Lineages Of Species Research Articles

Diverse lineages of pathogenic Leptospira species are widespread in the environment in Puerto Rico, USA.

BackgroundLeptospirosis, caused by Leptospira bacteria, is a common zoonosis worldwide, especially in the tropics. Reservoir species and risk factors have been identified but surveys for environmental sources are rare. Furthermore, understanding of environmental Leptospira containing virulence associated genes and possibly capable of causing disease is incomplete, which may convolute leptospirosis diagnosis, prevention, and epidemiology.Methodology/Principal findingsWe collected environmental samples from 22 sites in Puerto Rico during three sampling periods over 14-months (Dec 2018-Feb 2020); 10 water and 10 soil samples were collected at each site. Samples were screened for DNA from potentially pathogenic Leptospira using the lipL32 PCR assay and positive samples were sequenced to assess genetic diversity. One urban site in San Juan was sampled three times over 14 months to assess persistence in soil; live leptospires were obtained during the last sampling period. Isolates were whole genome sequenced and LipL32 expression was assessed in vitro.We detected pathogenic Leptospira DNA at 15/22 sites; both soil and water were positive at 5/15 sites. We recovered lipL32 sequences from 83/86 positive samples (15/15 positive sites) and secY sequences from 32/86 (10/15 sites); multiple genotypes were identified at 12 sites. These sequences revealed significant diversity across samples, including four novel lipL32 phylogenetic clades within the pathogenic P1 group. Most samples from the serially sampled site were lipL32 positive at each time point. We sequenced the genomes of six saprophytic and two pathogenic Leptospira isolates; the latter represent a novel pathogenic Leptospira species likely belonging to a new serogroup.Conclusions/SignificanceDiverse and novel pathogenic Leptospira are widespread in the environment in Puerto Rico. The disease potential of these lineages is unknown but several were consistently detected for >1 year in soil, which could contaminate water. This work increases understanding of environmental Leptospira diversity and should improve leptospirosis surveillance and diagnostics.

Molecular phylogeny of Ruppia maritima L. from Chilika Lake, Odhisa using nuclear and plastid genes

Aim: The present study aims to confirm the molecular identification of Ruppia maritima L. from Chilika Lake, Odhisa using different molecular markers and find out the evolutionary lineage of Ruppia species. Methodology: For molecular identification, R. maritima was collected from Chilika Lake and the rbcL, matK, and ITS gene sequences were investigated and analyzed using BLAST to verify the gene fragment. Phylogenetic tree was constructed using MEGA X software following Neighbor joining (NJ) and Maximum parsimony (MP) methods. Results: The nucleotide (ITS) and plastid gene (rbcL and matK) sequences of Ruppia maritima were examined. The tree topology of R. maritima rbcL and matK gene sequences revealed a paraphyletic cluster at 99 and 100% bootstrap. The conserved region was high in matK (74.8%), followed by rbcL (45.2%) and ITS (19.1%) with seagrass and freshwater species. ITS had the most significant proportion of variable sites (79.7%), followed by rbcL (52.4%) and matK (25.2%). The ITS region showed less parsimonious-informative character (66.1) than rbcL and matK region. Interpretation: The study concludes that the R. maritima was identified through molecular markers, which was a closed lineage with seagrasses than freshwater species.

Climate change will disproportionally affect the most genetically diverse lineages of a widespread African tree species

Global climate change is proceeding at an alarming rate with major ecological and genetic consequences for biodiversity, particularly in drylands. The response of species to climate change may differ between intraspecific genetic groups, with major implications for conservation. We used molecular data from 10 nuclear and two chloroplast genomes to identify phylogeographic groups within 746 individuals from 29 populations of Senegalia senegal, a savannah tree species in sub-Saharan Africa. Three phylogroups are identified corresponding to Sudano-Sahelian, Zambezian and Southern African biogeographic regions in West, East and Southern Africa. Genetic diversity was highest in Southern and Zambesian and lowest in the Sudano-Sahelian phylogroups. Using species distribution modeling, we infer highly divergent future distributions of the phylogroups under three climate change scenarios. Climate change will lead to severe reductions of distribution area of the genetically diverse Zambezian (− 41–− 54%) and Southern (− 63–− 82%) phylogroups, but to an increase for the genetically depauperate Sudano-Sahelian (+ 7– + 26%) phylogroups. This study improves our understanding of the impact of climate change on the future distribution of this species. This knowledge is particularly useful for biodiversity management as the conservation of genetic resources needs to be considered in complementary strategies of in-situ conservation and assisted migration.

Matamatas Chelus spp. (Testudines, Chelidae) have a remarkable evolutionary history of sex chromosomes with a long-term stable XY microchromosome system

The genus Chelus, commonly known as Matamata is one of the most emblematic and remarkable species among the Neotropical chelids. It is an Amazonian species with an extensive distribution throughout Negro/Orinoco and Amazonas River basins. Currently, two species are formally recognized: Chelus orinocensis and Chelus fimbriata and although it is still classified as "Least Concern" in the IUCN, the Matamatas are very appreciated and illegally sold in the international pet trade. Regardless, little is known regarding many aspects of its natural history. Chromosomal features for Chelus, for instance, are meagre and practically restricted to the description of the diploid number (2n = 50) for Chelus fimbriata, and its sex determining strategies are yet to be fully investigated. Here, we examined the karyotype of Chelus fimbriata and the newly described Chelus orinocensis, applying an extensive conventional and molecular cytogenetic approach. This allowed us to identify a genetic sex determining mechanism with a micro XY sex chromosome system in both species, a system that was likely present in their most common recent ancestor Chelus colombiana. Furthermore, the XY system found in Chelus orinocensis and Chelus fimbriata, as seen in other chelid species, recruited several repeat motifs, possibly prior to the split of South America and Australasian lineages, indicating that such system indeed dates back to the earliest lineages of Chelid species.

An integrative re-evaluation of Typhlatya shrimp within the karst aquifer of the Yucat\xe1n Peninsula, Mexico

The Yucatán Peninsula, Mexico is a carbonate platform well-known for extensive karst networks of densely stratified aquifer ecosystems. This aquifer supports diverse anchialine fauna, including species of the globally distributed anchialine shrimp genus Typhlatya (Atyidae). Four species (T. campecheae, T. pearsei, T. dzilamensis and T. mitchelli) are endemic to the Peninsula, of which three are federally listed in Mexico. This first integrative evaluation (i.e., molecular, morphological, broad geographic and type locality sampling, and environmental data) of Yucatán Typhlatya reveals considerable species identity conflict in prior phylogenetic assessments, broad species ranges, syntopy within cave systems and five genetic lineages (of which two are new to science). Despite sampling from the type locality of endangered T. campecheae, specimens (and molecular data) were indistinguishable from vulnerable T. pearsei. Ancestral/divergence reconstructions support convergent evolution of a low-salinity ancestor for a post-Paleogene arc Yucatán + Cuba Typhlatya clade within the anchialine Atyidae clade. A secondary adaptation for the coastal-restricted euryhaline (2–37 psu), Typhlatya dzilamensis (unknown conservation status) was identified, while remaining species lineages were low-salinity (< 5 psu) adapted and found within the meteoric lens of inland and coastal caves. This study demonstrates the need for integrative/interdisciplinary approaches when conducting biodiversity assessments in complex and poorly studied aquifers.

A New Species of Rhagoletis (Diptera: Tephritidae) from Switzerland, with Discussion of its Relationships within the Genus

Rhagoletis merzi sp. n., is described and illustrated based on specimens swept and reared from Juniperus sabina L. in Switzerland. A comparative review of Palaearctic species and a key to Palearctic and Nearctic species similar to R. merzi is provided. Based on DNA sequences from the COI, CAD, 28S, period, and AATS genes (4270 bp) of 92 isolates from two outgroup species (Anastrepha ludens, Euphranta canadensis), one species of Carpomya and 35 species representing most of species groups of Rhagoletis, a MrBayes analysis recovered a monophyletic lineage of Juniper-infesting species within a monophyletic cluster of R. fausta, R. batava, as well as the suavis, cingulata, pomonella, tabellaria and juniperina groups. Th e juniperina group includes both Nearctic (R. juniperina and undescribed forms) and Palaearctic species (R. fl avigenualis and R. merzi). Rhagoletis merzi is more similar to the Nearctic R. juniperina in both morphological characters (wing pattern, occiput, mesonotum and legs coloration, shape of male surstyli) and molecular sequences than to the Palearctic R. fl avigenualis.

Hypothesis: Trans-splicing Generates Evolutionary Novelty in the Photosynthetic Amoeba Paulinella.

Plastid primary endosymbiosis has occurred twice, once in the Archaeplastida ancestor and once in the Paulinella (Rhizaria) lineage. Both events precipitated massive evolutionary changes, including the recruitment and activation of genes that are horizontally acquired (HGT) and the redeployment of existing genes and pathways in novel contexts. Here we address the latter aspect in Paulinella micropora KR01 (hereafter, KR01) that has independently evolved spliced leader (SL) trans‐splicing (SLTS) of nuclear–derived transcripts. We investigated the role of this process in gene regulation, novel gene origination, and endosymbiont integration. Our analysis shows that 20% of KR01 genes give rise to transcripts with at least one (but in some cases, multiple) sites of SL addition. This process, which often occurs at canonical cis‐splicing acceptor sites (internal introns), results in shorter transcripts that may produce 5′‐truncated proteins with novel functions. SL–truncated transcripts fall into four categories that may show: (i) altered protein localization, (ii) altered protein function, structure, or regulation, (iii) loss of valid alternative start codons, preventing translation, or (iv) multiple SL addition sites at the 5′‐terminus. The SL RNA genes required for SLTS are putatively absent in the heterotrophic sister lineage of photosynthetic Paulinella species. Moreover, a high proportion of transcripts derived from genes of endosymbiotic gene transfer (EGT) and HGT origin contain SL sequences. We hypothesize that truncation of transcripts by SL addition may facilitate the generation and expression of novel gene variants and that SLTS may have enhanced the activation and fixation of foreign genes in the host genome of the photosynthetic lineages, playing a key role in primary endosymbiont integration.

Trait‐mediated responses to aridity and experimental drought by springtail communities across Europe

AbstractThe capacity to forecast the effects of climate change on biodiversity largely relies on identifying traits capturing mechanistic relationships with the environment through standardized field experiments distributed across relevant spatial scales. The effects of short‐term experimental manipulations on local communities may overlap with regional climate gradients that have been operating during longer time periods. However, to the best of our knowledge, there are no studies simultaneously assessing such long‐term macroecological drivers with local climate manipulations.We analysed this issue with springtails (Class Collembola), one of the dominant soil fauna groups, in a standardized climate manipulation experiment conducted across six European countries encompassing broad climate gradients. We combined community data (near 20K specimens classified into 102 species) with 22 eco‐morphological traits and reconstructed their phylogenetic relationships to track the evolution of adaptations to live at different soil depths, which is key to cope with desiccation. We then applied joint species distribution models to investigate the combined effect of the regional aridity gradient with the local experimental treatment (drought and warming) over the assembly of springtail communities and tested for significant trait–environment relationships mediating their community‐level responses.Our results show (1) a convergent evolution in all three major collembolan lineages of species adapted to inhabit at different soil strata; (2) a clear signature of aridity selecting traits of more epigeic species at a biogeographical scale and (3) the association of short‐term experimental drought with traits related to more euedaphic life‐forms.The hemiedaphic condition would be the plesiomorphic state for Collembola while the adaptations for an epigeic life would have been secondarily gained. Epigeic springtails are not only more resistant to drought, but also have a higher dispersal capacity that allows them to seek more favourable micro‐habitats after experiencing drier conditions. The observed relative edaphization of the springtail communities after short‐term experimental drought may thus be a transient community response.The disparity between macroecological trends and fast community‐level responses after climate manipulations highlights the need of simultaneously assessing long‐term and short‐term drivers at broad spatial scales to adequately interpret trait–environment relationships and better forecast biodiversity responses to climate change.Read the freePlain Language Summaryfor this article on the Journal blog.

Where have all the heathers gone?

Heathers have been cultivated for several centuries, both the hardy heaths (Calluna, Daboecia and Erica) from the northern hemisphere and the more frost-tender species of Erica from southern Africa known as Cape heaths. In the late 19th century, a number of heather gardens were created, especially in Britain, and the popularity of heathers as long-lasting garden plants reached its zenith in western Europe and temperate North America in the late 20th century. At about the same time, deliberate breeding and selecting of Calluna vulgaris (ling) for flowers that lack normal sexual parts and remain bud-like led to a revolution in heather production with tens of millions of these bud-bloomer Calluna propagated each year for an ephemeral trade dominated by throwaway plants. Concomitantly, the diversity of hardy heathers offered by the trade has declined sharply with a small number of artificially raised clones, protected by plant breeders’ rights, now dominating the market. In contrast, the discovery of living lineages of a few Erica species that are extinct in the wild in South Africa has led to successful reintroduction programmes, particularly of Erica verticillata. The Erica Conservation Consortium, inaugurated in 2020, aims to coordinate and prioritise ex situ conservation of endangered Cape heaths.

DNA Barcoding versus Morphological Variability of Pterostichus brevicornis brevicornis (Kirby, 1837) (Coleoptera, Carabidae) in the Arctic and Subarctic.

Simple SummaryTaxonomic studies on a polymorphic species inhabiting a region with relatively uniform environmental conditions (e.g., the Arctic) should involve an integrative approach. Ground beetles such as the subgenus Cryobius of the genus Pterostichus are a successful group in expansion in the tundra biome. The current taxonomy of Cryobius species is unclear and could be considered an obstacle to ecological studies; knowledge of their distribution patterns in the Arctic is rather limited. In this study, the first report on the phylogeography and phylogeny of the most abundant tundra subspecies, P. (Cryobius) brevicornis brevicornis (Kirby, 1837), within its continuous range throughout northern Eurasia and North America is presented. The results indicated that the male genitalia morphology of P. b. brevicornis from Eurasian populations shared a higher geographic variability compared with the pronotum shape and the mitochondrial DNA sequences.The geographic patterns of genetic and morphological variability in ground beetles were examined throughout Northern Eurasia and North America using the most abundant circumpolar tundra subspecies, Pterostichus (Cryobius) brevicornis brevicornis (Kirby, 1837), as a model. Phylogenetic structure was assessed on the basis of a Bayesian approach using two DNA markers (partial sequences of the COI and 28S rRNA genes), while phylogeographic patterns and population genetic diversity were estimated using the COI gene only. Morphological patterns were analysed using elliptical Fourier coefficients that were calculated based on the pronotum and male genitalia shape outlines. The subspecies shares 23 COI haplotypes throughout its entire circumpolar range, while eight haplotypes of 28S rRNA were detected in Northern Eurasia. Phylogenetic analysis did not reveal subdivided species lineages with strict geographical imprint. The network, FST and uncorrected pairwise divergence analyses showed that the genetic distances between populations increase by longitude from Northeastern Asia to Europe. The genetic variability among the five studied geographical population groups of P. b. brevicornis was relatively high. The MANOVA showed significant regional divergence between local populations in Northern Eurasia based on both morphological markers, but only male genitalia variability was geographically structured. Neither the pronotum shape nor the male genitalia shape aligned with the phylogeographic patterns discovered on the basis of COI sequences. The genetic (COI) marker had more variation within, rather than among, population groups in addition to morphology of pronotum but not male genitalia.

Uniparental genetic markers to investigate hybridization in wild-born marmosets with a mixed phenotype among Callithrix aurita and invasive species

The native marmoset of the Southeastern Atlantic Forest in Brazil is among the 25 most endangered primates of the world. Hybridization with alien species is one of its main threats registered since the early 2000s based on phenotype, so far, without genetic confirmation. Using uniparental molecular markers, we analyzed 18 putative hybrids, captured from 2004 to 2013 in different localities of the Atlantic Forest. A nine base pair deletion in the SRY gene of C. aurita was used to investigate paternal ancestry. Maternal ancestry was assessed by DNA sequencing of ca. 455 bp from the COX2 gene. Hybridization was confirmed for 16 out of the 18 marmosets since they inherited COX2 haplotypes of the alien C. penicillata or C. jacchus and the SRY deletion specific to C. aurita. Two individuals inherited both parental lineages of C. aurita, which is probably related to backcrossing or hybrid interbreeding. The direction of hybridization of females with the matrilineal lineage of invasive species with males descending from the native lineage was predominant in our sampling. This is the first time that hybridization between C. aurita and invasive species has been confirmed through genetic analysis.

Niche Divergence at Intraspecific Level in the Hyrcanian Wood Frog, Rana pseudodalmatina: A Phylogenetic, Climatic, and Environmental Survey

The role of ecological niche divergence in lineage speciation has recently stimulated the interest of evolutionary biologists and ecologists. Phylogenetic analysis has revealed that the Hyrcanian wood frog,Rana pseudodalmatina, has diverged into two western and eastern regional clades (WRC and ERC) within the Hyrcanian forest. The goal of this study was to investigate whether the ecological niches of WRC and ERC are conserved or diverged, as well as to figure out what variables promote niche conservatism or divergence. For this purpose, the maximum entropy model was employed to assess environmental niche modeling in geographical (G) space utilizing climatic and macro-environmental data. The niche overlap, equivalency, and similarity tests based on PCAenvanalyses were used to assess niche divergence or conservatism in environmental (E) space. The findings strongly support the hypothesis that WRC and ERC have undergone substantial niche divergence and are constrained by a unique set of climatic and macro-environmental conditions. This study by ecological niche comparisons based on phylogenetic data provides new insights into the exploration of species diversification processes in the Hyrcanian forests.

Discovery of a genetically distinct lineage in medaka species within Lake Towuti in central Sulawesi

Discovery of a genetically distinct lineage in medaka species within Lake Towuti in central Sulawesi

Comparative cytogenetics among Boana species (Anura, Hylidae): focus on evolutionary variability of repetitive DNA.

Boana comprises a diverse genus of Neotropical treefrogs, currently rearranged into seven taxonomic species groups. Although cytogenetic studies have demonstrated diversity in its representatives, the chromosomal mapping of repetitive DNA sequences is still scarce. In this study, Boana albopunctata, Boana faber, and Boana prasina were subjected to in situ localization of different repetitive DNA units to evaluate trends of chromosomal evolution in this genus. Boana faber and B. prasina had 2n=24 chromosomes, while B. albopunctata has 2n=22 and an intra-individual variation related to the presence/absence of one B chromosome. The location of 45S rDNA sites was different in the analyzed karyotypes, corroborating with what was found in the distinct phylogenetic groups of Boana. We presented the first description of 5S rDNA in a Boana species, which showed markings resulting from transposition/translocation mechanisms. In situ localization of microsatellite loci proved to be a helpful marker for karyotype comparison in Boana, commonly with cis accumulation in the heterochromatin. On the other hand, genomic dispersion of microsatellites may be associated with hitchhiking effects during the spreading of transposable elements. The obtained results corroborated the independent diversification of these lineages of species from three distinct phylogenetic groups of Boana.

Biogeography and Ecological Differentiation of Pseudasphondylia gall midges (Diptera: Cecidomyiidae) Distributed in Taiwan and Japan, with Description of a New Species P. kiwiphila sp. nov. and the Southernmost Record of P. elaeocarpi.

Pseudasphondylia species (Diptera: Cecidomyiidae) are known to induce fruit galls on Actinidia rufa (Siebold & Zucc.) Planch. ex Miq. and finger-like leaf galls on Elaeocarpus sylvestris (Lour.) Poir. in Taiwan, but their taxonomic positions remain undetermined. Based on gall morphology and host plants, they were supposed to be the same or allied species of known Japanese congeners, i.e., P. matatabi Yuasa & Kumazawa inducing flower-bud galls on Actinidia polygama (Sieb. et Zucc.) Maxim and P. elaeocarpi Tokuda & Yukawa inducing finger-like leaf galls on E. sylvestris. Species identifications of these Taiwanese species provide us an opportunity to study biogeographical aspects and transition of ecological features in these Pseudasphondylia species distributed in East Asian Arc. Morphological comparisons and species delimitation by molecular analysis indicated that the cecidomyiid on the fruit of A. rufa is distinct from P. matatabi and thus it is described as a species new to science, P. kiwiphila sp. nov. Lin, Tokuda, & Yang. The leaf galler on E. sylvestris was identical to P. elaeocarpi, whose southernmost distribution range extended to Taiwan, a new record of its distribution. COI-based phylogenetic tree (Bayesian inference and IQ tree) of Pseudasphondylia suggested that leaf galling habitat and univoltine life history are ancestral, whereas fruit or flower-bud galling and multivoltine life history are derived. In addition, the monophyletic Actinidia-associated species lineage is sistered to the clade including the remaining Japanese fruit and flower-bud gallers, suggesting that Pseudasphondylia has colonized on the host genus Actinidia once and later speciated on different plant species of the host genus. As a biogeographical aspect of P. elaeocarpi, 2.7% of the COI distance between Japanese and Taiwanese individuals indicates that they have diverged around 1.2 mya, which corresponds to the last but second separation of Taiwan and Japan in the Pleistocene. As for Actinidia-associated Pseudasphondylia species, the two valid species are allopatric and have distinct areas of origin, suggesting they may have speciated allopatrically. Nevertheless, there is still the possibility of ecological speciation due to the following reasons: (1) Host species (and varieties) and unidentified congener of Actinidia-associated Pseudasphondylia are occurring China, revealing potential occurrence of these gall midges. (2) The divergence time (2.2-2.9 mya) of the two known species corresponds to the late Pliocene to Pleistocene, when China, Taiwan, and Japan were part of the East Asian continent. During this period, their host species were sympatric in southeast China. (3) The host of two named Actinidia-associated Pseudasphondylia species each belong to different plant groups with distinct fruit features. These presume that the speciation might have been caused via sympatric host shift.

Demographic history and range modelling of the East Mediterranean Abies cilicica

The Mediterranean Basin is one of the 36 global hotspots of biodiversity and it is rich in endemic tree species. The complex geological history of the region throughout the Neogene and Quaternary periods that were marked with several palaeoclimatic transformations was a major factor triggering the genetic divergence of lineages in tree species in the region. The ongoing global climate change is the main factor threatening Mediterranean biodiversity. The risk of population decline related to aridization is the highest in the case of endemics, especially for cold-adapted conifers, such as Abies cilicica. The Cilician fir grows in the East Mediterranean mountains that constitute a local centre of endemism within the region. The species range is fragmented and small-size populations prevail. Previous studies have suggested that the last glacial cycle led to a significant reduction in the species range and might have initiated genetic divergence. As a result, two lineages are currently recognized at the subspecies level, A. cilicica subsp. isaurica (Turkey) and A. cilicica subsp. cilicica (Turkey, Syria, and Lebanon). The predictions about the impact of future climate changes in the East Mediterranean suggest a profound reduction of precipitation and overall warming that may put the remnant populations of A. cilicica at a risk of decline. Here, we used the Bayesian approach to investigate the demographic history of endemic A. cilicica. Specifically, we estimated the probable time of the intraspecies divergence to verify previous assumptions about the species’ evolutionary history. Additionally, niche modelling was used to outline the potential range of changes in the past and to indicate glacial refugia in where the species persisted climate crisis. This approach was also used to explore the possible influence of the future climate changes on the distribution of A. cilicica in the region. Our results demonstrate that the divergence between the Lebanese and the Turkish populations that occurred ~220 ka years BP coincided with the Riss glaciation. According to palaeoecological data, in the East Mediterranean, that glacial period caused a severe reduction in the populations of woody species due to the aridity of the climate. At that time, the Lebanese-Syrian part of the range was likely disconnected from the main range. The second split was induced by the last glacial cycle ~60 ka years BP and led to the separation of the Central Taurus and East Taurus population and, consequently, to the formation of the two subspecies. Niche modelling for the last glacial maximum has allowed us to locate the probable refugia for A. cilicica in the western Anatolia and Syria-Lebanon area. A projection of the future possible distribution of the species indicates a serious reduction of the range during this century.

Diversity of Land Snail Tribe Helicini (Gastropoda: Stylommatophora: Helicidae): Where Do We Stand after 20 Years of Sequencing Mitochondrial Markers?

Sequences of mitochondrial genes revolutionized the understanding of animal diversity and continue to be an important tool in biodiversity research. In the tribe Helicini, a prominent group of the western Palaearctic land snail fauna, mitochondrial data accumulating since the 2000s helped to newly delimit genera, inform species-level taxonomy and reconstruct past range dynamics. We combined the published data with own unpublished sequences and provide a detailed overview of what they revealed about the diversity of the group. The delimitation of Helix is revised by placing Helix godetiana back in the genus and new synonymies are suggested within the genera Codringtonia and Helix. The spatial distribution of intraspecific mitochondrial lineages of several species is shown for the first time. Comparisons between species reveal considerable variation in distribution patterns of intraspecific lineages, from broad postglacial distributions to regions with a fine-scale pattern of allopatric lineage replacement. To provide a baseline for further research and information for anyone re-using the data, we thoroughly discuss the gaps in the current dataset, focusing on both taxonomic and geographic coverage. Thanks to the wealth of data already amassed and the relative ease with which they can be obtained, mitochondrial sequences remain an important source of information on intraspecific diversity over large areas and taxa.

Multilocus-phylogeny of the lichen-forming genus Bacidia s. str. (Ramalinaceae, Lecanorales) with special emphasis on the Russian Far East

AbstractTo clarify deep relationships among species lineages within Bacidia s. str., and to investigate the robustness of the deeper branches, we combined data from three traditionally used RNA-coding genes (nrITS, nrLSU and mtSSU) with two protein-coding genes (RPB1 and RPB2). The multigene phylogeny contained 48 newly generated sequences from the Russian Far East and all Bacidia s. str. sequences from GenBank (131 sequences). We subjected the alignments for the single and concatenated data sets to Bayesian inference (BI) and two maximum likelihood (ML) analyses (RAxML and IQ-TREE). The topologies of phylogenetic trees recovered from BI and ML analyses were highly concordant. The multilocus phylogeny of Bacidia s. str. was congruent with previous results based on nrITS sequences from the Russian Far East but with considerably higher support values for most of the deeper branches. A correlation between the recovered clades and apothecial pigments in the upper part of the hymenium and lateral exciple was observed. Based on morphological and molecular evidence, Bacidia obtecta is described as new to science. It was recovered as the sister lineage of B. elongata. The two species are alike in having up to four enlarged lumina cells along the exciple edge, but B. obtecta differs in the abundant crystals found in the upper hymenium and lateral exciple, and by having spores with fewer septa.

Increased reproductive trait diversity, evolutionary history and distinctiveness during the succession of tropical forest

AbstractQuestionsDo old‐growth forests retain more evolutionary history and more reproductive trait diversity along the successional gradient? How similar are the phylogenetic branches and reproductive attributes at each phase? In which succession stages are distinct lineages of trees and shrubs present? Do distinct lineages have distinct traits? Is there a turnover of species, lineages and traits of trees and shrubs along the successional gradient?LocationAtlantic Forest, Reserva Natural Guaricica (25°19′ S, 45°42′ W) and Reserva Natural das Águas (25°21′ S, 48°46′ W), Antonina, Paraná, southern Brazil.MethodsWe assessed the variation of alpha and beta taxonomic, functional and phylogenetic diversities of tree and shrub communities along a successional gradient (phase 1, stand initiation phase, from 0 to 9 years old; phase 2, stem exclusion phase, 10–25 years old; and phase 3, understorey re‐initiation phase, 25–200 years old). We also evaluated the occurrence of distinct lineages and traits related to seed dispersal and pollination.ResultsIn addition to the expected change in species composition, lineages and trait states and values were replaced along the chronosequence, with stronger variation for trees. Old‐growth forests harbor distinct lineages and traits and a greater amount of evolutionary history and functional diversity of reproductive traits. We also found that distinct lineages were those that performed distinct functions.ConclusionsOur study showed that as the succession proceeds, turnover of lineages and traits occurred, with the understorey re‐initiation stage harboring the largest taxonomic, phylogenetic and functional diversity. In addition, understories of the re‐initiation stage are important for the occurrence of distinct lineages, such as magnoliids, and of distinct traits, such as large fruits and seeds, which highlights the importance of conservation of old‐growth forests, and its preservation can prevent the loss of distinct evolutionary histories and functions.

Pathogen-driven coevolution across the CBP60 plant immune regulator subfamilies confers resilience on the regulator module.

Components of the plant immune signaling network need mechanisms that confer resilience against fast-evolving pathogen effectors that target them. Among eight Arabidopsis CaM-Binding Protein (CBP) 60 family members, AtCBP60g and AtSARD1 are partially functionally redundant, major positive immune regulators, and AtCBP60a is a negative immune regulator. We investigated possible resilience-conferring evolutionary mechanisms among the CBP60a, CBP60g and SARD1 immune regulatory subfamilies. Phylogenetic analysis was used to investigate the times of CBP60 subfamily neofunctionalization. Then, using the pairwise distance rank based on the newly developed analytical platform Protein Evolution Analysis in a Euclidean Space (PEAES), hypotheses of specific coevolutionary mechanisms that could confer resilience on the regulator module were tested. The immune regulator subfamilies diversified around the time of angiosperm divergence and have been evolving very quickly. We detected significant coevolutionary interactions across the immune regulator subfamilies in all of 12 diverse core eudicot species lineages tested. The coevolutionary interactions were consistent with the hypothesized coevolution mechanisms. Despite their unusually fast evolution, members across the CBP60 immune regulator subfamilies have influenced the evolution of each other long after their diversification in a way that could confer resilience on the immune regulator module against fast-evolving pathogen effectors.