Frontiers of Biogeography

Technological and methodological advances in biogeography, phylogenetics, and bioinformatics during the past couple of decades provide greatly enhanced insights into the evolutionary history of birds in space and time. Molecular data, especially next-generation DNA sequencing, have produced a revolution in reconstructing the phylogenetic history of lineages. These advances shed a new light on the mode, tempo, and spatial context of differentiation processes that shaped the composition and structure of extant forest bird communities of temperate forests of the Northern Hemisphere. This paper offers a framework for understanding this history based on analytical tools that allow us to decipher the imprint of changes in the geographic configuration of land masses and in climates since the Mesozoic, with a focus on the temperate-tropical flyways that connect the massive forest blocks of the Northern to those of the Southern Hemispheres. Differentiation of most extant bird lineages and species has been shown to have begun in a deeper past than formerly thought, although recent analyses from molecular phylogenies also support the much-debated Late Pleistocene model of speciation. Geographical connections between tropical and temperate realms make north-south flyways important drivers of differentiation for many lineages. The histories of differentiation and colonisation of clades, including both resident and long-distance migrants, are discussed in relation to two alternative theories, the ‘southern home theory’ and the ‘northern home theory’. The region-specific characters of the bird faunas and differences between the main temperate forest blocks of the Northern Hemisphere are discussed in light of the hypotheses concerning dispersal processes related with geographical configuration of land masses. Differential dispersal-colonisation rates from tropical regions and subsequent diversification in temperate regions (and vice versa) are also considered. The causes of the observed decline in diversification rates during the Pleistocene are examined from phylogenetic reconstructions of various clades.

Estimates of species’ ranges can inform many aspects of biodiversity research and conservation-management decisions. Many practical applications need high-precision range estimates that are sufficiently reliable to use as input data in downstream applications. One solution has involved expert-generated maps that reflect on-the-ground field information and implicitly capture various processes that may limit a species’ geographic distribution. However, expert maps are often subjective and rarely reproducible. In contrast, species distribution models (SDMs) typically have finer resolution and are reproducible because of explicit links to data. Yet, SDMs can have higher uncertainty when data are sparse, which is an issue for most species. Also, SDMs often capture only a subset of the factors that determine species distributions (e.g., climate) and hence can require significant post-processing to better estimate species’ current realized distributions. Here, we demonstrate how expert knowledge, diverse data types, and SDMs can be used together in a transparent and reproducible modeling workflow. Specifically, we show how expert knowledge regarding species’ habitat use, elevation, biotic interactions, and environmental tolerances can be used to make and refine range estimates using SDMs and various data sources, including high-resolution remotely sensed products. This range-refinement approach is primed to use various data sources, including many with continuously improving spatial or temporal resolution. To facilitate such analyses, we compile a comprehensive suite of tools in a new R package, maskRangeR, and provide worked examples. These tools can facilitate a wide variety of basic and applied research that requires high-resolution maps of species’ current ranges, including quantifications of biodiversity and its change over time.

The island monarch (Monarcha cinerascens) was an original example of the “supertramp strategy”. This involves well-developed dispersal specialisation, enabling a species to colonise remote islands but leaving it competitively inferior. Supertramps are hypothesised to be excluded from larger islands by superior competitors. It is the only original Melanesian supertramp to occur in Wallacea, home also to the sedentary pale-blue monarch (Hypothymis puella). We interrogate the supertramp strategy and its biogeographical underpinnings by assessing the population structure of these two monarchs. We sampled island and pale-blue monarchs in Wallacea, collecting DNA and morphological data. We investigated monarch population structure by applying ABGD and Bayesian and Maximum Likelihood methods to their ND2 and ND3 genes. We constructed linear models to investigate the relationships between genetic divergence, dispersal ability, and island area, elevation, and isolation. Wallacea’s deep waters restrict gene flow even in a supertramp, as the Wallacean and Melanesian island monarchs are likely separate species (mean genetic distance: 2.7%). This mirrors the split of the pale-blue monarch from Asia’s black-naped monarch (Hypothymis azurea). We found further population structure within Wallacean and Melanesian island monarch populations. Their genetic divergence was related to elevation, area, and isolation of islands, as well as dispersal ability of birds. However, dispersal ability was independent of island elevation and area. Rather than being r-selected on small, disturbance-prone islands, our results support the view that the island monarch’s supertramp lifestyle is a temporary stage of the taxon cycle, i.e. supertramps may transition into resident species after colonisation. Our models suggest that more dispersive monarchs reach more distant islands, and divergence is promoted on islands that are more distant or larger or more permanent, without selection against dispersal ability per se. We suggest that supertramp lifestyle helps determine the distribution of species across islands, not necessarily the divergence occurring thereafter.

Microbes have a dominant role in nutrient cycling processes in the world’s deserts, where growth and activity are limited by the availability of water. In order to understand the dynamics of water availability in a desert system and how it may affect the soil microbiome, we analysed soil temperature and relative humidity fluctuations recorded between April 2018 and April 2020 across a precipitation gradient in the Namib Desert and compared them with recorded data from satellites and nearby weather stations. This allowed us to assess the possible impact of fog and rain events in terms of biologically-available water. Using published literature on the water activity limits for various physiological processes in microorganisms, we were able to infer the annual ‘metabolic windows’ for desert microbial communities across the longitudinal precipitation gradient. Specifically, soil surface microbial communities were estimated to have the capacity for active growth for an average of 184- 363 hours per year with the duration heavily dependent on intermittent rainfall events. During the relatively wet period of April 2018 - March 2019, the maximum growth window was found in the hyper-arid central region of the transect (approximately 100 km from the coast). During the dryer 2019- 2020 period, there was almost no predicted growth capacity in the hyper-arid region but substantial metabolic windows both near the coast and for the eastern inland areas, where water input comes in the form of fog and moist coastal air, and higher rainfall, respectively. As the first detailed study of the temperature and relative humidity characteristics of Namib Desert near-surface soils, this study provides valuable insights into the biogeography of microbial communities. In addition, the estimates for organismal functionality calculated in this study offer a baseline for future quantitation of the impacts of climate change on the functional capacity of desert soil microbiomes.

Disturbances of oceanic origin can severely affect plant communities on islands, but it is unclear whether they promote or deter biological invasions. Here, I collected floristic data from 97 small islands subject to different levels of ocean-borne disturbances (i.e. inside and outside Wellington Harbour, New Zealand). First, I tested how relationships between the richness of native and exotic species and island characteristics (e.g. area, isolation, height, distance from nearest dwelling) changed depending on island location. Next, I assessed compositional differences on inner and outer islands for both native and exotic species, and how they vary with geographic distance between islands (i.e. distance-decay). Results show that the richness of both native and exotic plant species was similarly related to island characteristics regardless of island location. Both native and exotic species richness consistently increased with area and nearest dwelling. However, only exotics richness always declined with isolation, while natives richness alone consistently increased with height (elevation). Natives on outer, more exposed islands were floristically more homogenous, and compositional differences changed less strongly with the distance between islands than inside Wellington harbour. In contrast, exotics exhibited similar distributional patterns regardless of island location. Different levels of ocean-borne disturbances might explain distinct distributional patterns in native species. Conversely, results for exotic species might reflect a lack of coastal specialists in the species pool. Perhaps time-lags in the invasion process and non-equilibrium dynamics play a role as well. Conservation bodies should similarly manage islands sustaining different levels of ocean-borne disturbances.

Marshall et al. recently estimated population densities, range sizes, instant and cumulative total population sizes for Tyrannosaurus rex with narrow ranges of uncertainly. I revisit the assumptions that led them to these conclusions and show that many of these parameters are associated with much wider margins of error than they estimated. Biogeographic estimates seem to have been especially unrealistic, seriously hampering the effort to calculate population level parameters. I posit that biogeographic and ecological uncertainties make it extremely unlikely to be able to estimate population sizes of long-extinct species.

Interested in the absolute preservation rate of one of the best understood dinosaurs, Tyrannosaurus rex, Marshall et al. (2021) estimated the total number that ever lived.  This required estimating its geographic range, longevity, and population density, which required estimating its body mass and physiology.  Meiri (2021) questions the precision of our estimates, emphasizing the difficulties in estimating population densities and geographic ranges for living species, and in error propagation.  He posits that estimating population sizes of extinct species is ‘extremely unlikely’.  While we agree that we did not quantify some sources of uncertainty (for example, in the physiology of T. rex), our calculations do not depend on short-term changes in population density and geographic range, but rather on their long-term averages, rendering many of Meiri’s (2021) concerns moot.  We also note that Monte Carlo Simulation propagates uncertainties robustly.  That is, we feel we have, in fact, developed a general method for estimating population sizes for extinct species, regardless of any shortfalls in implementation.

Review of:

The Species–Area Relationship: Theory and Application

Edited by Thomas J. Matthews, Kostas A. Triantis, Robert J. Whittaker

Cambridge University Press

March 2021

Online ISBN:9781108569422

https://doi.org/10.1017/9781108569422

Mammalian paleoecology: using the past to study the present, by Felisa A. Smith, 2021, Johns Hopkins University Press, 260 pp., ISBN 9781421441405 (hardcover).