Phylogenetic framework and the assignment of fossils to extant groups

The material presented in the chapters of Carnivorous Plants: Physiology, Ecology, and Evolution together provide a suite of common themes that could provide a framework for increasing progress in understanding carnivorous plants. All speciose genera would benefit from more robust, intra-generic classifications in a phylogenetic framework that uses a unified species concept. As more genomic, proteomic, and transcriptomic data accrue, new insights will emerge regarding trap biochemistry and regulation; interactions with commensals; and the importance of intraspecific variability on which natural selection works. Continued elaboration of field experiments will provide new insights into basic physiology; population biology; plant-animal and plant-microbe relationships; and evolutionary dynamics, all of which will aid conservation efforts and contribute to discussions of assisted migration as the climate continues to change.

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A Bayesian phylogenetic approach to estimating the stability of linguistic features and the genetic biasing of tone

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2010.1595 ◽

2010 ◽

Vol 278 (1704) ◽

pp. 474-479 ◽

Cited By ~ 26

Author(s):

Dan Dediu

Keyword(s):

Cultural Transmission ◽

Linguistic Diversity ◽

Large Set ◽

Linguistic Features ◽

Major Interest ◽

Software Implementations ◽

Phylogenetic Framework ◽

Linguistic Tone ◽

The Stability ◽

Stable Characteristic

Language is a hallmark of our species and understanding linguistic diversity is an area of major interest. Genetic factors influencing the cultural transmission of language provide a powerful and elegant explanation for aspects of the present day linguistic diversity and a window into the emergence and evolution of language. In particular, it has recently been proposed that linguistic tone —the usage of voice pitch to convey lexical and grammatical meaning—is biased by two genes involved in brain growth and development, ASPM and Microcephalin . This hypothesis predicts that tone is a stable characteristic of language because of its ‘genetic anchoring’. The present paper tests this prediction using a Bayesian phylogenetic framework applied to a large set of linguistic features and language families, using multiple software implementations, data codings, stability estimations, linguistic classifications and outgroup choices. The results of these different methods and datasets show a large agreement, suggesting that this approach produces reliable estimates of the stability of linguistic data. Moreover, linguistic tone is found to be stable across methods and datasets, providing suggestive support for the hypothesis of genetic influences on its distribution.

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Towards a phylogenetic framework for the evolution of shakes, rattles, and rolls in Myiarchus tyrant-flycatchers (Aves: Passeriformes: Tyrannidae)

Molecular Phylogenetics and Evolution ◽

10.1016/s1055-7903(03)00259-8 ◽

2004 ◽

Vol 31 (1) ◽

pp. 139-152 ◽

Cited By ~ 29

Author(s):

Leo Joseph ◽

Thomas Wilke ◽

Eldredge Bermingham ◽

Deryn Alpers ◽

Robert Ricklefs

Keyword(s):

Phylogenetic Framework ◽

Tyrant Flycatchers

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DNA barcodes provide evidence for the independent origin of the cultivated silkworms Samia ricini and Samia cynthia

Journal of Insects as Food and Feed ◽

10.3920/jiff2021.0077 ◽

2021 ◽

pp. 1-8

Author(s):

J.-C. Huang ◽

X.-Y. Li ◽

Y.-P. Li ◽

R.-S. Zhang ◽

D.-B. Chen ◽

...

Keyword(s):

Genetic Distance ◽

Phylogenetic Relationship ◽

Dna Barcode ◽

Distinct Species ◽

Coi Gene ◽

Molecular Evidence ◽

Dna Barcodes ◽

Close Relationship ◽

Molecular Phylogenetic ◽

Phylogenetic Framework

Samia ricini (Wm. Jones) and Samia cynthia (Drury) (Lepidoptera: Saturniidae) have been used as traditional sources of food as well as silk-producing insects. However, the phylogenetic relationship between the two silkworms remains to be addressed. In this study, the mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences corresponding to DNA barcodes from 13 Samia species were analysed, and a DNA barcode-based phylogenetic framework for these Samia species was provided. Phylogenetic analysis showed that multiple individuals of a species could be clustered together. Our analysis revealed a close relationship among Samia yayukae Paukstadt, Peigler and Paukstadt, Samia abrerai Naumann and Peigler, Samia kohlli Naumann and Peigler, Samia naessigi Naumann and Peigler, Samia naumanni Paukstadt, Peigler and Paukstadt, and Samia kalimantanensis Paukstadt and Paukstadt. The mixed clustering relationship and low Kimura-2-parameter (K2P) genetic distance (0.006) between individuals of S. ricini and Samia canningi (Hutton) indicated that the cultivated silkworm S. ricini was derived from the non-cultivated silkworm S. canningi. The remote phylogenetic relationship and high K2P genetic distance (0.039) indicated that S. ricini and S. cynthia are distinct species, thus providing solid molecular evidence that they had entirely independent origins. The relationships between S. kalimantanensis and S. naumanni and between S. cynthia and Samia wangi Naumann and Peigler, as well as the potential cryptic species within S. abrerai were also discussed. This is the first study to assess the DNA barcodes of the genus Samia, which supplements the knowledge of species identification and provides the first molecular phylogenetic framework for Samia species.

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Molecular Systematics of Tribe Physarieae (Brassicaceae) Based on Nuclear ITS, LUMINIDEPENDENS, and Chloroplast ndhF

Systematic Botany ◽

10.1600/036364421x16312067913318 ◽

2021 ◽

Author(s):

Sara Fuentes-Soriano ◽

Elizabeth A. Kellogg

Keyword(s):

Sequence Data ◽

Plastid Dna ◽

Sister Relationship ◽

Data Set ◽

Woody Perennial ◽

History Of ◽

Nuclear Its ◽

Phylogenetic Framework ◽

Phylogenetic Hypotheses ◽

Relationship Of

Physarieae is a small tribe of herbaceous annual and woody perennial mustards that are mostly endemic to North America, with its members including a large amount of variation in floral, fruit, and chromosomal variation. Building on a previous study of Physarieae based on morphology and ndhF plastid DNA, we reconstructed the evolutionary history of the tribe using new sequence data from two nuclear markers, and compared the new topologies against previously published cpDNA-based phylogenetic hypotheses. The novel analyses included ca. 420 new sequences of ITS and LUMINIDEPENDENS (LD) markers for 39 and 47 species, respectively, with sampling accounting for all seven genera of Physarieae, including nomenclatural type species, and 11 outgroup taxa. Maximum parsimony, maximum likelihood, and Bayesian analyses showed that these additional markers were largely consistent with the previous ndhF data that supported the monophyly of Physarieae and resolved two major clades within the tribe, i.e., DDNLS (Dithyrea, Dimorphocarpa, Nerisyrenia, Lyrocarpa, and Synthlipsis)and PP (Paysonia and Physaria). New analyses also increased internal resolution for some closely related species and lineages within both clades. The monophyly of Dithyrea and the sister relationship of Paysonia to Physaria was consistent in all trees, with the sister relationship of Nerisyrenia to Lyrocarpa supported by ndhF and ITS, and the positions of Dimorphocarpa and Synthlipsis shifted within the DDNLS Clade depending on the employed data set. Finally, using the strong, new phylogenetic framework of combined cpDNA + nDNA data, we discussed standing hypotheses of trichome evolution in the tribe suggested by ndhF.

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Comparing phylogenetics and linear morphometrics to solve the generic assignment ofParabolinella?triarthroidesHarrington (Trilobita, Olenidae)

Journal of Paleontology ◽

10.1017/jpa.2017.60 ◽

2017 ◽

Vol 91 (5) ◽

pp. 919-932 ◽

Cited By ~ 1

Author(s):

Daniela S. Monti ◽

Viviana A. Confalonieri

Keyword(s):

Phylogenetic Analysis ◽

Morphological Traits ◽

Good Description ◽

Sister Group ◽

Integrative Approach ◽

Original Matrix ◽

Quantitative Characters ◽

Phylogenetic Framework ◽

Methodological Approaches ◽

Source Of Information

AbstractThe use of different methodological approaches together with an exhaustive qualitative study has helped to recognize important morphological traits to distinguish species in a systematic and phylogenetic framework.Parabolinella triarthroidesHarrington, 1938 was described based on two cranidia from the Quebrada de Coquena, Purmamarca, Jujuy province. The generic assignment ofP. triarthroideshas been questioned by a phylogenetic analysis, which resolves this species as the sister group ofBienvilliaClark, 1924. To explore the generic assignment of this species, a revision of the type material, plus a morphometric analysis including specimens ofParabolinellaBrøgger, 1882 andBienvilliawere performed. In addition, the original matrix used in the published phylogeny was reviewed and enlarged, including more species ofBienvillia. Continuous characters were coded in different ways in order to compare how they could affect the ordering of specimens and their phylogenetic relationships. Finally, both methodologies were compared, especially in regard to the behavior of the quantitative characters included in the analyses. From the combined analyses, it is shown that similarities between the cranidium ofP. triarthroidesand all otherParabolinellaspecies are true homologies instead of a by-product of evolutionary convergence. Therefore,P. triarthroidesshould be considered a member of this genus. Finally, this study demonstrates that the best strategy for solving systematic problems in groups where the morphological variation is the only source of information (i.e., fossil taxa without living representatives) is the implementation of an integrative approach, combining different methodological techniques and a good description of specimens.

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Character evolution of modern fly-speck fungi and implications for interpreting thyriothecial fossils

10.1101/2020.03.13.989582 ◽

2020 ◽

Author(s):

Ludovic Le Renard ◽

André L. Firmino ◽

Olinto L. Pereira ◽

Ruth A. Stockey ◽

Mary. L. Berbee

Keyword(s):

Morphological Evolution ◽

Morphological Characters ◽

Small Subunit ◽

Leaf Surfaces ◽

The Matrix ◽

Character Matrix ◽

Phylogenetic Framework ◽

Single Hypha ◽

Objective Basis ◽

Ancestral Character States

AbstractPREMISE OF THE STUDYFossils show that fly-speck fungi have been reproducing with small, black thyriothecia on leaf surfaces for ∼250 million years. We analyze morphological characters of extant thyriothecial fungi to develop a phylogenetic framework for interpreting fossil taxa.METHODSWe placed 59 extant fly-speck fungi in a phylogeny of 320 Ascomycota using nuclear ribosomal large and small subunit sequences, including newly determined sequences from nine taxa. We reconstructed ancestral character states using BayesTraits and maximum likelihood after coding 11 morphological characters based on original observations and literature. We analyzed the relationships of three previously published Mesozoic fossils using parsimony and our morphological character matrix, constrained by the molecular phylogeny.KEY RESULTSThyriothecia evolved convergently in multiple lineages of superficial, leaf- inhabiting ascomycetes. The radiate and ostiolate scutellum organization is restricted to Dothideomycetes. Scutellum initiation by intercalary septation of a single hypha characterizes Asterinales and Asterotexiales, and initiation by coordinated growth of two or more adjacent hyphae characterizes Aulographaceae (order incertae sedis). Scutella in Microthyriales are initiated apically on a lateral hyphal branch. Patterns of hyphal branching in scutella contribute to distinguishing among orders. Parsimony resolves three fossil taxa as Dothideomycetes; one is further resolved as a member of a Microthyriales-Zeloasperisporiales clade within Dothideomycetes.CONCLUSIONSThis is the most comprehensive systematic study of thyriothecial fungi and their relatives to date. Parsimony analysis of the matrix of character states of modern taxa provides an objective basis for interpreting fossils, leading to insights into morphological evolution and geological ages of Dothideomycetes clades.

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The evolution of body size in termites

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2021.1458 ◽

2021 ◽

Vol 288 (1963) ◽

Author(s):

Nobuaki Mizumoto ◽

Thomas Bourguignon

Keyword(s):

Body Size ◽

Size Reduction ◽

Head Width ◽

Termite Species ◽

Fossil Species ◽

Modern Species ◽

Size Evolution ◽

Phylogenetic Framework ◽

Size Variability ◽

Width Measurements

Termites are social cockroaches. Because non-termite cockroaches are larger than basal termite lineages, which themselves include large termite species, it has been proposed that termites experienced a unidirectional body size reduction since they evolved eusociality. However, the validity of this hypothesis remains untested in a phylogenetic framework. Here, we reconstructed termite body size evolution using head width measurements of 1638 modern and fossil termite species. We found that the unidirectional body size reduction model was only supported by analyses excluding fossil species. Analyses including fossil species suggested that body size diversified along with speciation events and estimated that the size of the common ancestor of modern termites was comparable to that of modern species. Our analyses further revealed that body size variability among species, but not body size reduction, is associated with features attributed to advanced termite societies. Our results suggest that miniaturization took place at the origin of termites, while subsequent complexification of termite societies did not lead to further body size reduction.

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Conflicts in sperm: how do genitalia coevolve with elaborate sperm?

ARPHA Conference Abstracts ◽

10.3897/aca.2.e37158 ◽

2019 ◽

Vol 2 ◽

Author(s):

Antonio Gomez ◽

David Maddison

Keyword(s):

Reproductive Tract ◽

Sequence Data ◽

Ground Beetles ◽

Storage Space ◽

Male And Female ◽

Dna Sequence Data ◽

Sexual Conflicts ◽

Storage Volume ◽

Phylogenetic Framework ◽

Sperm Traits

Some sperm traits are now recognized as ornaments akin to peacock’s tails evolving under cryptic female choice or weapons in sexual conflicts, but there are still few studies addressing patterns and process in sperm-female evolution. We are studying sperm-female evolution in ground beetles of the genus Dyschirius. Male Dyschirius make groups of sperm, termed conjugates, by pairing sperm to non-cellular rods, or spermatostyles. This pairing creates a conflict for storage space in the female’s reproductive tract between sperm and the spermatostyle, which is incapable of fertilizing eggs. We speculate that the conjugates of some Dyschirius that include large spermatostyles with few sperm are ornaments. We hypothesize that increased spermathecal storage volume is positively correlated with larger spermatostyles and that male genitalic complexity is negatively correlated with elaboration of sperm. We gathered morphological trait data on sperm conjugates and male and female genitalia from several species of Dyschirius. We analyzed these data in a phylogenetic framework using a robust Dyschirius species tree derived from DNA sequence data. We present preliminary results from this ongoing study and solicit feedback from the ECM community.

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