Aim  Species diversity and genetic diversity within a taxon are intrinsic parts of global biodiversity. These two levels of biodiversity can show strong correlation due to a variety of reasons (i.e. parallel processes affecting both communities and populations, genotypes of a numerically or functionally dominant species affecting community composition, a species assemblage selecting for a particular genotype by affecting its selection regime). We examined correlations between species and genetic biodiversity in four isolated endemic‐rich spring systems in a hot desert and their potential link to environmental variables and physical isolation. Location  Chihuahuan Desert spring systems in the Pecos River basin of New Mexico and Texas, USA. Methods  We compared species richness of fish and benthic macroinvertebrate communities to within‐population allelic richness of amphipods (monophyletic Gammarus spp.) and Pecos gambusia (Gambusia nobilis) using Mantel tests. We also compared pairwise community similarities with pairwise genetic identities of populations among the same groups. We tested correlations among diversity, similarity and environmental variables after controlling for the effects of spatial distances using partial Mantel tests. We partitioned genetic and species diversity into three spatial scales (i.e. individual springs, individual spring systems, the entire region) using AMOVA and partition. Results  We found strong correlations between invertebrate species richness and mosquitofish allelic richness. We found even stronger correlations of amphipod and gambusia genetic identities with fish and invertebrate community similarities; these were best explained by geographic distance rather than abiotic environmental factors. Most of the taxa and communities exhibited the largest proportion of diversity at the regional level. Main conclusions  Our results suggest that drift and migration are the mechanisms that best explain our observations, and although α‐diversity among genes and species may not be strongly correlated, the pattern of species and allelic complementarity among these groups seems to be concordant at the regional level.

The endangered snails Juturnia kosteri and Pyrgulopsis roswellensis are endemic to springs on Bitter Lake National Wildlife Refuge, NM, USA. These species are small and difficult to distinguish by shell shape. A morphological analysis of these two species was conducted using geometric morphometrics, and a phylogenetic analysis using the mitochondrial DNA genes COI and ND1 was performed. Principal component analysis showed significant overlap in shell shape between the two species. Phylogenetic analysis showed that the two species formed monophyletic clades, with each containing low genetic diversity. Analysis of molecular variance for each species showed significant variation among populations. Both species showed significant isolation‐by‐distance, but only P. roswellensis showed a significant relationship between shell shape and geographic distance. The overlapping ranges and the similarity in shell morphology suggest that these micro‐endemic species are difficult to distinguish in the field, particularly by non‐specialists. This presents challenges to population management of these species. Divergence among populations within each species indicates isolation at very small geographic scales. Because these desert springs are home to endemic species within a variety of invertebrate groups, they are likely to contain significant amounts of yet‐to‐be‐discovered biodiversity; many of these unknown taxa are also likely to be of conservation concern. Copyright © 2013 John Wiley & Sons, Ltd.

Desert springs are highly threatened ecosystems inhabited by a substantial number of endemic species. Macroinvertebrate communities of five springs in the northern Chihuahuan Desert of west Texas and south‐eastern New Mexico were sampled seasonally. Rather than focusing on individual taxa, this study examined the community structure of springs to identify patterns that are likely to reflect both local conditions and potential dispersal barriers. In total, 46 774 individuals representing 109 taxa were collected with high relative abundances of gastropods, amphipods, and oligochaetes. Spatial variation in community composition was greater than temporal variation. Although there were differences in the salinity content and concentrations of several major anions and cations among sites, these were not significant predictors of difference in community structure. Two springs sharing the same groundwater source contained similar macroinvertebrate communities and had similar physicochemical conditions. Results from this study suggest that springs in the northern Chihuahuan Desert contain unique communities and endemic species owing to historical processes such as isolation and dispersal limitation, rather than contemporary processes such as environmental filtering and species sorting. Springs located in the northern Chihuahuan Desert, like those located in other arid regions of the world, are valuable for their biodiversity because of their distinct invertebrate communities and high rates of endemism. Thus, they should be conserved individually to ensure the preservation of unique species and communities.

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