Molecular phylogenetics and floral evolution of the Cirrhopetalum alliance (Bulbophyllum, Orchidaceae): Evolutionary transitions and phylogenetic signal variation

Abstract In flowering plants, the shift from outcrossing to selfing is associated with a set of correlated changes in morphological and reproductive features known as the ‘selfing syndrome’. Species of the sub-endemic Mediterranean genus Centaurium Hill (Gentianaceae) exhibit a wide array of flower traits related to pollination biology and different ploidy levels. We explored if the evolutionary transitions of seven flower traits and life cycle, typically associated with the selfing syndrome, are related to polyploidy, diversification patterns, divergence times and the geological and climatic history of the Mediterranean Basin. Using 26 species of Centaurium we reconstructed a phylogenetic tree, inferred the ancestral states of the selected traits, estimated their phylogenetic signal and tested the correlative evolution among them. We found a significant increase in diversification rates during the Quaternary. Anther length, flower size, herkogamy and polyploidy undergo rapid state transitions without phylogenetic signal that could be the result of adaptation for selfing. Changes in character states do not show evidence of correlative evolution among them, as would be predicted during the evolution of selfing syndrome. The evolution of reproductive traits in Centaurium has probably relied on a more diverse array of drivers than just reproductive assurance or polyploidy events.

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Molecular Phylogenetics of the Ramphastos Toucans: Implications for the Evolution of Morphology, Vocalizations, and Coloration

The Auk ◽

10.1093/auk/122.4.1191 ◽

2005 ◽

Vol 122 (4) ◽

pp. 1191-1209 ◽

Cited By ~ 2

Author(s):

Jason D. Weckstein

Keyword(s):

Mitochondrial Dna ◽

Molecular Phylogenetics ◽

Phylogenetic Signal ◽

Southeastern Brazil ◽

Mtdna Sequences ◽

Coloration Patterns ◽

Ancestral Character States

Abstract I reconstructed the phylogeny of 12 Ramphastos toucan taxa using mitochondrial DNA (mtDNA) sequences. This analysis identified two major groups, including a monophyletic smooth-billed yelping clade and a clade including most, but not all, the channel-keel-billed croakers. Within the R. tucanus and R. vitellinus groups, uncorrected mtDNA divergences are relatively low and mtDNA sequences from several subspecies are paraphyletic. One exception to low divergences within the R. vitellinus group is R. v. ariel from southeastern Brazil, which on average differs from all other R. vitellinus sampled by 2.9%. Character reconstructions on the phylogeny indicate that the ancestral Ramphastos was most likely a large-bodied channel- keel-billed croaker. Furthermore, an assessment of the patterns of bill shape, voice, and both plumage and bare-part coloration characters suggests that bill shape and voice have significant phylogenetic signal but that color characters do not. Sympatric Ramphastos taxa are not closely related in the phylogeny; therefore, character reconstructions indicate that the extreme similarity in coloration patterns between many sympatric Ramphastos pairs is most likely attributable to a combination of convergence or parallelism (homoplasy) and shared ancestral character states (symplesiomorphy). Filogenética Molecular de los Tucanes del Género Ramphastos: Implicaciones para la Evolución de la Morfología, las Vocalizaciones y la Coloración

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The unresolved phylogenomic tree of butterflies and moths (Lepidoptera): assessing the potential causes and consequences

10.1101/2021.04.09.439156 ◽

2021 ◽

Author(s):

Jadranka Rota ◽

Victoria Gwendoline Twort ◽

Andrea Chiocchio ◽

Carlos Pena ◽

Christopher W. Wheat ◽

...

Keyword(s):

Amino Acid ◽

Molecular Phylogenetics ◽

Phylogenetic Signal ◽

Tree Of Life ◽

Amino Acid Sequences ◽

Model Organisms ◽

Compositional Bias ◽

Sequencing Technologies ◽

Phylogenetic Hypotheses ◽

Phylogenomic Analyses

The field of molecular phylogenetics is being revolutionised with next-generation sequencing technologies making it possible to sequence large numbers of genomes for non-model organisms ushering us into the era of phylogenomics. The current challenge is no longer how to get enough data, but rather how to analyse the data and how to assess the support for the inferred phylogeny. We focus on one of the largest animal groups on the planet - butterflies and moths (order Lepidoptera). We clearly demonstrate that there are unresolved issues in the inferred phylogenetic relationships of the major lineages, despite several recent phylogenomic studies of the group. We assess the potential causes and consequences of the conflicting phylogenetic hypotheses. With a dataset consisting of 331 protein-coding genes and the alignment length over 290 000 base pairs, including 200 taxa representing 81% of lepidopteran superfamilies, we compare phylogenetic hypotheses inferred from amino acid and nucleotide alignments. The resulting two phylogenies are discordant, especially with respect to the placement of the superfamily Gelechioidea, which is likely due to compositional bias of both the nucleotide and amino acid sequences. With a series of analyses, we dissect our dataset and demonstrate that there is sufficient phylogenetic signal to resolve much of the lepidopteran tree of life. Overall, the results from the nucleotide alignment are more robust to the various perturbations of the data that we carried out. However, the lack of support for much of the backbone within Ditrysia makes the current butterfly and moth tree of life still unresolved. We conclude that taxon sampling remains an issue even in phylogenomic analyses, and recommend that poorly sampled highly diverse groups, such as Gelechioidea in Lepidoptera, should receive extra attention in the future.

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

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blaa009 ◽

2020 ◽

Vol 129 (3) ◽

pp. 652-663 ◽

Cited By ~ 1

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.

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Molecular phylogenetics and floral evolution in the sarracenioid clade (Actinidiaceae, Roridulaceae and Sarraceniaceae) of Ericales

Taxon ◽

10.12705/646.6 ◽

2015 ◽

Vol 64 (6) ◽

pp. 1209-1224 ◽

Cited By ~ 5

Author(s):

Stefan D. Löfstrand ◽

Jürg Schönenberger

Keyword(s):

Molecular Phylogenetics ◽

Floral Evolution

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Nuclear genomic signals of the ‘microturbellarian’ roots of platyhelminth evolutionary innovation

eLife ◽

10.7554/elife.05503 ◽

2015 ◽

Vol 4 ◽

Cited By ~ 81

Author(s):

Christopher E Laumer ◽

Andreas Hejnol ◽

Gonzalo Giribet

Keyword(s):

Nuclear Protein ◽

Phylogenetic Signal ◽

Evolutionary Relationships ◽

Free Living ◽

Evolutionary Transitions ◽

Protein Coding ◽

Protein Coding Genes ◽

Evolutionary Innovation ◽

Genomic Signals ◽

Shed Light

Flatworms number among the most diverse invertebrate phyla and represent the most biomedically significant branch of the major bilaterian clade Spiralia, but to date, deep evolutionary relationships within this group have been studied using only a single locus (the rRNA operon), leaving the origins of many key clades unclear. In this study, using a survey of genomes and transcriptomes representing all free-living flatworm orders, we provide resolution of platyhelminth interrelationships based on hundreds of nuclear protein-coding genes, exploring phylogenetic signal through concatenation as well as recently developed consensus approaches. These analyses robustly support a modern hypothesis of flatworm phylogeny, one which emphasizes the primacy of the often-overlooked ‘microturbellarian’ groups in understanding the major evolutionary transitions within Platyhelminthes: perhaps most notably, we propose a novel scenario for the interrelationships between free-living and vertebrate-parasitic flatworms, providing new opportunities to shed light on the origins and biological consequences of parasitism in these iconic invertebrates.

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Geography and major host evolutionary transitions shape the resource use of plant parasites

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1608381113 ◽

2016 ◽

Vol 113 (35) ◽

pp. 9840-9845 ◽

Cited By ~ 30

Author(s):

Joaquín Calatayud ◽

José Luis Hórreo ◽

Jaime Madrigal-González ◽

Alain Migeon ◽

Miguel Á. Rodríguez ◽

...

Keyword(s):

Resource Use ◽

Phylogenetic Signal ◽

Host Use ◽

Plant Interactions ◽

Evolutionary Transitions ◽

Use Patterns ◽

Parasite Communities ◽

Plant Parasites ◽

Theory Of Island Biogeography ◽

Globally Distributed

The evolution of resource use in herbivores has been conceptualized as an analog of the theory of island biogeography, assuming that plant species are islands separated by phylogenetic distances. Despite its usefulness, this analogy has paradoxically led to neglecting real biogeographical processes in the study of macroevolutionary patterns of herbivore–plant interactions. Here we show that host use is mostly determined by the geographical cooccurrence of hosts and parasites in spider mites (Tetranychidae), a globally distributed group of plant parasites. Strikingly, geography accounts for most of the phylogenetic signal in host use by these parasites. Beyond geography, only evolutionary transitions among major plant lineages (i.e., gymnosperms, commelinids, and eudicots) shape resource use patterns in these herbivores. Still, even these barriers have been repeatedly overcome in evolutionary time, resulting in phylogenetically diverse parasite communities feeding on similar hosts. Therefore, our results imply that patterns of apparent evolutionary conservatism may largely be a byproduct of the geographic cooccurrence of hosts and parasites.

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Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2019.05.022 ◽

2019 ◽

Vol 138 ◽

pp. 219-232 ◽

Cited By ~ 32

Author(s):

Deise J.P. Gonçalves ◽

Beryl B. Simpson ◽

Edgardo M. Ortiz ◽

Gustavo H. Shimizu ◽

Robert K. Jansen

Keyword(s):

Phylogenetic Signal ◽

Gene Trees ◽

Species Trees ◽

Signal Variation

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Compound Dynamics and Combinatorial Patterns of Amino Acid Repeats Encode a System of Evolutionary and Developmental Markers

Genome Biology and Evolution ◽

10.1093/gbe/evz216 ◽

2019 ◽

Vol 11 (11) ◽

pp. 3159-3178

Author(s):

Ilaria Pelassa ◽

Marica Cibelli ◽

Veronica Villeri ◽

Elena Lilliu ◽

Serena Vaglietti ◽

...

Keyword(s):

Amino Acid ◽

Evolutionary History ◽

Evolutionary Dynamics ◽

Phylogenetic Signal ◽

Regulatory System ◽

Evolutionary Transitions ◽

Quantitative Evidence ◽

Amino Acid Repeats ◽

Eukaryotic Proteomes ◽

History Of

Abstract Homopolymeric amino acid repeats (AARs) like polyalanine (polyA) and polyglutamine (polyQ) in some developmental proteins (DPs) regulate certain aspects of organismal morphology and behavior, suggesting an evolutionary role for AARs as developmental “tuning knobs.” It is still unclear, however, whether these are occasional protein-specific phenomena or hints at the existence of a whole AAR-based regulatory system in DPs. Using novel approaches to trace their functional and evolutionary history, we find quantitative evidence supporting a generalized, combinatorial role of AARs in developmental processes with evolutionary implications. We observe nonrandom AAR distributions and combinations in HOX and other DPs, as well as in their interactomes, defining elements of a proteome-wide combinatorial functional code whereby different AARs and their combinations appear preferentially in proteins involved in the development of specific organs/systems. Such functional associations can be either static or display detectable evolutionary dynamics. These findings suggest that progressive changes in AAR occurrence/combination, by altering embryonic development, may have contributed to taxonomic divergence, leaving detectable traces in the evolutionary history of proteomes. Consistent with this hypothesis, we find that the evolutionary trajectories of the 20 AARs in eukaryotic proteomes are highly interrelated and their individual or compound dynamics can sharply mark taxonomic boundaries, or display clock-like trends, carrying overall a strong phylogenetic signal. These findings provide quantitative evidence and an interpretive framework outlining a combinatorial system of AARs whose compound dynamics mark at the same time DP functions and evolutionary transitions.

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