Generic phylogeny, historical biogeography and character evolution of the cosmopolitan aquatic plant family Hydrocharitaceae

<p>Abstract</p> <p>Background</p> <p>Hydrocharitaceae is a fully aquatic monocot family, consists of 18 genera with approximately 120 species. The family includes both fresh and marine aquatics and exhibits great diversity in form and habit including annual and perennial life histories; submersed, partially submersed and floating leaf habits and linear to orbicular leaf shapes. The family has a cosmopolitan distribution and is well represented in the Tertiary fossil record in Europe. At present, the historical biogeography of the family is not well understood and the generic relationships remain controversial. In this study we investigated the phylogeny and biogeography of Hydrocharitaceae by integrating fossils and DNA sequences from eight genes. We also conducted ancestral state reconstruction for three morphological characters.</p> <p>Results</p> <p>Phylogenetic analyses produced a phylogeny with most branches strongly supported by bootstrap values greater than 95 and Bayesian posterior probability values of 1.0. <it>Stratiotes </it>is the first diverging lineage with the remaining genera in two clades, one clade consists of <it>Lagarosiphon, Ottelia, Blyxa, Apalanthe, Elodea </it>and <it>Egeria</it>; and the other consists of <it>Hydrocharis</it>-<it>Limnobium, Thalassia, Enhalus, Halophila, Najas, Hydrilla, Vallisneria, Nechamandra </it>and <it>Maidenia</it>. Biogeographic analyses (DIVA, Mesquite) and divergence time estimates (BEAST) resolved the most recent common ancestor of Hydrocharitaceae as being in Asia during the Late Cretaceous and Palaeocene (54.7-72.6 Ma). Dispersals (including long-distance dispersal and migrations through Tethys seaway and land bridges) probably played major roles in the intercontinental distribution of this family. Ancestral state reconstruction suggested that in Hydrocharitaceae evolution of dioecy is bidirectional, viz., from dioecy to hermaphroditism, and from hermaphroditism to dioecy, and that the aerial-submerged leaf habit and short-linear leaf shape are the ancestral states.</p> <p>Conclusions</p> <p>Our study has shed light on the previously controversial generic phylogeny of Hydrocharitaceae. The study has resolved the historical biogeography of this family and supported dispersal as the most likely explanation for the intercontinental distribution. We have also provided valuable information for understanding the evolution of breeding system and leaf phenotype in aquatic monocots.</p

Exploring the genetic diversity and population structure of Ailanthus altissima using chloroplast and nuclear microsatellite DNA markers across its native range

Understanding how anthropogenic disturbances affect the genetics of tree species is crucial; however, how tree populations in the wild can tolerate these activities remains unexplored. Given the ongoing and intensifying anthropogenic disturbances, we conducted a study using Ailanthus altissima to gain new insights into the effects of these pressures on genetic variability in undisturbed and disturbed forests. We analyzed the genetic diversity and population structure of A. altissima using nuclear (EST-SSR) and chloroplast (cpSSR) microsatellite markers. The genetic diversity across the 34 studied populations based on EST-SSRs was found to be moderate to high (nHE = 0.547–0.772) with a mean nHE of 0.680. Bayesian clustering, principal coordinate analysis (PCoA), and discriminant analysis of principal component (DAPC) consistently divided the populations into three distinct groups based on EST-SSRs. Allelic combinations of 92 different chloroplast size variants from 10 cpSSR loci resulted in a total of 292 chloroplast haplotypes. The mean haplotype diversity was relatively high (cpHE = 0.941), and the mean haplotype richness was 2.690, averaged across the 34 populations of A. altissima. Values of FST in A. altissima from chloroplast and nuclear markers were 0.509 and 0.126, respectively. Modeling results showed evidence for population range contraction during the Last Glacial Maximum with subsequent population expansion in the Holocene and the future. Although genetic variation did not differ substantially across disturbed and undisturbed sites, there were small trends indicating higher genetic diversity and population bottlenecks in disturbed forests. As a result, disrupted ecosystems might display surprising genetic patterns that are difficult to predict and should not be overlooked

Complete Chloroplast Genomes of Acanthochlamys bracteata (China) and Xerophyta (Africa) (Velloziaceae): Comparative Genomics and Phylogenomic Placement

Acanthochlamys P.C. Kao is a Chinese endemic monotypic genus, whereas XerophytaJuss. is a genus endemic to Africa mainland, Arabian Peninsula and Madagascar with ca.70 species. In this recent study, the complete chloroplast genome of Acanthochlamys bracteata was sequenced and its genome structure compared with two African Xerophyta species (Xerophyta spekei and Xerophyta viscosa) present in the NCBI database. The genomes showed a quadripartite structure with their sizes ranging from 153,843 bp to 155,498 bp, having large single-copy (LSC) and small single-copy (SSC) regions divided by a pair of inverted repeats (IR regions). The total number of genes found in A. bracteata, X. spekei and X. viscosa cp genomes are 129, 130, and 132, respectively. About 50, 29, 28 palindromic, forward and reverse repeats and 90, 59, 53 simple sequence repeats (SSRs) were found in the A. bracteata, X. spekei, and X. viscosa cp genome, respectively. Nucleotide diversity analysis in all species was 0.03501, Ka/Ks ratio average score was calculated to be 0.26, and intergeneric K2P value within the Order Pandanales was averaged to be 0.0831. Genomic characterization was undertaken by comparing the genomes of the three species of Velloziaceae and it revealed that the coding regions were more conserved than the non-coding regions. However, key variations were noted mostly at the junctions of IRs/SSC regions. Phylogenetic analysis suggests that A. bracteata species has a closer genetic relationship to the genus Xerophyta. The present study reveals the complete chloroplast genome of A. bracteata and gives a genomic comparative analysis with the African species of Xerophyta. Thus, can be useful in developing DNA markers for use in the study of genetic variabilities and evolutionary studies in Velloziaceae

Effect of Habitat Modification on the Distribution of the Endangered Aquatic Fern Ceratopteris pteridoides (Parkeriaceae) in China

Volume: 102Start Page: 136End Page: 14

A New Species of Asarum (Aristolochiaceae) from China

Volume: 14Start Page: 239End Page: 24

Phenotypic Diversity of Doum Palm (Hyphaene compressa), a Semi‐Domesticated Palm in the Arid and Semi‐Arid Regions of Kenya

Hyphaene compressa is an economically important palm in Africa. Despite its significant role in the livelihoods of rural communities, the diversity of doum palm is poorly documented and studied. In addition, it has no model descriptor that can aid such studies. Ninety H. compressa accessions collected from Northern, Eastern, and Coastal regions of Kenya were examined to determine the morphological variability of the vegetative and fruit traits of H. compressa and to identify its morphotypes for improvement. A total of 19 morphological characters including seven quantitative and 12 qualitative traits of fruit and vegetative traits were selected. Linear mixed-effects models, principal component analysis, and linear discriminant analyses were used to assess the variation in the morphological traits of doum palm based on the regions. Hierarchical clustering was performed to identify the morphotypes of H. compressa. There was variability in H. compressa morphological traits, particularly at the Kenyan Coast. All seven quantitative traits were able to effectively discriminate doum palm phenotypically p≤0.001. The 90 accessions clustered into five morphotypes designated as 1, 2, 3, 4, and 5. Morphotype 4 was specific only to the Coastal region. Morphotype 5 had the tallest trees with the biggest fruits and included palms from Eastern and Coastal regions making it the best morphotype for fruit traits. This study will inform the domestication, improvement, and conservation of H. compressa by selecting elite accessions

Health risk assessment by consumption of vegetables irrigated with reclaimed waste water: A case study in Thika (Kenya)

Current study was conducted to assess remediation efficiency of heavy metals in Thika waste water treatment plant, human health risk posed by consumption of vegetables irrigated with its reclaimed waste water, and vegetables supplied at Makongeni market. Concentration of Cu, Zn, Cr, Ni and Pb was investigated in the sludge, waste water and vegetables, spinach (Spinacea oleracea), kales (Brassica oleracea var. acephala) and coriander (Coriandrum sativum). Thika waste water treatment plant was efficient in heavy metal remediation. Effluent heavy metal concentration was within recommended concentration for irrigation. Dietary intake of heavy metals and target hazard quotient were used to evaluate health risk posed to consumers. Heavy metals concentrations of vegetables sampled and analyzed were within world health organization permissible limit. Thika waste water treatment plant was found to be efficient; however, regular dredging is essential to reduce accumulated heavy metals in the sludge. Moreover, the study outcome revealed that besides reclaimed waste water that may be perceived to pose great health risk to consumers, the whole food production and distribution chain should be monitored to guarantee food safety

Li et al. data of in four Epimedium species

Five data files as presented in main experiment of the article

Assessment of Cu, Zn, Mn, and Fe enrichment in Mt. Kenya soils: evidence for atmospheric deposition and contamination

Mountains are the preferred sites for studying long-range atmospheric transportation and deposition of heavy metals, due to their isolation and steep temperature decrease that favors cold trapping and condensation of particulate forms of heavy metals. Any enrichment of heavy metals in mountains is presumed to primarily occur through atmospheric deposition. In this particular study, we assessed the status of 27 subsurface soils collected along two elevation gradients of Mt. Kenya using enrichment factors (EFs) as the ecological risk assessments. The collected soils were analyzed for total organic carbon, zinc (Zn), iron (Fe), manganese (Mn), and copper (Cu). The mean concentration of Mn, Fe, Zn, and Cu was 0.376 mg/kg, 47.6 mg/kg, 12.3 mg/kg, and 4.88 mg/kg in Chogoria and 0.560 mg/kg, 113 mg/kg, 12.7 mg/kg, and 2.70 mg/kg in Naro Moru respectively. These concentrations were below the US-EPA maximum permissible levels for soils, implying that the levels recorded had low toxicity. Meanwhile, the mean enrichment factors for Mn, Cu, and Zn were 0.447, 131, and 78.8 in Chogoria and 0.463, 38.9, and 53.0 in Naro Moru respectively. This implied that Zn and Cu in Chogoria sites were extremely enriched, while in Naro Moru, enrichment levels ranged from significant to extreme. However, Mn was found to have minimal enrichment in all the sites. Lower montane forest and bamboo zone recorded relatively high enrichment due to distance from source of pollution. Ericaceous zone also had high mean enrichment due to influence of wind which favors higher deposition at mid-elevations