Elevational diversity patterns as an example for evolutionary and ecological dynamics in ferns and lycophytes

Evolutionary processes such as adaptation, ecological filtering, and niche conservatism involve the interaction of organisms with their environment and are thus commonly studied along environmental gradients. Elevational gradients have become among the most studied environmental gradients to understand large-scale patterns of species richness and composition because they are highly replicated with different combinations of geographical, environmental and historical factors. We here review the literature on using elevational gradients to understand evolutionary processes in ferns. Some phylogenetic studies of individual fern clades have considered elevation in the analysis or interpretation and postulated that fern diversification is linked to the colonization of mountain habitats. Other studies that have linked elevational community composition and hence ecological filtering with phylogenetic community composition and morphological traits, usually only found limited phylogenetic signal. However, these studies are ultimately only correlational, and there are few actual tests of the evolutionary mechanisms leading to these patterns. We identify a number of challenges for improving our understanding of how evolutionary and ecological processes are linked to elevational richness patterns in ferns: i) limited information on traits and their ecological relevance, ii) uncertainties on the dispersal kernels of ferns and hence the delimitation of regional species pools from which local assemblages are recruited, iii) limited genomic data to identify candidate genes under selection and hence actually document adaptation and selection, and iv) conceptual challenges in developing clear and testable hypotheses to how specific evolutionary processes can be linked to patterns in community composition and species richness.     

Elevational patterns of fern species assemblages and richness in central Japan

We conducted field surveys in 807 quadrats to evaluate the elevational belts, boundary and richness patterns of ferns and lycophytes in the temperate region of central Japan. We analysed fern species assemblages at 100 m elevational steps by cluster analysis and tested the number of upper and lower boundaries for elevational intervals against a null model of random distribution of elevational limits. We compared the pattern of fern species richness along the elevational gradients in central Japan with patterns in several locations to evaluate the fern flora in central Japan in relation to the rest of the world. We recorded 261 ferns species in total, which is one-third of the Japanese ferns. We found clear elevational boundaries of fern assemblages at 900 and 1,800 m and three fern elevational zones, which corresponded well to the elevational limits of forest types in central Japan. The pattern of fern species richness in central Japan was an asymmetric hump-shaped pattern that peaked close to the sea level, with the peak of local richness at lower elevations than that of regional richness. We found that the peak of fern species richness along the elevational gradient in Japan was located at lower elevations than that of fern elevational patterns in several locations around the world.     

A current perspective on apomixis in ferns

This review provides a synopsis of apogamous reproduction in ferns and highlights important progress made in recent studies of fern apomixis. First, a summary of the apomictic fern life cycle is provided, distinguishing between two pathways to diploid spore production that have been documented in apomictic ferns (premeiotic endomitosis and meiotic first division restitution) and briefly discussing the evolutionary implications of each. Next, recent trends in fern apomixis research are discussed, exposing a shift in focus from the observation and characterization of apomixis in ferns to more integrated studies of the evolutionary and ecological implications of this reproductive mode. Peer-reviewed contributions from the past decade are then summarized, spanning the identification of new apomictic lineages through to the developmental, phylogenetic, and population genetic insights that have been made in studies of fern apomixis during that time. Gaps in our understanding are also discussed, including the extent and implications of recombinant apomixis in ferns, the possible reversibility of reproductive mode (from apomictic to sexual) in ferns, and the genomic causes and consequences of apomixis in seed free vascular plants. To conclude, future directions for fern apomixis research are proposed in the context of modern technological advances and recent insights from studies of apomixis in other groups.     

Reconciling extreme branch length differences: decoupling time and rate through the evolutionary history of filmy ferns

The rate of molecular evolution is not constant across the Tree of Life. Characterizing rate discrepancies and evaluating the relative roles of time and rate along branches through the past are both critical to a full understanding of evolutionary history. In this study, we explore the interactions of time and rate in filmy ferns (Hymenophyllaceae), a lineage with extreme branch length differences between the two major clades. We test for the presence of significant rate discrepancies within and between these clades, and we separate time and rate across the filmy fern phylogeny to simultaneously yield an evolutionary time scale of filmy fern diversification and reconstructions of ancestral rates of molecular evolution. Our results indicate that the branch length disparity observed between the major lineages of filmy ferns is indeed due to a significant difference in molecular evolutionary rate. The estimation of divergence times reveals that the timing of crown group diversification was not concurrent for the two lineages, and the reconstruction of ancestral rates of molecular evolution points to a substantial rate deceleration in one of the clades. Further analysis suggests that this may be due to a genome-wide deceleration in the rate of nucleotide substitution.     

Fern species richness along a central Himalayan elevational gradient, Nepal

Aim The study explores fern species richness patterns along a central Himalayan elevational gradient (100–4800 m a.s.l.) and evaluates factors influencing the spatial increase and decrease of fern richness. Location The Himalayas stretch from west to east by 20°, i.e. 75–95° east, and Nepal is located from 80 to 88° east in this range. Methods We used published data of the distribution of ferns and fern allies to interpolate species elevational ranges. Defining species presence between upper and lower elevation limit is the basis for richness estimates. The richness pattern was regressed against the total number of rainy days, and gradients that are linearly related to elevation, such as length of the growing season, potential evapotranspiration (PET, energy), and a moisture index (MI = PET/mean annual rainfall). The regressions were performed by generalized linear models. Results A unimodal relationship between species richness and elevation was observed, with maximum species richness at 2000 m. Fern richness has a unimodal response along the energy gradients, and a linear response with moisture gradients. Main conclusions The study confirms the importance of moisture on fern distributions as the peak coincides spatially with climatic factors that enhance moisture levels; the maximum number of rainy days and the cloud zone. Energy‐related variables probably control species richness directly at higher elevations but at the lower end the effect is more probably related to moisture.     

Biodiversity patterns diverge along geographic temperature gradients

Models applying space-for-time substitution, including those projecting ecological responses to climate change, generally assume an elevational and latitudinal equivalence that is rarely tested. However, a mismatch may lead to different capacities for providing climatic refuge to dispersing species. We compiled community data on zooplankton, ectothermic animals that form the consumer basis of most aquatic food webs, from over 1200 mountain lakes and ponds across western North America to assess biodiversity along geographic temperature gradients spanning nearly 3750 m elevation and 30° latitude. Species richness, phylogenetic relationships, and functional diversity all showed contrasting responses across gradients, with richness metrics plateauing at low elevations but exhibiting intermediate latitudinal maxima. The nonmonotonic/hump-shaped diversity trends with latitude emerged from geographic interactions, including weaker latitudinal relationships at higher elevations (i.e. in alpine lakes) linked to different underlying drivers. Here, divergent patterns of phylogenetic and functional trait dispersion indicate shifting roles of environmental filters and limiting similarity in the assembly of communities with increasing elevation and latitude. We further tested whether gradients showed common responses to warmer temperatures and found that mean annual (but not seasonal) temperatures predicted elevational richness patterns but failed to capture consistent trends with latitude, meaning that predictions of how climate change will influence diversity also differ between gradients. Contrasting responses to elevation- and latitude-driven warming suggest different limits on climatic refugia and likely greater barriers to northward range expansion.     

Phylogenetic properties of Tertiary relict flora in the east Asian continental islands: imprint of climatic niche conservatism and in situ diversification

Understanding biodiversity patterns on islands has long been a central aim in ecology and conservation biology. Island‐specific biogeographical processes play substantial roles in the formation of endemic biota. Here, we examined how climate niche conservatism and geohistorical factors are interactively associated with in situ diversification of Tertiary relict flora in the east Asian continental islands. We generated two novel datasets for species distribution and phylogeny that included all of the known vascular plant species in Japan (5575). Then we tested phylogenetic signal of climatic tolerance, in terms of absolute minimum temperature and water balance, and explored environmental predictors of phylogenetic structure (evolutionary derivedness and clustering) of species assemblages. Although phylogenetic signal of climatic tolerance was significant across the phylogeny of most species, the strength of climatic niche conservatism differed among ferns, gymnosperms, angiosperm trees, and angiosperm herbs. For angiosperm trees, cold temperatures acted as environmental filters that generated phylogenetic derivedness/clustering of species assemblages. For fern and angiosperm herb species, however, phylogenetic properties were not associated with climatic harshness. These contrasting patterns among groups reflected climate niche evolution in vascular plants with different growth forms and traits; for example, diversification of angiosperm trees (but not fern and herb) occurred in response to historical climatic cooling. More importantly, geographical constraints contributed to evolutionary radiation that resulted from isolation by distance from the continent or by elevation. Quaternary climate change was also associated with clade‐specific radiation in refugial habitats. The degree to which geographical, geological, and palaeoclimatic variables explain the phylogenetic structure underscores the importance of isolation‐ and habitat‐stability‐related geohistorical processes in driving in situ diversification despite climatic niche conservatism. We propose that the highly endemic flora of the east Asian islands resulted from the interplay of idiosyncratic regional factors, and ecological and evolutionary processes, such as climate niche assembly and adaptive/nonadaptive radiation.     

Niche evolution and diversification in a Neotropical radiation of birds (Aves: Furnariidae)

Rapid diversification may be caused by ecological adaptive radiation via niche divergence. In this model, speciation is coupled with niche divergence and lineage diversification is predicted to be correlated with rates of niche evolution. Studies of the role of niche evolution in diversification have generally focused on ecomorphological diversification but climatic‐niche evolution may also be important. We tested these alternatives using a phylogeny of 298 species of ovenbirds (Aves: Furnariidae). We found that within Furnariidae, variation in species richness and diversification rates of subclades were best predicted by rate of climatic‐niche evolution than ecomorphological evolution. Although both are clearly important, univariate regression and multivariate model averaging more consistently supported the climatic‐niche as the best predictor of lineage diversification. Our study adds to the growing body of evidence, suggesting that climatic‐niche divergence may be an important driver of rapid diversification in addition to ecomorphological evolution. However, this pattern may depend on the phylogenetic scale at which rate heterogeneity is examined.     

Geographical and ecological patterns of range size in North American trees

We analysed the degree to which spatial, ecological and phylogenetic factors influenced geographic gradients in range size for all trees native to North America. We compared observed range sizes, measured in either one (latitudinal or longitudinal extent) or two dimensions (range area), with three null models that respected constraints imposed by the geometry of the continent; we tested whether climatic gradients could account for increasing range size with latitude – a Rapoport effect – in North American trees; and whether variation in range size was associated with phylogeny or ecological characteristics of species. We documented an excess of species with small ranges and a lack of widely distributed species compared with null expectations both with and without environmental constraints. We found evidence for a Rapoport effect in North American trees, at different taxonomic levels and for different groups defined by ecological characteristics. This pattern is not an outcome constrained by continental shape and does not depend on the metric for range size, but it is consistent with the climatic variability hypothesis proposed to explain the Rapoport pattern. Finally we showed that trees east of the Rocky Mountains have larger ranges on average than trees to the west or in Mexico and that the proportion of deciduous compared to evergreen species increases with range size. Variation in range size among North American trees is not spatially random, and has a phylogenetic and ecological signal. Consistent with the climatic variability hypothesis, range size of North American trees increases with increasing variability in annual temperature range at higher latitudes.     

The combined role of dispersal and niche evolution in the diversification of Neotropical lizards

Ecological requirements and environmental conditions can influence diversification across temporal and spatial scales. Understanding the role of ecological niche evolution under phylogenetic contexts provides insights on speciation mechanisms and possible responses to future climatic change. Large‐scale phyloclimatic studies on the megadiverse Neotropics, where biomes with contrasting vegetation types occur in narrow contact, are rare. We integrate ecological and biogeographic data with phylogenetic comparative methods, to investigate the relative roles of biogeographic events and niche divergence and conservatism on the diversification of the lizard genus Kentropyx Spix, 1825 (Squamata: Teiidae), distributed in South American rainforests and savannas. Using five molecular markers, we estimated a dated species tree, which recovered three clades coincident with previously proposed species groups diverging during the mid‐Miocene. Biogeography reconstruction indicates a role of successive dispersal events from an ancestral range in the Brazilian Shield and western Amazonia. Ancestral reconstruction of climatic tolerances and niche overlap metrics indicates a trend of conservatism during the diversification of groups from the Amazon Basin and Guiana Shield, and a strong signal of niche divergence in the Brazilian Shield savannas. Our results suggest that climatic‐driven divergence at dynamic forest‐savanna borders might have resulted in adaptation to new environmental niches, promoting habitat shifts and shaping speciation patterns of Neotropical lizards. Dispersal and ecological divergence could have a more important role in Neotropical diversification than previously thought.     

蕨类植物不同孢子裂缝类型在中国的分布格局

孢子在蕨类植物分类及有性生殖过程中具有重要地位, 一般都具有裂缝构造, 常见的是单裂缝和三裂缝, 极少数情况下有多裂缝的变异类型。我们统计了中国蕨类2,281种(含种下单位)的孢子裂缝类型, 来探讨两种不同裂缝类型的分布格局。结果表明: (1)具有单裂缝类型的物种数多于三裂缝类型, 单裂缝与三裂缝物种数目的比值(单/三比)与纬度和海拔呈正相关。随着温度下降以及降水量的降低, 具单裂缝孢子的物种比例增加。推测具单裂缝孢子的蕨类分布范围更广, 更适宜生活在干旱及高纬度或高海拔寒冷地区, 而具三裂缝孢子的蕨类更适宜存在于低纬度或低海拔的温暖地区; (2)蕨类植物孢子裂缝类型不是单次起源, 可能存在平行演化。本研究可以为蕨类植物的起源演化与生态适应等研究提供一定的证据。     

Climatic niche evolution in Smilacaceae (Liliales) drives patterns of species diversification and richness between the Old and New World

Geographical variation in species richness in plant groups is determined by the interplay between historical, evolutionary, and ecological processes. However, the processes underlying the striking disparity in species richness between Asia and the Americas remain poorly understood. Here, we synthesize global phylogenetic and macroecological data on the diversification of Smilacaceae, deciphering potential drivers underlying the species diversity pattern biased toward Asia. We compiled global distributions of all Smilacaceae species, and reconstructed the biogeographic history and niche evolution using a new time-calibrated phylogeny (eight genes, 135 species). Integrating these data sets, we estimated evolutionary histories and diversification rates for each region, and tested correlations among species diversification, niche evolution, and niche divergence. Smilacaceae probably originated during the Late Cretaceous/Early Palaeocene and began to diversify in middle to low latitudes in Central America and Eurasia during the Late Eocene. Both the Old and New World clades exhibited a steady, albeit slight, increase of species diversification from the Late Eocene to Early Miocene. However, the Old World clade experienced an abrupt increase in net diversification during the Late Miocene. Our findings also revealed that species diversification rates were positively correlated with ecological niche evolution and niche divergence. Niche shifts and climatic niche evolution since the Middle Miocene played crucial roles in species diversification dynamics within Smilacaceae. The high plant richness in Asia may be explained by greater diversification in this region, potentially promoted by heterogeneous environments.     

Latitudinal gradients in climatic‐niche evolution accelerate trait evolution at high latitudes

Despite the importance of divergent selection to the speed of evolution, it remains poorly understood if divergent selection is more prevalent in the tropics (where species richness is highest), or at high latitudes (where paleoclimate change has been most intense). We tested whether the rate of climatic‐niche evolution – one proxy for divergent selection – varies with latitude for 111 pairs of bird species. Using Brownian motion and Ornsetin–Ulhenbeck models, we show that evolutionary rates along two important axes of the climatic‐niche – temperature and seasonality – have been faster at higher latitudes. We then tested whether divergence of the climatic‐niche was associated with evolution in traits important in ecological differentiation (body mass) and reproductive isolation (song), and found that climatic divergence is associated with faster rates in both measures. These results highlight the importance of climate‐mediated divergent selection pressures in driving evolutionary divergence and reproductive isolation at high latitudes.     

二型花柱植物海仙花报春花部性状随地理梯度的变异

植物的花部性状在异质环境中表现出不均一的适应性进化, 其自然变异可能在时空格局上呈现一定的规律性。选择同一物种的不同地理居群进行花部表型变异分析, 能揭示花部性状随地理梯度的变异模式。海仙花报春(Primula poissonii)属于典型的二型花柱植物, 依赖昆虫传粉实现严格的型间异交。该物种广布于横断山地区亚高山-高山草甸, 其分布海拔跨度大且花部性状在种内具有较高变异, 但这些变异在不同地理梯度(海拔梯度和经纬度梯度)的特定选择因子作用下的变化规律尚不清楚。本研究选择海仙花报春16个居群, 对8个花部关键性状和二型花柱繁殖器官的互补度与海拔和经纬度的关系进行研究, 探究花部性状随地理梯度变异的模式及其潜在的选择因素。研究表明, 海仙花报春两种花型的花冠管开口大小、花药高度以及短柱花柱头高度与海拔均呈正相关, 但两种花型的花冠大小, 长柱花的花瓣长度、柱头到花冠管开口的距离, 以及短柱花的花冠管长度与海拔高度间均呈负相关, 其余性状与海拔无显著相关性。除短柱花中柱头高度以外的性状均随着纬度升高而逐渐减小。长柱花中除花药和柱头间的距离以及柱头到开口的距离外, 其余性状均随着经度的增加而减小; 短柱花的花瓣长度、花药高度以及花药和柱头间的距离随着经度的增加而变大, 其余性状均随着经度的增加而减小。繁殖器官间的互补度并不随地理环境的变化而变化。花部性状的地理变异可能受访花昆虫组成的地理变化驱动。繁殖器官间互补程度的高度保守表明非选型交配在居群二态性的维持和稳定过程中起关键作用。本研究为进一步深入开展报春花属(Primula)花部性状及其选择压力的地理变异研究奠定了基础。     

LATITUDINAL VARIATION IN SPECIATION MECHANISMS IN FROGS

Speciation often has a strong geographical and environmental component, but the ecological factors that potentially underlie allopatric and parapatric speciation remain understudied. Two ecological mechanisms by which speciation may occur on geographic scales are allopatric speciation through niche conservatism and parapatric or allopatric speciation through niche divergence. A previous study on salamanders found a strong latitudinal pattern in the prevalence of these mechanisms, with niche conservatism dominating in temperate regions and niche divergence dominating in the tropics, and related this pattern to Janzen's hypothesis of greater climatic zonation between different elevations in the tropics. Here, we test for latitudinal patterns in speciation in a related but more diverse group of amphibians, the anurans. Using data from up to 79 sister-species pairs, we test for latitudinal variation in elevational and climatic overlap between sister species, and evaluate the frequency of speciation via niche conservatism versus niche divergence in relation to latitude. In contrast to salamanders, we find no tendency for greater niche divergence in the tropics or for greater niche conservatism in temperate regions. Although our results support the idea of greater climatic zonation in tropical regions, they show that this climatic pattern does not lead to straightforward relationships between speciation, latitude, and niche evolution.     

Latitudinal patterns in rodent metabolic flexibility

Macrophysiology is defined as the study of variation in physiological traits-including physiological trait flexibility-over large geographical and temporal scales, and the ecological implications of this variation. A classic example of a macrophysiological trend is the one emerging from the climatic variability hypothesis, which states that as the range of climatic fluctuation experienced by terrestrial animals increases with latitude, individuals at higher latitudes should be more plastic than individuals inhabiting lower latitudes. In this context, we evaluate the correlation between absolute metabolic scope during cold exposure (an instantaneous measure of metabolic flexibility) and different geographic and climatic variables for 48 rodent species. Conventional and phylogenetic informed analyses indicated a positive correlation between metabolic scope and geographic latitude. These findings, together with previous reports on latitudinal pattern in phenotypic flexibility, suggest that an increase in physiological flexibility with latitude may hold for many phenotypic traits.     

Evidence for natural selection in a fern hybrid zone

Morphological characters, chloroplast DNA, and allozymes were used to analyze the distribution of individuals within a hybrid population of the ferns Polystichum munitum and P. imbricans in northwestern California. Microsites within the population were characterized according to soil moisture and light levels reaching the plants. In sites with low soil moisture and high light levels, all of the ferns were genetically and morphologically like P. imbricans. In contrast, ferns with the genetic and morphological identity of P. munitum predominated in moist shady sites. Intermediate sites supported very few P.munitum, a wide variety of hybrid recombinants, and a majority of ferns with P. imbricans characteristics. The pattern of variation within the population is noteworthy because of the close proximity of the habitat extremes and the long-range dispersal of fern spores. We conclude that natural selection along environmental gradients must be a major factor in determining the ecological and genetic associations within the hybrid zone. The results of this study are evaluated in the context of the fern life cycle and compared to the assumptions of models explaining the establishment and maintenance of hybrid zones, which vary in the role attributed to environmentally mediated natural selection.     

Neoendemism in Madagascan scaly tree ferns results from recent, coincident diversification bursts

More than 80% of Madagascar's 12,000 plant species are endemic with the degree of endemism reaching as much as 95% in the scaly tree ferns, an important species rich component of Madagascar's evergreen rainforests. Predominantly African or Asian ancestry and divergence times usually postdating the separation of Madagascar from the Gondwanan landmasses have been demonstrated for several Madagascan animal and angiosperm groups. However, evolutionary studies of rainforest-specific lineages are scarce and the ecological context of radiation events has rarely been investigated. Here, we examine the evolution of Madagascan tree ferns as a rainforest-specific model family, integrate results from bioclimatic niche analysis with a dated phylogenetic framework, and propose an evolutionary scenario casting new light on our knowledge of the evolution of large island endemic clades. We show that Madagascar's extant tree fern diversity springs from three distinct ancestors independently colonizing Madagascar in the Miocene and that these three monophyletic clades diversified in three coincident radiation bursts during the Pliocene, reaching exceptionally high diversification rates and most likely responding to a common climatic trigger. Recent diversification bursts may thus have played a major role in the evolution of the extant Madagascan rainforest biome, which hence contains a significant number of young, neoendemic taxa.     

Phylogenetic diversity,trait diversity and niches: species assembly of ferns along a tropical elevational gradient

Aim To analyse the structure of pteridophyte assemblages, based on phylogenetic relatedness and trait properties, along an elevational gradient. Ecological theory predicts that co‐occurring species may be: randomly selected from a regional pool; ecologically sorted so that they are functionally different hence resulting in reduced competition (overdispersion); or functionally similar as an adaptation to specific ecological conditions (clustering). Location Braulio Carrillo National Park and Cerro de la Muerte, Costa Rica, Central America. Methods We used an empirical dataset of the quantitative pattern of species occurrences and individual numbers of ferns within 156 plots along a tropical elevational gradient to test whether directed ecological sorting might cause deviations in patterns of trait and phylogenetic diversity. Mean pairwise distances of species based on phylogenetic and trait properties were compared with two different sets of null assemblages, one maintaining species frequency distributions (constrained) and one not (unconstrained). Results Applying different null models resulted in varying degrees of overdispersion and clustering, but overall patterns of deviation from random expectations remained the same. Contrary to theoretical predictions, phylogenetic and trait diversity were relatively independent from one another. Phylogenetic diversity showed no patterns along the elevational gradient, whereas trait diversity showed significant trends for epiphytes. Main conclusions Under stressful environmental conditions (drought at low elevations and frost at high elevations), epiphytic fern assemblages tended to be clustered with respect to trait characteristics, which suggests environmental filtering. Conversely, under less extreme environmental conditions (middle of the transect), the sorting was biased towards high differentiation (overdispersion), presumably because of interspecific competition and trait shifts among closely related species (character displacement).     

Life history, diversity and distribution: a study of Japanese pteridophytes

Many studies address the relationships between diversity or distribution and attributes of the physical environment. However, how these relationships are connected to variation in life history is poorly understood. This is particularly true in the case of pteridophytes. Japanese ferns and their allies comprise one of the best-known pteridophyte floras in the world. We analyzed ca 600 species of Japanese pteridophytes for which there is detailed information on distribution, reproduction, and chromosome number. Species richness was greatest in groups with a single reproductive mode (sexual, followed by apogamous), but distribution was greatest in species groups with multiple reproductive modes: sexual plus either sterile (irregular in meiosis) or apogamous. Geographical ranges varied greatly among species with small chromosome numbers but were uniformly small among species having high chromosome numbers. Seasonally green (mostly summer green) species had significantly larger distribution ranges than evergreen species. Endemic species had higher proportions of apogamy and sterility than non-endemic species. Seasonally green species had significantly larger distributional ranges, and a smaller proportion of species with apogamous reproduction, than evergreen species. There was no clear relationship between distribution and spore size, either among endemic species, non-endemic species, or all species combined. There was no relationship between spore size and chromosome number when all species were combined. However, positive relationships were detected within three of the nine largest genera, suggesting potential phylogenetic effects. We concluded that habitat availability, rather than dispersability, may be the limiting factor for the distribution of pteridophytes in Japan.