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Application of Phylogenetic Networks in Evolutionary Studies.
Abstract
The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, ...
... In order to analyze the nuclear fraction of our data, we mapped reads of each sample to our C. pyrenaica transcriptome reference (total length: 58,236,171 bp;Lopez et al., 2017). For 63 samples with sufficient nuclear sequence data quality (62 Cochlearia samples and Ionopsidium megalospermum), we generated a phylogenetic network using SplitsTree (Huson, 1998;Huson and Bryant, 2006) based on 447,919 biallelic SNPs. Concordant with our cytogenetic results, the network shows a clear separation of Arctic and European diploid taxa (Figure 3a and b; see Appendix 1-figure 11 for detailed SplitsTree output). ...
... Aside from the ML tree search, we used SplitsTree version 4.15.1 (Huson, 1998;Huson and Bryant, 2006) to investigate conflicting or reticulate phylogenetic relationships. The input file was generated from the 'all samples' vcf file (447,919 hard-filtered variant sites) using the Python script 'vcf2phylip' (Ortiz, 2019). ...
With accelerating global warming, understanding the evolutionary dynamics of plant adaptation to environmental change is increasingly urgent. Here we reveal the enigmatic history of the genus Cochlearia (Brassicaceae), a Pleistocene relic that originated from a drought-adapted Mediterranean sister genus during the Miocene. Cochlearia rapidly diversified and adapted to circum-Arctic regions and other cold-characterized habitat types during the Pleistocene. This sudden change in ecological preferences was accompanied by a highly complex, reticulate polyploid evolution, which was apparently triggered by the impact of repeated Pleistocene glaciation cycles. Our results illustrate that two early diversified arctic-alpine diploid gene pools contributed differently to the evolution of this young polyploid genus now captured in a cold-adapted niche. Metabolomics revealed central carbon metabolism responses to cold in diverse species and ecotypes, likely due to continuous connections to cold habitats that may have facilitated widespread adaptation to alpine and subalpine habitats, and which we speculate were coopted from existing drought adaptations. Given the growing scientific interest in adaptive evolution of temperature-related traits, our results provide much-needed taxonomic and phylogenomic resolution of a model system as well as first insights into the origins of its adaptation to cold.
... To further validate the evolutionary relationships of sect. Daghestanica, we used SplitsTree4 (Hudson and Bryant 2006) to reconstruct phylogenetic neighbour-net graphics just including the samples of sect. Daghestanica and A. carolinianum 1-4 collected in Qinghai. ...
... The inter-clade and interspecific relationships were also not well resolved by the tree-based phylogeny ( Fig. 3A and B). However, network methods provide a valuable tool for such uncertain phylogenetic science (Hudson and Bryant 2006). Our uncorrected_P-distance-based networks indicated that Asian A. maowenense, A. xinlongense and A. caroliniarum have a closer genetic relationship with Caucasian-European group; and Asian A. maowenense and Caucasian species could be at the base of sect. ...
The disjunctive distribution (Europe-Caucasus-Asia) and species diversification across Eurasia for the genus Allium sect. Daghestanica has fascinating attractions for researchers aiming to understanding the development and history of the modern Eurasia flora. However, no any studies have been carried out to address the evolutionary history of this section. Based on the nrITS and cpDNA fragments (trnL-trnF and rpl32-trnL), the evolutionary history of the third evolutionary line (EL3) of the genus Allium was reconstructed and we further elucidate the evolutionary line of sect. Daghestanica under this background. Our molecular phylogeny recovered two highly supported clades in sect. Daghestanica: the Clade I includes Caucasian-European species and Asian A. maowenense, A. xinlongense and A. carolinianum collected in Qinghai; the Clade II comprises Asian yellowish tepal species, A. chrysanthum, A. chrysocephalum, A. herderianum, A. rude and A. xichuanense. The divergence time estimation and biogeography inference indicated that Asian ancestor located in the QTP and the adjacent region could have migrated to Caucasus and Europe distributions around the Late Miocene and resulted in further divergence and speciation; Asian ancestor underwent the rapid radiation in the QTP and the adjacent region most likely due to the heterogeneous ecology of the QTP resulted from the orogeneses around 4–3 Mya. Our study provides a picture to understand the origin and species diversification across Eurasia for sect. Daghestanica.
... The Nei D A genetic distances were estimated in POPULATIONS v. 1.2.28 [23]. The Neighbor-Net method [24] as implemented in SPLITSTREE4 v. 4.14.4 software [25] was used to compute a network based on Nei distances to graphically represent breed relationships and admixture. The Factorial Correspondence Analysis (FCA) considering data for populations and groups of populations were performed using the GENETIX v. 4.04 software [22]. ...
American Criollo pigs are thought to descend mainly from those imported from the Iberian Peninsula starting in the late 15th century. Criollo pigs subsequently expanded throughout the Americas, adapting to very diverse environments, and possibly receiving influences from other origins. With the intensification of agriculture in the mid-20th century, cosmopolitan breeds largely replaced Criollo pigs, and the few remaining are mostly maintained by rural communities in marginal areas where they still play an important socioeconomic and cultural role. In this study, we used 24 microsatellite markers in samples from 1715 pigs representing 46 breeds with worldwide distribution, including 17 American Criollo breeds, with the major focus of investigating their genetic diversity, structure and breed relationships. We also included representatives of the Iberian, Local British, Hungarian, Chinese and Commercial breeds, as well as Wild Boar, in order to investigate their possible influence in the genetic composition of Criollos. Our results show that, when compared with the other breeds, Criollo pigs present higher levels of genetic diversity, both in terms of allelic diversity and expected heterozygosity. The various analyses indicate that breed differentiation overall explains nearly 21% of the total genetic diversity. Criollo breeds showed their own identity and shared a common genetic background, tending to cluster together in various analyses, even though they differ from each other. A close relationship of Criollos with Iberian breeds was revealed by all the different analyses, and the contribution of Iberian breeds, particularly of the Celtic breeds, is still present in various Criollo breeds. No influence of Chinese breeds was detected on Criollos, but a few were influenced by Commercial breeds or by wild pigs.
... To detect differences in clustering between populations, we compared the trees with and without outliers using the "cophylo" function in Phytools [39]. SplitsTree v4.19.0 [40] was used to create a distance-based split network using the neighbour-net algorithm. In population genomic research, the frequency of genetic recombination can be studied by Linkage Disequilibrium (LD) decay [41. ...
Fusarium graminearum is the main causal agent of Fusarium head blight (FHB) disease in wheat in Europe. To reveal population structure and to pinpoint genetic targets of selection we studied genomes of 96 strains of F . graminearum using population genomics. Bayesian and phylogenomic analyses indicated that the F . graminearum emergence in Europe could be linked to two independently evolving populations termed here as East European (EE) and West European (WE) population. The EE strains are primarily prevalent in Eastern Europe, but to a lesser extent also in western and southern areas. In contrast, the WE population appears to be endemic to Western Europe. Both populations evolved in response to population-specific selection forces, resulting in distinct localized adaptations that allowed them to migrate into their environmental niche. The detection of positive selection in genes with protein/zinc ion binding domains, transcription factors and in genes encoding proteins involved in transmembrane transport highlights their important role in driving evolutionary novelty that allow F . graminearum to increase adaptation to the host and/or environment. F . graminearum also maintained distinct sets of accessory genes showing population-specific conservation. Among them, genes involved in host invasion and virulence such as those encoding proteins with high homology to tannase/feruloyl esterase and genes encoding proteins with functions related to oxidation-reduction were mostly found in the WE population. Our findings shed light on genetic features related to microevolutionary divergence of F . graminearum and reveal relevant genes for further functional research aiming at better control of this pathogen.
... Branch support was accessed via 500 bootstrap replicates using ultrafast bootstrap (UFB) approximation (Hoang et al., 2018), with UFB values ≥ 95 being indicative of strongly supported clades (Minh et al., 2013;Hoang et al., 2018). To explore phylogenetic relationships within lineages of Sauromalus and to identify distinct populations without enforcing a strict bifurcating topology, phylogenetic networks were inferred using the neighborneT algorithm in spliTsTree v.4.15.1 (Hudson & Bryant, 2006). This approach has been used in similar studies to identify population clusters and to visualize phylogenetic conflict and uncertainty attributable to potential reticulated evolution (e.g. ...
Understanding how historical geological processes drive diversification and shape the contemporary distribution of species is fundamental to phylogeography. We take a genomic approach in order to elucidate the deep phylogeographical history and species limits of chuckwallas (Sauromalus), a conspicuous group of lizards of the arid lands of south-western North America. Phylogenetic and population genomic analyses of double digest restriction site-associated DNA sequencing data confirm the presence of at least two major lineages, peninsular and continental groups, within the widespread and morphologically variable common chuckwalla (Sauromalus ater). These lineages diversified in the vicinity of the head of the Gulf of California in north-eastern Baja California in the early Pliocene to late Miocene, during the formation of the northern gulf. The peninsular lineage of S. ater subsequently gave rise to the four insular endemic species of Sauromalus associated with the Baja California peninsula. Genomic analyses strongly support the continued recognition of the insular gigantics Sauromalus varius and Sauromalus hispidus as distinct species, although their relationship as sister species remains unresolved. Weaker phylogenetic signal for the insular species Sauromalus slevini and Sauromalus klauberi is provided by the genomic data; thus, it is advocated to continue recognizing these species until additional data can be analysed to evaluate their distinctiveness.
... To do this, we calculated the Shapley metric (SH; Volkmann et al. 2014), which can be calculated from unrooted trees. F ST estimates from pairwise comparisons of all five subspecies were used to build a NeighborNet network using the neighborNet function in the R package "phangorn" (Schliep 2011;Hudson and Bryant 2006). This network was then used to estimate the genetic contribution of individual tips (Volkmann et al. 2014), with higher SH values indicating higher priority for management. ...
Spatial variation in the environment can affect population fitness and individual phenotype by facilitating natural selection and local adaptation, and thereby enhance the diversity and adaptive capacity and persistence of species at regional to continental scales. The song sparrow subspecies complex endemic to the San Francisco Bay region, which has received over a century of close study, presents an opportunity to evaluate the adaptive potential of distinct subspecies faced with habitat loss, population decline, and threats of future environmental change. We used whole-genome sequences from 39 individuals representing five morphologically distinct song sparrow subspecies to evaluate the role of neutral and adaptive evolutionary processes in driving divergence within physiologically challenging habitats across multiple environmental clines. We found that natural selection for traits explained by ecological variables, including temperature and salinity, are drivers of adaptive genetic variation in these song sparrows. Differentiation was highest for candidate loci under selection (compared to neutral markers), as predicted if local ecological processes are at least partially responsible for the rapid radiation of these subspecies. Our findings inform management aimed at conserving and prioritizing population-level diversity in species displaying local adaptation and inhabiting a diverse range of environments.
... This alignment was used to calculate the nucleotide diversity (π), polymorphism level (diversity of haplotypes [Dh], number of haplotypes [h], and the average number of nucleotide differences [K]), using DnaSP v5 software (Librado & Rozas, 2009). The Genotype network was constructed in PopART, using the TCS inference method (Clement et al., 2000;Huson & Bryant, 2006). ...
There is a growing concern about the participation of wild hosts and reservoirs in the epidemiology of several pathogens, particularly within the context of environmental changes and the expansion of the One Health concept. The aim of this study was to investigate the presence of hemoplasmas in opossums rescued from the metropolitan region of Rio de Janeiro state, Brazil. Blood samples were collected from 15 Didelphis aurita and subjected to DNA extraction and PCR using primers for the 16S rRNA and 23S rRNA genes. Physical examination and hematological analysis were also performed. Three out of 15 opossums tested positive for hemotropic Mycoplasma spp. by PCR and showed hematological alterations such as anemia and leukocytosis. Clinical signs were non-specific and associated to traumatic lesions. The phylogenetic analysis indicated that the hemoplasma detected was positioned between ‘Ca. Mycoplasma haemodidelphis’ detected in D. virginiana from North American and hemoplasmas recently detected in D. aurita from the state of Minas Gerais, Brazil. This study indicates the existence of hemoplasma infections in D. aurita from the metropolitan region of Rio de Janeiro, and reinforce the need for new epidemiological inquiries to clarify the participation of these in the dynamics of circulation of tick-borne pathogens.
... See Li 2017 for details on the normalization of Sanskrit texts. 42 As implemented in SplitsTree(Huson & Bryant 2006).43 Fitch 1971. ...
Although the many extant Sanskrit versions of the story of King Śibi and the dove have been thoroughly studied, one version, from the Vahnipurāṇa, has so far escaped the attention of scholars. This paper presents a new, critical edition of the Sanskrit text, based on all available material — an existing edition, quotations, and a recently discovered Nepalese fragment — followed by a translation. Connections to Buddhist and Jain versions of the story are discussed. The long afterlife of the text presents an opportunity to study how it has been reused and recast over the course of many centuries, quoted in dharmanibandhas and harvested for material for other stories.
... . CC-BY-NC-ND 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made As these statistics are unable to measure gene flow between sister groups, we used SplitsTree 205 [69] to visualize the phylogenetic network as an 'admixture graph', using the seven files SplitsTree 206 output by IQtree (one for each of the 300 million base pair phylogenomic analyses). 207 208 (f) Rapidly evolving genes and gene ontology analysis 209 We used GWideCodeML [70], a python package to run the codeml function of PAML [71] in a 210 computationally efficient way using genome-wide data. ...
Intra-specific diversification in the northern hemisphere is a recent phenomenon, particularly for vertebrates, due to climatic oscillations during the Quaternary. Caribou (Rangifer tarandus) are a recently diversified, keystone species in North America with a continental-wide distribution and a large amount of phenotypic variation. We assess patterns of intra-specific genetic variation and adaptive divergence, which are of critical interest to the fields of evolutionary biology and conservation. We characterized the relationship among caribou ecotypes and rapidly evolving genes among intra-specific lineages using phylogenomic analyses and a newly assembled chromosome-scale reference genome and 66 high-coverage genomes. Nine phylogenomic lineages showed different levels of introgression, with some lineages highly introgressed. Despite this, dN/dS ratios of all genes in the caribou genome (>30,000) identified 700-800 genes with significant signatures of positive selection in each lineage. These genes function in diverse pathways ranging from immune responses to circulatory systems, with the most enriched molecular pathways found in lineages with high levels of introgression. Glacial cycles and repeated introgression events between caribou lineages likely inflated both neutral and adaptive genetic variation: findings that are particularly timely given the importance of intra-specific diversity and adaptive variation in wild species for resilience to global change.
... It is, therefore, more appropriate to deal with inbred or clonal lineages [50]. We used SPLITSTREE version 4 [112] to visualize relationships between genotypes in a phylogenetic network, with reticulations to represent the conflicting phylogenetic signals caused by homoplasy. Weir and Cockerham's F ST [111] was calculated using the same method as whole genome sequencing data. ...
[This corrects the article DOI: 10.1371/journal.ppat.1010687.].
... In biology, a phylogenetic tree was represented by a leaf-labeled tree (Huson and Bryant, 2006;Brandes and Cornelsen, 2009), while Mathur and Adlakha (2016) represented DNA using a combined tree. Hsu and Lin (2008) presented many graph theoretical concepts in engineering and computer science, and Al Etaiwi (2014) used the concepts of a complete graph, cycle graph, and minimum spanning tree to generate a complex cipher text. Priyadarsini (2015) explored the use of graph theory concepts, expander, and extremal graphs, in the design of some ciphers, whereas Ni et al. (2021) created ciphers using corona and bipartite graphs. ...
A graph that is connected G(V,E) is a graph in which there is at least one path connecting every two vertices in G; otherwise, it is called a disconnected graph. Labels or values can be assigned to the vertices or edges of a graph. A vertex-labeled graph is one in which only the vertices are labeled, and an edges-labeled graph is one in which only edges are assigned values or labels. If both vertices and edges are labeled, the graph is referred to as total labeling. If given n vertices and m edges, numerous graphs can be made, either connected or disconnected. This study will be discussed the number of disconnected vertices labeled graphs of order seven containing no parallel edges and may contain loops. The results show that number of vertices labeled connected graph of order seven with no parallel edges is N(G7,m, g)l= 6,727×Cm6; while for 7≤g≤ 21, N(G7,m, g)l= kg C(m−(g−6))g−1, where k7 =30,160, k8 = 30,765, k9=21,000, k10 =28,364, k11= 26,880, k12=26,460 , k13 = 20,790, k14 =10,290, k15 = 8,022, k16 = 2,940, k17 =4,417, k18 = 2,835, k19 =210, k20 = 21, k21= 1.
... Based on the distance matrices, a NeighbourNet network was generated by SplitsTree4 (version 4.13.1) [25]. ...
In Italy, serogroup C meningococci of the clonal complex cc11 (MenC/cc11) have caused several outbreaks of invasive meningococcal disease (IMD) during the past 20 years. Between December 2019 and January 2020, an outbreak of six cases of IMD infected with MenC/cc11 was identified in a limited area in the northern part of Italy. All cases presented a severe clinical picture, and two of them were fatal. This report is focused on the microbiological and molecular analysis of meningococcal isolates with the aim to reconstruct the chain of transmission. It further presents the vaccination strategy adopted to control the outbreak. The phylogenetic evaluation demonstrated the close genetic proximity between the strain involved in this outbreak and a strain responsible for a larger epidemic that had occurred in 2015 and 2016 in the Tuscany Region. The rapid identification and characterisation of IMD cases and an extensive vaccination campaign contributed to the successful control of this outbreak caused by a hyperinvasive meningococcal strain.
... The neighbour-net graphic was analysed in SplitsTree4 (Hudson and Bryant 2006) using an uncorrected P-distance method with 1000 replicates for bootstrapping to support and further ensure the phylogenetic relationships. DnaSP v5.10.01 (Librado and Rozas 2009) generated ribotypes among Carpinus species. ...
Carpinus (Betulaceae) has approximately 52 species distributed in the Northern Hemisphere, with many species of Carpinus found in China. However, the species boundaries and phylogenetic relationships remain poorly understood. This study reported ITS sequences for 225 individuals of 33 Carpinus species, mainly from China. We also included eight Ostrya species in our analyses, the closely related sister group of Carpinus. We aimed to delimit these species based on ITS sequences and clarify their phylogenetic relationships by constructing tree-like topology and networks at population level. We found that only 17 of 33 species could be delimited from the closely related ones based on species-specific mutations in ITS sequence variation, including all species of sect. Distegocarpus, and sect. Carpinus subsect. Carpinus. Carpinus subsect. Carpinus contained two endangered species, although one seemed to be a recently originated allopolyploid species with genetic additivity from two likely parents in the ITS sequence variation. 16 species of sect. Carpinus subsect. Polyneurae were classified into three species complexes, in each of which two or more could be not distinguished from each other. The closely related species of these complexes may still diverge at the early stage without genetic distinction in the nuclear ITS sequences because of too short of divergence time and frequent gene flow. Otherwise, some species may be established based on the intraspecific variations without genetic bases for an independently evolving unit.
... mics_general) (Table S3 of the Supplementary material available on Zenodo). Phylogenetic neighbor networks were then constructed from these three matrices with NeighbourNet in SplitsTree 4.16.1 (Hudson and Bryant 2006) to visualize the general structure of our SNP data (Fig. S2 of the Supplementary material available on Zenodo). We also assessed structure among our ingroup species with genomic principal components analysis (PCA). ...
Whole genome sequences are beginning to revolutionise our understanding of phylogenetic relationships. Yet, even whole genome sequences can fail to resolve the evolutionary history of the most rapidly radiating lineages, where incomplete lineage sorting, standing genetic variation, introgression, and other factors obscure the phylogenetic history of the group. To overcome such challenges, one emerging strategy is to integrate results across different methods. Most such approaches have been implemented on reduced representation genomic datasets, but whole genomes should provide the maximum possible evidence approach. Here, we test the ability of SNPs extracted from whole genome resequencing data, implemented in an integrative genomic approach, to resolve key nodes in the phylogeny of the mbuna, rock-dwelling cichlid fishes of Lake Malaŵi, which epitomise the phylogenetic intractability that often accompanies explosive lineage diversification. This monophyletic radiation has diversified at an unparalleled rate into several hundred species in less than two million years. Using an array of phylogenomic methods, we consistently recovered four major clades of mbuna, but a large basal polytomy among them. Although introgression between clades apparently contributed to the challenge of phylogenetic reconstruction, reduction of the dataset to non-introgressed sites still did not help to resolve the basal polytomy. On the other hand, relationships among six congeneric species pairs were resolved without ambiguity, even in one case where existing data led us to predict that resolution would be difficult. We conclude that the bursts of diversification at the earliest stages of the mbuna radiation may be phylogenetically unresolvable, but other regions of the tree are phylogenetically clearly supported. Integration of multiple phylogenomic approaches will continue to increase confidence in relationships inferred from these and other whole-genome datasets.
... When = 1, is simply the number of relevant classes having representatives in both and . The dissimilarity matrix ( ) 1≤ , ≤ can be given as input to a phylogenetic reconstruction software [23,32]. ...
The comparison of protein sequences has been for long a very effective tool in producing biological knowledge. It was initially based on the alignment of sequences, that is to say organizing the set of sequences in columns (of a spread-sheet) of sites which have evolved from a common site of the ancestral sequence. Alignments are generally obtained by minimizing an evolution or an edition cost. Sequence comparisons are now often performed without alignments by comparing the-mer compositions of the sequences. We present here the most popular methods used by biologists to compare sequences and place emphasis on an approach to augment the alphabet of a set of sequences in order to ease their comparison. The family of DNA topoisomerases, a set of ancient proteins whose history can be traced back 4 billion years, is used to illustrate this approach.
... We used SPLITSTREE v4 (Huson & Bryant, 2006) to visualize relationships 182 between isolates in a phylogenetic network based on pseudoassembled genomic 183 sequences generated from the tables of SNPs with the reference sequence as a template. 184 ...
Invasions by fungal plant pathogens pose a significant threat to the health of agriculture ecosystems. Despite limited standing genetic variation, many invasive fungal species can adapt and spread rapidly, resulting in significant losses in crop yields. Here, we report on the population genomics of Colletotrichum truncatum , a polyphagous pathogen that can infect more than 460 plant species, and an invasive pathogen on soybean in Brazil. We study the whole-genome sequences of 18 isolates representing 10 fields from two major regions of soybean production. We show that Brazilian C. truncatum is subdivided into three phylogenetically distinct lineages that exchange genetic variation through hybridization. Introgression affects 2 to 30% of the nucleotides of genomes and varies widely between the lineages. We find that introgressed regions comprise secreted protein-encoding genes, suggesting possible co-evolutionary targets for selection in those regions. We highlight the inherent vulnerability of genetically uniform crops in the agro-ecological environment, particularly when faced with pathogens that can take full advantage of the opportunities offered by an increasingly globalized world. Finally, we discuss "The Means, Motive, and Opportunity" of fungal pathogens and how they can become invasive species of crops. We call for more population genomic studies because such analyses can help identify geographic areas and pathogens that pose a risk, thereby helping to inform control strategies to better protect crops in the future.
... Pairwise Reynold's genetic distances between regions were automatically obtained by the hapFLK software (version 1.4, https://forge-dga.jouy.inra.fr/projects/hapflk, [22]) and they were graphically visualized using the NeighborNet graph in SplitsTree5 [23]. ...
In Greece, a number of local sheep breeds are raised in a wide range of ecological niches across the country. These breeds can be used for the identification of genetic variants that contribute to local adaptation. To this end, 50k genotypes of 90 local sheep from mainland Greece (Epirus, n = 35 and Peloponnesus, n = 55) were used, as well as 147 genotypes of sheep from insular Greece (Skyros, n = 21), Lemnos, n = 36 and Lesvos, n = 90). Principal components and phylogenetic analysis along with admixture and spatial point patterns analyses suggested genetic differentiation of ‘mainland-island’ populations. Genome scans for signatures of selection and genome-wide association analysis (GWAS) pointed to one highly differentiating marker on OAR4 (F ST = 0.39, FLK = 21.93, FDR p-value = 0.10) that also displayed genome wide significance (FDR p-value = 0.002) during GWAS. A total number of 6 positional candidate genes ( LOC106990429 , ZNF804B , TEX47 , STEAP4 , SRI and ADAM22 ) were identified within 500 kb flanking regions around the significant marker. In addition, two QTLs related to fat tail deposition are reported in genomic regions 800 kb downstream the significant marker. Based on gene ontology analysis and literature evidence, the identified candidate genes possess biological functions relevant to local adaptation that worth further investigation.
... Basic diversity indices (allelic diversity and heterozygosity) and genetic distances (pairwise Nei's genetic distance and pairwise inter-individual allele sharing distance) among South Indian cattle were estimated using MICROSATELLITE ANALYZER (MSA) version 4.05 [15]. A NeighborNet tree was constructed based on pairwise Nei's genetic distances using SplitsTree version 4.14.6 [16]. F statistics for each locus [17] was calculated and tested using the program FSTAT version 2.9.3.2. ...
The present study is the first comprehensive report on diversity, population structure, genetic admixture and mitochondrial DNA variation in South Indian draught type zebu cattle. The diversity of South Indian cattle was moderately high. A significantly strong negative correlation coefficient of-0.674 (P<0.05) was observed between the effective population size of different breeds and their estimated F IS. The genetic structure analysis revealed the distinct-ness of Kangayam, Vechur and Punganur cattle from the rest of the zebu breeds. The results showed the influence of Hallikar breed in the development of most Mysore type cattle breeds of South India with the exception of Kangayam. Bayesian clustering analysis was performed to assess the taurine admixture in South Indian zebu cattle using purebred Jersey and Holstein-Friesian as reference genotypes. Relatively high levels of taurine admix-ture (>6.25%) was observed in Punganur, Vechur, Umblachery and Pulikulam cattle breeds. Two major maternal haplogroups, I1 and I2, typical of zebu cattle were observed, with the former being predominant than the later. The pairwise differences among the I2 haplotypes of South Indian cattle were relatively higher than West Indian (Indus valley site) zebu cattle. The results indicated the need for additional sampling and comprehensive analysis of mtDNA control region variations to unravel the probable location of origin and domes-tication of I2 zebu lineage. The present study also revealed major concerns on South Indian zebu cattle (i) risk of endangerment due to small effective population size and high rate of inbreeding (ii) lack of sufficient purebred zebu bulls for breeding and (iii) increasing level of taurine admixture in zebu cattle. Availability of purebred semen for artificial insemination, incorporation of genomic/molecular information to identify purebred animals and increased awareness among farmers will help to maintain breed purity, conserve and improve these important draught cattle germplasms of South India.
... A neighbor-joining tree based on genome-wide pair-wise F ST estimates was drawn using Split-sTree [85]. Heterozygosity was calculated per breed at all biallelic sites found to be segregating in the entire data set. ...
Selective breeding for desirable traits in strictly controlled populations has generated an extraordinary diversity in canine morphology and behaviour, but has also led to loss of genetic variation and random entrapment of disease alleles. As a consequence, specific diseases are now prevalent in certain breeds, but whether the recent breeding practice led to an overall increase in genetic load remains unclear. Here we generate whole genome sequencing (WGS) data from 20 dogs per breed from eight breeds and document a ~10% rise in the number of derived alleles per genome at evolutionarily conserved sites in the heavily bottlenecked cavalier King Charles spaniel breed (cKCs) relative to in most breeds studied here. Our finding represents the first clear indication of a relative increase in levels of deleterious genetic variation in a specific breed, arguing that recent breeding practices probably were associated with an accumulation of genetic load in dogs. We then use the WGS data to identify candidate risk alleles for the most common cause for veterinary care in cKCs-the heart disease myxomatous mitral valve disease (MMVD). We verify a potential link to MMVD for candidate variants near the heart specific NEBL gene in a dachshund population and show that two of the NEBL candidate variants have regulatory potential in heart-derived cell lines and are associated with reduced NEBL isoform nebulette expression in papillary muscle (but not in mitral valve, nor in left ventricular wall). Alleles linked to reduced nebulette expression may hence predispose cKCs and other breeds to MMVD via loss of papillary muscle integrity.
... Calculation of MEK based on similarity indices used the Weighted Drift Similarity model (Oliehoek et al., 2006). The kinship matrix was transformed into a distance matrix and used as an input file for the SPLITSTREE v. 4.6 (Hudson and Bryant, 2006) to construct a phylogenetic network. ...
The overall goal of this study was to characterize the genetic diversity of the
Vietnamese local chicken breeds and to identify population priorities for conservation.
The specific aims were 1) to assess and explain the population genetic structure of the
Vietnamese breeds, 2) to characterize the Vietnamese breeds in relation to the Chinese
breeds and wild chickens, 3) to estimate conservation potentials for conservation
priorities of the Vietnamese breeds, and 4) to define an optimal allocation of limited
conservation funds to them
... We investigated genetic relationships among wild and cultivated samples with a splitstree and a principal component analysis (PCA). For the splitstree, we used the NeighborNet distance transformation and equal angle splits transformation implemented in SplitsTree v4 [22]. For the PCA, we used the dudi.pca ...
A road-map of the genetic and phenotypic diversities in both crops and their wild related species can help identifying valuable genetic resources for further crop breeding. The clary sage (Salvia sclarea L.), a perfume, medicinal and aromatic plant, is used for sclareol production and ornamental purposes. Despite its wide use in the field of cosmetics, the phenotypic and genetic diversity of wild and cultivated clary sages remains to be explored. We characterized the genetic and phenotypic variation of a collection of six wild S. sclarea populations from Croatia, sampled along an altitudinal gradient, and, of populations of three S. sclarea cultivars. We showed low level of genetic diversity for the two S. sclarea traditional cultivars used for essential oil production and for ornamental purposes, respectively. In contrast, a recent cultivar resulting from new breeding methods, which involve hybridizations among several genotypes rather than traditional recurrent selection and self-crosses over time, showed high genetic diversity. We also observed a marked phenotypic differentiation for the ornamental clary sage compared with other cultivated and wild clary sages. Instead, the two cultivars used for essential oil production, a traditional and a recent one, respectively, were not phenotypically differentiated from the wild Croatian populations. Our results also featured some wild populations with high sclareol content and early-flowering phenotypes as good candidates for future breeding programs. This study opens up perspectives for basic research aiming at understanding the impact of breeding methods on clary sage evolution, and highlights interesting avenues for clary breeding programs.
... A condensed tree is shown in figure 3A (the full tree can be found in supplementary figure 1). As the sequences are short, a Neighbor-Net analysis was also performed (figure 3B) and showed that the data were treelike, and that tree-based phylogenetic analysis was appropriate (Husan and Bryant, 2006). The cytochromes predicted to have a low redox midpoint potential, including those assigned as cytochromes c 6B and c 6C previously, all grouped to the exclusion of the predicted cytochrome c 6 sequences in both the phylogenetic tree (bootstrap value of 84%) and the Neighbor-Net analysis, and maintained a similar general topology to that of the cyanobacterial tree of figure 2. This distribution showed cytochrome c 6B as a clade derived from within the cytochrome c 6C clade, as with figure 2. ...
During photosynthesis, electrons are transferred between the cytochrome b6f complex and photosystem I. This is carried out by the protein plastocyanin in plant chloroplasts, or by either plastocyanin or cytochrome c6 in many cyanobacteria and eukaryotic algal species. There are three further cytochrome c6 homologues: cytochrome c6A in plants and green algae, and cytochromes c6B and c6C in cyanobacteria. The function of these proteins is unknown. Here, we present a comprehensive analysis of the evolutionary relationship between the members of the cytochrome c6 family in photosynthetic organisms. Our phylogenetic analyses show that cytochrome c6B and cytochrome c6C are likely to be orthologues that arose from a duplication of cytochrome c6, but that there is no evidence for separate origins for cytochrome c6B and c6C. We therefore propose re-naming cytochrome c6C as cytochrome c6B. We show that cytochrome c6A is likely to have arisen from cytochrome c6B rather than by an independent duplication of cytochrome c6, and present evidence for an independent origin of a protein with some of the features of cytochrome c6A in peridinin dinoflagellates. We conclude with a new comprehensive model of the evolution of the cytochrome c6 family which is an integral part of understanding the function of the enigmatic cytochrome c6 homologues.
... For this test, the concatenated sequences were constructed with the first locus (arcC) sequences appended to the end of the 7-locus concatenation to detect possible recombination between the last and first locus in the circular genome. The pairwise homoplasy index (PHI) for recombination was measured using the program implemented in SplitsTree [42,43]; recombination within and between sequences was considered positive if the PHI test yielded a p � 0.05. ...
Staphylococcus chromogenes is a common skin commensal in cattle and has been identified as a frequent cause of bovine mastitis and intramammary infections. We have developed a seven locus Multilocus Sequence Typing (MLST) scheme for typing S . chromogenes . Sequence-based typing systems, such as MLST, have application in studies of genetic diversity, population structure, and epidemiology, including studies of strain variation as a factor in pathogenicity or host adaptation. The S . chromogenes scheme was tested on 120 isolates collected from three geographic locations, Vermont and Washington State in the United States and Belgium. A total of 46 sequence types (STs) were identified with most of the STs being location specific. The utility of the typing scheme is indicated by a discrimination power of 95.6% for all isolates and greater than 90% for isolates from each of the three locations. Phylogenetic analysis placed 39 of the 46 STs into single core group consistent with a common genetic lineage; the STs in this group differ by less than 0.5% at the nucleotide sequence level. Most of the diversification in this lineage group can be attributed to mutation; recombination plays a limited role. This lineage group includes two clusters of single nucleotide variants in starburst configurations indicative of recent clonal expansion; nearly 50% of the isolates sampled in this study are in these two clusters. The remaining seven STs were set apart from the core group by having alleles with highly variable sequences at one or more loci. Recombination had a higher impact than mutation in the diversification of these outlier STs. Alleles with hypervariable sequences were detected at five of the seven loci used in the MLST scheme; the average sequence distances between the hypervariable alleles and the common core alleles ranged from 12 to 34 nucleotides. The extent of these sequence differences suggests the hypervariable alleles may be remnants of an ancestral genotype.
Earlier studies on Isothecium s.l. suggested potential interchange of genetic material between species that are nowadays known to belong to separate genera. In this study, we analyse the variation in three molecular markers (nuclear gpd; mitochondrial nad5; and plastid trnG) in a wide selection of Isothecium alopecuroides and Pseudisothecium myosuroides specimens to infer whether this potential exchange of genetic material is frequent. In addition, we explore the phylogeographic structure of these two species in Europe. Our results seem to show repeated genetic interchange for the nuclear and mitochondrial markers in both species, suggesting intergeneric hybridization, although horizontal gene transfer and/or incomplete lineage sorting could also explain the detected incongruences. The genetic lineages found indicate a complex biogeographical history for I. alopecuroides, including both post-glacial immigration from different glacial refugia and developing haplotypes potentially adapted to cold climates. As for P. myosuroides, genetic variants could either indicate a post-glacial immigration history or adaptation to oceanic conditions. Further studies including a larger set of more variable molecular markers could help to reach final conclusions on the results here presented.
The bryophyte genus Ulota has its main diversification area in Patagonia, with 18 currently accepted species, all of which are endemic to the area. Despite this richness, ongoing studies indicate the existence of hitherto unknown species in this territory. However, the strong resemblance between species often complicates the discrimination of new taxa, making the use of integrative taxonomy approaches compulsory. During surveys conducted in past decades, a morphotype of a Ulota, closely resembling Ulota macrodontia, was discovered coexisting with this species. Ulota macrodontia is characterized by unique peristomial features within the genus, and the variant morphotype shares these characteristics while displaying some distinct gametophytic and sporophytic features. Biometric analyses demonstrate that the differences are stable, and without intermediate states. The results obtained from the analyses of one nuclear and four plastid loci reveal a close relationship between both morphotypes, with the samples of U. macrodontia forming a well-supported monophyletic group. We propose to treat the new morphotype at species level (Ulota brachypoda sp. nov.), discussing why this is the most appropriate taxonomic rank, and we provide a detailed and illustrated description. Additionally, a distribution map of the two endemics is included.
Body size is a key morphological attribute, often used to delimit species boundaries among closely related taxa. But body size can evolve in parallel, reaching similar final states despite independent evolutionary and geographic origins, leading to faulty assumptions of evolutionary history. Here, we document parallel evolution in body size in the widely distributed leaf-nosed bat genus Hipposideros, which has misled both taxonomic and evolutionary inference. We sequenced reduced representation genomic loci and measured external morphological characters from three closely related species from the Solomon Islands archipelago, delimited by body size. Species tree reconstruction confirms the paraphyly of two morphologically designated species. The nonsister relationship between large-bodied H. dinops lineages found on different islands indicates that large-bodied ecomorphs have evolved independently at least twice in the history of this radiation. A lack of evidence for gene flow between sympatric, closely related taxa suggests the rapid evolution of strong reproductive isolating barriers between morphologically distinct populations. Our results position Solomon Islands Hipposideros as a novel vertebrate system for studying the repeatability of parallel evolution under natural conditions. We conclude by offering testable hypotheses for how geography and ecology could be mediating the repeated evolution of large-bodied Hipposideros lineages in the Solomon Islands.
Major histocompatibility complex (MHC) genes are commonly used markers for monitoring adaptive genetic and evolutionary potential of species. In this study, we investigated genetic variation of the MHC class II DRB locus in the chamois genus Rupicapra by using next-generation sequencing. Sequencing of 102 samples led to the identification of 25 alleles, 11 of which are novel. The high ratio of the relative rates of nonsynonymous to synonymous mutations (dN/dS) suggests a signal of positive selection on this locus. We analyzed patterns of genetic variation within and among 2 subspecies of Northern Chamois and compared them to previously published studies using neutral markers to provide a basis for assessing the effects of demographic processes. Our analyses have shown that alleles are likely to be maintained by balancing selection in different populations with similar frequencies and that this mechanism also works in small, isolated populations that are strongly affected by genetic drift.
The Mediterranean Basin is a hotspot of animal and plant diversity. Contrary to the Balkan and Iberian Peninsulas that were subject of many phylogeographic studies in past decades, the Apennine Peninsula and, in particular, the diversification of its flora has been neglected in contemporary phylogenetic studies. The few available studies showed a complex pattern of north–south differentiation of genetic diversity in Italy, both among the Alps, the Apuan Alps, and the Apennines, as well as within the Apennines. Here, we explore phylogeographic patterns within recently described Euphorbia adriatica, distributed in the central and northern Apennine Peninsula, the southern margin of the Eastern Alps and the north-western Balkan Peninsula, and its relationship to the southern Italian E. japygica. Our integrative approach using nuclear ITS sequences, amplified fragment length polymorphisms, relative genome size estimation combined with chromosome counting, as well as multivariate morphometrics inferred a weak genetic differentiation that only partly corresponds to the morphological differentiation. Whereas all southern populations have hairy capsules characteristic for E. japygica, only those in south-eastern Italy (Puglia and Basilicata) are genetically divergent. There are, however, additional morphological characters that differentiate them from other populations. Our data are thus in favour of recognizing a single species, E. japygica, which includes E. adriatica that should be treated as a subspecies, named E. japygica subsp. prostrata. We provide a revised taxonomic treatment for E. japygica, including the typification. Our study shows the necessity of further in-depth investigations of diversification of Italian biota.
We present an overview of the morphology, biogeography, and ecology of the fern genus Osmunda (i.e. without previously included taxa of Claytosmunda, Osmundastrum, and Plenasium), with a focus on the American O. spectabilis Willd. and Old World O. regalis L. While genetic data supports the separation of these taxa, commonly used morphologic characters to distinguish between O. regalis and O. spectabilis (maximum frond size; pinnae sessile vs. stalked; pinnules opposite vs. alternate; general pinnule proportions) are not infallible. We recorded morphometric differences among and between O. regalis and O. spectabilis and correlated these with spatio-environmental gradients. Our work provides an updated taxonomic overview with full synonymy and diagnostic key of Osmunda. We preliminarily recognize six informal subtaxa in O. regalis (‘regalis’, ‘abyssinica’, ‘huegeliana’, ‘longifolia’, ‘transvaalensis’, ‘obtusifolia’) and three in O. spectabilis (‘spectabilis’, ‘palustris’, ‘piresii’) that separate in a morphological traits-based principal component analysis. The morphotaxa appeared geographically structured and their distribution showed significant correlations with elevation, mean annual precipitation, annual mean temperature, and temperature seasonality. The taxonomic rank and validity of the proposed subtaxa has to be tested through a large-scale sampling, e.g. with comparative cp/nr genomic and cytogenetic analyses. Such future analyses may help to ascertain whether the observed morphologic peculiarities are conditioned solely by abiotic factors (which would allow addressing them as forms) or are manifested in the genome.
Alseuosmia (Alseuosmiaceae) is an endemic New Zealand genus of small trees and shrubs, which is unusual in that some taxa appear to morphologically mimic unrelated species. The taxonomy of the group has long been debated with the extreme morphological diversity in A. banksii causing much of the confusion. Here we use ddRADseq to examine the genetic relationships between the species, with a particular focus on the morphological forms of A. banksii. Our analyses revealed that for species in the northern part of the distribution, genetic relationships largely matched geography rather than species’ boundaries based on morphology, and that hybridisation between morphs appears to be common. A diversity of morphologies is present within these northern Alseuosmia, including multiple forms that appear to mimic unrelated genera, and these may constitute a single gene pool. Further south, two species (A. turneri and A. pusilla) were genetically distinct in sympatry. We suggest maintaining the current taxonomy until further research can be undertaken.
Pheromones mediate species-level communication in the search for mates, nesting, and feeding sites. Although the role of pheromones has long been discussed by various authors, their existence was not proven until the mid-twentieth century when the first sex pheromone was identified. From this finding, much has been speculated about whether this communication mechanism has acted as a regulatory agent in the process of speciation, competition, and sexual selection since it acts as an intraspecific barrier. Chrysomelidae is one of the major Phytophaga lineages, with approximately 40,000 species. Due to this immense diversity the internal relationships remain unstable when analyzed only with morphological data, consequently recent efforts have been directed to molecular analyses to establish clarity for the relationships and found their respective monophyly. Therefore, our goals are twofold 1) to synthesize the current literature on Chrysomelidae sex pheromones and 2) to test whether Chrysomelidae sex pheromones and their chemical structures could be used in phylogenetic analysis for the group. The results show that, although this is the first analysis in Chrysomelidae to use pheromones as a phylogenetic character, much can be observed in agreement with previous analyses, thus confirming that pheromones, when known in their entirety within lineages, can be used as characters in phylogenetic analyses, bringing elucidation to the relationships and evolution of organisms.
A novel Gram-staining-negative, aerobic and rod-shaped bacterium, designated WL0058T, was isolated from coastal sediment sample collected in Nantong city, Jiangsu province of China (120° 51′ 13″ E, 32° 6′ 26″ N) in October 2020. Strain WL0058T was found to grow at 4–37 °C (optimum, 28 °C) with 1.5–4.0% NaCl (optimum, 4.0%) and displayed alkaliphilic growth with the pH range of pH 6.0–10.0 (optimum, pH 6.0). Phylogenetic trees constructed based on 16S rRNA gene sequence indicated that strain WL0058T is a member of the family Rhizobiaceae, shared the highest similarity with “Hoeflea prorocentri” CCTCC AB 2016294T (97.7%) and constituted a sub-cluster within the family with it, while the similarity with others in the family Rhizobiaceae was lower than 97.0%. The G + C content of genomic DNA was 59.5 mol%. Polar lipids profile of strain WL0058T included phosphatidylcholine (PC), phosphatidylethanolamine (PE), and glycolipid (GL), phosphatidylmonomethylethanolamine (PME) and two unidentified polar lipids (L). The major isoprenoid quinone was determined to be Q-10 and the major fatty acids were C16:0, C18:0, summed features 4 (iso-C17:1 and/or anteiso-C17:1), and summed features 8 (C18:1ω6c and/or C18:1ω7c). As inferred from the morphology, physiology, and biochemical analysis, genotypic characteristics, and the phylogenetic trees, strain WL0058T ought to be recognized as a novel genus in the family Rhizobiaceae, for which the name Flavimaribacter sediminis gen. nov., sp. nov. The type strain of Flavimaribacter sediminis gen. nov., sp. nov. is WL0058T (= MCCC 1K06063T = JCM 34659T = GDMCC 1.2448T).
The enteric chicken astrovirus (CAstV) and avian nephritis virus (ANV) are the type species of the genus Avastrovirus (AAstV; Astroviridae family), capable of causing considerable production losses in poultry. Using next-generation sequencing of a cloacal swab from a backyard chicken in Tanzania, we assembled genome sequences of ANV and CAstV (6918 nt and 7318 nt in length, respectively, excluding poly(A) tails, which have a typical AAstV genome architecture (5'-UTR-ORF1a-ORF1b-ORF2-'3-UTR). They are most similar to strains ck/ANV/BR/RS/6R/15 (82.72%) and ck/CAstV/PL/G059/14 (82.23%), respectively. Phylogenetic and sequence analyses of the genomes and the three open reading frames (ORFs) grouped the Tanzanian ANV and CAstV strains with Eurasian ANV-5 and CAstV-Aii viruses, respectively. Compared to other AAstVs, the Tanzanian strains have numerous amino acid variations (substitutions, insertions and deletions) in the spike region of the capsid protein. Furthermore, CAstV-A has a 4018 nt recombinant fragment in the ORF1a/1b genomic region, predicted to be from Eurasian CAstV-Bi and Bvi parental strains. These data should inform future epidemiological studies and options for AAstV diagnostics and vaccines.
Sambucus L. is found in the family Viburnaceae (syn. Adoxaceae) and encompasses approximately 29 accepted species. The complex morphology of these species has caused continued confusion concerning their nomenclature, classification, and identification. Despite previous attempts to resolve taxonomic complexities in the Sambucus genus, there are still unclear phylogenetic relationships among several species. In this study, the newly obtained plastome of Sambucus williamsii Hance. as well as the populations of Sambucus canadensis L., Sambucus javanica Blume, and Sambucus adnata Wall. ex DC were sequenced, and their sizes, structural similarity, gene order, gene number, and guanine–cytosine (GC) contents were analyzed. The phylogenetic analyses were conducted using the whole chloroplast genomes and protein-coding genes (PCGs). The findings revealed that the chloroplast genomes of Sambucus species exhibited typical quadripartite double-stranded DNA molecules. Their lengths ranged from 158,012 base pairs (bp) ( S. javanica ) to 158,716 bp ( S. canadensis L). Each genome comprised a pair of inverted repeats (IRs), which separated the large single-copy (LSC) and small single-copy (SSC) regions. In addition, the plastomes contained 132 genes, encompassing 87 protein-coding, 37 tRNA, and four rRNA genes. In the simple sequence repeat (SSR) analysis, A/T mononucleotides had the highest proportion, with the most repetitive sequences observed in S. williamsii . The comparative genome analyses showed high similarities in structure, order, and gene contents. The hypervariable regions in the studied chloroplast genomes were trnT-GGU , trnF-GAA , psaJ , trnL-UAG , ndhF , and ndhE , which may be used as candidate barcodes for species discrimination in Sambucus genus. Phylogenetic analyses supported the monophyly of Sambucus and revealed the separation of S. javanica and S. adnata populations. Sambucus chinensis Lindl. was nested within S. javanica in the same clade, collaborating their conspecific treatment. These outcomes indicate that the chloroplast genome of Sambucus plants is a valuable genetic resource for resolving taxonomic discrepancies at the lower taxonomic levels and can be applied in molecular evolutionary studies.
Comparison of protein sequences has long been a very effective tool for producing biological knowledge. It was initially based on the alignment of sequences, that is to say organizing the set of sequences in columns (of a spreadsheet) of sites which have evolved from a common site of the ancestral sequence. Alignments are generally obtained by minimizing an evolution or an edition cost. Sequence comparisons are now often performed without alignments by comparing the N-mer compositions of the sequences. We present here the most popular methods used by biologists to compare sequences and place emphasis on an approach to augment the alphabet of a set of sequences in order to ease their comparison. The family of DNA topoisomerases, a set of ancient proteins whose history can be traced back 4 billion years, is used to illustrate this approach.
Amphipods have diversified greatly in the Ponto-Caspian region. Although many of these species are prominent invaders their systematics remains unclear. Taking an integrative approach, we investigate the taxonomy of Trichogammarus trichiatus, a widespread invader in European inland waters. It was initially described from the northeastern Black Sea coast as Chaetogammarus trichiatus by Martynov in 1932. A similar taxon, Chaetogammarus tenellus major, was described by Cărăușu from the western Black Sea in 1943 but later synonymized with C. trichiatus. Chaetogammarus trichiatus was itself shuffled between Chaetogammarus and the Atlanto-Mediterranean Echinogammarus, currently being assigned to Trichogammarus. Our analyses (six DNA markers, 60 measurements and scanning electron microscopic imaging) reveal that T. trichiatus and C. tenellus major are distinct species; the former is a Caucasian endemic, whereas the latter invaded Europe. Unexpectedly, T. trichiatus is an incipient species molecularly nested in Chaetogammarus ischnus, despite pronounced morphological and geographical differentiation. We also recover Chaetogammarus as polyphyletic, yet its member species are nested in the Ponto-Caspian radiation, thus distinct from Echinogammarus. Consequently, we reassign T. trichiatus to Chaetogammarus (Chaetogammarus trichiatus), synonymize Trichogammarus with Chaetogammarus and place C. tenellus major in the new genus Spirogammarus gen. nov. (Spirogammarus major comb. & stat. nov.).
Baleen whales are a clade of gigantic and highly specialized marine mammals. Their genomes have been used to investigate their complex evolutionary history and to decipher the molecular mechanisms that allowed them to reach these dimensions. However, many unanswered questions remain, especially about the early radiation of rorquals and how cancer resistance interplays with their huge number of cells. The pygmy right whale is the smallest and most elusive among the baleen whales. It reaches only a fraction of the body length compared to its relatives and it is the only living member of an otherwise extinct family. This placement makes the pygmy right whale genome an interesting target to update the complex phylogenetic past of baleen whales, because it splits up an otherwise long branch that leads to the radiation of rorquals. Apart from that, genomic data of this species might help to investigate cancer resistance in large whales, since these mechanisms are not as important for the pygmy right whale as in other giant rorquals and right whales.
Here, we present a first de novo genome of the species and test its potential in phylogenomics and cancer research. To do so, we constructed a multi-species coalescent tree from fragments of a whole-genome alignment and quantified the amount of introgression in the early evolution of rorquals. Furthermore, a genome-wide comparison of selection rates between large and small-bodied baleen whales revealed a small set of conserved candidate genes with potential connections to cancer resistance.
Our results suggest that the evolution of rorquals is best described as a hard polytomy with a rapid radiation and high levels of introgression. The lack of shared positive selected genes between different large-bodied whale species supports a previously proposed convergent evolution of gigantism and hence cancer resistance in baleen whales.
Root nodules of legume plants are primarily inhabited by rhizobial nitrogen-fixing bacteria. Here we propose two new Rhizobiales species isolated from root nodules of common sainfoin ( Onobrychis viciifolia ), as shown by core-gene phylogeny, overall genome relatedness indices and pan-genome analysis.
Mesorhizobium onobrychidis sp. nov., actively induces nodules, and achieves atmospheric nitrogen and carbon dioxide fixation. This species appears to be depleted in motility genes, and is enriched in genes for direct effects on plant growth performance. Its genome reveals functional and plant growth-promoting signatures like a large unique chromosomal genomic island with high density of symbiotic genetic traits. O nobrychidicola muellerharveyae gen. nov. sp. nov., is described as type species of the new genus O nobrychidicola in Rhizobiaceae . This species comprises unique genetic features and plant growth-promoting traits (PGPTs), which strongly indicate its function in biotic stress reduction and motility. We applied a newly developed bioinformatics approach for in silico prediction of PGPTs (PGPT-Pred), which supports the different lifestyles of the two new species and the plant growth-promoting performance of M. onobrychidis in the greenhouse trial.
Background
Moraxella bovis and Moraxella bovoculi both associate with infectious bovine keratoconjunctivitis (IBK), an economically significant and painful ocular disease that affects cattle worldwide. There are two genotypes of M. bovoculi (genotypes 1 and 2) that differ in their gene content and potential virulence factors, although neither have been experimentally shown to cause IBK. M. bovis is a causative IBK agent, however, not all strains carry a complete assortment of known virulence factors. The goals of this study were to determine the population structure and depth of M. bovis genomic diversity, and to compare core and accessory genes and predicted outer membrane protein profiles both within and between M. bovis and M. bovoculi.
Results
Phylogenetic trees and bioinformatic analyses of 36 M. bovis chromosomes sequenced in this study and additional available chromosomes of M. bovis and both genotype 1 and 2 M. bovoculi, showed there are two genotypes (1 and 2) of M. bovis. The two M. bovis genotypes share a core of 2015 genes, with 121 and 186 genes specific to genotype 1 and 2, respectively. The two genotypes differ by their chromosome size and prophage content, encoded protein variants of the virulence factor hemolysin, and by their affiliation with different plasmids. Eight plasmid types were identified in this study, with types 1 and 6 observed in 88 and 56% of genotype 2 strains, respectively, and absent from genotype 1 strains. Only type 1 plasmids contained one or two gene copies encoding filamentous haemagglutinin-like proteins potentially involved with adhesion. A core of 1403 genes was shared between the genotype 1 and 2 strains of both M. bovis and M. bovoculi, which encoded a total of nine predicted outer membrane proteins.
Conclusions
There are two genotypes of M. bovis that differ in both chromosome content and plasmid profiles and thus may not equally associate with IBK. Immunological reagents specifically targeting select genotypes of M. bovis, or all genotypes of M. bovis and M. bovoculi together could be designed from the outer membrane proteins identified in this study.
New Testament textual critics have for decades calculated the similarities between the manuscripts in a similar manner, using collations and variation units. This conventional methodology requires enormous amounts of time and manual work. Here is proposed a new method that does not require these preprocessing steps, enabling the establishment of quantitative relationships using manuscript transcriptions only. This is achieved by applying a technique called shingling, where the manuscript transcriptions are turned in a computerized manner into smaller pieces called tokens or k-grams. Then, a string metric is used to calculate the similarities between the tokenized strings. This method is efficient, meaning that it allows critics to consider all textual evidence in each manuscript tradition. At the same time, it returns similarity values that are compatible with those of conventional approaches.
The striped-back shrew group demonstrates remarkable variation in skull and body size, tail length, and brightness of the dorsal stripe; and karyotypic and DNA variation has been reported in recent years. In this study, we investigated the phylogenetic structure of the group, as well as speciation patterns and demographic history in Mountains of Southwestern China and adjacent mountains, including the southern Himalayas, Mts. Bashan, Wushan, and Qinling. We sequenced a total of 462 specimens from 126 localities in the known range of the group, which were sequenced and analyzed based on 6.2 kb of sequence data from two mitochondrial, six nuclear, and two Y chromosome markers. Phylogenetic analyses of the concatenated mtDNA data revealed 14 sympatric and independently evolving lineages within the striped-back shrew group, including Sorex bedfordiae, S. cylindricauda, S. excelsus, S. sinalis and several cryptic species. All concatenated data (ten genes) showed a consistent genetic structure compared to the mtDNA lineages for the group, whereas the nuclear and the Y chromosome data showed a discordant genetic structure compared to the mtDNA lineages for the striped-back shrew group. Species delimitation analyses and deep genetic distance clearly support the species status of the 14 evolving lineages. The divergence time estimation suggested that the striped-back shrew group began to diversify from the middle Pleistocene (2.34 Ma), then flourished at approximately 2.14 Ma, followed by a series of rapid diversifications through the Pleistocene. Our results also revealed multiple mechanisms of speciation in the Mountains of Southwestern China and Adjacent Mountains with complex landscapes and climate. The uplifting of the Qinghai-Tibetan Plateau, Quaternary climate oscillations, riverine barriers, ecological elevation gradients, topographical diversity, and their own low dispersal capacity may have driven the speciation, genetic structure, and phylogeographic patterns of the striped-back shrew group.
African sheep manifest diverse but distinct physio-anatomical traits, which are the outcomes of natural- and human-driven selection. Here, we generated 34.8 million variants from 150 indigenous northeast African sheep genomes sequenced at an average depth of ∼54× for 130 samples (Ethiopia, Libya) and ∼20× for 20 samples (Sudan). These represented sheep from diverse environments, tail morphology and post-Neolithic introductions to Africa. Phylogenetic and model-based admixture analysis provided evidence of four genetic groups corresponding to altitudinal geographic origins, tail morphotypes and possible historical introduction and dispersal of sheep into and across the continent. Running admixture at higher levels of K (6 ≤ K ≤ 25), revealed cryptic levels of genome intermixing as well as distinct genetic backgrounds in some sheep populations. Comparative genomic analysis identified targets of selection that spanned conserved haplotype structures which overlapped clusters of genes and gene families. These were related to hypoxia responses, ear morphology, caudal vertebrae and tail skeleton length, and tail fat-depot structures. Our findings provide novel insights underpinning morphological variation and response to human-driven selection and environmental adaptation in African indigenous sheep.
Invasive exotic pathogens pose a threat to trees and forest ecosystems worldwide, hampering the provision of essential ecosystem services such as carbon sequestration and water purification. Hybridization is a major evolutionary force that can drive the emergence of pathogens. Phytophthora ramorum, an emergent pathogen that causes the sudden oak and larch death, spreads as reproductively isolated divergent clonal lineages. We use a genomic biosurveillance approach by sequencing genomes of P. ramorum from survey and inspection samples and report the discovery of variants of P. ramorum that are the result of hybridization via sexual recombination between North American and European lineages. We show that these hybrids are viable, can infect a host and produce spores for long-term survival and propagation. Genome sequencing revealed genotypic combinations at 54,515 single nucleotide polymorphism loci not present in parental lineages. More than 6,000 of those genotypes are predicted to have a functional impact in genes associated with host infection, including effectors, carbohydrate-active enzymes and proteases. We also observed post-meiotic mitotic recombination that could generate additional genotypic and phenotypic variation and contribute to homoploid hybrid speciation. Our study highlights the importance of plant pathogen biosurveillance to detect variants, including hybrids, and inform management and control.
The human parasite Plasmodium malariae has relatives infecting African apes (Plasmodium rodhaini) and New World monkeys (Plasmodium brasilianum), but its origins remain unknown. Using a novel approach to characterise P. malariae-related sequences in wild and captive African apes, we found that this group comprises three distinct lineages, one of which represents a previously unknown, highly divergent species infecting chimpanzees, bonobos and gorillas across central Africa. A second ape-derived lineage is much more closely related to the third, human-infective lineage P. malariae, but exhibits little evidence of genetic exchange with it, and so likely represents a separate species. Moreover, the levels and nature of genetic polymorphisms in P. malariae indicate that it resulted from the zoonotic transmission of an African ape parasite, reminiscent of the origin of P. falciparum. In contrast, P. brasilianum falls within the radiation of human P. malariae, and thus reflects a recent anthroponosis. Plasmodium malariae is a cause of malaria in humans and related species have been identified in non-human primates. Here, the authors use genomic analyses to establish that human P. malariae arose from a host switch of an ape parasite whilst a species infecting New World monkeys can be traced to a reverse zoonosis.
Given n vertices and m edges, m ≥ 1, and for every vertex is given a label, there are lots of graphs that can be obtained. The graphs obtained may be simple or not simple, connected or disconnected. A graph G(V,E) is called simple if G(V,E) not containing loops nor parallel edges. An edge which has the same end vertex is called a loop, and parallel edges are two or more edges which connect the same set of vertices. Let N (G 7,m,t) as the number of connected vertex labeled graphs of order seven with m vertices and t (t is the number edges that connect different pair of vertices). The result shows that N (G 7,m,t) = c t C (m−1)
Pro-active approaches in preventing future epidemics include pathogen discovery prior to their emergence in human and/or animal populations. Playing an important role in pathogen discovery, high-throughput sequencing (HTS) enables the characterization of microbial and viral genetic diversity within a given sample. In particular, metagenomic HTS allows the unbiased taxonomic profiling of sequences; hence, it can identify novel and highly divergent pathogens such as viruses. Newly discovered viral sequences must be further investigated using genomic characterization, molecular and serological screening, and/or in-vitro and in-vivo characterization. Several outbreak and surveillance studies apply unbiased generic HTS to characterize whole genome sequences of suspected pathogens. In contrast, this study aimed to screen for novel and unexpected pathogens in previously generated HTS datasets and use this information as a starting point for the establishment of an early warning system (EWS). As a proof of concept, the EWS was applied to HTS datasets and archived samples from the 2018-19 West Nile virus (WNV) epidemic in Germany. A metagenomics read classifier detected sequences related to genome sequences of various members of Riboviria. We focused the further EWS investigation on viruses belonging to the families Peribunyaviridae and Reoviridae, under suspicion of causing co-infections in WNV-infected birds. Phylogenetic analyses revealed that the reovirus genome sequences clustered with sequences assigned to the species Umatilla virus, whereas a new peribunyavirid, tentatively named “Hedwig virus” belonged to a putative novel genus of the family Peribunyaviridae. In follow up studies, newly developed molecular diagnostic assays detected fifteen Umatilla virus-positive wild birds from different German cities and eight Hedwig virus-positive captive birds from two zoological gardens. Umatilla virus was successfully cultivated in mosquito C6/36 cells inoculated with a blackbird liver. In conclusion, this study demonstrates the power of the applied EWS for the discovery and characterization of unexpected viruses in repurposed sequence datasets, followed by virus screening and cultivation using archived sample material. The EWS enhances the strategies for pathogen recognition before causing sporadic cases and massive outbreaks and proves to be a reliable tool for modern outbreak preparedness.
Premise:
Although chestnuts and chinquapins are some of the best known and most widely loved of any plants in North America, relatively little genomic sequencing has been done, and much is still unknown about their evolution.
Methods:
We used double-digest restriction-site-associated DNA (ddRAD) sequencing data to infer the species-level phylogeny for Castanea and assess the phylogeography of the North American species using samples collected from populations that span the full extent of the species' ranges. We also constructed species distribution models using digitized herbarium specimens and observational data from field surveys.
Results:
We identified strong population structure within Castanea dentata (American chestnut) that reflects a stepwise northern migration since the last glacial maximum. Our species distribution models further confirmed this scenario and matched closely with the Castanea fossil pollen record. We also found significant structure within the Castanea pumila lineage, most notably a genetic cluster that corresponds to the frequently recognized Castanea pumila var. ozarkensis.
Conclusions:
The two North American Castanea species have contrasting patterns of population structure, but each is typical of plant phylogeography in North America. Within the C. pumila complex, we found novel genetic structure that provides new insights about C. pumila taxonomy. Our results also identified a series of distinctive populations that will be valuable in ongoing efforts to conserve and restore chestnuts and chinquapins in North America.
Genus Hypericum (Guttiferae, Hypericoideae) is perennial, belonging to the
Hypericaceae family, having 484 species in forms of trees, shrubs, and
herbs, distributed in 36 taxonomic sections. No detailed Random Amplified
Polymorphic DNA (RAPD) studies were conducted to study Hypericum genetic
diversity. Therefore, we collected and analyzed six species from five
provinces of Iran regions. Overall, seventy plant specimens were collected.
Our aims were 1) to assess genetic diversity among Hypericum species 2) is
there a correlation between species genetic and geographical distance? 3)
Genetic structure of populations and taxa. We showed significant differences
in quantitative morphological characters in plant species. H. dogonbadanicum
depicted unbiased expected heterozygosity (UHe) in the range of 0.10.
Shannon information was high (0.32) in H. perforaturm. H. dogonbadanicum
showed the lowest value, 0.17. The observed number of alleles (Na) ranged
from 0.22 to 0.53 in H. dogonbadanicum and H. elongaturn. Gene flow (Nm) was
relatively low (0.87) in Hypericum. The Mantel test showed correlation (r =
0.45, p=0.0001) between genetic and geographical distances. We reported high
genetic diversity, which clearly shows the Hypericum species can adapt to
changing environments since high genetic diversity is linked to species
adaptability. Present results highlighted the utility of RAPD markers and
morphometry methods to investigate genetic diversity in Hypericum species.
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