Regional influences on community structure across the tropical-temperate divide

The formation of the Indo-Pacific montane avifauna

The processes generating the earth's montane biodiversity remain a matter of debate. Two contrasting hypotheses have been advanced to explain how montane populations form: via direct colonization from other mountains, or, alternatively, via upslope range shifts from adjacent lowland areas. We seek to reconcile these apparently conflicting hypotheses by asking whether a species' ancestral geographic origin determines its mode of mountain colonization. Island-dwelling passerine birds at the faunal crossroads between Eurasia and Australo-Papua provide an ideal study system. We recover the phylogenetic relationships of the region's montane species and reconstruct their ancestral geographic ranges, elevational ranges, and migratory behavior. We also perform genomic population studies of three super-dispersive montane species/clades with broad island distributions. Eurasian-origin species populated archipelagos via direct colonization between mountains. This mode of colonization appears related to ancestral adaptations to cold and seasonal climates, specifically short-distance migration. Australo-Papuan-origin mountain populations, by contrast, evolved from lowland ancestors, and highland distribution mostly precludes their further colonization of island mountains. Our study explains much of the distributional variation within a complex biological system, and provides a synthesis of two seemingly discordant hypotheses for montane community formation.

Global determinants of insect mitochondrial genetic diversity

Understanding global patterns of genetic diversity is essential for describing, monitoring, and preserving life on Earth. To date, efforts to map macrogenetic patterns have been restricted to vertebrates, which comprise only a small fraction of Earth's biodiversity. Here, we construct a global map of predicted insect mitochondrial genetic diversity from cytochrome c oxidase subunit 1 sequences, derived from open data. We calculate the mitochondrial genetic diversity mean and genetic diversity evenness of insect assemblages across the globe, identify their environmental correlates, and make predictions of mitochondrial genetic diversity levels in unsampled areas based on environmental data. Using a large single-locus genetic dataset of over 2 million globally distributed and georeferenced mtDNA sequences, we find that mitochondrial genetic diversity evenness follows a quadratic latitudinal gradient peaking in the subtropics. Both mitochondrial genetic diversity mean and evenness positively correlate with seasonally hot temperatures, as well as climate stability since the last glacial maximum. Our models explain 27.9% and 24.0% of the observed variation in mitochondrial genetic diversity mean and evenness in insects, respectively, making an important step towards understanding global biodiversity patterns in the most diverse animal taxon.

Phylogenetic Partitioning of Gansu Flora: Unveiling the Core Transitional Zone of Chinese Flora

Floristic regions, conventionally established using species distribution patterns, have often overlooked the phylogenetic relationships among taxa. However, how phylogenetic relationships influence the historical interconnections within and among biogeographic regions remains inadequately understood. In this research, we compiled distribution data for seed plants in Gansu, a region of significant biogeographic diversity located in northwestern China.We proposed a novel framework for floristic regions within Gansu, integrating distribution data and phylogenetic relationships of genera-level native seed plants, aiming to explore the relationship between phylogenetic relatedness, taxonomic composition, and regional phylogenetic delineation. We found that (1) phylogenetic relatedness was strongly correlated with the taxonomic composition among floras in Gansu. (2) The southeastern Gansu region showed the lowest level of spatial turnover in both phylogenetic relationships and the taxonomic composition of floristic assemblages across the Gansu region. (3) Null model analyses indicated nonrandom phylogenetic structure across the region, where most areas showed higher phylogenetic turnover than expected given the underlying taxonomic composition between sites. (4) Our results demonstrated a consistent pattern across various regionalization schemes and highlighted the preference for employing the phylogenetic dissimilarity approach in biogeographical regionalization investigations. (5) Employing the phylogenetic dissimilarity approach, we identified nine distinct floristic regions in Gansu that are categorized into two broader geographical units, namely the northwest and southeast. (6) Based on the phylogenetic graphic regions of China across this area.

Predicting potential distribution and range dynamics of Aquilegia fragrans under climate change: insights from ensemble species distribution modelling

Climate change is one of the primary causes of species redistribution and biodiversity loss, especially for threatened and endemic important plant species. Therefore, it is vital to comprehend "how" and "where" priority medicinal and aromatic plants (MAPs) might be effectively used to address conservation-related issues under rapid climate change. In the present study, an ensemble modelling approach was used to investigate the present and future distribution patterns of Aquilegia fragrans Benth. under climate change in the entire spectrum of Himalayan biodiversity hotspot. The results of the current study revealed that, under current climatic conditions, the northwest states of India (Jammu and Kashmir, Himachal Pradesh and the northern part of Uttarakhand), the eastern and southern parts of Pakistan Himalaya have highly suitable climatic conditions for the growth of A. fragrans. The ensemble model exhibited high forecast accuracy, with temperature seasonality and precipitation seasonality as the main climatic variables responsible for the distribution of the A. fragrans in the biodiversity hotspot. Furthermore, the study predicted that future climate change scenarios will diminish habitat suitability for the species by -46.9% under RCP4.5 2050 and -55.0% under RCP4.5 2070. Likewise, under RCP8.5, the habitat suitability will decrease by -51.7% in 2050 and -94.3% in 2070. The current study also revealed that the western Himalayan area will show the most habitat loss. Some currently unsuitable regions, such as the northern Himalayan regions of Pakistan, will become more suitable under climate change scenarios. Hopefully, the current approach may provide a robust technique and showcases a model with learnings for predicting cultivation hotspots and developing scientifically sound conservation plans for this endangered medicinal plant in the Himalayan biodiversity hotspot.

What constitutes a community? A co-occurrence exploration of the Costa Rican avifauna

The concept of a "community" as a form of organization for natural biological systems is both widespread and widely accepted within the ecological and biological sciences. Communities have been defined as groups of organisms that interact in ways that denote interdependence between individuals and taxa (e.g. as defined by "food webs") but they have also been defined as groups of co-occurring organisms that are assumed to interact by virtue of their shared spatiotemporal existence. The latter definition has been debated and challenged in the literature, with mounting evidence for co-occurrence being more indicative of coincident ecological niches in space and time rather than being evidence of ecological interaction or dependency. Using a dataset of 460 Costa Rican bird species divided into breeding and non-breeding season datasets, we empirically demonstrate the ways in which co-occurrence can create illusory communities based on similar occupied ecological niches and similar patterns of co-occurrence at different times of year. We discuss the importance of discerning coincidental co-occurrence from true ecological interactions that would manifest a true community, and further address the importance of differentiating communities of co-occurrence from communities of demonstrable ecological interaction. While co-occurrence is a necessary aspect of interspecific interactions, we discuss and demonstrate here that such co-occurrence does not make a community, nor should explicit patterns of co-occurrence be seen as evidence for evolutionarily important ecological interactions.

Spatial phylogenetics of Japanese ferns: Patterns, processes, and implications for conservation

PREMISE

Biodiversity is often only measured with species richness; however, this metric ignores evolutionary history and is not sufficient for making conservation decisions. Here, we characterize multiple facets and drivers of biodiversity to understand how these relate to bioregions and conservation status in the ferns of Japan.

METHODS

We compiled a community data set of 1239 grid cells (20 × 20 km each) including 672 taxa based on >300,000 specimen records. We combined the community data with a phylogeny and functional traits to analyze taxonomic, phylogenetic, and functional diversity and modeled biodiversity metrics in response to environmental factors and reproductive mode. Hierarchical clustering was used to delimit bioregions. Conservation status and threats were assessed by comparing the overlap of significantly diverse grid cells with conservation zones and range maps of native Japanese deer.

RESULTS

Taxonomic richness was highest at mid-latitudes. Phylogenetic and functional diversity and phylogenetic endemism were highest in small southern islands. Relative phylogenetic and functional diversity were high at high and low latitudes, and low at mid-latitudes. Grid cells were grouped into three (phylogenetic) or four (taxonomic) major bioregions. Temperature and apomixis were identified as drivers of biodiversity patterns. Conservation status was generally high for grid cells with significantly high biodiversity, but the threat due to herbivory by deer was greater for taxonomic richness than other metrics.

CONCLUSIONS

Our integrative approach reveals previously undetected patterns and drivers of biodiversity in the ferns of Japan. Future conservation efforts should recognize that threats can vary by biodiversity metric and consider multiple metrics when establishing conservation priorities.

Grade of Membership models reveal geographical and environmental correlates of floristic structure in a temperate biodiversity hotspot

Identifying the contours and correlates of species turnover is central to understanding the nature of biogeographical regions. The Hengduan Mountains region of south-central China (HMR) is well known for its high diversity of plants, but its boundaries and internal floristic structure are poorly understood, especially in relation to geographical and environmental factors. With data on occurrences and elevational ranges of seed plants across the HMR and adjacent areas of the greater Qinghai-Tibet Plateau, we identified motifs (distinct species assemblages) by Grade of Membership models, and characterized relative contributions of geography, elevation, and climate to their spatial patterns. Motifs segregate primarily by latitude, elevation, and correlated environmental variables, most sharply across the tropical-temperate divide. Secondarily, they segregate by longitude and geographical features, and reveal a novel divide across the Jinsha River. A core set of motifs corresponds to previous delineations of the HMR. The HMR biodiversity hotspot is more a mosaic of floristic elements than a cohesive entity. Grade of Membership models effectively reveal the geographical contours of biotic structure, and are a valuable new tool for biogeographical analysis.

Southeast Asia as One of World’s Primary Sources of Biotic Recolonization Following Anthropocene Extinctions

The plight of Southeast Asia’s animals, plants and ecosystems in the face of unsustainable exploitation and habitat destruction has been illustrated in several recent studies, despite often falling outside the global discourse on global conservation priorities. Here, we collate biogeographic and phylogenetic information to argue that this beleaguered region is one of world’s primary macrorefugia, and possibly its best chance of regaining its natural biodiversity distribution patterns after the current Anthropocene upheaval. The region uniquely combines top diversity values in (a) ancient lineage diversity and (b) cosmopolitan lineage diversity, suggesting that it has acted in the past as a biodiversity museum and source of global colonization. This is at least partly due to the interplay between latitudinal diversity gradients and continental connectivity patterns. However, the peak values in South China/North Indochina for cosmopolitan tetrapods and their sister lineages suggest that a key feature is also the availability of diverse climatic conditions. In particular, the north-south orientation of the mountain ranges here has allowed for rapid recolonization within the region following past climatic changes, resulting in high survival values and overall exceptional relict lineage diversity. From this starting point, global colonization occurred on multiple occasions. It is hoped that, with urgent action, the region can once again fulfill this function.

Dispersal syndromes drive the formation of biogeographical regions, illustrated by the case of Wallace's Line

AIM

Biogeographical regions (realms) reflect patterns of co-distributed species (biotas) across space. Their boundaries are set by dispersal barriers and difficulties of establishment in new locations. We extend new methods to assess these two contributions by quantifying the degree to which realms intergrade across geographical space and the contributions of individual species to the delineation of those realms. As our example, we focus on Wallace's Line, the most enigmatic partitioning of the world's faunas, where climate is thought to have little effect and the majority of dispersal barriers are short water gaps.

LOCATION

Indo-Pacific.

TIME PERIOD

Present day.

MAJOR TAXA STUDIED

Birds and mammals.

METHODS

Terrestrial bird and mammal assemblages were established in 1-degree map cells using range maps. Assemblage structure was modelled using latent Dirichlet allocation, a continuous clustering method that simultaneously establishes the likely partitioning of species into biotas and the contribution of biotas to each map cell. Phylogenetic trees were used to assess the contribution of deep historical processes. Spatial segregation between biotas was evaluated across time and space in comparison with numerous hard realm boundaries drawn by various workers.

RESULTS

We demonstrate that the strong turnover between biotas coincides with the north-western extent of the region not connected to the mainland during the Pleistocene, although the Philippines contains mixed contributions. At deeper taxonomic levels, Sulawesi and the Philippines shift to primarily Asian affinities, resulting from transgressions of a few Asian-derived lineages across the line. The partitioning of biotas sometimes produces fragmented regions that reflect habitat. Differences in partitions between birds and mammals reflect differences in dispersal ability.

MAIN CONCLUSIONS

Permanent water barriers have selected for a dispersive archipelago fauna, excluded by an incumbent continental fauna on the Sunda shelf. Deep history, such as plate movements, is relatively unimportant in setting boundaries. The analysis implies a temporally dynamic interaction between a species' intrinsic dispersal ability, physiographic barriers, and recent climate change in the genesis of Earth's biotas.

200 Years of Research on Himalayan Biodiversity: Trends, Gaps, and Policy Implications

Global mountains, including the Himalaya, are highly vulnerable ecosystems, especially given climate and land-use changes. Here, we compile the literature on Himalayan biodiversity in order to assess spatial and taxonomic trends in research during the past 200 years. We identified 35,316 research outputs, including 28,120 journal articles, 3,725 doctoral theses, and 3,471 books. Nepal contributes the largest volume of published literature, followed by west Himalayan Indian states, with relatively few studies on the most biodiverse region lying to the east of Nepal. Publications on Himalayan biodiversity research have increased annually, especially after 1970, with an acceleration since 2000. Among the major taxonomic groups, the largest number of publications is on seed plants (angiosperms), followed by invertebrates (especially arthropods) and vertebrates. Some groups of organisms, notably fungi, bacteria, algae, bryophytes, pteridophytes, etc., are clearly understudied. Among various research disciplines, ecology is the most dominant field followed by agriculture, ethnobiology, and paleontology. Some newer disciplines, including molecular biology and climate change, have contributed to the growth in the number of papers appearing during the last two decades. Despite an encouraging and rapid increase in research papers during this century, they are largely in low-impact-factor journals, likely to be subject to poor peer review, and many doctoral theses remain unpublished. The Government of India's development initiative emphasizes the importance of research in the Himalaya, which can be enhanced by improved quality of peer review and local journals registering in global indexing services.

Hierarchical analyses of avian community biogeography in the Afromontane highlands

The Afromontane mountains are a complex series of highlands that have intermittently been connected by habitat corridors during climatic cycles, resulting in a mosaic of range disjunctions and allospecies complexes in the present day. Patterns of community relatedness between geographic regions are often determined through single-species analyses or spatial analyses of diversity and nestedness at the species level. To understand patterns of Afromontane community evolution and to assess the effects of taxonomy on our understanding of biogeographic patterns, I concatenated three lists of Afromontane bird taxa divided into five taxonomic hierarchies. These lists were converted into a presence-absence matrix across 42 montane regions and analyzed using a variety of clustering techniques based on a replicable coding pipeline. I used these lists and methods to determine patterns of relatedness between montane blocks, to assess the consistency with which biogeographic regions were recovered, and to shed light on the patterns of connectivity within the Afromontane region. My results reaffirm the distinctiveness of many biogeographic regions (e.g., the Cameroon Highlands) while also clarifying regional relationships and the presence of 'transition zones' between regions. Differences between lists illustrated how our understanding of taxonomy and distribution in the Afromontane highlands can also change our understanding of Afromontane biogeography. Most notably, I found evidence for an Expanded Eastern Arc that included the Eastern Arc Mountains and highlands in Malawi, Mozambique, and Zimbabwe. This study presents a rigorous yet easily adjustable pipeline for studying regional biogeography from multiple taxonomic perspectives using both traditional and novel approaches.

Climate Profiles in Brazilian Microregions

Brazil’s territory is considerably large and characterized by a variety of climate patterns, which allows the identification of regional climate specificities. The objective of this study was to identify a typology of climatic characteristics for the microregions of Brazil using the grade of membership (GoM) method, which is a multivariate technique based on the fuzzy sets theory. The meteorological variables used were: precipitation (mm), relative humidity (%), maximum and minimum temperature (°C) and wind speed (m/s), obtained from the interpolated database elaborated by Xavier comprising the period from January 1981 to December 2013. Three predominant homoclimatic profiles were found. The GoM method also allowed the identification of five mixed profiles, which is unprecedent in studies in Brazil and corroborates the regional climate diversity in the country. Furthermore, the heterogeneities of Brazilian climates could be better outlined. The extreme profiles—“predominant 1—P1”, “predominant 2—P2” and “predominant 3—P3”—accounted for 42.9% (236) of the total microregions. Additionally, approximately half (53.9%) of the microregions were classified as featuring characteristics of at least two profiles—that is, they presented mixed profiles with hybrid characteristics. These hybrid microregions were located mostly at transition zones between climates.

Evolutionary history of zoogeographical regions surrounding the Tibetan Plateau

The Tibetan Plateau (TP) and surrounding regions have one of the most complex biotas on Earth. However, the evolutionary history of these regions in deep time is poorly understood. Here, we quantify the temporal changes in beta dissimilarities among zoogeographical regions during the Cenozoic using 4,966 extant terrestrial vertebrates and 1,278 extinct mammal genera. We identify ten present-day zoogeographical regions and find that they underwent a striking change over time. Specifically, the fauna on the TP was close to the Oriental realm in deep time but became more similar to the Palearctic realms more recently. The present-day zoogeographical regions generally emerged during the Miocene/Pliocene boundary (ca. 5 Ma). These results indicate that geological events such as the Indo-Asian Collision, the TP uplift, and the aridification of the Asian interior underpinned the evolutionary history of the zoogeographical regions surrounding the TP over different time periods.

The projected timing of abrupt ecological disruption from climate change

As anthropogenic climate change continues the risks to biodiversity will increase over time, with future projections indicating that a potentially catastrophic loss of global biodiversity is on the horizon^1-3. However, our understanding of when and how abruptly this climate-driven disruption of biodiversity will occur is limited because biodiversity forecasts typically focus on individual snapshots of the future. Here we use annual projections (from 1850 to 2100) of temperature and precipitation across the ranges of more than 30,000 marine and terrestrial species to estimate the timing of their exposure to potentially dangerous climate conditions. We project that future disruption of ecological assemblages as a result of climate change will be abrupt, because within any given ecological assemblage the exposure of most species to climate conditions beyond their realized niche limits occurs almost simultaneously. Under a high-emissions scenario (representative concentration pathway (RCP) 8.5), such abrupt exposure events begin before 2030 in tropical oceans and spread to tropical forests and higher latitudes by 2050. If global warming is kept below 2 °C, less than 2% of assemblages globally are projected to undergo abrupt exposure events of more than 20% of their constituent species; however, the risk accelerates with the magnitude of warming, threatening 15% of assemblages at 4 °C, with similar levels of risk in protected and unprotected areas. These results highlight the impending risk of sudden and severe biodiversity losses from climate change and provide a framework for predicting both when and where these events may occur.

Ecological Limits as the Driver of Bird Species Richness Patterns along the East Himalayan Elevational Gradient

Variation in species richness across environmental gradients results from a combination of historical nonequilibrium processes (time, speciation, extinction) and present-day differences in environmental carrying capacities (i.e., ecological limits affected by species interactions and the abundance and diversity of resources). In a study of bird richness along the subtropical east Himalayan elevational gradient, we test the prediction that species richness patterns are consistent with ecological limits using data on morphology, phylogeny, elevational distribution, and arthropod resources. Species richness peaks at midelevations. Occupied morphological volume is roughly constant from low elevations to midelevations, implying that more species are packed into the same space at midelevations compared with low elevations. However, variance in beak length and differences in beak length between close relatives decline with elevation, which is a consequence of the addition of many small insectivores at midelevations. These patterns are predicted from resource distributions: arthropod size diversity declines from low elevations to midelevations, largely because many more small insects are present at midelevations. Weak correlations of species mean morphological traits with elevation also match predictions based on resources and habitats. Elevational transects in the tropical Andes, New Guinea, and Tanzania similarly show declines in mean arthropod size and mean beak length and, in these cases, likely contribute to declining numbers of insectivorous bird species richness along these gradients. The results imply that conditions for ecological limits are met, although historical nonequilibrium processes are likely to also contribute to the pattern of species richness.

Biochemical and structural insights into the cytochrome P450 reductase from Candida tropicalis

Cytochrome P450 reductases (CPRs) are diflavin oxidoreductases that supply electrons to type II cytochrome P450 monooxygenases (CYPs). In addition, it can also reduce other proteins and molecules, including cytochrome c, ferricyanide, and different drugs. Although various CPRs have been functionally and structurally characterized, the overall mechanism and its interaction with different redox acceptors remain elusive. One of the main problems regarding electron transfer between CPRs and CYPs is the so-called "uncoupling", whereby NAD(P)H derived electrons are lost due to the reduced intermediates' (FAD and FMN of CPR) interaction with molecular oxygen. Additionally, the decay of the iron-oxygen complex of the CYP can also contribute to loss of reducing equivalents during an unproductive reaction cycle. This phenomenon generates reactive oxygen species (ROS), leading to an inefficient reaction. Here, we present the study of the CPR from Candida tropicalis (CtCPR) lacking the hydrophobic N-terminal part (Δ2-22). The enzyme supports the reduction of cytochrome c and ferricyanide, with an estimated 30% uncoupling during the reactions with cytochrome c. The ROS produced was not influenced by different physicochemical conditions (ionic strength, pH, temperature). The X-ray structures of the enzyme were solved with and without its cofactor, NADPH. Both CtCPR structures exhibited the closed conformation. Comparison with the different solved structures revealed an intricate ionic network responsible for the regulation of the open/closed movement of CtCPR.

Latent Dirichlet Allocation reveals spatial and taxonomic structure in a DNA-based census of soil biodiversity from a tropical forest

High-throughput sequencing of amplicons from environmental DNA samples permits rapid, standardized and comprehensive biodiversity assessments. However, retrieving and interpreting the structure of such data sets requires efficient methods for dimensionality reduction. Latent Dirichlet Allocation (LDA) can be used to decompose environmental DNA samples into overlapping assemblages of co-occurring taxa. It is a flexible model-based method adapted to uneven sample sizes and to large and sparse data sets. Here, we compare LDA performance on abundance and occurrence data, and we quantify the robustness of the LDA decomposition by measuring its stability with respect to the algorithm's initialization. We then apply LDA to a survey of 1,131 soil DNA samples that were collected in a 12-ha plot of primary tropical forest and amplified using standard primers for bacteria, protists, fungi and metazoans. The analysis reveals that bacteria, protists and fungi exhibit a strong spatial structure, which matches the topographical features of the plot, while metazoans do not, confirming that microbial diversity is primarily controlled by environmental variation at the studied scale. We conclude that LDA is a sensitive, robust and computationally efficient method to detect and interpret the structure of large DNA-based biodiversity data sets. We finally discuss the possible future applications of this approach for the study of biodiversity.