Eggshell Types and Their Evolutionary Correlation with Life-History Strategies in Squamates

The eggshell is an important physiological structure for the embryo. It enables gas exchange, physical protection and is a calcium reserve. Most squamates (lizards, snakes, worm lizards) lay parchment-shelled eggs, whereas only some gekkotan species, a subgroup of lizards, have strongly calcified eggshells. In viviparous (live-bearing) squamates the eggshell is reduced or completely missing (hereafter “shell-less”). Recent studies showed that life-history strategies of gekkotan species differ between species with parchment- and rigid-shelled eggshells. Here we test if the three different eggshell types found in the squamates are also associated with different life-history strategies. We first investigated the influence of the phylogeny on the trait “eggshell type” and on six life-history traits of 32 squamate species. Phylogenetic principal component analysis (pPCA) was then conducted to identify an association between life-history strategies and eggshell types. Finally, we also considered adult weight in the pPCA to examine its potential effect on this association. Eggshell types in squamates show a strong phylogenetic signal at a low taxonomical level. Four out of the six life-history traits showed also a phylogenetic signal (birth size, clutch size, clutches per year and age at female maturity), while two had none (incubation time, maximum longevity). The pPCA suggested an association of life-history strategies and eggshell types, which disappeared when adult weight was included in the analysis. We conclude that the variability seen in eggshell types of squamates is weakly influenced by phylogeny. Eggshell types correlate with different life-history strategies, and mainly reflect differences in adult weights of species.     

Seasonal Food Resources of the Squirrel Sciurus ingrami in a Secondary Araucaria Forest in Southern Brazil

In a field study carried out over one year in a secondary Araucaria forest in eastern ParanÝ State, Brazil, foraging was observed in a population of the squirrel Sciurus ingrami. Seeds of Araucaria and about ten more species of native and exotic trees were the main food items besides mushrooms and fruits. Not all seeds were consumed immediately. Especially in autumn and winter, a large portion was cached, in particular of the Araucaria seeds. The relevance of this behaviour, well known in squirrels, for seed dispersion and forest regeneration is discussed.     

Seed Removal Increased by Scramble Competition with an Invasive Species

Competition for seeds has a major influence on the evolution of granivores and the plants on which they rely. The complexity of interactions and coevolutionary relationships vary across forest types. The introduction of non-native granivores has considerable potential to alter seed dispersal dynamics. Non-native species are a major cause of endangerment for native species, but the mechanisms are often unclear. As biological invasions continue to rise, it is important to understand mechanisms to build up strategies to mitigate the threat. Our field experiment quantified the impact of introduced Abert’s squirrels (Sciurus aberti) on rates of seed removal within the range of critically endangered Mount Graham red squirrels (Tamiasciurus hudsonicus grahamensis), which consumes similar foods. In the presence of invasive Abert’s squirrels, the time cones were removed was faster than when the invasive was excluded, accounting for a median removal time of cones available to red and Abert’s squirrels that is 32.8% less than that of cones available only to the rare native red squirrels. Moreover, in the presence of Abert’s squirrels, removal rates are higher at great distance from a territorial red squirrel larderhoard and in more open portions of the forest, which suggests differential patterns of seed dispersal. The impact on food availability as a result of cone removal by Abert’s squirrels suggests the potential of food competition as a mechanism of endangerment for the Mount Graham red squirrel. Furthermore, the magnitude and differential spatial patterns of seed removal suggest that non-native granivores may have impacts on forest regeneration and structure.     

Sensitivity to Seed Germination Schedule by Scatter‐Hoarding Pére David's Rock Squirrels During Mast and Non‐Mast Years

Mast seeding by oaks (Quercus) and other seed species has fundamental impacts on the behavior of individual scatter‐hoarding animals as well as their population and community dynamics. Scatter‐hoarding squirrels are highly sensitive to acorn germination schedule and stop germination by removing the embryo of non‐dormant acorns to prevent losses of energy and nutrients by rapid germination. However, we know little about how this behavior is affected by mast seeding. We investigated foraging decisions made by free‐ranging Pére David's rock squirrel (Sciurotamias davidianus) with three species that produce non‐dormant seeds and two species that produce dormant seeds (Fagaceae) during mast and non‐mast years in Central China from 2007–2010. Consistent with the food perishability hypothesis that squirrels make decisions to minimize the perishability of their caches, non‐dormant seeds were hoarded at a lower rate, but had a higher probability of embryo removal than dormant seeds. Compared with non‐mast years, a lower proportion of seeds were harvested during mast years, but a higher proportion of the harvested seeds were hoarded. In addition, the probability of embryo removal in the hoarded seeds was higher during mast years. Squirrels also dispersed seeds at shorter distances during mast years. Moreover, the interactions between mast seeding and seed germination schedule had significant effects on squirrel foraging decisions, including embryo removal. This study is the first to demonstrate that squirrels show greater sensitivity to seed germination potential when seeds are abundant.     

Geographic variation in walnut seed size correlates with hoarding behaviour of two rodent species

Seeds of the Japanese walnut, Juglans ailanthifolia, are usually scatter-hoarded by two rodent species, the Japanese squirrel Sciurus lis and the field mouse Apodemus speciosus, but only by the latter in several areas where S. lis is absent. We examined seed-size-mediated interactions of these three species across a wide geographic range. Field tracking of walnuts with miniature radio-transmitters revealed that squirrels hoarded larger seeds more frequently and at greater distances than smaller seeds. In contrast, mice hoarded smaller seeds more frequently and transported them farther than larger seeds. These seed dispersers could affect the evolution of seed size because seeds hoarded at sites farther from source trees are known to survive better until germination and as seedlings. We expect that larger seeds may be advantageous in regeneration if the main seed dispersers are squirrels, whereas smaller seeds may be advantageous if mice are the dominant dispersers. These predictions were supported by the fact that seed size was smaller on islands inhabited only by mice and at the edge of the squirrel distribution, compared to areas where mice and squirrels are both common.     

Seeds and seedlings of oaks suffer from mammals and molluscs close to phylogenetically isolated,old adults

Background and AimsMammals and molluscs (MaM) are abundant herbivores of tree seeds and seedlings, but how the trees and their environment affect MaM herbivory has been little studied. MaM tend to move much larger distances during the feeding stage than the more frequently studied insect herbivores. We hypothesize that MaM (1) select and stay within the patches that promise to be relatively the richest in seeds and seedlings, i.e. patches around adult trees that are old and within a distantly related, less productive neighborhood; and (2) try to remain sheltered from predators while foraging, i.e. mammals remain close to adult trees or to cover by herbs while foraging, and might force their mollusc prey to show the opposite distribution.MethodsWe exposed oak acorns and seedlings in a temperate forest along transects from adult conspecifics in different neighbourhoods. We followed acorn removal and leaf herbivory. We used exclusion experiments to separate acorn removal by ungulates vs. rodents and leaf herbivory by insects vs. molluscs. We measured the size of the closest conspecific adult tree, its phylogenetic isolation from the neighbourhood and the herbaceous ground cover.Key ResultsConsistent with our hypothesis, rodents removed seeds around adult trees surrounded by phylogenetically distant trees and by a dense herb cover. Molluscs grazed seedlings surrounding large conspecific adults and where herb cover is scarce. Contrary to our hypothesis, the impact of MaM did not change from 1 to 5 m distance from adult trees.ConclusionsWe suggest that foraging decisions of MaM repulse seedlings from old adults, and mediate the negative effects of herbaceous vegetation on tree recruitment. Also, an increase in mammalian seed predation might prevent trees from establishing in the niches of phylogenetically distantly related species, contrary to what is known from insect enemies.     

Intraspecific variation in seed dispersal of a Neotropical tree and its relationship to fruit and tree traits

The distribution of wind‐dispersed seeds around a parent tree depends on diaspore and tree traits, as well as wind conditions and surrounding vegetation. This study of a neotropical canopy tree, Platypodium elegans, explored the extent to which parental variation in diaspore and tree traits explained (1) rate of diaspore descent in still air, (2) distributions of diaspores dispersed from a 40‐m tower in the forest, and (3) natural diaspore distributions around the parent tree. The geometric mean rate of descent in still air among 20 parents was highly correlated with geometric mean wing loading^1/2 (r = 0.84). However, diaspore traits and rate of descent predicted less variation in dispersal distance from the tower, although descent rate⁻¹ consistently correlated with dispersal distance. Measured seed shadows, particularly their distribution edges, differed significantly among six parents (DBH range 62–181 cm) and were best fit by six separate anisotropic dispersal kernels and surveyed fecundities. Measured rate of descent and tree traits, combined in a mechanistic seed dispersal model, did not significantly explain variation among parents in natural seed dispersal distances, perhaps due to the limited power to detect effects with only six trees. Seedling and sapling distributions were at a greater mean distance from the parents than seed distributions; saplings were heavily concentrated at far distances. Variation among parents in the distribution tails so critical for recruitment could not be explained by measured diaspore or tree traits with this sample size, and may be determined more by wind patterns and the timing of abscission in relation to wind conditions. Studies of wind dispersal need to devote greater field efforts at recording the “rare” dispersal events that contribute to far dispersal distances, following their consequences, and in understanding the mechanisms that generate them.     

THE IMPACT OF TREE SQUIRRELS (TAMIASCIURUS) ON LIMBER PINE SEED DISPERSAL ADAPTATIONS

Tree squirrels (Tamiasciurus) are important selective agents on conifer reproductive strategies (Smith 1970, 1975). Although this is well established for wind-dispersed pines, the impact of tree squirrels on bird-dispersed pines has been largely ignored. I assessed the impact of tree squirrels on the allocation of reproductive energy in the bird-dispersed limber pine (Pinus flexilis) by comparing its cone and seed traits from three sites in the Rocky Mountains where tree squirrels (Tamiasciurus) are present to those from three mountain ranges in the Great Basin where tree squirrels are absent. As predicted, differences between the two regions in individual cone and seed traits are consistent with the hypothesis that tree squirrels are important selective agents on these traits. In the absence of tree squirrels, limber pine allocates more than twice as much energy to kernel compared with that invested in putative seed defenses (cone, resin, and seed coat) as does limber pine where tree squirrels are present. Such a large difference is particularly striking, because tree squirrels may have become extinct in the Great Basin in only the last 12,000 yr. Although many factors influence the allocation of energy to cones and seeds, no single factor other than the presence of tree squirrels is compatible with the large and consistent differences between limber pine in the Rocky Mountains and Great Basin. These results show that tree squirrels are an important constraint on the evolution of cone and seed traits that promote the dispersal of seeds by birds.     

Using Plant Functional Traits and Phylogenies to Understand Patterns of Plant Community Assembly in a Seasonal Tropical Forest in Lao PDR

Plant functional traits reflect different evolutionary responses to environmental variation, and among extant species determine the outcomes of interactions between plants and their environment, including other plant species. Thus, combining phylogenetic and trait-based information can be a powerful approach for understanding community assembly processes across a range of spatial scales. We used this approach to investigate tree community composition at Phou Khao Khouay National Park (18°14’-18°32’N; 102°38’- 102°59’E), Laos, where several distinct forest types occur in close proximity. The aim of our study was to examine patterns of plant community assembly across the strong environmental gradients evident at our site. We hypothesized that differences in tree community composition were being driven by an underlying gradient in soil conditions. Thus, we predicted that environmental filtering would predominate at the site and that the filtering would be strongest on sandier soil with low pH, as these are the conditions least favorable to plant growth. We surveyed eleven 0.25 ha (50x50 m) plots for all trees above 10 cm dbh (1221 individual trees, including 47 families, 70 genera and 123 species) and sampled soils in each plot. For each species in the community, we measured 11 commonly studied plant functional traits covering both the leaf and wood economic spectrum traits and we reconstructed a phylogenetic tree for 115 of the species in the community using rbcL and matK sequences downloaded from Genebank (other species were not available). Finally we compared the distribution of trait values and species at two scales (among plots and 10x10m subplots) to examine trait and phylogenetic community structures. Although there was strong evidence that an underlying soil gradient was determining patterns of species composition at the site, our results did not support the hypothesis that the environmental filtering dominated community assembly processes. For the measured plant functional traits there was no consistent pattern of trait dispersion across the site, either when traits were considered individually or when combined in a multivariate analysis. However, there was a significant correlation between the degree of phylogenetic dispersion and the first principle component axis (PCA1) for the soil parameters. Moreover, the more phylogenetically clustered plots were on sandier soils with lower pH. Hence, we suggest that the community assembly processes across our site may reflect the influence of more conserved traits that we did not measure. Nevertheless, our results are equivocal and other interpretations are possible. Our study illustrates some difficulties in combining trait and phylogenetic approaches that may result from the complexities of integrating spatial and evolutionary processes that vary at different scales.     

Bayesian Analysis of Congruence of Core Genes in Prochlorococcus and Synechococcus and Implications on Horizontal Gene Transfer

It is often suggested that horizontal gene transfer is so ubiquitous in microbes that the concept of a phylogenetic tree representing the pattern of vertical inheritance is oversimplified or even positively misleading. “Universal proteins” have been used to infer the organismal phylogeny, but have been criticized as being only the “tree of one percent.” Currently, few options exist for those wishing to rigorously assess how well a universal protein phylogeny, based on a relative handful of well-conserved genes, represents the phylogenetic histories of hundreds of genes. Here, we address this problem by proposing a visualization method and a statistical test within a Bayesian framework. We use the genomes of marine cyanobacteria, a group thought to exhibit substantial amounts of HGT, as a test case. We take 379 orthologous gene families from 28 cyanobacteria genomes and estimate the Bayesian posterior distributions of trees – a “treecloud” – for each, as well as for a concatenated dataset based on putative “universal proteins.” We then calculate the average distance between trees within and between all treeclouds on various metrics and visualize this high-dimensional space with non-metric multidimensional scaling (NMMDS). We show that the tree space is strongly clustered and that the universal protein treecloud is statistically significantly closer to the center of this tree space than any individual gene treecloud. We apply several commonly-used tests for incongruence/HGT and show that they agree HGT is rare in this dataset, but make different choices about which genes were subject to HGT. Our results show that the question of the representativeness of the “tree of one percent” is a quantitative empirical question, and that the phylogenetic central tendency is a meaningful observation even if many individual genes disagree due to the various sources of incongruence.     

Importance of fragmentation-tolerant species as seed dispersers in disturbed landscapes

Forest fragmentation can negatively affect plants if animal seed-dispersers become locally extinct in fragments. We conducted a 2-year experiment to evaluate the importance of tree squirrels (Sciurus) as seed dispersers for Quercus, Carya, and Juglans, and to assess dispersal consequences in patches where fragmentation-sensitive eastern gray squirrels (Sciurus carolinensis) are absent. We accounted for fates of ∼15,700 seeds from five tree species in four exclosure treatments at 18 fragments during a high (2003–2004) and low seed (2004–2005) year. Two treatments excluded Sciurus to mimic disperser loss. We sampled nut-tree seedling density at 259 sites across eight watersheds, half of which were too fragmented to support S. carolinensis, but supported fragmentation-tolerant fox squirrels (Sciurus niger). Autumn-to-spring seed survival was low (∼1%) for all species during low seed production. During high seed production, survival was higher for Juglans nigra (20%) and Carya ovata (16%) than for three Quercus species (∼4% for Quercus palustris and Quercus rubra in two exclosure types; ∼1% for Quercus alba in all treatments). Survival of J. nigra, C. ovata, and Q. rubra was ≥2.1–7.7 times higher for seeds in exclosures that Sciurus could access. Seed displacement distance was higher in the low seed than the seed-rich year, but the proportion of seeds surviving to greater distances was higher in seed-rich years for all seed types except Q. rubra. This affirms the importance of masting to seed survival and dispersal, but also suggests an advantage to trees of producing seed in non-mast years. Seedling densities were comparable in watersheds with and without S. carolinensis. These results demonstrate the importance of tree squirrels as dispersers of nut-bearing trees, but suggest that fragmentation may not disrupt dispersal of certain species if losing S. carolinensis from disturbed landscapes is compensated for by fragmentation-tolerant fox squirrels (S. niger).     

Long-term scatterhoarding by Eurasian red squirrels (Sciurus vulgaris)

Hoarding behavious, seed species hoarded and hoarding intensity by red squirrels ( Sclurus vulgaris L.) are described for two population; one in a coniferous woodland with few deciduous trees, the other in a mixed deciduous woodland with some conifers. Seasonal variation in the recovery of hoards and the importance of hoarded food with regard to a squirrel's annual energy demands are discussed. The importance of having hoards is compared among tree squirrel species.     

The Narrow Niche hypothesis: gray squirrels shed new light on primate origins

Current hypotheses for primate origins propose that nails and primate-like grasping hands and feet were important early adaptations for feeding in fine branches. Comparative research in this area has focused on instances of convergence in extant animals, showing that species with primate-like morphology feed predominantly from terminal branches. Little has been done to test whether animals without primate-like morphology engage in similar behavior. We tested the fine-branch niche hypothesis for primate origins by observing branch use in Eastern gray squirrels, Sciurus carolinensis, a species lacking primate grasping adaptations that has been understudied in the context of primate origins. We hypothesized that because gray squirrels lack primate-like grasping adaptations, they would avoid feeding and foraging in terminal branches. Instantaneous focal animal sampling was used to examine the locomotor and postural behaviors used while feeding and foraging. Our results demonstrate habitual and effective usage of terminal branches by gray squirrels while feeding and foraging, primarily on tree seeds (e.g., oak, maple, and elm). Discriminant function analysis indicates that gray squirrels feed and forage like primates, unlike some other tree squirrel species. Given the absence of primate-like features in gray squirrels, we suggest that although selection for fine-branch foraging may be a necessary condition for primate origins, it is not sufficient. We propose an alternative model of primate origins. The Narrow Niche hypothesis suggests that the primate morphological suite evolved not only from selection pressure for fine branch use, but also from a lack of engagement in other activities.     

Seed size and shade-tolerance: a comparative analysis of North American temperate trees

Large seed size is a trait associated with plant species of mature, closed habitats, and is thought to supply an ample nutrient reserve necessary for seedling establishment. While this relationship has been shown for annuals and short-lived perennials, it is poorly documented for trees. A comparative method was used to determine whether North American temperate tree species which typically establish in shady conditions have larger seeds than those requiring more open conditions. Both angiosperms (hardwoods) and gymnosperms (conifers) were involved in the study. A significant relationship was found between large seed mass and shade-tolerance for angiosperms, but not for gymnosperms. These contrasting results seem to relate to unique evolutionary opportunities or constraints in different taxa. The absence of a relationship for gymnosperms is discussed in terms of character traits which might prevent seed size selection in response to shade. The finding for angiosperms underlines the importance of the regeneration niche in promoting coexistence among temperate hardwood species through seed size differentiation. Received: 18 March 1997 / Accepted: 26 November 1997     

Seed dispersal of the Korean pine,Pinus koraiensis,by the red squirrel,Sciurus vulgaris

Seed hoarding behavior of the red squirrel,Sciurus vulgaris, was studied in relation to the amount of dispersed seeds of the Korean pine,Pinus koraiensis, and the distribution of its seedlings. After removing a cone from a tree, squirrels sat on the ground and ripped off its cone scales before transporting it. A mean of 3.2 seeds were scatter-hoarded per hole. Of 7.7×10⁴ mature seeds produced in a 0.21 ha planted Korean pine forest, 22% were estimated to be directly eaten by four squirrels, 9% were hoarded by them in the pine forest and 65% were cached outside the forest. Squirrels rediscovered hoarded seeds frequently, until the ground was covered with snow, during the period from snow fall until seed germination the next spring, few hoarded seeds were utilized. Korean pine seedlings were found up to 600 m from their mother trees. Scatter-hoarding by squirrels extensively contributes to seed dispersal to places suitable for the regeneration of the Korean pine. The large size of the cone, the absciss-layer at the cone penduncle, the infrequent dehiscence of cone scales, the large and wingless seeds, and the thick seed-coats have probably all been specialized to facilitate utilization by GenusSciurus.     

The anatomy of a range expansion: changes in cranial morphology and rates of energy extraction for North American red squirrels from different latitudes

Species with expanding ranges provide unique opportunities to examine environmentally induced adaptations in ecological traits and anatomical characteristics. Since the late 1800s, the North American red squirrel (Tamiasciurus hudsonicus) has expanded its range into the central hardwoods of the United States in conjunction with increasing agricultural fragmentation. We examined whether red squirrels from the central hardwoods (west‐central Indiana, USA) displayed differences in foraging behaviors and morphology relative to red squirrels from conifer‐dominated environments (upper peninsula of Michigan, USA), a biome in which red squirrels evolved. Specifically, we measured rates of energy extraction, variation in cranial morphology, and diet preference between red squirrels from both regions. In addition, we compared foraging behaviors of red squirrels from the central hardwoods to those of a competitor that coevolved with nut‐producing trees, the gray squirrel (Sciurus carolinensis). Red squirrels from Indiana and Michigan differed significantly in the efficiency with which they used food items, with individuals from each region extracting calories at a more rapid rate for items that were common in their region. The enhanced efficiency of southern red squirrels feeding on black walnuts (Juglans nigra) was correlated with geographic differences in cranial morphology; skulls of southern squirrels were larger, with longer jaws and higher metrics associated with greater mandibular force than northern squirrels. Contrary to our expectations, red squirrels from Indiana and Michigan did not differ qualitatively in preferences for food items, suggesting that diet choice may be governed by perishability of food items rather than by rates of energy extraction. Gray squirrels were more efficient than Indiana red squirrels in using all food items, and differed only slightly from red squirrels with regard to preference for food items. Measures of efficiency of resource use, after accounting for species‐specific metabolic requirements, suggest that red squirrels are unlikely to compensate ecologically for declining gray squirrel populations in fragmented portions of the central hardwoods, with potentially adverse effects for forest regeneration and succession. Our results demonstrate that invading species can display significant flexibility in adapting to new environments, but they may not be flexible enough to exploit resources in a manner comparable to native species.     

Comparing the Dispersal of Large-seeded Tree Species by Frugivore Assemblagesin Tropical Montane Forest in Africa

We examined frugivore visitation and seed dispersal of five large-seeded (≥ 5 mm) tree species in tropical montane forest based on their occurrence in frugivorous primate diets: Ekebergia capensis, Olea capensis, Parinari excelsa, Prunus africana , and Syzygium guineense. A total of 21 frugivores in five assemblages ( i.e. , chimpanzees, cercopithecines, large-bodied birds, small-bodied birds, and squirrels) were observed over the study period (August 2006 and October–April 2007). We observed seed dispersal in four of five tree species studied; no dispersal was observed for P. excelsa . Frugivore assemblages did not visit tree species equally. Primates spent the most time in trees and had the largest group size. Large-bodied birds (LB) and chimpanzees dispersed the highest number of seeds per minute. LB and cercopithecines potentially dispersed the greatest number of seeds for E. capensis , and chimpanzees for S. guineense . Our analyses indicated that the mean fruiting duration of the focal tree, time in the tree, and number of species present are important predictor variables for seed dispersal by small- and large-bodied birds, and cercopithecines. The number of fruiting trees in the immediate vicinity of the focal tree further predicted seed dispersal for small-bodied birds (SB). Large-bodied birdseed dispersal also was predicted by time in tree by SB, and the number of individuals for SB and cercopithecines. Cercopithecines (CS) were further explained by the time in tree and number of species (SB & LB), and number of individuals for CS. Our study highlights the complexity of describing the relative importance of a frugivore assemblage to the dispersal of a tree species seeds.     

Discriminating the effects of phylogenetic hypothesis,tree resolution and clade age estimates on phylogenetic signal measurements

Understanding how species traits evolved over time is the central question to comprehend assembly rules that govern the phylogenetic structure of communities. The measurement of phylogenetic signal (PS) in ecologically relevant traits is a first step to understand phylogenetically structured community patterns. The different methods available to estimate PS make it difficult to choose which is most appropriate. Furthermore, alternative phylogenetic tree hypotheses, node resolution and clade age estimates might influence PS measurements. In this study, we evaluated to what extent these parameters affect different methods of PS analysis, and discuss advantages and disadvantages when selecting which method to use. We measured fruit/seed traits and flowering/fruiting phenology of endozoochoric species occurring in Southern Brazilian Araucaria forests and evaluated their PS using Mantel regressions, phylogenetic eigenvector regressions (PVR) and K statistic. Mantel regressions always gave less significant results compared to PVR and K statistic in all combinations of phylogenetic trees constructed. Moreover, a better phylogenetic resolution affected PS, independently of the method used to estimate it. Morphological seed traits tended to show higher PS than diaspores traits, while PS in flowering/fruiting phenology depended mostly on the method used to estimate it. This study demonstrates that different PS estimates are obtained depending on the chosen method and the phylogenetic tree resolution. This finding has implications for inferences on phylogenetic niche conservatism or ecological processes determining phylogenetic community structure.     

Impacts of growth form and phylogenetic relatedness on seed germination: A large‐scale analysis of a subtropical regional flora

Plant regeneration strategy plays a critical role in species survival and can be used as a proxy for the evolutionary response of species to climate change. However, information on the effects of key plant traits and phylogenetic relatedness on seed germination is limited at large regional scales that vary in climate. To test the hypotheses that phylogenetic niche conservatism plays a critical force in shaping seed ecophysiological traits across species, and also drives their response to climatic fluctuation, we conducted a controlled experiment on seed germination and determined the percentage and rate of germination for 249 species in subtropical China under two temperature regimes (i.e., daily 25°C; daily alternating 25/15°C for each 12 hr). Germination was low with a skewed distribution (mean = 38.9% at 25°C, and 43.3% at 25/15°C). One fifth of the species had low (<10%) and slow (4–30 days) germination, and only a few (8%) species had a high (>80%) and rapid (1.2–6.6 days) germination. All studied plant traits (including germination responses) showed a significant phylogenetic signal, with an exception of seed germination percentage under the alternating temperature scenario. Generalized linear models (GLMs) and phylogenetic generalized estimation equations (GEEs) demonstrated that growth form and seed dispersal mode were strong drivers of germination. Our experimental study highlights that integrating plant key traits and phylogeny is critical to predicting seed germination response to future climate change.     

Special Care Is Needed in Applying Phylogenetic Comparative Methods to Gene Trees with Speciation and Duplication Nodes

How gene function evolves is a central question of evolutionary biology. It can be investigated by comparing functional genomics results between species and between genes. Most comparative studies of functional genomics have used pairwise comparisons. Yet it has been shown that this can provide biased results, as genes, like species, are phylogenetically related. Phylogenetic comparative methods should be used to correct for this, but they depend on strong assumptions, including unbiased tree estimates relative to the hypothesis being tested. Such methods have recently been used to test the “ortholog conjecture,” the hypothesis that functional evolution is faster in paralogs than in orthologs. Although pairwise comparisons of tissue specificity (τ) provided support for the ortholog conjecture, phylogenetic independent contrasts did not. Our reanalysis on the same gene trees identified problems with the time calibration of duplication nodes. We find that the gene trees used suffer from important biases, due to the inclusion of trees with no duplication nodes, to the relative age of speciations and duplications, to systematic differences in branch lengths, and to non-Brownian motion of tissue specificity on many trees. We find that incorrect implementation of phylogenetic method in empirical gene trees with duplications can be problematic. Controlling for biases allows successful use of phylogenetic methods to study the evolution of gene function and provides some support for the ortholog conjecture using three different phylogenetic approaches.