Basal Lineage Research Articles

Survey of Early-Diverging Lineages of Fungi Reveals Abundant and Diverse Mycoviruses.

Mycoviruses are widespread and purportedly common throughout the fungal kingdom, although most are known from hosts in the two most recently diverged phyla, Ascomycota and Basidiomycota, together called Dikarya. To augment our knowledge of mycovirus prevalence and diversity in underexplored fungi, we conducted a large-scale survey of fungi in the earlier-diverging lineages, using both culture-based and transcriptome-mining approaches to search for RNA viruses. In total, 21.6% of 333 isolates were positive for RNA mycoviruses. This is a greater proportion than expected based on previous taxonomically broad mycovirus surveys and is suggestive of a strong phylogenetic component to mycoviral infection. Our newly found viral sequences are diverse, composed of double-stranded RNA, positive-sense single-stranded RNA (ssRNA), and negative-sense ssRNA genomes and include novel lineages lacking representation in the public databases. These identified viruses could be classified into 2 orders, 5 families, and 5 genera; however, half of the viruses remain taxonomically unassigned. Further, we identified a lineage of virus-like sequences in the genomes of members of Phycomycetaceae and Mortierellales that appear to be novel genes derived from integration of a viral RNA-dependent RNA polymerase gene. The two screening methods largely agreed in their detection of viruses; thus, we suggest that the culture-based assay is a cost-effective means to quickly assess whether a laboratory culture is virally infected. This study used culture collections and publicly available transcriptomes to demonstrate that mycoviruses are abundant in laboratory cultures of early-diverging fungal lineages. The function and diversity of mycoviruses found here will help guide future studies into mycovirus origins and ecological functions.IMPORTANCE Viruses are key drivers of evolution and ecosystem function and are increasingly recognized as symbionts of fungi. Fungi in early-diverging lineages are widespread, ecologically important, and comprise the majority of the phylogenetic diversity of the kingdom. Viruses infecting early-diverging lineages of fungi have been almost entirely unstudied. In this study, we screened fungi for viruses by two alternative approaches: a classic culture-based method and by transcriptome-mining. The results of our large-scale survey demonstrate that early-diverging lineages have higher infection rates than have been previously reported in other fungal taxa and that laboratory strains worldwide are host to infections, the implications of which are unknown. The function and diversity of mycoviruses found in these basal fungal lineages will help guide future studies into mycovirus origins and their evolutionary ramifications and ecological impacts.

Marchantia TCP transcription factor activity correlates with three-dimensional chromatin structure.

Information in the genome is not only encoded within sequence or epigenetic modifications, but is also found in how it folds in three-dimensional space. The formation of self-interacting genomic regions, named topologically associated domains (TADs), is known as a key feature of genome organization beyond the nucleosomal level. However, our understanding of the formation and function of TADs in plants is extremely limited. Here we show that the genome of Marchantia polymorpha, a member of a basal land plant lineage, exhibits TADs with epigenetic features similar to those of higher plants. By analysing various epigenetic marks across Marchantia TADs, we find that these regions generally represent interstitial heterochromatin and their borders are enriched with Marchantia transcription factor TCP1. We also identify a type of TAD that we name 'TCP1-rich TAD', in which genomic regions are highly accessible and are densely bound by TCP1 proteins. Transcription of TCP1 target genes differs on the basis gene location, and those in TCP1-rich TADs clearly show a lower expression level. In tcp1 mutant lines, neither TCP1-bound TAD borders nor TCP1-rich TADs display drastically altered chromatin organization patterns, suggesting that, in Marchantia, TCP1 is dispensable for TAD formation. However, we find that in tcp1 mutants, genes residing in TCP1-rich TADs have a greater extent of expression fold change as opposed to genes that do not belong to these TADs. Our results suggest that, besides standing as spatial chromatin-packing modules, plant TADs function as nuclear microcompartments associated with transcription factor activities.

Improving Phylogenetic Signals of Mitochondrial Genes Using a New Method of Codon Degeneration.

Recovering deep phylogeny is challenging with animal mitochondrial genes because of their rapid evolution. Codon degeneration decreases the phylogenetic noise and bias by aiming to achieve two objectives: (1) alleviate the bias associated with nucleotide composition, which may lead to homoplasy and long-branch attraction, and (2) reduce differences in the phylogenetic results between nucleotide-based and amino acid (AA)-based analyses. The discrepancy between nucleotide-based analysis and AA-based analysis is partially caused by some synonymous codons that differ more from each other at the nucleotide level than from some nonsynonymous codons, e.g., Leu codon TTR in the standard genetic code is more similar to Phe codon TTY than to synonymous CTN codons. Thus, nucleotide similarity conflicts with AA similarity. There are many such examples involving other codon families in various mitochondrial genetic codes. Proper codon degeneration will make synonymous codons more similar to each other at the nucleotide level than they are to nonsynonymous codons. Here, I illustrate a “principled” codon degeneration method that achieves these objectives. The method was applied to resolving the mammalian basal lineage and phylogenetic position of rheas among ratites. The codon degeneration method was implemented in the user-friendly and freely available DAMBE software for all known genetic codes (genetic codes 1 to 33).

Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations

Anatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-genome sequence of a 2,500-year-old individual (IK002) from the main-island of Japan that is characterized with a typical Jomon culture. The phylogenetic analyses support multiple waves of migration, with IK002 forming a basal lineage to the East and Northeast Asian genomes examined, likely representing some of the earliest-wave migrants who went north from Southeast Asia to East Asia. Furthermore, IK002 shows strong genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration. This study highlights the power of ancient genomics to provide new insights into the complex history of human migration into East Eurasia.

Abstract 2802: Establishing and optimizing treatment-naïve prostate cancer patient-derived organoids culture: Implications for personalized medicine

Abstract Background: Prostate Cancer (PCa) is a heterogeneous disease. Currently available in vitro and in vivo cancer models fail to recapitulate the spectrum of clinical and biological challenges; accurate models for translational research remain a significant unmet need. Objective: The aim of this work is to employ fresh tissue specimens from a treatment-naïve cohort of patients with prostate cancer to optimize and establish 3D patient-derived organoids as an in vitro disease model for PCa progression and drug response. In addition, acknowledging the difficulty in establishing primary PCa cell lines, our aim was to generate novel PCa patient-derived cell lines. Methods: Fresh specimens were collected from treatment-naïve patients with prostate cancer during radical prostatectomy (one unaffected and one tumor). Briefly, fresh tissue samples were digested enzymatically, and the resulting cell suspensions were plated in a 3D environment that employs Matrigel as an extracellular matrix. At first, a cocktail of 12 factors, previously recognized, was used to establish organoids. Subsequently, we have optimized the recipe to a minimal 5-factors media for both organoids and cells. Organoids and the corresponding tissue specimens were characterized using immunofluorescent analysis and immunohistochemistry. Furthermore, patient-derived organoids were employed for the assessment of drug response. In addition, PCa patient-derived cell lines were generated and their culture conditions were optimized. These cells were further characterized using immunofluorescent analysis. Results: Fresh tissues were successfully established as organoids and as 2D cells using the same culture media that contains 12 original factors. The presence of prostate luminal (Cytokeratin 8, Androgen Receptor, and Prostate Specific Antigen) and basal (Cytokeratin 5 and P63) epithelial lineages was confirmed by immunohistochemical and immunofluorescent analyses. Notably, we have identified five essential components (NAC, NOG, A83, B27, and Nicotinamide) that support the establishment of organoids culture in a less expensive, more efficient manner. Moreover, we optimized the culture and maintenance of patient-derived 2D cells by plating on collagen type I and we have reduced the medium requirement to include EGF only as an essential component. Importantly, the results showed differential drug and radiation response between patient samples. Conclusion: This study provides a repertoire of novel patient-derived organoids and cells from a unique cohort of treatment-naïve patients, as our results demonstrate that we succeeded in delineating the essential components needed to grow prostate organoids and primary cells with a high success rate and long-term maintenance in culture. We hope that we can use this platform in the future to predict treatment response in a personalized fashion leading to better management of the disease. Citation Format: Katia Cheaito, Hisham Bahmad, Alissar Monzer, Farah Ballout, HIba Msheik, Ola Hadadeh, Christelle Dagher, Nour Saheb, Ayman Tawil, Marwan El-Sabban, Albert El-Hajj, Deborah Mukherji, Wassim G. Abou-Kheir. Establishing and optimizing treatment-naïve prostate cancer patient-derived organoids culture: Implications for personalized medicine [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2802.

Morphology and microstructure of Pellites hamiensis nov. sp., a Middle Jurassic liverwort from northwestern China and its evolutionary significance

Pelliales is a basal lineage of the simple thalloid liverworts. Here, we describe a simple thalloid liverwort from the Middle Jurassic Xishanyao Formation of the Turpan–Hami Basin, Xinjiang Uygur Autonomous Region in northwestern China. The thalloid fossil liverwort is described as a new species: Pellites hamiensis (Pelliaceae, Pelliales). Pellites hamiensis nov. sp. resembles the extant species of Pelliaceae in having ribbon-like segments, conspicuous costae that appear as ridges on the ventral surface, rectangular cells with thickened walls adjacent to the margin, and elongated cells in the middle part of the thallus. The occurrence of P. hamiensis nov. sp. extends the fossil records of Pellites back to the Aalenian-Bajocian or Bajocian (ca. 170 Ma) and suggests that the divergence time of the Pelliaceae is no later than the Middle Jurassic.

The first theropod dinosaur (Coelurosauria, Theropoda) from the base of the Romualdo Formation (Albian), Araripe Basin, Northeast Brazil

The Romualdo Formation (Araripe Basin) is worldwide known for the large number of well-preserved fossils but the dinosaur record is rather scarce. Here we describe a new coelurosaur, which is the first tetrapod recovered from the basal layers of this stratigraphic unit that consist of dark shales. Aratasaurus museunacionali gen. et sp. nov. is known by an incomplete but articulated right hind limb with the distal portion of the femur, proximal half of tibia and incomplete pes. The new species differs from other coelurosaurs by a medial fossa in the tibia and digits II, III and IV being symmetric. The phylogenetic analysis recovered Aratasaurus museunacionali closely related to Zuolong salleei, forming a basal coelurosaur lineage. The paleohistology indicate that the specimen is a juvenile, with an estimated body length around 3.12 m. The new taxon represents the first occurrence of basal coelurosaurians in the Araripe Basin and suggests a widespread distribution of this group during the Lower Cretaceous.

The complete mitochondrial genome and phylogenetic analysis of the European map butterfly Araschnia levana (Insecta: Lepidoptera: Nymphalidae)

The European map butterfly Araschnia levana (Linnaeus, 1758) is a species showing extreme seasonal polyphenism. The complete 15,207 bp circular A. levana mitogenome consisting of 81.6% AT nucleotides, was assembled by Illumina genome skimming. It includes 22 tRNAs, 13 protein-coding genes, 2 rRNAs, and a control region in the typical butterfly gene order. Araschnia levana COX1 features an atypical CGA start codon and ATP6, COX1, COX2, ND1, ND3, and ND4 have incomplete stop codons completed by 3′A residues added to the mRNA. Phylogenetic reconstruction places A. levana as a basal lineage within tribe Nymphalini, consistent with previous phylogenetic hypotheses.

Complete mitochondrial genome of Pterodecta felderi (Lepidoptera: Callidulidae)

We report the mitochondrial genome (mitogenome) of Pterodecta felderi (Callidulidae: Lepidoptera), which is the first mitogenome sequences in the family Callidulidae, a monotypic family in the superfamily Calliduloidea. The 15,340-bp long complete mitogenome consists of a typical set of genes (13 protein-coding genes [PCGs], 2 rRNA genes, and 22 tRNA genes) and 1 major non-coding A + T-rich region, which are arranged in a way that is frequently observed in Lepidoptera. Of the 13 PCGs, 12 P. felderi start with ATN, except for COI, which starts with CGA. The P. felderi mitogenome consists of 210-bp long intergenic-spacer sequences and 27-bp long overlaps. Phylogenetic analysis of superfamilial relationships in the lepidopteran clade Obtectomera with concatenated sequences of the 13 PCGs and 2 rRNA genes using the Bayesian inference method showed that Calliduloidea, which is only represented by P. felderi, was placed as the most basal lineage about Macroheterocera (Lasiocampoidea, Bombycoidea, Mimallonoidea, Noctuoidea, and Drepanoidea), Papilionoidea, and Pyraloidea.

Mitochondrial genome of the mason bee, Osmia pedicornis (Hymenopetra: Megachilidae)

The mason bee, Osmia pedicornis Cockerell, 1919, which is importantly used as the pollinator, particularly for apples in Korea. We sequenced the mitochondrial genome (mitogenome) of O. pedicornis as an initial study for species identification and subsequent population genetic study. The size of the incomplete genome was 14,505 bp, excluding the trnA, trnC, and the A + T-rich region that were unable to sequence, but including partially sequenced trnM and srRNA. The genome included typical sets of protein-coding genes (PCGs), rRNA genes, and one non-coding region, tRNAs, excluding two unidentified tRNAs. Although positions of the two tRNAs that were not sequenced are unknown the gene arrangement of O. pedicornis mitogenome has the tRNA arrangement, trnM-trnQ-trnI, at the A + T-rich region and ND2 junction that differed from that of previously published O. excavate, which has trnA-trnQ-trnI arrangement at the junction. Phylogenetic analyses were performed using concatenated sequences of the 13 PCGs genes and the maximum likelihood method with the inclusion of a total of 12 mitogenome sequences belonging to three families in the superfamily Apoidea. Current O. pedicornis was placed as the sister to the O. bicornis, with the highest nodal support. The Apidae and Megachilidae were placed as the sister group, with the placement of Colletidae as the basal lineage for the group with the highest nodal support.

Complete mitochondrial genome of Cerace xanthocosma and its phylogenetic position in the family Tortricidae

Cerace xanthocosma Diakonoff, 1950 belongs to the Tortricidae of Lepidoptera, distributed in China and Japan. Its mitochondrial genome is 15,344 bp in size, containing 37 genes (13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes) and a non-coding A + T-rich region. In the 37 genes, 14 genes are located on the minority-strand (N-strand) with the remaining genes on the majority-strand (J-strand). The A + T-rich region has a poly-T stretch and a motif ATAGA. Phylogenetic analysis using Bayesian Inference method shows the sister relationship between Tortricinae and Olethreutinae with the placement of C. xanthocosma as the basal lineage of Tortricinae.

Larvae of Abachrysa eureka (Banks) (Neuroptera: Chrysopidae: Belonopterygini): descriptions and a discussion of the evolution of myrmecophily in Chrysopidae.

Here we describe the first and third instars and the egg of the New World chrysopid Abachrysa eureka (Banks). Like other members of the tribe Belonopterygini, this species is myrmecophilic. Comparisons of Abachrysa larval and egg characteristics with those reported from four other belonopterygine genera indicate that Abachrysa more closely resembles the Old World Calochrysa and Italochrysa than the New World Vieira and Nacarina. The three genera Abachrysa, Calochrysa and Italochrysa all have large eggs, accelerated embryonic development, and an elaborate set of morphological modifications for larval debris carrying, an important defense against ant attack. This pattern of shared features is consistent with the phylogenies recovered in recent molecular studies that place the New World genera Vieira and Nacarina basal to Abachrysa and the Old World genera. Our assessment of current morphological information in relation to the molecular studies indicates the following sequence: (i) The form of belonopterygine myrmecophily that is currently expressed in the basal lineages (Nacarina and perhaps Vieira) originated in the New World and does not involve elaborate larval modifications for debris carrying. (ii) Myrmecophily that is based on a correlated set of developmental and morphological traits subserving debris carrying evolved in the New World when Abachrysa diverged. (iii) Subsequently, the debris-carrying clade of Belonopterygini underwent a significant radiation in the Old World, but not in the New World.

Trichome micromorphology in Alcea L. and allied genera (Malvaceae) and its systematic implication

Trichomes of 26 species of Alcea (Malvaceae) were investigated using light (LM) and scanning electron microscopy (SEM). The trichomes show a great micromorphological variation, which provides data useful for species delimitation in Alcea. Two basic types of trichomes could be distinguished in Alcea and allied genera: glandular and eglandular. The glandular trichomes could in turn be subdivided into two subtypes: capitate and clavate. The eglandular trichomes could be subdivided into five subtypes: simple, fascicled, stellate, fascicled‐stellate and pluri‐radiate. Characters of taxonomic interest are: trichome density (glabrous to dense), number of arms per trichome, orientation relative to the epidermal surface (appressed to erect) and presence/absence of a stalk. According to the results the species of Alcea can be divided into four informal groups based on trichome types. The results further support the exclusion of the annual Althaea species from the perennial ones and their close relationship to Malva. In addition, a close relationship between perennial Althaea and basal Alcea lineages is supported. Based on the evolutionary framework provided by recent molecular phylogenetic investigations, the following trends can be observed in the Malva alliance: long and narrow‐armed trichomes are primitive in relation to short and thick‐armed trichomes; dense indumentum coverage is primitive in relation to moderately dense or glabrous ones; presence of simple hairs on stem (particularly on leaves) is more advanced than their absence; spreading villous‐stellate and fascicled trichomes are more advanced than appressed stellate ones. Clavate trichomes, which were found exclusively in a few species of Alcea, should be considered as a derived state in relation to capitate ones, and they may provide a synapomorphy for the crown group of Alcea.

Phylogenetic reassignment of basal cyclostome braconid parasitoid wasps (Hymenoptera) with description of a new, enigmatic Afrotropical tribe with a highly anomalous 28S D2 secondary structure

AbstractA new tribe of braconid wasps provisionally included in the Rhyssalinae, Laibaleini trib. nov., type genus Laibalea gen. nov. (type species Laibalea enigmatica sp. nov.), from Kenya and the Central African Republic, is described. A molecular dataset, with emphasis on basally derived taxa based on four gene fragments (28S D2–D3 expansion region, COI barcode, elongation factor 1-alpha and 16S ribosomal DNA), was analysed both alone and in combination with a morphological dataset. Molecular phylogenetic placement of the new species into an existing subfamily is complicated by the extreme sequence divergence of the three sequences obtained for Laibalea. In both the combined sequence analysis and the combined DNA plus morphological tree, Laibalea is recovered as a sister group to the Rhyssalinae plus all non-cyclostome lineage braconids excluding Mesostoinae, Maxfischeriinae and Aphidiinae. A consensus of morphological characters and molecular analyses suggests inclusion of Laibalea either in the otherwise principally Holarctic subfamily Rhyssalinae or perhap more basally, in the principally Gondwanan Mesostoinae s.l., although we cannot exclude the possibility that it might represent a separate basal lineage. We place Laibalea in its own tribe, provisionally included in Rhyssalinae. The DNA sequence data are presented for several genera for the first time. Avga, the type genus of Avgini, is shown not to belong to Mesostoinae s.l. or Hormiinae, but its exact relationships remain uncertain. The generic compositions of Rhyssalinae and Mesostoinae s.l. are revised. Anachyra, Apoavga, Neptihormius, Neoavga and Opiopterus are shown to belong to Mesostoinae s.s. A key to the tribes of Rhyssalinae is provided.

Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage.

Thaumarchaeota constitute an abundant and ubiquitous phylum of Archaea that play critical roles in the global nitrogen and carbon cycles. Most well-characterized members of the phylum are chemolithoautotrophic ammonia-oxidizing archaea (AOA), which comprise up to 5 and 20% of the total single-celled life in soil and marine systems, respectively. Using two high-quality metagenome-assembled genomes (MAGs), here we describe a divergent marine thaumarchaeal clade that is devoid of the ammonia-oxidation machinery and the AOA-specific carbon-fixation pathway. Phylogenomic analyses placed these genomes within the uncultivated and largely understudied marine pSL12-like thaumarchaeal clade. The predominant mode of nutrient acquisition appears to be aerobic heterotrophy, evidenced by the presence of respiratory complexes and various organic carbon degradation pathways. Both genomes encoded several pyrroloquinoline quinone (PQQ)-dependent alcohol dehydrogenases, as well as a form III RuBisCO. Metabolic reconstructions suggest anaplerotic CO2 assimilation mediated by RuBisCO, which may be linked to the central carbon metabolism. We conclude that these genomes represent a hitherto unrecognized evolutionary link between predominantly anaerobic basal thaumarchaeal lineages and mesophilic marine AOA, with important implications for diversification within the phylum Thaumarchaeota.

Morphology, Ultrastructure, and Phylogeny of Two Novel Species of Ventrifissura (V. oblonga n. sp. and V. velata n. sp., Thecofilosea, Cercozoa)

Ventrifissura is a group of poorly studied heterotrophic biflagellates in the phylum Cercozoa. Despite a phylogenetic placement with only weak support and a lack of ultrastructural data, Ventrifissura was assigned to Thecofilosea. In the presented study, we established cultures of two novel species of Ventrifissura (V. oblonga n. sp. and V. velata n. sp.) isolated from coastal marine environments in Japan, and performed light and electron microscopy observations and molecular phylogenetic analysis. Transmission electron microscopy revealed that V. oblonga shares several ultrastructural characteristics with thecofilosean flagellates, including permanently condensed chromosomes, a extracellular theca, and slender extrusomes. Molecular phylogenetic analysis could not resolve the phylogenetic position, but the possibility that Ventrifissura clusters into Ventrifilosa was supported by approximately unbiased tests. Based on both morphological and phylogenetic findings, we concluded that Ventrifissura is a basal lineage of Thecofilosea.

Deep-Time Demographic Inference Suggests Ecological Release as Driver of Neoavian Adaptive Radiation

Assessing the applicability of theory to major adaptive radiations in deep time represents an extremely difficult problem in evolutionary biology. Neoaves, which includes 95% of living birds, is believed to have undergone a period of rapid diversification roughly coincident with the Cretaceous–Paleogene (K-Pg) boundary. We investigate whether basal neoavian lineages experienced an ecological release in response to ecological opportunity, as evidenced by density compensation. We estimated effective population sizes (Ne) of basal neoavian lineages by combining coalescent branch lengths (CBLs) and the numbers of generations between successive divergences. We used a modified version of Accurate Species TRee Algorithm (ASTRAL) to estimate CBLs directly from insertion–deletion (indel) data, as well as from gene trees using DNA sequence and/or indel data. We found that some divergences near the K-Pg boundary involved unexpectedly high gene tree discordance relative to the estimated number of generations between speciation events. The simplest explanation for this result is an increase in Ne, despite the caveats discussed herein. It appears that at least some early neoavian lineages, similar to the ancestor of the clade comprising doves, mesites, and sandgrouse, experienced ecological release near the time of the K-Pg mass extinction.

Arabidopsis Raf-like kinases act as positive regulators of subclass III SnRK2 in osmostress signaling.

SUMMARYGiven their sessile nature, land plants must use various mechanisms to manage dehydration under water‐deficit conditions. Osmostress‐induced activation of the SNF1‐related protein kinase 2 (SnRK2) family elicits physiological responses such as stomatal closure to protect plants during drought conditions. With the plant hormone ABA receptors [PYR (pyrabactin resistance)/PYL (pyrabactin resistance‐like)/RCAR (regulatory component of ABA receptors) proteins] and group A protein phosphatases, subclass III SnRK2 also constitutes a core signaling module for ABA, and osmostress triggers ABA accumulation. How SnRK2 is activated through ABA has been clarified, although its activation through osmostress remains unclear. Here, we show that Arabidopsis ABA and abiotic stress‐responsive Raf‐like kinases (AtARKs) of the B3 clade of the mitogen‐activated kinase kinase kinase (MAPKKK) family are crucial in SnRK2‐mediated osmostress responses. Disruption of AtARKs in Arabidopsis results in increased water loss from detached leaves because of impaired stomatal closure in response to osmostress. Our findings obtained in vitro and in planta have shown that AtARKs interact physically with SRK2E, a core factor for stomatal closure in response to drought. Furthermore, we show that AtARK phosphorylates S171 and S175 in the activation loop of SRK2E in vitro and that Atark mutants have defects in osmostress‐induced subclass III SnRK2 activity. Our findings identify a specific type of B3‐MAPKKKs as upstream kinases of subclass III SnRK2 in Arabidopsis. Taken together with earlier reports that ARK is an upstream kinase of SnRK2 in moss, an existing member of a basal land plant lineage, we propose that ARK/SnRK2 module is evolutionarily conserved across 400 million years of land plant evolution for conferring protection against drought.

Ontogeny and homology of cranial bones associated with lateral-line canals of the Senegal Bichir, Polypterus senegalus (Actinopterygii: Cladistii: Polypteriformes), with a discussion on the formation of lateral-line canal bones in fishes.

The association between lateral-line canals and skull bones in fishes has been the subject of several studies and raised a series of controversies, particularly with regard to the hypothesized role of lateral-line organs (i.e. neuromasts) in osteogenesis and the consequences for hypotheses of homology of the bones associated with lateral-line canals. Polypteridae, a group of freshwater fishes that occupies a key phylogenetic position as the most basal extant lineage of ray-finned fishes (Actinopterygii), provides an interesting model for the study of the relationships between lateral-line canals and skull bones. We describe the development of bones associated with lateral-line canals in the Senegal Bichir, Polypterus senegalus, and use these data to re-address previous hypotheses of homology of skull bones of polypterids. We demonstrate that the lateral-line canals constitute a separate component of the dermatocranium that may interact with a membranodermal component, thereby forming compound bones in the adult. Differences in the interactions between these components determine the characteristics of the development of each independent bone in the skull of adult P.senegalus. Our results shed light on long-standing controversies about the identity of skull bones such as the rostral, preopercle, and sphenotic in Polypteridae, and suggest the presence of an ancestral two-component pattern of formation of bones associated with lateral-line canals in bony fishes. These findings reveal the need to re-address previous hypotheses of homology of bones associated with lateral-line canals in different groups of bony fishes, especially fossil taxa.

Recently lost connectivity in the Western Palaearctic steppes: the case of a scarce specialist butterfly

Palaearctic steppes evolved under the Cenozoic cold arid climate and megaherbivore pressure. A large portion of the biome persisted into the Holocene but has recently been subjected to human land use alternation. Pseudophilotes bavius (Lepidoptera: Lycaenidae) is a steppe specialist sporadically distributed in Eastern Europe and Pontic-Caspian region (from Transylvania to Southern Urals), the Balkans, the South-Eastern Mediterranean and Irano-Anatolian regions. We used samples covering the distribution area to assess the phylogeography and population genetics of the species based on one mitochondrial and four nuclear genes. The basal lineages are situated in the Irano-Anatolian region, forming two Evolutionary Units. The species radiated to the Balkans and Pontic-Caspian steppes probably when the climatic conditions became suitable after the mid-Pleistocene transition and formation of vast steppe biome. In these parts of the range, the species survived both glacial and interglacial periods in situ, forming a third Evolutionary Unit. In the Balkans, the individual populations are distinct and have probably been isolated for a long time, owing to the diversity of Balkan habitats. In the Pontic-Caspian region, population connectivity probably existed until recently, since the life history of the species is unlikely to include long-distance dispersal. The distribution could have become fragmented with the conversion of steppes into cropland during the past centuries. Future conservation will require proper knowledge of the distribution and habitat needs of the species. Management of inhabited sites should respect historical disturbance-succession dynamics.