Dendrochronological dating of Rebel’s Rest (40FR512), Franklin County,Tennessee, USA

The structure named Rebel’s Rest was a two-story, Reconstruction-era house located on the campus of the University of the South in Sewanee, Tennessee, before being severely damaged by fire in July 2014. The house was constructed of squared timbers and round logs, with later additions built using sawn lumber. Dendrochronological analyses of timbers and logs salvaged from the house reveals wood from four genera: oak (Quercus spp.), tulip poplar (Liriodendron tulipifera L.), American chestnut (Castanea dentata [Marshall] Borkh.), and pine (Pinus spp.). We statistically and graphically crossdated a total of 251 samples (24,410 rings) with regional chronologies from the ITRDB, resulting in three dated chronologies comprised of oak (1645–1874), tulip poplar (1725–1865), and American chestnut (1710–1864). The majority of samples with cutting dates (95.6%) ended in years 1865–1866, confirming the historically reported construction date of 1866 for the initial structure. The cutting date analysis also confirms two rooms as later additions, Room M (1867) and Room B (1875). Based on ring count and the number of chronologies produced, this research represents the largest known dataset from a single historic structure in the Southeastern US.     

Reconstruction of source water using the δ18O of tree ring phenylglucosazone: A potential tool in paleoclimate studies

The oxygen isotope ratios of tree ring cellulose have a great potential as proxy for the oxygen isotope ratios of source water, which is related to climate. However, source water isotopic signatures can be masked by plant physiological and biochemical processes during cellulose synthesis. To minimize biochemical effects in the recording of source water, we modified the cellulose molecule to phenylglucosazone, which only has oxygen attached to carbon 3–6 (O_C3–6) of the cellulose glucose moieties, thus eliminating the oxygen attached to carbon 2 of the cellulose glucose moieties (O_C-2). Here we developed a method to use small amounts of inter and intra-annual tree ring cellulose for phenylglucosazone synthesis. Using this new method we tested if the oxygen isotope ratios of source water reconstructed from tree ring phenylglucosazone (δ¹⁸O_sw^PG) and the observed source water (δ¹⁸O_sw^obs) would have a better agreement than those reconstructed from the tree ring cellulose molecule. Annual tree ring samples were obtained from Pinus sylvestris (1997–2003) (Finland) and Picea abies (1971–1992) (Switzerland) and intra-annual tree ring samples were obtained from Pinus radiata (October 2004–March 2006) (New Zealand), each near a meteorological station where precipitation and relative humidity (RH) were measured periodically. The δ¹⁸O of tree ring cellulose and tree ring phenylglucosazone for each of the three species were then used to back calculate the δ¹⁸O of source water according to a previous published empirical equation. As expected, the δ¹⁸O of tree ring phenylglucosazone was superior than cellulose in the reconstruction of source water available to the plant. Deviation between δ¹⁸O_sw^PG and δ¹⁸O_sw^obs was in part correlated with variation in atmospheric relative humidity (RH) which was not observed for the cellulose molecule. We conclude that this new method can be applicable to inter and intra-annual tree ring studies and that the use of the tree ring phenylglucosazone will significantly improve the quality of paleoclimate studies.     

Oxygen isotope dendrochronology of Llwyn Celyn; One of the oldest houses in Wales

We report the application of oxygen isotope dendrochronology to date a high-status and remarkably unaltered late medieval hall house on the eastern border of South Wales. The oak timbers have either short and complacent ring series, or very strong growth disturbance, and none were suitable for ring-width dendrochronology. By using stable oxygen isotopes from the latewood cellulose, rather than ring widths, it was possible to cross-match and date all 14 timber samples and to provide felling dates related to several phases of building. The hall and solar cross-wing were constructed shortly after 1420CE, which is remarkably early. The house was upgraded using timbers felled in the winter of 1695/6CE by ceiling over of the hall and inserting a chimney. A separate small domestic building was added at the same time and the addition of the kitchen is likely to be contemporaneous. A substantial beast house was added a few years before the house was refurbished, emphasising the importance of cattle as the main source of wealth. A small barn with timbers felled in spring 1843 CE was added later. Llwyn Celyn is one of the most important domestic buildings in Wales, but without the new approach none of the phases of its evolution could have been dated precisely. Oxygen isotope dendrochronology has enormous potential for dating timbers that have small numbers of rings and/or show severe growth disturbance and it works well in regions where tree growth is not strongly constrained by climate. The research was generously supported by the Leverhulme Trust, Natural Environment Research Council, Landmark Trust and the UK National Lottery Heritage Fund.     

<Emphasis Type="Italic">In silico</Emphasis> analysis of pectin lyase and pectinase sequences

A total of 48 full-length protein sequences of pectin lyases from different source organisms available in NCBI were subjected to multiple sequence alignment, domain analysis, and phylogenetic tree construction. A phylogenetic tree constructed on the basis of the protein sequences revealed two distinct clusters representing pectin lyases from bacterial and fungal sources. Similarly, the multiple accessions of different source organisms representing bacterial and fungal pectin lyases also formed distinct clusters, showing sequence level homology. The sequence level similarities among different groups of pectinase enzymes, viz. pectin lyase, pectate lyase, polygalacturonase, and pectin esterase, were also analyzed by subjecting a single protein sequence from each group with common source organism to tree construction. Four distinct clusters representing different groups of pectinases with common source organisms were observed, indicating the existing sequence level similarity among them. Multiple sequence alignment of pectin lyase protein sequence of different source organisms along with pectinases with common source organisms revealed a conserved region, indicating homology at sequence level. A conserved domain Pec_Lyase_C was frequently observed in the protein sequences of pectin lyases and pectate lyases, while Glyco_hydro_28 domains and Pectate lyase-like β-helix clan domain are frequently observed in polygalacturonases and pectin esterases, respectively. The signature amino acid sequence of 41 amino acids, i.e. TYDNAGVLPITVN-SNKSLIGEGSKGVIKGKGLRIVSGAKNI, related with the Pec_Lyase_C is frequently observed in pectin lyase protein sequences and might be related with the structure and enzymatic function.     

Tree-rings and transportation in the New Zealand kauri (Agathis australis) timber industry: Investigating the time lag from tree to building

The interpretation of felling dates established by dendrochronological dating requires understanding of sample context and building practices, as well as knowledge of processes and timescales within the timber supply chain. In New Zealand (N.Z.), tree ring analysis of kauri from colonial-era (1840–1906) and early Dominion-era (1907–1920) buildings has been undertaken since 2000 and felling dates have been identified from several structures, providing a terminus post quem date for construction or modification of the building. What has been lacking is a good understanding of how long it took for a kauri tree to become timber used in a building or other structure. As a first estimate, felling dates from a small set of buildings were compared to documented construction dates, suggesting a delay of up to 5 years. To improve interpretation of felling dates, we investigated timescales associated with two stages of timber production within the 19th and early 20th century kauri timber industry: (a) transportation from stump to mill, and (b) seasoning of sawn timber. Documentary sources for ∼1850 until the 1920s were analysed, covering the development, expansion and decline of industrialised kauri timber production. The available evidence suggests that transportation to the sawmill was the most important variable. Logs could arrive within a few weeks of felling or potentially experience a delay of a year or more. Transportation times were affected by geography, weather, spatial differences and temporal changes in transportation methods and economic fluctuations. Seasoning of sawn timber probably contributed little to the time lag, as the balance of evidence suggests framing timber was not usually seasoned. In general, any delay associated with transportation and seasoning is unlikely to be more than a couple of years. The findings support the earlier use-date range of up to 5 years, but suggest it is generous. The dating of waney-edge timbers from buildings with accurate construction dates would help refine a use date range for kauri, as would further research into other stages of the production process including conversion of logs, transportation to market, and stockpiling in the timber yard and/or building site. The current study is also a starting point for further research in three related areas: (a) biography of timber; (b) technological change; and (c) trade networks.     

Refining the statistical parameters for constructing tree-ring chronologies using short-lived species: Alder (Alnus glutinosa Gaertn)

The dendrochronological potential of short-lived species has had varying degrees of success in the past. Where there has been a level of success with short sequenced assemblages, the focus has been on visual comparisons, based on the occurrence of signature rings. Of vital importance to alder’s ability to be cross-correlated is that it produces a significant amount of distinguishable signature rings. Between 2012 and 2013, a large artificial island (crannog) of medieval date was excavated at Drumclay, County Fermanagh, Northern Ireland, and revealed a site of significant longevity, dating from the 9th century AD to the Post-Medieval period. This excavation exposed a vast number of well-preserved waterlogged archaeological features, resulting in the retention of over 9,000 individual wood samples. Oak timbers were used scarcely in the construction of the crannog, with the dominant wood species identified during excavation being alder. While the oak timbers have proved successful in providing spot dates and indicating phases of activity, the full chronological potential of the wood assemblage lies in the ring patterns of the principal species, alder, particularly with respect to understanding construction phases and site evolution. Previous failures to build chronologies using alder have been attributed to the short-lived and site specific nature of the species. Here, we test whether the measurement of large numbers of samples from a single context within a single site overcomes the limitations posed by alder. We measured the ring-widths of 90 alder samples from archaeological features within the crannog’s infrastructure to test if a robust context chronology could be built. The average ring sequence length ranged from 30 to 60 rings, with one timber extending to 108 rings. Visual correlations were used to aid ring pattern matching in conjunction with statistical correlation. We used radiocarbon wiggle-matching to test the robustness of our constructed chronology and to anchor it to an absolute timescale. Our results to date show that problems of autocorrelation can arise when long alder sequences (>100 rings) are used in conjunction with short sequences (30 to 60 rings). Establishing a rigorous protocol for sample selection has enabled us to develop a more statistically refined methodology that has produced t-values as high as 8.3. We show that in order to construct the best possible alder chronology, multiple ring patterns need to be examined from each context. We recommend examining short-lived assemblages on their own merits; the best approach in these cases is not to look for the longest sequences but instead to focus on the those from the mean sequence range.     

Age and Growth Patterns of Brazil Nut Trees (Bertholletia excelsa Bonpl.) in Amazonia,Brazil

Various techniques have been used to estimate the age of Brazil nut trees (Bertholletia excelsa Bonpl.), but these techniques produce large discrepancies. Here, we first verified that two individuals of known ages from a plantation in central Amazonia, Brazil, have a congruent number of growth rings. The indexed average tree‐ring curve was significantly correlated with total precipitation during the rainy season (November–June) over a 50‐yr period, confirming the annual nature of the tree rings. Second, we analyzed Brazil nut trees from two populations in the Trombetas (eastern Amazon) and Purus (central Amazon) regions, performing tree‐ring analysis to estimate tree age and diameter increment rates. We compared age–diameter relationships, mean passage time through 10‐cm diameter size classes, and growth trajectories of individual trees. The maximum age of Brazil nut trees analyzed was 361 yr in the Purus and 401 yr in the Trombetas. Trees at the Purus site had higher mean diameter increment rates and showed more variation compared to trees at the Trombetas site. Individual growth trajectories show that the majority of trees attained the canopy by direct growth, while a smaller number passed through one release or one suppression event before becoming established in the canopy. None of the trees passed through multiple release and suppression events. The age estimations presented here are comparable to previous tree‐ring analyses for the species, and the observed growth patterns support earlier work indicating B. excelsa as a gap‐dependent tree species.     

New dendroarchaeological evidence of water well constructions reveals advanced Early Neolithic craftsman skills

The first European settlements accompanied by crop and livestock farming occurred approximately 7500 years ago. In this agrarian society, wood was one of the most important raw materials, most notably for construction, but only a little is known about wood use and woodworking technology. Hence, archaeological wooden finds are of particular importance. Dendroarchaeological studies combine the analysis of external and internal characteristics of archaeological wood: traces of tools on the wooden surfaces and the shape of timbers provide information about woodworking techniques, the tree rings allow dendrochronological dating and provide a paleoecological archive. In 2015 and 2016, two water wells with wooden linings from the Early Neolithic Period were discovered in the Czech Republic close to the towns of Velim (Bohemia) and Uničov (Moravia). The timbers were excellently preserved under waterlogged conditions. Here, we present a dendroarchaeological study including tree-ring and woodworking analyses. Furthermore, we consider former forest species composition. Overall, 15 lumbers from both wells were successfully dated by dendrochronology. The oaks used for the wells from Velim and Uničov were felled in 5196/5195 BCE and 5093–5085 BCE, respectively. Additionally, the taxa of 1859 wooden fragments, such as charcoals, branches and chips, were wood anatomically identified. The well lining from Velim with a hollowed tree trunk is already known from other Central European locations. In contrast, the construction from Uničov is unique for this period. Until now, the advanced construction design formed by four corner posts with longitudinal grooves and inserted horizontal planks was only known several thousands years later. The Early Neolithic wells from Uničov and Velim are the oldest archaeological discoveries of wooden artefacts in the Czech Republic that have been dendrochronologically dated. The tree-ring width series extend the Czech oak tree-ring width chronology more than 300 years into the past.     

沈阳清墓木质葬具的树种鉴定及生态环境的指示潜力

古墓葬器所用木材是我们了解当时植被、气候以及社会状况的重要材料。本文利用木材解剖学和树木年代学方法,对沈阳浑南水家村墓葬群出土的木质葬具进行树种识别与树木年轮定年研究。结果表明: 16个木质葬具样本中有7个为松科松属油松木材,有8个为松科落叶松属木材,很可能为长白落叶松,有1个为槭树科槭树属木材。这些树种至今在辽宁地区仍广泛分布,说明该地区森林结构(树种组成)相对稳定,在一定程度上反映了当时气候与现在相似。也表明清代盛京(今沈阳)地区平民墓葬木质葬具所用木材存在区域性的植物地理特征,并反映出当时的生产力发展水平,即均是低成本、易获得的乡土树种,且这些木材以针叶树为主,也有少量阔叶树。这些木材很可能来源于沈阳当地或辽东山区森林,浑河水道是木材运至沈阳的重要途径。部分油松和落叶松葬具木材可以较好地交叉定年,确定树木生长年代在1680s—1770s(清朝早期至中期)。这些样本的年轮宽度变化具有较好的一致性和较高的气候敏感度,反映出区域气候环境的一致性。这些木质葬具对清朝早期至中期的气候条件具有一定的指示潜力。     

A method for molecular phylogeny construction by direct use of nucleotide sequence data

Summary A method for molecular phylogeny construction is newly developed. The method, called the stepwise ancestral sequence method, estimates molecular phylogenetic trees and ancestral sequences simultaneously on the basis of parsimony and sequence homology. For simplicity the emphasis is placed more on parsiomony than on sequence homology in the present study, though both are certainly important. Because parsimony alone will sometimes generate plural candidate trees, the method retains not one but five candidates from which one can then single out the final tree taking other criteria into account.The properties and performance of the method are then examined by simulating an evolving gene along a model phylogenetic tree. The estimated trees are found to lie in a narrow range of the parsimony criteria used in the present study. Thus, other criteria such as biological evidence and likelihood are necessary to single out the correct tree among them, with biological evidence taking precedence over any other criterion. The computer simulation also reveals that the method satisfactorily estimates both tree topology and ancestral sequences, at least for the evolutionary model used in the present study.     

大兴安岭北部樟子松树轮δ13C的高向变化及其与树轮宽度的关系

通过对大兴安岭北部樟子松树轮样品高向的年轮宽度和稳定碳同位素比率(δ¹³C)进行测定,分析了高向上δ¹³C的变化特征及其与年轮宽度的关系.结果表明： 在木质部全轮、早材和树皮内皮3种成分中,样品高向δ¹³C均呈现由顶部至基部先显著增加,在冠层底部达到最大值,再向下迅速减少至谷值的变化趋势.早晚材平均宽度比由基部至顶部增大.高向上δ¹³C年均值序列与轮宽年均值序列呈现较为明显的反向对应关系,与早晚材宽度比年均值序列呈现在冠层以上较为一致的变化趋势.样本高向上年轮宽度序列及δ¹³C序列均存在不同程度的显著差异,δ¹³C值的高向变化与年际变化基本处于同一量级.树体高向δ¹³C序列逐年变化趋势基本一致,同一高度盘的δ¹³C序列与年轮宽度序列基本呈负相关,但不同高度的显著性有所差异.
     

Estimating phylogenetic trees from pairwise likelihoods and posterior probabilities of substitution counts

The field of phylogenetic tree estimation has been dominated by three broad classes of methods: distance-based approaches, parsimony and likelihood-based methods (including maximum likelihood (ML) and Bayesian approaches). Here we introduce two new approaches to tree inference: pairwise likelihood estimation and a distance-based method that estimates the number of substitutions along the paths through the tree. Our results include the derivation of the formulae for the probability that two leaves will be identical at a site given a number of substitutions along the path connecting them. We also derive the posterior probability of the number of substitutions along a path between two sequences. The calculations for the posterior probabilities are exact for group-based, symmetric models of character evolution, but are only approximate for more general models.     

Actin Gene Sequence from Euglena gracilis

ABSTRACT The full length coding sequence of the Euglena gracilis actin gene was determined by RT-PCR of Euglena gracilis mRNA. Conserved regions in the actin amino acid sequence were used as guides for the synthesis of degenerate primers. Sequence was obtained for 1.238 nucleotides, of which 1.131 were coding for 377 amino acids. Sequence comparisons showed a similarity with other actins of 56% to 80%. Even though most of the actin amino acid sequence was conserved, some regions showed high divergence, i.e. the DNase I-binding loop at the N-terminal region. The construction of a phylogenetic tree based on actin sequences from different organisms placed Euglena gracilis in a cluster with Trypanosoma brucei and Leishmania major.     

Molecular phylogeny of the hominoids: inferences from multiple independent DNA sequence data sets

Consensus on the evolutionary relationships of humans, chimpanzees, and gorillas has not been reached, despite the existence of a number of DNA sequence data sets relating to the phylogeny, partly because not all gene trees from these data sets agree. However, given the well-known phenomenon of gene tree-species tree mismatch, agreement among gene trees is not expected. A majority of gene trees from available DNA sequence data support one hypothesis, but is this evidence sufficient for statistical confidence in the majority hypothesis? All available DNA sequence data sets showing phylogenetic resolution among the hominoids are grouped according to genetic linkage of their corresponding genes to form independent data sets. Of the 14 independent data sets defined in this way, 11 support a human- chimpanzee clade, 2 support a chimpanzee-gorilla clade, and one supports a human-gorilla clade. The hypothesis of a trichotomous speciation event leading to Homo; Pan, and Gorilla can be firmly rejected on the basis of this data set distribution. The multiple-locus test (Wu 1991), which evaluates hypotheses using gene tree-species tree mismatch probabilities in a likelihood ratio test, favors the phylogeny with a Homo-Pan clade and rejects the other alternatives with a P value of 0.002. When the probabilities are modified to reflect effective population size differences among different types of genetic loci, the observed data set distribution is even more likely under the Homo-Pan clade hypothesis. Maximum-likelihood estimates for the time between successive hominoid divergences are in the range of 300,000-2,800,000 years, based on a reasonable range of estimates for long-term hominoid effective population size and for generation time. The implication of the multiple-locus test is that existing DNA sequence data sets provide overwhelming and sufficient support for a human-chimpanzee clade: no additional DNA data sets need to be generated for the purpose of estimating hominoid phylogeny. Because DNA hybridization evidence (Caccone and Powell 1989) also supports a Homo-Pan clade, the problem of hominoid phylogeny can be confidently considered solved.      

Dendroprovenancing: A preliminary assessment of potential to geo-locate kauri timbers in northern New Zealand

After 1840, New Zealand kauri (Agathis australis) became the focus of a large-scale timber industry in the upper North Island, which converted trees into timber that was then used in construction. Cities such as Auckland and Wellington relied on importing kauri to meet local demand for construction and other uses. Kauri timbers from buildings and in-ground features, mostly in Auckland city, have been collected for tree-dating and master chronology development. Although the use of timber at archaeological sites is understood, the geographic origin of the timber from within the natural range of kauri (north of 38 °S) is largely unknown. This limits interpretation of archaeological wood and constrains use of the tree-ring data in dendroclimatology. In this paper, we consider the potential to provenance kauri timbers used in 19^th and early 20^th century New Zealand buildings, using a combination of documentary sources, t-value mapping, and refined statistical matching using spatial patterns of correlations. Analysis of documentary sources for a test period of 1861–1865 CE indicates that there is sufficient information about the kauri timber industry to provide a geographic context for provenancing kauri in the upper North Island. The use of t-values for provenancing may be confounded by the relatively small size of the kauri growth region and a lack of sufficient spatial differentiation in growth patterns between the sub-regions. However, a new approach of using indexed residual chronologies and field correlations has promise for geo-locating timber in a relatively small region. The research highlights the value of establishing kauri provenance to New Zealand dendroclimatology, dendroarchaeology and environmental history.     

Global assessment of relationships between climate and tree growth

Tree‐ring records provide global high‐resolution information on tree‐species responses to global change, forest carbon and water dynamics, and past climate variability and extremes. The underlying assumption is a stationary (time‐stable), quasi‐linear relationship between tree growth and environment, which however conflicts with basic ecological and evolutionary theory. Indeed, our global assessment of the relevant tree‐ring literature demonstrates non‐stationarity in the majority of tested cases, not limited to specific proxies, environmental parameters, regions or species. Non‐stationarity likely represents the general nature of the relationship between tree‐growth proxies and environment. Studies assuming stationarity however score two times more citations influencing other fields of science and the science–policy interface. To reconcile ecological reality with the application of tree‐ring proxies for climate or environmental estimates, we provide a clarification of the stationarity concept, propose a simple confidence framework for the re‐evaluation of existing studies and recommend the use of a new statistical tool to detect non‐stationarity in tree‐ring proxies. Our contribution is meant to stimulate and facilitate discussion in light of our results to help increase confidence in tree‐ring‐based climate and environmental estimates for science, the public and policymakers.     

牛樟芝倍半萜合酶基因克隆及在不同培养基中的表达

牛樟芝(Antrodia camphorata)是一种珍稀食药用菌,能产生具有抗癌活性的倍半萜类化合物。对牛樟芝基因组进行分析,获得倍半萜合酶基因序列并设计特异引物,提取在Glu培养基(麦芽浸粉6 g/L,酵母提取物3 g/L,葡萄糖40 g/L)上生长的牛樟芝菌丝体的RNA,利用RT-PCR技术克隆得到倍半萜合酶基因AcTPS1。AcTPS1基因c DNA全长为969 bp,编码323个氨基酸,根据系统进化树可知AcTPS1氨基酸序列与其他9种真菌倍半萜合酶聚为一类。AcTPS1拥有典型倍半萜合酶的结构域(RRSRSATAEAYACFIW),之后检测AcTPS1在不同培养基上的菌丝中的表达结果显示不同碳源中,只有葡萄糖作为碳源时该基因表达,不同氮源中,以番茄浸粉和酪蛋白胨为氮源时该基因表达。说明AcTPS1是一类诱导型表达的基因。为利用发酵培养以及异源表达手段获得牛樟芝活性化合物提供参考。     

Long‐term growth‐increment chronologies reveal diverse influences of climate forcing on freshwater and forest biota in the Pacific Northwest

Analyses of how organisms are likely to respond to a changing climate have focused largely on the direct effects of warming temperatures, though changes in other variables may also be important, particularly the amount and timing of precipitation. Here, we develop a network of eight growth‐increment width chronologies for freshwater mussel species in the Pacific Northwest, United States and integrate them with tree‐ring data to evaluate how terrestrial and aquatic indicators respond to hydroclimatic variability, including river discharge and precipitation. Annual discharge averaged across water years (October 1–September 30) was highly synchronous among river systems and imparted a coherent pattern among mussel chronologies. The leading principal component of the five longest mussel chronologies (1982–2003; PC1_mussel) accounted for 47% of the dataset variability and negatively correlated with the leading principal component of river discharge (PC1_discharge; r = ?0.88; P < 0.0001). PC1_mussel and PC1_discharge were closely linked to regional wintertime precipitation patterns across the Pacific Northwest, the season in which the vast majority of annual precipitation arrives. Mussel growth was also indirectly related to tree radial growth, though the nature of the relationships varied across the landscape. Negative correlations occurred in forests where tree growth tends to be limited by drought while positive correlations occurred in forests where tree growth tends to be limited by deep or lingering snowpack. Overall, this diverse assemblage of chronologies illustrates the importance of winter precipitation to terrestrial and freshwater ecosystems and suggests that a complexity of climate responses must be considered when estimating the biological impacts of climate variability and change.     

Phylogenetic Signal,Congruence, and Uncertainty across Bacteria and Archaea

Reconstruction of the Tree of Life is a central goal in biology. Although numerous novel phyla of bacteria and archaea have recently been discovered, inconsistent phylogenetic relationships are routinely reported, and many inter-phylum and inter-domain evolutionary relationships remain unclear. Here, we benchmark different marker genes often used in constructing multidomain phylogenetic trees of bacteria and archaea and present a set of marker genes that perform best for multidomain trees constructed from concatenated alignments. We use recently-developed Tree Certainty metrics to assess the confidence of our results and to obviate the complications of traditional bootstrap-based metrics. Given the vastly disparate number of genomes available for different phyla of bacteria and archaea, we also assessed the impact of taxon sampling on multidomain tree construction. Our results demonstrate that biases between the representation of different taxonomic groups can dramatically impact the topology of resulting trees. Inspection of our highest-quality tree supports the division of most bacteria into Terrabacteria and Gracilicutes, with Thermatogota and Synergistota branching earlier from these superphyla. This tree also supports the inclusion of the Patescibacteria within the Terrabacteria as a sister group to the Chloroflexota instead of as a basal-branching lineage. For the Archaea, our tree supports three monophyletic lineages (DPANN, Euryarchaeota, and TACK/Asgard), although we note the basal placement of the DPANN may still represent an artifact caused by biased sequence composition. Our findings provide a robust and standardized framework for multidomain phylogenetic reconstruction that can be used to evaluate inter-phylum relationships and assess uncertainty in conflicting topologies of the Tree of Life.     

Nonannual tree rings in a climate‐sensitive Prioria copaifera chronology in the Atrato River,Colombia

In temperate climates, tree growth dormancy usually ensures the annual nature of tree rings, but in tropical environments, determination of annual periodicity can be more complex. The purposes of the work are as follows: (1) to generate a reliable tree‐ring width chronology for Prioria copaifera Griseb. (Leguminoceae), a tropical tree species dwelling in the Atrato River floodplains, Colombia; (2) to assess the climate signal recorded by the tree‐ring records; and (3) to validate the annual periodicity of the tree rings using independent methods. We used standard dendrochronological procedures to generate the P. copaifera tree‐ring chronology. We used Pearson correlations to evaluate the relationship of the chronology with the meteorological records, climate regional indices, and gridded precipitation/sea surface temperature products. We also evaluated 24 high‐precision ¹⁴C measurements spread over a range of preselected tree rings, with assigned calendar years by dendrochronological techniques, before and after the bomb spike in order to validate the annual nature of the tree rings. The tree‐ring width chronology was statistically reliable, and it correlated significantly with local records of annual and October–December (OND) streamflow and precipitation across the upper river watershed (positive), and OND temperature (negative). It was also significantly related to the Oceanic Niño Index, Pacific Decadal Oscillation, and the Southern Oscillation Index, as well as sea surface temperatures over the Caribbean and the Pacific region. However, ¹⁴C high‐precision measurements over the tree rings demonstrated offsets of up to 40 years that indicate that P. copaifera can produce more than one ring in certain years. Results derived from the strongest climate–growth relationship during the most recent years of the record suggest that the climatic signal reported may be due to the presence of annual rings in some of those trees in recent years. Our study alerts about the risk of applying dendrochronology in species with challenging anatomical features defining tree rings, commonly found in the tropics, without an independent validation of annual periodicity of tree rings. High‐precision ¹⁴C measurements in multiple trees are a useful method to validate the identification of annual tree rings.