scholarly journals Phylogeny and biogeography of the African Bathyergidae: a review of patterns and processes

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7730 ◽  
Author(s):  
Jacobus H. Visser ◽  
Nigel C. Bennett ◽  
Bettine Jansen van Vuuren
Keyword(s):  
Sequence Data ◽  
Population Level ◽  
Ecological Specialization ◽  
Subterranean Rodent ◽  
Systematic Revision ◽  
Biogeographic Patterns ◽  
Evolutionary Trajectories ◽  
Narrow Endemics ◽  
Suitable Habitats ◽  
Patterns And Processes

Background We review genealogical relationships, biogeographic patterns and broad historical drivers of speciation within the Bathyergidae, a group of endemic African rodents, as well as identify key taxa which need further research. Methods We sourced comparable cytochrome b sequence data (comparable data available for all members for the Family) and geographic information for all six genera of the African subterranean rodent. This information was combined into the most comprehensive and geographically representative evolutionary study for the Bathyergidae to date. Results Species richness within the Bathyergidae appears to be underestimated, with undescribed taxa in five of the six genera. Biogeographic patterns suggest large historical distributions, which were repeatedly fragmented by major landscape changes (especially rifting, uplift and drainage evolution) since the Miocene. Aside from vicariant events, other factors (ecological specialization, population-level responses and climatic change) may have been instrumental in driving divergences in the Bathyergidae. As such, adaptive differences may exist among both populations and species across their discrete ranges, driving independent evolutionary trajectories among taxa. In addition, highly fragmented distributions of divergent (and often relict) lineages indicates the possibility of narrow endemics restricted to diminishing suitable habitats. From this, it is clear that a systematic revision of the Bathyergidae is necessary; such a revision should include comprehensive sampling of all putative taxa, the addition of genomic information to assess adaptive differences, as well as ecological information.

scholarly journals The comparative ecology and biogeography of parasites

2011 ◽  
Vol 366 (1576) ◽  
pp. 2379-2390 ◽  
Author(s):  
Robert Poulin ◽  
Boris R. Krasnov ◽  
David Mouillot ◽  
David W. Thieltges
Keyword(s):  
Niche Breadth ◽  
Comparative Methods ◽  
Comparative Ecology ◽  
Host Interactions ◽  
Biogeographic Patterns ◽  
Parasite Communities ◽  
Fundamental Properties ◽  
Host Phylogeny ◽  
Patterns And Processes ◽  
Special Case

Comparative ecology uses interspecific relationships among traits, while accounting for the phylogenetic non-independence of species, to uncover general evolutionary processes. Applied to biogeographic questions, it can be a powerful tool to explain the spatial distribution of organisms. Here, we review how comparative methods can elucidate biogeographic patterns and processes, using analyses of distributional data on parasites (fleas and helminths) as case studies. Methods exist to detect phylogenetic signals, i.e. the degree of phylogenetic dependence of a given character, and either to control for these signals in statistical analyses of interspecific data, or to measure their contribution to variance. Parasite–host interactions present a special case, as a given trait may be a parasite trait, a host trait or a property of the coevolved association rather than of one participant only. For some analyses, it is therefore necessary to correct simultaneously for both parasite phylogeny and host phylogeny, or to evaluate which has the greatest influence on trait expression. Using comparative approaches, we show that two fundamental properties of parasites, their niche breadth, i.e. host specificity, and the nature of their life cycle, can explain interspecific and latitudinal variation in the sizes of their geographical ranges, or rates of distance decay in the similarity of parasite communities. These findings illustrate the ways in which phylogenetically based comparative methods can contribute to biogeographic research.

scholarly journals Reef development and Sea level changes drive Acanthaster Population Expansion in the Indo-Pacific region

2020 ◽  
Author(s):  
P.C. Pretorius ◽  
T.B. Hoareau
Keyword(s):  
Population Size ◽  
Sea Level ◽  
Environmental Changes ◽  
Sequence Data ◽  
Demographic History ◽  
Population Expansion ◽  
Population Level ◽  
Sea Level Changes ◽  
Reef Development ◽  
Curve Fitting Method

AbstractMolecular clock calibration is central in population genetics as it provides an accurate inference of demographic history, whereby helping with the identification of driving factors of population changes in an ecosystem. This is particularly important for coral reef species that are seriously threatened globally and in need of conservation. Biogeographic events and fossils are the main source of calibration, but these are known to overestimate timing and parameters at population level, which leads to a disconnection between environmental changes and inferred reconstructions. Here, we propose the Last Glacial Maximum (LGM) calibration that is based on the assumptions that reef species went through a bottleneck during the LGM, which was followed by an early yet marginal increase in population size. We validated the LGM calibration using simulations and genetic inferences based on Extended Bayesian Skyline Plots. Applying it to mitochondrial sequence data of crown-of-thorns starfish Acanthaster spp., we obtained mutation rates that were higher than phylogenetically based calibrations and varied among populations. The timing of the greatest increase in population size differed slightly among populations, but all started between 10 and 20 kya. Using a curve-fitting method, we showed that Acanthaster populations were more influenced by sea-level changes in the Indian Ocean and by reef development in the Pacific Ocean. Our results illustrate that the LGM calibration is robust and can probably provide accurate demographic inferences in many reef species. Application of this calibration has the potential to help identify population drivers that are central for the conservation and management of these threatened ecosystems.

Evolution of the south-western Pacific genus Melicytus (Violaceae): evidence from DNA sequence data, cytology and sex expression

2009 ◽  
Vol 22 (3) ◽  
pp. 143 ◽  
Author(s):  
A. D. Mitchell ◽  
P. B. Heenan ◽  
B. G. Murray ◽  
B. P. J. Molloy ◽  
P. J. de Lange
Keyword(s):  
New Zealand ◽  
Chromosome Numbers ◽  
Tree Species ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Sex Expression ◽  
The South ◽  
Shrub Species ◽  
Biogeographic Patterns ◽  
Norfolk Island

Phylogenetic analyses of nuclear DNA external transcribed spacer (ETS) and chloroplast DNA trnL–trnF markers were undertaken to reconstruct the evolutionary history of the South Pacific genus Melicytus. Bayesian analyses of the ETS sequence data produced a phylogenetic tree with several well supported groups, including clades comprising: (1) species from Australia, Tasmania and Lord Howe Island; (2) the Norfolk Island M. latifolius and New Zealand off-shore island M. novae-zelandiae subsp. novae-zelandiae; (3) the large-leaved M. ramiflorus complex; (4) M. fasciger and M. micranthus; and (5) M. obovatus and allies from the Cook Strait region. Phylogenetic analysis of trnL–trnF sequence data also retrieved some of these groups although, in general, was not as well resolved. The relationships of M. lanceolatus are equivocal, as in the ETS phylogeny it is sister to a clade comprising the large-leaved tree species M. fasciger and M. ramiflorus complex and the small-leaved M. micranthus, whereas in the trnL–trnF phylogeny it is sister to a clade of small-leaved shrub species such as M. alpinus and M. crassifolius. Several biogeographic patterns are evident, with dispersal to the west from New Zealand, to Australia, involving small-leaved shrub species. Dispersal to the north from New Zealand, to Norfolk Island and Fiji, involves large-leaved tree species. The sex expression is documented for all named species and undescribed entities, with these being either hermaphroditic or dioecious. When sex expression is mapped onto the phylogeny, the hermaphroditic system is inferred to have evolved from the dioecious system. New chromosome counts are presented for M. angustifolius (2n = 64) and M. dentatus (2n = 32), and earlier counts of 2n = 64 are confirmed for M. crassifolius and M. alpinus. An additional 17 counts are provided for two natural hybrids and several undescribed entities from Australia and New Zealand. The polyploid chromosome number of 2n = 64 occurs most frequently in small-leaved divariate plants with hermaphroditic flowers. When chromosome numbers are plotted onto the phylogeny it is inferred that high polyploids (e.g. 2n = 64) and small-leaved shrubs have evolved from large-leaved trees with functional diploid (e.g. 2n = 32) chromosome numbers.

scholarly journals A fully resolved backbone phylogeny reveals numerous dispersals and explosive diversifications throughout the history of Asteraceae

2019 ◽  
Vol 116 (28) ◽  
pp. 14083-14088 ◽  
Author(s):  
Jennifer R. Mandel ◽  
Rebecca B. Dikow ◽  
Carolina M. Siniscalchi ◽  
Ramhari Thapa ◽  
Linda E. Watson ◽  
...  
Keyword(s):  
Middle Eocene ◽  
Range Shift ◽  
Flowering Plant ◽  
Migration Routes ◽  
Biogeographic Patterns ◽  
Extant Species ◽  
The Family ◽  
History Of ◽  
Flowering Plant Species ◽  
Patterns And Processes

The sunflower family, Asteraceae, comprises 10% of all flowering plant species and displays an incredible diversity of form. Asteraceae are clearly monophyletic, yet resolving phylogenetic relationships within the family has proven difficult, hindering our ability to understand its origin and diversification. Recent molecular clock dating has suggested a Cretaceous origin, but the lack of deep sampling of many genes and representative taxa from across the family has impeded the resolution of migration routes and diversifications that led to its global distribution and tremendous diversity. Here we use genomic data from 256 terminals to estimate evolutionary relationships, timing of diversification(s), and biogeographic patterns. Our study places the origin of Asteraceae at ∼83 MYA in the late Cretaceous and reveals that the family underwent a series of explosive radiations during the Eocene which were accompanied by accelerations in diversification rates. The lineages that gave rise to nearly 95% of extant species originated and began diversifying during the middle Eocene, coincident with the ensuing marked cooling during this period. Phylogenetic and biogeographic analyses support a South American origin of the family with subsequent dispersals into North America and then to Asia and Africa, later followed by multiple worldwide dispersals in many directions. The rapid mid-Eocene diversification is aligned with the biogeographic range shift to Africa where many of the modern-day tribes appear to have originated. Our robust phylogeny provides a framework for future studies aimed at understanding the role of the macroevolutionary patterns and processes that generated the enormous species diversity of Asteraceae.

scholarly journals Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses

2020 ◽  
Vol 117 (29) ◽  
pp. 17104-17111
Author(s):  
Nicola F. Müller ◽  
Ugnė Stolz ◽  
Gytis Dudas ◽  
Tanja Stadler ◽  
Timothy G. Vaughan
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Population Level ◽  
Influenza Viruses ◽  
Monte Carlo Algorithm ◽  
Full Genome Sequence ◽  
Full Genome ◽  
Human Influenza ◽  
Fitness Benefits

Reassortment is an important source of genetic diversity in segmented viruses and is the main source of novel pathogenic influenza viruses. Despite this, studying the reassortment process has been constrained by the lack of a coherent, model-based inference framework. Here, we introduce a coalescent-based model that allows us to explicitly model the joint coalescent and reassortment process. In order to perform inference under this model, we present an efficient Markov chain Monte Carlo algorithm to sample rooted networks and the embedding of phylogenetic trees within networks. This algorithm provides the means to jointly infer coalescent and reassortment rates with the reassortment network and the embedding of segments in that network from full-genome sequence data. Studying reassortment patterns of different human influenza datasets, we find large differences in reassortment rates across different human influenza viruses. Additionally, we find that reassortment events predominantly occur on selectively fitter parts of reassortment networks showing that on a population level, reassortment positively contributes to the fitness of human influenza viruses.

scholarly journals Applying comparative genomics to plant disease epidemiology

2004 ◽  
Vol 85 (1) ◽  
pp. 45-48 ◽  
Author(s):  
Linda M. Kohn
Keyword(s):  
Magnaporthe Grisea ◽  
Sequence Data ◽  
Population Level ◽  
Avirulence Genes ◽  
Genome Database ◽  
Disease Epidemiology ◽  
Dna Sequence Data ◽  
Specific Pathogen ◽  
Pathogen Populations ◽  
Genomic Regions

Astract Phylogenetic or genealogical interpretation of DNA sequence data from multiple genomic regions has become the gold standard for species delimitation and population genetics. Precise species concepts can inform quarantine decisions but are likely to reflect evolutionary events too far in the past to impact disease management. On the other hand, multilocus approaches at the population level can identify patterns of endemism or migration directly associated with episodes of disease, including host shifts and associated changes in determinants of pathogenicity and avirulence. We used the genome database of Magnaporthe grisea to frame a comparative, multilocus genomics approach from which we demonstrate a single origin for rice infecting genotypes with concomitant loss of sex in pandemic clonal lineages, and patterns of gain and loss of avirulence genes. In the Sclerotinia sclerotiorum pathosystem, we identified significant associations of multilocus haplotypes with specific pathogen populations in North America. Following the introduction of a new crop, endemic pathogen genotypes and newly evolved migrant genotypes caused novel, early-season symptoms.

Eritreo-Arabian Affinities of the Socotran Flora as Revealed from the Molecular Phylogeny of Aerva (Amaranthaceae)

2006 ◽  
Vol 31 (3) ◽  
pp. 560-570 ◽  
Author(s):  
Mike Thiv ◽  
Mats Thulin ◽  
Norbert Kilian ◽  
H. Peter Linder
Keyword(s):  
Indian Ocean ◽  
Sequence Data ◽  
Plastid Dna ◽  
Molecular Dating ◽  
Tropical Asia ◽  
Biogeographic Patterns ◽  
Dna Sequence Data ◽  
Biogeographic History ◽  
History Of ◽  
Taxonomic Groups

We investigated the colonization of the Indian Ocean archipelago of Socotra through phylogenetic analysis of Aerva (Amaranthaceae) based on nuclear and plastid DNA sequence data. The biogeographic history of the genus was tracked using ancestral area reconstructions and molecular dating. Three independent colonization lineages from the Eritreo-Arabian subregion of the Sudano-Zambesian Region were revealed: one endemic clade comprising Aerva revoluta / A. microphylla and once within A. lanata and A. javanica. Our results provide further support for the dominance of Eritreo-Arabian affinities in the flora of Socotra, in contrast to more rare affinities to Madagascar, the Mascarenes, southern Africa, and tropical Asia. Our data point towards colonization via dispersal, rather than a vicariance origin of the island elements. The overall biogeographic patterns of Aerva show only limited concordance with other taxonomic groups distributed on Indian Ocean islands.

scholarly journals Synonymization of the male-based ant genus Phaulomyrma (Hymenoptera, Formicidae) with Leptanilla based upon Bayesian total-evidence phylogenetic inference

2020 ◽  
Author(s):  
Zachary H. Griebenow
Keyword(s):  
Sequence Data ◽  
Phylogenetic Inference ◽  
Morphological Characters ◽  
Molecular Data ◽  
Total Evidence ◽  
Morphological Data ◽  
Systematic Revision ◽  
Dna Sequence Data ◽  
Evidence Framework ◽  
Nuclear Loci

Abstract.Although molecular data have proven indispensable in confidently resolving the phylogeny of many clades across the tree of life, these data may be inaccessible for certain taxa. The resolution of taxonomy in the ant subfamily Leptanillinae is made problematic by the absence of DNA sequence data for leptanilline taxa that are known only from male specimens, including the monotypic genus Phaulomyrma Wheeler & Wheeler. Focusing upon the considerable diversity of undescribed male leptanilline morphospecies, the phylogeny of 35 putative morphospecies sampled from across the Leptanillinae, plus an outgroup, is inferred from 11 nuclear loci and 41 discrete male morphological characters using a Bayesian total-evidence framework, with Phaulomyrma represented by morphological data only. Based upon the results of this analysis Phaulomyrma is synonymized with Leptanilla Emery, and male-based diagnoses for Leptanilla that are grounded in phylogeny are provided, under both broad and narrow circumscriptions of that genus. This demonstrates the potential utility of a total-evidence approach in inferring the phylogeny of rare extant taxa for which molecular data are unavailable and begins a long-overdue systematic revision of the Leptanillinae that is focused on male material.

scholarly journals Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses

2019 ◽  
Author(s):  
Nicola F. Müller ◽  
Ugnė Stolz ◽  
Gytis Dudas ◽  
Tanja Stadler ◽  
Timothy G. Vaughan
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Population Level ◽  
Influenza Viruses ◽  
Monte Carlo Algorithm ◽  
Full Genome Sequence ◽  
Full Genome ◽  
Human Influenza ◽  
Fitness Benefits

AbstractReassortment is an important source of genetic diversity in segmented viruses and is the main source of novel pathogenic influenza viruses. Despite this, studying the reassortment process has been constrained by the lack of a coherent, model-based inference framework. We here introduce a novel coalescent based model that allows us to explicitly model the joint coalescent and reassortment process. In order to perform inference under this model, we present an efficient Markov chain Monte Carlo algorithm to sample rooted networks and the embedding of phylogenetic trees within networks. Together, these provide the means to jointly infer coalescent and reassortment rates with the reassortment network and the embedding of segments in that network from full genome sequence data. Studying reassortment patterns of different human influenza datasets, we find large differences in reassortment rates across different human influenza viruses. Additionally, we find that reassortment events predominantly occur on selectively fitter parts of reassortment networks showing that on a population level, reassortment positively contributes to the fitness of human influenza viruses.

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