Widespread Signals of Convergent Adaptation to High Altitude in Asia and America

Living at high altitude is one of the most difficult challenges that humans had to cope with during their evolution. Whereas several genomic studies have revealed some of the genetic bases of adaptations in Tibetan, Andean, and Ethiopian populations, relatively little evidence of convergent evolution to altitude in different continents has accumulated. This lack of evidence can be due to truly different evolutionary responses, but it can also be due to the low power of former studies that have mainly focused on populations from a single geographical region or performed separate analyses on multiple pairs of populations to avoid problems linked to shared histories between some populations. We introduce here a hierarchical Bayesian method to detect local adaptation that can deal with complex demographic histories. Our method can identify selection occurring at different scales, as well as convergent adaptation in different regions. We apply our approach to the analysis of a large SNP data set from low- and high-altitude human populations from America and Asia. The simultaneous analysis of these two geographic areas allows us to identify several candidate genome regions for altitudinal selection, and we show that convergent evolution among continents has been quite common. In addition to identifying several genes and biological processes involved in high-altitude adaptation, we identify two specific biological pathways that could have evolved in both continents to counter toxic effects induced by hypoxia.     

Plant Traits Demonstrate That Temperate and Tropical Giant Eucalypt Forests Are Ecologically Convergent with Rainforest Not Savanna

Ecological theory differentiates rainforest and open vegetation in many regions as functionally divergent alternative stable states with transitional (ecotonal) vegetation between the two forming transient unstable states. This transitional vegetation is of considerable significance, not only as a test case for theories of vegetation dynamics, but also because this type of vegetation is of major economic importance, and is home to a suite of species of conservation significance, including the world’s tallest flowering plants. We therefore created predictions of patterns in plant functional traits that would test the alternative stable states model of these systems. We measured functional traits of 128 trees and shrubs across tropical and temperate rainforest – open vegetation transitions in Australia, with giant eucalypt forests situated between these vegetation types. We analysed a set of functional traits: leaf carbon isotopes, leaf area, leaf mass per area, leaf slenderness, wood density, maximum height and bark thickness, using univariate and multivariate methods. For most traits, giant eucalypt forest was similar to rainforest, while rainforest, particularly tropical rainforest, was significantly different from the open vegetation. In multivariate analyses, tropical and temperate rainforest diverged functionally, and both segregated from open vegetation. Furthermore, the giant eucalypt forests overlapped in function with their respective rainforests. The two types of giant eucalypt forests also exhibited greater overall functional similarity to each other than to any of the open vegetation types. We conclude that tropical and temperate giant eucalypt forests are ecologically and functionally convergent. The lack of clear functional differentiation from rainforest suggests that giant eucalypt forests are unstable states within the basin of attraction of rainforest. Our results have important implications for giant eucalypt forest management.     

木质藤本及其在热带森林中的生态学功能

木质藤本是热带森林的一个重要组分,直接或间接地影响着森林中树木的生长和更新,改变森林树木的种类组成,并且可以通过改变森林碳固定量等方式在生态系统水平上发挥作用。全球气候的变化,以及热带森林片断化程度的加剧,将很大程度上影响着木质藤本的多样性和丰富度,其特殊的生物学特性将在森林动态中发挥更加重要的作用。本文结合国内外目前木质藤本研究现状,概述了木质藤本的一般知识（包括木质藤本的定义和生物学特性等）,介绍了木质藤本全球分布格局、其多样性维持机理以及木质藤本在森林生态系统中的功能与作用,并就存在的一些问题以及需进一步开展的工作展开了讨论。     

木质藤本及其在热带森林中的生态学功能

木质藤本是热带森林的一个重要组分, 直接或间接地影响着森林中树木的生长和更新, 改变森林树木的种类组成, 并且可以通过改变森林碳固定量等方式在生态系统水平上发挥作用。全球气候的变化, 以及热带森林片断化程度的加剧, 将很大程度上影响着木质藤本的多样性和丰富度, 其特殊的生物学特性将在森林动态中发挥更加重要的作用。本文结合国内外目前木质藤本研究现状, 概述了木质藤本的一般知识(包括木质藤本的定义和生物学特性等), 介绍了木质藤本全球分布格局、其多样性维持机理以及木质藤本在森林生态系统中的功能与作用, 并就存在的一些问题以及需进一步开展的工作展开了讨论。     

Simulating the Long-term Response of Tropical Wet Forests to Fragmentation

In the coming decades, a large fraction of the world's tropical forests will be fragmented into remnants surrounded by secondary vegetation, land-use areas, or roads. It is important to develop integrative tools to monitor the evolution of these fragmented ecosystems. We used the individual-oriented and process-based forest growth simulator FORMIND2.0 to investigate the spatial and temporal effects on standing biomass and functional diversity of various intensities and patterns of fragmentation within a forest landscape. The simulator was calibrated for an old-growth wet forest in French Guiana, South America. We found that the standing biomass of forest remnants was reduced significantly compared to a similar area of nonfragmented forest. When fewer but larger remnants were created rather than many small ones, the total loss in biomass and the increase in the abundance of early-successional species were significantly reduced, confirming that edge effects dominate the functioning of forest remnants. We also performed simulations of secondary succession after the landscape had been abandoned. The simulated recovery time in those secondary forests depends on both the size of cleared area and the spatial pattern of the remnant forests. Received 30 January 2002; accepted 16 July 2002.     

热带林下的砂仁栽培

阳春砂仁(Amomum villosumL。)是中国的传统药用植物,它的种子团称为砂仁,果皮称为砂壳,皆可入药,有温脾、健胃、消食、行气之功效,主治胃炎、积食不消等,是30多种中成药的主要成分,还可用作调味佐料等,具有很高的经济价值。阳春砂仁原产广东省阳     

Genome-Wide Analysis of Cold Adaptation in Indigenous Siberian Populations

Following the dispersal out of Africa, where hominins evolved in warm environments for millions of years, our species has colonised different climate zones of the world, including high latitudes and cold environments. The extent to which human habitation in (sub-)Arctic regions has been enabled by cultural buffering, short-term acclimatization and genetic adaptations is not clearly understood. Present day indigenous populations of Siberia show a number of phenotypic features, such as increased basal metabolic rate, low serum lipid levels and increased blood pressure that have been attributed to adaptation to the extreme cold climate. In this study we introduce a dataset of 200 individuals from ten indigenous Siberian populations that were genotyped for 730,525 SNPs across the genome to identify genes and non-coding regions that have undergone unusually rapid allele frequency and long-range haplotype homozygosity change in the recent past. At least three distinct population clusters could be identified among the Siberians, each of which showed a number of unique signals of selection. A region on chromosome 11 (chr11:66–69 Mb) contained the largest amount of clustering of significant signals and also the strongest signals in all the different selection tests performed. We present a list of candidate cold adaption genes that showed significant signals of positive selection with our strongest signals associated with genes involved in energy regulation and metabolism (CPT1A, LRP5, THADA) and vascular smooth muscle contraction (PRKG1). By employing a new method that paints phased chromosome chunks by their ancestry we distinguish local Siberian-specific long-range haplotype signals from those introduced by admixture.     

Independent Molecular Basis of Convergent Highland Adaptation in Maize

Convergent evolution is the independent evolution of similar traits in different species or lineages of the same species; this often is a result of adaptation to similar environments, a process referred to as convergent adaptation. We investigate here the molecular basis of convergent adaptation in maize to highland climates in Mesoamerica and South America, using genome-wide SNP data. Taking advantage of archaeological data on the arrival of maize to the highlands, we infer demographic models for both populations, identifying evidence of a strong bottleneck and rapid expansion in South America. We use these models to then identify loci showing an excess of differentiation as a means of identifying putative targets of natural selection and compare our results to expectations from recently developed theory on convergent adaptation. Consistent with predictions across a wide parameter space, we see limited evidence for convergent evolution at the nucleotide level in spite of strong similarities in overall phenotypes. Instead, we show that selection appears to have predominantly acted on standing genetic variation and that introgression from wild teosinte populations appears to have played a role in highland adaptation in Mexican maize.     

Genome-Wide Patterns of Adaptation to Temperate Environments Associated with Transposable Elements in Drosophila

Investigating spatial patterns of loci under selection can give insight into how populations evolved in response to selective pressures and can provide monitoring tools for detecting the impact of environmental changes on populations. Drosophila is a particularly good model to study adaptation to environmental heterogeneity since it is a tropical species that originated in sub-Saharan Africa and has only recently colonized the rest of the world. There is strong evidence for the adaptive role of Transposable Elements (TEs) in the evolution of Drosophila, and TEs might play an important role specifically in adaptation to temperate climates. In this work, we analyzed the frequency of a set of putatively adaptive and putatively neutral TEs in populations with contrasting climates that were collected near the endpoints of two known latitudinal clines in Australia and North America. The contrasting results obtained for putatively adaptive and putatively neutral TEs and the consistency of the patterns between continents strongly suggest that putatively adaptive TEs are involved in adaptation to temperate climates. We integrated information on population behavior, possible environmental selective agents, and both molecular and functional information of the TEs and their nearby genes to infer the plausible phenotypic consequences of these insertions. We conclude that adaptation to temperate environments is widespread in Drosophila and that TEs play a significant role in this adaptation. It is remarkable that such a diverse set of TEs located next to a diverse set of genes are consistently adaptive to temperate climate-related factors. We argue that reverse population genomic analyses, as the one described in this work, are necessary to arrive at a comprehensive picture of adaptation.     

The Emerging Era of Novel Tropical Forests

In 1966 Eugene P. Odum delivered a speech before the Ecological Society of America that transformed the way ecologists looked at succession. His comparison of mature and successional systems lead ecologists to place secondary forests in an inferior position relative to mature ones to the point that today, prominent tropical biologists argue for and against the conservation value of secondary forests. Nevertheless, we live in the era of secondary forests that is rapidly giving way to a new era of novel tropical forests. Research in Puerto Rico documents the emergence of novel forests, which are different in terms of species composition, dominance, and relative importance of species from forests that were present before the island was deforested. These novel forests emerged without assistance. They are a natural response to the new environmental conditions created by human activity. Natural processes have remixed or reassembled native and introduced plant and animal species into novel communities adapted to anthropogenic environmental conditions. Novel forests are expected to protect soils, cycle nutrients, support wildlife, store carbon, maintain watershed functions, and mitigate species extinctions. The dawn of the age of tropical novel forests is upon us and must not be ignored.     

Tropical Forests of Xishuangbanna,China1

Lowland tropical forests once covered a large fraction of tropical southern China, but currently have an extent of ca 633,800 ha, mostly in Xishuangbanna of southern Yunnan. The Xishuangbanna region has a typical monsoon climate with a mean annual temperature ranging between 15.1°C and 21.7°C, and precipitation between 1200 and 2500 mm. There is a pronounced dry season between November and April with frequent occurrence of heavy fog. Rainfall during the wet season between May and October accounts for over 80 percent of total annual precipitation. Water deposition from fog accounts for over one‐third of total water input during the dry season in the forests, suggesting an important role that fog may play in pushing up the northern limit of tropical rain forest in Southeast Asia.     

Deforestation Trends of Tropical Dry Forests in Central Brazil

Tropical dry forests are the most threatened forest type in the world yet a paucity of research about them stymies development of appropriate conservation actions. The Paranã River Basin has the most significant dry forest formations in the Cerrado biome of central Brazil and is threatened by intense land conversion to pastures and agriculture. We examined changes in Paranã River Basin deforestation rates and fragmentation across three time intervals that covered 31 yr using Landsat imagery. Our results indicated a 66.3 percent decrease in forest extent between 1977 and 2008, with an annual rate of forest cover change of 3.5 percent. Landscape metrics further indicated severe forest loss and fragmentation, resulting in an increase in the number of fragments and reduction in patch sizes. Forest fragments in flatlands have virtually disappeared and the only significant forest remnants are mostly found over limestone outcrops in the eastern part of the basin. If current patterns persist, we project that these forests will likely disappear within 25 yr. These patterns may be reversed with creation of protected areas and involvement of local people to preserve small fragments that can be managed for restoration.