Biogeographic Diversity Research Articles

Transition of survival strategies under global climate shifts in the grape family.

Faced with environmental changes, plants may either move to track their ancestral niches or evolve to adapt to new niches. Vitaceae, the grape family, has evolved diverse adaptive traits facilitating a global expansion in wide-ranging habitats, making it ideal for investigating transition between move and evolve strategies and exploring the underlying mechanisms. Here we inferred the patterns of biogeographic diversification and trait evolution in Vitaceae based on a robust phylogeny with dense sampling including 495 species (~52% of Vitaceae species). Vitaceae probably originated from Asia-the diversity centre of extant genera and the major source of dispersals. Boundaries of the Eocene, Oligocene and Miocene were identified as turning points in shifting strategies. A significant decrease in move strategy was identified during the Oligocene, followed by increases in move and evolve. After the Miocene, evolve began to dominate, during which increased niche opportunities and key trait innovations played important roles.

In Silico Comparative Analysis of Different vacA Genes of Helicobacter pylori

Helicobacter pylori is a class I carcinogen responsible for 90% of gastrointestinal and gastroduodenaldisorders, including gastric cancer and peptic ulcer disease. The virulence and pathogenicity peculiar to H. pylorihave been associated with several genes, including cytotoxin associated gene (cagA), vacuolating cytotoxin A(vacA), outer inflammatory protein A (oipA), and duodenal ulcer promoting (dupA). This study explored therelationship between African-generated vacA genes with genes from other regions with high gastrointestinaldisorder prevalence. Nucleotide sequences of 228 vacA genes of H. pylori were retrieved from the NationalCentre for Biotechnology Information (NCBI). Pairwise and multiple sequence alignment was carried out on228 vacA nucleotide sequences using MEGA 10.2.4 software to identify regions of similarities. Phylogeneticanalysis, also using MEGA software, was carried out to establish the evolutionary relationships between allextracted sequences. Analysis for conserved domain was also performed on the NCBI Conserved DomainDatabase to better understand each geographical data's properties. After the evolutionary analysis, it wasobserved that South African vacA genes were more closely related to genes from Mexico, Italy, Spain, andGermany—with Italy having the highest occurring relationship. Conserved domain analysis showed 2 highlyconserved superfamilies, cl20029 and cl22877, and 2 protein family models, pfam02691 and pfam03797.The results demonstrate relatedness of vacA genes from the African region to the European region; Italy,Mexico, and Spain. The study shows the biogeographical diversity among vacA genes and emphasizes thedegree of domain conservation across each gene. It also shows the need for a holistic assessment of thevirulent genes in H. pylori.

A DNA barcode inventory of the genus Ulva (Chlorophyta) along two Italian regions: updates and considerations

Abstract The genus Ulva Linnaeus 1753 is well known for its global distribution and containing many taxonomically debated species. Their morphological plasticity and cryptic nature overrepresent and underrepresent, respectively, the biodiversity of these species. The difficulty in morphologically identifying Ulva species has led to the accumulation of many species names that are currently considered synonyms. The correct identification of these species is crucial due to their significant role in marine ecosystems and mariculture. In the last 30 years, several checklists and taxonomic contributions have been made from the Italian coast on Ulva species, almost entirely based on morphological studies and only a few papers with molecular data have been published. In this study, samples deposited at the Institute of Marine Sciences (ISMAR) and Phycological Lab (PHL) herbaria have been reviewed by sequencing the chloroplast-encoded elongation factor Tu (tufA) barcode marker. The results obtained provide an update of the DNA barcode inventory of Ulva species for the Lagoon of Venice and the Strait of Messina, two ecosystems characterized by a high algal biogeographical diversity and continuous introduction due to anthropogenic activities. Here, ten Ulva species were identified based on molecular data. Furthermore, we record the presence of Ulva chaugulei on the coast of Tunisia.

Phylogenomics and biogeographical diversification of Collabieae (Orchidaceae) and its implication in the reconstruction of the dynamic history of Asian evergreen broadleaved forests

The tribe Collabieae (Epidendroideae, Orchidaceae) comprises approximately 500 species. Generic delimitation within Collabieae are confusing and phylogenetic interrelationships within the Collabieae have not been well resolved. Plastid genomes and nuclear internal transcribed spacer (ITS) sequences were used to estimate the phylogenetic relationships, ancestral ranges, and diversification rates of Collabieae. The results showed that Collabieae was subdivided into nine clades with high support. We proposed to combine Ancistrochilus and Pachystoma into Spathoglottis, merge Collabium and Chrysoglossum into Diglyphosa, and separate Pilophyllum and Hancockia as distinctive genera. The diversification of the nine clades of Collabieae might be associated with the uplift of the Himalayas during the Late Oligocene/Early Miocene. The enhanced East Asian summer monsoon in the Late Miocene may have promoted the rapid diversification of Collabieae at a sustained high diversification rate. The increased size of terrestrial pseudobulbs may be one of the drivers of Collabieae diversification. Our results suggest that the establishment and development of evergreen broadleaved forests facilitated the diversification of Collabieae.

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.

Biogeographic diversification of Actaea (Ranunculaceae): Insights into the historical assembly of deciduous broad-leaved forests in the Northern Hemisphere

The deciduous broad-leaved forests (DBLFs) cover large temperate and subtropical high-altitude regions in the Northern Hemisphere. They are home to rich biodiversity, especially to numerous endemic and relict species. However, we know little about how this vegetation in the Northern Hemisphere has developed through time. Here, we used Actaea (Ranunculaceae), an herbaceous genus almost exclusively growing in the understory of the Northern Hemisphere DBLFs, to shed light on the historical assembly of this biome in the Northern Hemisphere. We present a complete species-level phylogenetic analysis of Actaea based on five plastid and nuclear loci. Using the phylogenetic framework, we estimated divergence times, ancestral ranges, and diversification rates. Phylogenetic analyses strongly support Actaea as monophyletic. Sections Podocarpae and Oligocarpae compose a clade, sister to all other Actaea. The sister relationship between sections Chloranthae and Souliea is strongly supported. Section Dichanthera is not monophyletic unless section Cimicifuga is included. Actaea originated in East Asia, likely the Qinghai-Tibet Plateau, in the late Paleocene (c. 57 Ma), and subsequently dispersed into North America in the middle Eocene (c. 43 Ma) via the Thulean bridge. Actaea reached Europe twice, Japan twice, and Taiwan once, and all these five colonization events occurred in the late Miocene-early Pliocene, a period when sea level dropped. Actaea began to diversify at c. 43 Ma. The section-level diversification took place at c. 27–37 Ma and the species-level diversification experienced accelerations twice, which occurred at c. 15 Ma and c. 5 Ma, respectively. Our findings suggest that the Northern Hemisphere DBLFs might have risen in the middle Eocene and further diversified in the late Eocene-Oligocene, middle Miocene and early Pliocene, in association with climatic deterioration during these four periods.

The European freshwater landscape and hotspot areas of mass effects and regional connectivity

AbstractAimThe maintenance of broad‐scale connectivity patterns is suggested as a sustainable strategy for biodiversity preservation. However, explicit approaches for quantifying the functional role of different areas in biogeographic connectivity have been elusive. Freshwaters are spatially structured ecosystems critically endangered because of human activities and global change, demanding connectivity‐based approaches for their conservation. Mass effects—the increase in local diversity by immigration—and corridor effects—the connections with distant communities—are basic and relevant mechanisms connecting diversity with landscape configuration. Here, we identified freshwater hotspots areas for mass and corridor effects across Europe.LocationEurope.MethodsUsing satellite images, we quantified the areas of ephemeral, temporal and permanent freshwaters. The landscape structure of the freshwater ecoregions was represented as a directed‐graph, and the link weights were determined by the distance between cells and the water cover. Three centrality metrics were used to rank freshwater areas with respect to their potential role in dispersal‐mediated mechanisms. Out‐degree represents the potential of an area to operate as a diversity source to other regions. In‐degree reflects the importance that incoming dispersal may have in local diversity. Betweenness refers to the importance of local areas for connecting other distant areas.ResultsWe detected great concentrations of source hotspots on the northern regions associated to lentic ecosystems, main European rivers acting as ecological corridors for all freshwaters, and a mixed distribution of connectivity hotspots in southern and Mediterranean ecoregions, associated with lentic and/or lotic systems.Main ConclusionsWe showed an explicit connection between landscape structure and dispersal process at large geographic scales, highlighting hotspots of connectivity for the European waterscape. The spatial distribution of hotspots points to differences in landscape configurations potentially accounting for biogeographic diversity patterns and for mechanisms that have to be considered in conservation planning.

Time to reconsider the enigmatic tail of eastern Paleo-Tethys: New insights from Borneo

The rise of Tibet and growth of Asia resulted from successive accretion of Gondwana-derived continental fragments at the expense of Tethyan oceans, yet how and where the eastern Paleo-Tethys closed in SE Asia remain controversial. Here we report new and synthesized detrital zircon data from Borneo and relevant regions revealing that West and SW Borneo show consistent Precambrian age profiles resembling that of Northern Australia (Kimberley to Pine Creek), but contrasting with those of NW/NE Australia, Bird's Head, and Cathaysia/Indochina. Considering the questionable suture between West and SW Borneo, we suggest a united Borneo basement that originated from Northern Australia, with a position between Sumatra and Timor. Surprisingly, Borneo lacks NE Australia-sourced ca. 1700–1400 and 400–280 Ma zircons that prevail in Triassic-Jurassic strata of Timor, Babar, and Tanimbar offshore Northern Australia, which may be best explained by pre-Triassic rifting of the Borneo basement from Northern Australia. Combining with recent investigations, we propose a new tectonic scenario involving a Permian separation of Borneo (probably together with Sumatra) from northern Gondwana through opening of the Meso-Tethys Ocean followed by a Triassic docking with Eurasia that closed the eastern Paleo-Tethys. Thus, assembly of Sundaland (continental core of SE Asia) completed in the Late Triassic, rather than Cretaceous as previously thought, and the tail (or the southeasternmost section) of eastern Paleo-Tethys lies within the Kuching zone of Borneo. Our new reconstruction challenges current understanding of Gondwana dispersion and Asian accretion, shedding new light on Asian climate change and biogeographic diversity.

High Variation in Protist Diversity and Community Composition in Surface Sediment of Hot Springs in Himalayan Geothermal Belt, China

Hot springs are some of the most special environments on Earth. Many prokaryotic and eukaryotic microbes have been found to live in this environment. The Himalayan geothermal belt (HGB) has numerous hot springs spread across the area. Comprehensive research using molecular techniques to investigate eukaryotic microorganisms is still lacking; investigating the composition and diversity of eukaryotic microorganisms such as protists in the hot spring ecosystems will not only provide critical information on the adaptations of protists to extreme conditions, but could also give valuable contributions to the global knowledge of biogeographic diversity. In this study, we used high-throughput sequencing to illuminate the diversity and composition pattern of protist communities in 41 geothermal springs across the HGB on the Tibetan Plateau. A total of 1238 amplicon sequence variants (ASVs) of protists were identified in the hot springs of the HGB. In general, Cercozoa was the phylum with the highest richness, and Bacillariophyta was the phylum with the highest relative abundance in protists. Based on the occurrence of protist ASVs, most of them are rare. A high variation in protist diversity was found in the hot springs of the HGB. The high variation in protist diversity may be due to the different in environmental conditions of these hot springs. Temperature, salinity, and pH are the most important environmental factors that affect the protist communities in the surface sediments of the hot springs in the HGB. In summary, this study provides the first comprehensive study of the composition and diversity of protists in the hot springs of the HGB and facilitates our understanding of the adaptation of protists in these extreme habitats.

A complete genus-level phylogeny reveals the Cretaceous biogeographic diversification of the poppy family

Angiosperms, a trigger for the Cretaceous Terrestrial Revolution (KTR), underwent a rapid expansion and occupied all the environments during the Mid-Upper Cretaceous. Yet, Cretaceous biogeographic patterns and processes underlying the distribution of angiosperm diversity in the Northern Hemisphere are still poorly known. Here, we elucidated the biogeographic diversification of the angiosperm family Papaveraceae, an ancient Northern Hemisphere clade characterized by poor dispersal ability and high level of regional endemism. Based on both plastome and multi-locus datasets, we reconstructed a robust time-calibrated phylogeny that includes all currently recognized 45 genera of this family. Within the time-calibrated phylogenetic framework, we conducted 72 biogeographic analyses by testing the sensitivity of uncertainties of area delimitation, maxarea constraints, and the parameters of the model, i.e., j (describing jump-dispersal events) and w (modifying dispersal multiplier matrices), to ancestral range estimations. We also inferred ancestral habitat and ecological niches. Phylogenetic analyses strongly support Papaveraceae as monophyletic. Pteridophylloideae is strongly supported as sister to Hypecoideae-Fumarioideae. Our results indicate that the j parameter and number of predefined areas strongly affect ancestral range estimates, generating questionable ancestral ranges, whereas maxarea constraint and w parameter have no effect and improve model fit. After accounting for these uncertainties, our results indicate that Papaveraceae differentiated in Asian wet forests during the Lower Cretaceous and subsequently occupied the Asian and western North American arid and open areas. Three dispersals from Asia to western North America via the Bering land bridge occurred in the Mid-Upper Cretaceous, largely in agreement with the KTR. Habitat shift and ecological niche divergence resulted in the subsequent disjunctions between Asia and western North America. These findings suggest that the interplay of range expansion and niche divergence-driven vicariance might have shaped Cretaceous biogeographic patterns of angiosperms with Papaveraceae-like ecological requirements and dispersal abilities in the Northern Hemisphere, hence contributing to the knowledge on the geographic expansion of angiosperms during the KTR.

Species, growth form, and biogeographic diversity of summit vegetation along an elevation gradient in the tropical Andes: a baseline for climate change monitoring

Species, growth form, and biogeographic diversity of summit vegetation along an elevation gradient in the tropical Andes: a baseline for climate change monitoring

Aquatic Insects in Habitat-Forming Sponges: The Case of the Lower Mekong and Conservation Perspectives in a Global Context

Shallow water sponges settled on a raft along the Pong River (Lower Mekong Basin, Thailand) were investigated to highlight the taxonomic richness, composition, relative abundance and lifestyle of sponge-dwelling aquatic Insecta. The three-dimensional biogenic structures of the model sponges hosted 4 orders of Insecta, belonging to 10 families and 19 genera/species, able to strictly coexist at the level of the sponges in aquiferous canals and/or at the body surface, and/or dwelling in the extracellular matrix. On the basis of the identified 379 larvae and pupae, Trichoptera and Diptera were found to be the dominant inhabitants of Corvospongilla siamensis (Demospongiae: Spongillida), endemic to Southeast Asia. In the focused lotic ecosystem, dominated by soft bottoms, sponges play a functional role. Insecta use sponges as a substratum, nursery ground, food source, and shelter microhabitat, protecting them from predation and environmental aggression. Moreover, their feeding behavior indicates the insects’ adaptive traits to recycle sponge siliceous spicules as a source of exogenous material to strengthen the larval–pupal cases and the digestive system. The results of the Thai sponge model contribute to the inventory of global engineering species richness, ecosystem types, and biogeographic diversity, thus raising awareness for freshwater biodiversity conservation. In this regard, the present data, along with the worldwide inventory, focus on sponges as (a) key habitat-forming species for aquatic insect assemblages, (b) ecosystem engineers in river/lake/wetland ecosystems, providing water purification, the processing of organic matter, recycling of nutrients, and freshwater–terrestrial coupling, and (c) promising candidates in restoration projects of tropical freshwater ecosystems by bioremediation.

HAS 1: A natural product from soil-isolated Streptomyces species with potent activity against cutaneous leishmaniasis caused by Leishmania tropica.

Cutaneous Leishmaniasis (CL) is a neglected tropical disease, classified by the World Health Organization (WHO) as one of the most unrestrained diseases. The Syrian war and the significant displacement of refugees aggravated the spread of this ailment into several neighboring countries in the Eastern Mediterranean Region (EMR). In Syria, Leishmania tropica is identified as one of the most aggressive and endemic identified species, causing localized or generalized lesions, often chronic or relapsing. Pentavalent antimonial drugs are currently used as first line treatment against CL. Nonetheless, these drugs exhibit several limitations, including the repetitive painful injections, high cost, poor availability, and mainly systemic toxicity. Besides, the emergence of acquired parasitic resistance hinders their potency, stressing the need for new therapies to combat CL. Natural products (NPs) epitomize a valuable source in drug discovery. NPs are secondary metabolites (SMs) produced by plants, sponges, or a wide variety of organisms, including environmental microorganisms. The EMR is characterized by its immense biodiversity, yet it remains a relatively untapped area in drug discovery. NPs of the region were explored over the last 2 decades, but their discoveries lack biogeographical diversity and are limited to the Red Sea. Here, we isolated previously uncultured environmental soil-dwelling Streptomyces sp. HAS1, from Hasbaya region in southeast Lebanon. When fermented in one of our production media named INA, HAS1 produced a crude extract with significant potency against a clinical Leishmania tropica isolate. Using bio-guided fractionation, the bioactive compound was purified and the structure was elucidated by NMR and LC-HRMS. Our findings establish NPs as strong candidates for treating Leishmania tropica and further dwells on the importance of these natural sources to combat microbial infections.

The significance of recent diversification in the Northern Hemisphere in shaping the modern global flora revealed from the herbaceous tribe of Rubieae (Rubiaceae)

The global herbaceous flora is probably shaped by both ancient and/or recent diversification, companied with the impacts from geographic differences between the Northern and Southern Hemispheres. Therefore, its biogeographic pattern with respect to temporal and spatial divergence is far from full understanding. Tribe Rubieae, the largest herbaceous tribe in the woody-dominant Rubiaceae, provides an excellent opportunity for studying the macroevolution of worldwide colonization. Here, we aim to reconstruct the evolutionary history of Rubieae with regard to climate fluctuation and geological history in the Cenozoic. A total of 204 samples of Rubieae representing all the distribution areas of the tribe were used to infer its phylogenetic and biogeographic histories based on two nrDNA and six cpDNA regions. The ancestral area of Rubieae was reconstructed using a time-calibrated phylogeny in RASP and diversification rates were inferred using Bayesian analysis of macroevolutionary mixtures (BAMM). Our results show Rubieae probably originated in European region during the middle Oligocene, with the two subtribes separating at 26.8 million years ago (Ma). All the genera in Rubieae formed separate clades between 24.79 and 6.23 Ma. The ancestral area of the subtribe Rubiinae was the Madrean-Tethyan plant belt and the North Atlantic land bridge (NALB) provided passage between North America and Europe for Rubiinae. The subtribe Galiinae clade originated in Europe/central Asia during the late Oligocene. Two diversification shifts were detected within Rubieae in the late Neogene. Most extant Rubieae species diverged recently during the Neogene within clades that generally were established during the late Paleogene. The tribe shows complex migration/dispersal patterns within the North Hemisphere combined with multiple recent dispersals into Southern Hemisphere. Our results highlighted the important role of recent biogeographic diversification in the Northern Hemisphere in shaping the modern global herbaceous flora during the latest and rapid worldwide expansion in the Neogene.

Seven snail species hidden in one: Biogeographic diversity in an apparently widespread periwinkle in the Southern Ocean

AbstractAimThe Antarctic Circumpolar Current imparts significant structure to the Southern Ocean biota. The Antarctic Polar Front is a major barrier to dispersal, with separate species (or sometimes intraspecific clades) normally occurring either side of this feature. We examined the biogeographic structure of an apparent exception to this rule in a widespread genus of the Southern Ocean, the periwinkle snail, Laevilitorina.LocationSouthern Ocean.TaxonLittorinidae, Laevilitorininae, Laevilitorina.MethodsUsing 750 specimens from 16 Southern Ocean Laevilitorina populations across >8000 km, we analysed mitochondrial COI and nuclear 28S sequences to uncover the evolutionary history of these marine near‐shore snails. We utilized multi‐locus phylogenetic reconstructions, species‐delimitation analyses, divergence‐time estimations and geometric morphometrics.ResultsMolecular data revealed that the widespread nominal species L. caliginosa comprises seven species‐level clades, all supported by morphological data, whereas the Antarctic nominal species L. antarctica, L. claviformis and L. umbilicata are conspecific. Six “caliginosa” clades are restricted to southern South America, but one lineage extends from Antarctica to distant sub‐Antarctic islands on both sides of the APF. Geometric morphometrics also identified significant differences among these clades, but uncoupled from genetic differentiation.Main conclusionsThe apparent trans‐APF distribution of the poorly dispersing Laevilitorina caliginosa is largely illusory: this taxon consists of at least seven discrete species, only one of which has a trans‐APF distribution. Similar to most Laevilitorina species, the remaining six “caliginosa” clades are narrow endemics. Biogeographical patterns in Laevilitorina reflect the role of vicariance associated with geological processes together with recent long‐distance dispersal events. Laevilitorina originated near the Eocene/Oligocene boundary and diversified during the Miocene and the Pliocene. Laevilitorina is not a cryptic‐species complex: speciation was accompanied by hitherto unrecognized morphological differentiation. This study represents the most detailed molecular work on Southern‐Ocean littorinids and reveals unforeseen diversity across this globally important region.

Phylogeny and historical biogeography of the Panama‐hat family (Cyclanthaceae, Pandanales)

AbstractThe monocot family Cyclanthaceae (Pandanales) comprises ca. 230 known species in 12 genera restricted to the Neotropics. The family has not been the subject of a species‐level molecular phylogenetic study to date, with multiple evolutionary and biogeographic questions about Cyclanthaceae still unanswered. In this study, we address genus‐ and species‐level relationships and the historical biogeography of Cyclanthaceae based on a broadly sampled molecular phylogeny. Two low‐copy nuclear genes (phyC, rpb2) and five plastid regions (atpB‐rbcL, psbA‐trnH, trnL‐trnF, trnQ‐rps16, matK) representing 99 species and all genera of Cyclanthaceae were sampled, spanning the taxonomic and biogeographic diversity of the family. Our results strongly support the monophyly of all Cyclanthaceae genera and confirm previously proposed hypotheses of intergeneric relationships. Infrageneric relationships are generally well supported, with some exceptions in the genus Asplundia that may require a broader sampling to clarify. The early diversification of Cyclanthaceae is estimated to date back to the Paleocene‐Eocene period in South America, where the family possibly arrived through a boreotropical route. The origin of most genera is inferred from the Paleocene of the Tumbes‐Chocó‐Magdalena region, possibly indicating an earlier origin for this biodiversity hotspot. The current distribution of Cyclanthaceae is likely to have been strongly influenced by major biogeographical events in the Neotropics, such as the uplift of the Andes and the opening of the South America dry diagonal. Further studies that include a broader sample of the large Asplundia‐Dicranopygium clade and Sphaeradenia group are required.

Biogeography and Diversification of Bumblebees (Hymenoptera: Apidae), with Emphasis on Neotropical Species

A detailed phylogeny of bumblebees is urgently needed to understand speciation and biogeographic diversification in the Neotropical region. We sequenced autosomal and mtDNA loci from nine Brazilian bumblebee species and compiled it with the data already available to obtain highly resolved phylogenetic trees with fossil-calibrated dates. The ancestral Bombus lineage was estimated to diversify between 47.08 and 34.27 million years ago (Ma) in the Holarctic region, but largely restricted to the eastern Old World. The Neotropical region was initially colonized in the Late Miocene, where bumblebee diversification was shown to be consistent with geologic and climatic events of the Late Cenozoic. Neotropical bumblebees likely originated from Nearctic lineages, which dispersed towards South America after 29 Ma.

New Opportunities and Untapped Scientific Potential in the Abyssal Ocean

The abyssal ocean covers more than half of the Earth’s surface, yet remains understudied and underappreciated. In this Perspectives article, we mark the occasion of the Deep Submergence Vehicle Alvin’s increased depth range (from 4500 to 6500 m) to highlight the scientific potential of the abyssal seafloor. From a geologic perspective, ultra-slow spreading mid-ocean ridges, Petit Spot volcanism, transform faults, and subduction zones put the full life cycle of oceanic crust on display in the abyss, revealing constructive and destructive forces over wide ranges in time and space. Geochemically, the abyssal pressure regime influences the solubility of constituents such as silica and carbonate, and extremely high-temperature fluid-rock reactions in the shallow subsurface lead to distinctive and potentially unique geochemical profiles. Microbial residents range from low-abundance, low-energy communities on the abyssal plains to fast growing thermophiles at hydrothermal vents. Given its spatial extent and position as an intermediate zone between coastal and deep hadal settings, the abyss represents a lynchpin in global-scale processes such as nutrient and energy flux, population structure, and biogeographic diversity. Taken together, the abyssal ocean contributes critical ecosystem services while facing acute and diffuse anthropogenic threats from deep-sea mining, pollution, and climate change.

Adiantum japonicum, a new species of the Adiantum pedatum complex (Pteridaceae) from Japan

The Adiantum pedatum complex is disjunctly distributed in North America and eastern Asia. In this study, we carried out a detailed morphological study based on 137 specimens representing the biogeographic diversity of this complex. The sequences of eight chloroplast markers of 35 samples were analyzed with maximum likelihood and Bayesian inference. The morphological and phylogenetic analyses support the recognition of a new species of the A. pedatum complex from Japan. We propose the new species as A. japonicum based on the examinations of specimens from Japan and the comparative analyses of the whole complex. This new species can be distinguished from A. pedatum by the erect rhizome and shows significant molecular differences from other species in this complex. A taxonomic description with detailed morphological characters of the new species is presented.

Toward a unified diversity–area relationship (DAR) of species and gene diversity illustrated with the human gut metagenome

AbstractThe biogeographic diversity of the microbiome can be investigated from two perspectives: the spatiotemporal distribution of species (or any operational taxonomic unit) diversity and the spatiotemporal distribution of metagenomic gene diversity. Together, these provide a complementary understanding of taxonomic, ecological, evolutionary, and functional aspects of the microbiome. Here, we reformulate the species diversity–area relationship (DAR) to quantify and illustrate metagenomic diversity–area relationships (m‐DAR) with the gut metagenome from the human microbiome project (HMP). Using the m‐DAR, the estimated ranges of human gut metagenomic genes (MG) within and among individuals are 5.0–9.7 × 105 and 4.3–6.9 × 106, respectively; the among‐individual standard errors of these estimates (6.0–7.5 × 105) are of the same order of magnitude as the within‐individual ranges, suggesting high between‐individual variability. We similarly estimated the number of metagenome functional gene clusters (MFCG) to be 222–245 (SE = 1–2). More detailed analysis of the m‐DAR profile, pair‐wise diversity overlap (PDO), maximal accrual diversity (MAD), and ratio of individual‐ to population‐level diversity (RIP) of microbiomes of individuals with healthy guts and those with three microbiome‐associated diseases (obesity, diabetes, and inflammatory bowel disease) identified differences in m‐DAR parameters between healthy and diseased individuals. Methodologically, the m‐DAR and its associated parameters offer a unified toolset with which to study and analyze microbiomes from both species and metagenomic perspectives and to explore spatial scaling of metagenomic diversity within and among individuals. To the best of our knowledge, our illustration of m‐DAR with the human gut metagenome is the first statistically‐based estimate of the richness of human metagenomic genes at population scale.