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... The problem of ‘rogue taxa’ explored by Buenaventura et al. (2017, Cladistics 33: 109–133) is due to complementary patterns of missing data in their matrix, which are evident from perusal of their supplementary table S1. ...
... Mammalian taxonomy based on the diagnosability version of the Phylogenetic Species Concept has recently been declared the only sound approach to mammalian classification. In this article, based on the underlying evolutionary ontology of species taxa, I explain the fallacy of these arguments and hold that in a ‘grey area’ after lineage sundering, completely objective species delimitation is impossi ...
Laing, Adam M.; Doyle, Sharon; Gold, Maria Eugenia Leone; Nesbitt, Sterling J.; O'Leary, Maureen A.; Turner, Alan H.; Wilberg, Eric W.; Poole, Karen E.
... Simões et al. () argued that large matrices are linked to the construction of “problematic” characters, and that those characters negatively affect tree topology. In their re‐evaluation of two squamate datasets, however, Simões et al. () simply eliminated what they termed “problematic” characters, rather than recode them. This practice ignores potential sources of phylogenetic information and, if ...
... Niche differences are key to understanding the distribution and structure of biodiversity. To examine niche differences, we must first characterize how species occupy niche space, and two approaches are commonly used in the ecological literature. The first uses species traits to estimate multivariate trait space (so‐called functional trait diversity, FD); the second quantifies the amount of time o ...
... Genus Bonomyces is here reviewed. Multigene phylogenetic analysis suggests it is related with Cleistocybe in the Tricholomatineae. Morphological and genetical studies led to a new interpretation of the type species, B. sinopicus (=C. subsinopica), and the new combinations B. afrosinopicus and B. arnoldii. ...
... This paper discusses the problem of whether creating a matrix with all the character state combinations that have a fixed number of steps (or extra steps) on a given tree T, produces the same tree T when analyzed with maximum parsimony or maximum likelihood. Exhaustive enumeration of cases up to 20 taxa for binary characters, and up to 12 taxa for 4-state characters, shows that the same tree is re ...
... Fungi are prolific producers of natural products routinely screened for biotechnological applications, and those living endophytically within plants attract particular attention because of their purported chemical diversity. However, the harnessing of their biosynthetic potential is hampered by a large and often cryptic phylogenetic and ecological diversity, coupled with a lack of large‐scale natu ...
... The protracted speciation model presents a realistic and parsimonious explanation for the observed slowdown in lineage accumulation through time, by accounting for the fact that speciation takes time. A method to compute the likelihood for this model given a phylogeny is available and allows estimation of its parameters (rate of initiation of speciation, rate of completion of speciation and extinc ...
... A recent proposal that the genus Rymovirus be assimilated into the genus Potyvirus is examined, discussed, and rejected. It illustrates the danger of using ‘sequence identity’ as a proxy for phylogenetic relatedness to distinguish closely related but distinct groups of viruses. ...
phylogeny, etc ; Bayesian theory; Taeniidae; genes; mitochondria; mitochondrial genome; nucleotide sequences; Show all 7 Subjects
Abstract:
... The taxonomic concept for the family Paruterinidae is controversial, especially concerning the position of the genus Cladotaenia, since the latter genus has been placed sometimes in other families, i.e. in the Taeniidae or in the distinct family Cladotaeniidae; finding a solution based on morphological data is difficult and molecular data on paruterinids and related groups are scarce. In this stud ...
phylogeny, etc ; cluster analysis; ecosystem services; ecosystems; environmental indicators; trees; Japan; Show all 7 Subjects
Abstract:
... Phylogenetic diversity is expected to be an important predictor of ecosystem multifunctionality because distant relatives are often more functionally different than close relatives. However, the general extent of non-random linkages between phylogeny and ecosystem services remains unclear. In this study, we examined phylogenetic clustering and associations of beneficial attributes of tree species ...
phylogeny, etc ; Pycnogonida; arthropods; ecology; languages; Show all 5 Subjects
Abstract:
... Sea spiders (Pycnogonida) are a widespread and phylogenetically important group of marine arthropods. However, their biology remains understudied, and detailed information about their feeding ecology is difficult to find. Observations on pycnogonid feeding are scattered in the literature, often in older sources written in various languages, and have never been comprehensively summarized. Here we p ...
... Phylogenetic imputation has recently emerged as a potentially powerful tool for predicting missing data in functional traits datasets. As such, understanding the limitations of phylogenetic modelling in predicting trait values is critical if we are to use them in subsequent analyses. Previous studies have focused on the relationship between phylogenetic signal and clade‐level prediction accuracy, ...
phylogeny, etc ; autocorrelation; data collection; models; Show all 4 Subjects
Abstract:
... Eigenvector mapping techniques are widely used by ecologists and evolutionary biologists to describe and control for spatial and/or phylogenetic patterns in their data. The selection of an appropriate subset of eigenvectors is a critical step (misspecification can lead to highly biased results and interpretations), and there is no consensus yet on how to proceed. We conducted a ten‐year review of ...
phylogeny, etc ; Thalasseus; hybridization; water birds; Show all 4 Subjects
Abstract:
... We collected multi‐locus data to test whether hybridization has occurred between a critically endangered waterbird, the Chinese Crested Tern Thalasseus bernsteini, and the Greater Crested Tern Thalasseus bergii. Phylogenetic analysis shows these two tern species are sister species, having diverged < 1 million years ago. Our findings suggest a grave threat to the survival of the Chinese Crested Ter ...
... Continental islands are often dynamic in regard to the origin and evolution of their biota. Although colonizations from mainland Southeast Asia to Hainan Island have been reported, the role of Hainan Island as a source for continental biota has not been considered. Goniurosaurus is a genus comprised of nocturnal ground geckos. We reexamined the evolutionary history of Goniurosaurus using both mole ...
... The claim that parsimony can be statistically inconsistent remains the chief criticism of the cladistic approach, and also the main justification for alternative model‐based approaches such as maximum likelihood and Bayesian inference. Despite its refutation in the 1980s, this persistent myth of parsimony's Achilles’ heel is entrenched in the primary literature, and has metastasized into textbooks ...
... This paper provides a linear sequence of four subfamilies, 15 tribes and 106 genera of the magnoliid family Annonaceae, based on state-of-the-art and stable phylogenetic relationships. The linear sequence facilitates the organisation of Annonaceae herbarium specimens. ...
phylogeny, etc ; Dunaliella; asexual reproduction; chloroplasts; Show all 4 Subjects
Abstract:
... This study revisited the naked green flagellate strain ‘Nepal’, formerly identified as Dunaliella lateralis Pascher & Jahoda. This strain was concordant with the original description of motile cells, but different in features of the chloroplast morphology, eyespot position and asexual reproduction. Belonging to Oogamochlamydinia, this strain was distinguished from the walled species and another na ...