Extraordinary micro-endemism in Australian desert spring amphipods

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.

Phylogenomics and biogeography of arid-adapted Chlamydogobius goby fishes

The progressive aridification of the Australian continent from ∼ 20 million years ago posed severe challenges for the persistence of its resident biota. A key question involves the role of refugial habitats - specifically, their ability to mediate the effects of habitat loss and fragmentation, and their potential to shape opportunities for allopatric speciation. With freshwater species, for example, the patchiness, or absence, of water will constrain distributions. However, aridity may not necessarily isolate populations if disjunct refugia experience frequent hydrological connections. To investigate this potential dichotomy, we explored the evolutionary history of the Chlamydogobius gobies (Gobiiformes: Gobiidae), an arid-adapted genus of six small, benthic fish species that exploit all types of waterbodies (i.e. desert springs, waterholes and bore-fed wetlands, coastal estuarine creeks and mangroves) across parts of central and northern Australia. We used Anchored Phylogenomics to generate a highly resolved phylogeny of the group from sequence data for 260 nuclear loci. Buttressed by companion allozyme and mtDNA datasets, our molecular findings infer the diversification of Chlamydogobius in arid Australia, and provide a phylogenetic structure that cannot be simply explained by invoking allopatric speciation events reflecting current geographic proximity. Our findings are generally consistent with the existing morphological delimitation of species, with one exception: at the shallowest nodes of phylogenetic reconstruction, the molecular data do not fully support the current dichotomous delineation of C. japalpa from C. eremius in Kati Thanda-Lake Eyre-associated waterbodies. Together these findings illustrate the ability of structural (hydrological) connections to generate patterns of connectivity and isolation for an ecologically moderate disperser in response to ongoing habitat aridification. Finally, we explore the implications of these results for the immediate management of threatened (C. gloveri) and critically endangered (C. micropterus, C. squamigenus) congeners.

Spatial characterization of factors inherent in the microendemism of the dwarf pequi tree (Caryocar brasiliense subsp. intermedium (Wittm.) PRANCE & M. F. Silva)

The dwarf pequi tree, Caryocar brasiliense subsp. intermedium, is extremely restricted to ecological niches in the Cerrado biome. Thus, understanding the conditioning factors of the micro-endemism of this sub-species through its spatial distribution and the physical-chemical attributes of the soil was the objective of this research. The research was carried out in a fragment of rupestrian field. The area was divided into quadrants in which the number of pequi trees was quantified and the physicochemical characteristics of the soil were determined. The modeling of semivariograms was performed using semivariances, and ordinary kriging was used for spatial interpolation of variables with spatial dependence. The number of pequi trees, the altitude, the remaining phosphorus and the humidity showed a strong degree of spatial dependence, unlike the pH, the calcium and the magnesium, all of which had a pure nugget effect. The other variables showed a moderate degree of spatial dependence. The greater availability of bases (SB > 0.1 cmolc dm-3) and phosphorus (> 1.05 mg dm-3), the reduced percentage of moisture (< 5%) and low potential acidity (< 4.0 cmolc dm-3) were the factors positively related to the establishment and development of the dwarf pequi tree in the area.

Macroinvertebrate Community Composition in Wetlands of the Desert Southwest is Driven by wastewater-associated Nutrient Loading Despite Differences in Salinity

The relatively rare freshwater ecosystems in the arid southwestern United States serve as biodiversity hotspots, yet they remain among the most threatened systems in the world due to human impacts and climate change. Globally, arid region wetlands remain understudied with respect to their ecology, making assessments of quality or restoration efforts challenging. To address these needs, this project aims to better understand the factors that drive water quality and macroinvertebrate community composition of wetlands of the US desert Southwest. Water quality and macroinvertebrate data were collected over three years from 14 different wetland and riparian sites spanning across West Texas, New Mexico and Arizona. Principal Component Analysis (PCA) indicated that salinity related variables such as chloride, sulfate and conductivity were the greatest drivers of environmental variance (32%) among sampled desert wetlands. Nutrients such as nitrate and phosphate described a second axis, with 22% of variation in environmental data explained, where we found a clear distinction between wastewater and non-wastewater wetlands. Nutrients were shown to have the greatest impact on macroinvertebrate communities with wetlands receiving wastewater showing more uneven distribution of functional feeding groups and lower Simpson Index scores. These sites were dominated by filter feeders and had lower relative abundances of predator and collector-gatherer taxa. There was also a significant decrease in metrics related to diversity and environmental sensitivity such as % Ephemeroptera-Odonata-Trichoptera (EOT) within high nutrient sites. Increased salinity levels were also shown to correlate with lower Simpson Index scores indicating that increased salinity resulted in a decline in macroinvertebrate diversity and evenness. Overall, the nutrients within effluent water have shown to significantly alter community composition especially in desert wetlands where macroinvertebrates may be more adapted to high salinity. Though macroinvertebrate communities in wastewater sites may not fully resemble those of natural wetlands over time, creation of these sites can still benefit landscape level diversity.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13157-022-01647-2.

Micro-endemic species of snails and amphipods show population genetic structure across very small geographic ranges

Understanding variation in population genetic structure, even across small distances and for species with extremely limited ranges, is critical for conservation planning and the development of effective management strategies for imperiled species. Organisms that occupy the same geographic extent can maintain different population structures, ranging from highly diverged to panmictic. Such differences can result from differences in biological characteristics such as dispersal ability or demographic history. We used microsatellite loci to evaluate population genetic structure and variation of four desert spring invertebrates having high to low dispersal ability: the lung snail Physa acuta, two species of gilled snails (Juturnia kosteri and Pyrgulopsis roswellensis; family Hydrobiidae) and the amphipod Gammarus desperatus. The study location represents entire species ranges for the micro-endemic hydrobiids and G. desperatus, while P. acuta is ubiquitous throughout much of North America. We found little evidence of significant population genetic structure for P. acuta and J. kosteri, but much more for P. roswellensis and G. desperatus. Our results demonstrate differences in habitat preference and/or dispersal ability between the species. This information provides insight into how gene flow shapes varying population genetic structure between species across small spatial scales (<100 km2). Most importantly, our results suggest that conservation agencies should not consider these micro-endemic species to be composed of single populations, but rather, that management plans for such species should account for population genetic variation across the species' ranges.

High diversity and local endemism in Aotearoa New Zealand's groundwater crustacean fauna

We used DNA barcoding to assess the diversity and distribution of New Zealand's groundwater amphipods and isopods (Crustacea) and to determine whether biodiversity and endemism within tectonically active New Zealand are similar to those of more tectonically stable continents. Sixty-five wells were sampled in seven aquifers across four regions within the North and South islands of New Zealand, and resident invertebrates were morphologically identified and then assessed using sequencing of the mitochondrial DNA cytochrome c oxidase subunit one (COI) gene. Invertebrates were found in 54 wells. Of the 228 individual amphipods and isopods found in 36 of the wells, 154 individuals were successfully sequenced for COI (68% success rate) from 25 wells, with at least one well in each aquifer containing sequenced individuals. Of the 45 putative species identified using Barcode Index Numbers (BINs), 30 BINs (78% of all taxa and 83% of amphipods) were previously unrecorded. Substantial morphologically cryptic, species-level diversity was revealed, particularly within the amphipod Family Paraleptamphopidae. Similarly, one isopod taxon morphologically identified as Cruregens fontanus was assigned to five well-separated BINs based on COI sequences. Endemism appeared high, with all taxa regionally endemic; 87% of species were restricted to one aquifer and more than 50% restricted to one well. Non-saturated species accumulation curves indicated that, while additional sampling may increase the range of some currently identified taxa, additional range-restricted taxa are also likely to be discovered. Patterns of diversity and short-range endemism were similar to those found elsewhere, including locations which are more tectonically stable. The predominance of local endemism within New Zealand's groundwater fauna suggests that land-use activities and groundwater extraction require careful evaluation to minimize threats to groundwater biodiversity.

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.

Continental-scale patterns of hyper-cryptic diversity within the freshwater model taxon Gammarus fossarum (Crustacea, Amphipoda)

Traditional morphological diagnoses of taxonomic status remain widely used while an increasing number of studies show that one morphospecies might hide cryptic diversity, i.e. lineages with unexpectedly high molecular divergence. This hidden diversity can reach even tens of lineages, i.e. hyper cryptic diversity. Even well-studied model-organisms may exhibit overlooked cryptic diversity. Such is the case of the freshwater crustacean amphipod model taxon Gammarus fossarum. It is extensively used in both applied and basic types of research, including biodiversity assessments, ecotoxicology and evolutionary ecology. Based on COI barcodes of 4926 individuals from 498 sampling sites in 19 European countries, the present paper shows (1) hyper cryptic diversity, ranging from 84 to 152 Molecular Operational Taxonomic Units, (2) ancient diversification starting already 26 Mya in the Oligocene, and (3) high level of lineage syntopy. Even if hyper cryptic diversity was already documented in G. fossarum, the present study increases its extent fourfold, providing a first continental-scale insight into its geographical distribution and establishes several diversification hotspots, notably south-eastern and central Europe. The challenges of recording hyper cryptic diversity in the future are also discussed.

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.

The importance of naming cryptic species and the conservation of endemic subterranean amphipods

Molecular taxonomy often uncovers cryptic species, reminding us that taxonomic incompleteness is even more severe than previous thought. The importance of cryptic species for conservation is poorly understood. Although some cryptic species may be seriously threatened or otherwise important, they are rarely included in conservation programs as most of them remain undescribed. We analysed the importance of cryptic species in conservation by scrutinizing the South European cryptic complex of the subterranean amphipod Niphargus stygius sensu lato. Using uni- and multilocus delineation methods we show that it consists of 15 parapatric and sympatric species, which we describe using molecular diagnoses. The new species are not mere “taxonomic inflation” as they originate from several distinct branches within the genus and coexist with no evidence of lineage sharing. They are as evolutionarily distinct as average nominal species of the same genus. Ignoring these cryptic species will underestimate the number of subterranean endemics in Slovenia by 12 and in Croatia by four species, although alpha diversity of single caves remains unchanged. The new taxonomy renders national Red Lists largely obsolete, as they list mostly large-ranged species but omit critically endangered single-site endemics. Formal naming of cryptic species is critical for them to be included in conservation policies and faunal listings.

A review of the status of Coptotermes (Isoptera : Rhinotermitidae) species in Australia with the description of two new small termite species from northern and eastern Australia

Integrative taxonomy, including molecular, morphological, distributional and biological data, is applied in a review of the taxonomy of the Australian species of the pest termite genus Coptotermes. The validity of the previously described species is discussed, and two new species, Coptotermes nanus, sp. nov. and Coptotermes cooloola, sp. nov., are described from the Kimberley region of Western Australia and south-east Queensland respectively. Their delimitation is based on morphological and distributional data, and the results of generalised mixed Yule-coalescent analysis of mitochondrial DNA sequence data. Images of the external view of the two new species are provided, as well as a key, based on soldier characters, for all Australian species of Coptotermes.

Swimming through sand: connectivity of aquatic fauna in deserts

Freshwater ecosystems in arid regions range from highly fragmented to highly connected, and connectivity has been assumed to be a major factor in the persistence of aquatic biota in arid environments. This review sought to synthesize existing research on genetic estimation of population connectivity in desert freshwaters, identify knowledge gaps, and set priorities for future studies of connectivity in these environments. From an extensive literature search, we synthesized the approaches applied, systems studied, and conclusions about connectivity reached in population genetic research concerning desert freshwater connectivity globally. We restrict our scope to obligate aquatic fauna that disperse largely via freshwaters and exclude those with active aerial dispersal abilities. We examined 92 papers, comprising 133 studies, published from 1987 to 2014. Most described studies of fishes and invertebrates in the deserts of Australia and North America. Connectivity declined with increasing scale, but did not differ significantly among arid regions or taxonomic classes. There were significant differences in connectivity patterns between species with different dispersal abilities, and between spring and riverine habitats at local scales. Population connectivity in desert freshwaters is typically most influenced by the ecology of the species concerned and hydrological connectivity. Most studies did not assess predefined models of connectivity, but described gene flow and/or genetic structure. Climate change and anthropogenic impacts worldwide are likely to increase the incidence and impact of habitat fragmentation in already threatened desert freshwaters. To reduce this risk, biodiversity conservation and environmental management must address connectivity, but often the required information does not exist. Researchers can provide this by explicitly considering the effects of hydrology and species' ecology on connectivity, and incorporating these into connectivity models, which are vital for understanding connectivity in desert freshwaters.

Overlooked mountain rock pools in deserts are critical local hotspots of biodiversity

BACKGROUND

The world is undergoing exceptional biodiversity loss. Most conservation efforts target biodiversity hotspots at large scales. Such approach overlooks small-sized local hotspots, which may be rich in endemic and highly threatened species. We explore the importance of mountain rock pools (gueltas) as local biodiversity hotspots in the Sahara-Sahel. Specifically, we considered how many vertebrates (total and endemics) use gueltas, what factors predict species richness, and which gueltas are of most priority for conservation. We expected to provide management recommendations, improve local biodiversity conservation, and simultaneously contribute with a framework for future enhancement of local communities' economy. The identification of local hotspots of biodiversity is important for revaluating global conservation priorities.

METHODOLOGY/PRINCIPAL FINDINGS

We quantified the number of vertebrate species from each taxonomic group and endemics present in 69 gueltas in Mauritania, then compared these with species present in a surrounding area and recorded in the country. We evaluated the predictors of species number's present in each guelta through a multiple regression model. We ranked gueltas by their priority for conservation taking into account the percentage of endemics and threats to each guelta. Within a mere aggregate extent of 43 ha, gueltas hold about 32% and 78% of the total taxa analysed and endemics of Mauritania, respectively. The number of species present in each guelta increased with the primary productivity and area of gueltas and occurrence of permanent water. Droughts and human activities threaten gueltas, while 64% of them are currently unprotected.

CONCLUSION/SIGNIFICANCE

Gueltas are crucial for local biodiversity conservation and human activities. They require urgent management plans in Mauritania's mountains. They could provide refugia under climate change being important for long-term conservation of Sahara-Sahel biodiversity. Given their disproportional importance in relation to their size, they are local hotspots of biodiversity deserving global attention.

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.

Resolving phenotypic plasticity and species designation in the morphologically challenging Caulerpa racemosa-peltata complex (Chlorophyta, Caulerpaceae)

Although recent molecular studies have indicated the presence of a number of distinct species within the Caulerpa racemosa-peltata complex, due to the difficulties presented by high levels of phenotypic plasticity and the large number of synonyms, infra-specific taxa, and names of uncertain affinity, taxonomic proposals are yet to be made. In this study, we aimed to resolve the taxonomy of the complex and provide an example of how historical nomenclature can best be integrated into molecular based taxonomies. We accomplished this by first determining the number of genetic species within our globally sampled data set through a combination of phylogenetic and species-delimitation approaches of partial elongation factor TU and RUBISCO large subunit gene sequences. Guided by these results, comparative morphological examinations were then undertaken to gauge the extent of phenotypic plasticity within each species, as well as any morphological overlap between them. Our results revealed the presence of 11 distinct species within the complex, five of which showed high levels of phenotypic plasticity and partial overlap with other species. On the basis of observations of a large number of specimens, including type specimens/descriptions, and geographic inferences, we were able to confidently designate names for the lineages. Caulerpa peltata, C. imbricata and C. racemosa vars. laetevirens, occidentalis and turbinata were found to represent environmentally induced forms of a single species, for which the earlier-described C. chemnitzia, previously regarded as a synonym of C. racemosa var. turbinata, is reinstated. C. cylindracea, C. lamourouxii, C. macrodisca, C. nummularia and C. oligophylla are also reinstated and two new species, C. macra stat. nov. and C. megadisca sp. nov., are proposed.

Assessment of temporal genetic variability of two epibenthic amphipod species in an eastern Australian estuarine environment and their suitability as biological monitors

Population studies often assume temporally stable and consistent patterns of genetic variability. Violations of this assumption can lead to misrepresentation of the amount and patterns of genetic variability in natural populations, which can be problematic in basic research and environmental monitoring studies that are designed to detect environmental perturbation. We collected two endemic species of amphipods, Melita plumulosa and Melita matilda, in a major eastern Australian waterway between November 2009 and October 2011, and assessed genetic variation at the mitochondrial cytochromec oxidase subunitI locus. Overall, M. plumulosa was found to be more genetically variable than M. matilda. No distinct temporal trends in levels and patterns of genetic variation were identified in either species. These findings, combined with the published results demonstrating that M. plumulosa has greater sensitivity to a range of sediment-bound metals and organic contaminants, suggests it to be an informative species for environmental monitoring purposes.

16 microsatellite loci for the Australian Great Artesian Basin spring amphipod, Wangiannachiltonia guzikae

454 Next Generation sequencing was used to develop a set of microsatellite markers for the Great Artesian Basin (GAB) amphipod, Wangiannachiltonia guzikae. Primers were designed for 42 microsatellite loci. A total of 22 loci were successfully amplified and 16 characterised using 30 individuals from a single GAB spring population. Across these 16 loci, observed heterozygosity ranged from 0.000 to 0.818 (mean = 0.445) and the number of alleles per locus ranged from 2 to 12 (mean = 6.688). Of these 16 loci, however, only 10 were in Hardy–Weinberg equilibrium, though all 16 loci should be retained for further studies in the event that stochastic events affected equilibrium of this single population.