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Speciation is often portrayed as an "incomplete" or "incipient" process if two groups of organisms, technically distinguishable either by morphology or genetics, can exchange genes. The ultimate outcome of diversification, given this perspective, is complete reproductive isolation. But an increasing amount of evidence suggests that speciation is rarely complete and inter-fertility between different taxonomically accepted species is consistently maintained. In this issue of Molecular Ecology, Linan et al. (2021) provide results that bridge evolutionary processes from populations to phylogenies that indicate suites of closely related tree species in the Mascarene Islands actively exchange genes, evolving as a nested set of syngameons with a hierarchical pattern of interfertility. The deep insight into diversification provided by this study is particularly powerful because of the genomic scale of the data and the complete taxonomic sampling of an island clade evolving in situ. The prevalence of syngameon dynamics in a broad range of organisms indicates that we should adopt a fluid and comprehensive approach to defining evolutionary units for conservation and research. We should move beyond focusing on single endangered species in evolutionary and ecological isolation from other species but consider the entire network of potentially interfertile species and the potential for future adaptation and innovation, particularly in a human dominated world.

Synopsis The city and its urban biome provides an extreme laboratory for studying fundamental biological questions and developing best practices for sustaining biodiverse and well-functioning ecological communities within anthropogenic built environments. We propose by studying urban organisms, urban biotic communities, the urban biome, and the interactions between the urban biome and peri-urban built and natural environments, we can (1) discover new “rules of life” for the structure, function, interaction, and evolution of organisms; (2) use these discoveries to understand how novel emerging biotic communities affect and are affected by anthropogenic environmental changes in climate and other environmental factors; and (3) apply what we have learned to engage residents of the urban biome, and design cities that are more biologically diverse, are provided with more and better ecosystem services, and are more equitable and healthier places to live. The built environment of the urban biome is a place that reflects history, economics, technology, governance, culture, and values of the human residents; research on and applications of the rules of life in the urban biome can be used by all residents in making choices about the design of the cities where they live. Because inhabitants are directly invested in the environmental quality of their neighborhoods, research conducted in and about the urban environment provides a great opportunity to engage wide and diverse communities of people. Given the opportunity to engage a broad constituency—from basic researchers to teachers, civil engineers, landscape planners, and concerned citizens—studying the translation of the rules of life onto the urban environment will result in an integrative and cross-cutting set of questions and hypotheses, and will foster a dialog among citizens about the focus of urban biome research and its application toward making more equitable, healthy, livable, sustainable, and biodiverse cities.

Ficus (figs) and their agaonid wasp pollinators present an ecologically important mutualism that also provides a rich comparative system for studying functional co-diversification throughout its coevolutionary history (~75 million years). We obtained entire nuclear, mitochondrial, and chloroplast genomes for 15 species representing all major clades of Ficus. Multiple analyses of these genomic data suggest that hybridization events have occurred throughout Ficus evolutionary history. Furthermore, cophylogenetic reconciliation analyses detect significant incongruence among all nuclear, chloroplast, and mitochondrial-based phylogenies, none of which correspond with any published phylogenies of the associated pollinator wasps. These findings are most consistent with frequent host-switching by the pollinators, leading to fig hybridization, even between distantly related clades. Here, we suggest that these pollinator host-switches and fig hybridization events are a dominant feature of fig/wasp coevolutionary history, and by generating novel genomic combinations in the figs have likely contributed to the remarkable diversity exhibited by this mutualism., Figs and their wasp pollinators are a classic example of coevolution. By assembling and analysing genomes from across the Ficus clade, authors suggest that fig hybridization driven by pollinator host-switching in this obligate pollination system, is more common than previously thought.

The COVID-19 pandemic shut down undergraduate research programs across the United States. A group of 23 colleges, universities, and research institutes hosted remote undergraduate research programs in the life sciences during Summer 2020. Given the unprecedented offering of remote programs, we carried out a study to describe and evaluate them. Using structured templates, we documented how programs were designed and implemented, including who participated. Through focus groups and surveys, we identified programmatic strengths and shortcomings as well as recommendations for improvements from students' perspectives. Strengths included the quality of mentorship, opportunities for learning and professional development, and a feeling of connection with a larger community. Weaknesses included limited cohort building, challenges with insufficient structure, and issues with technology. Although all programs had one or more activities related to diversity, equity, inclusion, and justice, these topics were largely absent from student reports even though programs coincided with a peak in national consciousness about racial inequities and structural racism. Our results provide evidence for designing remote Research Experiences for Undergraduates (REUs) that are experienced favorably by students. Our results also indicate that remote REUs are sufficiently positive to further investigate their affordances and constraints, including the potential to scale up offerings, with minimal concern about disenfranchising students.

In-person undergraduate research experiences (UREs) promote students’ integration into careers in life science research. In 2020, the COVID-19 pandemic prompted institutions hosting summer URE programs to offer them remotely, raising questions about whether undergraduates who participate in remote research can experience scientific integration. To address this, we investigated indicators of scientific integration for students who participated in remote life science URE programs in summer 2020. We found that these students experienced gains in their scientific self-efficacy and scientific identity similar to results reported for in-person UREs. We also found that these students perceived high benefits and low costs of doing research at the outset of their programs, and their perceptions did not change despite the remote circumstances. Yet, their perceptions differed by program, indicating that programs differentially affected students’ perceptions of the costs of doing research. Finally, we observed that students with prior research experience made greater gains in self-efficacy and identity, as well as in their perceptions of the alignment of their values with those of the scientific community, in comparison to students with no prior research experience. This finding suggests that additional programming may be needed for undergraduates with no prior experience to benefit from remote research.

Trees can live many centuries with sustained fecundity and death is largely stochastic. We use a neutral stochastic model to examine the demographic patterns that emerge over time, across a range of population sizes and empirically observed mortality rates. A small proportion of trees (∼1% at 1.5% mortality) are life-history ‘lottery’ winners, achieving ages >10-20x median age. Maximum age increases with bigger populations and lower mortality rates. One quarter of trees (∼24%) achieve ages that are 3-4 times greater than median age. Three age classes (Mature, Old, and Ancient) contribute unique historical diversity across complex environmental cycles. Ancient trees are an emergent property of forests that requires many centuries to generate. They rradically change generation time variance and population fitness, bridging infrequent environmental cycles. These life-history ‘lottery’ winners are vital to future forest dynamics and invaluable data about environmental history and individual longevity. Old-growth forests contain trees that cannot be replaced through restoration or regeneration in the near future. They simply must be protected to preserve their unique diversity.

UAV-based photogrammetry can provide detailed, accurate, and consistent structural models of open-grown trees across different species and growth forms. Environmental and ambient light conditions impact the results. Our empirical knowledge of the complicated and highly dynamic three-dimensional structure of trees is limited. Drone-based photogrammetry offers a powerful and effective tool for capturing, analyzing, and monitoring adult trees, particularly individuals growing outside of the closed canopy forest (subsequently termed “open-grown”) in both natural and built environments. Here, we test the accuracy and consistency of high-resolution models of individual open-grown trees of three structurally distinct species. To validate model accuracy, we compared model estimates with direct measurements of branch diameter and internode length. We also examined the consistency of models of the same individual given different ambient light conditions by comparing corresponding measurements from two models of each tree. We use readily available equipment and software, so our protocol can be rapidly adopted by professional and citizen scientists alike. We found that the models captured diameter and interior internode length well (r2 = 0.87 and 0.98, respectively). Difference between measurements from different models of the same tree was less than 3 cm for diameters and interior internode lengths of most size classes. Thin distal branches were not captured well: measurements of terminal internodes in most size classes were underestimated by 50–60 cm. Models from overcast days were more accurate than models from sunny days (p = 0.0056), and a high-contrast background helps capture thin branches. Our approach constructs accurate and consistent three-dimensional models of individual open-grown trees that can provide the foundation for a wide range of physiological, behavioral, and growth studies.

The COVID-19 pandemic shut down undergraduate research programs across the U.S. Twenty-three sites offered remote undergraduate research programs in the life sciences during summer 2020. Given the unprecedented offering of remote research experiences, we carried out a study to describe and evaluate these programs. Using structured templates, we documented how programs were designed and implemented, including who participated. Through focus groups and surveys, we identified programmatic strengths and shortcomings as well as recommendations for improvements from the perspectives of participating students. Strengths included the quality of mentorship, opportunities for learning and professional development, and development of a sense of community. Weaknesses included limited cohort building, challenges with insufficient structure, and issues with technology. Although all programs had one or more activities related to diversity, equity, inclusion, and justice, these topics were largely absent from student reports even though programs coincided with a peak in national consciousness about racial inequities and structural racism. Our results provide evidence for designing remote REUs that are experienced favorably by students. Our results also indicate that remote REUs are sufficiently positive to further investigate their affordances and constraints, including the potential to scale up offerings, with minimal concern about disenfranchising students.

Premise Measuring plant productivity is critical to understanding complex community interactions. Many traditional methods for estimating productivity, such as direct measurements of biomass and cover, are resource intensive, and remote sensing techniques are emerging as viable alternatives. Methods We explore drone-based remote sensing tools to estimate productivity in a tallgrass prairie restoration experiment and evaluate their ability to predict direct measures of productivity. We apply these various productivity measures to trace the evolution of plant productivity and the traits underlying it. Results The correlation between remote sensing data and direct measurements of productivity varies depending on vegetation diversity, but the volume of vegetation estimated from drone-based photogrammetry is among the best predictors of biomass and cover regardless of community composition. The commonly used normalized difference vegetation index (NDVI) is a less accurate predictor of biomass and cover than other equally accessible vegetation indices. We found that the traits most strongly correlated with productivity have lower phylogenetic signal, reflecting the fact that high productivity is convergent across the phylogeny of prairie species. This history of trait convergence connects phylogenetic diversity to plant community assembly and succession. Discussion Our study demonstrates (1) the importance of considering phylogenetic diversity when setting management goals in a threatened North American grassland ecosystem and (2) the utility of remote sensing as a complement to ground measurements of grassland productivity for both applied and fundamental questions.

Dothideomycetes is the largest class of kingdom Fungi and comprises an incredible diversity of lifestyles, many of which have evolved multiple times. Plant pathogens represent a major ecological niche of the class Dothideomycetes and they are known to infect most major food crops and feedstocks for biomass and biofuel production. Studying the ecology and evolution of Dothideomycetes has significant implications for our fundamental understanding of fungal evolution, their adaptation to stress and host specificity, and practical implications with regard to the effects of climate change and on the food, feed, and livestock elements of the agro-economy. In this study, we present the first large-scale, whole-genome comparison of 101 Dothideomycetes introducing 55 newly sequenced species. The availability of whole-genome data produced a high-confidence phylogeny leading to reclassification of 25 organisms, provided a clearer picture of the relationships among the various families, and indicated that pathogenicity evolved multiple times within this class. We also identified gene family expansions and contractions across the Dothideomycetes phylogeny linked to ecological niches providing insights into genome evolution and adaptation across this group. Using machine-learning methods we classified fungi into lifestyle classes with >95 % accuracy and identified a small number of gene families that positively correlated with these distinctions. This can become a valuable tool for genome-based prediction of species lifestyle, especially for rarely seen and poorly studied species. This manuscript has been authored by an author at Lawrence Berkeley National Laboratory under Contract No. DE-AC02-05CH11231 with the U.S. Department of Energy. R. A. and I. V. G. were supported by the NSF grants DEB-1354625 and IOS-1456958. Sequencing of Dothideomycetes genomes were conducted as part of the 1000 Fungal Genomes Project supported by the JGI Community Sequencing Project #662.

Interspecific hybridization and genetic introgression are commonly observed in natural populations of many species, especially trees. Among oaks, gene flow between closely related species has been well documented. And yet, hybridization does not lead to a “melting pot”, i.e., the homogenization of phenotypic traits. Here, we explore how the combination of several common reproductive and genomic traits could create an avenue for interspecific gene flow that partially explains this apparent paradox. During meiosis, F1hybrids will produce approximately (½)n“reconstructed” parental gametes, where n equals the number of chromosomes. Crossing over would introduce a small amount of introgressive material. The resulting parental-type gametophytes would probably possess a similar fertilization advantage as conspecific pollen. The resulting “backcross” would actually be the genetic equivalent of a conspecific out-cross, with a small amount of heterospecific DNA captured through crossing over. Even with detailed genomic analysis, the resulting offspring would not appear to be a backcross. This avenue for rapid introgression between species through the F1hybrid will be viable for organisms that meet certain conditions: low base chromosome number, conserved genomic structure and size, production of billions of gametes/gametophytes during each reproductive event, and conspecific fertilization advantage.

Stone oaks, or Lithocarpus species of Fagaceae are ecologically important canopy trees in the tropical and subtropical forests over East Asia, and the fruits of which are important food sources for insects and vertebrates there. The great fruit morphological variation of this genus represents two fruit types, acorn and enclosed receptacle fruit types. However, the evolutionary mechanisms of differentiation into these two fruit types with contrasting morphology remain a puzzle. To reveal the morphogenetic properties of two fruit types, we observed tissue differentiation and development among 20 Lithocarpus species from fruit set to maturity. Unlike in fruits of Quercus, the endocarp differentiation in Lithocarpus fruits occurred later than exocarp and mesocarp. Cupules provided further protection of developing seeds, particularly of acorn-type fruits. Fruits of Lithocarpus and Quercus acorns share similar insect predators. At fruit set, both acorn and enclosed receptacle types were largely identical, with similar tissue morphology and the sequence of differentiation. The distinct difference between two fruit types at maturity came from varied rates and degrees of development between the pericarp and receptacle tissues. We found that heterochrony between two tissues could create substantially divergent ecological strategies for protection and dispersal of their seeds, which is essential for the evolution of two fruit types.

The eastern North American white oaks, a complex of approximately 16 potentially interbreeding species, have become a classic model for studying the genetic nature of species in a syngameon. Genetic work over the past two decades has demonstrated the reality of oak species, but gene flow between sympatric oaks raises the question of whether there are conserved regions of the genome that define oak species. Does gene flow homogenize the entire genome? Do the regions of the genome that distinguish a species in one part of its range differ from the regions that distinguish it in other parts of its range, where it grows in sympatry with different species? Or are there regions of the genome that are relatively conserved across species ranges? In this study, we revisit seven species of the eastern North American white oak syngameon using a set of 80 SNPs selected in a previous study because they show differences among, and consistency within, the species. We test the hypothesis that there exist segments of the genome that do not become homogenized by repeated introgression, but retain distinct alleles characteristic of each species. We undertake a rangewide sampling to investigate whether SNPs that appeared to be fixed based on a relatively small sample in our previous work are fixed or nearly fixed across the range of the species. Each of the seven species remains genetically distinct across its range, given our diagnostic set of markers, with relatively few individuals exhibiting admixture of multiple species. SNPs map back to all 12Quercuslinkage groups (chromosomes) and are separated from each other by an average of 7.47 million base pairs (± 8.74 million bp, s.d.), but are significantly clustered relative to a random null distribution, suggesting that our SNP toolkit reflects genome-wide patterns of divergence while potentially being concentrated in regions of the genome that reflect a higher-than-average history of among-species divergence. This application of a DNA toolkit designed for the simple problem of identifying species in the field has an important implication: the eastern North American white oak syngameon is composed of entities that most taxonomists would consider “good species,” and species in the syngameon retain their genetic cohesion because characteristic portions of the genome do not become homogenized despite a history of introgression.

In PNAS, Levi et al. (1) argue that near-neighbor exclusion zones of conspecifics suffice to maintain tropical biodiversity. Their argument, while supported by computer simulations, does not consider ( i ) the influence that demographic processes may have on species survival or ( ii ) the phylogenetic distribution of diversity found in tropical systems. We agree that the fine-scale spatial effects of enemies described by Levi et al. may play a role in hyperdiverse systems, but we do not believe that this effect is sufficient for the long-term maintenance of diversity. As first detailed experimentally by Allee and Bowen (2), populations … [↵][1]1To whom correspondence should be addressed: Email: ccannon{at}mortonarb.org. [1]: #xref-corresp-1-1

article The evolutionary diversifications of many taxonomic groups, especially those with limited dispersal ability, are often driven by key geological events, such as tectonic drift, continental collisions, and uplifts of mountains. Here, we use full range geographic sampling to create a dated molecular phylogeny for two genera of alpine gingers (Cautleya and Roscoea) in the Pan-Himalaya, and test the correlations between evolutionary diversifica- tion of this group and major geological events in the studied region. Our results revealed that the origination of their common ancestor and evolutionary split between the two genera occurred during the middle Eocene and the late Eocene to the early Oligocene, corresponding well to the proposed two early uplifts of the Himalayan- Tibetan Plateau.Roscoeaspecies,thehighest elevation gingers known, were then divided intodistinct Himalayan and Indochinese clades, simultaneous with the rapid extrusion of Indochina and accompanied by the third Himalayan uplift around the Oligocene/Miocene boundary. This study highlights the importance of evolutionary diversification of plants as an independent line of evidence to reflect tectonic events in the Himalayan- Indochinese region. © 2015 The Authors. Published by Elsevier B.V. on behalf of International Association for Gondwana Research. This is an open access article under the CC BY-NC-ND license

Wilf et al . (Research Articles, 7 June 2019, eaaw5139) claim that Castanopsis evolved in the Southern Hemisphere from where it spread to its modern distribution in Southeast Asia. However, extensive paleobotanical records of Antarctica and Australia lack evidence of any Fagaceae, and molecular patterns indicate shared biogeographic histories of Castanopsis , Castanea , Lithocarpus , and Quercus subgenus Cerris , making the southern route unlikely.

International audience; The eastern North American white oaks, a complex of approximately 16 potentially interbreeding species, have become a classic model for studying the genetic nature of species in a syngameon. Genetic work over the past two decades has demonstrated the reality of oak species, but gene flow between sympatric oaks raises the question of whether there are conserved regions of the genome that define oak species. Does gene flow homogenize the entire genome? Do the regions of the genome that distinguish a species in one part of its range differ from the regions that distinguish it in other parts of its range, where it grows in sympatry with different species? Or are there regions of the genome that are relatively conserved across species ranges? In this study, we revisit seven species of the eastern North American white oak syngameon using a set of 80 single-nucleotide polymorphisms (SNPs) selected in a previous study because they show differences among, and consistency within, the species. We test the hypothesis that there exist segments of the genome that do not become homogenized by repeated introgression, but retain distinct alleles characteristic of each species. We undertake a range-wide sampling to investigate whether SNPs that appeared to be fixed based on a relatively small sample in our previous work are fixed or nearly fixed across the range of the species. Each of the seven species remains genetically distinct across its range, given our diagnostic set of markers, with relatively few individuals exhibiting admixture of multiple species. SNPs map back to all 12 Quercus linkage groups (chromosomes) and are separated from each other by an average of 7.47 million bp ((+) 8.74 million bp, SD), but are significantly clustered relative to a random null distribution, suggesting that our SNP toolkit reflects genome-wide patterns of divergence while potentially being concentrated in regions of the genome that reflect a higher-than-average history of among-species divergence. This application of a DNA toolkit designed for the simple problem of identifying species in the field has two important implications. First, the eastern North American white oak syngameon is composed of entities that most taxonomists would consider "good species." Second, and more fundamentally, species in the syngameon are genetically coherent because characteristic portions of the genome remain divergent despite a history of introgression. Understanding the conditions under which some loci diverge while others introgress is key to understanding the origins and maintenance of global tree diversity.

Two fruit types can be distinguished among stone oaks (Lithocarpus) species: the ‘acorn’ (AC) and the ‘enclosed receptacle’ (ER) types. Our morphometric analysis of 595 nuts from 98 species (one third of all Lithocarpus spp.) found substantial transition in mechanical protection of the seed between two woody fruit tissues (exocarp and receptacle) of two fruit types. AC fruits were smaller in seed and fruit size and the thin brittle exocarp largely enclosed the seed, whereas ER fruits were larger and the seed was mostly enclosed by thick woody receptacle tissue. The differences in these two tissues were considerably greater between compared to within fruit type and species. Geospatial distribution showed that seed size of all examined species increased with elevation and decreased with latitude, the physical defense increased with both elevation and latitude, and ER-fruit species were more common at higher elevation. The two fruit types represent distinct suites of associated traits that respond differently to the various biotic and abiotic factors associated with geographic variation, profoundly impacting the evolution of the two fruit types. The co-occurrence of two fruit types in the same forest could be a consequence of distinct fruit and animal interactions.

In the megadiverse forests of Southeast Asia, hundreds of timber species are economically important but the population genetics of only a few taxa are known. Cross-specific amplification of microsatellite loci among closely related taxa could enhance our ability to study and manage previously unstudied species. We successfully utilized STMS markers in Shorea platyclados, originally developed for Shorea curtisii. The six primer pairs we tried successfully produced PCR products of expected sizes. The number of alleles observed ranged from 10 to 14 and an average of 12 alleles were detected per locus. A high expected and observed heterozygosity was observed and it ranges from 0.718 to 0.827 among all populations across all six loci tested. Microsatellite DNA markers are highly polymorphic, co-dominant, reproducible, and amenable to high throughput genetic analyses. Overall, the cross-specific amplification of microsatellite loci appears to be complicated by numerous factors. While the approach may be effective for local management and conservation of poorly known species, the results must be carefully interpreted.

International audience

Two fruit types can be distinguished among stone oaks (Lithocarpus) species: the 'acorn' (AC) and the 'enclosed receptacle' (ER) types. Our morphometric analysis of 595 nuts from 98 species (one third of all Lithocarpus spp.) found substantial transition in mechanical protection of the seed between two woody fruit tissues (exocarp and receptacle) of two fruit types. AC fruits were smaller in seed and fruit size and the thin brittle exocarp largely enclosed the seed, whereas ER fruits were larger and the seed was mostly enclosed by thick woody receptacle tissue. The differences in these two tissues were considerably greater between compared to within fruit type and species. Geospatial distribution showed that seed size of all examined species increased with elevation and decreased with latitude, the physical defense increased with both elevation and latitude, and ER-fruit species were more common at higher elevation. The two fruit types represent distinct suites of associated traits that respond differently to the various biotic and abiotic factors associated with geographic variation, profoundly impacting the evolution of the two fruit types. The co-occurrence of two fruit types in the same forest could be a consequence of distinct fruit and animal interactions.

Interspecific hybridization and genetic introgression are commonly observed in natural populations of many species, especially trees. Among oaks, gene flow between closely related species has been well documented. And yet, hybridization does not lead to a "melting pot", i.e., the homogenization of phenotypic traits. Here, we explore how the combination of several common reproductive and genomic traits could create an avenue for interspecific gene flow that partially explains this apparent paradox. During meiosis, F

One of the remarkable aspects of the tremendous biodiversity found in tropical forests is the wide range of evolutionary strategies that have produced this diversity, indicating many paths to diversification. We compare two diverse groups of trees with profoundly different biologies to discover whether these differences are reflected in their genomes. Ficus (Moraceae), with its complex co-evolutionary relationship with obligate pollinating wasps, produces copious tiny seeds that are widely dispersed. Lithocarpus (Fagaceae), with generalized insect pollination, produces large seeds that are poorly dispersed. We hypothesize that these different reproductive biologies and life history strategies should have a profound impact on the basic properties of genomic divergence within each genus. Using shallow whole genome sequencing for six species of Ficus, seven species of Lithocarpus, and three outgroups, we examined overall genomic diversity, how it is shared among the species within each genus, and the fraction of this shared diversity that agrees with the major phylogenetic pattern. A substantially larger fraction of the genome is shared among species of Lithocarpus, a considerable amount of this shared diversity was incongruent with the general background history of the genomes, and each fig species possessed a substantially larger fraction of unique diversity than Lithocarpus.

Tropical Southeast (SE) Asia harbors extraordinary species richness and in its entirety comprises four of the Earth's 34 biodiversity hotspots. Here, we examine the assembly of the SE Asian biota through time and space. We conduct meta-analyses of geological, climatic, and biological (including 61 phylogenetic) data sets to test which areas have been the sources of long-term biological diversity in SE Asia, particularly in the pre-Miocene, Miocene, and Plio-Pleistocene, and whether the respective biota have been dominated by in situ diversification, immigration and/or emigration, or equilibrium dynamics. We identify Borneo and Indochina, in particular, as major "evolutionary hotspots" for a diverse range of fauna and flora. Although most of the region's biodiversity is a result of both the accumulation of immigrants and in situ diversification, within-area diversification and subsequent emigration have been the predominant signals characterizing Indochina and Borneo's biota since at least the early Miocene. In contrast, colonization events are comparatively rare from younger volcanically active emergent islands such as Java, which show increased levels of immigration events. Few dispersal events were observed across the major biogeographic barrier of Wallace's Line. Accelerated efforts to conserve Borneo's flora and fauna in particular, currently housing the highest levels of SE Asian plant and mammal species richness, are critically required.

Given predicted rapid climate change, an understanding of how environmental factors affect genetic diversity in natural populations is important. Future selection pressures are inherently unpredictable, so forest management policies should maintain both overall diversity and identify genetic markers associated with the environmental factors expected to change most rapidly, like temperature and rainfall. In this study, we genotyped 648 individuals in 28 populations of Castanopsis fargesii (Fagaceae) using 32 expressed sequence tag (EST)-derived microsatellite markers. After removing six loci that departed from Hardy–Weinberg equilibrium, we measured genetic variation, population structure and identified candidate loci putatively under selection by temperature and precipitation. We found that C. fargesii populations possessed high genetic diversity and moderate differentiation among them, indicating predominant outcrossing and few restrictions to gene flow. These patterns reduce the possible impact of stochastic effects or the influence of genetic isolation. Clear footprints of divergent selection at four loci were discovered. Frequencies of five alleles at these loci were strongly correlated with environmental factors, particularly extremes in precipitation. These alleles varied from being near fixation at one end of the gradient to being completely absent at the other. Our study species is an important forest tree in the subtropical regions of China and could have a major role in future management and reforestation plans. Our results demonstrate that the gene flow is widespread and abundant in natural populations, maintaining high diversity, while diversifying selection is acting on specific genomic regions.

Xishuangbanna has been largely transformed from biodiverse natural forests and mixed-use farms into monoculture rubber plantations in just twenty years. This conversion has expanded into forests previously protected by the community and onto marginal sites at high-elevation. Market-based ecosystem payments, especially carbon financing, are potential tools to prevent further forest loss in China. Here, we compare rubber net present value (NPV), carbon sequestration, and seed-plant species diversity for Xishuangbanna given three land-use scenarios: Business-As-Usual (BAU), Economic Oriented Scenario (EOS) and Conservation Oriented Scenario (COS) using a previously published spatial map of rubber profitability. The EOS achieved the greatest rubber profit but caused substantial reductions in natural forest area, biodiversity and carbon stocks. The EOS also requires substantial immigration of workers into a remote and ecologically important region with little social infrastructure for basic security, food security, health-care and education, causing frequently ignored costs. As expected, the COS will maintain the highest levels of natural forest area, sequester 57% more carbon, and 71% more biodiversity than EOS. Given the conservation value of the carbon stores and rich biodiversity residing in Xishuangbanna's natural forests, reducing rubber NPV only marginally would probably cost less than attempting to recover these resources. We recommend that rubber plantations be limited to established, productive lowland areas whilst protecting intact high-elevation forest and reforesting low-productivity plantations. These actions will enhance carbon sequestration and biodiversity conservation. Management policies focused solely on profits, like the EOS scenario, will fail to sustain the entire range of natural resources and ecosystem services. The prices in the carbon market would have to be considerably larger than they are currently to compete with the profitability of rubber.

Polyploidization is a major source of diversification among plants, particularly during cladogenesis, but most evidence involves herbaceous temperate species. The prevalence of polyploidy among woody taxa is largely unknown, especially among tropical groups. In this study, we examined genome size variation globally and at several taxonomic levels within the Fagaceae. This family has diversified in the northern temperate zone (Quercus) and at least twice in the Asian tropics (Lithocarpus and Castanopsis), allowing us to examine genomic size evolution across a broad latitudinal range. We compared nuclear DNA contents from 78 species in six genera, including new measurements for 171 individuals from 47 Chinese species using standard flow cytometry methods. No evidence suggests that polyploidization or whole genome duplication has occurred in the family. Genome size varied among genera, but limited variation was present in each genus and species. In general, tropical species had larger genomes than temperate species, but the ancestral state cannot be determined given current evidence. Partial duplication does seem to occur among species as within genus variation was larger than within species variation. A review of the literature suggests that genome size and even chromosome structure is highly conserved among woody plants and trees. We propose that ploidy level and genome size are conserved among trees because they participate in diverse syngameons. This behavior would provide similar benefits to polyploidization but avoid exclusion from the syngameon. This conservatism in genome size and structure should enhance ongoing whole genome studies.

In Xishuangbanna, southwest China, rubber plantations are lucrative and have expanded dramatically in the past two decades, leaving little natural forest. The local government hopes to use eco-compensation mechanisms to promote forest restoration without forcing smallholders to forego profits. Based on a landscape productivity model for two management systems and given a range of prices, we assessed the feasibility of this concept by constructing a spatially explicit map of net present value (NPV) of rubber plantations. We found that roughly 7% of existing plantations generally had negative NPV, therefore opportunity costs would be negligible. But to restore forest in buffer zones along roads and rivers as recommended by the state government, more substantial opportunity costs were observed because these areas have high NPV values. Additionally, plantations situated above 900 m elevation or on slopes > 24° were not profitable and a conversion ban should be enforced. Opportunity costs and plant species biodiversity are positively correlated, so any policy to protect species-rich areas must take this relationship into consideration. Eco-compensation schemes can feasibly promote forest restoration on marginal lands and spatially-explicit mapping of NPV can provide monetary targets to adequately recover opportunity costs for smallholders.

Aim A wide range of forests distributed across steep environmental gradients are found in Yunnan, southwest China. Climate change could profoundly change these forests by affecting species ranges. We produce predictions about species suitable habitat shifts and use these to (1) evaluate species range size change, loss and turn-over under no- and full-dispersal and nine climate change scenarios and (2) identify environmental variables responsible for current species richness and future local species losses. Location Yunnan Province, Southwest China. Methods Using MaxEnt, we modelled current distributions of 2319 woody plant species, corrected for collecting bias and found that 1996 had significant spatial association with environmental factors. Using three General Circulation Models (GCMs: CGCM, CSIRO and HADCM3) for the years 2070–2099 (2080s), based on three emission scenarios for each GCM (A1b, A2a and B2a), we predicted the future geographic position of suitable habitat for each species. Results Although most species were predicted to persist within Yunnan, with a maximum extinction rate of c. 6% under the most extreme climate change scenario, up to 1400 species (of the 1996 tested) are expected to lose more than 30% of their current range under the most extreme climate change scenario. Assuming no- or unlimited dispersal minimally affected these outcomes. Species losses were associated with increasing temperature variability and declining precipitation during the dry season. Main conclusions To conserve Yunnan’s woody flora, management efforts should focus on providing elevational migration routes at local scales, with priority for those areas located within previously identified conservation hotspots. As almost all species show range contractions, storage of genetic diversity in seed banks and botanical gardens would be sensible. A change in Yunnan’s conservation policy will be needed to counter the predicted negative impacts of climate change on its flora.

To protect biodiversity and improve environmental conditions, China has invested billions of dollars in reforestation and payments for ecosystem service programs. Here, we examine the Sloping Land Conversion Program, the largest such program in the world and found that after 13 years of implementation at our study site, it has had negative impacts on natural tropical forests. GIS and remote sensing techniques revealed that both natural forests and natural shrub and grasslands were replaced by non-native monocultural plantations on Hainan Island, China, a key tropical biodiversity hotspot. Under current Chinese policy, these plantations are classified simply as "forests", with the assumption that they are equivalent to natural forests. This lack of a distinction in forest quality has led to substantial deforestation and plantation expansion, including encroachment into protected areas on Hainan. Additional social and economic drivers of these changes were identified by examining the participants in this program and their actions. Without a new ecologically based definition of forests and new goals for reforestation, such programs designed to improve ecosystem services, and forest quality may actually threaten remaining natural forests and other vegetation types in Hainan and in other areas of mainland China.

Legumes (family Fabaceae) are globally important crops due to their nitrogen fixing ability. Papilionoideae, the best-studied subfamily, have undergone a Whole Genome Duplication (WGD) around 59 million years ago. Recent study found varying WGD ages in subfamilies Mimosoideae and Caesalpinioideae and proposed multiple occurrences of WGD across the family based on gene duplication patterns. Despite that, the genome evolution of legume ancestor into modern legumes after the WGD is not well-understood. We aimed to study genome evolution at the subfamily level using gene-based linkage maps for Acacia auriculiformis and A. mangium (Mimosoideae) and we discovered evidence for a WGD event in Acacia. In additional to synonymous substitution rate (Ks) analysis, we used ancestral karyotype prediction to further corroborate this WGD and elucidate underlying mechanisms of karyotype evolution in Fabaceae. Using publicly available transcriptome resources from 25 species across the family Fabaceae and 2 species from order Fabales, we found that the variations in WGD ages highly correlate (R=0.8606, p-valueVitis vinifera as an outgroup. If the variation of Ks is corrected, the age of WGDs of the family Fabaceae should be the same and therefore, parsimony would favour a single WGD near the base of Fabaceae over multiple independent WGDs across Fabaceae. In addition, we demonstrated that genome comparison of Papilionoideae with other subfamily provide important insights in understanding genome evolution in legumes.

Many animals scatter-hoard seeds to ensure an even supply of food throughout the year and this behavior requires similar foraging decisions. Seed-traits have been shown to affect the final foraging decision but little is known about the decision process itself. Here, we first defined four sequential steps comprising the decision process of scatter-hoarding rodents: 1) upon encountering a seed, should it be ignored or manipulated; 2) if manipulated, should it be eaten in situ or removed elsewhere; 3) upon removal, how far away should it be carried; and finally 4) whether to eat or cache the removed seed. Using experimental seeds with controlled differences in size, tannin and nutrient content, we evaluated how different traits influence each step in this decision process. We found that different traits had distinct effects on each step. Seed size affected all four steps, while nutrient and tannin content primarily affected the first and third steps. By dissecting foraging behavior in relation to experimentally controlled seed-traits, we have created an effective framework within which to understand the unique relationship between scatter-hoarding rodents that both predate and disperse plant seeds.

Part of the Himalayan biodiversity hotspot, Yunnan province in China is a highly diverse terrestrial region, particularly in the wide range of natural forest types. These forests are under considerable conversion pressure as land use intensifies with expanding human population and economic development. Conservation strategies based on the geographic patterns of botanical species richness, including the identification of meaningful floristic regions and priority areas for conservation, could improve the effectiveness of forest policy and management. These strategies should also include current threats of loss due to forest conversion to address the more urgent challenges for sustainable development. Here, we produce distribution models at similar to 10 km(2) resolution for 2319 plant species, using geo-referenced herbarium collections, corrected for spatial bias using a null model, and detailed environmental variables. Based on 1996 species with significant non-random habitat preferences, we identify four important aspects of plant species distribution in Yunnan: (1) species diversity hotspots; (2) seven major floristic regions, using a cluster analysis of species presence/absence; (3) priority areas for conservation based on the concept of the 'irreplaceability' value of planning units and (4) the percentage remaining natural forest among the species rich and conservation priority areas, to assess the level of endangerment. Our maps provide clear priorities for the development of a sustainable and feasible biodiversity conservation strategy for Yunnan. (C) 2012 Elsevier Ltd. All rights reserved.

We describe a new species of Lithocarpus from the central Kelabit Highlands of Sarawak, Malaysia with a distribution extending north to Mt. Kinabalu, Sabah. This species was included in a previous morphometric and phylogenetic study of the section Synaedrys, mistakenly identified as L. rotundatus. Several individuals were observed on the western slopes of Mt. Kinabalu between the elevation of 1200–1500 meters. The species has a distinctive cupule, which usually completely encloses the nut and is very dark in color, almost black with a brittle texture similar to charcoal. The fruit is semi-hemispheric in shape and the bracts on the cupule are entirely fused, relatively sparse, stiff, brittle, and prominent.

Summary China’s collective forest tenure reform will have a profound impact on the livelihoods of rural people. For the equitable implementation of reform, rural smallholders need sufficient knowledge and understanding of the opportunities and limitations offered by reform. Here, we examine rural smallholder’s awareness and attitude towards the reform, across the socio-economic range, in three villages of Zhang Guying Township, Hunan province. Income level and educational background played a consistent role in knowledge and understanding of the reform, as people with low income and no formal education were more likely to be unaware and have no clear understanding of the reform. Additionally, low -income rural smallholders were more likely to convert forest to cash crops, undercutting the central government’s stated objectives for the forest reform to improve forest condition. Given our results, the government needs to ensure equitable distribution of information, specifically targeting low- income villagers without formal education. The strong disparity in knowledge and understanding between wealthy and poor creates a situation where the wealthy effectively benefit from the reform, while the poor miss its opportunity. This inequality has great potential for generating future unrest and conflict and for damaging forest condition due to unsustainable or uninformed practices.

The recent mass fruiting of forest trees in Borneo is an urgent wakeup call: existing policy instruments, financial mechanisms, and forestry infrastructure are inadequate to take full advantage of these infrequent opportunities for forest restoration and conservation. Tropical forest restoration can provide substantial benefits for biodiversity conservation, climate change mitigation, and poverty alleviation. Yet the unpredictability of the synchronized flowering and consequent mass fruiting of many forest trees in Borneo presents a distinctive set of challenges for forest restoration. Significant financing and a considerable coordinated effort are required to prepare for future mass fruiting events if we are to capitalize on opportunities for ecological restoration. The continued high rate of forest clearance in this region and the rarity of mass fruiting events suggest that there may be few remaining opportunities to prevent widespread species extinctions. In this article we propose a facilitatory policy framework for forest restoration in Borneo to stimulate action in advance of the next mass fruiting of forest trees.

Large parts of the everwet tropics have been burned, leaving many unburned–burned forest edges. Here we studied a Bornean forest edge to determine: (1) how unburned and burned forest differ in vegetation structure, diversity, composition and plant functional traits 7 yr after fire, and (2) if these variables showed significant edge effects. Environmental and inventory data from 120 plots (0.01 ha each), covering both sides of a � 1.3 km forest boundary were sampled. Differences in vegetation structure, diversity, composition and plant functional traits were analyzed in relation to disturbance type (Mann–Whitney tests) and edge distance (partial correlation analysis that controlled for confounding effects of elevation, slope and fire intensity). Seven years after fire, burned forest differed significantly from unburned forest in most measured variables while few significant edge effects were detected, i.e., there existed a sharp delimitation between the two forest types. The regeneration of the burned forest depended almost entirely on in situ recruitment with little input of late successional species from the neighboring old growth forest. On the other hand, old growth forest showed few signs of edge degradation. A possible explanation for these results might be related to the absence of a mast fruiting event during these first 7 yr of forest recovery, resulting in low levels of late successional species seed input into the burned forest, combined with the quick development of a closed canopy in the burned forest by early successional species that shielded the unburned forest from adverse edge effects.

Most comparative genomic analyses of short-read sequence (SRS) data rely upon the prior assembly of a reference sequence. Here, we present an assembly free analysis of SRS data that discovers sequence variants among focal genomes by tabulating the presence and frequency of 'complex' fragments in the data. Using data from nine tree species, we compare genomic diversity from populations to families. As a control, we simulated SRS data for three known plant genomes. The results provide insight into the quality and distributional bias of the sequencing reaction. Three main types of informative complexmers were identified, each possessing unique statistical properties. Type I complexmers are unique to a genome but suffer from a high false positive rate, being highly dependent on read coverage and distribution. Type II complexmers are shared between two genomes and can highlight potential copy-number differences. Type III complexmers are exclusive to a subset of genomes and can be useful for associating genetic differences with phenotypic or geographic variation. At the population level in an endangered timber species, numerous markers were identified that could potentially determine geographic origin of individuals and regulate international trade. We observed that the genomic data for the four fig species were more divergent than for stone oak species, possibly due to their complex pollination syndrome and high rates of gene flow. Our approach greatly enhances the application of SRS technology to the study of non-model organisms and directly identifies the most informative genetic elements for more detailed study and assembly.