Ancestral state, phylogenetic signal and convergence among anuran distress calls

2018 ◽  
Vol 274 ◽  
pp. 1-5 ◽  
Author(s):  
Lucas Rodriguez Forti ◽  
Camila Zornosa-Torres ◽  
Rafael Márquez ◽  
Luís Felipe Toledo
Keyword(s):  
Phylogenetic Signal ◽  
Ancestral State ◽  
Distress Calls

scholarly journals Ancestry and evolution of seasonal migration in the Parulidae

2011 ◽  
Vol 279 (1728) ◽  
pp. 610-618 ◽  
Author(s):  
Benjamin M. Winger ◽  
Irby J. Lovette ◽  
David W. Winkler
Keyword(s):  
Phylogenetic Signal ◽  
Rapid Change ◽  
Large Family ◽  
Seasonal Migration ◽  
Ancestral State ◽  
Migratory Behaviour ◽  
Wood Warbler ◽  
Wood Warblers ◽  
History Of ◽  
The Tropics

Seasonal migration in birds is known to be highly labile and subject to rapid change in response to selection, such that researchers have hypothesized that phylogenetic relationships should neither predict nor constrain the migratory behaviour of a species. Many theories on the evolution of bird migration assume a framework that extant migratory species have evolved repeatedly and relatively recently from sedentary tropical or subtropical ancestors. We performed ancestral state reconstructions of migratory behaviour using a comprehensive, well-supported phylogeny of the Parulidae (the ‘wood-warblers’), a large family of Neotropical and Nearctic migratory and sedentary songbirds, and examined the rates of gain and loss of migration throughout the Parulidae. Counter to traditional hypotheses, our results suggest that the ancestral wood-warbler was migratory and that losses of migration have been at least as prevalent as gains throughout the history of Parulidae. Therefore, extant sedentary tropical radiations in the Parulidae represent losses of latitudinal migration and colonization of the tropics from temperate regions. We also tested for phylogenetic signal in migratory behaviour, and our results indicate that although migratory behaviour is variable within some wood-warbler species and clades, phylogeny significantly predicts the migratory distance of species in the Parulidae.

scholarly journals Reconstructing the ancestral phenotypes of great apes and humans (Homininae) using subspecies-level phylogenies

2019 ◽  
Author(s):  
Keaghan J Yaxley ◽  
Robert A Foley
Keyword(s):  
Dna Sequences ◽  
Phenotypic Variation ◽  
Common Ancestor ◽  
Phylogenetic Signal ◽  
Great Apes ◽  
Last Common Ancestor ◽  
Ancestral State ◽  
Great Ape ◽  
Subspecies Level ◽  
African Great Apes

Abstract Owing to their close affinity, the African great apes are of interest in the study of human evolution. Although numerous researchers have described the ancestors we share with these species with reference to extant great apes, few have done so with phylogenetic comparative methods. One obstacle to the application of these techniques is the within-species phenotypic variation found in this group. Here, we leverage this variation, modelling common ancestors using ancestral state reconstructions (ASRs) with reference to subspecies-level trait data. A subspecies-level phylogeny of the African great apes and humans was estimated from full-genome mitochondrial DNA sequences and used to implement ASRs for 14 continuous traits known to vary between great ape subspecies. Although the inclusion of within-species phenotypic variation increased the phylogenetic signal for our traits and improved the performance of our ASRs, whether this was done through the inclusion of subspecies phylogeny or through the use of existing methods made little difference. Our ASRs corroborate previous findings that the last common ancestor of humans, chimpanzees and bonobos was a chimp-like animal, but also suggest that the last common ancestor of humans, chimpanzees, bonobos and gorillas was an animal unlike any extant African great ape.

scholarly journals Much more than a clasp: evolutionary patterns of amplexus diversity in anurans

2020 ◽  
Vol 129 (3) ◽  
pp. 652-663 ◽  
Author(s):  
Juan D Carvajal-Castro ◽  
Yelenny López-Aguirre ◽  
Ana María Ospina-L ◽  
Juan C Santos ◽  
Bibiana Rojas ◽  
...  
Keyword(s):  
Morphological Traits ◽  
Sexual Size Dimorphism ◽  
Phylogenetic Signal ◽  
Evolutionary Relationships ◽  
Behavioural Ecology ◽  
Ancestral State ◽  
Evolutionary Patterns ◽  
Evolutionary Transitions ◽  
Size Dimorphism ◽  
Reproductive Modes

Abstract The evolution and diversification of animal reproductive modes have been pivotal questions in behavioural ecology. Amphibians present the highest diversity of reproductive modes among vertebrates, involving various behavioural, physiological and morphological traits. One such feature is the amplexus, which is the clasp or embrace of males on females during reproduction and is found almost universally in anurans. Hypotheses about the origin of amplexus are limited and have not been tested thoroughly, nor have they taken into account evolutionary relationships in most comparative studies. However, these considerations are crucial to an understanding of the evolution of reproductive modes. Here, using an evolutionary framework, we reconstruct the ancestral state of amplexus in 685 anuran species. We investigate whether the type of amplexus has a strong phylogenetic signal and test whether sexual size dimorphism could have influenced amplexus type or male performance while clasping females. Overall, we found evidence of ≥34 evolutionary transitions in amplexus type across anurans. We found that amplexus type exhibits a high phylogenetic signal and that amplexus type does not evolve in association with sexual size dimorphism. We discuss the implications of our findings for the diversity of amplexus types across anurans.

scholarly journals The evolution of multi-component visual signals in darters (genus Etheostoma)

2011 ◽  
Vol 57 (2) ◽  
pp. 125-139 ◽  
Author(s):  
Jennifer M. Gumm ◽  
Tamra C. Mendelson
Keyword(s):  
Complex Traits ◽  
Phylogenetic Signal ◽  
The Body ◽  
Visual Signals ◽  
Recent Common Ancestor ◽  
Ancestral State ◽  
Complex Signals ◽  
Evolutionary Forces ◽  
Most Recent Common Ancestor ◽  
Body Regions

Abstract As complex traits evolve, each component of the trait may be under different selection pressures and could respond independently to distinct evolutionary forces. We used comparative methods to examine patterns of evolution in multiple components of a complex courtship signal in darters, specifically addressing the question of how nuptial coloration evolves across different areas of the body. Using spectral reflectance, we defined 4 broad color classes present on the body and fins of 17 species of freshwater fishes (genus Etheostoma) and quantified differences in hue within each color class. Ancestral state reconstruction suggests that most color traits were expressed in the most recent common ancestor of sampled species and that differences among species are mostly due to losses in coloration. The evolutionary lability of coloration varied across body regions; we found significant phylogenetic signal for orange color on the body but not for most colors on fins. Finally, patterns of color evolution and hue of the colors were correlated among the two dorsal fins and between the anterior dorsal and anal fins, but not between any of the fins and the body. The observed patterns support the hypothesis that different components of complex signals may be subject to distinct evolutionary pressures, and suggests that the combination of behavioral displays and morphology in communication may have a strong influence on patterns of signal evolution.

scholarly journals Mitochondrial copper and phosphate transporter specificity was defined early in the evolution of eukaryotes

2020 ◽  
Author(s):  
Xinyu Zhu ◽  
Aren Boulet ◽  
Katherine M. Buckley ◽  
Casey B. Phillips ◽  
Micah G. Gammon ◽  
...  
Keyword(s):  
Protein Function ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Phosphate Transport ◽  
Site Directed Mutagenesis ◽  
Specific Gene ◽  
Ancestral State ◽  
Gene Duplications ◽  
Substrate Selection ◽  
Mitochondrial Carrier Family

AbstractMitochondrial carrier family (MCF/SLC25) proteins are selective transporters that maintain the mitochondrial metabolome. Here we combine computational, biochemical and phenotypic approaches to understand substrate selectivity of SLC25A3. In mammals, SLC25A3 transports both copper and phosphate, yet in Saccharomyces cerevisiae the transport of these substrates is partitioned across two paralogs: PIC2, which transports copper, and MIR1, which transports phosphate. To understand whether the ancestral state of this transporter was a single promiscuous transporter that duplicated and gained selectivity, we explored the evolutionary relationships of PIC2 and MIR1 orthologs across the eukaryotic tree of life. Phylogenetic analyses reveal that PIC2-like and MIR1-like orthologs are present in all major eukaryotic supergroups, indicating that the gene duplication that created these paralogs occurred early in eukaryotic evolution. Frequent lineage-specific gene duplications and losses suggest that substrate specificity may be evolutionarily labile. To link this phylogenetic signal to protein function and resolve the residues involved in substrate selection, we used structural modelling and site-directed mutagenesis to identify PIC2 residues involved in copper and phosphate transport activities. Based on these analyses, we generated a Leu175Ala variant of mouse SLC25A3 that retains the ability to transport copper, but not phosphate, and rescues the cytochrome c oxidase defect in SLC25A3 knockout cells. Taken together, this work uses an evolutionary framework to uncover amino acids involved in substrate recognition by MCF proteins responsible for copper and phosphate transport.

scholarly journals Phylogenetic Patterns in Mouth Posture and Echolocation Emission Behavior of Phyllostomid Bats

2021 ◽  
Vol 9 ◽  
Author(s):  
Gloria Gessinger ◽  
Rachel Page ◽  
Lena Wilfert ◽  
Annemarie Surlykke ◽  
Signe Brinkløv ◽  
...  
Keyword(s):  
High Speed ◽  
Feeding Habits ◽  
Phylogenetic Signal ◽  
Ancestral State ◽  
Sound Emission ◽  
Behavioral Differences ◽  
Open Mouth ◽  
Echolocation Calls ◽  
Sister Clade ◽  
Emission Behavior

While phyllostomid bats show an impressive range of feeding habits, most of them emit highly similar echolocation calls. Due to the presence of an often prominent noseleaf, it has long been assumed that all phyllostomids emit echolocation calls exclusively through the nostrils rather than through the mouth. However, photo evidence documents also phyllostomid bats flying with an opened mouth. We hypothesized that all phyllostomid species emit echolocation calls only through the nostrils and therefore fly consistently with a closed mouth, and that observations of an open mouth should be a rare and random behavior among individuals and species. Using a high-speed camera and standardized conditions in a flight cage, we screened 40 phyllostomid species. Behavior varied distinctly among the species and mouth posture shows a significant phylogenetic signal. Bats of the frugivorous subfamilies Rhinophyllinae and Carolliinae, the nectarivorous subfamilies Glossophaginae and Lonchophyllinae, and the sanguivorous subfamily Desmodontinae all flew consistently with open mouths. So did the animalivorous subfamilies Glyphonycterinae, Micronycterinae and Phyllostominae, with the notable exception of species in the omnivorous genus Phyllostomus, which consistently flew with mouths closed. Bats from the frugivorous subfamily Stenodermatinae also flew exclusively with closed mouths with the single exception of the genus Sturnira, which is the sister clade to all other stenodermatine species. Further, head position angles differed significantly between bats echolocating with their mouth closed and those echolocating with their mouths opened, with closed-mouth phyllostomids pointing only the nostrils in the direction of flight and open-mouth phyllostomids pointing both the nostrils and mouth gape in the direction of flight. Ancestral trait reconstruction showed that the open mouth mode is the ancestral state within the Phyllostomidae. Based on the observed behavioral differences, we suggest that phyllostomid bats are not all nasal emitters as previously thought and discuss possible reasons. Further experiments, such as selectively obstructing sound emission through nostrils or mouth, respectively, will be necessary to clarify the actual source, plasticity and ecological relevance of sound emission of phyllostomid bats flying with their mouths open.

scholarly journals Macroevolutionary Trade-Offs and Trends in Life History Traits of Cephalopods Through a Comparative Phylogenetic Approach

2021 ◽  
Vol 8 ◽  
Author(s):  
Christian M. Ibáñez ◽  
Mariana Díaz-Santana-Iturrios ◽  
Sergio A. Carrasco ◽  
Fernando A. Fernández-Álvarez ◽  
David A. López-Córdova ◽  
...  
Keyword(s):  
Body Length ◽  
Phylogenetic Signal ◽  
Reproductive Traits ◽  
Evolutionary Trend ◽  
Ancestral State ◽  
Potential Fecundity ◽  
Correlated Evolution ◽  
Phylogenetic Methods ◽  
Trade Offs ◽  
Concomitant Reduction

One of the major mechanisms responsible for the animals’ fitness dynamics is fecundity. Fecundity as a trait does not evolve independently, and rather interacts with other traits such as body and egg size. Here, our aim was to correctly infer the macroevolutionary trade-offs between body length, egg length, and potential fecundity, using cephalopods as study model. The correlated evolution among those traits was inferred by comparative phylogenetic methods. Literature data on biological and reproductive traits (body length, egg length, and potential fecundity) was obtained for 90 cephalopod species, and comparative phylogenetic methods based on a previous molecular phylogeny were used to test the correlated evolution hypothesis. Additionally, we estimated the phylogenetic signal and fitted five different evolutionary models to each trait. All traits showed high phylogenetic signal, and the selected model suggested an evolutionary trend toward increasing body length, egg length, and fecundity in relation to the ancestral state. Evidence of correlated evolution between body length and fecundity was observed, although this relationship was not detected between body length and egg length. The robust inverse relationship between fecundity and egg length indicates that cephalopods evolved a directional selection that favored an increase of fecundity and a reduction of egg length in larger species, or an increase in egg length with the concomitant reduction of fecundity and body length in order to benefit offspring survival. The use of phylogenetic comparative methods allowed us to properly detect macroevolutionary trade-offs.

scholarly journals RASP 4: Ancestral State Reconstruction Tool for Multiple Genes and Characters

2019 ◽  
Vol 37 (2) ◽  
pp. 604-606 ◽  
Author(s):  
Yan Yu ◽  
Christopher Blair ◽  
Xingjin He
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Signal ◽  
Graphic User Interface ◽  
Ancestral State ◽  
Ancestral Reconstruction ◽  
Phylogenetic Studies ◽  
Reconstruction Methods ◽  
Ancestral States ◽  
Genome Scale ◽  
The Relationship

Abstract With the continual progress of sequencing techniques, genome-scale data are increasingly used in phylogenetic studies. With more data from throughout the genome, the relationship between genes and different kinds of characters is receiving more attention. Here, we present version 4 of RASP, a software to reconstruct ancestral states through phylogenetic trees. RASP can apply generalized statistical ancestral reconstruction methods to phylogenies, explore the phylogenetic signal of characters to particular trees, calculate distances between trees, and cluster trees into groups. RASP 4 has an improved graphic user interface and is freely available from http://mnh.scu.edu.cn/soft/blog/RASP (program) and https://github.com/sculab/RASP (source code).

scholarly journals Mitochondrial copper and phosphate transporter specificity was defined early in the evolution of eukaryotes

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Xinyu Zhu ◽  
Aren Boulet ◽  
Katherine M Buckley ◽  
Casey B Phillips ◽  
Micah G Gammon ◽  
...  
Keyword(s):  
Protein Function ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Phosphate Transport ◽  
Site Directed Mutagenesis ◽  
Ancestral State ◽  
Mitochondrial Carrier ◽  
Family Protein ◽  
Mitochondrial Carrier Family ◽  
Transport In Mitochondria

The mitochondrial carrier family protein SLC25A3 transports both copper and phosphate in mammals yet in Saccharomyces cerevisiae the transport of these substrates is partitioned across two paralogs: PIC2 and MIR1. To understand the ancestral state of copper and phosphate transport in mitochondria, we explored the evolutionary relationships of PIC2 and MIR1 orthologs across the eukaryotic tree of life. Phylogenetic analyses revealed that PIC2-like and MIR1-like orthologs are present in all major eukaryotic supergroups, indicating an ancient gene duplication created these paralogs. To link this phylogenetic signal to protein function, we used structural modelling and site-directed mutagenesis to identify residues involved in copper and phosphate transport. Based on these analyses, we generated a L175A variant of mouse SLC25A3 that retains the ability to transport copper but not phosphate. This work highlights the utility of using an evolutionary framework to uncover amino acids involved in substrate recognition by mitochondrial carrier family proteins.

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