Parallel decay of vision genes in subterranean water beetles.

In the framework of neutral theory of molecular evolution, genes specific to the development and function of eyes in subterranean animals living in permanent darkness are expected to evolve by relaxed selection, ultimately becoming pseudogenes. However, definitive empirical evidence for the role of neutral processes in the loss of vision over evolutionary time remains controversial. In previous studies, we characterized an assemblage of independently-evolved water beetle (Dytiscidae) species from a subterranean archipelago in Western Australia, where parallel vision and eye loss have occurred. Using a combination of transcriptomics and exon capture, we present evidence of parallel coding sequence decay, resulting from the accumulation of frameshift mutations and premature stop codons, in eight phototransduction genes (arrestins, opsins, ninaC and transient receptor potential channel genes) in 32 subterranean species in contrast to surface species, where these genes have open reading frames. Our results provide strong evidence to support neutral evolutionary processes as a major contributing factor to the loss of phototransduction genes in subterranean animals, with the ultimate fate being the irreversible loss of a light detection system.

Continental risk assessment for understudied taxa post-catastrophic wildfire indicates severe impacts on the Australian bee fauna.

The 2019-2020 Australian Black Summer wildfires demonstrated that single events can have widespread and catastrophic impacts on biodiversity, causing a sudden and marked reduction in population size for many species. In such circumstances, there is a need for conservation managers to respond rapidly to implement priority remedial management actions for the most-affected species to help prevent extinctions. To date, priority responses have been biased towards high-profile taxa with substantial information bases. Here, we demonstrate that sufficient data are available to model the extinction risk for many less well-known species, which could inform much broader and more effective ecological disaster responses. Using publicly available collection and GIS datasets, combined with life-history data, we modelled the extinction risk from the 2019-2020 catastrophic Australian wildfires for 553 Australian native bee species (33% of all described Australian bee taxa). We suggest that two species are now eligible for listing as Endangered and nine are eligible for listing as Vulnerable under IUCN criteria, on the basis of fire overlap, intensity, frequency, and life-history traits: this tally far exceeds the three Australian bee species listed as threatened prior to the wildfire. We demonstrate how to undertake a wide-scale assessment of wildfire impact on a poorly understood group to help to focus surveys and recovery efforts. We also provide the methods and the script required to make similar assessments for other taxa or in other regions.

A method to generate multilocus barcodes of pinned insect specimens using MiSeq.

For molecular insect identification, amplicon sequencing methods are recommended because they offer a cost-effective approach for targeting small sets of informative genes from multiple samples. In this context, high-throughput multilocus amplicon sequencing has been achieved using the MiSeq Illumina sequencing platform. However, this approach generates short gene fragments of <500 bp, which then have to be overlapped using bioinformatics to achieve longer sequence lengths. This increases the risk of generating chimeric sequences or leads to the formation of incomplete loci. Here, we propose a modified nested amplicon sequencing method for targeting multiple loci from pinned insect specimens using the MiSeq Illumina platform. The modification exists in using a three-step nested PCR approach targeting near full-length loci in the initial PCR and subsequently amplifying short fragments of between 300 and 350 bp for high-throughput sequencing using Illumina chemistry. Using this method, we generated 407 sequences of three loci from 86% of all the specimens sequenced. Out of 103 pinned bee specimens of replicated species, 71% passed the 95% sequence similarity threshold between species replicates. This method worked best for pinned specimens aged between 0 and 5 years, with a limit of 10 years for pinned and 14 years for ethanol-preserved specimens. Hence, our method overcomes some of the challenges of amplicon sequencing using short read next generation sequencing and improves the possibility of creating high-quality multilocus barcodes from insect collections.

The genus Amegilla (Hymenoptera, Apidae, Anthophorini) in Australia: a revision of the subgenus Asaropoda.

The species in the subgenus Amegilla (Asaropoda) are revised. Species delineation was decided based on diagnostic morphological characters as well as an incomplete phylogeny based on mitochondrial cytochrome oxidase 1 sequence data. Strong support was obtained for separating the Australian species of Amegilla into the three subgenera previously proposed on the basis of morphology. The subgenus Asaropoda was found to comprise 21 species, including ten new species: A. albiclypeata Leijs, sp. nov., A. aurantia Leijs, sp. nov., A. batleyi Leijs, sp. nov., A. crenata Leijs, sp. nov., A. griseocincta Leijs, sp. nov., A. incognita Leijs, sp. nov., A. nitidiventris Leijs, sp. nov., A. scoparia Leijs, sp. nov., A. xylocopoides Leijs, sp. nov., and A. youngi Leijs, sp. nov. The subspecies A. preissi frogatti is raised to species level, and 16 new synonymies are proposed. Keys to the species of both sexes and descriptions or redescriptions are provided. Distribution maps, data on flower visitation and phenology are given.

Twenty six new species of Leioproctus (Colletellus): Australian Neopasiphaeinae, all but one with two submarginal cells (Hymenoptera, Colletidae, Leioproctus).

Twenty six new species of Australian Leioproctus (subgenusColletellus) (Hymenoptera, Colletidae) are described: aberrans Leijs, sp. n., alatus Leijs, sp. n., albipilosus Leijs, sp. n., albiscopis Leijs, sp. n., aliceafontanus Leijs, sp. n., altispinosus Leijs, sp. n., aratus Leijs, sp. n., auricorneus Leijs, sp. n., bidentatus Leijs, sp. n., centralis Leijs, sp. n., ciliatus Leijs, sp. n., claviger Leijs, sp. n., consobrinus Leijs, sp. n., constrictus Leijs, sp. n., laciniosus Leijs, sp. n., longivultu Leijs, sp. n., lucidus Leijs, sp. n., nitidifuscus Leijs, sp. n., pectinatus Leijs, sp. n., pilotapilus Leijs, sp. n., quadripinnatus Leijs, sp. n., rubicundus Leijs, sp. n., rubricinctus Leijs, sp. n., similis Leijs, sp. n., splendens Leijs, sp. n., submetallicus Leijs, sp. n. High resolution images of diagnostic characters for all type specimens are included. Identification keys are provided.

The genus Amegilla (Hymenoptera, Apidae, Anthophorini) in Australia: A revision of the subgenera Notomegilla and Zonamegilla.

The Australian bees in the subgenera Notomegilla and Zonamegilla of the genus Amegilla are revised. Commonly in Australia the species in these subgenera are called blue-banded bees, although not all species have blue bands. A phylogeny based on mitochondrial cytochrome oxidase 1 sequence data was used to delineate the species and a set of morphological criteria was developed for species identification. Strong support was obtained for separating the Australian species into the three subgenera previously proposed on the basis of morphology. Two species, are recognised in the subgenus Notomegilla and eleven new synonymies are proposed. Twelve Australian species are recognised in the subgenus Zonamegilla including four new species: indistincta, karlba, paeninsulae and viridicingulata, and twenty new synonymies are proposed. Keys to the species of both sexes and descriptions or redescriptions of all species are provided. Distribution maps, data on flower visitation and phenology are given.

Stygofauna enhance prokaryotic transport in groundwater ecosystems.

More than 97% of the world's freshwater reserves are found in aquifers, making groundwater one of the most important resources on the planet. Prokaryotic communities in groundwater underpin the turnover of energy and matter while also maintaining groundwater purity. Thus, knowledge of microbial transport in the subsurface is crucial for maintaining groundwater health. Here, we describe for the first time the importance of stygofauna as vectors for prokaryotes. The "hitch-hiking" prokaryotes associated with stygofauna may be up to 5 orders of magnitude higher in abundance and transported up to 34× faster than bulk groundwater flow. We also demonstrate that prokaryotic diversity associated with stygofauna may be higher than that of the surrounding groundwater. Stygofauna are a newly recognized prokaryotic niche in groundwater ecosystems that have the potential to transport remediating, water purifying and pathogenic prokaryotes. Therefore, stygofauna may influence ecosystem dynamics and health at a microbial level, and at a larger scale could be a new source of prokaryotic diversity in groundwater ecosystems.

New species of Goniocolletes and Trichocolletes (Hymenoptera, Colletidae) from southern Australia.

Goniocolletes comatus Maynard, 2013 is redescribed. Goniocolletes wanni sp. n. and the male of Trichocolletes luteorufus Batley & Houston, 2012 are described.

The Evolution of Functionally Redundant Species; Evidence from Beetles.

While species fulfill many different roles in ecosystems, it has been suggested that numerous species might actually share the same function in a near neutral way. So-far, however, it is unclear whether such functional redundancy really exists. We scrutinize this question using extensive data on the world's 4168 species of diving beetles. We show that across the globe these animals have evolved towards a small number of regularly-spaced body sizes, and that locally co-existing species are either very similar in size or differ by at least 35%. Surprisingly, intermediate size differences (10-20%) are rare. As body-size strongly reflects functional aspects such as the food that these generalist predators can eat, these beetles thus form relatively distinct groups of functional look-a-likes. The striking global regularity of these patterns support the idea that a self-organizing process drives such species-rich groups to self-organize evolutionary into clusters where functional redundancy ensures resilience through an insurance effect.

DNA barcoding of euryglossine bees and the description of new species of Euhesma Michener (Hymenoptera, Colletidae, Euryglossinae).

This paper launches an open access DNA barcoding project "AUSBS" under the Barcoding of Life Datasystems (BOLD). The aims of the project are to help scientists who lack the necessary morphological knowledge to identify known species using molecular markers, to aid native bee specialists with the recognition of species groups that morphologically are difficult to define, and, eventually, to assist with the recognition of new species among known species. Using integrative taxonomy, i.e. morphological comparison to type specimens in Australian museum collections combined with phylogenetic analysis of a fragment of the mitochondrial DNA cytochrome c oxidase subunit I (mtCOI) gene sequences led to the recognition of four new species of Euhesma Michener (Hymenoptera: Colletidae: Euryglossini) collected during intensive surveys in remote Australian conservation areas, which are described. The new species are Euhesma micans, Euhesma lyngouriae, and Euhesma aulaca in a species group associated with Eremophila flowers, and Euhesma albamala in the walkeriana species group.

The Evolution of Epigean and Stygobitic Species of Koonunga Sayce, 1907 (Syncarida: Anaspidacea) in Southern Australia, with the Description of Three New Species.

Three new species of Koonunga were discovered in surface and subterranean waters in southern Australia, and were defined using mtDNA analyses and morphology. The new species are: Koonunga hornei Leijs & King; K. tatiaraensis Leijs & King and K. allambiensis Leijs & King. Molecular clock analyses indicate that the divergence times of the species are older than the landscape that they currently inhabit. Different scenarios explaining this apparent discrepancy are discussed in the context of the palaeography of the area. A freshwater epigean origin for Koonunga is considered the most likely hypothesis, whereby some lineages made the transition to the subterranean environment within the last few million years influenced by significant climatic cooling/drying. We discuss the possibility that one stygobitic lineage secondarily regained some of its body pigmentation as adaptation to increased photic conditions after cave collapse and forming of cenotes during the last glacial maximum.

Repeated parallel evolution reveals limiting similarity in subterranean diving beetles.

The theory of limiting similarity predicts that co-occurring species must be sufficiently different to coexist. Although this idea is a staple of community ecology, convincing empirical evidence has been scarce. Here we examine 34 subterranean beetle communities in arid inland Australia that share the same habitat type but have evolved in complete isolation over the past 5 million years. Although these communities come from a range of phylogenetic origins, we find that they have almost invariably evolved to share a similar size structure. The relative positions of coexisting species on the body size axis were significantly more regular across communities than would be expected by chance, with a size ratio, on average, of 1.6 between coexisting species. By contrast, species' absolute body sizes varied substantially from one community to the next. This suggests that self-organized spacing according to limiting-similarity theory, as opposed to evolution toward preexisting fixed niches, shaped the communities. Using a model starting from random sets of founder species, we demonstrate that the patterns are indeed consistent with evolutionary self-organization. For less isolated habitats, the same model predicts the coexistence of multiple species in each regularly spaced functional group. Limiting similarity, therefore, may also be compatible with the coexistence of many redundant species.

Evolution of blind beetles in isolated aquifers: a test of alternative modes of speciation.

Evidence is growing that not only allopatric but also sympatric speciation can be important in the evolution of species. Sympatric speciation has most convincingly been demonstrated in laboratory experiments with bacteria, but field-based evidence is limited to a few cases. The recently discovered plethora of subterranean diving beetle species in isolated aquifers in the arid interior of Australia offers a unique opportunity to evaluate alternative modes of speciation. This naturally replicated evolutionary experiment started 10-5 million years ago, when climate change forced the surface species to occupy geographically isolated subterranean aquifers. Using phylogenetic analysis, we determine the frequency of aquifers containing closely related sister species. By comparing observed frequencies with predictions from different statistical models, we show that it is very unlikely that the high number of sympatrically occurring sister species can be explained by a combination of allopatric evolution and repeated colonisations alone. Thus, diversification has occurred within the aquifers and likely involved sympatric, parapatric and/or microallopatric speciation.