scholarly journals Pleistocene origin and colonization history of Lobelia columnaris Hook. f. (Campanulaceae: Lobelioideae) across sky islands of West Central Africa

2021 ◽  
Author(s):  
Miguel Perez Perez ◽  
Wen-Bin Yu
Keyword(s):  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Central Africa ◽  
Sky Islands ◽  
Lowland Forest ◽  
Colonization History ◽  
Bioko Island ◽  
Climatic Oscillations ◽  
Chloroplast Genomes ◽  
Sky Island

We aimed to infer the phylogenetic relationships of populations of Lobelia columnaris using chloroplast genomes and estimate the divergence time to reconstruct its historical colonization on the sky islands of Bioko and Cameroon. Specifically, we aim to answer the following questions: (1) What is the phylogenetic relationship among Bioko Island and Cameroon populations? (2) Are the older populations found on the older sky islands? (3) Does the colonization history reflect the age of the sky islands? We assembled novel plastomes from 20 individuals of L. columnaris from five mountain systems. The plastome data was explored with phylogenetic analyses using Maximum likelihood and Bayesian Inference. The complete plastome size varied from 164,609 bp to 165,368 bp. The populations of L. columnaris have a monophyletic origin, subdivided into three plastome-geographic clades. The plastid phylogenomic results and age of the sky islands indicate that L. columnaris colonized first along the Cameroon Volcanic Line’s young sky islands. The earliest divergent event (1.54 Ma) split the population in South Bioko from those on the mainland and North Bioko. The population of South Bioko was likely isolated during cold and dry conditions in forest refugia. Presumably, the colonization history occurred during the middle-late Pleistocene from South Bioko’s young sky island to North Bioko and the northern old sky islands in Cameroon. Furthermore, the central depression with lowland forest between North and South Bioko is a current geographic barrier that keeps separate the populations of Bioko from each other and the mainland populations. The Pleistocene climatic oscillations led to the divergence of the Cameroon and Bioko populations into three clades. L. columnaris colonized the older sky island in mainland Cameroon after establishing South Bioko’s younger sky islands. The biogeography history was an inverse progression concerning the age of the Afromontane sky islands.

scholarly journals Phylogenetics of the freshwater crab (Potamonautes MacLeay, 1838) fauna from ‘sky islands’ in Mozambique with the description of a new species (Brachyura: Potamoidea: Potamonautidae)

2020 ◽  
Author(s):  
Savel R. Daniels ◽  
Gabriela B. Bittencourt-Silva ◽  
Vanessa Muianga ◽  
Julian Bayliss
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
12S Rrna ◽  
Sky Islands ◽  
Freshwater Crab ◽  
Crab Species ◽  
African Species ◽  
Island Species ◽  
Sky Island

Patterns and processes of cladogenesis among taxa living on the Mozambique ‘sky islands’ remain poorly studied. During the present study, we report on a new freshwater crab species from Mount Lico, an inselberg and ‘sky island’ in the Zambezia Province of Mozambique. Phylogenetic analyses using three mitochondrial DNA sequence loci (12S rRNA, 16S rRNA and COI) were used to determine the evolutionary placement of the freshwater crab specimens from Mount Lico. The freshwater crab specimens from Mount Lico were retrieved sister to Potamonautes choloensis. The new species, Potamonautes licoensis sp. nov., is described and compared with other southern African freshwater crab species. Divergence time estimations for the Mozambican freshwater crab species suggest a Miocene / Plio–Pleistocene diversification. Some endemic ‘sky island’ species form an early branching and are sister to other predominantly East African species, while other ‘sky island’ species are more recently derived and nested within a predominantly southern African clade. The present study presents the description of the fourth endemic freshwater crab species from Mozambique and suggests that the species diversity in the country is likely highly underrepresented, reiterating the call for renewed systematic surveys. An argument for the conservation of these mountainous ‘sky islands’ is presented.

scholarly journals Chloroplast phylogenomics in Camelina (Brassicaceae) reveals multiple origins of polyploid species and the maternal lineage of C. sativa

2022 ◽  
Vol 9 ◽  
Author(s):  
Jordan R Brock ◽  
Terezie Mandáková ◽  
Michael McKain ◽  
Martin A Lysak ◽  
Kenneth M Olsen
Keyword(s):  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Diploid Species ◽  
Time Estimation ◽  
Polyploid Species ◽  
Chromosome Counts ◽  
Diploid Parent ◽  
Divergence Time Estimation ◽  
Multiple Origins ◽  
Chloroplast Genomes

Abstract The genus Camelina (Brassicaceae) comprises 7–8 diploid, tetraploid, and hexaploid species. Of particular agricultural interest is the biofuel crop, C. sativa (gold-of-pleasure or false flax), an allohexaploid domesticated from the widespread weed, C. microcarpa. Recent cytogenetics and genomics work has uncovered the identity of the parental diploid species involved in ancient polyploidization events in Camelina. However, little is known about the maternal subgenome ancestry of contemporary polyploid species. To determine the diploid maternal contributors of polyploid Camelina lineages, we sequenced and assembled 84 Camelina chloroplast genomes for phylogenetic analysis. Divergence time estimation was used to infer the timing of polyploidization events. Chromosome counts were also determined for 82 individuals to assess ploidy and cytotypic variation. Chloroplast genomes showed minimal divergence across the genus, with no observed gene-loss or structural variation. Phylogenetic analyses revealed C. hispida as a maternal diploid parent to the allotetraploid Camelina rumelica, and C. neglecta as the closest extant diploid contributor to the allohexaploids C. microcarpa and C. sativa. The tetraploid C. rumelica appears to have evolved through multiple independent hybridization events. Divergence times for polyploid lineages closely related to C. sativa were all inferred to be very recent, at only ~65 thousand years ago. Chromosome counts confirm that there are two distinct cytotypes within C. microcarpa (2n = 38 and 2n = 40). Based on these findings and other recent research, we propose a model of Camelina subgenome relationships representing our current understanding of the hybridization and polyploidization history of this recently-diverged genus.

scholarly journals Comparative Chloroplast Genomics of Litsea Lam. (Lauraceae) and Its Phylogenetic Implications

Forests ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 744
Author(s):  
Yunyan Zhang ◽  
Yongjing Tian ◽  
David Y. P. Tng ◽  
Jingbo Zhou ◽  
Yuntian Zhang ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Eastern China ◽  
Chloroplast Microsatellites ◽  
Endangered Tree ◽  
Protein Coding ◽  
Intergenic Spacers ◽  
Chloroplast Genomes ◽  
Phylogenetic Implications ◽  
Chloroplast Genome Sequence

Litsea Lam. is an ecological and economic important genus of the “core Lauraceae” group in the Lauraceae. The few studies to date on the comparative chloroplast genomics and phylogenomics of Litsea have been conducted as part of other studies on the Lauraceae. Here, we sequenced the whole chloroplast genome sequence of Litsea auriculata, an endangered tree endemic to eastern China, and compared this with previously published chloroplast genome sequences of 11 other Litsea species. The chloroplast genomes of the 12 Litsea species ranged from 152,132 (L. szemaois) to 154,011 bp (L. garrettii) and exhibited a typical quadripartite structure with conserved genome arrangement and content, with length variations in the inverted repeat regions (IRs). No codon usage preferences were detected within the 30 codons used in the chloroplast genomes, indicating a conserved evolution model for the genus. Ten intergenic spacers (psbE–petL, trnH–psbA, petA–psbJ, ndhF–rpl32, ycf4–cemA, rpl32–trnL, ndhG–ndhI, psbC–trnS, trnE–trnT, and psbM–trnD) and five protein coding genes (ndhD, matK, ccsA, ycf1, and ndhF) were identified as divergence hotspot regions and DNA barcodes of Litsea species. In total, 876 chloroplast microsatellites were located within the 12 chloroplast genomes. Phylogenetic analyses conducted using the 51 additional complete chloroplast genomes of “core Lauraceae” species demonstrated that the 12 Litsea species grouped into four sub-clades within the Laurus-Neolitsea clade, and that Litsea is polyphyletic and closely related to the genera Lindera and Laurus. Our phylogeny strongly supported the monophyly of the following three clades (Laurus–Neolitsea, Cinnamomum–Ocotea, and Machilus–Persea) among the above investigated “core Lauraceae” species. Overall, our study highlighted the taxonomic utility of chloroplast genomes in Litsea, and the genetic markers identified here will facilitate future studies on the evolution, conservation, population genetics, and phylogeography of L. auriculata and other Litsea species.

scholarly journals Chloroplast genome variation and phylogenetic relationships of Atractylodes species

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yiheng Wang ◽  
Sheng Wang ◽  
Yanlei Liu ◽  
Qingjun Yuan ◽  
Jiahui Sun ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Herbal Medicines ◽  
Structural Genomic ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Original Plant ◽  
Morphological Differences ◽  
Rna Genes

Abstract Background Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing. Results The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT(GGU), and trnT(UGU)-trnL, and a total of 42–47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus. Conclusions Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.

scholarly journals Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jiawei Zhou ◽  
Shuo Zhang ◽  
Jie Wang ◽  
Hongmei Shen ◽  
Bin Ai ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Population Level ◽  
Gene Content ◽  
Sequencing Data ◽  
Cellular Functions ◽  
Chloroplast Evolution ◽  
Chloroplast Genomes ◽  
Genome Features ◽  
Genome Annotations ◽  
Genome Analyses

AbstractThe chloroplast is one of two organelles containing a separate genome that codes for essential and distinct cellular functions such as photosynthesis. Given the importance of chloroplasts in plant metabolism, the genomic architecture and gene content have been strongly conserved through long periods of time and as such are useful molecular tools for evolutionary inferences. At present, complete chloroplast genomes from over 4000 species have been deposited into publicly accessible databases. Despite the large number of complete chloroplast genomes, comprehensive analyses regarding genome architecture and gene content have not been conducted for many lineages with complete species sampling. In this study, we employed the genus Populus to assess how more comprehensively sampled chloroplast genome analyses can be used in understanding chloroplast evolution in a broadly studied lineage of angiosperms. We conducted comparative analyses across Populus in order to elucidate variation in key genome features such as genome size, gene number, gene content, repeat type and number, SSR (Simple Sequence Repeat) abundance, and boundary positioning between the four main units of the genome. We found that some genome annotations were variable across the genus owing in part from errors in assembly or data checking and from this provided corrected annotations. We also employed complete chloroplast genomes for phylogenetic analyses including the dating of divergence times throughout the genus. Lastly, we utilized re-sequencing data to describe the variations of pan-chloroplast genomes at the population level for P. euphratica. The analyses used in this paper provide a blueprint for the types of analyses that can be conducted with publicly available chloroplast genomes as well as methods for building upon existing datasets to improve evolutionary inference.

Phylogeographic structure and gene flow of Himalayan snowcock (Tetraogallus himalayensis)

2010 ◽  
Vol 60 (4) ◽  
pp. 449-465
Author(s):  
Wen Longying ◽  
Zhang Lixun ◽  
An Bei ◽  
Luo Huaxing ◽  
Liu Naifa ◽  
...  
Keyword(s):  
Demographic History ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Population Expansion ◽  
Population History ◽  
Tibet Plateau ◽  
Phylogeographic Structure ◽  
Mitochondrial Cytochrome B ◽  
History Of ◽  
Qinghai Tibet Plateau

AbstractWe have used phylogeographic methods to investigate the genetic structure and population history of the endangered Himalayan snowcock (Tetraogallus himalayensis) in northwestern China. The mitochondrial cytochrome b gene was sequenced of 102 individuals sampled throughout the distribution range. In total, we found 26 different haplotypes defined by 28 polymorphic sites. Phylogenetic analyses indicated that the samples were divided into two major haplogroups corresponding to one western and one eastern clade. The divergence time between these major clades was estimated to be approximately one million years. An analysis of molecular variance showed that 40% of the total genetic variability was found within local populations, 12% among populations within regional groups and 48% among groups. An analysis of the demographic history of the populations suggested that major expansions have occurred in the Himalayan snowcock populations and these correlate mainly with the first and the second largest glaciations during the Pleistocene. In addition, the data indicate that there was a population expansion of the Tianshan population during the uplift of the Qinghai-Tibet Plateau, approximately 2 million years ago.

scholarly journals Mice as stowaways? Colonization history of Danish striped field mice

2017 ◽  
Vol 13 (7) ◽  
pp. 20170064 ◽  
Author(s):  
Liselotte Wesley Andersen ◽  
Magnus Jacobsen ◽  
Christina Vedel-Smith ◽  
Thomas Secher Jensen
Keyword(s):  
Eastern Europe ◽  
Divergence Time ◽  
Mitochondrial Genomes ◽  
Field Mouse ◽  
Colonization History ◽  
Striped Field Mouse ◽  
Steppe Region ◽  
History Of ◽  
Field Mice ◽  
Human Introduction

Species from the steppe region of Eastern Europe likely colonized northwestern Europe in connection with agriculture after 6500 BP. The striped field mouse ( Apodemus agrarius Pallas, 1783), is a steppe-derived species often found in human crops. It is common on the southern Danish islands of Lolland and Falster, which have been isolated from mainland Europe since approximately 10 300–8000 BP. Thus, this species could have been brought in with humans in connection with agriculture, or it could be an earlier natural invader. We sequenced 86 full mitochondrial genomes from the northwestern range of the striped field mouse, analysed phylogenetic relationships and estimated divergence time. The results supported human-induced colonization of Denmark in the Subatlantic or Subboreal period. A newly discovered population from Central Jutland in Denmark diverged from Falster approximately 100–670 years ago, again favouring human introduction. One individual from Sweden turned out to be a recent introduction from Central Jutland.

Tigridiopalma longmenensis (Melastomataceae), a new species from Guangdong, China

Phytotaxa ◽  
2021 ◽  
Vol 500 (3) ◽  
pp. 241-247
Author(s):  
HUI-FENG WANG ◽  
ZHENG-FENG WANG ◽  
QIAO-MEI QIN ◽  
HONG-LIN CAO ◽  
XIAO-MING GUO
Keyword(s):  
New Species ◽  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Monotypic Genus ◽  
Distribution Map ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genomes ◽  
A New Species

Tigridiopalma longmenensis, a new species from Guangdong, China, is described. This species differs from its ally, T. magnifica, by the polychasium consisting of scorpioid cymes, hypanthium with carinas on angles, and longer stamens with a conspicuously white or pink spur at the connective base of anther. A diagnosis and a distribution map of the two species are also provided. The complete chloroplast genome of T. longmenensis was reported here. Phylogenetic analyses based on complete chloroplast genomes from T. longmenensis and other 15 Melastomataceae species indicated that T. longmenensis is sister to T. magnifica. The discovery of T. longmenensis terminates Tigridiopalma as a monotypic genus.

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