Phylogenetic analysis of the Digenea (Platyhelminthes: Cercomeria) with comments on their adaptive radiation

1985 ◽  
Vol 63 (2) ◽  
pp. 411-443 ◽  
Author(s):  
Daniel R. Brooks ◽  
Richard T. O'Grady ◽  
David R. Glen
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Morphological Change ◽  
Adaptive Radiation ◽  
Parallel Evolution ◽  
Morphological Diversification ◽  
Ecological Diversification ◽  
Low Degree ◽  
Adaptive Radiations ◽  
Low Levels

Phylogenetic analysis of 63 digenean family groups, based on 113 adult characters and 90 larval characters, produced a phylogenetic tree comprising nine orders. Adult characters alone resolved 76% of the phylogenetic tree, whereas larval characters alone resolved 74%. There was no disagreement in phylogenetic inferences drawn from only larval or only adult characters, and yet the larval forms of digeneans do not seem to be recapitulations of ancestral adult forms. The consistency index for the tree is 74%, indicating a low degree of parallel evolution in digenean morphology. Diversification in six sets of ecological characteristics combined resolves 26% of the phylogenetic tree. The combination of (i) larval and adult congruence in the absence of recapitulation, (ii) low levels of parallel evolution in morphology, and (iii) ecological diversification lagging far behind morphological change discounts traditional notions of adaptive radiations. Digeneans have experienced great morphological diversification constrained by their developmental programs and history, and have maintained their functional intergrity with few changes caused by extrinsic, "adaptive," forces.

scholarly journals Parallel and non-parallel changes of the gut microbiota during trophic diversification in repeated young adaptive radiations of sympatric cichlid fish

2019 ◽  
Author(s):  
Andreas Härer ◽  
Julián Torres-Dowdall ◽  
Sina Rometsch ◽  
Elizabeth Yohannes ◽  
Gonzalo Machado-Schiaffino ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Trophic Ecology ◽  
Crater Lake ◽  
Parallel Evolution ◽  
Cichlid Fish ◽  
Crater Lakes ◽  
Functional Changes ◽  
Ecological Diversification ◽  
Early Stages ◽  
Adaptive Radiations

AbstractRecent increases in understanding the ecological and evolutionary roles of microbial communities has underscored their importance for their hosts’ biology. Yet, little is known about gut microbiota dynamics during early stages of ecological diversification and speciation. We studied the gut microbiota of extremely young adaptive radiations of Nicaraguan crater lake cichlid fish (Amphilophus cf. citrinellus) to test the hypothesis that parallel evolution in trophic ecology is associated with parallel changes of the gut microbiota. Bacterial communities of the water (eDNA) and guts were highly distinct, indicating that the gut microbiota is shaped by host-specific factors. Across individuals of the same crater lake, differentiation in trophic ecology was associated with gut microbiota differentiation, suggesting that diet affects the gut microbiota. However, differences in trophic ecology were much more pronounced across than within species whereas little evidence was found for similar patterns in taxonomic and functional changes of the gut microbiota. Across the two crater lakes, we could not detect evidence for parallel changes of the gut microbiota associated with trophic ecology. Similar cases of non-parallelism have been observed in other recently diverged fish species and might be explained by a lack of clearly differentiated niches during early stages of ecological diversification.

scholarly journals Adaptive Divergence in Experimental Populations of Pseudomonas fluorescens. IV. Genetic Constraints Guide Evolutionary Trajectories in a Parallel Adaptive Radiation

Genetics ◽  
2009 ◽  
Vol 183 (3) ◽  
pp. 1041-1053 ◽  
Author(s):  
Michael J. McDonald ◽  
Stefanie M. Gehrig ◽  
Peter L. Meintjes ◽  
Xue-Xian Zhang ◽  
Paul B. Rainey
Keyword(s):  
Adaptive Radiation ◽  
Parallel Evolution ◽  
Adaptive Divergence ◽  
Genetic Constraints ◽  
Regulatory Modules ◽  
Fitness Effects ◽  
Evolutionary Trajectories ◽  
Adaptive Radiations ◽  
Encoding Gene ◽  
Do So

The capacity for phenotypic evolution is dependent upon complex webs of functional interactions that connect genotype and phenotype. Wrinkly spreader (WS) genotypes arise repeatedly during the course of a model Pseudomonas adaptive radiation. Previous work showed that the evolution of WS variation was explained in part by spontaneous mutations in wspF, a component of the Wsp-signaling module, but also drew attention to the existence of unknown mutational causes. Here, we identify two new mutational pathways (Aws and Mws) that allow realization of the WS phenotype: in common with the Wsp module these pathways contain a di-guanylate cyclase-encoding gene subject to negative regulation. Together, mutations in the Wsp, Aws, and Mws regulatory modules account for the spectrum of WS phenotype-generating mutations found among a collection of 26 spontaneously arising WS genotypes obtained from independent adaptive radiations. Despite a large number of potential mutational pathways, the repeated discovery of mutations in a small number of loci (parallel evolution) prompted the construction of an ancestral genotype devoid of known (Wsp, Aws, and Mws) regulatory modules to see whether the types derived from this genotype could converge upon the WS phenotype via a novel route. Such types—with equivalent fitness effects—did emerge, although they took significantly longer to do so. Together our data provide an explanation for why WS evolution follows a limited number of mutational pathways and show how genetic architecture can bias the molecular variation presented to selection.

Revision and phylogenetic analysis of the Amphilinidea Poche, 1922 (Platyhelminthes: Cercomeria: Cercomeromorpha)

1987 ◽  
Vol 65 (5) ◽  
pp. 1110-1128 ◽  
Author(s):  
Susan M. Bandoni ◽  
Daniel R. Brooks
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Geographic Distribution ◽  
Homologous Series ◽  
Consistency Index ◽  
Low Degree ◽  
Systematic Relationships ◽  
Index Value ◽  
High Degree

Systematic relationships of amphilinidean platyhelminth species were investigated. Eight species and three genera are considered valid. Analysis of 46 character states comprising 34 homologous series produced a single phylogenetic tree with a consistency index value of 87%, indicating a very low degree of parallelism in the evolution of amphilinidean morphology. Comparison of host and parasite phylogenies produced a fit of 70%, suggesting a high degree of coevolution between amphilinideans and their teleostean hosts. The geographic distribution of the amphilinideans was compared with four current hypotheses of area relationship for the southern land masses. Consistency index values obtained range from 87.5% to 100%, indicating that vicariance may be sufficient to explain the biogeographic distribution of amphilinidean platyhelminths.

Revision and phylogenetic analysis of the Gyrocotylidea Poche, 1926 (Platyhelminthes: Cercomeria: Cercomeromorpha)

1987 ◽  
Vol 65 (10) ◽  
pp. 2369-2389 ◽  
Author(s):  
Susan M. Bandoni ◽  
Daniel R. Brooks
Keyword(s):  
Phylogenetic Analysis ◽  
Initial Phase ◽  
Phylogenetic Trees ◽  
Parallel Evolution ◽  
Tectonic Plate ◽  
Low Degree ◽  
Two Phases ◽  
Index Value ◽  
Dispersal Events ◽  
Later Phase

Phylogenetic analysis of 10 gyrocotylidean platyhelminth species, based on 24 character states comprising 13 homologous series, produced two similar phylogenetic trees of equal length. The consistency index value for each tree is 87.5%, indicating a low degree of parallel evolution in the morphology of gyrocotylidean platyhelminths. Slightly more than half of the observed associations between gyrocotylideans and holocephalan hosts can be attributed to coevolution. Remaining associations must be attributed to colonization, but these represent recolonizations of plesiomorphic hosts. The geographic distribution of gyrocotylideans remains enigmatic, as part of it seems to predate tectonic plate movements. Extensive dispersal has occurred; dispersal events are correlated with host transfers. It is hypothesized that the origin of gyrocotylideans predates separation of the continents, and that there were two phases in the evolution of the gyrocotylideans, an initial phase of coevolution and a later phase of colonization and dispersal.

scholarly journals SARS-CoV-2 within-host diversity and transmission

Science ◽  
2021 ◽  
Vol 372 (6539) ◽  
pp. eabg0821 ◽  
Author(s):  
Katrina A. Lythgoe ◽  
Matthew Hall ◽  
Luca Ferretti ◽  
Mariateresa de Cesare ◽  
George MacIntyre-Cockett ◽  
...  
Keyword(s):  
United Kingdom ◽  
Severe Acute Respiratory Syndrome ◽  
Phylogenetic Tree ◽  
Immune Escape ◽  
Clinical Samples ◽  
Diversity Patterns ◽  
Host Diversity ◽  
Viral Loads ◽  
The United Kingdom ◽  
Low Levels

Extensive global sampling and sequencing of the pandemic virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have enabled researchers to monitor its spread and to identify concerning new variants. Two important determinants of variant spread are how frequently they arise within individuals and how likely they are to be transmitted. To characterize within-host diversity and transmission, we deep-sequenced 1313 clinical samples from the United Kingdom. SARS-CoV-2 infections are characterized by low levels of within-host diversity when viral loads are high and by a narrow bottleneck at transmission. Most variants are either lost or occasionally fixed at the point of transmission, with minimal persistence of shared diversity, patterns that are readily observable on the phylogenetic tree. Our results suggest that transmission-enhancing and/or immune-escape SARS-CoV-2 variants are likely to arise infrequently but could spread rapidly if successfully transmitted.

scholarly journals Adaptive radiation and hybridization in Wallace's Dreamponds: evidence from sailfin silversides in the Malili Lakes of Sulawesi

2006 ◽  
Vol 273 (1598) ◽  
pp. 2209-2217 ◽  
Author(s):  
Fabian Herder ◽  
Arne W Nolte ◽  
Jobst Pfaender ◽  
Julia Schwarzer ◽  
Renny K Hadiaty ◽  
...  
Keyword(s):  
New Species ◽  
Adaptive Radiation ◽  
Introgressive Hybridization ◽  
Reticulate Evolution ◽  
Species Group ◽  
Potential Force ◽  
Major Interest ◽  
Key Factor ◽  
Adaptive Radiations ◽  
Malili Lakes

Adaptive radiations are extremely useful to understand factors driving speciation. A challenge in speciation research is to distinguish forces creating novelties and those relevant to divergence and adaptation. Recently, hybridization has regained major interest as a potential force leading to functional novelty and to the genesis of new species. Here, we show that introgressive hybridization is a prominent phenomenon in the radiation of sailfin silversides (Teleostei: Atheriniformes: Telmatherinidae) inhabiting the ancient Malili Lakes of Sulawesi, correlating conspicuously with patterns of increased diversity. We found the most diverse lacustrine species-group of the radiation to be heavily introgressed by genotypes originating from streams of the lake system, an effect that has masked the primary phylogenetic pattern of the flock. We conclude that hybridization could have acted as a key factor in the generation of the flock's spectacular diversity. To our knowledge, this is the first empirical evidence for massive reticulate evolution within a complex animal radiation.

Rhizocarpon smaragdulum, a new monosporic yellow-thalline species and some additional species of the genus Rhizocarpon from the Altai Mountains (Siberia)

2017 ◽  
Vol 49 (5) ◽  
pp. 457-466 ◽  
Author(s):  
Evgeny A. DAVYDOV ◽  
Lidia S. YAKOVCHENKO
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Altai Mountains ◽  
Additional Species ◽  
Sister Relationship

AbstractRhizocarpon smaragdulum Davydov & Yakovchenko sp. nov. is described and a phylogenetic analysis (ITS, mtSSU) is presented, confirming its distinctiveness and indicating a sister relationship with R. suomiense and R. subgeminatum. The species is unique among yellow Rhizocarpon species in having a single hyaline ascospore per ascus. The phylogenetic tree suggests that the number of ascospores per ascus has been reduced in Rhizocarpon more than once during the course of its evolution. Two new distributional records are also reported: Rhizocarpon atroflavescens is new for Siberia and R. norvegicum is new for the Altai Mountains. Rhizocarpon norvegicum in this region grows on rocks and is also lichenicolous on Acarospora bullata.

scholarly journals Phylogenetic Analysis of Kobuvirus and Astrovirus From Korean Wild Boars: 2016-2018

2021 ◽  
Author(s):  
Jihye Shin ◽  
SeEun Choe ◽  
Bang-Hun Hyun ◽  
Dong-Jun An
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Porcine Kobuvirus ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Wild Boars ◽  
Porcine Astrovirus ◽  
The One

Abstract The prevalence of porcine kobuvirus (PKoV) and porcine astrovirus (PAstV) in 845 Korean wild boars (KWB) during 2016-2018 were 28.0% and 10.6%, respectively, and co-infection of two viruses showed 5.1%. Phylogenetic tree analysis also revealed that 236 PKoVs from KWB were divided to diverse lineages within Aichivirus C group but the one strain (WKoV16CN-8627) was included the same cluster with bovine kobuvirus (Achivirus B). Eighty-nine PAstVs from KWB was belonged predominantly to lineage PAstV4 and only one strain (WAst17JN-10931) included novel to lineage PAstV2. Two viruses are epidemic more in young (≤ 12 months) than in old pigs (> 12 months).

scholarly journals Eutherians experienced elevated evolutionary rates in the immediate aftermath of the Cretaceous–Palaeogene mass extinction

2016 ◽  
Vol 283 (1833) ◽  
pp. 20153026 ◽  
Author(s):  
Thomas John Dixon Halliday ◽  
Paul Upchurch ◽  
Anjali Goswami
Keyword(s):  
Phylogenetic Analysis ◽  
Adaptive Radiation ◽  
Mass Extinction ◽  
Fossil Record ◽  
Morphological Evolution ◽  
Placental Mammal ◽  
Stochastic Methods ◽  
Ecological Niches ◽  
Evolutionary Radiation ◽  
Quantitative Analyses

The effect of the Cretaceous–Palaeogene (K–Pg) mass extinction on the evolution of many groups, including placental mammals, has been hotly debated. The fossil record suggests a sudden adaptive radiation of placentals immediately after the event, but several recent quantitative analyses have reconstructed no significant increase in either clade origination rates or rates of character evolution in the Palaeocene. Here we use stochastic methods to date a recent phylogenetic analysis of Cretaceous and Palaeocene mammals and show that Placentalia likely originated in the Late Cretaceous, but that most intraordinal diversification occurred during the earliest Palaeocene. This analysis reconstructs fewer than 10 placental mammal lineages crossing the K–Pg boundary. Moreover, we show that rates of morphological evolution in the 5 Myr interval immediately after the K–Pg mass extinction are three times higher than background rates during the Cretaceous. These results suggest that the K–Pg mass extinction had a marked impact on placental mammal diversification, supporting the view that an evolutionary radiation occurred as placental lineages invaded new ecological niches during the Early Palaeocene.

scholarly journals Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua

2012 ◽  
Vol 22 (3) ◽  
pp. 650-669 ◽  
Author(s):  
Tereza Manousaki ◽  
Pincelli M. Hull ◽  
Henrik Kusche ◽  
Gonzalo Machado-Schiaffino ◽  
Paolo Franchini ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Parallel Evolution ◽  
Ecological Divergence ◽  
Cichlid Fishes ◽  
Adaptive Radiations ◽  
Differential Gene
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