Predictive modelling of tree species distributions on the Iberian Peninsula during the Last Glacial Maximum and Mid-Holocene

This paper reports a bioclimatic envelope model study of the potential distribution of 19 tree species in the Iberian Peninsula during the Last Glacial Maximum (LGM; 21 000 yr BP) and the Mid-Holocene (6000 yr BP). Current patterns of tree species richness and distributions are believed to have been strongly influenced by the climate during these periods. The modelling employed novel machine learning techniques, and its accuracy was evaluated using a threshold-independent method. Two atmospheric general circulation models, UGAMP and ECHAM3 (generated by the Palaeoclimate Modelling Intercomparison Project, PMIP), were used to provide climate scenarios under which the distributions of the 19 tree species were modelled. The results obtained for these scenarios were assessed by agreement measure analysis; they differed significantly for the LGM, but were more similar for the Mid-Holocene.
The results for the LGM support the inferred importance of pines in the Iberian Peninsula at this time, and the presence of evergreen Quercus in the south. Important differences in the altitude at which the modelled species grew were also predicted. During the LGM, some normally higher mountain species potentially became re-established in the foothills of the Pyrenees. The warm Mid-Holocene climate is clearly reflected in the predicted expansion of broad-leaved forests during this period, including the colonization of the northern part of the Iberian Peninsula by evergreen Quercus species.     

Tropical tree species diversity: a test of the Janzen-Connell model

To test the premises and predictions of the Janzen-Connell model (Janzen's spacing mechanism), seeds of the rainforest canopy tree, Brosimum alicastrum, were placed at different distances from the parent tree and their removal observed over 3 weeks. The number and density of naturally occurring seeds at different distances from the parent tree were also estimated. Predation was not greater near the parent tree, except on the very small spatial scale: the proportion of experimental seeds removed was greater 1 m from the trunk than it was 5–25 m from the trunk. Predation was negatively correlated with seed density, not positively as the Janzen-Connell model assumes-presumably due to predator satiation. The density of seeds after predation peaked 5 m from the tree trunk, but this is well within the crown radius of the parent tree. There is a peak in the number of potential recruits at a distance of 10 m from the parent tree, due to the peaked initial distribution of seeds. This peak is caused by the interaction between the seed density curve and the increasing area of an annulus around the parent tree at increasing distances, not by the product of the density curve and the predation curve. However, it is important to realize that it is not the presence of a peak in recruitment away from the parent that is essential to maintaining tropical tree species diversity, but frequency-dependent recruitment induced by poor recruitment near conspecifics. Predator satiation seems to be an important factor in the survival of B. alicastrum seeds, possibly at several spatial scales. The number of seeds produced by the tree is negatively correlated with the loss to predators, and trees that have a fruiting conspecific nearby also suffer lower levels of predation. Seed predation increases as one moves from the forest edge into the interior, creating an edge effect that may have long-term effects on the forest composition and tree species diversity. More studies are needed, for other species, other localities, and larger spatial and temporal scales, on both the Janzen-Connell mechanism and this edge effect.     

A nonparametric estimator of species overlap

For two communities, species overlap has been defined by Smith, Solow, and Preston (1996, Biometrics 52, 1472-1477) as the probability that a randomly selected species is present in both communities given that it is present in at least one community. Species overlap can thus be used to describe the similarity of two communities. In contrast with the parametric estimator of Smith et al., we propose a nonparametric maximum likelihood estimator (NPMLE). We prove that the NPMLE is consistent and asymptotically normally distributed and show that computation of the NPMLE and its standard error is straightforward. We also compare the NPMLE and the estimator of Smith et al. for a variety of situations.     

Indirect interactions among tropical tree species through shared rodent seed predators: a novel mechanism of tree species coexistence

The coexistence of numerous tree species in tropical forests is commonly explained by negative dependence of recruitment on the conspecific seed and tree density due to specialist natural enemies that attack seeds and seedlings (‘Janzen–Connell’ effects). Less known is whether guilds of shared seed predators can induce a negative dependence of recruitment on the density of different species of the same plant functional group. We studied 54 plots in tropical forest on Barro Colorado Island, Panama, with contrasting mature tree densities of three coexisting large seeded tree species with shared seed predators. Levels of seed predation were far better explained by incorporating seed densities of all three focal species than by conspecific seed density alone. Both positive and negative density dependencies were observed for different species combinations. Thus, indirect interactions via shared seed predators can either promote or reduce the coexistence of different plant functional groups in tropical forest.     

Quickly identifying tree species susceptible to extinction: a case study of seven tree species at Northeast China Transect

Quickly predicting which species are most susceptible to extirpation in a defined area is important for conservation and environmental monitoring. We hypothesised that the susceptibility of tree species to extinction in an area could be inferred by the spatial and temporal dynamics of its populations. Here we use change in population size, population spatial variability, spatial autocorrelation, spatial cohesion, crash rate, and recovery rate to characterise the relative susceptibility to extirpation for seven tree species along the Northeast China Transect from 1986 to 1994. Betula dahurica Pall. and Populus davidiana Dode. were found to have a higher susceptibility to loss than Pinus koraiensis Siebold et Zucc., Betula costata Trautv., and Larix olgensis A. Henry in this area during this time period. The same methods could be useful to monitor and predict the susceptibility of species extinction at a larger regional scale.     

Maximum likelihood estimation of oncogenetic tree models

We present a new approach for modelling the dependences between genetic changes in human tumours. In solid tumours, data on genetic alterations are usually only available at a single point in time, allowing no direct insight into the sequential order of genetic events. In our approach, genetic tumour development and progression is assumed to follow a probabilistic tree model. We show how maximum likelihood estimation can be used to reconstruct a tree model for the dependences between genetic alterations in a given tumour type. We illustrate the use of the proposed method by applying it to cytogenetic data from 173 cases of clear cell renal cell carcinoma, arriving at a model for the karyotypic evolution of this tumour.     

A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree

ABSTRACT: BACKGROUND: The ancestries of genes form gene trees which do not necessarily have the same topology as the species tree due to incomplete lineage sorting. Available algorithms determining the probability of a gene tree given a species tree require exponential computational runtime. RESULTS: In this paper, we provide a polynomial time algorithm to calculate the probability of a ranked gene tree topology for a given species tree, where a ranked tree topology is a tree topology with the internal vertices being ordered. The probability of a gene tree topology can thus be calculated in polynomial time if the number of orderings of the internal vertices is a polynomial number. However, the complexity of calculating the probability of a gene tree topology with an exponential number of rankings for a given species tree remains unknown. CONCLUSIONS: Polynomial algorithms for calculating ranked gene tree probabilities may become useful in developing methodology to infer species trees based on a collection of gene trees, leading to a more accurate reconstruction of ancestral species relationships.     

No evidence for consistent long‐term growth stimulation of 13 tropical tree species: results from tree‐ring analysis

The important role of tropical forests in the global carbon cycle makes it imperative to assess changes in their carbon dynamics for accurate projections of future climate–vegetation feedbacks. Forest monitoring studies conducted over the past decades have found evidence for both increasing and decreasing growth rates of tropical forest trees. The limited duration of these studies restrained analyses to decadal scales, and it is still unclear whether growth changes occurred over longer time scales, as would be expected if CO₂‐fertilization stimulated tree growth. Furthermore, studies have so far dealt with changes in biomass gain at forest‐stand level, but insights into species‐specific growth changes – that ultimately determine community‐level responses – are lacking. Here, we analyse species‐specific growth changes on a centennial scale, using growth data from tree‐ring analysis for 13 tree species (~1300 trees), from three sites distributed across the tropics. We used an established (regional curve standardization) and a new (size‐class isolation) growth‐trend detection method and explicitly assessed the influence of biases on the trend detection. In addition, we assessed whether aggregated trends were present within and across study sites. We found evidence for decreasing growth rates over time for 8–10 species, whereas increases were noted for two species and one showed no trend. Additionally, we found evidence for weak aggregated growth decreases at the site in Thailand and when analysing all sites simultaneously. The observed growth reductions suggest deteriorating growth conditions, perhaps due to warming. However, other causes cannot be excluded, such as recovery from large‐scale disturbances or changing forest dynamics. Our findings contrast growth patterns that would be expected if elevated CO₂ would stimulate tree growth. These results suggest that commonly assumed growth increases of tropical forests may not occur, which could lead to erroneous predictions of carbon dynamics of tropical forest under climate change.     

Complexity of the simplest species tree problem

The multispecies coalescent model provides a natural framework for species tree estimation accounting for gene-tree conflicts. Although a number of species tree methods under the multispecies coalescent have been suggested and evaluated using simulation, their statistical properties remain poorly understood. Here, we use mathematical analysis aided by computer simulation to examine the identifiability, consistency, and efficiency of different species tree methods in the case of three species and three sequences under the molecular clock. We consider four major species-tree methods including concatenation, two-step, independent-sites maximum likelihood, and maximum likelihood. We develop approximations that predict that the probit transform of the species tree estimation error decreases linearly with the square root of the number of loci. Even in this simplest case, major differences exist among the methods. Full-likelihood methods are considerably more efficient than summary methods such as concatenation and two-step. They also provide estimates of important parameters such as species divergence times and ancestral population sizes,whereas these parameters are not identifiable by summary methods. Our results highlight the need to improve the statistical efficiency of summary methods and the computational efficiency of full likelihood methods of species tree estimation.     

Nutrient distribution in a Swedish tree species experiment

The influence of four tree species on the distribution of nutrients between different compartments of the ecosystem was examined. In a randomized block (n=3) experiment in south-western Sweden, Ca, Mg and K were determined as exchangeable amounts in the mineral soil and as total amounts in the O+A₁ horizons (topsoil) and in the aboveground tree biomass. N contents were determined in all compartments as well as P contents of the aboveground tree biomass and the topsoil. The four tree species planted were: silver fir [Abies alba Mill.] (AA), grand fir [Abies grandis Lindl.] (AG), Norway spruce [Picea abies L. Karst.] (PA) and Japanese larch [Larix leptolepis (Sieb. och Zucc.) Endl.] (LL). At the age of 35–36 years, the total stemwood production of the most productive species, AG, was estimated at 471 m³ ha⁻¹. In relation to AG, LL had produced 80%, PA 73% and AA 37%. The system totals [aboveground tree biomass total + topsoil total + exchangeable (Ca, Mg, K) or total (N) in the mineral soil] of Ca, K and N did not differ significantly at the 5% level between the investigated species. For Mg, the system total in LL was significantly higher than for the other species. There was an indication that LL and AA contained higher amounts of Ca, Mg, K and N in the topsoil but less in the biomass than did AG and PA (partly significant). In the mineral soil, there were no significant differences in the exchangeable pools of Ca and K, nor in the total amounts of N. The biomass nutrient concentrations generally decreased in the order: AA > PA > AG > LL. At stem or whole-tree harvest, the Ca export per biomass unit would more than double in the case of PA compared to LL. LL also contained less N in the biomass than the other species. However, the N content in the biomass did not differ between the most (AG) and the least (AA) productive species, although the production of dry weight biomass (standing + harvested) of AG had been twice that of AA. It is concluded that the nutrient budget of a managed forest may vary considerably depending on the choice of tree species.     

Inventory, differentiation, and proportional diversity: a consistent terminology for quantifying species diversity

Almost half a century after Whittaker (Ecol Monogr 30:279–338, 1960) proposed his influential diversity concept, it is time for a critical reappraisal. Although the terms alpha, beta and gamma diversity introduced by Whittaker have become general textbook knowledge, the concept suffers from several drawbacks. First, alpha and gamma diversity share the same characteristics and are differentiated only by the scale at which they are applied. However, as scale is relative––depending on the organism(s) or ecosystems investigated––this is not a meaningful ecological criterion. Alpha and gamma diversity can instead be grouped together under the term “inventory diversity.” Out of the three levels proposed by Whittaker, beta diversity is the one which receives the most contradictory comments regarding its usefulness (“key concept” vs. “abstruse concept”). Obviously beta diversity means different things to different people. Apart from the large variety of methods used to investigate it, the main reason for this may be different underlying data characteristics. A literature review reveals that the multitude of measures used to assess beta diversity can be sorted into two conceptually different groups. The first group directly takes species distinction into account and compares the similarity of sites (similarity indices, slope of the distance decay relationship, length of the ordination axis, and sum of squares of a species matrix). The second group relates species richness (or other summary diversity measures) of two (or more) different scales to each other (additive and multiplicative partitioning). Due to that important distinction, we suggest that beta diversity should be split into two levels, “differentiation diversity” (first group) and “proportional diversity” (second group). Thus, we propose to use the terms “inventory diversity” for within-sample diversity, “differentiation diversity” for compositional similarity between samples, and “proportional diversity” for the comparison of inventory diversity across spatial and temporal scales. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Phenology is a major determinant of tree species range

Global warming is expected to have a major impact on plant distributions, an issue of key importance in biological conservation. However, very few models are able to predict species distribution accurately, although we know species respond individually to climate change. Here we show, using a process-based model ( PHENOFIT ), that tree species distributions can be predicted precisely if the biological processes of survival and reproductive success only are incorporated as a function of phenology. These predictions showed great predictive power when tested against present distributions of two North American species – quaking aspen and sugar maple – indicating that on a broad scale, the fundamental niche of trees coincides with their realized niche. Phenology is shown here to be a major determinant of plant species range and should therefore be used to assess the consequences of global warming on plant distributions, and the spread of alien plant species.     

Genetic and palaeo-climatic evidence for widespread persistence of the coastal tree species Eucalyptus gomphocephala (Myrtaceae) during the Last Glacial Maximum

Background and Aims

Few phylogeographic studies have been undertaken of species confined to narrow, linear coastal systems where past sea level and geomorphological changes may have had a profound effect on species population sizes and distributions. In this study, a phylogeographic analysis was conducted of Eucalyptus gomphocephala (tuart), a tree species restricted to a 400 × 10 km band of coastal sand-plain in south west Australia. Here, there is little known about the response of coastal vegetation to glacial/interglacial climate change, and a test was made as to whether this species was likely to have persisted widely through the Last Glacial Maximum (LGM), or conforms to a post-LGM dispersal model of recovery from few refugia.

Methods

The genetic structure over the entire range of tuart was assessed using seven nuclear (21 populations; n = 595) and four chloroplast (24 populations; n = 238) microsatellite markers designed for eucalypt species. Correlative palaeodistribution modelling was also conducted based on five climatic variables, within two LGM models.

Key Results

The chloroplast markers generated six haplotypes, which were strongly geographically structured (G_ST = 0·86 and R_ST = 0·75). Nuclear microsatellite diversity was high (overall mean H_E 0·75) and uniformly distributed (F_ST = 0·05), with a strong pattern of isolation by distance (r² = 0·362, P = 0·001). Distribution models of E. gomphocephala during the LGM showed a wide distribution that extended at least 30 km westward from the current distribution to the palaeo-coastline.

Conclusions

The chloroplast and nuclear data suggest wide persistence of E. gomphocephala during the LGM. Palaeodistribution modelling supports the conclusions drawn from genetic data and indicates a widespread westward shift of E. gomphocephala onto the exposed continental shelf during the LGM. This study highlights the importance of the inclusion of complementary, non-genetic data (information on geomorphology and palaeoclimate) to interpret phylogeographic patterns.     

Effects of tree species on soil organic carbon density: A common garden experiment of five temperate tree species

Aims Forest trees alter litter inputs, turnover and rhizospheric activities, modify soil physical, chemical and biological properties, and consequently affect soil organic carbon (SOC) storage and carbon sink strength. That how to select appropriate tree species in afforestation, reforestation and management practices is critical to enhancing forest carbon sequestration. The objective of this study was to determine the effects of tree species on SOC density and vertical distributions.Methods A common garden experiment with the same climate, soil, and management history was established in Maoershan Forest Ecosystem Station, Northeast China, in 2004. The experimental design was a completely randomized arrangement with twenty 25 m × 25 m plots, consisting of monocultures of five tree species, including white birch (Betula platyphylla), Manchurian walnut (Juglans mandshurica), Manchurian ash (Fraxinus mandshurica), Dahurian larch (Larix gmelinii), and Mongolian pine (Pinus sylvestris var. mongolica), each with four replicated plots. A decade after the establishment (2013-2014), we measured carbon density and related factors (i.e., bulk density, total nitrogen concentration, microbial biomass carbon, microbial biomass nitrogen, pH value) in soils of the 0-40 cm depth for these monocultures. Important findings Results showed that tree species significantly influenced the SOC density in the 0-40 cm depth (p < 0.05). SOC density in the 0-10 cm depth varied from 2.79 to 3.08 kg·m^-2, in the order of walnut > ash> birch > larch > pine, in the 10-20 cm depth from 1.56 to 2.19 kg·m^-2, in the order of pine > walnut > ash > birch > larch, in the 20-30 cm depth from 1.17 to 2.10 kg·m^-2, and in the 20-40 cm depth from 0.84 to 1.43 kg·m^-2. The greatest SOC density occurred in the birch stands in the 20-40 cm depth. The vertical distributions of SOC density varied with tree species. The percentage of SOC in the 0-10 cm depth over the total SOC in the soil profile was significantly higher in the walnut and larch stands than in others, while the percentage of SOC in the 20-40 cm depth over the total SOC was highest in the birch stands. SOC concentration and soil bulk density differed significantly among the stands of different tree species, and were negatively correlated. SOC density was positively correlated with soil microbial biomass and soil pH in the walnut, ash, and larch stands, and with total nitrogen density in all the stands. We conclude that tree species modifies soil properties and microbial activity, thereby influencing SOC density, and that different patterns of vertical distributions of SOC density among monocultures of different tree species may be attributed to varying SOC controls at each soil depth.     

An estimator of number of species from quadrat sampling

We consider the problem of estimating the number of distinct species S in a study area from the recorded presence or absence of species in each of a sample of quadrats. A generalized jackknife estimator of S is derived, along with an estimate of its variance. It is compared with the jackknife estimator for S proposed by Heltshe and Forrester and the empirical Bayes estimator of Mingoti and Meeden. We show that the empirical Bayes estimator has the form of a generalized jackknife estimator under a specific model for species distribution. We compare the new estimators of S to the empirical Bayes estimator via simulation. We characterize circumstances under which each is superior.     

Limits to the abundance of rare species: an experimental test with a tree aphid

Abstract. 1. The birch ( Betula )-feeding aphid, Monaphis antennata, is always found at low densities on individual hosts and has low local abundance, but another birch-feeding aphid, Euceraphis betulae , is often found at high densities on individual hosts and has high local abundance.
2. This work attempts to establish whether the interaction between M. antennata and its host or the behaviour of individuals limits its densities.
3. Both species were reared on saplings, and population sizes were monitored for 6 weeks. Two levels of host quality were used and feeding space was kept constant throughout the experiment. Adults were prevented from leaving the saplings by clipping their wings, and predators were excluded.
4. On plants of similar host quality, both species achieved similar population sizes.
5. It is concluded that resource availability or the interactions between individuals are unlikely to be important causes of rarity.     

Scale-area curves: a tool for understanding the ecology and distribution of invasive tree species

Scale-area curves are increasingly used in ecology to predict population trajectories, based on the assumption that observed patterns are indicative of population dynamics. However, for introduced species, scale-area curves might be strongly influenced by introduction history. We examined the spatial structure of an invasive tree species (Acacia elata; Fabaceae) introduced to South Africa as an ornamental plant and compared our findings with previous work done on a species introduced for dune stabilization (A. longifolia). A fractal sampling method was used to map the occupancy of A. elata at twelve spatial scales for ten quarter-degree grid cells throughout South Africa. Based on the fractal dimension (D _ij ) calculated at different spatial scales we found that populations were more contiguous at plot (2.5–25 m) and regional scales (2.5–25 km) than at local and landscape scales (0.025–2.5 km). We argue that the lack of contiguous A. elata populations over 250 m to 2.5 km is not indicative of a low risk, but the result of the spatial structure of available land in suburban environments. When working with introduced species, scale-area curves representing fragmented populations at the edge of invasions should not be considered to indicate a lack of invasive spread/threat. Rather they can be used to identify “missing links” in the invasive introduction-naturalization-invasion continuum, but only if the life-history traits, introduction history, and area suitable for invasion are well understood and are used in interpreting the results. We suggest that their greatest value will lie in their use as a method for long-term monitoring of introduced species.