All species concepts are rooted in reproductive, and ultimately genealogical, relations. Genetic data are thus the most important source of information for species delimitation. Current ease of access to genomic data and recent computational advances are blooming a plethora of coalescent-based species delimitation methods. Despite their utility as objective approaches to identify species boundaries, coalescent-based methods (1) rely on simplified demographic models that may fail to capture some attributes of biological species, (2) do not make explicit use of the geographic information contained in the data, and (3) are often computationally intensive. In this article, we present a case of species delimitation in the Erebia tyndarus species complex, a taxon regarded as a classic example of problematic taxonomic resolution. Our approach to species delimitation used genomic data to test predictions rooted in the biological species concept and in the criterion of coexistence in sympatry. We (1) obtained restriction-site associated DNA (RAD) sequencing data from a carefully designed sample, (2) applied two genotype clustering algorithms to identify genetic clusters, and (3) performed within-clusters and between-clusters analyses of isolation by distance as a test for intrinsic reproductive barriers. Comparison of our results with those from a Bayes factor delimitation coalescent-based analysis, showed that coalescent-based approaches may lead to overconfident splitting of allopatric populations, and indicated that incorrect species delimitation is likely to be inferred when an incomplete geographic sample is analyzed. While we acknowledge the theoretical justification and practical usefulness of coalescent-based species delimitation methods, our results stress that, even in the phylogenomic era, the toolkit for species delimitation should not dismiss more traditional, biologically grounded, approaches coupling genomic data with geographic information.

Since the last glacial maximum, soil formation related to ice‐cover shrinkage has been one major sink of carbon accumulating as soil organic matter (SOM), a phenomenon accelerated by the ongoing global warming. In recently deglacierized forelands, processes of SOM accumulation, including those that control carbon and nitrogen sequestration rates and biogeochemical stability of newly sequestered carbon, remain poorly understood. Here, we investigate the build‐up of SOM during the initial stages (up to 410 years) of topsoil development in 10 glacier forelands distributed on four continents. We test whether the net accumulation of SOM on glacier forelands (i) depends on the time since deglacierization and local climatic conditions (temperature and precipitation); (ii) is accompanied by a decrease in its stability and (iii) is mostly due to an increasing contribution of organic matter from plant origin. We measured total SOM concentration (carbon, nitrogen), its relative hydrogen/oxygen enrichment, stable isotopic (13C, 15N) and carbon functional groups (C‐H, C=O, C=C) compositions, and its distribution in carbon pools of different thermal stability. We show that SOM content increases with time and is faster on forelands experiencing warmer climates. The build‐up of SOM pools shows consistent trends across the studied soil chronosequences. During the first decades of soil development, the low amount of SOM is dominated by a thermally stable carbon pool with a small and highly thermolabile pool. The stability of SOM decreases with soil age at all sites, indicating that SOM storage is dominated by the accumulation of labile SOM during the first centuries of soil development, and suggesting plant carbon inputs to soil (SOM depleted in nitrogen, enriched in hydrogen and in aromatic carbon). Our findings highlight the potential vulnerability of SOM stocks from proglacial areas to decomposition and suggest that their durability largely depends on the relative contribution of carbon inputs from plants.

Glaciers are retreating globally, and the resulting ice-free areas provide an experimental system for understanding species colonization patterns, community formation, and dynamics. The last several years have seen crucial advances in our understanding of biotic colonization after glacier retreats, resulting from the integration of methodological innovations and ecological theories. Recent empirical studies have demonstrated how multiple factors can speed up or slow down the velocity of colonization and have helped scientists develop theoretical models that describe spatiotemporal changes in community structure. There is a growing awareness of how different processes (e.g., time since glacier retreat, onset or interruption of surface processes, abiotic factors, dispersal, biotic interactions) interact to shape community formation and, ultimately, their functional structure through succession. Here, we examine how these studies address key theoretical questions about community dynamics and show how classical approaches are increasingly being combined with environmental DNA metabarcoding and functional trait analysis to document the formation of multitrophic communities, revolutionizing our understanding of the biotic processes that occur following glacier retreat. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Historically, where forest habitats are deemed as the pristine landscape state, anthropogenic habitats such as managed grasslands or open spaces are often perceived to be antagonistic and of secondary conservation priority. Traditionally, studies on biodiversity responses to ecological variation, i.e. edge effect, have mostly focused on forest habitats. Yet recently there has been increased attention on communities beyond the forest edge in an effort to better understand how interactions between forests and adjacent habitats may potentially affect regional biodiversity. However, in Europe and the Mediterranean basin (a biodiversity hotspot), areas with high landscape heterogeneity and high edge density, there is a paucity of studies analysing the community responses across forest and "beyond edge" habitats across ecotones. In a protected area of central Italy, we investigated the responses of ground-dwelling arthropods (Araneae [spiders], Chilopoda [centipedes] and Carabidae [ground beetles]), which were differentiated into habitat-specific guilds (forest, edge and grassland species) across a forest-grassland ecotone. We investigated the extent to which a habitat edge influenced communities of arthropods associated with either the forest or grassland, and how far from the edge this effect penetrated into each habitat. Twelve 150 m-transects perpendicular to a forest-grassland edge were established and arthropods were sampled at nine progressive distances across the ecotone. An indicator species analysis (ISA) was used to detect species significantly associated with forest, edge-belt or grassland habitats, which were assumed representative of the respective communities. Logistic models of indicator species richness and abundances were used to describe responses of grassland and forest communities across the ecological boundaries. We found that grassland and edge habitats had habitat specialists and higher species richness compared to the forest habitat. Moreover, the occurrence of grassland-specific species was influenced by the presence of an edge up to 15 m from the habitat border. In contrast forest-associated indicator species were not affected by proximity to the habitat edge, rather individuals typical of forest habitats tended to "spill over" into grassland habitats. These findings support the hypothesis that in a forest-grassland mosaic, forest species are less sensitive to an edge and influence the community beyond the forest edge and into the grassland more than the reverse, i.e. the effect was asymmetric. From these data, we estimated that a minimum grassland habitat width of 600 m is necessary for grassland species to maintain a core area that is relatively unaffected by the spillover of species from adjacent forest habitats. Incorporating the directional influences of adjacent communities on each other allows for an empirical 3 assessment of habitat vulnerability that doesn't a priori value the conservation of one habitat over another.

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Understanding the factors affecting the dynamics of spatially‐structured populations (SSP) is a central topic of conservation and landscape ecology. Invasive alien species are increasingly important drivers of the dynamics of native species. However, the impacts of invasives are often assessed at the patch scale, while their effects on SSP dynamics are rarely considered. We used long‐term abundance data to test whether the impact of invasive crayfish on subpopulations can also affect the whole SSP dynamics, through their influence on source populations. From 2010 to 2018, we surveyed a network of 58 ponds and recorded the abundance of Italian agile frog clutches, the occurrence of an invasive crayfish, and environmental features. Using Bayesian hierarchical models, we assessed relationhips between frog abundance in ponds and a) environmental features; b) connectivity within the SSP; c) occurrence of invasive species at both the patch‐ and the SSP‐levels. If spatial relationships between ponds were overlooked, we did not detect effects of crayfish presence on frog abundance or trends. When we jointly considered habitat, subpopulation and SSP features, processes acting at all these levels affected frog abundance. At the subpopulation scale, frog abundance in a year was related to habitat features, but was unrelated to crayfish occurrence at that site during the previous year. However, when we considered the SSP level, we found a strong negative relationship between frog abundance in a given site and crayfish frequency in surrounding wetlands during the previous year. Hence, SSP‐level analyses can identify effects that would remain unnoticed when focussing on single patches. Invasive species can affect population dynamics even in not invaded patches, through the degradation of subpopulation networks. Patch‐scale assessments of the impact of invasive species can thus be insufficient: predicting the long‐term interplay between invasive and native populations requires landscape‐level approaches accounting for the complexity of spatial interactions.

The Italian endemic genus Salamandrina has been historically regarded as monotypic but, recently, studies based on both mitochondrial and nuclear markers have indicated the existence of two distinct species of spectacled salamanders: Salamandrina perspicillata, in central and northern Italy, and Salamandrina terdigitata, in southern Italy. We analyzed nucleotide variation at mitochondrial and nuclear genes [cytochrome b, 12S and 16S rRNA, recombination activating gene (RAG 1)] in 223 individuals from 56 locations, aiming to investigate their genetic structure and recent evolutionary histories. Phylogenetic and phylogeographical analyses revealed the existence of three and two genetically distinct groups of populations in northern and southern salamander, respectively. Historical demographic analyses led to the inference of range expansion for both species in the late Pleistocene. During the last glacial stage, each salamander survived in a single refugium, namely the southern in Calabria and the northern in central Italy. At the end of this period, both lineages expanded northward and established secondary contact. Spatial distribution of RAG 1 haplotype variation revealed two differentiated population groups corresponding to the major mitochondrial (mt)DNA clades. Nuclear pattern of introgressive hybridization was more extensive than the highly limited introgression of mtDNA markers. From a conservation standpoint, southern Latium and Calabria proved to be the major genetic diversity reservoirs, thus deserving particular conservation effort

Aim Worldwide distribution patterns of living animals are structured in multiple zoogeographical regions, characterized by faunas with homogeneous composition that are separated by sharp boundaries. These zoogeographical regions can differ depending on the considered animal group, probably because they have distinct characteristics such as dispersal, metabolism, or evolutionary history, and thus divergent responses to major biogeographical drivers, such as tectonic movements, abrupt climate transitions and orographic barriers. Here, we tested if the drivers of biogeographical boundaries are different between vertebrate classes with strongly divergent traits and evolutionary history. Location Global. Time period Present. Major taxa studied Amphibians, birds and mammals. Methods We focused on terrestrial biogeographical boundaries, considering multiple potential drivers: spatial heterogeneity of present‐day climate, altitudinal variation, long‐term tectonic movements and past climate change (temperature). We used spatially explicit regression models and geographically weighted regressions to select and quantify the factors explaining the position of the biogeographical boundaries between vertebrate classes. Results For mammals, tectonic movements, abrupt climatic transitions and orographic barriers jointly determined extant biogeographical boundaries, with tectonic movements being the most important. For birds, abrupt climatic transitions played the strongest role, while the effect of orographic barriers was weak. For amphibians, biogeographical boundaries mostly corresponded to areas with abrupt climatic transitions. The strongest transitions of amphibian faunas occur in areas with abrupt shifts of temperature and precipitation regimes. Main conclusions Our analyses confirmed that different drivers have jointly shaped the global vertebrate biogeographical regions, and highlight that taxa with different features show heterogeneous responses across the globe. Eco‐physiological constraints likely increase the importance of spatial heterogeneity of climate, while dispersal limitations magnify the relevance of physical barriers (mountain chains and long‐term tectonic instability). Integrating among‐taxa heterogeneity into analyses thus provides a more complete view of how different processes determine biodiversity variation across the globe.