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Open Access Publications from the University of California

Frontiers of Biogeography

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Frontiers of Biogeography (FoB) is the scientific journal of the International Biogeography Society (IBS,, a not-for-profit organization dedicated to promotion of and public understanding of the biogeographical sciences.  IBS launched FoB to provide an independent forum for biogeographical science, with the academic standards expected of a journal operated by and for an academic society.

Issue cover
Acropora intermedia (Brook, 1891) in the southeastern channel of Ant (Ahnd) Atoll, Pohnpei, Federated States of Micronesia, 2018.  See the article by Cacciapaglia and colleagues, in this issue, on how legacies of an ice-age world may explain contemporary biogeographical provinces of corals. Photo by Robert van Woesik.

Opinions, Perspectives & Reviews

Sonoric geography – addressing the silence of biogeography

In 2015, we called upon our colleagues to address a glaring oversight of a potentially transformative frontier in biogeography – the geography of sound (Lomolino et al. 2015).  Our purpose here is to lay the conceptual foundations, based on the fundamental unifying principles of biogeography, to guide the development of the nascent field of sonoric geography.  We define sonoric geography as an emerging subdiscipline of biogeography that attempts to discover and articulate patterns of geographic variation in the acoustic properties of biological communities and identify the underlying, causal explanations for those patterns.

We see at least two major benefits to this initiative.  First, it will advance the field of biogeography by expanding the spectrum of biological properties studied – demonstrating how the field’s fundamental, unifying principles can be applied to a novel component of biological diversity – sound and acoustic assemblages across the principal geographic dimensions (area, isolation, elevation/depth, and latitude).  Second, a research program in sonoric geography will, in synergism, advance the fields of soundscape ecology (Pijanowski et al. 2011, Slabbekoorn 2018) and acoustic ecology (Wrightson 2000) by integrating an explicit geographic context into their conceptual foundations, empirical investigations, and applications for conserving biological diversity, sensu lato—again, all this guided by the fundamental unifying principles of biogeography.

Dispersal vs. vicariance: the origin of India’s extant tetrapod fauna

Given the Indian block’s ancient association with Gondwana and subsequent separation from Africa, then Madagascar, then the Seychelles, vicariance has often been invoked to explain the distribution of some of India’s extant biota that might have had Gondwanan origins. Here I review phylogenetic studies and fossil data of Indian tetrapods to ascertain the contribution of dispersal and vicariance in shaping the assemblage. Paleogene dispersal into India accounts for almost all of the tetrapod clades in India. Vicariance is invoked for three groups, all fossorial; the caecilians, the frog family Nasikabatrachidae and the blindsnake family Gerrhopilidae. This review concludes that practically all of India’s Late Cretaceous tetrapod fauna (of Gondwanan origin) was extirpated during the Cretaceous-Paleogene mass extinction, which may have been exacerbated by the coeval volcanism associated with the emplacement of the Deccan Trap large igneous province. Subsequently, the tetrapod fauna was built up by incoming elements as India advanced towards Asia, docking with the continent in the Paleogene.


Thresholds and the species–area relationship: a set of functions for fitting, evaluating and plotting a range of commonly used piecewise models in R

An increasing number of studies have focused on identifying thresholds in the species–area relationship (SAR). The most common approach in such studies is to use piecewise regression models. While a few software packages are available for fitting piecewise models, these resources are general regression packages (i.e., they are not specifically designed for the analysis of SAR data) and tend to only provide functions for fitting a subset of the piecewise models proposed in the SAR literature. Given the large number of SAR studies now fitting piecewise models, there is a need for a software package that provides functions for fitting a range of piecewise models, including continuous, left-horizontal and discontinuous models in addition to supplementary functions for analysing model fits, in the context of SAR data. To this end, we provide a set of functions for fitting six piecewise regression models to SAR data, calculating confidence intervals around the breakpoint estimates (for certain models), comparing the models using various information criteria, and plotting the resultant model fits. Here, we present these functions and illustrate them using a selection of empirical datasets. These functions are implemented in the freely available and open-source R package ‘sars.’

Research Letters

On the scaling and standardization of charcoal data in paleofire reconstructions

Understanding the biogeography of past and present fire events is particularly important in tropical forest ecosystems, where fire rarely occurs in the absence of human ignition. Open science databases have facilitated comprehensive and synthetic analyses of past fire activity, but charcoal datasets must be standardized (scaled) because of variations in measurement strategy, sediment type, and catchment size.  Here, we: i) assess how commonly used metrics of charcoal scaling perform on datasets from tropical forests; ii) introduce a new method called proportional relative scaling, which down-weights rare and infrequent fire; and iii) compare the approaches using charcoal data from four lakes in the Peruvian Amazon. We found that Z-score transformation and relative scaling (existing methods) distorted the structure of the charcoal peaks within the record, inflating the variation in small-scale peaks and minimizing the effect of large peaks. Proportional relative scaling maintained the structure of the original non-scaled data and contained zero values for the absence of fire. Proportional relative scaling provides an alternative scaling approach when the absence of fire is central to the aims of the research or when charcoal is infrequent and occurs in low abundances.

Research Articles

Another rejection of the more-individuals-hypothesis: Carrion beetles (Silphidae, Coleoptera) in the Southern Rocky Mountains

Beetles are the most diverse animal clade on the planet, and understanding the mechanisms underlying their diversity patterns is critical to understanding animal biodiversity in general. Using carrion beetles (Silphidae; Coleoptera), I test the more-individuals hypothesis (MIH), consisting of positive climatic impacts on food resources leading to increased abundance and then diversity. I also test competing mechanistic hypotheses, including interacting effects of climate, local vegetation, habitat diversity, habitat heterogeneity, soil diversity, and elevational area. Carrion beetle species richness and abundances were estimated using 40 standardized pitfall traps set for 90 days at 30 survey sites on two elevational gradients in the Front Range and San Juan Mountains, Colorado, USA. Standardized measurements assessed 13 vegetative characteristics, food resources (mammal abundances), soil diversity, habitat diversity, elevational area, temperature, precipitation and net primary productivity at each site. Structural equation models were used to test competing diversity hypotheses and mechanisms. Species richness peaked at intermediate elevations on both gradients, whereas abundance was unimodal on one gradient and decreasing on the other. The MIH mechanism was rejected; all four potential SEM model constructions were unsupported and the majority of all SEM models did not support relationships between abundance and diversity or climate and food resources. The best SEM model included direct influences of temperature, vegetation biomass, and food resources but with separate effects on diversity and abundance. Carrion beetles were more diverse and abundant in sites with dense understory vegetation and warm temperatures, while higher abundances were also linked to more food resources. This climate-biotic relationship is likely due to a need for microclimates and microhabitats to mediate physiological tradeoffs of desiccation and thermoregulation with predation. This suggests a general hypothesis for beetle diversity and abundance, particularly on arid-based mountains globally.

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Devising a method to remotely model and map the distribution of natural landscapes in Europe with the greatest recreational amenity value (cultural services)

With a growing emphasis on the societal benefits gained through recreation outdoors, a method is needed to identify which spaces are most valuable for providing those benefits. Social media platforms offer a wealth of useful information on where people prefer to enjoy the outdoors. We combined geotagged images from Flickr with several environmental metrics in a Maxent model to calculate the probability of a photograph being taken (the potential supply of recreational amenity). We then built a set of population density kernels to express the potential demand of recreational amenity. Linear regression was used to compare supply and demand layers to visitation records from 540 recreation sites across Europe. The result was a map estimating the number of visitors/km2/year. Our analysis showed that natural areas near population centres deliver more recreational benefit than attractive sites in remote locations. The former should therefore be prioritised by planners and policymakers seeking to protect or improve recreational amenity.

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Northern Fennoscandia via the British Isles: evidence for a novel post-glacial recolonization route by winter moth (Operophtera brumata)

The frequency and severity of outbreaks by pestiferous insects is increasing globally, likely as a result of human-mediated introductions of non-native organisms. However, it is not always apparent whether an outbreak is the result of a recent introduction of an evolutionarily naïve population, or of recent disturbance acting on an existing population that arrived previously during natural range expansion.  Here we use approximate Bayesian computation to infer the colonization history of a pestiferous insect, the winter moth, Operophtera brumata L. (Lepidoptera: Geometridae), which has caused widespread defoliation in northern Fennoscandia. We generated genotypes using a suite of 24 microsatellite loci and find that populations of winter moth in northern Europe can be assigned to five genetically distinct clusters that correspond with 1) Iceland, 2) the British Isles, 3) Central Europe and southern Fennoscandia, 4) Eastern Europe, and 5) northern Fennoscandia. We find that the northern Fennoscandia winter moth cluster is most closely related to a population presently found in the British Isles, and that these populations likely diverged around 2,900 years ago. This result suggests that current outbreaks are not the result of a recent introduction, but rather that recent climate or habitat disturbance is acting on existing populations that may have arrived to northern Fennoscandia via pre-Roman traders from the British Isles, and/or by natural dispersal across the North Sea likely using the Orkney Islands of northern Scotland as a stepping-stone before dispersing up the Norwegian coast.

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Disjunct plant species in South American seasonally dry tropical forests responded differently to past climatic fluctuations

Seasonally dry tropical forests (STDFs) are a main component of open seasonally dry areas in South America and their biogeography is understudied compared to evergreen forests. In this work, we identify vascular plant species with long-distance disjunctions across STDF patches of South America based on information available in online repositories and on species taxonomy and distribution, to explore species’ biogeographic patterns. Specifically, we combine distribution data from the Brazilian Flora 2020 Project (BFG) and the Global Biodiversity Information Facility (GBIF) to identify species with a peri-Amazonian distribution, and then use species distribution models to discuss possible scenarios of peri-Amazonian distributions under Pleistocene climatic fluctuations. We identified 81 candidate species for peri-Amazonian distributions in STDFs, including shrubs, herbs, trees and lianas, and provided a summary of their main fruit dispersion syndrome based on the literature to identify prevalent dispersal patterns. The study species responded differently to Pleistocene climatic fluctuations, with both contractions and expansions through time in different rates and do not show consistent larger distributions during past climate conditions. Our results show that a peri-Amazonian distribution is also present in growth-forms other than trees. Also, the prevalence of species with long-distance dispersal strategies such as wind or vertebrate-dispersed can suggest, although biased for Neotropical taxa, an alternative scenario of long-distance dispersal, possibly using stepping-stones of azonal vegetation. We argue that such an alternative scenario, especially for species disjunct with long-dispersal abilities, should be considered to test if STDF disjunctions are relics of a past widespread distribution or not.

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Legacies of an ice-age world may explain the contemporary biogeographical provinces of corals

This study hindcast the geographic distribution of 18 Indo-Pacific scleractinian coral species, with different sensitivities to modern heat stress, into the last glacial maximum (LGM), some 18,000 years ago, when sea-surface temperatures were 2–4oC cooler and sea level was ~130 m lower than on contemporary reefs. Identifying geographic provinces from the past may provide clues into genetic affiliations through time and provide some insight into how some coral species might respond to contemporary climate change. Coral habitat in the Indo-Pacific was reduced by 70% in the LGM. We identified five Indo-Pacific biogeographical provinces for corals during the LGM — (i) the western Indian Ocean, (ii) Southeast Asia, (iii) Indonesia and northwestern Australia, (iv) northeastern Australia and the Pacific Islands, and (v) the eastern Pacific. These provinces align with provinces recently identified using genetic markers. Given that the Quaternary was dominated by glacial conditions, the distributional legacies left through glacial dominance over that 2.6 million-year period may have also left evolutionary legacies. These glacial legacies may explain why contemporary corals live close to their upper thermal thresholds, which in turn have major consequences as we move into unprecedented rates of ocean warming.

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Global biodiversity and biogeography of rhodolith-forming species

Unattached nodules of calcareous red algae (Rhodophyta), known as rhodoliths, are widely reported and studied in places that extend from the tropics to polar latitudes. Factors controlling the distribution of the rhodolith-forming species remain poorly understood. A review of the global distribution of present-day rhodolith beds was undertaken, collating information on 106 rhodolith-forming species from 10 families, representing 21 genera distributed through 11 realms: 1) Arctic, 2) Temperate Northern Atlantic, 3) Temperate Northern Pacific, 4) Tropical Atlantic, 5) Western Indo-Pacific, 6) Central Indo-Pacific, 7) Eastern Indo-Pacific, 8) Tropical Eastern Pacific, 9) Temperate South America, 10) Temperate Australasia, and 11) Southern Ocean. The Central Indo-Pacific and Temperate Australasia proved to be the most diverse realms. Of 62 provinces across these realms, the Tropical Southwestern Atlantic, the Mediterranean Sea and the Tropical East Pacific feature the highest diversity of rhodolith-forming species. A significant proportion of the 106 species (14.2%; 15 species) are endemic to a single biogeographic province. Species richness is weakly related to sampling effort (r2=0.573) and unrelated to littoral area (r2=0.012). Even when high latitude provinces are excluded from the analysis, no correlation between species richness and littoral was found (r2 = 0.0005). A wider, evolutionary-time framework revealed that the existence of marine barriers and the geological age of their final emplacement are key elements to explaining compositional differences between the rhodoliths of former contiguous areas (e.g., Pacific versus Atlantic shores of Panama and Costa Rica, in the Central America; eastern Mediterranean Sea versus Red Sea and Gulf of Aden). Finally, we propose that the lower diversity of the rhodolith-forming species in the tropical Pacific Ocean when compared to the Atlantic Ocean (23 versus 33 spp.), may be linked to the higher abundance of corals and coral reefs in the Pacific, which act as competitors with coralline algae for space.

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A comprehensive monograph on the ecology and distribution of the House bunting (Emberiza sahari) in Algeria

The House bunting (Emberiza sahari Levaillant, 1850) is a human commensal passerine bird species, characteristic of urban environments in the Sahara Desert of Algeria. Its distribution in Algeria, with particular emphasis in Ghardaïa, was investigated using two sampling methods: progressive frequency sampling and point abundance index, with ecological field data collected during 2017-2019. Morphological biometric measurements were carried out on free-living individuals for each sex. Reproduction phenology and success were surveyed through the breeding season (February‒September) during 2018‒2019. Trophic behavior was studied by direct observations of foraging individuals. Results showed that the species range in Algeria is larger than shown by data from the literature, with expansion northwards within the country. At a finer scale, in Saharan cities, the species prefers old and traditional urban environments, where its densities are higher than within modern urban habitats. At a national scale, we found that the species range is not restricted to desert climates, but extends towards the north of Algeria, including the semi-arid steppe rangelands of the Hauts-Plateaux region. Range changes are attributed to changes in building practices and climate change. Adult females were heavier and slightly larger than males, whose head plumage had different coloration patterns compared to females. Nests weighed 82.03 ± 20.77 g (mean ± standard deviation) and consisted of 72% plant materials, 19% animal-origin materials and 9% inert constituents. The nest cups were oval in form, top-lined and stuffed with diverse material. House buntings nest under the roofs of uninhabited houses, in stairwells, traditional water wells, and holes within walls. Nesting height averaged 2.14 ± 0.8 m. In Ghardaia, courtship and pair formation began mid-February. Females can raise up to three successive broods (March-September), with 31‒34 days/brood including 14‒15 days for egg incubation. Clutch size is typically 2‒3 eggs. The diet of the House bunting included seeds of annual grasses dominated by Poaceae species. The species also fed on anthropogenic food remains, and sometimes on insects, especially during the breeding period.

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FB Information



Acropora intermedia (Brook, 1891) in the southeastern channel of Ant (Ahnd) Atoll, Pohnpei, Federated States of Micronesia, 2018.  See the article by Cacciapaglia and colleagues, in this issue, on how legacies of an ice-age world may explain contemporary biogeographical provinces of corals. Photo by Robert van Woesik.