Cladistics最新文献

Halting biodiversity decline is one of the most critical challenges for humanity, but monitoring biodiversity is hampered by taxonomic impediments. One impediment is the large number of undescribed species (here called “dark taxon impediment”) whereas another is caused by the large number of superficial species descriptions, that can only be resolved by consulting type specimens (“superficial description impediment”). Recently, Sharkey et al. (2021) proposed to address the dark taxon impediment for Costa Rican braconid wasps by describing 403 species based on COI barcode clusters (“BINs”) computed by BOLD Systems. More than 99% of the BINs (387 of 390) were converted into species by assigning binominal names (e.g. BIN “BOLD:ACM9419” becomes Bracon federicomatarritai) and adding a minimal diagnosis (consisting only of a consensus barcode for most species). We here show that many of Sharkey et al.’s species are unstable when the underlying data are analyzed using different species delimitation algorithms. Add the insufficiently informative diagnoses, and many of these species will become the next “superficial description impediment” for braconid taxonomy because they will have to be tested and redescribed after obtaining sufficient evidence for confidently delimiting species. We furthermore show that Sharkey et al.’s approach of using consensus barcodes as diagnoses is not functional because it cannot be applied consistently. Lastly, we reiterate that COI alone is not suitable for delimiting and describing species, and voice concerns over Sharkey et al.’s uncritical use of BINs because they are calculated by a proprietary algorithm (RESL) that uses a mixture of public and private data. We urge authors, reviewers and editors to maintain high standards in taxonomy by only publishing new species that are rigorously delimited with open-access tools and supported by publicly available evidence.

The genus Thuridilla Bergh, 1872 comprises mostly tropical sap-sucking sea slugs species with flamboyantly coloured forms. However, the potential for cryptic or pseudocryptic species masked by convergent or polymorphic colour patterns has not been tested using molecular characters. In this study, we sampled 20 of the 23 recognized worldwide species and performed the most comprehensive molecular phylogenetic analysis of the genus to date using a multi-locus approach combining two mitochondrial (cytochrome c oxidase subunit I, 16S rRNA) and two nuclear (Histone H3, 28S rRNA) genes using maximum likelihood, maximum-parsimony and Bayesian criteria. Three molecular species delimitation methods (ABGD, GMYC, bPTP) and the morphology of radular teeth were additionally used to aid in species delimitation. Our analyses supported 35 species within Thuridilla, of which more than one-third (13) are part of a single radiation here named the Thuridilla gracilis (Risbec, 1928) species-complex. This complex includes T. gracilis, T. splendens (Baba, 1949), T. bayeri (Er. Marcus, 1965), and T. ratna (Er. Marcus, 1965), plus nine additional undescribed species. All 13 species are distinguishable by radular characters, external morphology and their DNA. The detection of this radiation led diversity of Thuridilla to be underestimated by about 25% and provides a new comparative system for studying the role of colour patterns in marine diversification.

The systematics of Megalopodidae is not adequately known, in spite of it being a relatively small group of phytophagous beetles. The first phylogenetic analysis of Megalopodidae with a comprehensive generic representation (25 genera of 30 described, 10 subgenera and 77 species) is undertaken. A parsimony analysis under equal and implied weights was carried out based on 147 adult and larval morphological characters. Subfamilies Palophaginae and Zeugophorinae were recovered as monophyletic, by contrast with Megalopodinae, which proved to be paraphyletic. Atelederinae are proposed as a new subfamily. Also, three tribes and three subtribes within Megalopodinae are proposed: Leucasteini trib.n., Sphondyliini trib.n. and Megalopodini, the latter including Macrolophina subtrib.n., Temnaspidina subtrib.n. and Megalopodina. The genera Macrolopha, Kuilua, Poecilomorpha, Temnaspis, Antonaria, Agathomerus, Megalopus and Bothromegalopus were recovered as non-monophyletic. New delimitations of the polyphyletic genera Poecilomorpha and Macrolopha are proposed, Clythraxeloma is resurrected, and the subgenera of Agathomerus are suppressed. The following new combinations are proposed: Kuilua apicata (Fairmaire), K. nyassae (Jacoby), Poecilomorpha cribricollis (Pic), P. minuta (Pic), Clythraxeloma assamensis (Jacoby), C. bipartita (Lacordaeri), C. discolineata (Pic), C. downesii (Baly), C. gerstaeckeri (Westwood), C. laosensis (Pic), C. maculata (Pic), C. mouhoti (Baly), C. nigrocyanea (Motschulsky), C. pretiosa (Reineck), Temnaspis tricoloripes (Pic) and Barticaria faciatus (Dalman). Clythraxeloma cyanipennis Kraatz is a restored combination. Distribution patterns of Megalopodidae largely conform to the breakup of Gondwanaland, with its main clades having particular distributions: Andean-Australian (Palophaginae), Ethiopian (Leucasteini, Sphondyliini, and Macrolophina), Neotropical (Ateledrinae and Megalopodina) and Ethiopian-Oriental-Palaearctic (Temnaspidina the result of a secondary expansion. Zeugophorinae present a worldwide distribution, except for the Neotropical and Andean regions, which may be the result of geodispersal. The findings of the present study also shed light on groups with taxonomic issues, where phylogenetic analyses are strongly needed.

Calaphidinae is the second-largest subfamily in the family Aphididae. Despite their species diversity and some taxonomic controversy, no phylogenetic studies have been conducted on them thus far. Herein, we report the first molecular phylogeny of Calaphidinae and two related lineages, Phyllaphidinae and Saltusaphidinae, based on five genes (3418 bp) for 126 taxa. Maximum parsimony, maximum-likelihood and Bayesian inference phylogenetic analyses were performed on the multilocus dataset. Divergence time estimation, biogeographical reconstruction, ancestral host plant reconstruction and PhyloType analyses were performed to identify evolutionary trends in Calaphidinae. Our phylogenetic results lead to several conclusions: Phyllaphidinae is a sister group to Calaphidinae s.l.; Calaphidinae is paraphyletic with respect to the former “Saltusaphidinae”; the ingroup clade was subdivided into nine newly recognized lineages; and three subtribes of Calaphidinae (Monaphidina, Calaphdina and Panaphidina) and many genera were not recovered as monophyletic. A new classification is proposed with eight tribal divisions that reflect our phylogenetic results, including three new tribes (Pterocallidini trib.n., Pseudochromaphidini trib.n. and Shivaphidini trib.n.) and three new statuses (Saltusaphidini stat.n., Therioaphidini stat.n. and Myzocallidini stat.n.). The ancestral reconstruction results imply that the ingroup taxa’s common ancestor originated in the Eastern Palaearctic and might have fed on Fagaceae in the Late Cretaceous. Later, multiple host shifts and an expanding geographical distribution led to the current species diversity of Calaphidinae. Our reconstructions suggest that species diversification cannot solely be explained by speciation via host shifts and that geographical isolation probably also played a key role. Our results provide new insight into the natural classification and history of the host plant associations and biogeography of Calaphidinae s.l.

Pollen, the microgametophyte of seed plants, has an important role in plant reproduction and, therefore, evolution. Pollen is variable in, for example, size, shape, aperture number; these features are particularly diverse in some plant taxa and can be diagnostic. In one family, Boraginaceae, the range of pollen diversity suggests the potential utility of this family as a model for integrative studies of pollen development, evolution and molecular biology. In the present study, a comprehensive survey of the diversity and evolution of pollen from 538 species belonging to 72 genera was made using data from the literature and additional scanning electron microscopy examination. Shifts in diversification rates and the evolution of various quantitative characters were detected, and the results revealed remarkable differences in size, shape and number of apertures. The pollen of one subfamily, Boraginoideae, is larger than that in Cynoglossoideae. The diversity of pollen shapes and aperture numbers in one tribe, Lithospermeae, is greater than that in the other tribes. Ancestral pollen for the family was resolved as small, prolate grains that bear three apertures and are iso-aperturate. Of all the tribes, the greatest number of changes in pollen size and aperture number were observed in Lithospermeae and Boragineae, and the number of apertures was found to be stable throughout all tribes of Cynoglossoideae. In addition, the present study showed that diversification of Boraginaceae cannot be assigned to a single factor, such as pollen size, and the increased rate of diversification for species-rich groups (e.g. Cynoglossum) is not correlated with pollen size or shape evolution. The palynological data and patterns of character evolution presented in the study provide better resolution of the roles of geographical and ecological factors in the diversity and evolution of pollen grains of Boraginaceae, and provide suggestions for future palynological research across the family.

Baripus is a ground beetle genus endemic to southern South America, currently distributed across grassland and shrub habitats in mountain and lowland regions. The species of this genus are known to have been affected by the Andean orogeny and the climate changes that occurred during this process. In this study, we seek to understand how the orogeny of the Andes may have led to changes in the climatic niches of the species of Baripus over time. We integrated former ecological and historical biogeographic hypotheses, exploring the use of parsimony optimization of phylogenetically structured climate variables and ancestral character state reconstruction methods. We then performed regression analyses of the optimized climatic niche variables within the phylogenetic tree of Baripus. We were able to infer significant climatic niche constraints, and niche changes that provide new insights to the existing knowledge, supporting former ecological and biogeographic hypotheses for this genus. Such trends in climatic niche could be explained by the rain shadow effect caused by the Andean uplift as well as with other climate shifts associated with temperature and precipitation swings that occurred in this region from the Middle Miocene to the Pliocene.

Phylogenetic graph structures used in empirical and theoretical analysis have expanded beyond trees to more general directed acyclic graphs including networks and forests. Several methods to reconcile multiple such graphs are presented and discussed here, extending existing consensus and supertree techniques to form a set of phylogenetic supergraph methods. These graphs can be used as the summary of analytical results, or as heuristic initial graphs for further phylogenetic analysis.

A new troodontid (LH PV39) recovered from the Upper Cretaceous Wulansuhai Formation, Inner Mongolia, China, is described, highlighting the dorsoventrally compressed sacral centra. The completely fused neurocentral junctions indicate that LH PV39 had reached adulthood at the time of death, but its size is nevertheless 20% smaller than that of the sympatric Philovenator, demonstrating that it is the second small-bodied troodontid recovered from the Wulansuhai Formation. Phylogenetic analyses scoring LH PV39 using different strategies and performed with different algorithms unambiguously recovered it as a troodontid. While the parsimony-based analysis scoring LH PV39 as an independent OTU with all of its available characteristics included recovered it as a basal troodontid, the Bayesian analysis suggests a closer relationship of LH PV39 to Almas and an unnamed troodontid from Ukhaa Tolgod, Mongolia (MPC-D100/1126+D100/3500). Body size analysis confirmed a single trend of gigantism throughout the evolution of troodontids, and suggests that the Late Cretaceous troodontids evolved in two directions: (i) several size-independent characteristics evolved while retaining the small sizes that are typical of the Early Cretaceous relatives, resulting in the Late Cretaceous small-bodied troodontids; and (ii) size-dependent characteristics (e.g., the elongation of the rostrum) evolved accompanying the size increase, resulting in large-bodied derived troodontids. The mosaic features of the Late Cretaceous small-bodied troodontids place them intermediate between their Early Cretaceous basal relatives and the Late Cretaceous large-bodied taxa in a well-resolved phylogeny, which is crucial for understanding the size and morphological evolution of troodontids.