Desert springs: deep phylogeographic structure in an ancient endemic crustacean (Phreatomerus latipes)

Genetic approaches reveal a healthy population and an unexpectedly recent origin for an isolated desert spring fish

Foskett Spring in Oregon's desert harbors a historically threatened population of Western Speckled Dace (Rhinichthys klamathensis). Though recently delisted, the dace's recruitment depends upon regular removal of encroaching vegetation. Previous studies assumed that Foskett Dace separated from others in the Warner Valley about 10,000 years ago, thereby framing an enigma about the population's surprising ability to persist for so long in a tiny habitat easily overrun by plants. To investigate that persistence and the effectiveness of interventions to augment population size, we assessed genetic diversity among daces inhabiting Foskett Spring, a refuge at Dace Spring, and three nearby streams. Analysis revealed a robust effective population size (Ne) of nearly 5000 within Foskett Spring, though Ne in the Dace Spring refuge is just 10% of that value. Heterozygosity is slightly lower than expected based on random mating at all five sites, indicating mild inbreeding, but not at a level of concern. These results confirm the genetic health of Foskett Dace. Unexpectedly, genetic differentiation reveals closer similarity between Foskett Dace and a newly discovered population from Nevada's Coleman Creek than between Foskett Dace and dace elsewhere in Oregon. Demographic modeling inferred Coleman Creek as the ancestral source of Foskett Dace fewer than 1000 years ago, much more recently than previously suspected and possibly coincident with the arrival of large herbivores whose grazing may have maintained open water suitable for reproduction. These results solve the enigma of persistence by greatly shortening the duration over which Foskett Dace have inhabited their isolated spring.

Drainage Network Morphology Influences Population Structure and Gene Flow of the Andean Water Frog Telmatobius pefauri (Anura: Telmatobiidae) of the Atacama Desert, Northern Chile

Desert aquatic species tend to show isolated and disconnected populations due to the fragmented nature of their environment; however, the morphology of the hydrographic basins, added to humid climatic conditions, can allow dispersion between populations in a desert environment. The aim of this study was to examine the influence of drainage morphology on the phylogeographic structure and gene flow (using a fragment of the mitochondrial control region and seven microsatellite markers) of an endemic taxon of the Andean Precordillera in the Atacama Desert, the aquatic frog species Telmatobius pefauri. We detected three genetic clusters, one cluster present in the Lluta basin and two clusters in the Azapa basin. The results suggest that the genetic structure of T. pefauri is influenced by the morphology of the drainage network formed by the Lluta and Azapa basins: localities present in the same drainage, Tignamar River, were less differentiated and showed higher gene flow levels among them than to their conspecifics belonging to the other drainage in the same basin, Seco River, and those belonging to the other basin, Lluta basin. Gene flow patterns and genetic structure to populations Atacama Andean aquatic taxa would be influenced by basin morphology, with dispersion being stimulated in dendritic hydrological systems, and eventually by humid climatic (regional) events.

Insight into the evolutionary history of Indoplanorbis exustus (Bulinidae: Gastropoda) at the scale of population and species

The history of a lineage is intertwined with the history of the landscape it inhabits. Here we showcase how the geo-tectonic and climatic evolution of South Asia and surrounding landmasses have shaped the biogeographical history of Indoplanorbis exustus, a tropical Asian, freshwater snail. We amplified partial COI gene fragments from all over India and combined this with a larger dataset from South and Southeast Asia to carry out phylogenetic reconstruction, species delimitation analysis and population genetic analyses. Two nuclear genes were also amplified from a few individuals per putative species to carry out divergence dating and ancestral area reconstruction analyses. The results suggest that I. exustus dispersed out of Africa into India during the Eocene. Furthermore, molecular data suggest I. exustus is a species complex consisting of multiple putative species. Primary diversification took place in the Northern Indian plains or in Northeast India. The speciation events appear to be primarily allopatric caused by a series of aridification events starting from the late Miocene to early Pleistocene. None of the species appears to have any underlying genetic structure suggestive of high vagility. All the species underwent population fluctuations during the Pleistocene, probably driven by the Quaternary climatic fluctuations.

Addressing the Linnean shortfall in a cryptic species complex

Biodiversity is being lost at an alarming rate, but the rate of this loss is likely to be underestimated as a result of a deficit in taxonomic knowledge (i.e. the Linnean shortfall). This knowledge gap is more extensive for morphologically indistinct taxa. The advancement of molecular techniques and delimitation methods has facilitated the identification of such cryptic species, but a majority of these taxa remain undescribed. To investigate the effects of taxonomic uncertainty on understanding of biodiversity, we applied the general lineage concept of species to an amphipod species complex, the Gammaruslacustris lineage that occupies springs of the northern Chihuahuan Desert, which is emerging in contemporary times. We investigated species boundaries using a validation-based approach and examined genetic structure of the lineage using a suite of microsatellite markers to identify independently evolving metapopulations. Our results show that each spring contains a genetically distinct population that is geographically isolated from other springs, suggesting evolutionary independence and status as separate species. Additionally, we observed subtle interspecific morphological variation among the putative species. We used multiple lines of evidence to formally describe four new species (Gammarus langi sp. nov., G. percalacustris sp. nov., G. colei sp. nov. and G. malpaisensis sp. nov.) endemic to the northern Chihuahuan Desert. Cryptic speciation is likely to be high in other aquatic taxa within these ecosystems, and across arid landscapes throughout North America and elsewhere, suggesting that the magnitude of the Linnean shortfall is currently underestimated in desert springs worldwide.

Extreme genetic diversity among springtails (Collembola) in subterranean calcretes of arid Australia

The subterranean islands hypothesis for calcretes of the Yilgarn region in Western Australia applies to many stygobitic (subterranean-aquatic) species that are "trapped" evolutionarily within isolated aquifers due to their aquatic lifestyles. In contrast, little is known about the distribution of terrestrial-subterranean invertebrates associated with the calcretes. We used subterranean Collembola from the Yilgarn calcretes to test the hypothesis that troglobitic species, those inhabiting the subterranean unsaturated (non-aquatic) zone of calcretes, are also restricted in their distribution and represent reciprocally monophyletic and endemic lineages. We used the barcoding fragment of the mtDNA cytochrome c oxidase subunit 1 (COI) gene from 183 individuals to reconstruct the phylogenetic history of the genus Pseudosinella Schäffer (Collembola, Lepidocyrtidae) from 10 calcretes in the Yilgarn. These calcretes represent less than 5% of the total possible calcretes in this region, yet we show that their diversity for subterranean Collembola comprises a minimum of 25 new species. Regionally, multiple levels of diversity exist in Pseudosinella, indicative of a complex evolutionary history for this genus in the Yilgarn. These species have probably been impacted by climatic oscillations, facilitating their dispersal across the landscape. The results represent a small proportion of the undiscovered diversity in Australia's arid zone.

Communities at the extreme: Aquatic food webs in desert landscapes

Studying food webs across contrasting abiotic conditions is an important tool in understanding how environmental variability impacts community structure and ecosystem dynamics. The study of extreme environments provides insight into community-wide level responses to environmental pressures with relevance to the future management of aquatic ecosystems. In the western Lake Eyre Basin of arid Australia, there are two characteristic and contrasting aquatic habitats: springs and rivers. Permanent isolated Great Artesian Basin springs represent hydrologically persistent environments in an arid desert landscape. In contrast, hydrologically variable river waterholes are ephemeral in space and time. We comprehensively sampled aquatic assemblages in contrasting ecosystem types to assess patterns in community composition and to quantify food web attributes with stable isotopes. Springs and rivers were found to have markedly different invertebrate communities, with rivers dominated by more dispersive species and springs associated with species that show high local endemism. Qualitative assessment of basal resources shows autochthonous carbon appears to be a key basal resource in both types of habitat, although the particular sources differed between habitats. Food-web variables such as trophic length, trophic breadth, and community isotopic niche size were relatively similar in the two habitat types. The basis for the similarity in food-web structure despite differences in community composition appears to be broader isotopic niches for predatory invertebrates and fish in springs as compared with rivers. In contrast to published theory, our findings suggest that the food webs of the hydrologically variable river sites may show less dietary generalization and more compact food-web modules than in springs.

Species, ESUs or populations? Delimiting and describing morphologically cryptic diversity in Australian desert spring amphipods

Cryptic species are frequently being discovered in refugial habitats, such as desert springs and groundwater systems. Unfortunately, many of these taxa remain as unnamed entities years after their initial discovery. Recent advances in the use of molecular data and coalescent analyses allow DNA-based delimitation of species to move from single locus, tree-based methods to multilocus coalescent analyses. This study compares two DNA-based approaches to delimit species of putatively cryptic freshwater amphipods (Chiltoniidae) from desert springs in central Australia. In addition, a morphometric analysis of 11 characters was undertaken to determine whether the DNA-delimited species were morphologically distinguishable. The single locus method results in identification of lineages that are not supported as species under the multilocus coalescent analyses. We conclude that Wangiannachiltonia guzikae King, 2009, as currently circumscribed, represents six genetically distinct amphipod species, and we describe and name these species despite no clear diagnosable morphological differences. Critically, all of these newly recognised species have extremely limited distributions, which increases the biodiversity significance of their desert spring habitat.

Molecular evidence for mid-Pleistocene divergence of populations of three freshwater amphipod species (Talitroidea : Chiltoniidae) on Kangaroo Island, South Australia, with a new spring-associated genus and species

Recent molecular and morphological analyses have shown that chiltoniid amphipods, once thought to be a relictual group, are a diverse and speciose family of Australian freshwater amphipods. As part of a larger examination of the family, chiltoniids from Kangaroo Island in South Australia were collected and analysed using molecular (COI and 28S) and morphological methods in order to understand species distributional patterns and relationships. Kartachiltonia moodyi gen. nov., sp. nov., a spring-associated species endemic to the island, was discovered and populations of three additional mainland species (Austrochiltonia australis, A. dalhousiensis and A. subtenuis) were examined. The island populations of A. australis, A. dalhousiensis and A. subtenuis were found to form natural groups with differing haplotype coalescence times dating from the Early to Mid-Pleistocene. Numerous cycles of regional climate change throughout the Pleistocene are likely to have driven speciation in chiltoniid amphipods in southern Australia and the presence of multiple chiltoniid species at Kangaroo Island indicates that it exists at a likely convergence of species distribution patterns. Three possible hypotheses to explain the evolution and diversity of chiltoniids in southern Australia are discussed as are evidence for potential introduction and long-distance dispersal events.

Extraordinary micro-endemism in Australian desert spring amphipods

Increasing pressure for water in the Australian arid zone is placing enormous stress on the diverse endemic communities inhabiting desert springs. Detailed information about the evolutionary processes occurring within and between individual endemic species will help to develop effective and biologically relevant management strategies this fragile ecosystem. To help determine conservation priorities, we documented the genetic structure of the endemic freshwater amphipod populations in springs fed by the Great Artesian Basin in central Australia. Phylogenetic and phylogeographic history and genetic diversity measures were examined using nuclear and mitochondrial DNA from approximately 500 chiltoniid amphipods across an entire group of springs. Pronounced genetic diversity was identified, demonstrating that levels of endemism have been grossly underestimated in these amphipods. Using the GMYC model, 13 genetically divergent lineages were recognized as Evolutionarily Significant Units (ESUs), all of which could be considered as separate species. The results show that due to the highly fragmented ecosystem, these taxa have highly restricted distributions. Many of the identified ESUs are endemic to a very small number of already degraded springs, with the rarest existing in single springs. Despite their extraordinarily small ranges, most ESUs showed relative demographic stability and high levels of genetic diversity, and genetic diversity was not directly linked to habitat extent. The relatively robust genetic health of ESUs does not preclude them from endangerment, as their limited distributions ensure they will be highly vulnerable to future water extraction.