Phylogenetic Network Analysis Research Articles

Phylogenomics and species delimitation in the Lepidophyma sylvaticum complex (Squamata: Xantusiidae) using ddRADseq and morphological data.

The Lepidophyma sylvaticum complex occurs from west-central Nuevo León to the Sierra de Chiconquiaco in central Veracruz, Mexico. Morphological studies have revealed population groups that are "moderately divergent from each other" within the complex. In addition, a molecular phylogenetic study found L. sylvaticum to be strongly structured and paraphyletic with respect to L. micropholis. We used ddRADseq and morphological data to evaluate the phylogenetic relationships and species boundaries within the complex. Phylogenetic analyses performed using both concatenation and coalescent methods estimated the same well-supported tree, composed of five allopatric, strongly supported lineages of L. sylvaticum (from Nuevo León [NL]; Sierra de Álvarez, San Luis Potosí [ASLP]; southeastern San Luis Potosí, Querétaro, Hidalgo, and northwestern Veracruz [HSQV]; Tamaulipas [T]; and Puebla and northern Veracruz [PV]) branching off (in that order) from the base of the tree, with L. micropholis as the sister taxon to the last of them. A population genetics analysis revealed one pattern of genetic structure in L. micropholis and three in L. sylvaticum: one in the L. sylvaticum NL and ASLP lineages, another in the L. sylvaticum HSQV and T lineages, and a third in the L. sylvaticum PV lineage. The six lineages identified were genetically distinctive across our phylogenetic and population genetics analyses, and congruent with geography. Species tree and phylogenetic network analyses, considering the six lineages as potentially independent, inferred trees identical to the concatenated tree. Additionally, the phylogenetic network analysis detected a recent introgression event from the L. sylvaticum T lineage into L. micropholis. A time-calibrated tree indicated that the diversification of the complex began in the late Miocene and continued into the Pleistocene. A species delimitation analysis, based on the genealogical divergence index, suggested that the L. sylvaticum NL, ASLP, and PV lineages are independent evolutionary lineages. A morphological analysis showed that L. micropholis and the L. sylvaticum NL and ASLP lineages were distinguishable from each other and from the remaining L. sylvaticum lineages. We conclude that the L. sylvaticum NL and ASLP lineages, the two oldest in the complex, represent independent evolutionary lineages, and propose recognizing the other four lineages as subspecies (historical sublineages) of L. sylvaticum sensu stricto.

Intraspecific genetic variation in the lymphatic filariasis vector Mansonia dives (Diptera: Culicidae) in Thailand: Hidden species or genetically divergent populations?

Mansonia dives is recognized as a vector for brugian filariasis in Thailand. A recent study analyzing the cytochrome c oxidase subunit I (COI) gene revealed two distinct clades within the Ma. dives population in Thailand. This study aimed to examine the genetic diversity and structure of Ma. dives using the COI gene and the internal transcribed spacer 2 (ITS2) region to determine the presence of distinct species or genetically divergent populations. We analyzed 60 COI and 60 ITS2 sequences from Ma. dives populations in Narathiwat, Ranong, Tak, and Trat. The results showed a nucleotide diversity of 0.019 and a haplotype diversity of 0.979 for the COI gene, while the ITS2 region displayed a nucleotide diversity of 0.005 and a haplotype diversity of 0.545. Phylogenetic and haplotype network analyses of the COI gene identified two genetic lineages: one confined to Trat and another encompassing the other sites. However, species delimitation methods suggested that these genetic differences were insufficient to classify the lineages as distinct species. In contrast, the ITS2 analysis indicated a uniform genetic pattern across all populations. We conducted neutrality tests and mismatch distribution to examine the demographic history. For the COI gene, Tajima's D was slightly positive and non-significant (0.014), while Fu's Fs was negative (-9.750), indicating a potential expansion phase. Conversely, for the ITS2 region, Tajima's D and Fu's Fs were positive and non-significant, suggesting that the population might be in equilibrium or undergoing contraction. Moreover, the mismatch distribution analysis for the ITS2 region was inconclusive. The apparent discrepancies between these markers indicate the presence of genetically divergent populations, rather than distinct species.

Synergistic effects of microplastics and sulfonamide on greenhouse gas emissions in agricultural ditch sediments: Insights into microbial interactions

Recently, concerns have been raised regarding concurrent pollution by microplastics and antibiotics in agricultural aquatic ecosystems. However, knowledge gaps remain regarding their combined effects on greenhouse gas (GHG) emissions and bacterial community assembly mechanisms. To address this, a microcosm experiment was performed to investigate the GHG (CH4, CO2, and N2O) emission characteristics and bacterial community assembly mechanisms in agricultural ditch sediments under co-exposure to different microplastics (polythene (PE), polylactic acid (PLA)), and sulfanilamide (SA). The global warming potential (GWP) of the different treatments was ranked as follows: SA+PLA (162.96 mg/m2/h) > PLA (123.49 mg/m2/h) > SA (121.75 mg/m2/h) > SA+PE (102.33 mg/m2/h) > CK (without microplastics or antibiotics, 84.67 mg/m2/h) > PE (78.29 mg/m2/h). Additionally, a phylogenetic bin-based null model and molecular ecological network analysis indicated that SA-induced selective pressures reduced compositional turnover, whereas microplastics enhanced drift effects and decreased network robustness. The co-contamination of SA with different microplastics exhibited the opposite effect on the network and assembly process, suggesting that disturbance-mediated species dominance alters the colonization of rare species. Collectively, these findings provide valuable evidence that the synergistic effects of biodegradable microplastic and SA can promote GHG emissions and influence the mechanisms underlying community assembly processes.

Multiple Maternal Lineages of <i>Strauchbufo raddei</i> (Strauch, 1876) in Mongolia Revealed by Mitochondrial DNA

The Mongolian toad Strauchbufo raddei (Strauch, 1876) is one of widely distributed and dominated amphibian species in eastern Asian, including Mongolia. In this study, we amplified and sequenced a total of 50 samples of S. raddei, from three main regions in its Mongolian distribution range namely, Northern, Eastern, and Gobi regions. Our phylogenetic trees (Bayesian inference; BI and time-calibrated) and network analysis clearly support presence of multiple maternal mitochondrial DNA lineages for S. raddei in Mongolia. As expected, samples from these three regions were clustered separately in BI tree (Bayesian posterior probability (BPP 0.52). In addition, the population specific haplotypes, estimated genetic distances (e.g. uncorrelated p distance; ranged from 1% to 25%) and hierarchical AMOVA suggested relatively strong population genetic structure of S. raddei across Mongolia. Time-calibrated tree and ancestral range analysis showed that the first colonization of S. raddei may have occurred in Northern part of Mongolia approximately 9.63 mya, then dispersed over other parts of the country. Estimated approximate time for crossing event of S. raddei over dry steppe and semi-desert regions in Mongolia was 5.02 – 2.50 mya. Finally, high level of genetic diversity (overall; haplotype diversity, Hd = 0.93; nucleotide diversity, π = 0.011) of S. raddei were observed in Mongolia. Importantly, through this study, we contributed to closing sampling gaps in distribution range of S. raddei in Eastern Asia, which is key to better understanding species history, as well as describing cryptic lineages.

Prezygotic barriers effectively limit hybridization in a rapid evolutionary radiation.

Hybridization is increasingly recognized as an important evolutionary process across the tree of life. In many clades, phylogenomic approaches have permitted unparalleled insight into the extent and frequency of hybridization. However, we continue to lack a deep understanding of the factors that limit and shape patterns of hybridization, especially in evolutionary radiations. In this study, we characterized patterns of introgression across Costus (Costaceae), a young evolutionary radiation of tropical understory plants that maintain widespread interfertility despite exhibiting strong prezygotic reproductive isolation. We analyzed a phylogenomic dataset of 756 genes from 54 Costus species using multiple complementary approaches - D-statistics, gene-tree-based tests, and phylogenetic network analyses - to detect and characterize introgression events throughout the evolutionary history of the radiation. Our results identified a moderate number of introgression events, including a particularly ancient, well-supported event spanning one of the deepest divergences in the clade. Most introgression events occurred between taxa or ancestral lineages that shared the same pollination syndrome (bee-pollinated or hummingbird-pollinated). These findings suggest that prezygotic barriers, including pollinator specialization, have been key to the balance between introgression and reproductive isolation in Costus.

Inferring the origin of new D-loop haplotypes of loggerhead sea turtles (Testudinata: Cheloniidae) from the Southwest Atlantic lineage

The populations of the loggerhead turtles, Caretta caretta, present four main D-loop mitochondrial haplogroups that are distributed across the Indo-Pacific, Mediterranean, and Atlantic oceans. The Southwestern Atlantic (SWA) is one of the Regional Management Units (RMUs) of loggerheads, characterized by unique haplotypes, high nest density, and distinct life history traits. Detecting new D-loop haplogroups is important, particularly endemic ones, as they can enhance our understanding of their life history within the RMUs and contribute to the resolution of mixed stock analysis. In this study, we conducted a series of phylogenetic delimitation and network analyses to identify, validate, and infer the origin of four new D-loop haplotypes detected in the loggerhead populations from the SWA. Our findings demonstrate that these new D-loop haplotypes are valid and unique to the SWA lineage, potentially aiding in the delimitation of individuals’ origins and the inference of their lineage.

Reticulate evolution and rapid development of reproductive barriers upon secondary contact in a forest fungus

Reproductive barriers between sister species of the mushroom-forming fungi tend to be stronger in sympatry, leading to speculation on whether they are being reinforced by selection against hybrids. We have used population genomic analyses together with invitro crosses of a global sample of the wood decay fungus Trichaptum abietinum to investigate reproductive barriers within this species complex and the processes that have shaped them. Our phylogeographic analyses show that T.abietinum is delimited into six major genetic groups: one in Asia, two in Europe, and three in North America. The groups present in Europe are interfertile and admixed, whereas our crosses show that the North American groups are reproductively isolated. In Asia, a more complex pattern appears, with partial intersterility between subgroups that likely originated independently and more recently than the reproductive barriers in North America. We found pre-mating barriers in T.abietinum to be moderately correlated with genomic divergence, whereas mean growth reduction of the mated hybrids showed a strong correlation with increasing genomic divergence. Genome-wide association analyses identified candidate genes with programmed cell death annotations, which are known to be involved in intersterility in distantly related fungi, although their link here remains unproven. Our demographic modeling and phylogenetic network analyses fit a scenario where reproductive barriers in Trichaptum abietinum could have been reinforced upon secondary contact between groups that diverged in allopatry during the Pleistocene glacial cycles. Our combination of experimental and genomic approaches demonstrates how T.abietinum is a tractable system for studying speciation mechanisms.

Phylogenomic Analysis of Target Enrichment and Transcriptome Data Uncovers Rapid Radiation and Extensive Hybridization in Slipper Orchid Genus Cypripedium L.

Cypripedium is the most widespread and morphologically diverse genus of slipper orchids. Despite several published phylogenies, the topology and monophyly of its infrageneric taxa remained uncertain. Here, we aimed to reconstruct a robust section-level phylogeny of Cypripedium and explore its evolutionary history using target capture data for the first time. We used the orchid-specific bait set Orchidaceae963 in combination with transcriptomic data to reconstruct the phylogeny of Cypripedium based on 913 nuclear loci, covering all 13 sections. Subsequently, we investigated discordance among nuclear and chloroplast trees, estimated divergence times and ancestral ranges, searched for anomaly zones, polytomies, and diversification rate shifts, and identified potential gene (genome) duplication and hybridization events. All sections were recovered as monophyletic, contrary to the two subsections within sect. Cypripedium. The two subclades within this section did not correspond to its subsections but matched the geographic distribution of their species. Additionally, we discovered high levels of discordance in the short backbone branches of the genus and within sect. Cypripedium, which can be attributed to hybridization events detected based on phylogenetic network analyses, and incomplete lineage sorting caused by rapid radiation. Our biogeographic analysis suggested a Neotropical origin of the genus during the Oligocene (~30 Ma), with a lineage of potentially hybrid origin spreading to the Old World in the Early Miocene (~22 Ma). The rapid radiation at the backbone likely occurred in Southeast Asia around the Middle Miocene Climatic Transition (~15-13 Ma), followed by several independent dispersals back to the New World. Moreover, the Pliocene-Quaternary glacial cycles may have contributed to further speciation and reticulate evolution within Cypripedium. Our study provided novel insights into the evolutionary history of Cypripedium based on high-throughput molecular data, shedding light on the dynamics of its distribution and diversity patterns from its origin to the present.

Unraveling microbial community variation along a salinity gradient and indicative significance to groundwater salinization in the coastal aquifer

Saltwater intrusion poses a global environmental challenge in coastal regions, profoundly influencing groundwater microbial communities and biogeochemical processes. This study aims to elucidate the origin of groundwater salinity and understand the response of microbial interactions to groundwater salination through stable isotopes and 16S rDNA gene sequencing. The findings reveal a significant increase in groundwater TDS from inland to the coastline, ranging from 0.5 g/L to 144.6 g/L. Ionic relationship and isotopic fractionation indicate that the high salinity in groundwater originates not only from paleo–seawater but also from the dissolution of halite. Salty groundwater exhibits lower species richness and diversity than fresh groundwater. TDS, SO42–, and NO2– are the pivotal factors shaping the microbial community of salty groundwater, while NO3– and H2SiO3 are dominant variables influencing fresh groundwater community. This study identifies the order Alteromonadales, family Alteromonadaceae, and genus Marinobacter as potential biomarkers of seawater or paleo–seawater sources. Phylogenetic molecular network analysis of microbial communities illustrates that groundwater salinization results in a more compact microbial network but enhances microbial interactions. Predicted functional genes indicate that sulfate reduction genes (sat, met3, aprA, aprB, dsrA, and dsrB) are more abundant in salty groundwater than in fresh groundwater, suggesting a high metabolic potential for sulfate. These results elucidate the pivotal role of groundwater salinization in microbial community evolution, shaping specific functional zones in coastal groundwater.

Seek, and you will find: Cryptic diversity of the cardiopulmonary nematode Angiostrongylus vasorum in the Americas

Angiostrongylus vasorum is a metastrongylid parasite infecting wild canids and domestic dogs. Its patchy distribution, high pathogenicity and taxonomical classification makes the evolutionary history of A. vasorum intriguing and important to study. First larval stages of A. vasorum were recovered from feces of two grey foxes, Urocyon cinereoargenteus, from Costa Rica. Sequencing and phylogenetic and haplotypic analyses of the ITS2, 18S and cytochrome oxidase subunit 1 (cox1) fragments were performed. Then p- and Nei´s genetic distance, nucleotide substitution rates and species delimitation analyses were conducted with cox1 data of the specimens collected herein and other Angiostrongylus spp. Cophylogenetic congruence and coevolutionary events of Angiostrongylus spp. and their hosts were evaluated using patristic and phenetic distances and maximum parsimony reconciliations. Specimens from Costa Rica clustered in a separate branch from European and Brazilian A. vasorum sequences in the phylogenetic and haplotype network analyses using the ITS2 and cox1 data. In addition, cox1 p-distance of the sequences derived from Costa Rica were up to 8.6 % different to the ones from Europe and Brazil, a finding mirrored in Nei´s genetic distance PCoA. Species delimitation analysis supported a separate group with the sequences from Costa Rica, suggesting that these worms may represent cryptic variants of A. vasorum, a new undescribed taxon or Angiocaulus raillieti, a synonym species of A. vasorum described in Brazil. Moreover, nucleotide substitution rates in A. vasorum were up to six times higher than in the congener Angiostrongylus cantonensis. This finding and the long time elapsed since the last common ancestor between both species may explain the larger diversity in A. vasorum. Finally, cophylogenetic congruence was observed between Angiostrongylus spp. and their hosts, with cospeciation events occurring at deeper taxonomic branching of host order. Altogether, our data suggest that the diversity of the genus Angiostrongylus is larger than expected, since additional species may be circulating in wild canids from the Americas.

Phylogenetic Network Analyses Reveal the Influence of Transmission Clustering on the Spread of HIV Drug Resistance in Quebec from 2002 to 2022.

HIV drug resistance (HIV-DR) may jeopardize the benefit of antiretroviral therapy (ART) in treatment and prevention. This study utilized viral phylogenetics to resolve the influence of transmission networks on sustaining the spread of HIV-DR in Quebec spanning 2002 to 2022. Time trends in acquired (ADR) and transmitted drug resistance (TDR) were delineated in treatment-experienced (n = 3500) and ART-naïve persons (n = 6011) with subtype B infections. Similarly, non-B-subtype HIV-DR networks were assessed pre- (n = 1577) and post-ART experience (n = 488). Risks of acquisition of resistance-associated mutations (RAMs) were related to clustering using 1, 2-5, vs. 6+ members per cluster as categorical variables. Despite steady declines in treatment failure and ADR since 2007, rates of TDR among newly infected, ART-naive persons remained at 14% spanning the 2007-2011, 2012-2016, and 2017-2022 periods. Notably, half of new infections among men having sex with men and heterosexual groups were linked in large, clustered networks having a median of 35 (14-73 IQR) and 16 (9-26 IQR) members per cluster, respectively. Cluster membership and size were implicated in forward transmission of non-nucleoside reverse transcriptase inhibitor NNRTI RAMs (9%) and thymidine analogue mutations (TAMs) (5%). In contrast, transmission of M184V, K65R, and integrase inhibitors (1-2%) remained rare. Levels of TDR reflected viral replicative fitness. The median baseline viremia in ART-naïve groups having no RAMs, NNRTI RAMs, TAMs, and M184VI were 46.088, 38,447, 20,330, and 6811 copies/mL, respectively (p < 0.0001). Phylogenetics emphasize the need to prioritize ART and pre-exposure prophylaxis strategies to avert the expansion of transmission cascades of HIV-DR.

Uncovering ghost introgression through genomic analysis of a distinct eastern Asian hickory species.

Ghost introgression, or the transfer of genetic material from extinct or unsampled lineages to sampled species, has attracted much attention. However, conclusive evidence for ghost introgression, especially in plant species, remains scarce. Here, we newly assembled chromosome-level genomes for both Carya sinensis and Carya cathayensis, and additionally re-sequenced the whole genomes of 43 C. sinensis individuals as well as 11 individuals representing 11 diploid hickory species. These genomic datasets were used to investigate the reticulation and bifurcation patterns within the genus Carya (Juglandaceae), with a particular focus on the beaked hickory C. sinensis. By combining the D-statistic and BPP methods, we obtained compelling evidence that supports the occurrence of ghost introgression in C. sinensis from an extinct ancestral hickory lineage. This conclusion was reinforced through the phylogenetic network analysis and a genome scan method VolcanoFinder, the latter of which can detect signatures of adaptive introgression from unknown donors. Our results not only dispel certain misconceptions about the phylogenetic history of C. sinensis but also further refine our understanding of Carya's biogeography via divergence estimates. Moreover, the successful integration of the D-statistic and BPP methods demonstrates their efficacy in facilitating a more precise identification of introgression types.

Evolutionary and Phylogenetic Dynamics of SARS-CoV-2 Variants: A Genetic Comparative Study of Taiyuan and Wuhan Cities of China.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-sense, single-stranded RNA genome-containing virus which has infected millions of people all over the world. The virus has been mutating rapidly enough, resulting in the emergence of new variants and sub-variants which have reportedly been spread from Wuhan city in China, the epicenter of the virus, to the rest of China and all over the world. The occurrence of mutations in the viral genome, especially in the viral spike protein region, has resulted in the evolution of multiple variants and sub-variants which gives the virus the benefit of host immune evasion and thus renders modern-day vaccines and therapeutics ineffective. Therefore, there is a continuous need to study the genetic characteristics and evolutionary dynamics of the SARS-CoV-2 variants. Hence, in this study, a total of 832 complete genomes of SARS-CoV-2 variants from the cities of Taiyuan and Wuhan in China was genetically characterized and their phylogenetic and evolutionary dynamics studied using phylogenetics, genetic similarity, and phylogenetic network analyses. This study shows that the four most prevalent lineages in Taiyuan and Wuhan are as follows: the Omicron lineages EG.5.1.1, followed by HK.3, FY.3, and XBB.1.16 (Pangolin classification), and clades 23F (EG.5.1), followed by 23H (HK.3), 22F (XBB), and 23D (XBB.1.9) (Nextclade classification), and lineage B followed by the Omicron FY.3, lineage A, and Omicron FL.2.3 (Pangolin classification), and the clades 19A, followed by 22F (XBB), 23F (EG.5.1), and 23H (HK.3) (Nextclade classification), respectively. Furthermore, our genetic similarity analysis show that the SARS-CoV-2 clade 19A-B.4 from Wuhan (name starting with 412981) has the least genetic similarity of about 95.5% in the spike region of the genome as compared to the query sequence of Omicron XBB.2.3.2 from Taiyuan (name starting with 18495234), followed by the Omicron FR.1.4 from Taiyuan (name starting with 18495199) with ~97.2% similarity and Omicron DY.3 (name starting with 17485740) with ~97.9% similarity. The rest of the variants showed ≥98% similarity with the query sequence of Omicron XBB.2.3.2 from Taiyuan (name starting with 18495234). In addition, our recombination analysis results show that the SARS-CoV-2 variants have three statistically significant recombinant events which could have possibly resulted in the emergence of Omicron XBB.1.16 (recombination event 3), FY.3 (recombination event 5), and FL.2.4 (recombination event 7), suggesting some very important information regarding viral evolution. Also, our phylogenetic tree and network analyses show that there are a total of 14 clusters and more than 10,000 mutations which may have probably resulted in the emergence of cluster-I, followed by 47 mutations resulting in the emergence of cluster-II and so on. The clustering of the viral variants of both cities reveals significant information regarding the phylodynamics of the virus among them. The results of our temporal phylogenetic analysis suggest that the variants of Taiyuan have likely emerged as independent variants separate from the variants of Wuhan. This study, to the best of our knowledge, is the first ever genetic comparative study between Taiyuan and Wuhan cities in China. This study will help us better understand the virus and cope with the emergence and spread of new variants at a local as well as an international level, and keep the public health authorities informed for them to make better decisions in designing new viral vaccines and therapeutics. It will also help the outbreak investigators to better examine any future outbreak.

Genetic diversity, phylogeography, and maternal origin of yak (Bos grunniens)

BackgroundThere is no consensus as to the origin of the domestic yak (Bos grunniens). Previous studies on yak mitochondria mainly focused on mitochondrial displacement loop (D-loop), a region with low phylogenetic resolution. Here, we analyzed the entire mitochondrial genomes of 509 yaks to obtain greater phylogenetic resolution and a comprehensive picture of geographical diversity.ResultsA total of 278 haplotypes were defined in 509 yaks from 21 yak breeds. Among them, 28 haplotypes were shared by different varieties, and 250 haplotypes were unique to specific varieties. The overall haplotype diversity and nucleotide diversity of yak were 0.979 ± 0.0039 and 0.00237 ± 0.00076, respectively. Phylogenetic tree and network analysis showed that yak had three highly differentiated genetic branches with high support rate. The differentiation time of clades I and II were about 0.4328 Ma, and the differentiation time of clades (I and II) and III were 0.5654 Ma. Yushu yak is shared by all haplogroups. Most (94.70%) of the genetic variation occurred within populations, and only 5.30% of the genetic variation occurred between populations. The classification showed that yaks and wild yaks were first clustered together, and yaks were clustered with American bison as a whole. Altitude had the highest impact on the distribution of yaks.ConclusionsYaks have high genetic diversity and yak populations have experienced population expansion and lack obvious phylogeographic structure. During the glacial period, yaks had at least three or more glacial refugia.

Epidemic characteristics of local HIV-2 transmission across Hunan province, China

ObjectiveTo elucidate the epidemiological features of HIV-2 in Hunan Province, China, utilizing sequence analysis. MethodsThirteen individuals diagnosed with HIV-2 infection in Hunan Province, China, from 2017 to 2023 were included in this study. Amplification of HIV-2 env and pol regions was conducted, followed by Sanger sequencing. Phylogenetic and molecular transmission network analyses were performed to delineate molecular features and transmission dynamics. ResultsAll 14 individuals contracted HIV-2 through heterosexual intercourse, comprising 7 males and 7 females, with a median age of 58 years. Among them, three couples (HN001 and HN013, HN010 and HN011, HN008 and HN009) were identified, along with commercial sexual activity engagement reported for subject HN004. Notably, subjects HN001, HN003, HN008, and HN010 engaged in commercial sexual activities at the same location as subject HN004. Phylogenetic analysis of the pol gene revealed close proximity of sequences from all subjects to reference sequences from Gambia (Sub-type A). Employing a genetic distance threshold of 1.5 %, eight out of the 14 subjects formed a molecular transmission network, with HN002 and HN004 identified as central nodes. ConclusionFrom 2017 to 2023, all HIV-2-infected individuals in Hunan Province, China, acquired the virus through identifiable routes, indicating transmission of similar HIV-2 strains among them.

Variations and trade-offs in leaf and culm functional traits among 77 woody bamboo species

BackgroundWoody bamboos are the only diverse large perennial grasses in mesic-wet forests and are widely distributed in the understory and canopy. The functional trait variations and trade-offs in this taxon remain unclear due to woody bamboo syndromes (represented by lignified culm of composed internodes and nodes). Here, we examined the effects of heritable legacy and occurrence site climates on functional trait variations in leaf and culm across 77 woody bamboo species in a common garden. We explored the trade-offs among leaf functional traits, the connection between leaf nitrogen (N), phosphorus (P) concentrations and functional niche traits, and the correlation of functional traits between leaves and culms.ResultsThe Bayesian mixed models reveal that the combined effects of heritable legacy (phylogenetic distances and other evolutionary processes) and occurrence site climates accounted for 55.10–90.89% of the total variation among species for each studied trait. The standardized major axis analysis identified trade-offs among leaf functional traits in woody bamboo consistent with the global leaf economics spectrum; however, compared to non-bamboo species, the woody bamboo exhibited lower leaf mass per area but higher N, P concentrations and assimilation, dark respiration rates. The canonical correlation analysis demonstrated a positive correlation (ρ = 0.57, P-value < 0.001) between leaf N, P concentrations and morphophysiology traits. The phylogenetic principal components and trait network analyses indicated that leaf and culm traits were clustered separately, with leaf assimilation and respiration rates associated with culm ground diameter.ConclusionOur study confirms the applicability of the leaf economics spectrum and the biogeochemical niche in woody bamboo taxa, improves the understanding of woody bamboo leaf and culm functional trait variations and trade-offs, and broadens the taxonomic units considered in plant functional trait studies, which contributes to our comprehensive understanding of terrestrial forest ecosystems.

Increased geographic sampling suggests incomplete lineage sorting and recent introgression between Pyrrhosoma nymphula (Sulzer, 1776) and P. elisabethae Schmidt, 1948 in the Western Palearctic

We analysed COI and ITS sequences from a total of 69 European Pyrrhosoma nymphula (Sulzer, 1776) and three P. elisabethae Schmidt, 1948 to explore species boundaries and phylogeographic patterns in their Western Palearctic distributions. We found that phylogenetic and haplotype network analyses support previous results that the widespread P. nymphula and the endangered P. elisabethae are distinct species, and that P. nymphula in North Africa are distinct from P. nymphula in Europe. However, our results also suggest that neither diversification is complete as we found evidence for introgression of mitochondrial DNA between P. elisabethae and eastern Europe P. nymphula, as well as possible incomplete lineage sorting. Finally, our results indicate that while P. nymphu­la likely recolonized most of Europe from an Iberian Peninsula refugium following the Weichsel Glaciation, separate refugia possibly existed in North Africa, southern Italy, and for P. elisabethae in the southwestern Balkan.

Spatiotemporal Distribution of PRRSV-1 Clades in Hungary with a Focus on the Era of Disease Eradication.

Porcine reproductive and respiratory syndrome (PRRS) is the cause of the most severe economic losses in the pig industry worldwide. PRRSV is extremely diverse in Europe, which poses a significant challenge to disease control within a country or any region. With the combination of phylogenetic reconstruction and network analysis, we aimed to uncover the major routes of the dispersal of PRRSV clades within Hungary. In brief, by analyzing >2600 ORF5 sequences, we identified at least 12 clades (including 6 clades within lineage 1 and 3 clades within lineage 3) common in parts of Western Europe (including Denmark, Germany and the Netherlands) and identified 2 novel clades (designated X1 and X2). Of interest, some genetic clades unique to other central European countries, such as the Czech Republic and Poland, were not identified. The pattern of PRRSV clade distribution is consistent with the route of the pig trade among countries, showing that most of the identified clades were introduced from Western Europe when fatteners were transported to Hungary. As a result of rigorous implementation of the national eradication program, the swine population was declared officially free from PRRSV. This map of viral diversity and clade distribution will serve as valuable baseline information for the maintenance of PRRSV-free status in the post-eradication era.

Phylogenomic analyses and chromosome ploidy identification reveal multiple cryptic species in Allium sikkimense complex (Amaryllidaceae).

Polyploidization is a process that typically leads to instantaneous reproductive isolation and has, therefore, been considered as one of the major evolutionary forces in the species-rich Hengduan Mountains (HM), yet this topic remains poorly studied in the region. Allium sikkimense and its relatives (about eight species) compose a natural diploid-polyploid complex with the highest diversity in the HM and adjacent areas. A combination of nuclear ribosomal DNA (nrDNA), plastome, transcriptome, and ploidy identification through chromosome counting and flow cytometry is employed to reconstruct the phylogenetic relationships in this complex and to investigate the frequency and the evolutionary significance of polyploidy in the complex. The plastome failed to resolve the phylogenetic relationships of the different species in the A. sikkimense complex, and the phylogenetic tree based on nrDNA also has limited resolution. However, our study reveals a well-resolved phylogenetic framework for species in the A. sikkimense complex using more than 1,000 orthologous genes from the transcriptome data. Previously recognized morphospecies A. sikkimense are non-monophyletic and comprise at least two independently evolved lineages (i.e., cryptic species), each forming a clade with different diploid species in this complex. The embedded pattern of octoploid A. jichouense and tetraploid A. sp. nov. within different polyploid samples of A. sikkimense supports a possible scenario of budding speciation (via niche divergence). Furthermore, our results reveal that co-occurring species in the A. sikkimense complex usually have different ploidy levels, suggesting that polyploidy is an important process for reproductive isolation of sympatric Allium species. Phylogenetic network analyses suggested that the phylogenetic relationships of the A. sikkimense complex, allowing for reticulation events, always fit the dataset better than a simple bifurcating tree. In addition, the included or exserted filaments, which have long been used to delimit species, are highly unreliable taxonomically due to their extensive parallel and convergent evolution.

Phylogenetic and network analysis of Pediculus humanus in Nigeria reveal the presences of clade E body lice and novel haplotypes.

An investigation was conducted for the first time to determine the prevalence and genetic diversity of human lice, for the first time in Nigeria, using conventional PCR and sequencing methods. Three mitochondrial genes, cytochrome oxidase subunit 1 (cox1), cytochrome b (cytb), and 12S rRNA of Nigerian human lice, were amplified, sequenced, and analyzed. Overall, high prevalence (72.5%; 103/142) of lice infestation was recorded among the examined volunteers. Head lice infestation was more common 63 (61.2%) than body lice infestation 34 (33.0%). Co-infestation with both head and body lice was recorded in six humans (5.8%). The Nigerian human lice specimens were placed mostly into clade A with few in clade E, including body lice for the first time. Six, three, and eight haplotypes of Nigerian human lice were obtained for the cytb, cox1, and 12S rRNA genes, respectively. Additionally, one (E51), three (A31, A32, and E5), and six (A20, A21, A23, A24, A30, and E1) novel haplotypes were recorded for cox1, cytb, and 12S rRNA, respectively, from the Nigerian specimens which were corroborated by the ML phylogenetic trees and MJ network analyses. Genetic diversity indices indicate minimal variation in the parameters analyzed among the clades of the three genes. However, a statistically significant Snn test, negative Tajima's D test for clade A (cox1 and 12S rRNA genes), and negative Fu and Li's D test in clade A for cox1 gene indicate a geographical structure and the signature of population expansion of the Nigerian human lice. The findings from this study provide additional data on the human lice structure in Africa.