Biogeographical Research Research Articles

Introduction, Establishment, Invasion, Accommodation: innovation and disruption in biogeographic publishing

Author(s): Dawson, Michael N; Field, Richard; Hortal, Joaquin; Stigall, Alycia L. | Abstract: Frontiers of Biogeography launched eight years ago, merging the missions of a newsletter and a book, to deliver a series of integrative and interdisciplinary volumes to a diverse community of biogeographers. The journal purposefully was pitched as a 'magazine' aiming to distinguish itself from existing biogeography journals with syntheses and prospectives that would push forward the boundaries of biogeography philosophy and practice. Here, we review the development of the journal since 2009, we survey the journal's current niche in the biogeography publishing ecosystem, and we look forward to changes in the coming year(s) that will further advance our mission to enhance your biogeographical research.

A plant growth form dataset for the New World.

This dataset provides growth form classifications for 67,413 vascular plant species from North, Central, and South America. The data used to determine growth form were compiled from five major integrated sources and two original publications: the Botanical Information and Ecology Network (BIEN), the Plant Trait Database (TRY), the SALVIAS database, the USDA PLANTS database, Missouri Botanical Garden's Tropicos database, Wright (2010), and Boyle (1996). We defined nine plant growth forms based on woodiness (woody or non-woody), shoot structure (self-supporting or not self-supporting), and root traits (rooted in soil, not rooted in soil, parasitic or aquatic): Epiphyte, Liana, Vine, Herb, Shrub, Tree, Parasite, or Aquatic. Species with multiple growth form classifications were assigned the growth form classification agreed upon by the majority (>2/3) of sources. Species with ambiguous or otherwise not interpretable growth form assignments were excluded from the final dataset but are made available with the original data. Comparisons with independent estimates of species richness for the Western hemisphere suggest that our final dataset includes the majority of New World vascular plant species. Coverage is likely more complete for temperate than for tropical species. In addition, aquatic species are likely under-represented. Nonetheless, this dataset represents the largest compilation of plant growth forms published to date, and should contribute to new insights across a broad range of research in systematics, ecology, biogeography, conservation, and global change science.

Biogeographia: a brief historical outline of the Società Italiana di Biogeografia (SIB)

Biogeographia – The Journal of Integrative Biogeography 31 (2016): 1 – 2 Biogeographia: a brief historical outline of the Societa Italiana di Biogeografia (SIB) VALERIO SBORDONI Department of Biology, Universita di Roma “Tor Vergata”, Roma, Italy e-mail corresponding author: valerio.sbordoni@uniroma2.it EDITORIAL On September 1954, during the 27 th Congress of the Unione Zoologica Italiana (UZI), a small group of academic scholars, including one geologist, two botanists and five zoologists, gave rise to a scientific association called “Gruppo Italiano Biogeografi”, literally the Italian group of biogeographers. The team aimed at promoting research in Biogeography, and networking researchers engaged in floristic and faunal studies with emphasis on the Mediterranean Region. Starting from 41 fellows, the membership regularly increased up to 200 fellows through the following decade. Since 1962, the association shifted its denomination into “Societa Italiana di Biogeografia”, SIB, namely the Italian Society of Biogeography, and its main activity was the organization of conferences. For the most part, these conferences focused on the study of the biota of given geographic areas of Italy, or to particular habitat types. By this way the SIB initiated its great role as main organizer of systematic research of the Italian flora and fauna and results of the surveys found place in the journal that, since the year 1970, became the SIB Journal “Lavori della Societa Italiana di Biogeografia”, which in 1984 turned under the name “Biogeographia”. A great merit of the SIB has been its role in encouraging collaborative research of botanists and zoologists, stimulating joint surveys in given geographic areas, since the Executive Board anticipated the location of any conference a few years in advance. Accordingly, the journal has also served for years the main repository of the georeferenced data of biodiversity of Italy and of a few other areas investigated by Italian biogeographers. From 1970 to 2011, 30 volumes have been published focusing on themes like the biota of the main mountain compartments of the Alps and Apennines, Sicily, Sardinia, as well as the small Tyrrhenian archipelagos. Other conference themes included the cave habitat, the inland waters, the coastal areas, and the Mediterranean Sea, the biogeographic consequences of Pleistocene climate. A few conferences with the relative volumes concerned methodological issues. Finally, some

Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa.

Rapidly growing biological data—including molecular sequences and fossils—hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyze these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction. Here we introduce a modular framework termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of evolutionary and biogeographical research. This framework assembles comprehensive data sets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data produced through next-generation sequencing techniques. We exemplify the application of our method by presenting phylogenetic and dating analyses for the mammal order Primates and for the plant family Arecaceae (palms). We believe that this framework will provide a valuable tool for a wide range of hypothesis-driven research questions in systematics, biogeography, and evolution. SUPERSMART will also accelerate the inference of a “Dated Tree of Life” where all node ages are directly comparable.

Challenges, advances and perspectives in island biogeography

Island biogeographical research is becoming more and more fashionable, with the continuous identification of new challenges that are critical for the advancement of science. In this contribution we identify biases and limitations associated with island biogeographical studies, and also describe recent advances and propose new perspectives. The main proposals include: 1) downscaling island biogeographical studies to local/plot scale; 2) investigating geographical patterns of intra-specific genetic variation to infer dispersal processes among and within islands; 3) using applied biogeographical research to respond to the current island biodiversity crisis; and 4) applying new computer-intensive methods such as artificial intelligence (AI) approaches.

Challenges, advances and perspectives in island biogeography

Island biogeographical research is becoming more and more fashionable, with the continuous identification of new challenges that are critical for the advancement of science. In this contribution we identify biases and limitations associated with island biogeographical studies, and also describe recent advances and propose new perspectives. The main proposals include: 1) downscaling island biogeographical studies to local/plot scale; 2) investigating geographical patterns of intra-specific genetic variation to infer dispersal processes among and within islands; 3) using applied biogeographical research to respond to the current island biodiversity crisis; and 4) applying new computer-intensive methods such as artificial intelligence (AI) approaches.

Island-Biogeographical Characteristics of Insular Flora in Southern Sea of Jeollanamdo, Korea

Present work aims to establish the countermeasure for the better maintenance and preservation of insular floristic diversity at the South Sea of Jeollanamdo Province, ROK, where unique ecosystems are under threat due to climate change, anthropogenic disturbance and habitat destruction. Numerous flora reports from 15 inhabited islands and 60 uninhabited islands as well as field survey data are collated for the compilation of floristic data base and island biogeographical analysis. Out of the 1,940 vascular plant species from 180 families occurring in studies areas, 30.1 percentage or 584 plant species are physiognomically belonging to arboreal plants. Average number of species at individual island is numbered about 222 species, but it varies from about 591 species at the inhabited islands to 129 species at the uninhabited islands. Only 0.15 percentage of species with high proportion above 0.9 in its relative occurrence rate occurs at 68 islands and it includes three species, such as Pinus thunbergii, Eurya japonica and Pteridium aquilinum var. latiusculum. However, about 68 percentage of plant species occurring in study area is confined their distribution to less than seven islands. Presence of high proportion of notable plants in small islands, i.e., 10 critically endangered species compared with 5.5 species in average, 9 endangered species (average 4.2 spp.) at Sonjookdo, and 7 critically endangered species, 8 endangered species at Sokomundo may due to existence of diverse geological and topographical environmental diversity as well as lower human population density and remoteness from the mainland. Since island is small in size and geographically isolated, minor environmental and ecological burdens can cause the critical damages to the diversity of flora and vegetation, urgent island biogeographical research is needed for the scientific conservation and management of island biodiversity.

New directions in island biogeography

ABSTRACTAimMuch of our current understanding of ecological and evolutionary processes comes from island research. With the increasing availability of data on distributions and phylogenetic relationships and new analytical approaches to understanding the processes that shape species distributions and interactions, a re‐evaluation of this ever‐interesting topic is timely.LocationIslands globally.MethodsWe start by arguing that the reasons why island research has achieved so much in the past also apply to the future. We then critically assess the current state of island biogeography, focusing on recent changes in emphasis, including research featured in this special issue ofGlobal Ecology and Biogeography. Finally, we suggest promising themes for the future. We cover both ecological and evolutionary topics, although the greater emphasis on island ecology reflects our own backgrounds and interests.ResultsMuch ecological theory has been directly or indirectly influenced by research on island biotas. Currently, island biogeography is renascent, with research focusing on, among other things, patterns and processes underlying species interaction networks, species coexistence and the assembly of island communities through ecological and evolutionary time. Continuing island research should provide additional insight into biological invasions and other impacts of human activities, functional diversity and ecosystem functioning, extinction and diversification, species pools and more. Deeper understanding of the similarities and differences between island and mainland systems will aid transferability of island theory to continental regions.Main conclusionsAs research in biogeography and related fields expands in new directions, islands continue to provide opportunities for developing insights, both as natural laboratories for ecology and evolution and because of the exceptions islands often present to the usual ‘rules’ of ecology. New data collection initiatives are needed on islands world‐wide and should be directed towards filling gaps in our knowledge of within‐island distributions of species, as well as the functional traits and phylogenetic relationships of island species.

Mapping ignorance: 300 years of collecting flowering plants in Africa

AbstractAimSpatial and temporal biases in species‐occurrence data can compromise broad‐scale biogeographical research and conservation planning. Although spatial biases have been frequently scrutinized, temporal biases and the overall quality of species‐occurrence data have received far less attention. This study aims to answer three questions: (1) How reliable are species‐occurrence data for flowering plants in Africa? (2) Where and when did botanical sampling occur in the past 300 years? (3) How complete are plant inventories for Africa?LocationAfrica.MethodsBy filtering a publicly available dataset containing 3.5 million records of flowering plants, we obtained 934,676 herbarium specimens with complete information regarding species name, date and location of collection. Based on these specimens, we estimated inventory completeness for sampling units (SUs) of 25 km × 25 km. We then tested whether the spatial distribution of well‐sampled SUs was correlated with temporal parameters of botanical sampling. Finally, we determined whether inventory completeness in individual countries was related to old or recently collected specimens.ResultsThirty‐one per cent of SUs contained at least one specimen, whereas only 2.4% of SUs contained a sufficient number of specimens to reliably estimate inventory completeness. We found that the location of poorly sampled areas remained almost unchanged for half a century. Moreover, there was pronounced temporal bias towards old specimens in South Africa, the country that holds half of the available data for the continent. There, high inventory completeness stems from specimens collected several decades ago.Main conclusionsDespite the increasing availability of species occurrence data for Africa, broad‐scale biogeographical research is still compromised by the uncertain quality and spatial and temporal biases of such data. To avoid erroneous inferences, the quality and biases in species‐occurrence data should be critically evaluated and quantified prior to use. To this end, we propose a quantification method based on inventory completeness using easily accessible species‐occurrence data.

Multidimensional biases, gaps and uncertainties in global plant occurrence information.

Plants are a hyperdiverse clade that plays a key role in maintaining ecological and evolutionary processes as well as human livelihoods. Biases, gaps and uncertainties in plant occurrence information remain a central problem in ecology and conservation, but these limitations remain largely unassessed globally. In this synthesis, we propose a conceptual framework for analysing gaps in information coverage, information uncertainties and biases in these metrics along taxonomic, geographical and temporal dimensions, and apply it to all c. 370000 species of land plants. To this end, we integrated 120million point-occurrence records with independent databases on plant taxonomy, distributions and conservation status. We find that different data limitations are prevalent in each dimension. Different metrics of information coverage and uncertainty are largely uncorrelated, and reducing taxonomic, spatial or temporal uncertainty by filtering out records would usually come at great costs to coverage. In light of these multidimensional data limitations, we discuss prospects for global plant ecological and biogeographical research, monitoring and conservation and outline critical next steps towards more effective information usage and mobilisation. Our study provides an empirical baseline for evaluating and improving global floristic knowledge, along with a conceptual framework that can be applied to study other hyperdiverse clades.

Phylogeographic concordance factors quantify phylogeographic congruence among co-distributed species in the Sarracenia alata pitcher plant system.

Comparative phylogeographic investigations have identified congruent phylogeographic breaks in co-distributed species in nearly every region of the world. The qualitative assessments of phylogeographic patterns traditionally used to identify such breaks, however, are limited because they rely on identifying monophyletic groups across species and do not account for coalescent stochasticity. Only long-standing phylogeographic breaks are likely to be obvious; many species could have had a concerted response to more recent landscape events, yet possess subtle signs of phylogeographic congruence because ancestral polymorphism has not completely sorted. Here, we introduce Phylogeographic Concordance Factors (PCFs), a novel method for quantifying phylogeographic congruence across species. We apply this method to the Sarracenia alata pitcher plant system, a carnivorous plant with a diverse array of commensal organisms. We explore whether a group of ecologically associated arthropods have co-diversified with the host pitcher plant, and identify if there is a positive correlation between ecological interaction and PCFs. Results demonstrate that multiple arthropods share congruent phylogeographic breaks with S. alata, and provide evidence that the level of ecological association can be used to predict the degree of similarity in the phylogeographic pattern. This study outlines an approach for quantifying phylogeographic congruence, a central concept in biogeographic research.

Phylogenetics and biogeography of the endemic Madagascan millipede assassin bugs (Hemiptera: Reduviidae: Ectrichodiinae)

For at least the past 80my, Madagascar, a major biodiversity hotspot, has been isolated from all other landmasses. This long-term isolation, along with geologic and climatic factors within Madagascar and throughout the Indian Ocean, has undoubtedly influenced the evolution of the island’s biota. However, few systematic analyses incorporating modern divergence dating and biogeographic analyses have focused on Madagascan insects. The diverse Madagascan millipede assassin bugs (Heteroptera: Reduviidae: Ectrichodiinae) offer an opportunity to contribute to a limited body of insect-related research that explores Madagascar’s historical biogeography. A molecular dataset (COI mtDNA and 18S, 28S D2 and D3–D5 rDNAs) for 56 taxa (39 ingroup) and a combined morphological (145 characters) and molecular dataset for 110 taxa (93 ingroup) are analyzed with maximum likelihood (ML) and parsimony approaches. Based on the molecular ML phylogeny, divergence times were estimated using fossil and secondary calibrations and biogeographic analyses performed using DIVA, DEC, and DEC+j models to determine the role and patterns of vicariance and dispersal in the origin of Madagascan Ectrichodiinae. Results indicate that Ectrichodiinae in Madagascar do not form a monophyletic group, different clades are closely related to Afrotropical and Oriental lineages, and have colonized the island via transoceanic dispersal at least twice from the Oriental region and once from the Afrotropical region in the last ∼68my. Additionally, the DEC+j and DIVA models infer a single out-of-Madagascar dispersal event to the Afrotropical region. Oceanic and geologic factors that may have facilitated dispersal between these three regions are discussed. Results of the combined analyses are used to explore character support for Madagascan taxa and inform taxonomic diagnoses. Our results are congruent with the small but growing body of biogeographic research supporting Cenozoic transoceanic dispersal for Madagascan invertebrates to and from Oriental and Afrotropical regions.

Plant responses to global change: next generation biogeography

Global change has become a major ecological concern that has the potential to dramatically alter plant distributions and assemblages worldwide. The specific response of plants to global change will depend on their ability to move, evolve, or adjust through phenotypic plasticity. Advances in biogeographic research are on the verge of a giant leap forward if we can take advantage of emerging tools in genetics and genomics. In this review, we appraise how new, post-Sanger, high-throughput sequencing and associated technologies can be used by next generation biogeographers to assess plant responses to global change. First, we briefly review the recent advances in genome sequencing and available approaches of genomic analysis. Secondly, we discuss the three main plant responses to global change: migration, adaptation, and phenotypic plasticity. This review is intended to spark the interest of biogeographers who do not traditionally use genetics but could benefit from including genetic and genomic tools into their research. Our goal is to illustrate that their use can contribute to new perspective and add an additional level of resolution into future biogeographic research.

Genome Sequence Analysis of CsRV1: A Pathogenic Reovirus that Infects the Blue Crab Callinectes sapidus Across Its Trans-Hemispheric Range.

The blue crab, Callinectes sapidus Rathbun, 1896, which is a commercially important trophic link in coastal ecosystems of the western Atlantic, is infected in both North and South America by C. sapidus Reovirus 1 (CsRV1), a double stranded RNA virus. The 12 genome segments of a North American strain of CsRV1 were sequenced using Ion Torrent technology. Putative functions could be assigned for 3 of the 13 proteins encoded in the genome, based on their similarity to proteins encoded in other reovirus genomes. Comparison of the CsRV1 RNA-dependent RNA polymerase (RdRP) sequence to genomes of other crab-infecting reoviruses shows that it is similar to the mud crab reovirus found in Scylla serrata and WX-2012 in Eriocheir sinensis, Chinese mitten crab, and supports the idea that there is a distinct “Crabreo” genus, different from Seadornavirus and Cardoreovirus, the two closest genera in the Reoviridae. A region of 98% nucleotide sequence identity between CsRV1 and the only available sequence of the P virus of Macropipus depurator suggests that these two viruses may be closely related. An 860 nucleotide region of the CsRV1 RdRP gene was amplified and sequenced from 15 infected crabs collected from across the geographic range of C. sapidus. Pairwise analysis of predicted protein sequences shows that CsRV1 strains in Brazil can be distinguished from those in North America based on conserved residues in this gene. The sequencing, annotation, and preliminary population metrics of the genome of CsRV1 should facilitate additional studies in diverse disciplines, including structure-function relationships of reovirus proteins, investigations into the evolution of the Reoviridae, and biogeographic research on the connectivity of C. sapidus populations across the Northern and Southern hemispheres.

On the integration of biotic interaction and environmental constraints at the biogeographical scale

Biogeography is primarily concerned with the spatial distribution of biodiversity, including performing scenarios in a changing environment. The efforts deployed to develop species distribution models have resulted in predictive tools, but have mostly remained correlative and have largely ignored biotic interactions. Here we build upon the theory of island biogeography as a first approximation to the assembly dynamics of local communities embedded within a metacommunity context. We include all types of interactions and introduce environmental constraints on colonization and extinction dynamics. We develop a probabilistic framework based on Markov chains and derive probabilities for the realization of species assemblages, rather than single species occurrences. We consider the expected distribution of species richness under different types of ecological interactions. We also illustrate the potential of our framework by studying the interplay between different ecological requirements, interactions and the distribution of biodiversity along an environmental gradient. Our framework supports the idea that the future research in biogeography requires a coherent integration of several ecological concepts into a single theory in order to perform conceptual and methodological innovations, such as the switch from single‐species distribution to community distribution.

Cafioquedus gularis Sharp, 1886 and other poorly understood Staphylinini: a review of the New Zealand fauna of the tribe with discussion of its potential for biogeography (Insecta: Coleoptera: Staphylinidae)

ABSTRACTThe formation of New Zealand's terrestrial biota is a subject where conclusions depend strongly on the properties of the focal organisms. Here, we bring the systematic knowledge of the New Zealand fauna of the very diverse rove beetle tribe Staphylinini closer to the level appropriate for biogeographic research. In particular, the hitherto puzzling New Zealand endemic genus Cafioquedus is considered a member of the Creophilus-complex (Staphylinina), while several other endemic species proved to be misidentifications of common introduced species. With these taxonomic updates, and taking into account the relative age and extant distributions of lineages that occur in New Zealand, we conclude the following: 1. the New Zealand Staphylinini are dominated (66%) by the endemic members of the subtribe Amblyopinina, which are likely Gondwanan paleoendemics; 2. species from the Creophilus- and Cafius-complexes (Staphylinina and Philonthina, respectively), are neoendemics (15%), possibly resulting from trans-oceanic colonisation; 3. human-transported adventive species (19%) form the notable, most recent and taxonomically heterogeneous component of the New Zealand fauna. Cafioquedus gularis Sharp, 1886 is redescribed. The following new combinations and synonymies are proposed: Philonthus longicornis Stephens, 1832 = Philonthus burrowsi (Broun, 1915), comb. nov., syn. nov.; Philonthus politus (Linnaeus, 1758) = Philonthus ohiaensis (Broun, 1923), syn. nov.; Philonthus umbratilis (Gravenhorst, 1802) = Philonthus insularis (Bernhauer and Schubert, 1916), syn. nov.; Sphingoquedius novaezeelandiae (Duvivier, 1883), comb. nov. = Sphingoquedius mannaiaensis (Cameron, 1945), comb. nov., syn. nov.; Quediomimus hybridus (Erichson, 1840), comb. nov. = Quediomimus taurus (Blackburn, 1888), comb. nov. = Quediomimus brookesi Cameron, 1948, syn. nov. A lectotype is designated for Philonthus insularis (Bernhauer and Schubert, 1916).

Ecology and Biogeography, Future Perspectives: Example Marine Parasites

Ecology and Biogeography, Future Perspectives: Example Marine Parasites This article draws attention to some perspective that must be considered in future research in biogeography and ecology. Both disciplines are closely connected: biogeography, the study of biodiversity and its patterns in space and time, depends on ecology, the study of interactions between organisms and their environment, for elucidating reasons for the patterns.

Geographic body size variation in ectotherms: effects of seasonality on an anuran from the southern temperate forest.

BackgroundBody size variation has played a central role in biogeographical research, however, most studies have aimed to describe trends rather than search for underlying mechanisms. In order to provide a more comprehensive understanding of the causes of intra-specific body size variation in ectotherms, we evaluated eight hypotheses proposed in the literature to account for geographical body size variation using the Darwin’s frog (Rhinoderma darwinii), an anuran species widely distributed in the temperate forests of South America. Each of the evaluated hypotheses predicted a specific relationship between body size and environmental variables. The level of support for each of these hypotheses was assessed using an information-theoretic approach and based on data from 1015 adult frogs obtained from 14 sites across the entire distributional range of the species.ResultsThere was strong evidence favouring a single model comprising temperature seasonality as the predictor variable. Larger body sizes were found in areas of greater seasonality, giving support to the “starvation resistance” hypothesis. Considering the known role of temperature on ectothermic metabolism, however, we formulated a new, non-exclusive hypothesis, termed “hibernation hypothesis”: greater seasonality is expected to drive larger body size, since metabolic rate is reduced further and longer during colder, longer winters, leading to decreased energy depletion during hibernation, improved survival and increased longevity (and hence growth). Supporting this, a higher post-hibernation body condition in animals from areas of greater seasonality was found.ConclusionsDespite largely recognized effects of temperature on metabolic rate in ectotherms, its importance in determining body size in a gradient of seasonality has been largely overlooked so far. Based on our results, we present and discuss an alternative mechanism, the “hibernation hypothesis”, underlying geographical body size variation, which can be helpful to improve our understanding of biogeographical patterns in ectotherms.

Global biogeography of marine fungi is shaped by the environment

Abstract Fungi are essential components of marine ecosystems, yet very little is known about their global distribution and diversity in the marine environment. In this study, we analyzed marine fungal community structure at a global scale using the International Census of Marine Microbes dataset. Marine fungal communities sampled from both the water column and sediments were compared. Based on the sequences of the nuclear ribosomal small subunit V9 region, 2200 operational taxonomic units (OTUs) were identified at 97% similarity. There was a significant distinction between the pelagic and benthic communities, with 15.4% OTUs shared between the two realms. Environmental factors, particularly sample depth, oxygen, and nitrate, strongly correlated with the fungal community composition and explained more variance than did geographic distance. This study represents the first global-scale analysis of marine fungal community structure, and highlights potential opportunities for research in marine fungal ecology and biogeography.

Effects of Tree Size, Shade Tolerance, and Spatial Pattern on the Mortality of Woody Plants in a Seminatural Forest in Central Kentucky

Previous biogeographical research has investigated the mortality of woody plants, emphasizing tree size, shade tolerance, and competition individually as critical factors. Few researchers, though, have empirically evaluated the simultaneous and relative importance of these three factors in a single study. Based on a thirty-five-year study within the University of Kentucky Arboretum, we report that none of the factors exerted an overriding influence on the tree survivorship alone. Rather, they were tightly intertwined in a complex way. Our study indicates that the three factors have contributed perhaps equally or at least simultaneously to the overall demographic processes in the woodland.