Genetic diversity and species limits in Veltheimia (Asparagaceae: Scilloideae): insights from noncoding cpDNA sequence data

Phytotaxa ◽  
2020 ◽  
Vol 429 (3) ◽  
pp. 239-247
Author(s):  
NIGEL P. BARKER ◽  
TAMIKA FELLOWS ◽  
NTOMBIFIKILE PHALISO ◽  
JOHN ROURKE
Keyword(s):  
Genetic Diversity ◽  
Bayesian Analysis ◽  
Southern Africa ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Summer Rainfall ◽  
Coastal Forests ◽  
Lineage Sorting ◽  
Dna Sequence Data ◽  
Cpdna Sequence

Veltheimia is a genus of two species of bulbous flowering angiosperms restricted to southern Africa. Both parsimony and Bayesian analysis of 1829 nucleotides of DNA sequence data, from three non-coding chloroplast regions from multiple samples of both species, indicates that specimens of V. bracteata form a monophyletic clade together with three specimens named as V. capensis. This clade receives low support and is embedded within a paraphyletic grade of specimens of V. capensis. A Median Joining Network analysis of a subset of samples revealed nine haplotypes, the relationships of which mirrored the relationships resolved by the Bayesian analysis. With the exception of the V. capensis members of the V. bracteata clade, the remaining specimens are from the summer rainfall thicket and coastal forests. The samples of the basal V. capensis grade are found in the winter rainfall regions of southern Africa. These results indicate that there is limited genetic diversity within the genus, and there is no clear distinction between these two species based on plastid non-coding DNA data. This may be due to their recent divergence and incomplete lineage sorting, or recent or ongoing hybridisation and / or introgression.

Phylogeny, biogeography and foliar manganese accumulation of Gossia (Myrtaceae)

2018 ◽  
Author(s):  
Todd McLay ◽  
Gareth D. Holmes ◽  
Paul I. Forster ◽  
Susan E. Hoebee ◽  
Denise R. Fernando
Keyword(s):  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Position ◽  
Strongly Correlated ◽  
Lineage Sorting ◽  
Dna Sequence Data ◽  
Australian Species ◽  
Wide Range ◽  
Single Clade ◽  
The Relationship

The rainforest genus Gossia N.Snow & Guymer (Myrtaceae) occurs in Australia, Melanesia and Malesia, and is capable of hyperaccumulating the heavy metal manganese (Mn). Here, we used nuclear ribosomal and plastid spacer DNA-sequence data to reconstruct the phylogeny of 19 Australian species of Gossia and eight New Caledonian taxa. Our results indicated that the relationship between Gossia and Austromyrtus (Nied.) Burret is not fully resolved, and most Australian species were supported as monophyletic. Non-monophyly might be related to incomplete lineage sorting or inaccurate taxonomic classification. Bark type appears to be a morphological synapomorphy separating two groups of species, with more recently derived lineages having smooth and mottled ‘python’ bark. New Caledonian species were well resolved in a single clade, but were not the first diverging Gossia lineage, calling into doubt the results of a recent study that found Zealandia as the ancestral area of tribe Myrteae. Within Australia, the evolution of multiple clades has probably been driven by well-known biogeographic barriers. Some species with more widespread distributions have been able to cross these barriers by having a wide range of soil-substrate tolerances. Novel Mn-hyperaccumulating species were identified, and, although Mn hyperaccumulation was not strongly correlated with phylogenetic position, there appeared to be some difference in accumulation levels among clades. Our study is the first detailed phylogenetic investigation of Gossia and will serve as a reference for future studies seeking to understand the origin and extent of hyperaccumulation within the Myrteae and Myrtaceae more broadly.

scholarly journals Interspecific hybridization in North American Polygala (Polygalaceae)

2020 ◽  
Vol 14 (1) ◽  
pp. 47-56
Author(s):  
Kurt M. Neubig ◽  
J. Richard Abbott
Keyword(s):  
Interspecific Hybridization ◽  
North American ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Molecular Tools ◽  
Lineage Sorting ◽  
Sympatric Populations ◽  
Dna Sequence Data ◽  
Phylogenetic Studies ◽  
Species Pairs

As a part of ongoing systematic and phylogenetic studies in Polygalaceae, field collections of two pairs of North American species (Polygala balduinii and P. ramosa, and P. lutea and P. rugelii) had morphologically intermediate forms and grew sympatrically, and so were suspected to be interspecific hybrids. Although hybrids among plants are often invoked in taxonomic and floristic literature based on morphologic intermediacy, they are rarely documented and substantiated using molecular tools. We found that the morphologically intermediate individuals within intermixed populations of both species pairs did indeed share all of the variable nucleotide sites in nrITS among the parent species. Likewise, using plastid sequence data (trnL-F), we determined that in both species pairs, the parentage was bidirectional. Although some DNA inheritance phenomena (e.g. incomplete lineage sorting) can result in similar polymorphic DNA sequence data, the intermediacy in both morphology and sequence data within sympatric populations is more indicative of interspecific hybridization.

scholarly journals Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts

2019 ◽  
Author(s):  
Joshua I Brian ◽  
Simon K Davy ◽  
Shaun P Wilkinson
Keyword(s):  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Reticulate Evolution ◽  
Next Generation Sequencing Data ◽  
Putative Hybrid ◽  
Its2 Region ◽  
Sequencing Data ◽  
Lineage Sorting ◽  
Evolutionary Potential ◽  
Unbiased Test

Coral reefs rely on their intracellular dinoflagellate symbionts (family Symbiodiniaceae) for nutritional provision in nutrient-poor waters, yet this association is threatened by thermally stressful conditions. Despite this, the evolutionary potential of these symbionts remains poorly characterised. In this study, we tested the potential for divergent Symbiodiniaceae types to sexually reproduce (i.e. hybridise) within Cladocopium, the most ecologically prevalent genus in this family. With sequence data from three organelles (cob gene, mitochondria; psbAncr region, chloroplast; and ITS2 region, nucleus), we utilised the Incongruence Length Difference test, Approximately Unbiased test, tree hybridisation analyses and visual inspection of raw data in stepwise fashion to highlight incongruences between organelles, and thus provide evidence of reticulate evolution. Using this approach, we identified three putative hybrid Cladocopium samples among the 158 analysed, at two of the seven sites sampled. These samples were identified as the common Cladocopium types C40 or C1 with respect to the mitochondria and chloroplasts, but the rarer types C3z, C3u and C1# with respect to their nuclear identity. These five Cladocopium types have previously been confirmed as evolutionarily distinct and were also recovered in non-incongruent samples multiple times, which is strongly suggestive that they sexually reproduced to produce the incongruent samples. A concomitant inspection of Next Generation Sequencing data for these samples suggests that other plausible explanations, such as incomplete lineage sorting, are much less likely. The approach taken in this study allows incongruences between gene regions to be identified with confidence, and brings new light to the evolutionary potential within Symbiodiniaceae.

Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment

Zootaxa ◽  
2020 ◽  
Vol 4750 (3) ◽  
pp. 328-348 ◽  
Author(s):  
DAVID A. GRAY ◽  
DAVID B. WEISSMAN ◽  
JEFFREY A. COLE ◽  
EMILY MORIARTY LEMMON
Keyword(s):  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
The United States ◽  
Field Cricket ◽  
Future Research ◽  
Gene Trees ◽  
Lineage Sorting ◽  
The Bahamas ◽  
Field Crickets ◽  
Anchored Hybrid Enrichment

We present the first comprehensive molecular phylogeny of Gryllus field cricket species found in the United States and Canada, select additional named Gryllus species found in Mexico and the Bahamas, plus the European field cricket G. campestris Linnaeus and the Afro-Eurasian cricket G. bimaculatus De Geer. Acheta, Teleogryllus, and Nigrogryllus were used as outgroups. Anchored hybrid enrichment was used to generate 492,531 base pairs of DNA sequence from 563 loci. RAxML analysis of concatenated sequence data and Astral analysis of gene trees gave broadly congruent results, especially for older branches and overall tree structure. The North American Gryllus are monophyletic with respect to the two Old World taxa; certain sub-groups show rapid recent divergence. This is the first Anchored Hybrid Enrichment study of an insect group done for closely related species within a single genus, and the results illustrate the challenges of reconstructing the evolutionary history of young rapidly diverged taxa when both incomplete lineage sorting and probable hybridization are at play. Because Gryllus field crickets have been used extensively as a model system in evolutionary ecology, behavior, neuro-physiology, speciation, and life-history and life-cycle evolution, these results will help inform, interpret, and guide future research in these areas. 

scholarly journals A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis

2019 ◽  
Vol 37 (4) ◽  
pp. 1211-1223 ◽  
Author(s):  
Tomáš Flouri ◽  
Xiyun Jiao ◽  
Bruce Rannala ◽  
Ziheng Yang
Keyword(s):  
Gene Flow ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Mosquito Species ◽  
Phylogenomic Analysis ◽  
Data Sets ◽  
Lineage Sorting ◽  
Coalescent Model ◽  
Multispecies Coalescent

Abstract Recent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer introgression events and to estimate the timing and intensity of introgression, providing an important means to advance our understanding of the role of gene flow in speciation. Here, we implement the multispecies-coalescent-with-introgression model, an extension of the multispecies-coalescent model to incorporate introgression, in our Bayesian Markov chain Monte Carlo program Bpp. The multispecies-coalescent-with-introgression model accommodates deep coalescence (or incomplete lineage sorting) and introgression and provides a natural framework for inference using genomic sequence data. Computer simulation confirms the good statistical properties of the method, although hundreds or thousands of loci are typically needed to estimate introgression probabilities reliably. Reanalysis of data sets from the purple cone spruce confirms the hypothesis of homoploid hybrid speciation. We estimated the introgression probability using the genomic sequence data from six mosquito species in the Anopheles gambiae species complex, which varies considerably across the genome, likely driven by differential selection against introgressed alleles.

scholarly journals Analysis of Genetic Diversity of Fusarium tupiense, the Main Causal Agent of Mango Malformation Disease in Southern Spain

Plant Disease ◽  
2016 ◽  
Vol 100 (2) ◽  
pp. 276-286 ◽  
Author(s):  
M. Crespo ◽  
F. M. Cazorla ◽  
A. de Vicente ◽  
E. Arrebola ◽  
J. A. Torés ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sequence Data ◽  
Random Amplified Polymorphic Dna ◽  
Phylogenetic Analyses ◽  
Southern Spain ◽  
Fusarium Fujikuroi ◽  
Dna Sequence Data ◽  
Fusarium Fujikuroi Species Complex ◽  
Polymerase Chain ◽  
Mango Malformation

Mango malformation disease (MMD) has become an important global disease affecting this crop. The aim of this study was to identify the main causal agents of MMD in the Axarquía region of southern Spain and determine their genetic diversity. Fusarium mangiferae was previously described in the Axarquía region but it represented only one-third of the fusaria recovered from malformed trees. In the present work, fusaria associated with MMD were analyzed by arbitrary primed polymerase chain reaction (ap-PCR), random amplified polymorphic DNA (RAPD), vegetative compatibility grouping (VCG), a PCR screen for mating type idiomorph, and phylogenetic analyses of multilocus DNA sequence data to identify and characterize the genetic diversity of the MMD pathogens. These analyses confirmed that 92 of the isolates were F. tupiense, which was previously only known from Brazil and Senegal. In addition, two isolates of a putatively novel MMD pathogen were discovered, nested within the African clade of the Fusarium fujikuroi species complex. The F. tupiense isolates all belonged to VCG I, which was first described in Brazil, and the 11 isolates tested showed pathogenicity on mango seedlings. Including the prior discovery of F. mangiferae, three exotic MMD pathogenic species have been found in southern Spain, which suggests multiple independent introductions of MMD pathogens in the Axarquía region.

The genus Iare Barbalho and Penteado-Dias (Hymenoptera: Braconidae: Doryctinae) in Mexico, with the description of two new species

Zootaxa ◽  
2010 ◽  
Vol 2685 (1) ◽  
pp. 30 ◽  
Author(s):  
JUAN JOSÉ MARTÍNEZ ◽  
FADIA SARA CECCARELLI ◽  
ALEJANDRO ZALDÍVAR-RIVERÓN
Keyword(s):  
New Species ◽  
Bayesian Analysis ◽  
Dna Sequence ◽  
Sequence Data ◽  
Tropical Dry Forest ◽  
Sister Group ◽  
Dry Forest ◽  
Dna Sequence Data ◽  
Single Clade ◽  
Two New Species

Two new species of the doryctine genus Iare, I. mexicanus sp. nov. and I. cheguevarai sp. nov., are genetically and morphologically described from a tropical dry forest in Jalisco, Mexico. Iare belokobylskiji Marsh is also reported for the latter region. These species represent the northernmost distribution records for the genus. A simultaneous Bayesian analysis with COI and 28S DNA sequence data recovered the three examined species of Iare within a single clade, though with low support. This genus appears nested within a large doryctine Neotropical clade as sister group of a cluster containing species of Callihormius Ashmead, Leluthia Cameron, Histeromeroides Marsh and Panama Marsh.

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