Phylogenetic relationships within an endemic group of Malagasy ‘assassin spiders’ (Araneae, Archaeidae): ancestral character reconstruction, convergent evolution and biogeography

2007 ◽  
Vol 45 (2) ◽  
pp. 612-619 ◽  
Author(s):  
Hannah M. Wood ◽  
Charles E. Griswold ◽  
Greg S. Spicer
Keyword(s):  
Phylogenetic Relationships ◽  
Convergent Evolution ◽  
Character Reconstruction ◽  
Ancestral Character Reconstruction

scholarly journals Coping with the extremes: comparative osteology of the tepui-associated toad Oreophrynella and its bearing on the evolution of osteological novelties in the genus

2020 ◽  
Vol 190 (1) ◽  
pp. 114-139
Author(s):  
Philippe J R Kok ◽  
Milan A J van der Velden ◽  
D Bruce Means ◽  
Sebastian Ratz ◽  
Iván Josipovic ◽  
...  
Keyword(s):  
Body Weight ◽  
High Resolution ◽  
Vertebral Column ◽  
Relative Length ◽  
Single Species ◽  
Microcomputed Tomography ◽  
X Ray ◽  
Character Reconstruction ◽  
Ancestral Character Reconstruction ◽  
Comparative Osteology

Abstract The only study of the osteology of the toad genus Oreophrynella dates back to 1971 and was based on a single species. Here, we use high-resolution X-ray microcomputed tomography to analyse the osteology of all nine described Oreophrynella species, which are compared with representatives of other bufonid lineages. Oreophrynella is unique among bufonids in having opposable digits. Osteological synapomorphies confirmed for the genus are as follows: presence of parietal fontanelles and exposed frontoparietal fontanelle, absence of quadratojugal, five presacral vertebrae, distally enlarged terminal phalanges and urostyle greatly expanded into flanges. Ancestral character reconstruction indicates that arboreal habits in some Oreophrynella species are likely to have evolved after the evolution of opposable digits. Opposable digits, in combination with an extension of the interdigital integument and the relative length/orientation of the digits, are likely to be adaptations to facilitate life on rocky tepui summits and an exaptation to arboreality. Cranial simplification in Oreophrynella, in the form of cranial fontanelles and absence of the quadratojugal, is possibly driven by a reduction of developmental costs, increase in flexibility and reduction of body weight. Cranial simplification combined with the shortening of the vertebral column and the shift towards a partly firmisternal girdle might be adaptations to the peculiar tumbling behaviour displayed by Oreophrynella.

Towards uncovering evolution of lineage-specific calcium oxalate crystal patterns in Piperales

Botany ◽  
2015 ◽  
Vol 93 (3) ◽  
pp. 159-169 ◽  
Author(s):  
Harry T. Horner ◽  
Marie-Stéphanie Samain ◽  
Sarah T. Wagner ◽  
Stefan Wanke
Keyword(s):  
Calcium Oxalate ◽  
Recent Common Ancestor ◽  
Calcium Oxalate Crystal ◽  
Character Reconstruction ◽  
Most Recent Common Ancestor ◽  
Molecular Phylogenetic ◽  
Crystal Type ◽  
Phylogenetic Hypotheses ◽  
Crystal Sand ◽  
Ancestral Character Reconstruction

Piperales is among the largest and most diverse angiosperm orders (>4000 species), occurring broadly in tropical and temperate habitats. Twenty-four of the species from 12 genera, representing all lineages of Piperales, except the holoparasitic Hydnoraceae, display a mixture of leaf calcium oxalate crystal types found in previous studies of the two genera of Piperaceae subfamily Piperoideae (Peperomia Ruiz & Pav. and Piper L.). Crystal macropatterns, a result of varying leaf anatomies and diverse habitats, are investigated in a comparative way by using clearings and recent molecular phylogenetic hypotheses to trace crystal types and macropattern evolution. Ancestral character reconstruction reveals that the most recent common ancestor of Piperales had either crystal sand or druses or both and that prisms, raphides, and styloids are derived from the ancestral crystal type(s). These results are also recovered for both the ancestors of the perianth-less and the perianth-bearing Piperales. Raphides or druses are found in the two other subfamilies of Piperaceae (Verhuellioideae and Zippelioideae). Asaraceae and Lactoridaceae display crystal sand, whereas Aristolochia L. (Aristolochiaceae) species display mainly druses. Our crystal investigation, combined with ancestral character reconstruction, suggests that styloids, raphides, and prisms are derived within Piperales from crystal sand or druses.

scholarly journals The phylogenetic relationships of neosuchian crocodiles and their implications for the convergent evolution of the longirostrine condition

2019 ◽  
Author(s):  
Sebastian S Groh ◽  
Paul Upchurch ◽  
Paul M Barrett ◽  
Julia J Day
Keyword(s):  
Bayesian Methods ◽  
Phylogenetic Relationships ◽  
Convergent Evolution ◽  
Morphological Characters ◽  
Late Triassic ◽  
Continuous Data ◽  
Comprehensive Review ◽  
Phylogenetic Studies ◽  
History Of ◽  
First Time

Abstract Since their origin in the Late Triassic, crocodylomorphs have had a long history of evolutionary change. Numerous studies examined their phylogeny, but none have attempted to unify their morphological characters into a single, combined dataset. Following a comprehensive review of published character sets, we present a new dataset for the crocodylomorph clade Neosuchia consisting of 569 morphological characters for 112 taxa. For the first time in crocodylian phylogenetic studies, quantitative variation was treated as continuous data (82 characters). To provide the best estimate of neosuchian relationships, and to investigate the origins of longirostry, these data were analysed using a variety of approaches. Our results show that equally weighted parsimony and Bayesian methods cluster unrelated longirostrine forms together, producing a topology that conflicts strongly with their stratigraphic distributions. By contrast, applying extended implied weighting improves stratigraphic congruence and removes longirostrine clustering. The resulting topologies resolve the major neosuchian clades, confirming several recent hypotheses regarding the phylogenetic placements of particular species (e.g. Baryphracta deponiae as a member of Diplocynodontinae) and groups (e.g. Tethysuchia as non-eusuchian neosuchians). The longirostrine condition arose at least three times independently by modification of the maxilla and premaxilla, accompanied by skull roof changes unique to each longirostrine clade.

scholarly journals Convergent evolution of ‘creepers’ in the Hawaiian honeycreeper radiation

2008 ◽  
Vol 5 (2) ◽  
pp. 221-224 ◽  
Author(s):  
Dawn M Reding ◽  
Jeffrey T Foster ◽  
Helen F James ◽  
H. Douglas Pratt ◽  
Robert C Fleischer
Keyword(s):  
Natural Selection ◽  
Adaptive Radiation ◽  
Phylogenetic Relationships ◽  
Convergent Evolution ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Evolutionary Patterns ◽  
Dna Sequence Data ◽  
Hawaiian Honeycreepers ◽  
Mtdna Introgression

Natural selection plays a fundamental role in the ecological theory of adaptive radiation. A prediction of this theory is the convergent evolution of traits in lineages experiencing similar environments. The Hawaiian honeycreepers are a spectacular example of adaptive radiation and may demonstrate convergence, but uncertainty about phylogenetic relationships within the group has made it difficult to assess such evolutionary patterns. We examine the phylogenetic relationships of the Hawaii creeper ( Oreomystis mana ), a bird that in a suite of morphological, ecological and behavioural traits closely resembles the Kauai creeper ( Oreomystis bairdi ), but whose mitochondrial DNA (mtDNA) and osteology suggest a relationship with the amakihis ( Hemignathus in part) and akepas ( Loxops ). We analysed nuclear DNA sequence data from 11 relevant honeycreeper taxa and one outgroup to test whether the character contradiction results from historical hybridization and mtDNA introgression, or convergent evolution. We found no evidence of past hybridization, a phenomenon that remains undocumented in Hawaiian honeycreepers, and confirmed mtDNA and osteological evidence that the Hawaii creeper is most closely related to the amakihis and akepas. Thus, the morphological, ecological and behavioural similarities between the evolutionarily distant Hawaii and Kauai creepers represent an extreme example of convergent evolution and demonstrate how natural selection can lead to repeatable evolutionary outcomes.

scholarly journals An Extraordinary Rosette and Resurrection New Spikemoss, Selaginella iridescens (Selaginellaceae) from Hainan Island, China

Taxonomy ◽  
2021 ◽  
Vol 1 (4) ◽  
pp. 302-312
Author(s):  
Jie Yang ◽  
Meng-Hua Zhang ◽  
Ya-Rong Wang ◽  
Lang-Xing Yuan ◽  
Xian-Chun Zhang
Keyword(s):  
New Species ◽  
Hainan Island ◽  
Main Stem ◽  
Molecular Evidence ◽  
Character Reconstruction ◽  
Ancestral Character Reconstruction ◽  
A New Species

Selaginella iridescens (Selaginellaceae), a new species of spikemoss from Hainan Island, China, is described based on morphological and molecular evidence. The new species morphologically resembles S. pseudotamariscina from Vietnam which was recently recognized and segregated from S. tamariscina and S. pulvinata. Some characters of S. iridescens, including the iridescent leaves and long arista (0.35–1.20 mm long), the widely membranaceous margin of axillary leaves (ca. 2/3), dorsal leaves sulcate extending to the top, and slender main stem, dorsoventrally prostrate, distinguish it from S. pseudotamariscina. Phylogenetic results based on rbcL of 28 Selaginella species indicate that S. iridescens is sister to S. pseudotamariscina, and distant from the S. tamariscina-S.pulvinata clade. The ancestral character reconstruction result reveals that the rosette is apomorphic and has evolved independently at least six times in Selaginella.

Phylogenetic relationships within the genus Hypnea (Cystocloniaceae, Rhodophyta): convergent evolution and its implications in the infrageneric classification

2019 ◽  
Vol 62 (6) ◽  
pp. 563-575 ◽  
Author(s):  
Priscila Barreto de Jesus ◽  
Fabio Nauer ◽  
Goia de Mattos Lyra ◽  
Valter Loureiro de Araújo ◽  
Igor Araújo Santos de Carvalho ◽  
...  
Keyword(s):  
South America ◽  
Genetic Markers ◽  
Phylogenetic Relationships ◽  
Convergent Evolution ◽  
Taxonomic Status ◽  
Morphological Data ◽  
Infrageneric Classification ◽  
Taxonomic History ◽  
Commercial Source ◽  
Morphological Differences

Abstract Hypnea is a monophyletic genus with a complex nomenclatural and taxonomic history, and is an important commercial source of carrageenan. Phylogenies of this genus have been accessed based primarily on Asian species; however, recent studies performed in South America revealed a great diversity of species, for which phylogenetic relationships need to be evaluated. Three infrageneric sections are recognized in the genus: Pulvinatae, Spinuligerae, and Virgatae; however, morphological and molecular circumscriptions within each section lack clarity. In this study, we analyzed three distinct markers to establish phylogenetic relationships among Hypnea species. To assign each species to the correct section, morphological data were obtained from original descriptions, reference literature, and comparisons with type/topotype and herbaria specimens. Our analyses recovered robust phylogenies for the genus and provided new insights on the taxonomic status and relationships among and within Hypnea species. The combination of three genetic markers increased the resolution and support, resulting in the largest and best-resolved phylogeny of the genus to date. Single and combined analyses revealed that the three sections of the genus Hypnea are taxonomically irrelevant, as currently recognized. Morphological differences are not associated with monophyletic groups and similarities among clades could be better explained by convergent evolution in thallus habit.

scholarly journals Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Mark S Hibbins ◽  
Matthew JS Gibson ◽  
Matthew W Hahn
Keyword(s):  
Theoretical Consideration ◽  
Phylogenetic Relationships ◽  
Convergent Evolution ◽  
Incomplete Lineage Sorting ◽  
Large Datasets ◽  
Comparative Methods ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Statistical Inferences ◽  
Biological Sources

The incongruence of character states with phylogenetic relationships is often interpreted as evidence of convergent evolution. However, trait evolution along discordant gene trees can also generate these incongruences – a phenomenon known as hemiplasy. Classic comparative methods do not account for discordance, resulting in incorrect inferences about the number, timing, and direction of trait transitions. Biological sources of discordance include incomplete lineage sorting (ILS) and introgression, but only ILS has received theoretical consideration in the context of hemiplasy. Here, we present a model that shows introgression makes hemiplasy more likely, such that methods that account for ILS alone will be conservative. We also present a method and software (HeIST) for making statistical inferences about the probability of hemiplasy and homoplasy in large datasets that contain both ILS and introgression. We apply our methods to two empirical datasets, finding that hemiplasy is likely to contribute to the observed trait incongruences in both.

scholarly journals Assessing bivalve phylogeny using Deep Learning and Computer Vision approaches

2021 ◽  
Author(s):  
Steffen Kiel
Keyword(s):  
Computer Vision ◽  
Deep Learning ◽  
Phylogenetic Relationships ◽  
Convergent Evolution ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Morphological Data ◽  
Future Directions ◽  
Classification Tasks

ABSTRACTPhylogenetic analyses using morphological data currently require hand-crafted character matrices, limiting the number of taxa that can be included. Here I explore how Deep Learning and Computer Vision approaches typically applied to image classification tasks, may be used to infer phylogenetic relationships among bivalves. A convolutional neural network (CNN) was trained on thousands of images showing species of 75 bivalve families. The predictions of the CNN on a large number of bivalve images are then interpreted as an indication of how similar these bivalves are to each other, are averaged by the families to which the species belonged, and visualized in a cluster diagram. In this cluster diagram, significantly more families clustered with members of their subclasses than expected by chance, confirming the feasibility of the approach. To address the issue of convergent evolution, two further CNNs were trained, on the same images but grouped by the orders and subclasses to which the species belonged. Combining predictions for the same images but on different taxonomic levels improved the inferred phylogenetic relationships also of families that the CNNs had not been trained on. Finally, this combined tree is merged with five published phylogenetic trees into a supertree, representing the largest single phylogeny of the Bivalvia to date, encompassing 128 families, including six exclusively fossil families and nine extant families for which presently no molecular data are available. Issues inherent to the approach and suggestions for future directions are discussed.

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