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SUMMARY: Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole‐genome resequencing, that represents both genic and intergenic regions. This array was designed following a two‐step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full‐sib family trios, breeding population, and range‐wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype–environment and genotype–phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high‐confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high‐throughput fundamental and applied research of Scots pine and other pine species. Significance Statement: In this paper, we present the first high‐throughput single nucleotide polymorphism genotyping array for a pine species developed from whole‐genome resequencing, and thus spanning genic as well as intergenic regions. This array was developed for Scots pine and successfully tested in six other pine species from North America and Eurasia, being useful for fundamental and applied studies in the fields of population genetics, evolution, genomic selection, and breeding. [ABSTRACT FROM AUTHOR]

Ecological restoration is a viable strategy to recover floristic, structural, and functional attributes of the very vulnerable and widely degraded tropical mountain forests. Most restoration efforts in these highly diverse and narrowly distributed systems involve unassisted forest regeneration or enrichment planting with a small number of species, usually those with commercial value and success evaluated after a few years. We assessed changes in soil attributes, forest composition and structure in four sites with plots under unassisted forest regeneration or enrichment planting. The sites are in the limestone massif of the central highlands of Chiapas (Mexico) and share geological, edaphic and climatic conditions, but differ in level of previous disturbance and the time elapsed since the enrichment planting (16–30 years). No changes in soil variables (contents of C, N, P, and K, cation exchange capacity, and pH) were detected. Total density of juveniles was not consistently related to unassisted forest regeneration or enrichment planting but was highest in the two sites that had severe disturbance level. Influence of enrichment planting on forest regeneration depended on the composition and structure of the surrounding stands, and more so when opportunistic trees like pines and other shade‐intolerant species are available. Yet long‐lived shade‐tolerant species, including oaks, which may have synergistic effects during forest recovery, were well represented in sites with original severe disturbance level. [ABSTRACT FROM AUTHOR]

This article is a Commentary on Buck et al. (2023), 237: 2435–2449. [ABSTRACT FROM AUTHOR]

Premise: Accurate species delimitation is essential for evolutionary biology, conservation, and biodiversity management. We studied species delimitation in North American pinyon pines, Pinus subsection Cembroides, a natural group with high levels of incomplete lineage sorting. Methods: We used coalescent‐based methods and multivariate analyses of low‐copy number nuclear genes and nearly complete high‐copy number plastomes generated with the Hyb‐Seq method. The three coalescent‐based species delimitation methods evaluated were the Generalized Mixed Yule Coalescent (GMYC), Poisson Tree Process (PTP), and Trinomial Distribution of Triplets (Tr2). We also measured admixture in populations with possible introgression. Results: Our results show inconsistencies among GMYC, PTP, and Tr2. The single‐locus based GMYC analysis of plastid DNA recovered a higher number of species (up to 24 entities, including singleton lineages and clusters) than PTP and the multi‐locus coalescent approach. The PTP analysis identified 10 species whereas Tr2 recovered 13, which agreed closely with taxonomic treatments. Conclusions: We found that PTP and GMYC identified species with low levels of ILS and high morphological divergence (P. maximartinezii, P. pinceana, and P. rzedowskii). However, GMYC method oversplit species by identification of more divergent samples as singletons. Moreover, both PTP and GMYC were incapable of identifying some species that are readily identified morphologically. We suggest that the divergence times between lineages within North American pinyon pines are so disparate that GMYC results are unreliable. Results of the Tr2 method coincided well with previous delimitations based on morphology, DNA, geography, and secondary chemistry. [ABSTRACT FROM AUTHOR]

With the current rate of biodiversity loss, conservation management practices require a comprehensive understanding of eco‐evolutionary relationships, history, and genetic structure of species. Assessments of genetic diversity are crucial, especially in rare, endemic, or threatened forest tree species with small and isolated populations, such as peat bog pine (Pinus uliginosa N.). Here, we used a novel approach, combining genetic diversity assessment, ecological niche modeling, and population demography inference to explore the complex history of a few remnant populations of this endangered pine. To asses the relative influence of isolation and fragmentation on genetic diversity in the taxonomic context, the patterns of genetic variation found in P. uliginosa were contrasted with those observed in its close relatives with much bigger distribution ranges and larger populations (Pinus sylvestris, Pinus mugo, and Pinus uncinata). We found a similar level of genetic diversity across the species at nuclear loci but contrasting patterns of variability distribution at chloroplast markers. We detected the signatures of an ancient genetic bottleneck dated at around 26 400 years ago, indicating a drastic reduction in the population size of P. uligionosa during the Last Glacial Maximum. In addition, we found substantial differentiation between current populations as a result of enhanced genetic drift during long‐lasting isolation. The research suggests potential conservation management strategies for peat bog pine and emphasizes the importance of using complementary approaches for their successful development. [ABSTRACT FROM AUTHOR]

The conversion of agricultural land to forest plantations is a major driver of global land-use change, and considering that large portions of the planet are covered by forest plantations, understanding their impact on biodiversity is a research priority. The aim of our study was to quantify the long-term response of two lizard species to the transformation of the matrix surrounding remnant habitat patches (from agricultural land to pine plantations). We used a large-scale (115 sites), long-term (16 years) fully replicated and controlled landscape scale 'natural experiment' (the ' Nanangroe experiment', Australia) to compare the response of lizard populations to plantation establishment. The study entailed detailed surveys of reptiles in 50 eucalypt patches surrounded by maturing pine P inus radiata plantations ( treatments) and populations inhabiting 55 eucalypt patches surrounded by grazing land ( controls). We found that the eastern three-toed earless skink H emiergis talbingoensis was advantaged by the establishment of the pine plantations (increasing colonization of eucalypt patches embedded within plantations). In contrast, we found that the southern rainbow skink C arlia tetradactyla was negatively affected by surrounding areas of maturing plantations. Thus, our results show that plantations acted as a barrier for one species and increased connectivity for the other. We suggest that leaving areas of land devoid of pines between remnant eucalypt patches may enhance the connectivity for species that respond negatively to plantation establishment while maintaining the beneficial increase in connectivity for others. [ABSTRACT FROM AUTHOR]

The article presents information on a research which compares the invasive ability of the North American exotic organism Heterobasidion irregulare with Italian Heterobasidion annosum. It informs that geostatistical and statistical analyses were performed to test the association between both species. It also informs that H. annosum is negatively associated with deciduous oaks while it shows a positive association with pines.

1. Fire is an important process in Mediterranean-ecosystem shrublands, and prescribed burning is often used to manage these ecosystems. Analyses of past fire regimes are required to interpret biotic responses to fire, as well as to assess the degree to which management interventions have been able to influence the fire regime. 2. We used a spatial data base of fires within 10 protected areas covering >720 000 ha to examine the frequency, seasonality, size and cause of fires over four decades. Our study covered five fire climate zones and a range of mountain fynbos shrubland types. We examined whether regular prescribed burning would be necessary to rejuvenate the vegetation, and also to reduce the incidence and extent of wildfires. 3. Cumulative fire frequency distributions indicated that the probability of fire was not strongly affected by post-fire age, with 50% of the area experiencing a successive fire within 10–13 years after the previous fire in most areas. This suggests that the accumulation of fuel did not limit the occurrence of wildfires, and that regular prescribed burning would not necessarily reduce the risk of wildfires. 4. Inland zones experienced more severe fire weather than coastal zones (∼35% vs. 11–19% of days with high to very high fire danger, respectively). Despite these differences, fire return periods were similar (10–13 years), suggesting that the availability of ignitions, and not fuel or weather, limited the occurrence of wildfires. 5. Despite a policy that promoted prescribed burning, a relatively small area (between 4·6% and 32·4% of the area of all fires) burned in prescribed burns. Seasonal restrictions for safety and ecological reasons, the imperative to integrate planned fires with invasive alien plant treatments and unplanned wildfires have all contributed to the relatively small area that burnt in prescribed burns. 6. Synthesis and applications. Recurrent wildfires,... [ABSTRACT FROM AUTHOR]

1. In pine ecosystems, the role of the larval nests of the Mediterranean defoliator Thaumetopoea pityocampa as shelter of other arthropods, was studied for the first time. In Portugal, Pinus stands which differed in understorey plant diversity and level of attack by T. pityocampa were compared. 2. The arthropod fauna found sheltering inside the nests consisted of 60 species, representing 12 foraging types. Both arthropod richness and abundance were positively correlated with nest size, expressed as larval biomass. Arthropod richness was further positively correlated with understorey plant diversity, while no correlation was detected between arthropod richness and nest density. 3. Spiders accounted for up to 50% of the species richness, while 80% of the individuals collected were either juveniles, or females with brood, implying that T. pityocampa nests are used for overwintering and brood care. Seventy-six per cent of the Araneae were nocturnal ground foragers and specialised cryptic hunters, demonstrating the occurrence of indirect interactions among species belonging to different communities, namely ground vegetation layers and forest pine coppice. 4. It was concluded that, in Mediterranean pine ecosystems, T. pityocampa nests (i) create habitat diversification and contribute to improve overwintering survival of a wide range of arthropod species; (ii) play a functional role in the food web of pine ecosystems, by promoting indirectly mediated interactions among species from different communities; and (iii) do not contribute to create habitat for symtopic phytophagous arthropods, since contrary to literature references for different types of shelters, 98% of the associated species belonged to foraging types other than T. pityocampa. [ABSTRACT FROM AUTHOR]

The longer-term effects of afforestation with Pinus radiata and Eucalyptus grandis on streamflows were analyzed using data from two paired-catchment experiments in South Africa. The experiments are rare in that they have been maintained over longer periods than the typical rotation period for industrial timber plantations in the tropics or subtropics. In both experiments the planting treatments led to large reductions in streamflow, which increased with the age of the trees and were positively related to water availability. The pine plantation caused peak reductions in yield over a 5-year period of 44 mm a−1 or 7.7% a−1 for each 10% of catchment planted when the trees were between 10 and 20 years old. The eucalypt plantation caused peak reductions over a 3-year period of 48 mm a−1 and 10% a−1 for each 10% of catchment planted. However, as the plantations matured (over 30 years of age in the case of pines and over 15 years of age in the case of eucalypts) the flow reduction trend was reversed, and streamflow effects appear to be tending toward preafforestation levels. The longer-term effects of planted forests need not be as harmful on the water yield of catchments as has been predicted from shorter-term studies. The implication of these results is that if trees are grown on very long rotations, they may be used for restoring degraded catchments or as a means of storing carbon without completely denuding available water resources. [ABSTRACT FROM AUTHOR]

Effects of substantial increase in area of pine plantations from 1960 to 2000 on runoff in a large catchment in southeastern Australia are quantified. Reliable land use maps were prepared for 1960-1979, 1980-1989, and 1990-2000 conditions from various data sources. Land use changes in the subcatchments have occurred at varying rates (16 to 28%) with pines replacing pasture and native woody vegetation. On the basis of long-term trends in rainfall-runoff relationships, flow duration curves, and history of land use changes, it is shown that there is strong evidence of reduction in runoff over a wide range. Modeling methodology using a lumped catchment-scale rainfall-runoff model (SMAR) and landscape-scale ecohydrological models (CLASS U3M-1D, CLASS PGM, and 3PG+) was implemented in a catchment framework to partition the effects of land use change and climate variability during 1960-2000. Runoff reductions from land use change in the range 22-52 mm/yr are estimated for different subcatchments. Annual yield impact per 10% of the catchment forested (AYI/10%) from catchment-scale modeling is estimated to vary between 14.3 to 19.2 mm/yr for the subcatchments. AYI/10% from landscape-scale modeling is estimated to vary between 12.8 to 21.3 mm/yr. [ABSTRACT FROM AUTHOR]

The article focuses on a study on identifying functional groups of trees in west gulf coast forests in the U.S. by using tree-ring approach. Topics discussed include effect of climate on tree radial growth in southeasternmost section of the Eastern Deciduous Forest/Southern Evergreen Forest, using rotated principal components analysis for analyzing species from the genera Pinus, Quercus, and Fagus, and response of phylogenetic groups of trees to climate.

Summary 1. Senescing, shade-suppressed, or broken branches of Monterey pine Pinus radiata are infested by twig beetles in the genus Pityophthorus (Coleoptera: Scolytidae). The studies reported here tested whether twig beetles can discriminate between healthy and pitch canker-diseased branches, whether diseased branch tips produce more ethylene than undamaged controls, and whether ethylene and other volatiles, produced by the plant in response to tissue damage, are utilised by twig beetles in host location. 2. Significantly greater numbers of twig beetles were reared from pitch canker-symptomatic than from pitch canker-asymptomatic branches of Monterey pine collected in the field. 3. Needles of Monterey pine branches inoculated with the pitch canker fungal pathogen Fusarium circinatum produced significantly higher levels of ethylene than needles of control branches, and this was evident just prior to, and during, symptom expression. 4. In trapping studies in which pheromone production was prevented, there was no evidence of attraction of twig beetles to a source of ethylene alone, to cut host branches, or to cut branches treated with the ethylene-releasing compound, ethephon. The results suggest that twig beetles identify weakened branches after landing. [ABSTRACT FROM AUTHOR]

Variation in paternally inherited chloroplast microsatellite (cpSSR) DNA was used to study population genetic structure in red pine (Pinus resinosa Ait.), a species characterized by morphological uniformity, no allozyme variation, and limited RAPD variation. Using nine cpSSR loci, a total of 23 chloroplast haplotypes and 25 cpSSR alleles were found among 159 individuals surveyed in seven widely separated populations. The total genetic diversity, HT, was 0.618, but haplotype differentiation among populations was low (GST = 0.121). All populations were distinguished from each other by their haplotype compositions, and only one haplotype was common among all populations. Based on average squared composite cpSSR length differences (stepwise haplotypes), within-population diversity was relatively high for only one population (D2SH = 0.443). Frequency distributions of pairwise SSR differences among individuals within different populations, as well as branch length differences in neighbour-joining dendrograms, indicated recovery from one or more population bottlenecks, and may be explained by metapopulation dynamics. [ABSTRACT FROM AUTHOR]

The article reports on the study on the utility of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA in pines. The ITS region is used as a marker to determine hybridization in pines, since it has been proven to be an efficient source of characters for phylogenetic research. Through the assistance of the Institute of Forest Genetics, 14 individuals of certain hybrids and matching parental lines were observed, species including the Pinus flexilis and P. strobiformis. Information regarding the polymerase chain reaction amplifications of the ITS area is also presented.