Intraspecific Genetic Variation Research Articles

Evidence for multiple refugia and hotspots of genetic diversity for Westralunio carteri, a threatened freshwater mussel in south‐western Australia

Abstract Intraspecific genetic diversity provides the evolutionary potential to adapt to changing environments and ‘hotspots’ of high intraspecific diversity are recognized as key targets for conservation. In south‐western Australia, intraspecific genetic diversity for mesic taxa is not uniformly distributed. Many species comprise highly divergent lineages with unique haplotypes resulting from contraction to refugia during historical arid cycles. Sampling strategies in studies of the region’s unique and ancient freshwater fauna have often focused on broad distributional range, making it difficult to determine boundaries between lineages and the location of genetic hotspots. This study explored the spatial distribution of intraspecific genetic diversity in the threatened freshwater mussel, Westralunio carteri. Mitochondrial DNA sequences for 164 specimens, sampled from all basins within the distribution of the species, were used to describe lineage boundaries and the location of hotspots, and to reconstruct historical demographics. There was strong evidence for three subregions of genetic diversity based on the largely non‐overlapping distributions of three evolutionarily significant units. Spatial and demographic analyses suggest that these evolutionarily significant units persisted through past arid cycles in separate refugia. The majority of haplotypes were unique to a single location, indicating limited connectivity among populations in recent times. Hotspots were identified throughout the region. Most notably, a significant hotspot in the south‐western corner probably arose through the overlap of lineages in historical refugia. Conservation assessments often focus on the species as a whole, even though sublineages, hotspots and the threats faced are not evenly distributed across the species range. This paper highlights that effective conservation of spatially structured taxa requires targeted management of multiple genetic units. Given the importance of formal taxonomic description for conservation listings, further investigation of the potential for species delimitation within W. carteri is required.

Population genetic analysis of the Humboldt’s flying squirrel using high-throughput sequencing

Abstract The San Bernardino flying squirrel (Glaucomys oregonensis californicus) is thought to be the southernmost population of the Humboldt’s flying squirrel (G. oregonensis) and is restricted to the San Bernardino and San Jacinto Mountains in California. However, recent surveys indicate they have been extirpated from the latter locality. In this study, we characterized the intraspecific genetic structure and diversity of G. oregonensis. We amplified and sequenced at least 300 bp of the mitochondrial cytochrome-b gene and 11 nuclear microsatellites to provide baseline genetic data for this species and subspecies, investigate G. oregonensis genetic structure with a focus on the subspecies distributed in California, and finally evaluate the genetic diversity within G. o. californicus. Population and phylogenetic analyses were performed on a total of 147 samples (tissue, hair, and museum specimen) using the Illumina high-throughput sequencing (HTS) platform, thereby bioinformatically coding microsatellite alleles using established pipelines. Our results indicate reduced genetic diversity in G. o. californicus and highlight genetic distinctiveness of the San Jacinto population. In addition, the differences in genetic diversity between the mitochondrial and nuclear markers suggest sex-biased dispersal and historic separation of the species in multiple refugia followed by more recent gene flow among subpopulations in northern California. This study contributes valuable information toward understanding the genetic variation within G. oregonensis, provides information for future conservation decisions for G. o. californicus, and has novel implications for HTS genotyping-by-sequencing.

Integrated Approaches for the Identification of Mosquitoes (Diptera: Culicidae) from the Volcanoes of Central America Physiographic Subprovince of the State of Chiapas, Mexico.

Nowadays, there is a lack of information on the mosquito's fauna and DNA barcoding sequence reference library from many areas in Mexico, including the Volcanoes of Central America physiographic subprovince in the state of Chiapas. Consequently, a survey was undertaken to delineate the mosquito (Diptera: Culicidae) fauna in this region across different seasons using different collecting techniques. All species were identified by morphology and DNA barcoding, and their ecological features were also defined. In total, 62 taxa were morphologically examined, 60 of these were successfully identified based on morphological characteristics, but two were unable to be identified at the species level. The genera Aedes, Anopheles, Culex, and Wyeomyia are the most diverse among mosquito genera collected and include several species of medical and veterinary importance. Ecological characteristics of the immature habitats indicated that they were grouped into four categories namely, (1) large water bodies at ground level, (2) small and shady phytotelmata (e.g., tree holes and bamboo internodes), (3) large phytotelmata (e.g., plant leaves and axis bromeliad), and (4) artificial containers. The cytochrome c oxidase subunit I (COI) DNA barcoding sequences successfully separated the majority of these species, although specific species showed >2% intraspecific genetic divergences.

Investigating Liriomyza (Diptera: Agromyzidae) Populations From Northeastern Brazil: mtDNA Analyses of the Global Pests L. sativae and L. huidobrensis

Abstract Species of Liriomyza Mik (Diptera: Agromyzidae) occur worldwide and are economically important leafminers. However, populations of some pest species, although very similar morphologically, show highly divergent mtDNA sequences, suggesting that nominal species are in fact complexes of cryptic species. This study focuses on two globally invasive pests, L. huidobrensis (Blanchard) and L. sativae Blanchard, already known to be highly destructive in Brazilian crops, although only a few studies on morphological and genetic divergences of them have been made. A total of 63 sequences of the mitochondrial cytochrome oxidase I (COI) and cytochrome oxidase II (COII) from Brazilian populations of L. huidobrensis and L. sativae collected from six crops (gypsophila, chrysanthemum, melon, watermelon, tomato, and onion) in Northeastern Brazil were generated to investigate their genetic structure together with available sequences from the Americas, Europe, Asia, Africa, and Australia. Genetic structure was not found to be correlated to neither host plant nor geographical locality. Liriomyza huidobrensis showed an overall low intraspecific global genetic divergence in both genes. On the other hand, high intraspecific divergences for L. sativae and its phylogenetic position confirm a divergent clade currently found only in Brazil and suggest it may be a global complex of cryptic species. Considering the possibility of cryptic species (in the latter case), we provided detailed redescriptions of these Brazilian populations for future studies and local management of these global pests. Finally, our results also revealed a new synonym herein proposed, L. strigosa Spencer as a junior synonym of L. huidobrensis.

Insights into the phylogenetic position and phylogeography of the monospecific skink-parasite genus

Neoentomelas asatoi Hasegawa, 1989 is a parasitic nematode that infests only the scincid lizard Ateuchosaurus pellopleurus (Hallowell, 1861) that inhabits the forest floor in the Northern and Central Ryukyu Archipelago, Japan. As a member of Rhabdiasidae, the reproductive mode of N. asatoi is characterised by the alternation of the protandrous hermaphroditic mode and gonochoristic mode throughout the life cycle. The intrafamily phylogenetic position and intraspecific diversity of this nematode species were inferred by molecular phylogenetic analyses. The results revealed the phylogenetic distinctiveness of Neoentomelas Hasegawa, 1989 in Rhabdiasidae that supports the unique generic status of Neoentomelas within the family. The intraspecific phylogenetic analyses of N. asatoi revealed a minor concordant phylogenetic pattern with the host and mosaic geographic arrangement of the major clades that was discordant with the host. The analyses and distribution pattern of subclades suggested that this geographic arrangement can be explained by at least three dispersal events and subsequent switching to indigenous host populations. Colonisation events might be promoted by the high establishment rate of new populations stemming from the parthenogenesis-like reproduction mode of N. asatoi. This study demonstrated that reproductive modes can affect the intraspecific genetic diversity of parasites.

Population structure and population history of the black fly Simulium chumpornense (Diptera: Simuliidae) from Thailand

Understanding genetic structure and diversity of insect vectors is crucial for disease epidemiology. In this study, mitochondrial cytochrome c oxidase I sequences were used to infer genetic diversity, genetic structure and population history of the black fly, Simulium chumpornense Takaoka and Kuvangkadilok, a suspected vector of blood protozoa of the genus Leucocytozoon and Trypanosoma. High intraspecific genetic divergence (max. 3.76%) was found among 142 specimens obtained from 19 locations across Thailand. A median joining network revealed two genetic lineages (A and B) that were geographically associated. Lineage A is representative of central and northeastern regions. Lineage B represents specimens from diverse locations in northern, western, and southern Thailand, including the type locality. Mismatch distribution and the neutrality tests provided signals of past population expansions in both lineages. The expansion time dating back to the end of last glaciations at 12,000 - 15,000 years ago is possibly related to increasing of precipitation at the end of last glacial period. Despite recent population history, population pairwise FST analysis revealed that almost all population comparisons were genetically significantly different. The high level of genetic structuring is possibly a result of historical isolation of the population that survived in different refugia sites during the dry conditions during glaciations.

Description and molecular characterisation of Pelecitus copsychi Uni, Mat Udin & Martin n. sp. (Nematoda: Onchocercidae) from the white-rumped shama Copsychus malabaricus (Scopoli) (Passeriformes: Muscicapidae) of Pahang, Malaysia

Species of the genus Pelecitus Railliet & Henry, 1910 the most widely distributed avian filariae in Africa and South America. Zoonotic cases in humans were reported in South America. While investigating the filarial fauna of wild animals in Malaysia, we discovered an undescribed filaria from the swollen footpad of the left leg of Copsychus malabaricus (Scopoli) in Pahang, Peninsular Malaysia. Adults of both sexes have a corkscrew-shaped body. Based on comparison of their morphological characteristics (i.e. pre-oesophageal cuticular ring distinct, oesophagus divided, vulva protuberant and situated at the level of anterior half of oesophagus, spicules strongly sclerotized and left spicule with broad blade) with other Pelecitus species, they are here described as Pelecitus copsychi Uni, Mat Udin & Martin n. sp. Multi-locus sequence analyses based on seven genes (12S rDNA, cox1, 18S rDNA, 28S rDNA, MyoHC, rbp1 and hsp70) were performed to determine the phylogenetic position of the new species. The calculated p-distance between the cox1 gene sequences for P. copsychi n. sp. and Pelecitus fulicaeatrae (Diesing, 1861) was 14.1%. Intraspecific genetic variation between two individuals of the new species was 0.4%. In both the Bayesian inference and maximum-likelihood trees, P. copsychi n. sp. was positioned in the second clade of ONC5, containing three genera of the subfamily Dirofilariinae (Foleyella Seurat, 1917, Pelecitus and Loa Stiles, 1905). Immunostaining and molecular analyses remained negative for the presence of Wolbachia endosymbionts. Our findings corroborate the division of the subfamily Dirofilariinae into ONC3 with Dirofilaria Railliet & Henry, 1911 and ONC5 with Pelecitus.

Intraspecific genetic variation among

Context The genus Sehima is an important component of grasslands worldwide and is the dominant grass of Sehima–Dichanthium grasslands of India. It is an excellent fodder and a good source of lignocellulosic material and several industrially important biomolecules. Aims We aimed to characterise and conserve locally adapted diverse germplasm of S. nervosum, collected from different agro-climatic zones, for effective utilisation. Methods Morphological and nutritive traits were measured and statistically analysed for diversity in a germplasm collection of S. nervosum genotypes from diverse agro-climatic conditions of India, and a representative core subset was created. Key results Morphological traits and nutritive parameters such as crude protein content and digestibility showed wide variability among accessions. Principal component analysis established that plant height, number of tillers per tussock and number of nodes per tiller accounted for half of the variation present. Tiller internode length, stem diameter, and leaf blade length and width also contributed >5 unit points each to the cumulative proportion of variance accounted for. Conclusions The set of germplasm, possessing substantial variability, is a valuable genetic resource for developing new cultivars. Genotypes identified with high protein content could be used as forage, and those with high cellulose and hemicelluloses as a biofuel resource. Implications Genotypes can be separately identified for forage and biofuel, and the core subset can effectively be used for evaluation and selection of genotypes in target environments. Additionally, the core subset can be used to establish and rejuvenate sustainable pastures by allowing natural selection.

Identification and Distribution of Wedge Clams (Donacidae: Bivalvia) in Thailand by Geometric Morphometric and Molecular Analysis.

The phylogenetic relationship of living Thai Donacidae was herein studied. Two methodologies, geometric morphometrics (GM) and genetic analysis of COI sequences, were combined and applied to identify the valid taxa and explain biodiversity and the distribution pattern in this family. A total of 587 living specimens were tested to analyze the shape and size patterns by Elliptic Fourier Analysis (EFA). Shell identification and GenBank sequences were added to construct the phylogenetic relationship and haplotype network. Centroid size was used to identify the specimens to the subgenus level. Donax (Hecuba) scortum, was easily distinguished from other species by Principal Component analysis (PCA) of shell size and shape. Donax (Dentilatona) incarnatus and Donax (Deltachion) semisulcatus semisulcatus were identified using Canonical Variates Analysis (CVA). Pairwise comparison of EFA was used for species level recognition, particularly shape overlap was observed for medium and small shell size. Based on genetic distance and haplotype network of COI sequences, Donax (Latona) faba and D. (Latona) solidus could be grouped in the same clade. Intraspecific and interspecific genetic data variation of some common species in different geographical localities of Thailand was observed. Three distribution patterns of Donax species were observed along the two-marine system of Thailand.

Historical persistence and isolation by distance of

Context Empirical studies of intraspecific genetic diversity and population structure can inform the evolutionary and demographic history of individual species and of landscapes at the bioregional level. Aims We aimed to assess intraspecific genetic variation at macroevolutionary and microevolutionary temporal scales for Mirbelia viminalis, a key species present on the Hamersley Range in the ancient and highly diverse landscape of the Pilbara bioregion of northwest Western Australia. Methods We sampled extant populations and assessed diversity and structure using sequences (chloroplast DNA, 1759 base pairs) and microsatellite markers (nuclear DNA, 15 loci) data. Key results Significant phylogeographic structure and a lack of historical demographic signals of population contraction or expansion suggest historical population persistence. Moderate chloroplast haplotype diversity (h = 15) and moderate divergence among extant haplotypes indicates a degree of historical connectivity via seed dispersal across central populations on the Hamersley Range. Levels of nuclear genetic diversity were low to moderate (allelic richness = 3.554, expected heterozygosity = 0.489, observed heterozygosity = 0.462) and depauperate compared to another member of the Mirbelia genus present further south in the Midwest region. Nuclear diversity revealed a strong signal of isolation by distance with localised admixture among populations and some contemporary genetic clustering along a north-west to south-east transect of the Hamersley Range. Conclusions Low nuclear genetic diversity may be related to recent reductions in population size for M. viminalis. Historical population persistence with few barriers to dispersal other than geographic distance may be common for members of the Fabaceae across the Hamersley Range.

Highlighted articles for January 2022.

Highlighted articles for January 2022.

An unusually high upper thermal acclimation potential for rainbow trout.

Thermal acclimation, a compensatory physiological response, is central to species survival especially during the current era of global warming. By providing the most comprehensive assessment to date for the cardiorespiratory phenotype of rainbow trout (Oncorhynchus mykiss) at six acclimation temperatures from 15°C to 25°C, we tested the hypothesis that, compared with other strains of rainbow trout, an Australian H-strain of rainbow trout has been selectively inbred to have an unusually high and broad thermal acclimation potential. Using a field setting at the breeding hatchery in Western Australia, thermal performance curves were generated for a warm-adapted H-strain by measuring growth, feed conversion efficiency, specific dynamic action, whole-animal oxygen uptake (ṀO2) during normoxia and hypoxia, the critical maximum temperature and the electrocardiographic response to acute warming. Appreciable growth and aerobic capacity were possible up to 23°C. However, growth fell off drastically at 25°C in concert with increases in the time required to digest a meal, its total oxygen cost and its peak ṀO2. The upper thermal tipping points for appetite and food conversion efficiency corresponded with a decrease in the ability to increase heart rate during warming and an increase in the cost to digest a meal. Also, comparison of upper thermal tipping points provides compelling evidence that limitations to increasing heart rate during acute warming occurred well below the critical thermal maximum (CTmax) and that the faltering ability of the heart to deliver oxygen at different acclimation temperatures is not reliably predicted by CTmax for the H-strain of rainbow trout. We, therefore, reasoned the remarkably high thermal acclimation potential revealed here for the Australian H-strain of rainbow trout reflected the existing genetic variation within the founder Californian population, which was then subjected to selective inbreeding in association with severe heat challenges. This is an encouraging discovery for those with conservation concerns for rainbow trout and other fish species. Indeed, those trying to predict the impact of global warming should more fully consider the possibility that the standing intra-specific genetic variation within a fish species could provide a high thermal acclimation potential, similar to that shown here for rainbow trout.

Population subdivision promoted by a sea-level-change-driven bottleneck: A glimpse from the evolutionary history of the mangrove plant Aegiceras corniculatum.

Historic climate changes drive geographical populations of coastal plants to contract and recover dynamically, even die out completely. Species suffering from such bottlenecks usually lose intraspecific genetic diversity, but how do these events influence population subdivision patterns of coastal plants? Here, we investigated this question in the typical coastal plant: mangrove species Aegiceras corniculatum. Inhabiting the intertidal zone of the tropical and subtropical coast of the Indo-West Pacific oceans, its populations are deemed to be greatly shaped by historic sea-level fluctuations. Using dual methods of Sanger and Illumina sequencing, we found that the 18sampled populations were structured into two groups, namely, the "Indo-Malayan" group, comprising three subgroups (the northern South China Sea, Gulf of Bengal, and Bali), and the "Pan-Australasia" group, comprising the subgroups of the southern South China Sea and Australasia. Based on the approximate Bayesian computations and Stairway Plot, we inferred that the southern South China Sea subgroup, which penetrates the interior of the "Indo-Malayan" group, originated from the Australasia subgroup, accompanied by a severe bottleneck event, with a spot of gene flow from both the Australasia and "Indo-Malayan" groups. Geographical barriers such as the Sundaland underlie the genetic break between Indian and Pacific Oceans, but the discontinuity between southern and northern South China Sea was originated from genetic drift in the bottleneck event. Hence, we revealed a case evidencing that the bottleneck event promoted population subdivision. This conclusion may be applicable in other taxa beyond coastal plants.

Molecular identification of seven Sarcocystis species in red deer (Cervus elaphus) from Lithuania

The diaphragm muscles of 77 free-ranging red deer (Cervus elaphus) were examined for Sarcocystis species in Lithuania. Sarcocysts were detected in 61 out of 77 (79.2%) animals investigated. A total of 60 isolated sarcocysts were identified to species using subunit I of cytochrome c oxidase (cox1) sequence analysis. Overall, seven species, S. entzerothi, S. hjorti, S. iberica, S. linearis, S. pilosa, S. truncata and S. venatoria, were confirmed in Lithuanian red deer. Sarcocystis entzerothi was reported in red deer for the first time. Previously this species was shown to use sika deer as well as roe deer and fallow deer as an intermediate host. Based on cox1, with the addition of the current data, altogether 13 Sarcocystis species have so far been shown to use red deer as an intermediate host. Species detected in red deer demonstrated considerable differences in intraspecific genetic variation at cox1. Genetic distances between different samples of S. hjorti and S. linearis were calculated using principal coordinates analysis (PCoA), implying molecular divergence of same Sarcocystis species using different hosts in the same geographical area and divergence of those employing same intermediate host species from different areas.

Revealing the diversity of Fusarium micromycetes in agroecosystems of the North Caucasus plains for replenishing the State Collection of Phytopathogenic Microorganisms of the All-Russian Scientif ic Research Institute of a Phytopathology.

In order to prevent crop yield losses from the most dangerous and economically important pathogenic organisms, it is necessary not only to monitor the virulence gene pool, but also to study the nature of pathogen variability and determine the potential for the emergence of new genes and races. This requires centralized collections of fungal cultures characterized by a set of stable strains to provide for phytopathological, immunological, breeding, genetic, toxicological, parasitological and other studies. The State Collection of Phytopathogenic Microorganisms of the ARSRIP is the State Depository of Phytopathogenic microorganisms that are non-pathogenic to humans or farmed animals. Currently, it has more than 4,500 accessions of plant pathogenic strains of fungi, oomycetes, bacteria, viruses, phytoplasmas, and the collection is updated annually. For this purpose, the study of the inter- and intraspecific genetic diversity of genus Fusarium was carried out in agricultural systems of the Krasnodar Territory. In 2020, the State Collection of Phytopathogenic Microorganisms was supplemented with 13 strains of Fusarium fungi isolated from tissues of winter wheat plants collected in several locations of the Krasnodar region. The complex of Fusarium fungi revealed on winter wheat usually included Fusarium oxysporum, F. culmorum, F. lolii, F. graminearum, F. fujikuroi, F. sporotrichioides, etc. The effect of the preceding crop on the frequency of Fusarium species isolated from winter wheat was observed. After series cloning of collected isolates, 21 strains of different fungal species characterized by stable morphology traits and known pathogenic and phytotoxic properties were selected for collection replenishment. Significant differences in pathogenic activity were revealed between fungi belonging to either the same or different species; the manifestation of this activity varied from the absence of any effect of spore suspensions on seedling development to a complete inhibition of their growth. The phytotoxic activity towards wheat seedlings varied from medium to high. Species possessing a high intensity of phytotoxic activities are the most dangerous for wheat, since they promote accumulation of dangerous phytotoxins in plant tissues.

A review of intraspecific genetic diversity on wild plants in Korea estimated from varying nuclear DNA markers

Given the significant impact of molecular markers on the genetic diversity assessment, understanding genetic diversity pattern across diverse marker types in a comparative manner is of great importance. In Korea, within the last 10 years population genetics studies of wild plants have drawn much attention as varying DNA markers have developed. To investigate the pattern of among-population and within-population level genetic diversity of wild plants in Korea, we reviewed the extent of population genetic parameters across four DNA markers (RAPD, AFLP, ISSR, SSR). We compiled 73 data sets from research papers published between 2010 and 2019. ISSR markers were the most frequently used in population genetics studies conducted on Korean wild plants. Overall, genetic diversity patterns greatly varied across the different marker types. On average, endangered species exhibited low within-population genetic variation and high among-population genetic diversity. Species with wide geographic distribution showed greater within-population diversity values than the ones residing in a restricted area except for AFLP data. Populations were genetically less differentiated in long distance dispersal species with wide geographic ranges. Our review indicates that the studies on the genetic diversity of wild plants may be improved by expanding the scope and increasing the sample sizes.

SSR-Sequencing Reveals the Inter- and Intraspecific Genetic Variation and Phylogenetic Relationships among an Extensive Collection of Radish (Raphanus) Germplasm Resources.

Raphanus has undergone a lengthy evolutionary process and has rich diversity. However, the inter- and intraspecific phylogenetic relationships and genetic diversity of this genus are not well understood. Through SSR-sequencing and multi-analysis of 939 wild, semi-wild and cultivated accessions, we discovered that the European wild radish (EWR) population is separated from cultivated radishes and has a higher genetic diversity. Frequent intraspecific genetic exchanges occurred in the whole cultivated radish (WCR) population; there was considerable genetic differentiation within the European cultivated radish (ECR) population, which could drive radish diversity formation. Among the ECR subpopulations, European primitive cultivated radishes (EPCRs) with higher genetic diversity are most closely related to the EWR population and exhibit a gene flow with rat-tail radishes (RTRs) and black radishes (BRs)/oil radishes (ORs). Among Asian cultivated radishes (ACRs), Chinese big radishes (CBRs) with a relatively high diversity are furthest from the EWR population, and most Japanese/Korean big radishes (JKBRs) are close to CBR accessions, except for a few old Japanese landraces that are closer to the EPCR. The CBR and JKBR accessions are independent of RTR accessions; however, phylogenetic analysis indicates that the RTR is sister to the clade of CBR (including JWR), which suggests that the RTR may share the most recent common ancestry with CBRs and JWRs. In addition, Japanese wild radishes (JWRs), (namely, R. sativus forma raphanistroides) are mainly scattered between CBRs and EPCRs in PCoA analysis. Moreover, JWRs have a strong gene exchange with the JKBR, OR and RTR subpopulations. American wild radishes (AWRs) are closely related to European wild and cultivated radishes, and have a gene flow with European small radishes (ESRs), suggesting that the AWR developed from natural hybridization between the EWR and the ESR. Overall, this demonstrates that Europe was the origin center of the radish, and that Europe, South Asia and East Asia appear to have been three independent domestication centers. The EPCR, AWR and JWR, as semi-wild populations, might have played indispensable transitional roles in radish evolution. Our study provides new perspectives into the origin, evolution and genetic diversity of Raphanus and facilitates the conservation and exploitation of radish germplasm resources.

Plant genotype controls wetland soil microbial functioning in response to sea-level rise

Abstract. Climate change can strongly alter soil microbial functioning via plant–microbe interactions, often with important consequences for ecosystem carbon and nutrient cycling. Given the high degree of intraspecific trait variability in plants, it has been hypothesized that genetic shifts within plant species yield a large potential to control the response of plant–microbe interactions to climate change. Here we examined if sea-level rise and plant genotype interact to affect soil microbial communities in an experimental coastal wetland system, using two known genotypes of the dominant salt-marsh grass Elymus athericus characterized by differences in their sensitivity to flooding stress – i.e., a tolerant genotype from low-marsh environments and an intolerant genotype from high-marsh environments. Plants were exposed to a large range of flooding frequencies in a factorial mesocosm experiment, and soil microbial activity parameters (exo-enzyme activity and litter breakdown) and microbial community structure were assessed. Plant genotype mediated the effect of flooding on soil microbial community structure and determined the presence of flooding effects on exo-enzyme activities and belowground litter breakdown. Larger variability in microbial community structure, enzyme activities, and litter breakdown in soils planted with the intolerant plant genotype supported our general hypothesis that effects of climate change on soil microbial activity and community structure can depend on plant intraspecific genetic variation. In conclusion, our data suggest that adaptive genetic variation in plants could suppress or facilitate the effects of sea-level rise on soil microbial communities. If this finding applies more generally to coastal wetlands, it yields important implications for our understanding of ecosystem–climate feedbacks in the coastal zone.

Molecular epidemiology of Paracoccidiodes spp. recovered from patients with paracoccidioidomycosis in a teaching hospital from Minas Gerais State of Brazil.

IntroductionParacoccidioidomycosis (PCM) is caused by several species of the Paracoccidioides genus which can be differentiated by interspecific genetic variations, morphology and geographic distribution. Intraspecific variability correlation with clinical and epidemiological aspects of these species still remains unclear. This study aimed to sequence the loci GP43, exon 2 and ARF of 23 clinical isolates of Paracoccidioides spp. from patients in the Southeast Region of Brazil.Methodology and main findingsGenBank was used to compare the present (23) with previous described sequences (151) that included ARF and GP43. It was identified a high polymorphism rate among the 23 isolates in comparison to the other 151. Among the isolates, 22 (95.66%) were S1/P. brasiliensis and 1 (4.34%) was identified as PS2/P. americana. A total of 45 haplotypes were found as follows: 19 from S1/P. brasiliensis (13 from the present study), 15 from P. lutzii, 6 from PS2/P. americana (1 from the present study), 3 from PS3/P. restrepiensis and 2 from PS4/P. venezuelensis. Moreover, exclusive haplotypes according to clinical origin and geographical area were found. S1/P. brasiliensis (HD = 0.655 and K = 4.613) and P. lutzii (HD = 0.649 and K = 2.906) presented the highest rate of polymorphism among all species, from which 12 isolates of the present study were clustered within S1b/P. brasiliensis. The GP43 locus showed a higher variability and was found to be the main reason for the species differentiation.ConclusionsThe results herein decribed show a high intraspecific genetic variability among S1/P. brasiliensis isolates and confirm the predominance of this species in the Southeast region of Brazil. The finding of exclusive haplotypes according to clinical origin and geographical area would suggest correlation between the molecular profile with the clinical form and geographic origin of patients with PCM.

Genetic divergence and local adaptation of Liriodendron driven by heterogeneous environments.

Ecological adaptive differentiation alters both the species diversity and intraspecific genetic diversity in forests, thus affecting the stability of forest ecosystems. Therefore, knowledge of the genetic underpinnings of the ecological adaptive differentiation of forest species is critical for effective species conservation. In this study, single-nucleotide polymorphisms (SNPs) from population transcriptomes were used to investigate the spatial distribution of genetic variation in Liriodendron to assess whether environmental variables can explain genetic divergence. We examined the contributions of environmental variables to population divergence and explored the genetic underpinnings of local adaptation using a landscape genomic approach. Niche models and statistical analyses showed significant niche divergence between L. chinense and L. tulipifera, suggesting that ecological adaptation may play a crucial role in driving interspecific divergence. We detected a new fine-scale genetic structure in L. chinense, and divergence of the six groups occurred during the late Pliocene to early Pleistocene. Redundancy analysis (RDA) revealed significant associations between genetic variation and multiple environmental variables. Environmental association analyses identified 67 environmental association loci (EALs; nonsynonymous SNPs) that underwent interspecific or intraspecific differentiation, 28 of which were associated with adaptive genes. These 28 candidate adaptive loci provide substantial evidence for local adaptation in Liriodendron. Our findings reveal ecological adaptive divergence pattern between Liriodendron species and provide novel insight into the role of heterogeneous environments in shaping genetic structure and driving local adaptation among populations, informing future L. chinense conservation efforts.