scholarly journals Hybridization underlies localized trait evolution in cavefish

iScience ◽  
2022 ◽  
pp. 103778
Author(s):  
Rachel L. Moran ◽  
James B. Jaggard ◽  
Emma Y. Roback ◽  
Kenzior Alexander ◽  
Rohner Nicolas ◽  
...  
Keyword(s):  
2021 ◽  
Vol 7 (6) ◽  
pp. 478
Author(s):  
Xue-Wei Wang ◽  
Tom W. May ◽  
Shi-Liang Liu ◽  
Li-Wei Zhou

Hyphodontia sensu lato, belonging to Hymenochaetales, accommodates corticioid wood-inhabiting basidiomycetous fungi with resupinate basidiocarps and diverse hymenophoral characters. Species diversity of Hyphodontia sensu lato has been extensively explored worldwide, but in previous studies the six accepted genera in Hyphodontia sensu lato, viz. Fasciodontia, Hastodontia, Hyphodontia, Kneiffiella, Lyomyces and Xylodon were not all strongly supported from a phylogenetic perspective. Moreover, the relationships among these six genera in Hyphodontia sensu lato and other lineages within Hymenochaetales are not clear. In this study, we performed comprehensive phylogenetic analyses on the basis of multiple loci. For the first time, the independence of each of the six genera receives strong phylogenetic support. The six genera are separated in four clades within Hymenochaetales: Fasciodontia, Lyomyces and Xylodon are accepted as members of a previously known family Schizoporaceae, Kneiffiella and Hyphodontia are, respectively, placed in two monotypic families, viz. a previous name Chaetoporellaceae and a newly introduced name Hyphodontiaceae, and Hastodontia is considered to be a genus with an uncertain taxonomic position at the family rank within Hymenochaetales. The three families emerged between 61.51 and 195.87 million years ago. Compared to other families in the Hymenochaetales, these ages are more or less similar to those of Coltriciaceae, Hymenochaetaceae and Oxyporaceae, but much older than those of the two families Neoantrodiellaceae and Nigrofomitaceae. In regard to species, two, one, three and 10 species are newly described from Hyphodontia, Kneiffiella, Lyomyces and Xylodon, respectively. The taxonomic status of additional 30 species names from these four genera is briefly discussed; an epitype is designated for X. australis. The resupinate habit and poroid hymenophoral configuration were evaluated as the ancestral state of basidiocarps within Hymenochaetales. The resupinate habit mainly remains, while the hymenophoral configuration mainly evolves to the grandinioid-odontioid state and also back to the poroid state at the family level. Generally, a taxonomic framework for Hymenochaetales with an emphasis on members belonging to Hyphodontia sensu lato is constructed, and trait evolution of basidiocarps within Hymenochaetales is revealed accordingly.


Diversity ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 88
Author(s):  
Eric K. Moody ◽  
Fernando Alda ◽  
Krista A. Capps ◽  
Oscar Puebla ◽  
Benjamin L. Turner

Variation in nutrient excretion rates and stoichiometric ratios (e.g., nitrogen to phosphorus) by consumers can have substantial effects on aquatic ecosystem function. While phylogenetic signals within an assemblage often explain variation in nutrient recycling rates and stoichiometry, the phylogenetically conserved traits that underlie this phenomenon remain unclear. In particular, variation in nutrient excretion stoichiometry across a phylogeny might be driven by phylogenetic patterns in either diet or body stoichiometry. We examined the relative importance of these traits in explaining variation in nutrient recycling rates and stoichiometry in a diverse family of Neotropical-armored catfishes, Loricariidae, in Panamanian streams. We found significant variation in nutrient mineralization traits among species and subfamilies, but variation in nutrient excretion stoichiometry among species was best explained by trophic position rather than body stoichiometry. The variation in trophic position among Panamanian species was consistent with variation in the trophic niche of their genera across South America, suggesting that phylogenetic patterns underpin the evolution of trophic and nutrient excretion traits among these species. Such geographical variation in nutrient mineralization patterns among closely related species may be common, given that trophic variation in fish lineages occurs widely. These results suggest that information on trophic trait evolution within lineages will advance our understanding of the functional contribution of animals to biogeochemical cycling.


2011 ◽  
Vol 7 (3) ◽  
pp. 443-448 ◽  
Author(s):  
Alexander E. Quinn ◽  
Stephen D. Sarre ◽  
Tariq Ezaz ◽  
Jennifer A. Marshall Graves ◽  
Arthur Georges

Sex in many organisms is a dichotomous phenotype—individuals are either male or female. The molecular pathways underlying sex determination are governed by the genetic contribution of parents to the zygote, the environment in which the zygote develops or interaction of the two, depending on the species. Systems in which multiple interacting influences or a continuously varying influence (such as temperature) determines a dichotomous outcome have at least one threshold. We show that when sex is viewed as a threshold trait, evolution in that threshold can permit novel transitions between genotypic and temperature-dependent sex determination (TSD) and remarkably, between male (XX/XY) and female (ZZ/ZW) heterogamety. Transitions are possible without substantive genotypic innovation of novel sex-determining mutations or transpositions, so that the master sex gene and sex chromosome pair can be retained in ZW–XY transitions. We also show that evolution in the threshold can explain all observed patterns in vertebrate TSD, when coupled with evolution in embryonic survivorship limits.


2017 ◽  
Author(s):  
Meng Wu ◽  
Jamie L. Kostyun ◽  
Matthew W. Hahn ◽  
Leonie Moyle

ABSTRACTPhylogenetic analyses of trait evolution can provide insight into the evolutionary processes that initiate and drive phenotypic diversification. However, recent phylogenomic studies have revealed extensive gene tree-species tree discordance, which can lead to incorrect inferences of trait evolution if only a single species tree is used for analysis. This phenomenon—dubbed “hemiplasy”—is particularly important to consider during analyses of character evolution in rapidly radiating groups, where discordance is widespread. Here we generate whole-transcriptome data for a phylogenetic analysis of 14 species in the plant genus Jaltomata (the sister clade to Solanum), which has experienced rapid, recent trait evolution, including in fruit and nectar color, and flower size and shape. Consistent with other radiations, we find evidence for rampant gene tree discordance due to incomplete lineage sorting (ILS) and several introgression events among the well-supported subclades. Since both ILS and introgression increase the probability of hemiplasy, we perform several analyses that take discordance into account while identifying genes that might contribute to phenotypic evolution. Despite discordance, the history of fruit color evolution in Jaltomata can be inferred with high confidence, and we find evidence of de novo adaptive evolution at individual genes associated with fruit color variation. In contrast, hemiplasy appears to strongly affect inferences about floral character transitions in Jaltomata, and we identify candidate loci that could arise either from multiple lineage-specific substitutions or standing ancestral polymorphisms. Our analysis provides a generalizable example of how to manage discordance when identifying loci associated with trait evolution in a radiating lineage.


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