods. Despite the importance of genetic information in safeguarding natural seaweed resources, knowledge of the population genetics of Chondrus in the northwest Pacific is limited. In this study, genetic diversity and phylogeographic structure of 45 populations (777 specimens) of Chondrus from Korea, China, and Japan were evaluated based on mitochondrial COI- 5P gene sequences, and phylogenetic relationships were confirmed based on plastid rbcL gene sequences. Molecular analyses assigned the specimens in this study to three Chondrus species: C. nipponicus, C. ocellatus, and C. giganteus; phenotype-based species classification was impossible owing to their high morphological plasticity. We found moderate intraspecific genetic diversity and a shallow phylogeographic structure in both for C. nipponicus and C. ocellatus, and low intraspecific genetic diversity in C. giganteus. Each of the three species exhibited high-level intraspecific gene flow among regions based on the most common haplotypes (CN1 for C. nipponicus, CO1 for C. ocellatus, and CG1 for C. giganteus). Our comprehensive genetic information provides insights into the phylogeographic patterns and intraspecific diversity of the economically important Chondrus species. It also highlights the need to conserve existing natural Chondrus resources through continuous monitoring of genetic diversity and phylogeographic pattern.

SSR-based evaluation of genetic diversity in populations of Agriophyllum squarrosum L. and Agriophyllum minus Fisch. & Mey. collected in South-East Kazakhstan.

The development of informative polymorphic DNA markers for poorly studied genera is an important step in population analyses of living organisms, including those that play very important ecological roles in harsh environments, such as desert and semi-desert area. Examples of those poorly studied desert species are Agriophyllum squarrosum L. and Agriophyllum minus Fisch. & Mey. However, a recent RNA-sequencing project in A. squarrosum has proposed a large set of hypothetical SSR (simple sequence repeat) markers. In this work, 11 novel polymorphic SSRs were found due to the screening of 24 randomly selected SSRs for three populations of A. squarrosum and one population of A. minus. The analysis of 11 SSRs revealed 16 polymorphic loci in two Agriophyllum species, 8 polymorphic loci within three populations of A. squarrosum, and 6 polymorphic loci in the population of A. minus. Statistical analyses showed high interspecific, but relatively low intraspecific genetic diversity. The phylogenetic clusterization and population structure analysis have demonstrated a clear segregation of A. minus from A. squarrosum, as well as the separation of population 1 from populations 2 and 3 of A. squarrosum. Thus, we identified the set of novel and informative SSR markers suitable for the study of genetic diversity in Agriophyllum.

Low genetic variation is associated with low mutation rate in the giant duckweed

Mutation rate and effective population size (Ne) jointly determine intraspecific genetic diversity, but the role of mutation rate is often ignored. Here we investigate genetic diversity, spontaneous mutation rate and Ne in the giant duckweed (Spirodela polyrhiza). Despite its large census population size, whole-genome sequencing of 68 globally sampled individuals reveals extremely low intraspecific genetic diversity. Assessed under natural conditions, the genome-wide spontaneous mutation rate is at least seven times lower than estimates made for other multicellular eukaryotes, whereas Ne is large. These results demonstrate that low genetic diversity can be associated with large-Ne species, where selection can reduce mutation rates to very low levels. This study also highlights that accurate estimates of mutation rate can help to explain seemingly unexpected patterns of genome-wide variation.

Low intraspecific genetic diversity indicates asexuality and vertical transmission in the fungal cultivars of ambrosia beetles

Abstract Ambrosia beetles farm ascomycetous fungi in tunnels within wood. These ambrosia fungi are regarded asexual, although population genetic proof is missing. Here we explored the intraspecific genetic diversity of Ambrosiella grosmanniae and Ambrosiella hartigii (Ascomycota: Microascales), the mutualists of the beetles Xylosandrus germanus and Anisandrus dispar. By sequencing five markers (ITS, LSU, TEF1α, RPB2, β-tubulin) from several fungal strains, we show that X. germanus cultivates the same two clones of A. grosmanniae in the USA and in Europe, whereas A. dispar is associated with a single A. hartigii clone across Europe. This low genetic diversity is consistent with predominantly asexual vertical transmission of Ambrosiella cultivars between beetle generations. This clonal agriculture is a remarkable case of convergence with fungus-farming ants, given that both groups have a completely different ecology and evolutionary history.

Low genetic diversity and recent demographic expansion in the red starfish Echinaster sepositus (Retzius 1816).

Understanding the phylogeography and genetic structure of populations and the processes responsible of patterns therein is crucial for evaluating the vulnerability of marine species and developing management strategies. In this study, we explore how past climatic events and ongoing oceanographic and demographic processes have shaped the genetic structure and diversity of the Atlanto-Mediterranean red starfish Echinaster sepositus. The species is relatively abundant in some areas of the Mediterranean Sea, but some populations have dramatically decreased over recent years due to direct extraction for ornamental aquariums and souvenir industries. Analyses across most of the distribution range of the species based on the mitochondrial cytochrome c oxidase subunit I gene and eight microsatellite loci revealed very low intraspecific genetic diversity. The species showed a weak genetic structure within marine basins despite the a priori low dispersal potential of its lecithotrophic larva. Our results also revealed a very recent demographic expansion across the distribution range of the species. The genetic data presented here indicate that the species might be highly vulnerable, due to its low intraspecific genetic diversity.

Contribution to the study of Acanthodactylus (Sauria: Lacertidae) mtDNA diversity focusing on the A. boskianus species group

The Acanthodactylus boskianus species group includes three species (A. boskianus, A. nilsoni, and A. schreiberi) of unclear phylogeny and phylogeographic history. By sequencing fragments of two mtDNA genes and performing phylogenetic, demographic, and chronophylogenetic analyses, we aimed at identifying their phylogenetic relationships while unravelling their biogeographic history. The analyses indicated that A. boskianus is a species complex, while A. s. schreiberi and A. s. ataturi show, both, low intraspecific genetic diversity. From a biogeographic point of view, the ancestor of A. s. schreiberi colonized Cyprus from the Middle East through overseas dispersal during the Pleistocene, whereas A. s. ataturi is considered to be a relict of a previously wider distribution.

Analysis of the genetic diversity of Candida isolates obtained from diabetic patients and kidney transplant recipients.

Yeasts of the genus Candida have high genetic variability and are the most common opportunistic pathogenic fungi in humans. In this study, we evaluated the genetic diversity among 120 isolates of Candida spp. obtained from diabetic patients, kidney transplant recipients and patients without any immune deficiencies from Paraná state, Brazil. The analysis was performed using the ITS1-5.8S-ITS2 region and a partial sequence of 28S rDNA. In the phylogenetic analysis, we observed a consistent separation of the species C. albicans, C. dubliniensis, C. glabrata, C. tropicalis, C. parapsilosis, C. metapsilosis and C. orthopsilosis, however with low intraspecific variability. In the analysis of the C. albicans species, two clades were formed. Clade A included the largest number of isolates (91.2%) and the majority of isolates from GenBank (71.4%). The phylogenetic analysis showed low intraspecific genetic diversity, and the genetic polymorphisms between C. albicans isolates were similar to genetic divergence found in other studies performed with isolates from Brazil. This low genetic diversity of isolates can be explained by the geographic proximity of the patients evaluated. It was observed that yeast colonisation was highest in renal transplant recipients and diabetic patients and that C. albicans was the species most frequently isolated.

Co-Speciation of the Ectoparasite Gyrodactylus teuchis (Monogenea, Platyhelminthes) and Its Salmonid Hosts.

Co-speciation is a fundamental concept of evolutionary biology and intuitively appealing, yet in practice hard to demonstrate as it is often blurred by other evolutionary processes. We investigate the phylogeographic history of the monogenean ectoparasites Gyrodactylus teuchis and G. truttae on European salmonids of the genus Salmo. Mitochondrial cytochrome oxidase subunit 1 and the nuclear ribosomal internal transcribed spacer 2 were sequenced for 189 Gyrodactylus individuals collected from 50 localities, distributed across most major European river systems, from the Iberian- to the Balkan Peninsula. Despite both anthropogenic and naturally caused admixture of the principal host lineages among major river basins, co-phylogenetic analyses revealed significant global congruence for host and parasite phylogenies, providing firm support for co-speciation of G. teuchis and its salmonid hosts brown trout (S. trutta) and Atlantic salmon (S. salar). The major split within G. teuchis, coinciding with the initial divergence of the hosts was dated to ~1.5 My BP, using a Bayesian framework based on an indirect calibration point obtained from the host phylogeny. The presence of G. teuchis in Europe thus predates some of the major Pleistocene glaciations. In contrast, G. truttae exhibited remarkably low intraspecific genetic diversity. Given the direct life cycle and potentially high transmission potential of gyrodactylids, this finding is interpreted as indication for a recent emergence (<60 ky BP) of G. truttae via a host-switch. Our study thus suggests that instances of two fundamentally different mechanisms of speciation (co-speciation vs. host-switching) may have occurred on the same hosts in Europe within a time span of less than 1.5 My in two gyrodactylid ectoparasite species.

Discovered just before extinction? The first endemic ant from the Balearic Islands (Lasius balearicus sp. nov.) is endangered by climate change

AbstractAimWe analyse the taxonomic status, phylogenetic relationships, distribution and age of a newly discovered ant taxon found in the mountaintops of the island of Mallorca (Spain). We also consider the potential impact of short‐term climate change on the survival of this ant and make proposals on its conservation status, risks and management.LocationBalearic Islands (Spain).MethodsWe used morphological, molecular and ecological evidence to assess the specific status of the potential new species. We gathered distribution data to conduct climate‐based distribution modelling of present and future occupancy under several SRES emission scenarios.ResultsThe existence of a new non‐cryptic species of ant (Lasius balearicus Talavera, Espadaler &amp; Vila, sp. nov.) is described from the island of Mallorca. Its distribution was found to be extremely restricted (Serra de Tramuntana) and elevationally constrained to island summits (between 800 and 1400 m a.s.l.). Molecular dating indicated that this species diverged about 1.51 million years ago from its nearest relatives, from which it can be distinguished based on several morphological traits. Ecological niche modelling shows a dramatic reduction of areas with suitable climatic conditions under the different scenarios studied.Main conclusionsLasius balearicus represents the first endemic ant to be described in the Balearic Islands, as well as the first endemic Lasius species in the Mediterranean islands. Distribution modelling predictions, the low intraspecific genetic diversity observed, and the geographical and elevational isolation of the populations indicated a low probability for the survival of the species in the short term, thus making it a potential model to study real‐time climate‐based biodiversity loss. As a consequence, we strongly recommend including L. balearicus in the IUCN Red List of Threatened Species under the category ‘Endangered’. This case illustrates that a fraction of biodiversity remains unexplored even within Europe, arguably the best‐studied region of the planet, and that the available time‐window for us to study and protect it may be in some instances notably narrow.

Conservation genetics and population diversity of Erigeron breviscapus (Asteraceae), an important Chinese herb

Erigeron breviscapus (Vant.) Hand.-Mazz. is an important Chinese herb in treating cerebral infarction and heart diseases, which is increasingly endangered because of over-harvesting and habitat fragmentation. We applied AFLP method to investigate its genetic diversity and population structure in order to make efficient conservation strategies. The results indicated a relatively low intraspecific genetic diversity and feeble genetic differentiation among populations, and no Evolutionarily Significant Units (ESUs) was detected. The relationships between population genetic diversity and populations' distributions (latitude, longitude and altitude) were tested, and the genetic diversity of each population (H-POP) positively correlated with the populations' distribution altitudes. The suitable germinating and growing conditions and less human disturbance at the higher latitude regions might be attributable for this phenomenon. For conservation purpose, an ex situ conservation measure for the populations of E. breviscapus with large size in higher altitude regions should be conserved in priority. (c) 2013 Elsevier Ltd. All rights reserved.

Geographic Origins and Genetic Diversity of Air-Potato (Dioscorea bulbifera) in Florida

AbstractIn Florida, air-potato is an invasive weed with high management priority, which may soon be targeted using classical biological control. This yam was introduced during the early 20th century by the United States Department of Agriculture (USDA) from areas throughout its extensive range. Our objectives were to characterize the genetic diversity of the invasive population in Florida and to identify the source regions of introduction. Authorities have often asserted the African provenance of the species in Florida, but our analyses, conducted using chloroplast markers, indicate that Florida air-potato is more similar to specimens examined from China than to those from Africa. Low intraspecific genetic diversity in Florida indicates that the invasive population was the result of at least two introductions becoming established in Florida.

Mitochondrial DNA sequence variation of the bumblebee, Bombus ardens (Hymenoptera: Apidae)

The bumblebee, Bombus ardens, is a valuable natural resource, and is most notably utilized for greenhouse pollination. In order to gain a greater understanding of the population genetic structure and the genetic diversity of this species, we sequenced a portion of the mitochondrial COI gene corresponding to the “DNA Barcode” region (658 bp) from 160 individuals collected over 15 Korean localities. Uncorrected pairwise distances among the eight haplotypes suggested low intraspecific genetic diversity, with a maximum sequence divergence of 0.3%. Such a low level of intraspecific genetic diversity was further reflected in local populations, particularly to islet populations, such as those of Youngheungdo, Jakyakdo, and Ulleugdo, which had zero genetic diversity. Geographically, one haplotype (BARBA01) was widespread and dominant, with a frequency of 90.6% (145 among 160 individuals). Other haplotypes were restricted to one to three localities and had low frequency. Overall, a very high rate of per generation female migration ratio ( Nm = 4.6 to infinite) and a very low level of genetic fixation ( F ST = 0 to 0.099) were detected between pairs of localities, suggesting that the B. ardens populations on the Korean peninsula are panmictic, which is consistent with our understanding of their dispersal capability.

Quantifying Spatial and Temporal Genotypic Changes in White Clover Populations by RAPD Technology

In established white clover (Trifolium repens L.) populations, seedling recruitment is rare and plants spread by clonal growth, which could lead to low intraspecific genetic diversity. To assess how populations of white clover maintain high genetic variability in grazed swards during a growing season, we examined spatial and temporal changes in white clover clones by identifying genotypes by RAPD (random amplified polymorphic DNA) profiles. Trifoliate leaf samples were taken from plants at up to 37 specific sampling points in each of four 2.8‐m2 permanent quadrats in a grazed pasture from April to October 1997. RAPD profiles (genotype) based on 28 markers were determined for genomic DNA prepared from leaf samples. The number of sampled clones per quadrat ranged from zero to 10 and the sampled members per clone ranged from two to 34 over the growing season. Some clones were found more than once. During the study, numbers of clonal members increased or decreased, clones were found on one to three dates, and clones were found in one to two quadrats. The clonal diversity index D (probability that any two sampled plants have different genotypes) ranged from 0.89 to 0.99 for the eight dates, showing that genotypic diversity of populations was affected by number of clones and number of clonal members. We report here the first use of dominant RAPD markers to document dynamic changes of white clover population structure. These data show that white clover clones undergo dynamic spatial and temporal variability at a local scale, which accounts for much of the genetic diversity within field populations.