Evaluating Population Genetic Structure and Demographic History of Quercus spinosa (Fagaceae) Based on Specific Length Amplified Fragment Sequencing

Speciation patterns of related species under the hybrid zone: A case study of three sclerophyllous oaks in the east Himalaya-Hengduan Mountains

Speciation is often accompanied by frequent gene exchanges, which have been gradually recognized as a common phenomenon in nature. Although gene flow may influence different reproductive isolations, the specific mechanism of the process still requires more experimental evidence, especially in hybrid populations that have no significant differentiation and isolation. To address this challenge, this study aims to elucidate the underlying mechanisms of sympatry and parapatry in related species. Three sclerophyllous oaks (Quercus spinosa, Quercus aquifolioides and Quercus rehderiana), which are mainly distributed in the sympatry/parapatry of the East Himalaya-Hengduan Mountains and adjacent regions, were used to explore the population dynamics and evolutionary history. Based on 12,420 genome-wide single nucleotide polymorphism datasets, gene flow detection showed that the three species did not present any obvious genetic barriers. Evolutionary analysis indicated that the three species diverged during the Tertiary Period, and no migration events occurred in the early stages of species divergence. Combined with the data of 19 ecological factors, geological movements and climatic turbulence caused the rapid radiated differentiation of the three species during the Neocene, and similar selective pressures resulted in the same evolutionary pattern based on demographic history analysis. In addition, the predicted niche occupancy profiles and Generalized Dissimilarity Modelling revealed that the three species occupied distinct niches and had significant differences in ecological adaptation, which may explain the specific morphological characteristics of the different species. Therefore, we believe that the populations of the three related species underwent adaptive evolution in different habitats during the early stages of divergence. This study provides new experimental evidence of the formation patterns of parallel speciation.

Genetic diversity and signatures of selection in four indigenous horse breeds of Iran

Indigenous Iranian horse breeds were evolutionarily affected by natural and artificial selection in distinct phylogeographic clades, which shaped their genomes in several unique ways. The aims of this study were to evaluate the genetic diversity and genomewide selection signatures in four indigenous Iranian horse breeds. We evaluated 169 horses from Caspian (n = 21), Turkmen (n = 29), Kurdish (n = 67), and Persian Arabian (n = 52) populations, using genomewide genotyping data. The contemporary effective population sizes were 59, 98, 102, and 113 for Turkmen, Caspian, Persian Arabian, and Kurdish breeds, respectively. By analysis of the population genetic structure, we classified the north breeds (Caspian and Turkmen) and west/southwest breeds (Persian Arabian and Kurdish) into two phylogeographic clades reflecting their geographic origin. Using the de-correlated composite of multiple selection signal statistics based on pairwise comparisons, we detected a different number of significant SNPs under putative selection from 13 to 28 for the six pairwise comparisons (FDR < 0.05). The identified SNPs under putative selection coincided with genes previously associated with known QTLs for morphological, adaptation, and fitness traits. Our results showed HMGA2 and LLPH as strong candidate genes for height variation between Caspian horses with a small size and the other studied breeds with a medium size. Using the results of studies on human height retrieved from the GWAS catalog, we suggested 38 new putative candidate genes under selection. These results provide a genomewide map of selection signatures in the studied breeds, which represent valuable information for formulating genetic conservation and improved breeding strategies for the breeds.

Electrochemical fingerprinting sensor for plant phylogenetic investigation: A case of sclerophyllous oak

Electrochemical fingerprinting can collect the electrochemical behavior of electrochemically active molecules in plant tissues, so it is regarded as a new plant analysis technology. Because the signal of electrochemical fingerprinting is positively correlated with the amount and type of electrochemically active molecules in plant tissues, it can also be used to reflect genetic differences between different species. Previous electrochemical fingerprinting techniques have been frequently used in phylogenetic studies of herbaceous plants. In this work, 19 Quercus species (17 evergreen or semi evergreen species and 2 deciduous species) were selected for investigation. The results indicated the electrochemical fingerprint of some species share similar features but can be distinguished after changing the recording condition (extraction solvent and electrolyte). The two sets of electrochemical fingerprint data can be used to construct different pattern recognition technology, which further speeds up the recognition efficiency. These electrochemical fingerprints were further used in phylogenetic investigations. The phylogenetic results deduced from electrochemical fingerprinting were divided mainly into three clusters. These can provide evidence for some of these arguments as well as new results.

Population and Landscape Genetics Provide Insights Into Species Conservation of Two Evergreen Oaks in Qinghai-Tibet Plateau and Adjacent Regions

The combination of population and landscape genetics can facilitate the understanding of conservation strategy under the changing climate. Here, we focused on the two most diverse and ecologically important evergreen oaks: Quercus aquifolioides and Quercus spinosa in Qinghai-Tibetan Plateau (QTP), which is considered as world's biodiversity hotspot. We genotyped 1,657 individuals of 106 populations at 15 nuclear microsatellite loci throughout the species distribution range. Spatial patterns of genetic diversity were identified by mapping the allelic richness (AR) and locally common alleles (LCA) according to the circular neighborhood methodology. Migration routes from QTP were detected by historical gene flow estimation. The response pattern of genetic variation to environmental gradient was assessed by the genotype-environment association (GEA) analysis. The overall genetic structure showed a high level of intra-species genetic divergence of a strong west-east pattern. The West-to-East migration route indicated the complex demographic history of two oak species. We found evidence of isolation by the environment in Q. aqu-East and Q. spi-West lineage but not in Q. aqu-West and Q. spi-East lineage. Furthermore, priority for conservation should be given to populations that retain higher spatial genetic diversity or isolated at the edge of the distribution range. Our findings indicate that knowledge of spatial diversity and migration route can provide valuable information for the conservation of existing populations. This study provides an important guide for species conservation for two oak species by the integration of population and landscape genetic methods.

Genetic structure and temporal environmental niche dynamics of sideoats grama [Bouteloua curtipendula (Michx.) Torr.] populations in Mexico

In the past years, several plant breeding programs have been done to select outstanding genotypes of sideoats grama (Bouteloua curtipendula) for restoration purposes. Such programs have been focused mainly on agronomic traits; however, little attention has been paid to the genetic structure and environmental adaptation of the selected genotypes. Thus, in this study we evaluated the genetic structure of 85 sideoats grama populations in Mexico. In addition, we modeled the past, present and future environmental niche of the genetic clusters of this species. Ninety sideoats grama populations were genetically analyzed through AFLP (Amplified Fragment Length Polymorphisms) markers. The environmental niche of the population clusters was modeled by using the maximum entropy method. The genetic analysis separated the populations into two genetically different clusters (p = 0.0003). The differentiation of these lineages can be partially explained by the paleoclimatic events experienced during the last interglacial and glacial maximums. Consequently, the genetic clusters have different environmental niche at the present time. Suitability areas for the distribution of Cluster I are mainly located in the central part of the country while the environmental niche of Cluster II is located in the semiarid region, close to the mountain range of the Sierra Madre Occidental. Thus, selection and restoration programs with sideoats grama must be carried out using local germplasm from each environmental niche. Given the environmental niche of both genetic clusters will suffer changes in the near and mid-century future, climate change must be considered for genotypes selection and restoration programs.

A selection signatures study among Middle Eastern and European sheep breeds

Selection, both natural and artificial, leaves patterns on the genome during domestication of animals and leads to changes in allele frequencies among populations. Detecting genomic regions influenced by selection in livestock may assist in understanding the processes involved in genome evolution and discovering genomic regions related to traits of economic and ecological interests. In the current study, genetic diversity analyses were conducted on 34,206 quality-filtered SNP positions from 450 individuals in 15 sheep breeds, including six indigenous breeds from the Middle East, namely Iranian Balouchi, Afshari, Moghani, Qezel, Karakas and Norduz, and nine breeds from Europe, namely East Friesian Sheep, Ile de France, Mourerous, Romane, Swiss Mirror, Spaelsau, Suffolk, Comisana and Engadine Red Sheep. The SNP genotype data generated by the Illumina OvineSNP50 Genotyping BeadChip array were used in this analysis. We applied two complementary statistical analyses, F_ST (fixation index) and xp-EHH (cross-population extended haplotype homozygosity), to detect selection signatures in Middle Eastern and European sheep populations. F_ST and xp-EHH detected 629 and 256 genes indicating signatures of selection, respectively. Genomic regions identified using F_ST and xp-EHH contained the CIDEA, HHATL, MGST1, FADS1, RTL1 and DGKG genes, which were reported earlier to influence a number of economic traits. Both F_ST and xp-EHH approaches identified 60 shared genes as the signatures of selection, including four candidate genes (NT5E, ADA2, C8A and C8B) that were enriched for two significant Gene Ontology (GO) terms associated with the adenosine metabolic procedure. Knowledge about the candidate genomic regions under selective pressure in sheep breeds may facilitate identification of the underlying genes and enhance our understanding on these genes role in local adaptation.

Divergent lineages in a semi-arid mallee species, Eucalyptus behriana, correspond to a major geographic break in southeastern Australia

AIM

To infer relationships between populations of the semi-arid, mallee eucalypt, Eucalyptus behriana, to build hypotheses regarding evolution of major disjunctions in the species' distribution and to expand understanding of the biogeographical history of southeastern Australia.

LOCATION

Southeastern Australia.

TAXON

Eucalyptus behriana (Myrtaceae, Angiospermae).

METHODS

We developed a large dataset of anonymous genomic loci for 97 samples from 11 populations of E. behriana using double digest restriction site-associated DNA sequencing (ddRAD-seq), to determine genetic relationships between the populations. These relationships, along with species distribution models, were used to construct hypotheses regarding environmental processes that have driven fragmentation of the species' distribution.

RESULTS

Greatest genetic divergence was between populations on either side of the Lower Murray Basin. Populations west of the Basin showed greater genetic divergence between one another than the eastern populations. The most genetically distinct population in the east (Long Forest) was separated from others by the Great Dividing Range. A close relationship was found between the outlying northernmost population (near West Wyalong) and those in the Victorian Goldfields despite a large disjunction between them.

CONCLUSIONS

Patterns of genetic variation are consistent with a history of vicariant differentiation of disjunct populations. We infer that an early disjunction to develop in the species distribution was that across the Lower Murray Basin, an important biogeographical barrier separating many dry sclerophyll plant taxa in southeastern Australia. Additionally, our results suggest that the western populations fragmented earlier than the eastern ones. Fragmentation, both west and east of the Murray Basin, is likely tied to climatic changes associated with glacial-interglacial cycles although it remains possible that major geological events including uplift of the Mount Lofty Ranges and basalt flows in the Newer Volcanics Province also played a role.

Fine-scale genetic structure of the overwintering Chilo suppressalis in the typical bivoltine areas of northern China

The rice stem borer (RSB), Chilo suppressalis (Lepidoptera: Pyralidae), is an important agricultural pest that has caused serious economic losses in the major rice-producing areas of China. To effectively control this pest, we investigated the genetic diversity, genetic differentiation and genetic structure of 16 overwintering populations in the typical bivoltine areas of northern China based on 12 nuclear microsatellite loci. Moderate levels of genetic diversity and genetic differentiation among the studied populations were detected. Neighbour-joining dendrograms, Bayesian clustering and principal coordinate analysis (PCoA) consistently divided these populations into three genetic clades: western, eastern and northern/central. Isolation by distance (IBD) and spatial autocorrelation analyses demonstrated no correlation between genetic distance and geographic distance. Bottleneck analysis illustrated that RSB populations had not undergone severe bottleneck effects in these regions. Accordingly, our results provide new insights into the genetic relationships of overwintering RSB populations and thus contribute to developing effective management strategies for this pest.

The Zagros Mountains acting as a natural barrier to gene flow in the Middle East: more evidence from the evolutionary history of spiny-tailed lizards (Uromasticinae: Saara)

We investigated the phylogeographic structure of the genus Saara and studied whether the Zagros Mountain ranges influence the gene flow and dispersal at the landscape scale between the Iranian Saara species, including S. asmussi in the central Iranian plateau and S. loricata in the Mesopotamian lowlands. Phylogenetic analyses clearly show three well-supported species, including S. loricata, S. asmussi and S. hardwickii, that are distinct from Uromastyx species. The S-DIVA and BBM analyses demonstrate that species of Saara originated from an ancestor somewhere in the Iranian Plateau and then dispersed to its current geographical range. Our results indicate that the separation of S. loricata from S. asmussi coincides with the orogenic events of the Zagros Mountains during the Pliocene, and thus it may show a vicariance event. Diversification within populations of S. loricata and S. assmussi are estimated to have occurred during the Pleistocene. The haplotype network indicates one haplogroup for each of the Iranian Saara species. Population genetic analyses shows signals of demographic expansions at the beginning of the Holocene for S. loricata. Our results support the hypothesis that the Zagros Mountains act as a barrier for gene flow and Quaternary climatic oscillations affected intraspecific genetic divergences of S. loricata and S. asmussi.

Mitochondrial DNA diversity and population structure of Laodelphax striatellus across a broad geographic area in China

The small brown planthopper (SBPH), Laodelphax striatellus Fallén (Hemiptera: Delphacidae), is a crucial devastating rice pest in East Asia. To effectively control this pest, we investigate the genetic diversity, genetic differentiation and genetic structure of 49 populations in China based on a 596 bp fragment of the mitochondrial DNA cytochrome c oxidase subunit I (mtDNA COI) gene. Overall, 83 haplotypes were detected in 1253 mtDNA COI sequences. High levels of genetic variability (Hd = 0.756 ± 0.009, π = 0.00416 ± 0.00011) and genetic differentiation (F _ST = 0.262, p < .001) were observed. Bayesian inference phylogenetic and median-joining haplotype network analyses indicated no obvious geographical distribution pattern among haplotypes. Hierarchical AMOVA and SAMOVA revealed no genetically distinct groups and lack of obvious phylogeographic structure. Isolation by distance (IBD) analysis results demonstrated no correlation between genetic differentiation and geographic distance. Finally, the demographic history of SBPH examined by neutrality tests and mismatch distribution analyses illustrated a sudden population expansion at the large spatial scale in China.

Framework Phylogeny, Evolution and Complex Diversification of Chinese Oaks

Oaks (Quercus L.) are ideal models to assess patterns of plant diversity. We integrated the sequence data of five chloroplast and two nuclear loci from 50 Chinese oaks to explore the phylogenetic framework, evolution and diversification patterns of the Chinese oak's lineage. The framework phylogeny strongly supports two subgenera Quercus and Cerris comprising four infrageneric sections Quercus, Cerris, Ilex and Cyclobalanopsis for the Chinese oaks. An evolutionary analysis suggests that the two subgenera probably split during the mid-Eocene, followed by intergroup divergence within the subgenus Cerris around the late Eocene. The initial diversification of sections in the subgenus Cerris was dated between the mid-Oligocene and the Oligocene-Miocene boundary, while a rapid species radiation in section Quercus started in the late Miocene. Diversification simulations indicate a potential evolutionary shift on section Quercus, while several phenotypic shifts likely occur among all sections. We found significant negative correlations between rates of the lineage diversification and phenotypic turnover, suggesting a complex interaction between the species evolution and morphological divergence in Chinese oaks. Our infrageneric phylogeny of Chinese oaks accords with the recently proposed classification of the genus Quercus. The results point to tectonic activity and climatic change during the Tertiary as possible drivers of evolution and diversification in the Chinese oak's lineage.