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Aim: Discontinuity in the distribution of genetic diversity (often based on mtDNA) is usually interpreted as evidence for phylogeographic breaks, underlying vicariant units. However, a misleading signal of phylogeographic break can arise in the absence of barrier to gene flow, under mechanisms of isolation by distance (IBD). How and under which conditions phylogeographic breaks can be reliably differentiated from populations evolving under IBD remain unclear. Here, we use multi-locus sequence data from a widely distributed lizard species to address these questions in an empirical setting. Location: Morocco. Taxon: Spiny-footed lizard (Acanthodactylus erythrurus), Squamata: Lacertidae. Methods: Using 325 samples from 40 localities, we identified genetic discontinuities within A. erythrurus based on a mitochondrial fragment and nine nuclear markers independently. Using the nuclear markers, we then applied linear regression models to investigate whether genetic divergence could be explained by geographical distances alone, or barriers to gene flow (real phylogeographic breaks). Results: A. erythrurus is characterized by an important mitochondrial diversity, with 11 strongly supported phylogeographic lineages with a crown age of 6 Mya. Nuclear markers, however, yielded weak phylogenetic support for these lineages. Using clustering methods based on genotypes at nine nuclear loci, we identified phylogeographic clusters that were partly discordant with the mtDNA lineages. Tests of IBD delimited at least four groups of populations separated by barriers to gene flow, but unambiguous separation of vicariance from IBD remained challenging in several cases. Main conclusions: The genetic diversity of A. erythrurus originates from a mix of IBD and vicariance, which were difficult to distinguish, and resulted in similar levels of mitochondrial differentiation. These results highlight that phylogeographic breaks inferred from mitochondrial data should be further investigated using multi-locus data and explicit testing to rule out alternative processes generating discontinuities in mitochondrial diversity, including IBD. We identified four groups of populations within A. erythrurus, separated by barriers to gene flow, but even using nine independent nuclear makers the power of our approach was limited, and further investigation using genome-wide data will be required to resolve the phylogeographic history of this species.

Elucidating the evolutionary process of animal adaptation to deserts is key to understanding adaptive responses to climate change. Here we generated 82 individual whole genomes of four fox species (genus Vulpes) inhabiting the Sahara Desert at different evolutionary times. We show that adaptation of new colonizing species to a hot arid environment has probably been facilitated by introgression and trans-species polymorphisms shared with older desert resident species, including a putatively adaptive 25 Mb genomic region. Scans for signatures of selection implicated genes affecting temperature perception, non-renal water loss and heat production in the recent adaptation of North African red foxes (Vulpes vulpes), after divergence from Eurasian populations approximately 78 thousand years ago. In the extreme desert specialists, Rueppell's fox (V. rueppellii) and fennec (V. zerda), we identified repeated signatures of selection in genes affecting renal water homeostasis supported by gene expression and physiological differences. Our study provides insights into the mechanisms and genetic underpinnings of a natural experiment of repeated adaptation to extreme conditions.

We describe changes in the cropland distribution for physiographic and bioregions of continental Ecuador between 2000 and 2016 using Landsat satellite data and government statistics. The cloudy conditions in Ecuador are a major constraint to satellite data analysis. We developed a two-stage cloud filtering algorithm to create cloud-free multi-temporal Landsat composites that were used in a Random Forest model to identify cropland. The overall accuracy of the model was 78% for the Coast region, 86% for the Andes, and 98% for the Amazon region. Cropland density was highest in the coastal lowlands and in the Andes between 2500 and 4400 m. During this period, cropland expansion was most pronounced in the Páramo, Chocó Tropical Rainforests, and Western Montane bioregions. There was no cropland expansion detected in the Eastern Foothill forests bioregion. The satellite data analysis further showed a small contraction of cropland (4%) in the Coast physiographic region, and cropland expansion in the Andes region (15%), especially above 3500m, and in the Amazon region (57%) between 2000 and 2016. The government data showed a similar contraction for the Coast (7%) but, in contrast with the satellite data, they showed a large agricultural contraction in the Andes (39%) and Amazon (50%). While the satellite data may be better at estimating relative change (trends), the government data may provide more accurate absolute numbers in some regions, especially the Amazon because separating pasture and tree crops from forest with satellite data is challenging. These discrepancies illustrate the need for careful evaluation and comparison of data from different sources when analyzing land use change.

One of the most celebrated textbook examples of physiological adaptations to desert environments is the unique ability that desert mammals have to produce hyperosmotic urine. Commonly perceived as an adaptation mainly observed in small rodents, the extent to which urine-concentrating ability has evolved independently in distinct mammalian lineages has not previously been assessed using modern phylogenetic approaches. We review urine-concentrating ability data from the literature in 121 mammalian species with geographic ranges encompassing varying climatic conditions. We explicitly test the general hypothesis that desert-dwelling mammals have evolved greater ability to concentrate urine than non-desert species, controlling for body mass, phylogenetic affinity and other covariates. Ancestral state reconstruction across our dataset’s phylogeny shows that the ability to produce hyperosmotic urine, measured as maximum urine osmolality, has evolved convergently in mammalian species with geographic ranges characterised by low mean annual aridity index. Phylogenetic generalised least-squares (PGLS) models show that the mean annual aridity index of a species’ geographic range largely predicts its urine-concentrating ability, even when accounting for body mass differences, phylogenetic correlations, the specific condition under which urine osmolality was measured, the method used to measure urine osmolality, and the species’ diet. In contrast, we find much weaker correlations between mass-adjusted basal metabolic rate and environmental variables when analysing 84 of the species included in the urine osmolality analysis. Taken together, our results not only show that desert mammals effectively concentrate more urine than non-desert mammals, but further suggest that aridity is likely to have been one of the main selective pressures leading to increasing maximum urine-concentrating ability and driving its repeated evolution in different desert mammalian lineages.

Deserts are among the harshest environments on Earth. The multiple ages of different deserts and their global distribution provide a unique opportunity to study repeated adaptation at different timescales. Here, we summarize recent genomic research on the genetic mechanisms underlying desert adaptations in mammals. Several studies on different desert mammals show large overlap in functional classes of genes and pathways, consistent with the complexity and variety of phenotypes associated with desert adaptation to water and food scarcity and extreme temperatures. However, studies of desert adaptation are also challenged by a lack of accurate genotype-phenotype-environment maps. We encourage development of systems that facilitate functional analyses, but also acknowledge the need for more studies on a wider variety of desert mammals.