Phylogenetic relationships in Chinese oaks (Fagaceae, Quercus): Evidence from plastid genome using low-coverage whole genome sequencing.

China is a second center of oak diversity but with less intensively systematic studies. Here, with 49 species representing all four sections in China, we firstly gave insight into the comprehensive phylogenetic relationships of Chinese oaks based on 54 complete plastid genomes. Our results recovered a robust phylogenetic framework and provided strong support for most nodes. The phylogenetic tree supported Quercus section Ilex as not monophyletic, in which Quercus section Cyclobalanopsis and Quercus section Cerris were nested. Most likely, incomplete lineage sorting and/or introgression among ancestral lineages in these three sections resulted in this complex pattern. The current distribution, diversification and molecular differentiation of Q. sect. Ilex in China are likely consequences of local adaptation to the geographic and paleoclimatic changes, which were driven by the uplift of Tibetan Plateau, the Hengduan Mountains and the Himalayas.

Niche Filling Dynamics of Ragweed (Ambrosia artemisiifolia L.) during Global Invasion.

Determining whether the climatic ecological niche of an invasive alien plant is similar to that of the niche occupied by its native population (ecological niche conservatism) is essential for predicting the plant invasion process. Ragweed (Ambrosia artemisiifolia L.) usually poses serious threats to human health, agriculture, and ecosystems within its newly occupied range. We calculated the overlap, stability, unfilling, and expansion of ragweed's climatic ecological niche using principal component analysis and performed ecological niche hypothesis testing. The current and potential distribution of A. artemisiifolia was mapped by ecological niche models to identify areas in China with the highest potential risk of A. artemisiifolia invasion. The high ecological niche stability indicates that A. artemisiifolia is ecologically conservative during the invasion. Ecological niche expansion (expansion = 0.407) occurred only in South America. In addition, the difference between the climatic and native niches of the invasive populations is mainly the result of unpopulated niches. The ecological niche model suggests that southwest China, which has not been invaded by A. artemisiifolia, faces an elevated risk of invasion. Although A. artemisiifolia occupies a climatic niche distinct from native populations, the climatic niche of the invasive population is only a subset of the native niche. The difference in climatic conditions is the main factor leading to the ecological niche expansion of A. artemisiifolia during the invasion. Additionally, human activities play a substantial role in the expansion of A. artemisiifolia. Alterations in the A. artemisiifolia niche would help explain why this species is so invasive in China.

Environmental factors influencing potential distribution of Schisandra sphenanthera and its accumulation of medicinal components.

Schisandrae Sphenantherae Fructus (SSF), the dry ripe fruit of Schisandra sphenanthera Rehd. et Wils., is a traditional Chinese medicine with wide application potential. The quality of SSF indicated by the composition and contents of secondary metabolites is closely related to environmental factors, such as regional climate and soil conditions. The aims of this study were to predict the distribution patterns of potentially suitable areas for S. sphenanthera in China and pinpoint the major environmental factors influencing its accumulation of medicinal components. An optimized maximum entropy model was developed and applied under current and future climate scenarios (SSP1-RCP2.6, SSP3-RCP7, and SSP5-RCP8.5). Results show that the total suitable areas for S. sphenanthera (179.58×104 km2) cover 18.71% of China's territory under the current climatic conditions (1981-2010). Poorly, moderately, and highly suitable areas are 119.00×104 km2, 49.61×104 km2, and 10.98×104 km2, respectively. The potentially suitable areas for S. sphenanthera are predicted to shrink and shift westward under the future climatic conditions (2041-2070 and 2071-2100). The areas of low climate impact are located in southern Shaanxi, northwestern Guizhou, southeastern Chongqing, and western Hubei Provinces (or Municipality), which exhibit stable and high suitability under different climate scenarios. The contents of volatile oils, lignans, and polysaccharides in SSF are correlated with various environmental factors. The accumulation of major secondary metabolites is primarily influenced by temperature variation, seasonal precipitation, and annual precipitation. This study depicts the potential distribution of S. sphenanthera in China and its spatial change in the future. Our findings decipher the influence of habitat environment on the geographical distribution and medicinal quality of S. sphenanthera, which could have great implications for natural resource conservation and artificial cultivation.

Using MaxEnt to Predict the Potential Distribution of the Little Fire Ant (Wasmannia auropunctata) in China.

Invasive ants are some of the most destructive species in ecosystems and can have serious ecological and socioeconomic impacts. The little fire ant, Wasmannia auropunctata, is native to Central and South America and was listed as one of the 100 most threatening major invasive organisms in the world by the International Union for Conservation of Nature (IUCN). The presence of W. auropunctata was first reported on the Chinese mainland in January 2022, but its distribution in China is still unclear. In this study, MaxEnt was used to predict the potential distribution of W. auropunctata in China based on known distribution points and climatic variables. The prediction results showed that most of the area south of the Yangtze River is potentially suitable for W. auropunctata, and temperature is the main factor affecting its distribution. The contemporary total suitable living area of W. auropunctata is 1,954,300 km2, accounting for 20.36% of China's total land area. Further attention should be given to the potential impact of W. auropunctata invasions, and effective measures should be taken to eliminate the introduced population in China.

Intraspecific support for the polygyny-vs.-polyandry hypothesis in the bulldog ant Myrmecia brevinoda.

The number of queens per colony and the number of matings per queen are the most important determinants of the genetic structure of ant colonies, and understanding their interrelationship is essential to the study of social evolution. The polygyny-vs.-polyandry hypothesis argues that polygyny and polyandry should be negatively associated because both can result in increased intracolonial genetic variability and have costs. However, evidence for this long-debated hypothesis has been lacking at the intraspecific level. Here, we investigated the colony genetic structure in the Australian bulldog ant Myrmecia brevinoda. The numbers of queens per colony varied from 1 to 6. Nestmate queens within polygynous colonies were on average related (r(qq) = 0.171 ± 0.019), but the overall relatedness between queens and their mates was indistinguishable from zero (r(qm) = 0.037 ± 0.030). Queens were inferred to mate with 1-10 males. A lack of genetic isolation by distance among nests indicated the prevalence of independent colony foundation. In accordance with the polygyny-vs.-polyandry hypothesis, the number of queens per colony was significantly negatively associated with the estimated number of matings (Spearman rank correlation R = -0.490, P = 0.028). This study thus provides the rare intraspecific evidence for the polygyny-vs.-polyandry hypothesis. We suggest that the high costs of multiple matings and the strong effect of multiple mating on intracolonial genetic diversity may be essential to the negative association between polygyny and polyandry and that any attempt to empirically test this hypothesis should place emphasis upon these two key underlying aspects.

Characterization of polymorphic microsatellites in the giant bulldog ant, Myrmecia brevinoda and the jumper ant, M. pilosula.

The ant genus Myrmecia Fabricius (Hymenoptera: Formicidae) is endemic to Australia and New Caledonia, and has retained many biological traits that are considered to be basal in the family Formicidae. Here, a set of 16 dinucleotide microsatellite loci were studied that are polymorphic in at least one of the two species of the genus: the giant bulldog ant, M. brevinoda Forel, and the jumper ant, M. pilosula Smith; 13 are novel loci and 3 are loci previously published for the genus Nothomyrmecia Clark (Hymenoptera: Formicidae). In M. brevinoda, the total of 12 polymorphic microsatellites yielded a total of 125 alleles, ranging from 3 to 18 with an average of 10.42 per locus; the observed and expected heterozygosities ranged from 0.4000 to 0.9000 and from 0.5413 to 0.9200, respectively. In M. pilosula, the 9 polymorphic loci yielded a total of 67 alleles, ranging from 3 to 12 with an average of 7.44 per locus; the observed and expected heterozygosities ranged from 0.5625 to 0.9375 and from 0.4863 to 0.8711, respectively. Five loci were polymorphic in both target species. In addition, 15 out of the 16 loci were successfully amplified in M. pyriformis. These informative microsatellite loci provide a powerful tool for investigating the population and colony genetic structure of M. brevinoda and M. pilosula, and may also be applicable to a range of congeners considering the relatively distant phylogenetic relatedness between M. pilosula and the other two species within the genus Myrmecia.

Strong phylogeographic pattern of cpDNA variation reveals multiple glacial refugia for Saruma henryi Oliv. (Aristolochiaceae), an endangered herb endemic to China.

Saruma henryi Oliv. (Aristolochiaceae) is an endangered herb endemic to China. In this study, chloroplast microsatellites (cpSSRs) and sequences of the atpB-rbcL intergenic spacers were employed to reveal its genetic diversity and phylogeographic patterns. We detected high within-species genetic diversity (H(T)=0.939 for cpSSR; H(T)=0.862 for atpB-rbcL) and pronounced among-population genetic differentiation (H(S)=0.182, G(ST)=0.811, R(ST)=0.9, F(ST)=0.93 for cpSSR; H(S)=0.238, G(ST)=0.724, N(ST)=0.758, F(ST)=0.79 for atpB-rbcL) with a strong phylogeographic pattern (R(ST)>G(ST), P<0.01 for cpSSR; N(ST)>G(ST), U=0.25 for atpB-rbcL). Eleven haplotypes were distinguished by cpSSRs and atpB-rbcL intergenic spacers, respectively. The molecular phylogenetic data, together with the geographic distribution of the haplotypes, suggested the existence of multiple localized glacial refugia in Mts. Qinling, eastern Mts. Bashan and the southeastern edge of Yunnan-Guizhou Plateau. Nested clade analysis (NCA) and population genetic analyses supported the limited gene flow (caused by low dispersal capacity and complex topography of its habitats) as the major factor responsible for the strong population differentiation and phylogeographic pattern. Past fragmentation and allopatric fragmentation were inferred as important processes responsible for the modern phylogeograhpic pattern. In addition, contiguous range expansions occurred in western Mts. Qinling and eastern Mts. Bashan.

Polyploid origins in Gynostemma pentaphyllum (Cucurbitaceae) inferred from multiple gene sequences.

The genus Gynostemma (Cucurbitaceae) constitutes a polyploid group of perennial creeping herbs, in whose evolution polyploidization is a key component. With the largest variety of cytotypes (2n=22, 44, 66 and 88) in Gynostemma, G. pentaphyllum is also the most widespread species in this genus. In the present study, we inferred the origins of polyploids in G. pentaphyllum using sequences of the plastid intergenic spacers (trnL-trnF, psbB-psbF and rpl20-rps12) and cloned DNA sequences from two nuclear regions (RPB2 and nrDNA ITS). Phylogenetic analyses of the separate and the combined nuclear gene datasets all supported autoploid origins of polyploids in G. pentaphyllum. Three polyploid populations were more closely related, indicating that significant genetic differentiation may have occurred between diploids and polyploids. We concluded that polyploidization might be an important evolutionary mechanism in the diversification of G. pentaphyllum. On the other hand, no chloroplast DNA (cpDNA) variation was detected in ingroups except the octoploid DL 8x, which possessed a different cpDNA haplotype from the other populations of G. pentaphyllum. This can be explained by limited sample sizes, possible extinction of its diploid progenitors and/or the occurrence of chloroplast transfer through hybridization with other Gynostemma species. However, the distribution of cytotypes in G. pentaphyllum was not as typical as many other autopolyploid complexes. Polyploidization failed to contribute significantly to the expansion of its geographic range. The geographic distribution of diploids and polyploids in G. pentaphyllum may be associated with the past ecological environments of different areas, especially during the glacial period.

Overall grazing tolerance index (overall GTI) is not an ideal predictor for describing a single-species tolerance to grazing.

Plants' pattern of compensatory growth is often used to intuitively estimate their grazing tolerance. However, this tolerance is sometimes measured by the overall grazing tolerance index (overall GTI), which assumes that tolerance is a multivariate linear function of various underlying mechanisms. Because the interaction among mechanisms is not independent, the grazing tolerance expression based on overall GTI may be inconsistent with that based on compensatory growth. Through a manipulative field experiment from 2007 to 2012, we measured the responses of 12 traits of Elymus nutans to clipping under different resource availabilities in an alpine meadow and explored the compensatory aboveground biomass and the overall GTI to assess the possible differences between the two expressions of tolerance. Our results showed that these two expressions of tolerance were completely opposite. The expression based on overall GTI was over-compensatory and did not vary with clipping and resource availability, while the expression based on compensatory aboveground biomass was under-compensatory and altered to over-compensation after fertilization. The over-expression of highly variable traits with extremely high negative mean GTI to defoliation damage, the influence of random errors contained in traits considered, and the doubling weight of functional redundant traits greatly inflated the overall GTI, which leads to the inconsistency of the two tolerance expressions. This inconsistency is also associated with the different determining mechanisms of the two tolerance expressions. Our data suggest that plants' grazing tolerance is not a multivariate linear function of traits or mechanisms that determine grazing tolerance; the overall GTI is only a measure of traits' variability to defoliation damage. Our findings highlight that the tolerance of E. nutans mainly depends on the response of traits with lower variability to defoliation, and the overall GTI is not an ideal predictor for describing a single-species tolerance to grazing.

Different mitogenomic codon usage patterns between damselflies and dragonflies and nine complete mitogenomes for odonates.

Damselflies and dragonflies, of the order Odonata, have distinct body plans and predatory abilities. Knowledge of their various evolutionary histories will allow for an understanding of the genetic and phenotypic evolution of insects. Mitogenomes are suitable materials to elucidate this, but the mitogenome of only a few odonates have been annotated. Herein, we report the complete mitogenome of nine odonates, including seven dragonflies and two damselflies, and a comprehensive analysis of the codon usage in 31 Odonata mitogenomes with the aim to estimate their evolutionary characteristics. Overall, a weak codon bias exists among odonate mitogenomes, although this favours AT-ending codons. Damselflies have a weaker codon usage bias than dragonflies, and 37 codons have significantly different usages. Both directional mutation and purifying selection shape damselfly and dragonfly mitogenomes. Although inevitable, directional mutation bias plays a minor role, whereas purifying selection pressure is the dominant evolutionary force. A higher selection pressure is observed in dragonflies than in damselflies, but it mainly acts on codon usage patterns rather than amino acid translation. Our findings suggest that dragonflies might have more efficient mitochondrial gene expression levels than damselflies, producing more proteins that support their locomotion and predatory abilities.

The complete mitogenome of the Cydno Longwing Heliconius cydno (Insecta: Lepidoptera: Nymphalidae).

The complete mitogenome of the Cydno Longwing Heliconius cydno has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 15,367 bp in length, and consists of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs) and 1 D-loop region. PCGs are mostly initiated with the ATN codons (COII, COIII, Cytb, ND2, ND3, ND4, ND4L, ND5, ND6, ATP6 & ATP8), except for the ND1 and COI genes with TTG and the unusual CGA as their initiation codons, respectively. Some PCGs harbor TAG (ND3) or incomplete termination codon T (COI, COII & ND4), while all the others use TAA as their termination codons. The nucleotide composition is highly asymmetric (39.3% A, 42.1% T, 7.6% G, 11.0% C) with an overall GC content of 18.6%.

The complete mitogenome of the dampwood termite Zootermopsis nevadensis (Insecta: Isoptera: Termopsidae).

The complete mitogenome of the dampwood termite Zootermopsis nevadensis was reconstructed from whole-genome Illumina sequencing data with an average coverage of 7052×. The circular genome is 15,444 bp in length, and consists of 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs) and one D-loop region. All PCGs are initiated with ATN codons, except for the ND1 and ND5 genes with the start codon GTG. Some PCGs harbor TAG (ND1) or incomplete stop codon T (COII, ND5 & Cytb), while the others use TAA as their stop codons. The nucleotide composition is asymmetric (45.8% A, 19.8% C, 10.9% G, 23.5% T) with an overall GC content of 30.7%. These data would contribute to the design of novel molecular markers for population and evolutionary studies of this and related termite species.

Characterization of the complete mitochondrial genome of Bombyx huttoni (Lepidoptera: Bombycidae).

The complete mitochondrial genome of the wild silk moth Bombyx huttoni has been reconstructed from the whole-genome Illumina sequencing data. The circular genome was determined to be 15,638 bp in length, consisting of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one A+T-rich D-loop or control region. Twelve PCGs (COX2, COX3, CYTB, ND1, ND2, ND3, ND4, ND4L, ND5, ND6, ATP6, and ATP) are initiated with the typical ATN codons, whereas COX1 was tentatively determined to use the unusual CGA as its start codon. All PCGs are terminated with the TAA codon, except for ND1 and the other two PCGs (COX1 and COX2) with the TAG and the incomplete T stop codon, respectively. The nucleotide composition is highly asymmetric (43.8% A, 38.0% T, 7.1% G, and 11.1% C) with an overall A+T content of 81.8%.

Characterization of the complete mitochondrial genome of Formica selysi (Insecta: Hymenoptera: Formicidae: Formicinae).

The complete mitochondrial genome of Formica selysi has been assembled from Illumina sequencing data with an average coverage of 2733X. The circular genome was 16,752 bp in length, and consists of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs) and one D-loop region. All PCGs initiated with ATN codons and terminated with the TAA codon. The nucleotide composition was highly asymmetric (40.33% A, 11.07% C, 5.66% G and 42.94% T) with an overall GC content of 16.73%. Unlike those of most other insects, the mitochondrial genome of F. selysi was characterized by an obviously high proportion of intergenic spacers. These data would contribute to the evolutionary studies of this and related ant taxa.

The complete mitochondrial genome of the Sara Longwing Heliconius sara (Insecta: Lepidoptera: Nymphalidae).

The complete mitochondrial genome of the Sara Longwing Heliconius sara has been reconstructed from the whole-genome Illumina sequencing data. The mitochondrial genome is 15,372 bp in size with the highly asymmetric overall A + T content of 80.6%. Annotation of mitochondrial genome revealed a total of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs) and 1 D-loop region. Most PCGs are initiated with the ATN codons, while COX1 and ND1 start with CGA and TTG, respectively. COX1, COX2, and ND4 harbor the incomplete stop codon T, while all the others are terminated with the TAR codons. The complete mitochondrial genome of H. Sara would contribute to our further understanding of the phylogeny and evolution of the genus Heliconius and related taxa.

The complete chloroplast genome of Armand pine Pinus armandii, an endemic conifer tree species to China.

The complete chloroplast genome (cpDNA) sequence of an endemic conifer species, Armand pine Pinus armandii Franch., is determined in this study. The cpDNA was 117,265 bp in length, containing a pair of 475 bp inverted repeat (IR) regions those distinguished in large and small single copy (LSC and SSC) regions of 64,548 and 51,767 bp in length, respectively. The cpDNA contained 114 genes, including 74 protein-coding genes (74 PCG species), 4 ribosomal RNA genes (four rRNA species) and 36 transfer RNA genes (33 tRNA species). Out of these genes, 12 harbor a single intron and most of the genes occurred in a single copy. The overall AT content of the Armand pine cpDNA was 61.2%, while the corresponding values of the LSC, SSC and IR regions were 62.0%, 60.2% and 62.7%, respectively. A phylogenetic analysis revealed that P. armandii chloroplast genome is closely related to that of the P. koraiensis within the genus Pinus.

Genetic Structure and Evolutionary History of Three Alpine Sclerophyllous Oaks in East Himalaya-Hengduan Mountains and Adjacent Regions.

The East Himalaya-Hengduan Mountains (EH-HM) region has a high biodiversity and harbors numerous endemic alpine plants. This is probably the result of combined orographic and climate oscillations occurring since late Tertiary. Here, we determined the genetic structure and evolutionary history of alpine oak species (including Quercus spinosa, Quercus aquifolioides, and Quercus rehderiana) using both cytoplasmic-nuclear markers and ecological niche models (ENMs), and elucidated the impacts of climate oscillations and environmental heterogeneity on their population demography. Our results indicate there were mixed genetic structure and asymmetric contemporary gene flow within them. The ENMs revealed a similar demographic history for the three species expanded their ranges from the last interglacial (LIG) to the last glacial maximum (LGM), which was consistent with effective population sizes changes. Effects of genetic drift and fragmentation of habitats were responsible for the high differentiation and the lack of phylogeographic structure. Our results support that geological and climatic factors since Miocene triggered the differentiation, evolutionary origin and range shifts of the three oak species in the studied area and also emphasize that a multidisciplinary approach combining molecular markers, ENMs and population genetics can yield deep insights into diversification and evolutionary dynamics of species.

Analysis of genetic diversity and population differentiation of Larix potaninii var. chinensis using microsatellite DNA.

Larix potaninii var. chinensis is endemic to China and is found only on several peaks of the Qinling Mountains in Shaanxi Province. In China, it is classified in the second class of national protected rare plants. To estimate genetic diversity and to analyze population genetic structure of L. potaninii var. chinensis, 120 individual samples from six natural populations were assessed using seven Larix SSR primer pairs. The results indicate that the level of genetic diversity of L. potaninii var. chinensis is very high, with a mean number of alleles per locus of 4.71. On the other hand, correspondingly low genetic differentiation was found between populations, with an F (ST) value of 0.116, suggesting that more than four-fifths of the genetic variation resides within populations. Besides the influence of habitat heterogeneity and historical distribution, the high level of genetic diversity of L. potaninii var. chinensis is also attributed to its biological characteristics. The definite genetic differentiation among populations, however, is attributed to the effects of genetic drift and natural selection, which are most likely due to the spatial isolation and inclement climate of the species' habitat. This study also revealed evidence that L. potaninii var. chinensis could be endangered, and some conservation strategies are suggested.