A molecular systematic analysis of the N eotropical banner winged damselflies ( P olythoridae: O donata)

Dermatophagoides farinae (Acari: Pyroglyphidae) has been reported as one of the major sources of indoor allergens that trigger allergic disease in humans. In this study, the genetic diversity and differentiation of nine geographic populations of D. farinae were investigated by analyzing mitochondrial and nuclear genes (COI, Cytb, COI+Cytb, and ITS). The results showed high genetic diversity across the D. farinae populations. The BX (Benxi) population showed the lowest genetic diversity, possibly due to climatic causes. Significant genetic differentiation was observed among D. farinae populations based on mitochondrial genes. The analysis of molecular variance (AMOVA) results elucidated that the contribution to the rate of variation was primarily from among populations. Phylogenetic analysis and haplotype network based on mitochondrial genes both indicated significant geographic structure among D. farinae populations. The nine geographic populations of D. farinae were divided into two groups with the Qinling Mountains-Huai River Line serving as the boundary for spatial analysis of molecular variance analysis (SAMOVA). However, the Mantel test analysis showed no association between genetic differentiation and geographic distance because of the high level of gene flow among some populations through the transportation of stored food. Overall, these results indicate both significant genetic differentiation among D. farinae populations, but also significant gene exchange between them. Results from the analysis of the nuclear gene ITS differed from the mitochondrial genes due to differences in molecular markers between mitochondrial genes and nuclear genes. These observations improve our understanding of the genetic diversity and structure of D. farinae populations.

Two species ofCallithrix,C. jacchus(Linnaeus, 1758) andC. penicillata(É. Geoffroy, 1812), are considered invasive in Rio de Janeiro. This study determined the genetic and morphological diversity and verified the species involved in the hybridization of 10 individuals from the municipalities of Silva Jardim (N = 9) and Rio das Ostras (N = 1). We compared the external morphology and skull ofC. jacchus(N = 15) andC. penicillata(N = 14) specimens deposited in the collection of the National Museum of Rio de Janeiro (MN- UFRJ). Phylogenetic (maximum likelihood and Bayesian inference) and phylogeographical analyses (network analysis) were performed based on cytochrome b sequences. These analyses included hybrids from the metropolitan region of Rio de Janeiro (N = 3),C. penicillata(N = 2),C. jacchus(N = 2),C. geoffroyi(N = 2),C. kuhlii(N = 2),C. aurita(N = 1), and as outgroups,Mico emiliae(N = 1) andSaguinus mystax(N = 1). The pelage and skull characters of most hybrids were more closely related toC. jacchus. Skull morphometric analysis revealed an intermediate state for the hybrids. Phylogenetic analyses revealed a high similarity between the hybrids andC. penicillata. Six haplotypes of hybrids were identified. Network analysis including them andC. penicillatarecovered the topology generated by phylogenetic analysis. The results corroborate thatC. jacchusandC. penicillataparticipate in the hybridization process. There was no geographic structure between hybrids from the coastal lowlands and from the metropolitan region of Rio de Janeiro.

Taxonomic recommendations for British birds: seventh report

BackgroundThe earliest fossil evidence of terrestrial animal activity is from the Ordovician, ~450 million years ago (Ma). However, there are earlier animal fossils, and most molecular clocks suggest a deep origin of animal phyla in the Precambrian, leaving open the possibility that animals colonized land much earlier than the Ordovician. To further investigate the time of colonization of land by animals, we sequenced two nuclear genes, glyceraldehyde-3-phosphate dehydrogenase and enolase, in representative arthropods and conducted phylogenetic and molecular clock analyses of those and other available DNA and protein sequence data. To assess the robustness of animal molecular clocks, we estimated the deuterostome-arthropod divergence using the arthropod fossil record for calibration and tunicate instead of vertebrate sequences to represent Deuterostomia. Nine nuclear and 15 mitochondrial genes were used in phylogenetic analyses and 61 genes were used in molecular clock analyses.ResultsSignificant support was found for the unconventional pairing of myriapods (millipedes and centipedes) with chelicerates (spiders, scorpions, horseshoe crabs, etc.) using nuclear and mitochondrial genes. Our estimated time for the divergence of millipedes (Diplopoda) and centipedes (Chilopoda) was 442 ± 50 Ma, and the divergence of insects and crustaceans was estimated as 666 ± 58 Ma. Our results also agree with previous studies suggesting a deep divergence (~1100 – 900 Ma) for arthropods and deuterostomes, considerably predating the Cambrian Explosion seen in the animal fossil record.ConclusionsThe consistent support for a close relationship between myriapods and chelicerates, using mitochondrial and nuclear genes and different methods of analysis, suggests that this unexpected result is not an artefact of analysis. We propose the name Myriochelata for this group of animals, which includes many that immobilize prey with venom. Our molecular clock analyses using arthropod fossil calibrations support earlier studies using vertebrate calibrations in finding that deuterostomes and arthropods diverged hundreds of millions of years before the Cambrian explosion. However, our molecular time estimate for the divergence of millipedes and centipedes is close to the divergence time inferred from fossils. This suggests that arthropods may have adapted to the terrestrial environment relatively late in their evolutionary history.

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Phelipanche aegyptiaca is one of the most noxious parasitic weedy broomrapes in Xinjiang, China. Understanding its morphological polymorphism and genetic diversity can support effective control strategies. This study investigated the morphological and genetic diversity among and within populations from different geographical regions and host species across Xinjiang to characterize their relationships. Thirteen ISSR primers were used, resulting in 173 clear bands, 172 of which (99%) were polymorphic. Significant genetic variations were observed within regional and host groups, while variation among groups was relatively low. Gene flow was frequent, with a significant correlation of 1.57 between geographic regions and 5.57 between host species groups. Morphological traits exhibited substantial variability, with diverse coefficients ranging from 16% to 50%. Canonical correspondence analysis indicated that samples primarily clustered by region, not by host species. There was a significant correlation between morphological and genetic diversity across geographical groups. The findings suggest that genetic and morphological diversity are key factors in the expansion of P. aegyptiaca's host-range and its spread. Morphological diversity appears to result from the interaction between genetic variation and environmental factors. This study offers new insights into the adaptation and evolution of P. aegyptiaca in relation to its genetic, morphological diversity and dissemination. © 2024 Society of Chemical Industry.

With its distinctive evolutionary rate and inheritance patterns separate from the nuclear genome, mitochondrial genome analysis has become a prominent focus of current research. Dendrobium hancockii Rolfe, a species of orchid with both medicinal and horticultural value, will benefit from the application of the fully assembled and annotated mitochondrial genome. This will aid in elucidating its phylogenetic relationships, comparative genomics, and population genetic diversity. Based on sequencing results from Illumina combined with PacBio and Nanopore, the mitochondrial genome map of D. hancockii was constructed. Comparative analysis was conducted from the perspectives of phylogeny across multiple species, selection pressure on protein-coding genes, and homologous segments. The population diversity of D. hancockii was analyzed using single nucleotide polymorphism (SNP) data from the mitochondrial genome and single-copy nuclear genes. This research constructed a circular mitochondrial map for D. hancockii, spanning 523,952 bp, containing 40 unique protein-coding genes, 37 transfer RNA genes, and 4 ribosomal RNA genes. Comparative analysis of mitochondrial genes from 26 land plants revealed a conserved gene cluster, "rpl16-ccmFn-rps3-rps19," particularly within the Dendrobium genus. The mitochondrial genome of D. hancockii exhibits a lower point mutation rate but significant structural variation. Analysis of 103 resequencing samples identified 19,101 SNP sites, dividing D. hancockii into two major groups with limited gene flow between them, as supported by population diversity, genetic structure analysis, principal component analysis, and phylogenetic trees. The geographical distribution and genetic differentiation of D. hancockii into two major groups suggest a clear phytogeographical division, likely driven by ancient geological or climatic events. The close alignment of mitochondrial data with nuclear gene data highlights the potential of the mitochondrial genome for future studies on genetic evolution in this species.

Phylogenetic relationships among Boleosoma darter species (Percidae: Etheostoma)

Animal phylogeny

Understanding the genetic diversity and distribution patterns of seaweeds species is crucial for evaluating key regions of high genetic diversity. Identifying hotspots of high intraspecific diversity is an important step for developing conservation strategies. Grateloupia is a diverse genus of Rhodophyta, many of which are resource of numerous useful bioactive compounds; therefore, the genus is valuable target for conservation. The aim of this study is to examine the genetic diversity and population structure of two Grateloupia species, Grateloupia asiatica and Grateloupia jejuensis, with the understanding of the phylogeography of the Korean genetic diversity hotspot for two species. Plastid rbcL gene sequences of 134 specimens of G. asiatica and 112 specimens of G. jejuensis collected from the Korean coast were analyzed. We evaluated the number of haplotypes, genetic diversity (haplotype and nucleotide diversity), and haplotype networks of two species. Historical demographic was inferred by calculating neutrality tests and genetic differentiation was estimated using the fixation index, FST. Our results show that both species are generally similar in geographical distribution patterns, that is, relatively homogeneous with few haplotypes derived from the most frequent haplotype. The east coast of Korea is identified as a 'hotspot' with the highest genetic diversity for both species, whereas Jeju Island is identified as a 'cold spot' with the lowest genetic diversity for G. jejuensis. Analyses across most distribution ranges of the two species in Korea reveal low genetic and haplotype diversities, which could indicate that these two Grateloupia species have either experienced a historical lack of diversity or a recent reduction in diversity due to high gene flow. The low genetic diversity values found in the present study raise considerable concern about the conservation status of these two Grateloupia species and highlight the need to locate further hotspots of genetic diversity to strengthen their resilience against further decline.

Raspberry bushy dwarf virus (RBDV) is a long-known virus naturally infecting Rubus and grapevine. It is also one of the economically most important viruses of raspberries, but there are only a limited number of sequences covering a substantial part of the genome available in the databases. The aim of this study was: i) to study the geographic distribution of RBDV in Slovenia, and ii) to sequence RNA2 of several red raspberry and grapevine RBDV isolates and study their phylogeny and population structure. Geographic distribution studies were performed over a period of 13 years in three wine-growing regions of Slovenia (Primorska, Podravje and Posavje). The highest incidence of RBDV was found in Podravje (58.8%) and the lowest in Primorska (5.1%). Big differences were observed between Vipavska dolina (10.2%) and three other wine-growing districts of Primorska region (0.4–1.2%). Almost complete RNA2 sequences were obtained for four red raspberry isolates and seven grapevine isolates. Additionally, only coat protein sequences were obtained for three red raspberry isolates. Phylogenetic and population diversity analyses were performed on all available RBDV sequences. Phylogenetic analysis has shown clear differences in sequences from Rubus and grapevine that form two highly supported clades. In RNA2 analysis additional two sub-clades were found in grapevine clade. Two major subclades were identified also in the Rubus clade with further differentiation within these subclades. Purifying or stabilizing selection was found to be acting on both, CP and MP genes while few codons were found to be under positive selection.

Five chloroplast coding and non-coding regions, one mitochondrial gene and its associated intron, and part of one nuclear ribosomal gene were sequenced, giving a total included aligned length of 7,845 bp. Samples from six collections, representing five species of Jensenia from South America, Malaysia, and New Zealand, four collections belonging to three species of Pallavicinia and one collection of Podomitrium phyllanthus comprised the ingroup, which was rooted on Symphyogyna marginata. Phylogenetic analysis under the maximum parsimony and maximum likelihood criteria support Jensenia as monophyletic. Within Jensenia, two monophyletic clades are resolved, one comprising the four Latin American collections and the other, the Malayasian and New Zealand species; however, this is based on only 16 parsimony informative characters. The lack of informative characters within Jensenia suggests that the divergence among taxa is relatively recent, rather than Gondwanan, as has been hypothesized based on geographical distribution. A corollary of this is that the present day distribution of Jensenia is likely the product of dispersal rather than vicariance.

Aim In this study we present a molecular phylogenetic and phylogeographical analysis of Peltophryne (Anura: Bufonidae), an endemic genus of Antillean toads, to investigate the spatial and temporal origins of the genus, with particular focus on the eight Cuban species.Location Greater Antilles, with extensive sampling of the Cuban archipelago.Methods We obtained DNA sequence data from two mitochondrial genes, cytochrome c oxidase subunit I (COI) and ribosomal RNA (16S), for 124 toads representing all eight Cuban species, and combined this with published data from Hispaniola (one of three species) and Puerto Rico (one of one species) to establish a molecular phylogeny for Peltophryne. In addition, we explored the phylogeographical structure of widespread Cuban species. For a subset of 42 toads we also obtained DNA sequence data from two nuclear genes, recombination activator‐1 (RAG‐1) and chemokine receptor 4 (CXCR‐4). We combined our molecular data with published DNA sequences from a global sample of bufonid toads to place the spatial and temporal origins of Peltophryne in the Caribbean within a fuller geographical and phylogenetic context.Results All phylogenetic analyses supported the monophyly of West Indian toads. The ancestor of Peltophyrne diverged from its mainland source around the Eocene–Oligocene boundary, with a subsequent radiation across the Caribbean islands taking place during the Miocene. Cuban species are monophyletic with a basal split in the early–middle Miocene that separates extant small‐bodied from large‐bodied species. Extensive mitochondrial DNA (mtDNA) sampling within widespread Cuban species revealed contrasting phylogeographical patterns. Peltophryne taladai and P. empusa showed deeply divergent lineages, whereas no geographical structure was observed in the widespread P. peltocephala.Main conclusions Our timeline for Peltophryne diversification is consistent with a biogeographical model requiring no long‐distance overwater dispersal. Although confidence intervals on divergence time estimates are wide, the stem age of Peltophyrne coincides with the hypothesized GAARlandia landspan or archipelago, which may have connected South America briefly with the Antilles. The ages of Peltophryne for Puerto Rico, Hispaniola and Cuba are consistent with a recently proposed vicariance scenario for the region. Our molecular results support the recognition of all eight species in Cuba, and provide evidence of possible cryptic species.

Chagas disease remains the most important parasitic infection in Latin America. The aetiological agent, Trypanosoma cruzi (Kinetoplastida: Trypanosomatidae), is a complex vector-borne zoonosis transmitted in the faeces of hematophagous triatomine bugs (Hemiptera: Reduviidae: Triatominae), and maintained by mammalian reservoir hosts ranging from the southern United States to Argentinean Patagonia. In the absence of chemotherapy, infection is life-long and can lead to a spectrum of pathological sequelae ranging from subclinical to lethal cardiac and/or gastrointestinal complications in up to 30% of patients. T. cruzi displays remarkable genetic diversity, which has long been suspected to contribute to the considerable variation in clinical symptoms observed between endemic regions. Currently, isolates of T. cruzi can be assigned to a minimum of six stable genetic lineages or discrete typing units (DTUs) (TcI-TcVI), which are broadly associated with disparate ecologies, transmission cycles and geographical distributions. The principal mode of reproduction among T. cruzi strains is the subject of an intense, decades-old debate. Despite the existence of two recent natural hybrid lineages (TcV and TcVI), which resemble meiotic F1 progeny, a pervasive view is that recombination has been restrained at an evolutionary scale and is of little epidemiological relevance to contemporary parasite populations. The aim of this PhD project was to investigate T. cruzi genetic diversity through significant development of phylogenetic markers and their application to the characterization of natural parasite population structures and genetic exchange mechanisms. Multiple, single-copy, chromosomally-independent, nuclear housekeeping genes were assessed initially for their ability to allocate isolates to DTU-level, to facilitate higher resolution intra-lineage analyses and finally for their inclusion alongside additional targets in a standardized T. cruzi multilocus sequence typing (nMLST) scheme. For the immediate future, nuclear MLST, using a panel of four to seven nuclear loci, is a robust, reproducible and highly discriminatory method that has potential to become the new gold standard for T. cruzi DTU assignment. To investigate natural parasite population structures and uncover evidence of genetic exchange, a high resolution mitochondrial MLST (mtMLST) scheme, based on ten gene fragments, was developed and evaluated against current nuclear markers (multilocus microsatellite typing; MLMT) using isolates belonging to the oldest and most widely distributed lineage (TcI). Observations of gross nuclear-mitochondrial phylogenetic incongruence indicate that recombination is ongoing, geographically widespread and continues to influence natural populations, challenging the traditional paradigm of clonality in T. cruzi. Application of this combined nuclear-mitochondrial methodology to intensively sampled, minimally-subdivided TcI populations revealed extensive mitochondrial introgression within a disease focus in North-East Colombia as well as among arboreal transmission cycles in Bolivia. Failure to detect any reciprocal nuclear hybridization among recombinant strains ! 4 may be indicative of alternate, cryptic mating strategies in T. cruzi, which are challenging to reconcile with both in vitro parasexual mechanisms of genetic exchange described, and patterns of Mendelian allele inheritance among natural hybrid DTUs. High resolution genotyping of TcI populations was also undertaken to explore the interaction between parasite genetic heterogeneity and ecological biodiversity, exposing the significant impact human activity has had on T. cruzi evolution. Reduced genetic diversity, accelerated parasite dissemination between densely populated areas and mitochondrial gene flow between domestic and sylvatic populations, suggests humans may have played a crucial role in T. cruzi dispersal across the Bolivian highlands. Parallel reductions in genetic diversity were observed among isolates from the Brazilian Atlantic Forest, attributable to ongoing anthropogenic habitat fragmentation. By comparison domestic TcI isolates (TcIDOM) are divergent from their sylvatic counterparts, but also genetically homogeneous, and likely to have originated in North/Central America before distribution southwards. Molecular dating of Colombian TcIDOM clones confirmed that this clade emerged 23,000 ± 12,000 years, coinciding with the earliest human migration into South America. Lastly, Illumina amplicon deep sequencing markers were developed to explore the interaction between parasite multiclonality and clinical status of chronic Chagas disease. An unprecedented level of intra-host genetic diversity was detected, highlighting putative diversifying selection affecting antigenic surface proteases, which may facilitate survival in the mammalian host. In lieu of comparative genomics of representative T. cruzi field isolates, not yet a reality, as is the case with other more experimentally-tractable trypanosomatids, presented herein are some of the highest resolution genotyping techniques developed in T. cruzi to date, which have the potential to expand our current understanding of parasite genetic diversity and its relevance to clinical outcome of Chagas disease.

Gene–Gene Concordance and the Phylogenetic Relationships among Rare and Widespread Pygmy Sunfishes (Genus Elassoma)