Salvia miltiorrhiza is an outcrossing and perennial herb native to China. Although well-known for its medicinal value, there is a lack of knowledge regarding its natural population genetics. Here, we used 12 microsatellite markers to investigated population genetic diversity and structure of 215 samples from populations naturally distributed in central eastern China. A moderate level of genetic diversity was detected probably due to the over-mining of its roots. The allelic richness (AR) ranged from 3.034 to 4.889 with an average of 3.891. Moreover, pairwise estimates of FST among the populations of S. miltiorrhiza varied from 0.036 to 0.312 and two clusters were obtained by STRUCTURE and discriminant analysis of principal components. It is likely that the genetic differentiation of these two clusters was formed during glacial periods. Our result provides insights into the conservation of this valuable medicinal plant.

Sticta canariensis is a lichen which is rare in all parts of its range in Atlantic Europe and Macaronesia, where it occurs in laurisilva forests, a habitat highly threatened by global change. Thus, this species is of high priority for inclusion in conservation programmes where genetic diversity should be considered. We have established new microsatellite loci and generated a dataset that demonstrates the genetic diversity of the lichen-forming fungus S. canariensis from eight locations across its disjunct range, in Macaronesia, Norway and England. We genotyped 25 microsatellite loci for 65 specimens and detected five genetic clusters which resemble major geographical divisions, specifically among the Macaronesian archipelagos. The total number of observed alleles ranged from 2 to 22. These are the first microsatellite markers developed for S. canariensis and they will be useful for population genetic studies and for conservation assessments.

Archaeology and cultural evolution theory both predict that environmental variation and population size drive the likelihood of inventions (via individual learning) and their conversion to population-wide innovations (via social uptake). We use the case study of the adoption of the bow and arrow in the Great Basin to infer how patterns of cultural variation, invention, and innovation affect investment in new technologies over time and the conditions under which we could predict cultural innovation to occur. Using an agent-based simulation to investigate the conditions that manifest in the innovation of technology, we find the following: (1) increasing ecological variation results in a greater reliance on individual learning, even when this decreases average fitness due to the costs of learning; (2) decreasing population size increases variability in the types of learning strategies that individuals use; among smaller populations drift-like processes may contribute to randomization in interpopulation cultural diffusion; (3) increasing the mutation rate affects the variability in learning patterns at different rates of environmental variation; and (4) increasing selection pressure increases the reliance on social learning. We provide an open-source R script for the model and encourage others to use it to test additional hypotheses.

The North-Eastern region (NER) of India falls under the Eastern Himalayan region and it is a bio-diversity hub. Diverse maize landraces with wide adaptability to extreme climatic and soil scenario like heavy rainfall, drought and acidic soil conditions have been grown in NER since time immemorial. However, maize diversity in NER region has drastically reduced due to introduction of high yielding varieties and hybrids. Modern maize breeding programmes are focused on high yield but other unique traits like stay green trait, prolificacy (more than one fertile ear per plant), self-fertilizing ability are also important and the local germplasm of the NER region can contribute with these unique traits. Prior to the selection of any lines in several breeding programmes, assessment of genetic diversity and population structure are basic requirements. Hence, in the present study assessment of genetic diversity and population structure study in 30 maize inbreds developed from different germplasm of NER was undertaken using SSR markers, selected for their broad distribution throughout the genome, in order to assess the extent of allelic diversity among the lines and whether any population structure could be established. In addition to assessing molecular diversity, the study aims to evaluate the potential for yield and other beneficial and unique alleles that have high potential to contribute in the genetic enhancement programme of maize.

The article presents the results of the search for microsatellite or simple sequence repeat (SSR) loci with tri-, tetra-, penta- and hexanucleotide tandem repeat motifs in the draft de novo assembly of the Siberian fir (Abies sibirica Ledeb.) genome and the development of convenient relatively highly and moderately polymorphic markers that can be easily genotyped even by simple gel electrophoresis. In total, 64 pairs of oligonucleotide polymerase chain reaction (PCR) primers for 32 detected microsatellite loci were designed and tested. Based on the testing results, 10 most promising polymorphic loci were selected and genotyped in eight natural populations of Siberian fir. Homologous microsatellite loci in the genome of European silver fir (Abies alba Mill.) were also identified by mapping Siberian fir contigs, containing SSR loci to the European silver fir genome assembly. A multiplex panel of 14 universal microsatellite loci was developed and genotyped in samples from four natural populations of A. alba and a small sample of eight Nordmann fir (Abies nordmanniana (Steven) Spach) trees.

Genetic diversity and genetic relatedness among 50 genotypes from eight countries, including Iran, Afghanistan, Turkmenistan, Syria, Lebanon, India, Yemen, and the United States located in two continents of Asia and the America, were assessed using SCoT markers. A total of 213 bands were produced; 100% of them were polymorphic; the average polymorphism information content (PIC) was 0.39. The mean Nei's gene diversity and Shannon's index were 0.33 and 0.49, respectively. Analysis of molecular variance suggested significant genetic differences within pomegranate populations. 99% of variance occurs within the populations, whereas 1% of the variation was recorded among the populations of pomegranate. Cluster analysis using SCoT markers able to group genotypes based on their geographical origins. Based on cluster analysis, the genotypes studied were divided into two main groups. The first group included most Asian genotypes, while American genotypes along with some Asian genotypes were in the second group. In the first group, Iranian genotypes were grouped with genotypes from Afghanistan and India. In the second group, the genotypes belonging to the America were in the same group as most of the genotypes of Turkmenistan. According to the present study, SCoT markers can be used to evaluate genetic diversity, identification and DNA fingerprinting pomegranate genotypes of different origins. This information can be used in breeding programs and the management of pomegranate collections.

Fluted pumpkin (Telfairia occidentalis Hook F.) is an underutilized indigenous leafy vegetable with enormous prospects for food security in sub-Saharan Africa. However, relatively little is known about genetic relationships and population structure in the species. In this study, 32 landraces of fluted pumpkin collected across three southern geographical regions in Nigeria were assessed for genetic diversity and population structure using 8 start codon-targeted (SCoT) makers. The polymorphic information content of the SCoT markers ranged from 0.48 in SCoT36 to 0.94 in SCoT28, with an average of 0.77. Hierarchical cluster dendrogram based on Ward's method and principal component analysis grouped the landraces into four clusters without affiliation to provenance. Overall, the mean values of the population genetic diversity parameters – Nei's gene diversity (H) and Shannon's information index (I) showed values of 0.28 ± 0.01 and 0.43 ± 0.02, respectively, implying a narrow genetic base for the landraces. The result was further corroborated by a very close Nei's genetic distance and identity among populations of the landraces. Furthermore, the south-west population exhibited the higher genetic diversity (H = 0.31 ± 0.02 and I = 0.45 ± 0.03). Population structure analysis inferred three subpopulations for the accessions with varying degrees of allelic admixture. An analysis of molecular variance revealed that almost all the genetic variation occurred within (99%) than between (1%) populations. The findings shed light on the genetic diversity of southern Nigerian fluted pumpkin and have significant implications for the characterisation, conservation, exploitation and improvement of the species.

Availability of resistance sources among cultivated varieties helps in easy utilization as donor owing to no deleterious linkage drag. In the present investigation, 121 rice varieties were screened for their resistance against a virulent isolate of Fusarium fujikuroi (Ff-10) and genotyped using reported microsatellite markers. Among 121 varieties, only eight varieties, namely Luna Sankhi, Improved Tapaswini, Sarasa, Sadabahar, CR-311, Kshira, Wifa-10 and Binadhan-8, were found to be highly resistant (HR), seven varieties were resistant (R), 31 were moderately resistant (MR), 10 were moderately susceptible (MS), 11 were susceptible (S) and the rest 54 were highly susceptible (HS). The allele diversity of molecular markers classified the population into three clusters. The highly resistant varieties were grouped in major clusters II and III, whereas the remaining genotypes were distributed in all three clusters. Analysis of molecular variance (AMOVA) resulted in 95% of the maximum diversity within the test population and 5% diversity between populations. Population structure analysis grouped the genotypes into two sub-populations based on relatedness, where most of the resistant genotypes were grouped into one sub-population and other genotypes were distributed among sub-populations. Re-examination of reported markers' trait associations with bakanae resistance in the experimental population identified marker RM-3698 as associated with resistance accounting 8.4% explained phenotypic variation. This study shows that simple sequence repeat markers can be used to assess allelic diversity and population structure of bakanae resistance in rice varieties. The highly resistant genotypes, along with resistance markers, could be used as donors in marker-assisted bakanae improvement breeding programmes.

Next generation sequencing technologies have facilitated a shift from a few targeted loci in population genetic studies to whole genome approaches. Here, we review the types of questions and inferences regarding the population biology and evolution of parasitic helminths being addressed within the field of population genomics. Topics include parabiome, hybridization, population structure, loci under selection and linkage mapping. We highlight various advances, and note the current trends in the field, particularly a focus on human-related parasites despite the inherent biodiversity of helminth species. We conclude by advocating for a broader application of population genomics to reflect the taxonomic and life history breadth displayed by helminth parasites. As such, our basic knowledge about helminth population biology and evolution would be enhanced while the diversity of helminths in itself would facilitate population genomic comparative studies to address broader ecological and evolutionary concepts.

In this article I show how ubiquitous hybridity is in cultures. It is enabled by layers of population movements and contacts since the dispersal of Homo sapiens out of Africa around 50,000 years ago. I demonstrate how hybridization has proceeded in the emergence of creole language varieties and show that the same process has also driven, for instance, the emergence and differential evolution of English and the speciation of Vulgar Latin into the Romance languages. Differences in outcomes are determined by the specificities of the contact ecologies, including population structure, differences in the demographic proportions of the populations in contact and power relations between them, as well as patterns of population growth, among other factors. I argue that hybridity is not unique to languages. It is conspicuous in other domains of culture, including cuisine, music, clothing fashions, and technologies, for example. I submit a uniformitarian approach inspired by evolutionary biology to better understand how hybridization occurs.

The members of the Aegilops genus serve as a vast pool of allele discovery for wheat improvement in abiotic and biotic stress responses. Aegilops mutica Boiss (Amblyopyrym muticum (Boiss) Eig) is an unexplored candidate with significant potential. Even though it has been used in cytogenetics applications within the last century, natural population diversity and allele discovery have been neglected. As an endemic species for Anatolia and the lower Caucasian region, it has an unexplored population structure. Here, seventy-five genotypes from five different newly collected populations from central Anatolia were evaluated with 29 polymorphic SSR loci. Significant diversity within (83%) and between (17%) the populations was obtained. Three of the populations were clearly separated, while two had some level of the mixture. Relatively easy cross-species hybridization and introgressions make Ae. mutica a good candidate for novel allele discovery and pre-breeding. Here, for the first time, representative natural populations of Ae. mutica were compared and population structures were revealed with SSR markers which may clear the misty vision that geneticists might have regarding Ae. mutica. This could be exploited in genetic resource conservation and breeding programs and maybe a point for further studies.

Muskmelon, which is an important cucurbit of the tropical and subtropical region of the world, shows great diversity, with six different botanical or horticultural groups and fifteen varietal groups. In this study, a total of fifty (50) simple sequence repeat (SSR) markers were used to investigate the genetic diversity and population structure of 46 muskmelon accessions of different horticultural or varietal groups. Thirty-eight (38) of the fifty SSR markers were highly polymorphic. A total of 99 alleles were generated by the polymorphic markers, with an average of 2.06 alleles per loci. Heterozygosity among accessions for individual loci varied from 0.00 to 0.21, with the highest (0.21) reported for the CMCTN71 marker. The gene diversity and polymorphism information content (PIC) values varied between 0.08 to 0.72 and 0.07 to 0.67, with an average of 0.47 and 0.38, respectively. The primer that showed the highest gene diversity and PIC values was DM0913. The unweighted pair-group method for arithmetic average (UPGMA)-based dendrogram classified all the 46 accessions into two major clusters. Population structure analysis classified 46 muskmelon accessions into 2 subpopulations. The subpopulation I contained 29 accessions from the cantalupensis group, and subpopulation II contained 17 accessions from momordica, inodorus and conomon groups, respectively. Analysis of variance indicated that 18 and 68% of variance was due to subpopulations and differences among individuals, respectively. The present study supports the existence of sufficient variation among musk melon genetic resources in India, and their classification based on molecular markers will be helpful to accelerate the breeding programme for specific traits.

Common bean (Phaseolus vulgaris L.) is a highly economically important crop worldwide and a particularly important source of protein and minerals for people in less developed countries. Improving yield is a vital objective to meet the increasing demand for food due to the expanding human population. The present study was undertaken to study the genetic architecture of agronomic traits of common bean in India, particularly in the north-western Himalayan region. Marker-trait association (MTA) analysis was performed in a population of 100 common bean accessions using polymorphic microsatellite markers. Population structure analysis based on SSR markers divided the accessions into three main subpopulations. Ten significant MTAs were found using general linear model (GLM) and mixed linear model (MLM) approaches. We found two markers i.e. BM142 and J04555 associated with 100 seed weight and pods per plant common in both the GLM and MLM approach markers. All the MTAs were considered as major MTAs contributing more than 25% phenotypic variation. The significant quantitative trait loci identified in this study could be used in marker-assisted breeding to accelerate the genetic improvement of yield and development of high yielding common beans lines.

Hermit crabs have soft abdomens and therefore must use empty gastropod shells as protection. Shell choices do not occur at random, and the animals often occupy shells with the best fit among the available ones. To live in intertidal and sublittoral zones, regions subjected to daily variations in abiotic factors, hermit crabs present a locomotory circadian rhythm. Clibanarius antillensis has been the object of several studies in Brazil's south-east, so this study was aimed at describing its population in the south of Brazil and its movement activity under laboratory conditions during night-time and daytime, while using two different shells. The animals were sampled from the Sepultura and Lagoinha beaches, in the state of Santa Catarina through free diving. Sex ratio was skewed for males, with ovigerous females present during the whole year but with a spring peak. Males were more abundant than females, ovigerous females and intersex individuals, being predominant in all size-classes analysed. The hermit crabs occupied mainly two gastropod shells: Cerithium atratum and Agathistoma viridulum, and ovigerous females used only the first. Clibanarius antillensis showed nocturnal activity and the animals using C. atratum shells were more active than those using A. viridulum. Cerithium atratum shells are lighter and less bulky than A. viridulum, implying that there might be a tradeoff in which the hermit crabs use lighter shells, that provide less protection in order to expend less energy and be more active.

This study focuses on the role of the population structure of Leishmania spp. on the adaptive capacity of the parasite. Herein, we investigate the contribution of subpopulations of the L. (V.) braziliensis Thor strain (Thor03, Thor10 and Thor22) in the profile of murine macrophages infection. Infection assays were performed with binary combinations of these subpopulations at stationary phases. The initial interaction time showed major effects on the combination assays, as demonstrated by the significant increase in the infection rate at 5 h. Based on the endocytic index (EI), Thor10 (EI = 563.6) and Thor03 (EI = 497) showed a higher infection load compared to Thor22 (EI = 227.3). However, the EI decreased in Thor03 after 48 h (EI = 447) and 72 h (EI = 388.3) of infection, and showed changes in the infection level in all Thor10/Thor22 combinations. Assays with CellTrace CFSE-labelled Thor22 promastigotes indicated an increase (~1.5 fold) in infection by this subpopulation in the presence of Thor10 when compared to the infection profile of Thor03/Thor22 combinations in the same proportions. In addition, the potential of these subpopulations, alone or in binary combinations, to modulate the expression of cytokines and nitric oxide (NO) in vitro was investigated. Lower NO and tumour necrosis factor-α production levels were observed for all Thor10/Thor22 combinations at 24 h compared to these subpopulations alone. In contrast, Thor03/Thor22 combination assays increased IL-10 production at this time. Collectively, these results provide in vitro evidence on the potential of L. (V.) braziliensis population structure to play a relevant role in a host infection by this parasite.

Humpback whales (Megaptera novaeangliae) exhibit maternally driven fidelity to feeding grounds, and yet occasionally occupy new areas. Humpback whale sightings and mortalities in the New York Bight apex (NYBA) have been increasing over the last decade, providing an opportunity to study this phenomenon in an urban habitat. Whales in this area overlap with human activities, including busy shipping traffic leading into the Port of New York and New Jersey. The site fidelity, population composition and demographics of individual whales were analysed to better inform management in this high-risk area. Whale watching and other opportunistic data collections were used to identify 101 individual humpback whales in the NYBA from spring through autumn, 2012–2018. Although mean occurrence was low (2.5 days), mean occupancy was 37.6 days, and 31.3% of whales returned from one year to the next. Individuals compared with other regional and ocean-basin-wide photo-identification catalogues (N = 52) were primarily resighted at other sites along the US East Coast, including the Gulf of Maine feeding ground. Sightings of mother-calf pairs were rare in the NYBA, suggesting that maternally directed fidelity may not be responsible for the presence of young whales in this area. Other factors including shifts in prey species distribution or changes in population structure more broadly should be investigated.

A detailed study of rice genetic resources in Bangladesh's coastal areas is necessary. This understanding is a necessary requirement for its utilization in selective breeding. The study reports on the qualitative morphological trait-based assessment of 150 local rice samples collected from Bangladesh's coastal zone, including 50 advanced lines developed from coastal germplasm. Six of the thirteen analysed characters had a substantial gene contribution, whereas the average was 0.694. The most impressive diversity was in leaf blade intensity of green colour (LBIGC: 0.705). The total morpho-qualitative diversity was calculated to be 0.412. The character efficiency content ranged from 0.655 (LBIGC) to 0.136 (Leaf Sheath: Anthocyanin colouration, Leaf Blade: Presence/Absence, and Leaf Blade: Anthocyanin. Colouration). As per the morphological variance study, 93% of morphological changes were detected within individuals, whereas 7% were found in populations. The 150 germplasm samples were divided into four subpopulations using STRUCTURE-based population analysis. A moderate genotypic difference was detected amongst all groups, with an Fst value of 0.111. The G statistic backed up the record as well. The Shannon mutual information index reached a value of 1.252 between populations 2 and 3. In terms of gene exchange, the highest value was found between populations 3 and 4. Our data indicate a high degree of diversity in Bangladesh's coastline rice germplasm. The findings will aid in conferring the farmers' Intellectual Property Rights on the investigated rice germplasm.