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Although previous phylogenetic analyses suggested that the araphid diatom family Plagiogrammaceae is monophyletic, there is still not a clear understanding of relationships among the genera, and the taxonomy of several genera--Dimeregramma and Plagiogramma--remains questionable in light of paraphyly for both genera using molecular and morphological data. We have expanded the available DNA for molecular work for dozens of plagiogrammacean clones and analyzed 29 morphological characters from plagiogrammarian taxa and closely related genera, to increase understanding of the evolutionary history and systematics of the family and re-evaluate the current taxonomical classification of plagiogrammacean genera. The addition of more taxa and more data confirm the results from previous molecular phylogenies: most plagiogrammacean genera are monophyletic, except for Dimeregramma and Plagiogramma. Interestingly, the morphological analysis resolves only Talaroneis and Glyphodesmis as monophyletic. Given these results, we feel there is limited support for retaining Dimeregramma and Plagiogramma as distinct genera, and formally propose amending Plagiogramma and transferring six Dimeregramma species. As the Plagiogrammaceae is also one of the first-diverging clades of pennate diatoms, we also used these molecular data to estimate the age of the family, based on multiple calibration points derived from fossil taxa within or close to the Plagiogrammaceae. The results indicated that the Plagiogrammaceae evolved more than 114 million year ago and its diversification appears to correspond to a time of climate cooling. Additionally, we described a new monotypic genus (Coccinelloidea) with one new species C. gracilis, and five new species within established genera, e.g. Plagiogramma marginalis, Plagiogramma harenae, Plagiogramma porcipellis, Neofragilaria montgomeryii and Psammogramma anacarae., (Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved.)

Background: Conures are a morphologically diverse group of Neotropical parrots classified as members of the tribe Arini, which has recently been subjected to a taxonomic revision. The previously broadly defined Aratinga genus of this tribe has been split into the 'true' Aratinga and three additional genera, Eupsittula, Psittacara and Thectocercus. Popular markers used in the reconstruction of the parrots' phylogenies derive from mitochondrial DNA. However, current phylogenetic analyses seem to indicate conflicting relationships between Aratinga and other conures, and also among other Arini members. Therefore, it is not clear if the mtDNA phylogenies can reliably define the species tree. The inconsistencies may result from the variable evolution rate of the markers used or their weak phylogenetic signal. To resolve these controversies and to assess to what extent the phylogenetic relationships in the tribe Arini can be inferred from mitochondrial genomes, we compared representative Arini mitogenomes as well as examined the usefulness of the individual mitochondrial markers and the efficiency of various phylogenetic methods., Results: Single molecular markers produced inconsistent tree topologies, while different methods offered various topologies even for the same marker. A significant disagreement in these tree topologies occurred for cytb, nd2 and nd6 genes, which are commonly used in parrot phylogenies. The strongest phylogenetic signal was found in the control region and RNA genes. However, these markers cannot be used alone in inferring Arini phylogenies because they do not provide fully resolved trees. The most reliable phylogeny of the parrots under study is obtained only on the concatenated set of all mitochondrial markers. The analyses established significantly resolved relationships within the former Aratinga representatives and the main genera of the tribe Arini. Such mtDNA phylogeny can be in agreement with the species tree, owing to its match with synapomorphic features in plumage colouration., Conclusions: Phylogenetic relationships inferred from single mitochondrial markers can be incorrect and contradictory. Therefore, such phylogenies should be considered with caution. Reliable results can be produced by concatenated sets of all or at least the majority of mitochondrial genes and the control region. The results advance a new view on the relationships among the main genera of Arini and resolve the inconsistencies between the taxa that were previously classified as the broadly defined genus Aratinga. Although gene and species trees do not always have to be consistent, the mtDNA phylogenies for Arini can reflect the species tree.

abtract The presence of bare facial area distinguishes Macaws from other members of the Arini tribe. Genera and species of the Macaw group differ in pattern of this bare skin as well as in body size. Individuals of the genera: Diopsittaca, Orthopsittaca, and Primolius are significantly smaller than the members of the genera: Anodorhynchus, Cyanopsitta, and the most species of the genus Ara. The genus Primolius contains three species: P. auricollis, P. couloni, and P. maracana, which are classified as medium-sized Macaws. So far, mitochondrial genome representative for the genus was sequenced only for Primolius couloni species. Primolius maracana mitogenome, which was sequenced in this study, will be indispensable to refine the phylogenetic relationships between Primolius species, as results of molecular researches seems to be inconsistent with Primolius species morphology.

The Yellow-shouldered Amazon (Amazona barbadensis) is the sole parrot of the genus Amazona that inhabits only dry forests. Its population has been dropping; therefore it has been the topic of many studies and conservation efforts. However, the phylogenetic relationship of this species to potential relatives classified within the Yellow-Headed Amazon (YHA) complex are still not clear. Therefore, we used more extensive data sets, including the newly sequenced mitochondrial genome of A. barbadensis, to conduct phylogenetic analyses. Various combinations of genes and many phylogenetic approaches showed that A. barbadensis clustered significantly with A. ochrocephala ochrocephala from Colombia and Venezuela, which created the Northern South American (NSA) lineage, clearly separated from two other lineages within the YHA complex, the Central (CA) and South American (SA). Tree topology tests and exclusion of rapidly evolving sites provided support for a NSA+SA grouping. We propose an evolutionary scenario for the YHA complex and its colonization of the American mainland. The NSA lineage likely represents the most ancestral lineage, which derived from Lesser Antillean Amazons and colonized the northern coast of Venezuela about a million years ago. Then, Central America was colonized through the Isthmus of Panama, which led to the emergence of the CA lineage. The southward expansion to South America and the origin of the SA lineage happened almost simultaneously. However, more intensive or prolonged gene flow or migrations have led to much weaker geographic differentiation of genetic markers in the SA than in the CA lineage.

Background: An important role in the evolution of intracellular trafficking machinery in eukaryotes played small GTPases belonging to the Rab family known as pivotal regulators of vesicle docking, fusion and transport. The Rab family is very diversified and divided into several specialized subfamilies. We focused on the VII functional group comprising Rab7 and Rab9, two related subfamilies, and analysed 210 sequences of these proteins. Rab7 regulates traffic from early to late endosomes and from late endosome to vacuole/lysosome, whereas Rab9 participates in transport from late endosomes to the trans-Golgi network., Results: Although Rab7 and Rab9 proteins are quite small and show heterogeneous rates of substitution in different lineages, we found a phylogenetic signal and inferred evolutionary relationships between them. Rab7 proteins evolved before radiation of main eukaryotic supergroups while Rab9 GTPases diverged from Rab7 before split of choanoflagellates and metazoans. Additional duplication of Rab9 and Rab7 proteins resulting in several isoforms occurred in the early evolution of vertebrates and next in teleost fishes and tetrapods. Three Rab7 lineages emerged before divergence of monocots and eudicots and subsequent duplications of Rab7 genes occurred in particular angiosperm clades. Interestingly, several Rab7 copies were identified in some representatives of excavates, ciliates and amoebozoans. The presence of many Rab copies is correlated with significant differences in their expression level. The diversification of analysed Rab subfamilies is also manifested by non-conserved sequences and structural features, many of which are involved in the interaction with regulators and effectors. Individual sites discriminating different subgroups of Rab7 and Rab9 GTPases have been identified., Conclusion: Phylogenetic reconstructions of Rab7 and Rab9 proteins were performed by a variety of methods. These Rab GTPases show diversification both at the phylogenetic, expression and structural levels. The presence of many Rab7 and Rab9 isoforms suggests their functional specialization and complexity of subcellular trafficking even in unicellular eukaryotes. The identified less conserved regions in analysed Rab sequences may directly contribute to such a differentiation.

The rearrangement of 37 genes with one control region, firstly identified in Gallus gallus mitogenome, is believed to be ancestral for all Aves. However, mitogenomic sequences obtained in recent years revealed that many avian mitogenomes contain duplicated regions that were omitted in previous genomic versions. Their evolution and mechanism of duplication are still poorly understood. The order of Accipitriformes is especially interesting in this context because its representatives contain a duplicated control region in various stages of degeneration. Therefore, we applied an appropriate PCR strategy to look for duplications within the mitogenomes of the early diverged species Sagittarius serpentarius and Cathartiformes, which is a sister order to Accipitriformes. The analyses revealed the same duplicated gene order in all examined taxa and the common ancestor of these groups. The duplicated regions were subjected to gradual degeneration and homogenization during concerted evolution. The latter process occurred recently in the species of Cathartiformes as well as in the early diverged lineages of Accipitriformes, that is, Sagittarius serpentarius and Pandion haliaetus. However, in other lineages, that is, Pernis ptilorhynchus , as well as representatives of Aegypiinae, Aquilinae, and five related subfamilies of Accipitriformes (Accipitrinae, Circinae, Buteoninae, Haliaeetinae, and Milvinae), the duplications were evolving independently for at least 14–47 Myr. Different portions of control regions in Cathartiformes showed conflicting phylogenetic signals indicating that some sections of these regions were homogenized at a frequency higher than the rate of speciation, whereas others have still evolved separately. [ABSTRACT FROM AUTHOR]

We have recently found that β-actin-like protein 2 (actbl2) forms complexes with gelsolin in human melanoma cells and can polymerize. Phylogenetic and bioinformatic analyses showed that actbl2 has a common origin with two non-muscle actins, which share a separate history from the muscle actins. The actin groups' divergence started at the beginning of vertebrate evolution, and actbl2 actins are characterized by the largest number of non-conserved amino acid substitutions of all actins. We also discovered that ACTBL2 is expressed at a very low level in several melanoma cell lines, but a small subset of cells exhibited a high ACTBL2 expression. We found that clones with knocked-out ACTBL2 (CR-ACTBL2) or overexpressing actbl2 (OE-ACTBL2) differ from control cells in the invasion, focal adhesion formation, and actin polymerization ratio, as well as in the formation of lamellipodia and stress fibers. Thus, we postulate that actbl2 is the seventh actin isoform and is essential for cell motility. [ABSTRACT FROM AUTHOR]

The identification and designation of land snail species in the genus Trochulus on the basis of shell characteristics are problematic because of their great phenotypic plasticity. Some genetic analyses have proved inconclusive, with much variation within populations and apparent gene flow among them. We examined this issue by morphometric and molecular approaches on the morphologically similar species T. coelomphala, T. hispidus and T. striolatus, co‐occurring in the Alpenvorland of Germany. While these species differed in shell and reproductive system morphology, there were forms that turned out intermediate in shell characters between T. coelomphala and T. hispidus but had genital morphology similar to T. coelomphala. Phylogenetic analysis, however, showed that these forms clustered neither with T. coelomphala nor T. hispidus but are sister to T. striolatus from the same region, which suggests that they evolved by way of sympatric speciation. Further, these analyses suggest that T. coelomphala diverged within T. hispidus; a crossing experiment indicated that they were interfertile. Expanding the study to include all available Trochulus sequences enabled us to infer evolutionary relationships between them and showed that T. hispidus is polyphyletic. Some Trochulus samples of one nominal species were grouped within others. The combination of phenotypic plasticity and possible mitochondrial DNA introgression illustrates the complex nature of evolutionary processes and the need for caution in the application of traditional taxonomic practice. [ABSTRACT FROM AUTHOR]

Mitogenomes are valuable data sources for phylogeographic and evolutionary studies of relatively closely related organisms. Here we describe eight complete sequences of moose mitogenomes belonging to the three clades of the European lineage and compare them with those of the Asian lineage. Mitochondrial genomes of moose and other cervids were used to infer highly resolved phylogenetic relationships and estimate divergence times. The analyses clearly distinguished two mtDNA lineages of moose and supported the division of the European lineage into three clades: East, West, and Central. The divergence of the European and Asian mtDNA lineages occurred in the Middle Pleistocene (ca. 443 kya), which significantly exceeds the fossil records of modern Alces alces dated to 100-200 kya. It indicates that the evolutionary history of the moose is more complex and could encompass inheritance of the ancestral variation. Our estimates also showed rapid diversification of present-day clades of the European lineage, which coincided with the transition from the Penultimate Glacial Period (MIS 6) and the Eemian interglacial (MIS 5) approximately 100 kya. Despite the strong division of the nucleotide sequences, we detected no evidence for the divergence ofamino acid sequences between Clade Central and Clade East. The recent diversification of A. alces clades, incombinationwiththeirevidentreciprocal monophyly, could be a result of low effective population size over its evolutionary history, augmented by severe bottlenecks during the Last Glacial Period. Our results are in agreement with the presence of different glacial refugia recently proposed for three identified clades of the European lineage and suggested the relict character of the Scandinavian (from Clade West) and the Biebrza moose population in northeastern Poland (belonging to Clade Central). [ABSTRACT FROM AUTHOR]

Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass. [ABSTRACT FROM AUTHOR]

The proper identification of species has significant implications for conservation and general knowledge of ecosystem variety. It is especially important for biodiversity hotspots and former Pleistocene refugia, such as the Balkans. In this paper, we evaluate the taxonomic status of the endemic Balkan species Fruticicola waldemari A. J. Wagner, 1912, using both recently collected material and museum specimens. Phylogenetic analyses based on two mitochondrial markers, 16S rRNA and cytochrome c oxidase subunit I, show that this species is closely related to the representatives of Xerocampylaea, including a conchologically similar and partly sympatric species, X. erjaveci. Analyses of shell and genital morphology as well as mitochondrial DNA sequences indicate that X. waldemari and X. erjaveci are separate but closely related species. These species differ in shell morphology (size, umbilicus diameter, microsculpture) as well as genital morphology. Nevertheless, a further study with more comprehensive sampling of both taxa is required to fully understand the complex pattern of genetic and morphological variation observed. [ABSTRACT FROM AUTHOR]

Summary: The vast biodiversity of the microbial world and how little is known about it, has already been revealed by extensive metagenomics analyses. Our rudimentary knowledge of microbes stems from difficulties concerning their isolation and culture in laboratory conditions, which is necessary for describing their phenotype, among other things, for biotechnological purposes. An important component of the understudied ecosystems is methanogens, archaea producing a potent greenhouse‐effect gas methane. Therefore, we created PhyMet2, the first database that combines descriptions of methanogens and their culturing conditions with genetic information. The database contains a set of utilities that facilitate interactive data browsing, data comparison, phylogeny exploration and searching for sequence homologues. The most unique feature of the database is the web server MethanoGram, which can be used to significantly reduce the time and cost of searching for the optimal culturing conditions of methanogens by predicting them based on 16S RNA sequences. The database will aid many researchers in exploring the world of methanogens and their applications in biotechnological processes. PhyMet2 with the MethanoGram predictor is available at http://metanogen.biotech.uni.wroc.pl [ABSTRACT FROM AUTHOR]

The present distribution of many species is a result of climatic changes during the Pleistocene and human activity. The impact of climate has been accompanied by restrictions of populations into refugia during glacial periods, and subsequent expansions during more favourable conditions, whereas human influence has been associated with hunting practices and translocations. One mammalian species that has been subject to such transformations is the red deer, Cervus elaphus, but the exact nature of these changes has been difficult to determine using only modern DNA. In this study, we obtained new cytochrome b sequences from subfossil remains of deer found in the Crimean Peninsula. A comparison of these sequences with the available recent and ancient sequences allowed to us to reconstruct phylogeographic relationships between Cervus lineages and to determine their potential migration routes at both local and Eurasian scales. Our analyses showed that the Crimean Peninsula was not a glacial refugium for red deer, but rather that red deer colonized Crimea in three independent waves from both Western and Eastern red deer populations. The immigrations were related to local extinctions and replacements of native populations. [ABSTRACT FROM AUTHOR]

Medium-sized neotropical parrots from Pionus genus are represented by at least eight species. However, their taxonomy should be revised because some external morphological characters together with genetic data recognize 19 taxa. At present, only two mitochondrial markers are available for most of these taxa and obtained phylogenies are not well resolved. Therefore, we sequenced Pionus chalcopterus chalcopterus mitogenome to gain more molecular data required for future studies of the taxonomical status and phylogenetic relationships between Pionus taxa. Performed phylogenetic analyses showed seven monophyletic clades including at least two sequences assigned to one species. However, not all subspecies sequences were monophyletic. [ABSTRACT FROM AUTHOR]

One of the key evolutionary events on the scale of the biosphere was an endosymbiosis between a heterotrophic eukaryote and a cyanobacterium, resulting in a primary plastid. Such an organelle is characteristic of three eukaryotic lineages, glaucophytes, red algae and green plants. The three groups are usually united under the common name Archaeplastida or Plantae in modern taxonomic classifications, which indicates they are considered monophyletic. The methods generally used to verify this monophyly are phylogenetic analyses. In this article we review up-to-date results of such analyses and discussed their inconsistencies. Although phylogenies of plastid genes suggest a single primary endosymbiosis, which is assumed to mean a common origin of the Archaeplastida, different phylogenetic trees based on nuclear markers show monophyly, paraphyly, polyphyly or unresolved topologies of Archaeplastida hosts. The difficulties in reconstructing host cell relationships could result from stochastic and systematic biases in data sets, including different substitution rates and patterns, gene paralogy and horizontal/endosymbiotic gene transfer into eukaryotic lineages, which attract Archaeplastida in phylogenetic trees. Based on results to date, it is neither possible to confirm nor refute alternative evolutionary scenarios to a single primary endosymbiosis. Nevertheless, if trees supporting monophyly are considered, relationships inferred among Archaeplastida lineages can be discussed. Phylogenetic analyses based on nuclear genes clearly show the earlier divergence of glaucophytes from red algae and green plants. Plastid genes suggest a more complicated history, but at least some studies are congruent with this concept. Additional research involving more representatives of glaucophytes and many understudied lineages of Eukaryota can improve inferring phylogenetic relationships related to the Archaeplastida. In addition, alternative approaches not directly dependent on phylogenetic methods should be developed. [ABSTRACT FROM AUTHOR]

The taxonomic status of Trochulus phorochaetius and its phylogenetic relationships to Trochulus plebeius and Trochulus hispidus were evaluated based on molecular, morphological, and genital anatomy data. The canonical discriminant analysis ( CDA) of shell morphology allowed the clear differentiation between these three nominal species, whereas the genitalia revealed their high similarity. Analyses of cytochrome c oxidase subunit I ( COI) sequences were not always congruent with the differentiation between these three species by shell characters. None of them formed a monophyletic group covering all its sequences. Instead, many sequences obtained from individuals classified to the same morphospecies, and/or usually collected from the same region or country, created highly supported separate clades and delimited clusters. Three distinct clades containing sequences of two morphospecies originating from the same country were identified in molecular phylogenetic and species delimitation studies: (1) T. plebeius + T. hispidus from Great Britain; (2) T. plebeius + T. hispidus from Poland; and (3) T. phorochaetius + T. hispidus from France. In the latter case some of the sequences were even identical. Their genetic similarity could indicate the ability to hybridize, which may be evidenced by the lack of major differences in their reproductive system. The assignment of distinctive morphospecies, and thus existing taxonomic names, to genetically defined evolutionary lineages is premature and arbitrary to some extent at this stage. © 2013 The Linnean Society of London [ABSTRACT FROM AUTHOR]

Background: It is commonly assumed that a heterotrophic ancestor of the supergroup Archaeplastida/Plantae engulfed a cyanobacterium that was transformed into a primary plastid; however, it is still unclear how nuclearencoded proteins initially were imported into the new organelle. Most proteins targeted to primary plastids carry a transit peptide and are transported post-translationally using Toc and Tic translocons. There are, however, several proteins with N-terminal signal peptides that are directed to higher plant plastids in vesicles derived from the endomembrane system (ES). The existence of these proteins inspired a hypothesis that all nuclear-encoded, plastidtargeted proteins initially carried signal peptides and were targeted to the ancestral primary plastid via the host ES. Results: We present the first phylogenetic analyses of Arabidopsis thaliana α-carbonic anhydrase (CAH1), Oryza sativa nucleotide pyrophosphatase/phosphodiesterase (NPP1), and two O. sativa α-amylases (αAmy3, αAmy7), proteins that are directed to higher plant primary plastids via the ES. We also investigated protein disulfide isomerase (RB60) from the green alga Chlamydomonas reinhardtii because of its peculiar dual post- and cotranslational targeting to both the plastid and ES. Our analyses show that these proteins all are of eukaryotic rather than cyanobacterial origin, and that their non-plastid homologs are equipped with signal peptides responsible for co-translational import into the host ES. Our results indicate that vesicular trafficking of proteins to primary plastids evolved long after the cyanobacterial endosymbiosis (possibly only in higher plants) to permit their glycosylation and/or transport to more than one cellular compartment. Conclusions: The proteins we analyzed are not relics of ES-mediated protein targeting to the ancestral primary plastid. Available data indicate that Toc- and Tic-based translocation dominated protein import into primary plastids from the beginning. Only a handful of host proteins, which already were targeted through the ES, later were adapted to reach the plastid via the vesicular trafficking. They represent a derived class of higher plant plastidtargeted proteins with an unusual evolutionary history. [ABSTRACT FROM AUTHOR]