scholarly journals The Evolution of Wahlenbergia (Campanulaceae) in Australasia

2021 ◽  
Author(s):  
◽  
Jessica Mary Prebble
Keyword(s):  
South Africa ◽  
New Zealand ◽  
Dna Marker ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Molecular Dating ◽  
The Other ◽  
Lineage Sorting ◽  
Low Genetic Diversity ◽  
Plant Groups

<p>Wahlenbergia is a large genus of flowering plants within the family Campanulaceae. In this thesis the first molecular phylogeny of Wahlenbergia was reconstructed from approximately 20% of the genus, based on the nuclear ribosomal ITS (nrITS) DNA marker and the chloroplast trnL-F DNA marker, with samples from South Africa, Europe, Australia and New Zealand. Additionally a large phylogeny with increased within-species sampling focusing on addressing taxonomic questions among the 45 Australasian species of Wahlenbergia was also reconstructed based on nrITS and trnL-F, plus an additional chloroplast DNA marker, trnK. Relationships and species limits of the New Zealand species of Wahlenbergia were further analysed using amplified fragment length polymorphisms (AFLPs). Wahlenbergia was found to be polyphyletic, though most of the species form a clade. Tree topologies and molecular dating analysis showed that the genus originated in South Africa about 16.2 million years ago (mya), then dispersed to Australasia before radiating there about 3.7 mya, thus refuting the hypothesis of Gondwanan vicariance for the Australasian species. Two dispersals from Australia to New Zealand are hypothesised, one leading to a radiation of species with the rhizomatous growth from about 1.0 mya and the other leading to a radiation of species with the radicate growth form 0.49 mya, although the radicate species might not form a clade. Low levels of genetic variation among individuals from Australia and New Zealand was revealed with all markers, and the phylogenies were poorly resolved as a result. The low genetic diversity is probably due to rapid and recent evolution during a period of geological and climatic change, coupled with incomplete lineage sorting and hybridisation. Phylogenies reconstructed using AFLPs were also poorly resolved, although AFLPs were found to be useful for species delimitation, as has been shown in studies of other plant groups. Despite the poor resolution, several morphological species and subspecies were recovered as monophyletic with DNA sequence data, notably the morphologically distinctive New Zealand W. cartilaginea, W. matthewsii and W. congesta subsp. congesta. Further research into species boundaries within the W. albomarginata/W. pygmaea complex is needed. Members of the New Zealand lowland radicate W. gracilis complex may all belong to the same morphologically variable species, although further research is needed to justify such a taxonomic change. The other New Zealand radicate species, W. vernicosa, is probably a separately evolving lineage, and is not conspecific with the Australian W. littoricola.</p>

scholarly journals The Evolution of Wahlenbergia (Campanulaceae) in Australasia

2021 ◽  
Author(s):  
◽  
Jessica Mary Prebble
Keyword(s):  
South Africa ◽  
New Zealand ◽  
Dna Marker ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Molecular Dating ◽  
The Other ◽  
Lineage Sorting ◽  
Low Genetic Diversity ◽  
Plant Groups

<p>Wahlenbergia is a large genus of flowering plants within the family Campanulaceae. In this thesis the first molecular phylogeny of Wahlenbergia was reconstructed from approximately 20% of the genus, based on the nuclear ribosomal ITS (nrITS) DNA marker and the chloroplast trnL-F DNA marker, with samples from South Africa, Europe, Australia and New Zealand. Additionally a large phylogeny with increased within-species sampling focusing on addressing taxonomic questions among the 45 Australasian species of Wahlenbergia was also reconstructed based on nrITS and trnL-F, plus an additional chloroplast DNA marker, trnK. Relationships and species limits of the New Zealand species of Wahlenbergia were further analysed using amplified fragment length polymorphisms (AFLPs). Wahlenbergia was found to be polyphyletic, though most of the species form a clade. Tree topologies and molecular dating analysis showed that the genus originated in South Africa about 16.2 million years ago (mya), then dispersed to Australasia before radiating there about 3.7 mya, thus refuting the hypothesis of Gondwanan vicariance for the Australasian species. Two dispersals from Australia to New Zealand are hypothesised, one leading to a radiation of species with the rhizomatous growth from about 1.0 mya and the other leading to a radiation of species with the radicate growth form 0.49 mya, although the radicate species might not form a clade. Low levels of genetic variation among individuals from Australia and New Zealand was revealed with all markers, and the phylogenies were poorly resolved as a result. The low genetic diversity is probably due to rapid and recent evolution during a period of geological and climatic change, coupled with incomplete lineage sorting and hybridisation. Phylogenies reconstructed using AFLPs were also poorly resolved, although AFLPs were found to be useful for species delimitation, as has been shown in studies of other plant groups. Despite the poor resolution, several morphological species and subspecies were recovered as monophyletic with DNA sequence data, notably the morphologically distinctive New Zealand W. cartilaginea, W. matthewsii and W. congesta subsp. congesta. Further research into species boundaries within the W. albomarginata/W. pygmaea complex is needed. Members of the New Zealand lowland radicate W. gracilis complex may all belong to the same morphologically variable species, although further research is needed to justify such a taxonomic change. The other New Zealand radicate species, W. vernicosa, is probably a separately evolving lineage, and is not conspecific with the Australian W. littoricola.</p>

Ein föderales Imperium?

2021 ◽  
Author(s):  
Patrick Rummel
Keyword(s):  
South Africa ◽  
New Zealand ◽  
Great Britain ◽  
British Empire ◽  
19Th Century ◽  
Military Personnel ◽  
The Other ◽  
The 19Th Century

The previously ignored model of Greek colonisation attracted numerous actors from the 19th century British empire: historians, politicians, administrators, military personnel, journalists or anonymous commentators used the ancient paradigm to advocate a global federation exclusively encompassing Great Britain and the settler colonies in Canada, Australia, New Zealand and South Africa. Unlike other historical templates, Greek colonisation could be viewed as innovative and unspent: innovative because of the possibility of combining empire and liberty and unspent due to its very novelty, which did not contain the ‘imperial vice’ the other models had so often shown and which had always led to their political and cultural decline.

Molecular phylogeny of Australasian anopsobiine centipedes (Chilopoda : Lithobiomorpha)

2004 ◽  
Vol 18 (3) ◽  
pp. 235 ◽  
Author(s):  
Gregory D. Edgecombe ◽  
Gonzalo Giribet
Keyword(s):  
South Africa ◽  
New Species ◽  
New Zealand ◽  
New Caledonia ◽  
Sequence Data ◽  
Mitochondrial Protein ◽  
Molecular Data ◽  
12S Rrna ◽  
28S Rrna ◽  
16S Rna

Species assigned to the anopsobiine centipede genera Anopsobius Silvestri, 1899, and Dichelobius Attems, 1911, are widely distributed on fragments of the Gondwanan supercontinent, including temperate and tropical Australia, New Zealand, New Caledonia, the Cape region of South Africa, and southern South America. Phylogenetic relationships between Australasian and other Gondwanan Anopsobiinae are inferred based on parsimony and maximum likelihood analyses (via direct optimisation) of sequence data for five markers: nuclear ribosomal 18S rRNA and 28S rRNA, mitochondrial ribosomal 12S rRNA and 16S RNA, and the mitochondrial protein-coding cytochrome c oxidase subunit I. New molecular data are added for Anopsobius from South Africa and New Zealand, Dichelobius from New Caledonia, and a new species from Queensland, Australia, Dichelobius etnaensis, sp. nov. The new species is based on distinctive morphological and molecular data. The molecular phylogenies indicate that antennal segmentation in the Anopsobiinae is a more reliable taxonomic character than is spiracle distribution. The former character divides the Gondwanan clade into a 17-segmented group (Dichelobius) and a 15-segmented group (Anopsobius). Confinement of the spiracles to segments 3, 10 and 12 has at least two origins in the Gondwanan clade. The area cladogram for Dichelobius (Queensland (Western Australia + New Caledonia)) suggests a relictual distribution pruned by extinction.

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.

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 &amp; 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 A Bayesian implementation of the multispecies coalescent model with introgression for comparative genomic analysis

2019 ◽  
Author(s):  
Thomas Flouris ◽  
Xiyun Jiao ◽  
Bruce Rannala ◽  
Ziheng Yang
Keyword(s):  
Gene Flow ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Mosquito Species ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Lineage Sorting ◽  
Multispecies Coalescent ◽  
Important Means

AbstractRecent 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 (MSci) model, an extension of the multispecies-coalescent (MSC) model to incorporate introgression, in our Bayesian Markov chain Monte Carlo (MCMC) program BPP. The MSci 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. Re-analysis of datasets 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 Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7178 ◽  
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, mitochondrion; 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 or the presence of co-dominance, 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.

scholarly journals Faithfulness and fidelity across identities and contexts for SOTL in the global South

2021 ◽  
Vol 5 (2) ◽  
Author(s):  
KC Lee ◽  
Zach Simpson
Keyword(s):  
Higher Education ◽  
South Africa ◽  
Social Work ◽  
New Zealand ◽  
Teaching And Learning ◽  
Global South ◽  
The Other ◽  
Scholarship Of Teaching ◽  
Aotearoa New Zealand

Issue 5.2 of SOTL in the South features four peer-reviewed articles, one reflective piece and one book review. The peer-reviewed articles include two articles about broader concerns related to the scholarship of teaching and learning in higher education, namely the discursive and negotiated work of producing SoTL work and the importance of considering diverse worldviews regarding research ethics. In addition, there are two detailed accounts of instances of SoTL, one from Lesotho, addressing the challenges facing students from rural contexts, and the other from South Africa, investigating the implementation of collaborative learning in a fourth-year social work classroom. The issue concludes with a reflection on an action-oriented workshop held in Aotearoa New Zealand aimed at increasing the number of Māori and Pasifika academics, and a review of The Bloomsbury Handbook of the Internationalization of Higher Education in the Global South.

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