Browsing by Subject "TREE"

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  • Liao, Ziyan; Zhang, Lin; Nobis, Michael P.; Wu, Xiaogang; Pan, Kaiwen; Wang, Keqing; Dakhil, Mohammed A.; Du, Mingxi; Xiong, Qinli; Pandey, Bikram; Tian, Xianglin (2020)
    Aim As a prominent geographical distribution centre for the dark coniferous forests, mountains of Southwest China (MSWC) is experiencing an unprecedented warming trend, posing severe challenges to the survival of dominant fir (Abies) species. Although plant's migration ability is a prerequisite for its survival in changing environments, it has often been ignored in species distribution models (SDMs). This study aimed to quantify the magnitude and direction of range changes by the year 2080 for six dominant fir species, that is Abies recurvata, Abies faxoniana, Abies squamata, Abies ernestii, Abies forrestii and Abies georgei, with an emphasis on exploring the relationship between migration ability and projected distributions. Location The mountains of Southwest China. Methods We applied the Maximum Entropy (Maxent) algorithm to calibrate ecological niche models and to project the climatically suitable areas (CSAs) of each species under two emission scenarios (RCP 4.5 and RCP 8.5). Additionally, we delimited future species ranges by three migration scenarios (full-, no- and partial-migration scenarios). Results The simulations showed the distinctive responses of the six fir species to anthropogenic climate change (ACC). By 2080, the distribution areas of Abies recurvata were projected to decline only in the no-migration scenario but increase under the full- and partial-migration scenarios, while the other five species were projected to decline in the majority of emission x migration scenarios. Fir species in the southern region were predicted to be more vulnerable to ACC due to the larger losses in CSAs and a stronger effect of the partial-migration scenario on the newly colonized areas of this group. The studied species showed a simulated migration trend (northward and westward) to the interior Qinghai-Tibet Plateau under ACC. Main conclusions Benefits or losses for species under ACC depended on the geographical location, their ecological niches and migration abilities, which provide essential insights for a spatial conservation assessment of biodiversity hotspots in the future.
  • Abdullah; Henriquez, Claudia L.; Mehmood, Furrukh; Carlsen, Monica M.; Islam, Madiha; Waheed, Mohammad Tahir; Poczai, Peter; Croat, Thomas B.; Ahmed, Ibrar (2020)
    The subfamily Pothoideae belongs to the ecologically important plant family Araceae. Here, we report the chloroplast genomes of two species of the subfamily Pothoideae:Anthurium huixtlense(size: 163,116 bp) andPothos scandens(size: 164,719 bp). The chloroplast genome ofP. scandensshowed unique contraction and expansion of inverted repeats (IRs), thereby increasing the size of the large single-copy region (LSC: 102,956 bp) and decreasing the size of the small single-copy region (SSC: 6779 bp). This led to duplication of many single-copy genes due to transfer to IR regions from the small single-copy (SSC) region, whereas some duplicate genes became single copy due to transfer to large single-copy regions. The rate of evolution of protein-coding genes was affected by the contraction and expansion of IRs; we found higher mutation rates for genes that exist in single-copy regions as compared to those in IRs. We found a 2.3-fold increase of oligonucleotide repeats inP. scandenswhen compared withA. huixtlense, whereas amino acid frequency and codon usage revealed similarities. The ratio of transition to transversion mutations was 2.26 inP. scandensand 2.12 inA. huixtlense. Transversion mutations mostly translated in non-synonymous substitutions. The phylogenetic inference of the limited species showed the monophyly of the Araceae subfamilies. Our study provides insight into the molecular evolution of chloroplast genomes in the subfamily Pothoideae and family Araceae.
  • Feng, Shaohong; Stiller, Josefin; Deng, Yuan; Armstrong, Joel; Fang, Qi; Reeve, Andrew Hart; Xie, Duo; Chen, Guangji; Guo, Chunxue; Faircloth, Brant C.; Petersen, Bent; Wang, Zongji; Zhou, Qi; Diekhans, Mark; Chen, Wanjun; Andreu-Sanchez, Sergio; Margaryan, Ashot; Howard, Jason Travis; Parent, Carole; Pacheco, George; Sinding, Mikkel-Holger S.; Puetz, Lara; Cavill, Emily; Ribeiro, Angela M.; Eckhart, Leopold; Fjeldsa, Jon; Hosner, Peter A.; Brumfield, Robb T.; Christidis, Les; Bertelsen, Mads F.; Sicheritz-Ponten, Thomas; Tietze, Dieter Thomas; Robertson, Bruce C.; Song, Gang; Borgia, Gerald; Claramunt, Santiago; Lovette, Irby J.; Cowen, Saul J.; Njoroge, Peter; Dumbacher, John Philip; Ryder, Oliver A.; Fuchs, Jerome; Bunce, Michael; Burt, David W.; Cracraft, Joel; Meng, Guanliang; Hackett, Shannon J.; Ryan, Peter G.; Jønsson, Knud Andreas; Jamieson, Ian G.; da Fonseca, Rute R.; Braun, Edward L.; Houde, Peter; Mirarab, Siavash; Suh, Alexander; Hansson, Bengt; Ponnikas, Suvi; Sigeman, Hanna; Stervander, Martin; Frandsen, Paul B.; van der Zwan, Henriette; van der Sluis, Rencia; Visser, Carina; Balakrishnan, Christopher N.; Clark, Andrew G.; Fitzpatrick, John W.; Bowman, Reed; Chen, Nancy; Cloutier, Alison; Sackton, Timothy B.; Edwards, Scott V.; Foote, Dustin J.; Shakya, Subir B.; Sheldon, Frederick H.; Vignal, Alain; Soares, Andre E. R.; Shapiro, Beth; Gonzalez-Solis, Jacob; Ferrer-Obiol, Joan; Rozas, Julio; Riutort, Marta; Tigano, Anna; Friesen, Vicki; Dalen, Love; Urrutia, Araxi O.; Szekely, Tamas; Liu, Yang; Campana, Michael G.; Corvelo, Andre; Fleischer, Robert C.; Rutherford, Kim M.; Gemmell, Neil J.; Dussex, Nicolas; Mouritsen, Henrik; Thiele, Nadine; Delmore, Kira; Liedvogel, Miriam; Franke, Andre; Hoeppner, Marc P.; Krone, Oliver; Fudickar, Adam M.; Mila, Borja; Ketterson, Ellen D.; Fidler, Andrew Eric; Friis, Guillermo; Parody-Merino, Angela M.; Battley, Phil F.; Cox, Murray P.; Lima, Nicholas Costa Barroso; Prosdocimi, Francisco; Parchman, Thomas Lee; Schlinger, Barney A.; Loiselle, Bette A.; Blake, John G.; Lim, Haw Chuan; Day, Lainy B.; Fuxjager, Matthew J.; Baldwin, Maude W.; Braun, Michael J.; Wirthlin, Morgan; Dikow, Rebecca B.; Ryder, T. Brandt; Camenisch, Glauco; Keller, Lukas F.; DaCosta, Jeffrey M.; Hauber, Mark E.; Louder, Matthew I. M.; Witt, Christopher C.; McGuire, Jimmy A.; Mudge, Joann; Megna, Libby C.; Carling, Matthew D.; Wang, Biao; Taylor, Scott A.; Del-Rio, Glaucia; Aleixo, Alexandre; Vasconcelos, Ana Tereza Ribeiro; Mello, Claudio V.; Weir, Jason T.; Haussler, David; Li, Qiye; Yang, Huanming; Wang, Jian; Lei, Fumin; Rahbek, Carsten; Gilbert, M. Thomas P.; Graves, Gary R.; Jarvis, Erich D.; Paten, Benedict; Zhang, Guojie (2020)
    Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
  • Horesh, Gal; Taylor-Brown, Alyce; McGimpsey, Stephanie; Lassalle, Florent; Corander, Jukka; Heinz, Eva; Thomson, Nicholas R. (2021)
    The pan-genome is defined as the combined set of all genes in the gene pool of a species. Pan-genome analyses have been very useful in helping to understand different evolutionary dynamics of bacterial species: an open pan-genome often indicates a free-living lifestyle with metabolic versatility, while closed pan-genomes are linked to host-restricted, ecologically specialized bacteria. A detailed understanding of the species pan-genome has also been instrumental in tracking the phylodynamics of emerging drug resistance mechanisms and drug-resistant pathogens. However, current approaches to analyse a species' pan-genome do not take the species population structure into account, nor do they account for the uneven sampling of different lineages, as is commonplace due to over -sampling of clinically relevant representatives. Here we present the application of a population structure- aware approach for classify-ing genes in a pan-genome based on within-species distribution. We demonstrate our approach on a collection of 7500 Escherichia coli genomes, one of the most-studied bacterial species and used as a model for an open pan-genome. We reveal clearly distinct groups of genes, clustered by different underlying evolutionary dynamics, and provide a more biologically informed and accurate description of the species' pan-genome.
  • Guo, Qingxue; Song, Haifeng; Kang, Jieyu; Korpelainen, Helena; Li, Chunyang (2018)
    Knowledge of how competition and facilitation affect photosynthetic traits and nitrogen metabolism contributes to understanding of plant-plant interaction mechanisms. We transplanted two larch species, Larix kaempferi and L. olgensis, to establish intra- and interspecific interaction experiments under different types of soil. Experiment 1: Two different soil types were selected, one from a c. twenty years old L. kaempferi plantation (named larch soil) and another from a secondary natural forest (named mixed forest soil). The experiment included three types of plant interactions (L kaempferi + L. kaempferi, L. olgensis + L. olgensis, and L. kaempferi + L. olgensis) and two soil types. Experiment 2: N fertilization was applied to larch soil. The experiment included the same three types of plant interactions as in Experiment 1 and two N treatments. The growth of L kaempferi was negatively affected by larch soil and accelerated by N fertilization, particularly under interspecific interaction. The effects of soil type combined with plant-plant interactions or N fertilization influenced the chlorophyll pigment content, net photosynthetic rate (Pn), photosynthetic N use efficiency (PNUE) and total non-structural carbohydrates of leaves (TNC). CM a/Chl b (ratio of chlorophyll a to chlorophyll b) was higher when the growth of L. kaempferi was facilitated by the presence of L olgensis in mixed forest soil. However, the ratio significantly declined when L. kaempferi confronted strong competition from L. olgensis in larch soil without N fertilization. Under N fertilization in larch soil, Chl a/Chl b of L. olgensis significantly increased by the presence of L. kaempferi. Plant-plant interactions and soil types affected the number of chloroplasts, especially in L. kaempferi, which had a greater number of chloroplasts under interspecific interactions than in monoculture when growing in mixed forest soil. L. olgensis enhanced its ability to absorb N-NO3- under interspecific interactions in larch N- soil, while L. kaempferi enhanced its ability to absorb N-NH4+ under interspecific competition in mixed forest soil. Competition or facilitation modified the photosynthetic traits and nitrogen metabolism depending on the type of soil. Differences in these physiological processes contribute to divergent performance among individuals growing under interspecific or intraspecific competition, or in isolation.
  • Huang, Yongjiang; Jacques, Frederic M. B.; Su, Tao; Ferguson, David K.; Tang, Hui; Chen, Wenyun; Zhou, Zhekun (2015)
    Cenozoic plant relicts are those groups that were once widespread in the Northern Hemisphere but are now restricted to some small isolated areas as a result of drastic climatic changes. They are good proxies to study how plants respond to climatic changes since their modern climatic requirements are known. Herein we look at the modern distribution of 65 palaeoendemic genera in China and compare it with the Chinese climatic pattern, in order to find a link between the plant distribution and climate. Central China and Taiwan Island are shown to be diversity centres of Cenozoic relict genera, consistent with the fact that these two regions have a shorter dry season with comparatively humid autumn and spring in China. Species distribution models indicate that the precipitation parameters are the most important variables to explain the distribution of relict genera. The Cenozoic wide-scale distribution of relict plants in the Northern Hemisphere is therefore considered to be linked to the widespread humid climate at that time, and the subsequent contraction of their distributional ranges was probably caused by the drying trend along with global cooling.
  • Dukat, Paulina; Ziemblinska, Klaudia; Olejnik, Janusz; Malek, Stanislaw; Vesala, Timo; Urbaniak, Marek (2021)
    The accurate estimation of an increase in forest stand biomass has remained a challenge. Traditionally, in situ measurements are done by inventorying a number of trees and their biometric parameters such as diameter at the breast height (DBH) and height; sometimes these are complemented by carbon (C) content studies. Here we present the estimation of net primary productivity (NPP) over a two years period (2019-2020) at a 25-year-old Scots pine stand. Research was based on allometric equations made by direct biomass analysis (tree extraction) and carbon content estimations in individual components of sampled trees, combined with a series of stem diameter increments recorded by a network of band dendrometers. Site-specific allometric equations were obtained using two different approaches: using the whole tree biomass vs DBH (M1), and total dry biomass-derived as a sum of the results from individual tree components' biomass vs DBH (M2). Moreover, equations for similar forest stands from the literature were used for comparison. Gross primary productivity (GPP) estimated from the eddy-covariance measurements allowed the calculation of carbon use efficiency (CUE = NPP/GPP). The two investigated years differed in terms of the sum and patterns of precipitation distribution, with a moderately dry year of 2019 that followed the extremely dry 2018, and the relatively average year of 2020. As expected, a higher increase in biomass was recorded in 2020 compared to 2019, as determined by both allometric equations based on in situ and literature data. For the former approach, annual NPP estimates reached ca. 2.0-2.1 t C ha(-1) in 2019 and 2.6-2.7 t C ha(-1) in 2020 depending on the "in situ equations" (M1-M2) used, while literature-derived equations for the same site resulted in NPP values ca. 20-30% lower. CUE was higher in 2020, which resulted from a higher NPP total than in 2019, with lower summer and spring GPP in 2020. However, the CUE values were lower than those reported in the literature for comparable temperate forest stands. A thorough analysis of the low CUE value would require a full interpretation of interrelated physiological responses to extreme conditions.
  • Elshibli, Sakina; Korpelainen, Helena (2018)
    Background: Medemia argun is a rare wild palm tree species. Its global existence is assumed to include the main population of about 1000 trees in the Nubian Desert of Sudan and some scattered individuals in southern Egypt. The species had previously been assumed to be extinct, but then reported to be extant about 20 years ago. Aims: To assess genetic variation and explore population genetic structure of M. argun, through development and analysis of microsatellite markers. Methods: The genome sequence mining approach was applied in order to identify microsatellites in the chloroplast genome of Bismarckia nobilis, a species closely related of M. argun. A set of 49 markers were designed, and their characteristics are now provided. Seven chloroplast DNA markers were developed for use in the genetic characterisation of this threatened species. Results: Five markers were found polymorphic in M. argun, which enabled the assessment of the genetic diversity of the species. Significant genetic differentiation was observed among generations and collection sites, accompanied by low genetic variation. The seven markers developed were polymorphic among the wild relatives Hyphaene thebaica and Borassus aethiopum. Conclusions: This is the first study to report molecular markers for M. argun. Our results suggest that the genetic consequences of population fragmentation in M. argun are beginning to be evident.
  • Murphy, Robert; Palm, Martin; Mustonen, Ville; Warringer, Jonas; Farewell, Anne; Parts, Leopold; Moradigaravand, Danesh (2021)
    Escherichia coli is a common bacterial species in the gastrointestinal tracts of warm-blooded animals and humans. Pathogenicity and antimicrobial resistance in E. coli may emerge via host switching from animal reservoirs. Despite its potential clinical importance, knowledge of the population structure of commensal E. coli within wild hosts and the epidemiological links between E. coli in nonhuman hosts and E. coli in humans is still scarce. In this study, we analyzed the whole-genome sequencing data of a collection of 119 commensal E. coli strains recovered from the guts of 55 mammal and bird species in Mexico and Venezuela in the 1990s. We observed low concordance between the population structures of E. coli isolates colonizing wild animals and the phylogeny, taxonomy, and ecological and physiological attributes of the host species, with distantly related E. coli strains often colonizing the same or similar host species and distantly related host species often hosting closely related E. coli strains. We found no evidence for recent transmission of E. coli genomes from wild animals to either domesticated animals or humans. However, multiple livestockand human-related virulence factor genes were present in E. coli of wild animals, including virulence factors characteristic of Shiga toxin-producing E. coli (STEC) and atypical enteropathogenic E. coli (aEPEC), where several isolates from wild hosts harbored the locus of enterocyte effacement (LEE) pathogenicity island. Moreover, E. coli isolates from wild animal hosts often harbored known antibiotic resistance determinants, including those against ciprofloxacin, aminoglycosides, tetracyclines, and beta-lactams, with some determinants present in multiple, distantly related E. coli lineages colonizing very different host animals. We conclude that genome pools of E. coli colonizing the guts of wild animals and humans share virulence and antibiotic resistance genes, underscoring the idea that wild animals could serve as reservoirs for E. coli pathogenicity in human and livestock infections. IMPORTANCE Escherichia coli is a clinically important bacterial species implicated in humanand livestock-associated infections worldwide. The bacterium is known to reside in the guts of humans, livestock, and wild animals. Although wild animals are recognized as potential reservoirs for pathogenic E. coli strains, the knowledge of the population structure of E. coli in wild hosts is still scarce. In this study, we used fine resolution of whole-genome sequencing to provide novel insights into the evolution of E. coli genomes from a small yet diverse collection of strains recovered within a broad range of wild animal species (including mammals and birds), the coevolution of E. coli strains with their hosts, and the genetics of pathogenicity of E. coli strains in wild hosts in Mexico. Our results provide evidence for the clinical importance of wild animals as reservoirs for pathogenic strains and highlight the need to include nonhuman hosts in the surveillance programs for E. coli infections.
  • Qiao, Wanjin; Liu, Fulu; Wan, Xing; Qiao, Yu; Li, Ran; Wu, Zhenzhou; Saris, Per Erik Joakim; Xu, Haijin; Qiao, Mingqiang (2022)
    Lactococcus lactis is a commonly used fermenting bacteria in cheese, beverages and meat products. Due to the lack of simplified chassis strains, it has not been widely used in the fields of synthetic biology. Thus, the construction of lactic acid bacteria chassis strains becomes more and more important. In this study, we performed whole genome sequencing, annotation and analysis of L. lactis N8. Based on the genome analysis, we found that L. lactis N8 contains two large plasmids, and the function prediction of the plasmids shows that some regions are related to carbohydrate transport/metabolism, multi-stress resistance and amino acid uptake. L. lactis N8 contains a total of seven prophage-related fragments and twelve genomic islands. A gene cluster encoding a hybrid NRPS-PKS system that was found in L. lactis N8 reveals that the strain has the potential to synthesize novel secondary metabolites. Furthermore, we have constructed a simplified genome chassis of L. lactis N8 and achieved the largest amount of deletion of L. lactis so far. Taken together, the present study offers further insights into the function and potential role of L. lactis N8 as a model strain of lactic acid bacteria and lays the foundation for its application in the field of synthetic biology.
  • Kulha, Niko; Pasanen, Leena; Aakala, Tuomas (2018)
    Time series of repeat aerial photographs currently span decades in many regions. However, the lack of calibration data limits their use in forest change analysis. We propose an approach where we combine repeat aerial photography, tree-ring reconstructions, and Bayesian inference to study changes in forests. Using stereopairs of aerial photographs from five boreal forest landscapes, we visually interpreted canopy cover in contiguous 0.1-ha cells at three time points during 1959-2011. We used tree-ring measurements to produce calibration data for the interpretation, and to quantify the bias and error associated with the interpretation. Then, we discerned credible canopy cover changes from the interpretation error noise using Bayesian inference. We underestimated canopy cover using the historical low-quality photographs, and overestimated it using the recent high-quality photographs. Further, due to differences in tree species composition and canopy cover in the cells, the interpretation bias varied between the landscapes. In addition, the random interpretation error varied between and within the landscapes. Due to the varying bias and error, the magnitude of credibly detectable canopy cover change in the 0.1-ha cells depended on the studied time interval and landscape, ranging from -10 to -18 percentage points (decrease), and from +10 to +19 percentage points (increase). Hence, changes occurring at stand scales were detectable, but smaller scale changes could not be separated from the error noise. Besides the abrupt changes, also slow continuous canopy cover changes could be detected with the proposed approach. Given the wide availability of historical aerial photographs, the proposed approach can be applied for forest change analysis in biomes where tree-rings form, while accounting for the bias and error in aerial photo interpretation.
  • Oversti, Sanni; Onkamo, Paivi; Stoljarova, Monika; Budowle, Bruce; Sajantila, Antti; Palo, Jukka U. (2017)
    In Europe, modern mitochondrial diversity is relatively homogeneous and suggests an ubiquitous rapid population growth since the Neolithic revolution. Similar patterns also have been observed in mitochondrial control region data in Finland, which contrasts with the distinctive autosomal and Y-chromosomal diversity among Finns. A different picture emerges from the 843 whole mitochondrial genomes from modern Finns analyzed here. Up to one third of the subhaplogroups can be considered as Finn-characteristic, i.e. rather common in Finland but virtually absent or rare elsewhere in Europe. Bayesian phylogenetic analyses suggest that most of these attributed Finnish lineages date back to around 3,000-5,000 years, coinciding with the arrival of Corded Ware culture and agriculture into Finland. Bayesian estimation of past effective population sizes reveals two differing demographic histories: 1) the 'local' Finnish mtDNA haplotypes yielding small and dwindling size estimates for most of the past; and 2) the 'immigrant' haplotypes showing growth typical of most European populations. The results based on the local diversity are more in line with that known about Finns from other studies, e.g., Y-chromosome analyses and archaeology findings. The mitochondrial gene pool thus may contain signals of local population history that cannot be readily deduced from the total diversity.
  • Beigaite, Rita; Tang, Hui; Bryn, Anders; Skarpaas, Olav; Stordal, Frode; Bjerke, Jarle W.; Zliobaite, Indre (2022)
    The global distribution of vegetation is largely determined by climatic conditions and feeds back into the climate system. To predict future vegetation changes in response to climate change, it is crucial to identify and understand key patterns and processes that couple vegetation and climate. Dynamic global vegetation models (DGVMs) have been widely applied to describe the distribution of vegetation types and their future dynamics in response to climate change. As a process-based approach, it partly relies on hard-coded climate thresholds to constrain the distribution of vegetation. What thresholds to implement in DGVMs and how to replace them with more process-based descriptions remain among the major challenges. In this study, we employ machine learning using decision trees to extract large-scale relationships between the global distribution of vegetation and climatic characteristics from remotely sensed vegetation and climate data. We analyse how the dominant vegetation types are linked to climate extremes as compared to seasonally or annually averaged climatic conditions. The results show that climate extremes allow us to describe the distribution and eco-climatological space of the vegetation types more accurately than the averaged climate variables, especially those types which occupy small territories in a relatively homogeneous ecological space. Future predicted vegetation changes using both climate extremes and averaged climate variables are less prominent than that predicted by averaged climate variables and are in better agreement with those of DGVMs, further indicating the importance of climate extremes in determining geographic distributions of different vegetation types. We found that the temperature thresholds for vegetation types (e.g. grass and open shrubland) in cold environments vary with moisture conditions. The coldest daily maximum temperature (extreme cold day) is particularly important for separating many different vegetation types. These findings highlight the need for a more explicit representation of the impacts of climate extremes on vegetation in DGVMs.
  • Ramírez-Valiente, José-Alberto; Aranda, Ismael; Sanchez-Gomez, David; Rodriguez-Calcerrada, Jesus; Valladares, Fernando; Robson, Thomas Matthew (2019)
    In Mediterranean-type ecosystems, drought is considered the main ecological filter for seedling establishment. The evergreen oaks Quercus ilex L. and Quercus suber L. are two of the most abundant tree species in the Mediterranean Basin. Despite their shared evergreen leaf habit and ability to resist low soil water potentials, traditionally it has been suggested that Q. ilex is better suited to resist dry conditions than Q. suber. In this study, we examined how seedlings of Q. ilex and Q. suber grown in sandy soils responded to different levels of water availability using natural dry conditions and supplemental watering. Specifically, we estimated survival and water status of seedlings and explored the role of acorn mass and belowground biomass in seedling performance. To our surprise, Q. suber was better able to survive the summer drought in our experiment than Q. ilex. Nearly 55% of the Q. suber seedlings remained alive after a 2-month period without rain or supplemental water, which represents almost 20% higher survival than Q. ilex over the same period. At the end of the dry period, the surviving seedlings of Q. suber had strikingly higher water potential, potential maximum quantum yield of photosystem II (F-v/F-m) and stomatal conductance (g(s)) than those of Q. ilex. Acorn mass was associated with the probability of survival under dry conditions; however, it did not explain the differences in survival or water status between the species. In contrast, Q. suber had a higher root ratio and root: shoot ratio than Q. ilex and these traits were positively associated with predawn leaf water potential, F-v/F-m, g(s) and survival. Taken together, our results suggest that the higher relative investment in roots by Q. suber when growing in a sandy acidic substrate allowed this species to maintain better physiological status and overall condition than Q. ilex, increasing its probability of survival in dry conditions.
  • Lee, Kyung Min; Kivelä, Sami M.; Ivanov, Vladislav; Hausmann, Axel; Kaila, Lauri; Wahlberg, Niklas; Mutanen, Marko (2018)
    A rapid shift from traditional Sanger sequencing-based molecular methods to the phylogenomic approach with large numbers of loci is underway. Among phylogenomic methods, restriction site associated DNA (RAD) sequencing approaches have gained much attention as they enable rapid generation of up to thousands of loci randomly scattered across the genome and are suitable for nonmodel species. RAD data sets however suffer from large amounts of missing data and rapid locus dropout along with decreasing relatedness among taxa. The relationship between locus dropout and the amount of phylogenetic information retained in the data has remained largely uninvestigated. Similarly, phylogenetic hypotheses based on RAD have rarely been compared with phylogenetic hypotheses based on multilocus Sanger sequencing, even less so using exactly the same species and specimens. We compared the Sanger-based phylogenetic hypothesis (8 loci; 6172 bp) of 32 species of the diverse moth genus Eupithecia (Lepidoptera, Geometridae) to that based on double-digest RAD sequencing (3256 loci; 726,658 bp). We observed that topologies were largely congruent, with some notable exceptions that we discuss. The locus dropout effect was strong. We demonstrate that number of loci is not a precise measure of phylogenetic information since the number of single-nucleotide polymorphisms (SNPs) may remain low at very shallow phylogenetic levels despite large numbers of loci. As we hypothesize, the number of SNPs and parsimony informative SNPs (PIS) is low at shallow phylogenetic levels, peaks at intermediate levels and, thereafter, declines again at the deepest levels as a result of decay of available loci. Similarly, we demonstrate with empirical data that the locus dropout affects the type of loci retained, the loci found in many species tending to show lower interspecific distances than those shared among fewer species. We also examine the effects of the numbers of loci, SNPs, and PIS on nodal bootstrap support, but could not demonstrate with our data our expectation of a positive correlation between them. We conclude that RAD methods provide a powerful tool for phylogenomics at an intermediate phylogenetic level as indicated by its broad congruence with an eight-gene Sanger data set in a genus of moths. When assessing the quality of the data for phylogenetic inference, the focus should be on the distribution and number of SNPs and PIS rather than on loci.
  • Bravo, Gustavo A.; Whitney, Bret M.; Belmonte-Lopes, Ricardo; Bornschein, Marcos R.; Aristizabal, Natalia; Beco, Renata; Battilana, Jaqueline; Naka, Luciano N.; Aleixo, Alexandre; Pie, Marcio R.; Silveira, Luis F.; Derryberry, Elizabeth P.; Brumfield, Robb T. (2021)
    The family Thamnophilidae is a species-rich Neotropical radiation of passerine birds. Current classification of its 235 species is mostly based on morphological similarities, but recent studies integrating comprehensive phenotypic and phylogenetic data have redefined taxonomic limits of several taxa. Here, we assess generic relationships of Herpsilochmus, Sakesphorus, Thamnophilus, Biatas, and Dysithamnus using DNA sequences from the mitochondrion, nuclear exons, and ultraconserved elements, with further attention to interspecific relationships within Herpsilochmus. We show that Herpsilochmus and Sakesphorus are not monophyletic. We resolve Herpsilochmus sellowi as a deep-branch sister to the monotypic genus Biatas and Sakesphorus cristatus as sister to a clade comprising Herpsilochmus sensu stricto and Dysithamnus. These results are consistent across loci, obtained via concatenation and coalescent-based analyses, and supported by likelihood-ratio tests of the distribution of our sampled coalescent histories. The phenotypic distinctiveness of both H. sellowi and Biatas argues against merging them into a single genus. Because no generic name is available for H. sellowi, we describe a monotypic genus. The polyphyly of Sakesphorus warrants recognition of the available generic name Sakesphoroides for the distinctive and monotypic S. cristatus. Furthermore, we recover 6 well-supported species groups within Herpsilochmus sensu stricto. Within the context of the family as a whole, the ubiquity of long terminal branches representing monotypic genera points to extinction events among ancestors of these lineages. We suggest that retention of ancestral characters or random genetic drift coupled with extensive extinction could explain the high degree of morphological and ecological similarity across these taxa, but we highlight the potential role of the environment in driving adaptive phenotypic convergence. Finally, our results send a cautionary message against the blind use of phylogenies containing imputed data based on taxonomy due to the increasingly frequent mismatches between traditional taxonomic classification and molecular phylogenies.
  • Zhu, Qiyun; Huang, Shi; Gonzalez, Antonio; McGrath, Imran; McDonald, Daniel; Haiminen, Niina; Armstrong, George; Vazquez-Baeza, Yoshiki; Yu, Julian; Kuczynski, Justin; Sepich-Poore, Gregory D.; Swafford, Austin D.; Das, Promi; Shaffer, Justin P.; Lejzerowicz, Franck; Belda-Ferre, Pedro; Havulinna, Aki S.; Meric, Guillaume; Niiranen, Teemu; Lahti, Leo; Salomaa, Veikko; Kim, Ho-Cheol; Jain, Mohit; Inouye, Michael; Gilbert, Jack A.; Knight, Rob (2022)
    We introduce the operational genomic unit (OGU) method, a metagenome analysis strategy that directly exploits sequence alignment hits to individual reference genomes as the minimum unit for assessing the diversity of microbial communities and their relevance to environmental factors. This approach is independent of taxonomic classification, granting the possibility of maximal resolution of community composition, and organizes features into an accurate hierarchy using a phylogenomic tree. The outputs are suitable for contemporary analytical protocols for community ecology, differential abundance, and supervised learning while supporting phylogenetic methods, such as UniFrac and phylofactorization, that are seldom applied to shotgun metagenomics despite being prevalent in 16S rRNA gene amplicon studies. As demonstrated in two real-world case studies, the OGU method produces biologically meaningful patterns from microbiome data sets. Such patterns further remain detectable at very low metagenomic sequencing depths. Compared with taxonomic unit-based analyses implemented in currently adopted metagenomics tools, and the analysis of 16S rRNA gene amplicon sequence variants, this method shows superiority in informing biologically relevant insights, including stronger correlation with body environment and host sex on the Human Microbiome Project data set and more accurate prediction of human age by the gut microbiomes of Finnish individuals included in the FINRISK 2002 cohort. We provide Woltka, a bioinformatics tool to implement this method, with full integration with the QIIME 2 package and the Qiita web platform, to facilitate adoption of the OGU method in future metagenomics studies. IMPORTANCE Shotgun metagenomics is a powerful, yet computationally challenging, technique compared to 16S rRNA gene amplicon sequencing for decoding the composition and structure of microbial communities. Current analyses of metagenomic data are primarily based on taxonomic classification, which is limited in feature resolution. To solve these challenges, we introduce operational genomic units (OGUs), which are the individual reference genomes derived from sequence alignment results, without further assigning them taxonomy. The OGU method advances current read-based metagenomics in two dimensions: (i) providing maximal resolution of community composition and (ii) permitting use of phylogeny-aware tools. Our analysis of real-world data sets shows that it is advantageous over currently adopted metagenomic analysis methods and the finest-grained 16S rRNA analysis methods in predicting biological traits. We thus propose the adoption of OGUs as an effective practice in metagenomic studies.
  • Runnel, Kadri; Miettinen, Otto; Lohmus, Asko (2021)
    Polyporous fungi, a morphologically delineated group of Agaricomycetes (Basidiomycota), are considered well studied in Europe and used as model group in ecological studies and for conservation. Such broad interest, including widespread sampling and DNA based taxonomic revisions, is rapidly transforming our basic understanding of polypore diversity and natural history. We integrated over 40,000 historical and modern records of polypores in Estonia (hemiboreal Europe), revealing 227 species, and including Polyporus submelanopus and P. ulleungus as novelties for Europe. Taxonomic and conservation problems were distinguished for 13 unresolved subgroups. The estimated species pool exceeds 260 species in Estonia, including at least 20 likely undescribed species (here documented as distinct DNA lineages related to accepted species in, e.g., Ceriporia, Coltricia, Physisporinus, Sidera and Sistotrema). Four broad ecological patterns are described: (1) polypore assemblage organization in natural forests follows major soil and tree-composition gradients; (2) landscape-scale polypore diversity homogenizes due to draining of peatland forests and reduction of nemoral broad-leaved trees (wooded meadows and parks buffer the latter); (3) species having parasitic or brown-rot life-strategies are more substrate-specific; and (4) assemblage differences among woody substrates reveal habitat management priorities. Our update reveals extensive overlap of polypore biota throughout North Europe. We estimate that in Estonia, the biota experienced ca. 3-5% species turnover during the twentieth century, but exotic species remain rare and have not attained key functions in natural ecosystems. We encourage new regional syntheses on long studied fungal groups to obtain landscape-scale understanding of species pools, and for elaborating fungal indicators for biodiversity assessments.
  • Cayuela, Hugo; Lemaitre, Jean-Francois; Lena, Jean-Paul; Ronget, Victor; Martinez-Solano, Inigo; Muths, Erin; Pilliod, David S.; Schmidt, Benedikt R.; Sanchez-Montes, Gregorio; Gutierrez-Rodriguez, Jorge; Pyke, Graham; Grossenbacher, Kurt; Lenzi, Omar; Bosch, Jaime; Beard, Karen H.; Woolbright, Lawrence L.; Lambert, Brad A.; Green, David M.; Jreidini, Nathalie; Garwood, Justin M.; Fisher, Robert N.; Matthews, Kathleen; Dudgeon, David; Lau, Anthony; Speybroeck, Jeroen; Homan, Rebecca; Jehle, Robert; Baskale, Eyup; Mori, Emiliano; Arntzen, Jan W.; Joly, Pierre; Stiles, Rochelle M.; Lannoo, Michael J.; Maerz, John C.; Lowe, Winsor H.; Valenzuela-Sanchez, Andres; Christiansen, Ditte G.; Angelini, Claudio; Thirion, Jean-Marc; Merilä, Juha; Colli, Guarino R.; Vasconcellos, Mariana M.; Boas, Taissa C. V.; Arantes, isis da C.; Levionnois, Pauline; Reinke, Beth A.; Vieira, Cristina; Marais, Gabriel A. B.; Gaillard, Jean-Michel; Miller, David A. W. (2022)
    Sex-related differences in mortality are widespread in the animal kingdom. Although studies have shown that sex determination systems might drive lifespan evolution, sex chromosome influence on aging rates have not been investigated so far, likely due to an apparent lack of demographic data from clades including both XY (with heterogametic males) and ZW (heterogametic females) systems. Taking advantage of a unique collection of capture-recapture datasets in amphibians, a vertebrate group where XY and ZW systems have repeatedly evolved over the past 200 million years, we examined whether sex heterogamy can predict sex differences in aging rates and lifespans. We showed that the strength and direction of sex differences in aging rates (and not lifespan) differ between XY and ZW systems. Sex-specific variation in aging rates was moderate within each system, but aging rates tended to be consistently higher in the heterogametic sex. This led to small but detectable effects of sex chromosome system on sex differences in aging rates in our models. Although preliminary, our results suggest that exposed recessive deleterious mutations on the X/Z chromosome (the "unguarded X/Z effect") or repeat-rich Y/W chromosome (the "toxic Y/W effect") could accelerate aging in the heterogametic sex in some vertebrate clades.
  • Chen, Juan; Han, Qingquan; Duan, Baoli; Korpelainen, Helena; Li, Chunyang (2017)
    Lead (Pb) contamination seriously threatens agroforestry production and safety. We aim to determine the interactive influence of Pb and sexual competition on the growth performance, photosynthetic and biochemical traits, ultrastructure and phytoremediation-related parameters of males and females. In the present study, eco-physiological responses and phytoremediation traits of Populus cathayana females and males were evaluated under interactive treatments of Pb and competition. There were significant sex-specific competition effects on biomass partition, photosynthetic activities, carbohydrate contents, nitrogen and phosphorus use efficiencies, ultrastructure and phytoremediation under Pb stress. When competition within the same sex was compared, females were more sensitive to Pb stress, while males possessed greater Pb contents, and a higher bioconcentration factor and tolerance index. Under inter-sexual competition, males alleviated competition effects through greater Pb absorption, and lower photosynthetic rates, nutrient use efficiencies and biomass accumulation. Moreover, Pb stress altered competition intensities of both sexes. Sex-specific competition and neighbor effects may regulate responses and phytoremediation under heavy metal stress in dioecious plants. In the future, more attention should be paid on the effects of inter- and intra-sexual competition on dioecious species in the process of forestation and restoration of contaminated soil.