Population demography influences climatic niche evolution: evidence from diploid American Hordeum species (Poaceae)

In this study, we explore the interplay of population demography with the evolution of ecological niches during or after speciation in Hordeum. While large populations maintain a high level of standing genetic diversity, gene flow and recombination buffers against fast alterations in ecological adaptation. Small populations harbour lower allele diversity but can more easily shift to new niches if they initially survive under changed conditions. Thus, large populations should be more conservative regarding niche changes in comparison to small populations. We used environmental niche modelling together with phylogenetic, phylogeographic and population genetic analyses to infer the correlation of population demography with changes in ecological niche dimensions in 12 diploid Hordeum species from the New World, forming four monophyletic groups. Our analyses found both shifts and conservatism in distinct niche dimensions within and among clades. Speciation due to vicariance resulted in three species with no pronounced climate niche differences, while species originating due to long‐distance dispersals or otherwise encountering genetic bottlenecks mostly revealed climate niche shifts. Niche convergence among clades indicates a niche‐filling pattern during the last 2 million years in South American Hordeum. We provide evidence that species, which did not encounter population reductions mainly showed ecoclimatic niche conservatism, while major niche shifts occurred in species which have undergone population bottlenecks. Our data allow the conclusion that population demography influences adaptation and niche shifts or conservatism in South American Hordeum species.     

Phylogeography and species biogeography of montane Great Basin stoneflies

Sky islands are ideal systems for determining the effects of climatic oscillations on species distributions and genetic structure. Our study focused on montane stonefly populations in the Great Basin of western North America. We used niche-based distribution modelling, phylogeography and traditional species-based biogeography to test several hypotheses as follows: (i) genetic differentiation among Doroneuria baumanni populations will be independent of hydrologic connectivity (headwater model); (ii) Sky islands were colonized when habitat was more continuous and populations likely experienced multiple expansions and contractions; (iii) Colonization events were coincident with the late Pleistocene and Holocene; and (iv) Shared topography and climate history will result in concordant patterns of genetic differentiation in D. baumanni and occurrences of 32 stonefly species across the region. Overall, Φ(ST) 's and coalescent-based estimates of migration were consistent with the headwater model. Maximum likelihood and Bayesian gene trees identified three major nonoverlapping east-west clades. Distribution modelling indicated more suitable habitat in the Great Basin during the Last Glacial Maximum than at present, but none during the last interglacial period. Demographic analyses showed evidence of population expansion in one of the three major east-west clades. Intra-clade divergence times (60,000-183,000ybp) were well within the late Pleistocene while among-clade divergence times (499.000-719,000ybp) were deeper. Genetic differentiation in D. baumanni and distributions of stonefly species were significantly concordant. These results imply that climatic oscillations have played major roles in shaping the genetic structure and distributions of Great Basin stoneflies, but that divergence among clades occurred much earlier than our late Pleistocence/early Holocene predictions.     

Does GARP really fail miserably? A response to Stockman et al. (2006)

Stockman et al. (2006 ) found that ecological niche models built using DesktopGARP ‘failed miserably’ to predict trapdoor spider (genus Promyrmekiaphila) distributions in California. This apparent failure of GARP (Genetic Algorithm for Rule‐Set Production) was actually a failure of the authors’ methods, that is, attempting to build ecological niche models using single data points. In this paper, we present a re‐analysis of their original data using standard methods with the data appropriately partitioned into training/testing subsets. This re‐evaluation generated accurate distributional predictions that we contrast with theirs. We address the consequences of model‐building using single data points and the need for a foundational understanding of the principles of ecological niche modelling.     

Influence of environmental heterogeneity on genetic diversity and structure in an endemic southern Californian oak

Understanding how specific environmental factors shape gene flow while disentangling their importance relative to the effects of geographical isolation is a major question in evolutionary biology and a specific goal of landscape genetics. Here, we combine information from nuclear microsatellite markers and ecological niche modelling to study the association between climate and spatial genetic structure and variability in Engelmann oak (Quercus engelmannii), a wind-pollinated species with high potential for gene flow. We first test whether genetic diversity is associated with climatic niche suitability and stability since the Last Glacial Maximum (LGM). Second, we use causal modelling to analyse the potential influence of climatic factors (current and LGM niche suitability) and altitude in the observed patterns of genetic structure. We found that genetic diversity is negatively associated with local climatic stability since the LGM, which may be due to higher immigration rates in unstable patches during favourable climatic periods and/or temporally varying selection. Analyses of spatial genetic structure revealed the presence of three main genetic clusters, a pattern that is mainly driven by two highly differentiated populations located in the northern edge of the species distribution range. After controlling for geographic distance, causal modelling analyses showed that genetic relatedness decreases with the environmental divergence among sampling sites estimated as altitude and current and LGM niche suitability. Natural selection against nonlocal genotypes and/or asynchrony in reproductive phenology may explain this pattern. Overall, this study suggests that local environmental conditions can shape patterns of genetic structure and variability even in species with high potential for gene flow and relatively small distribution ranges.     

Functional traits reveal the expansion and packing of ecological niche space underlying an elevational diversity gradient in passerine birds

Variation in species richness across environmental gradients may be associated with an expanded volume or increased packing of ecological niche space. However, the relative importance of these alternative scenarios remains unknown, largely because standardized information on functional traits and their ecological relevance is lacking for major diversity gradients. Here, we combine data on morphological and ecological traits for 523 species of passerine birds distributed across an Andes-to-Amazon elevation gradient. We show that morphological traits capture substantial variation in species dietary (75%) and foraging niches (60%) when multiple independent trait dimensions are considered. Having established these relationships, we show that the 14-fold increase in species richness towards the lowlands is associated with both an increased volume and density of functional trait space. However, we find that increases in volume contribute little to changes in richness, with most (78%) lowland species occurring within the range of trait space occupied at high elevations. Taken together, our results suggest that high species richness is mainly associated with a denser occupation of functional trait space, implying an increased specialization or overlap of ecological niches, and supporting the view that niche packing is the dominant trend underlying gradients of increasing biodiversity towards the lowland tropics.     

Four cleaved amplified polymorphic sequence (CAPS) markers for the detection of the Juglans ailantifolia chloroplast in putatively native J. cinerea populations

Hybridization between butternut (Juglans cinerea), a forest tree native to eastern North America, and Japanese walnut (J. ailantifolia), a tree tolerant to the lethal fungal disease butternut canker, casts doubt on the genetic identity of the remaining butternuts. We report a diagnostic test to distinguish the J. cinerea chloroplast from the J. ailantifolia chloroplast using cleaved amplified polymorphic sequences resolvable in 1.5% agarose gels. J. ailantifolia maternal ancestry in naturally regenerated stands provides a site selection criterion for studies of introgression dynamics when the non-native parent and the hybrids tolerate a disease to which the native species is susceptible.