Contrasting insights provided by single and multispecies data in a regional comparative phylogeographic study

Unravelling the taxonomy and identification of a problematic group of benthic fishes from tropical rivers (Gobiidae: Glossogobius)

Flathead gobies (genus Glossogobius) include c. 40 small- to medium-sized benthic fishes found primarily in freshwater habitats across the Indo-Pacific, having biodiversity value as well as cultural and economic value as food fishes, especially in developing countries. To help resolve considerable confusion regarding the identification of some of the larger-growing Glossogobius species, a systematic framework was established using nuclear genetic markers, mitochondrial DNA barcoding and phenotypic evidence for a geographically widespread collection of individuals from the waterways of tropical northern Australia. Species boundaries and distribution patterns were discordant with those previously reported, most notably for the tank goby Glossogobius giuris, which included a cryptic species. Genetic divergence was matched with accompanying unique visual characters that aid field identification. Additional taxonomic complexity was also evident, by comparison with DNA barcodes from international locations, suggesting that the specific names applicable for two of the candidate species in Australia remain unresolved due to confusion surrounding type specimens. Although flathead gobies are assumed to be widespread and common, this study demonstrates that unrealised taxonomic and ecological complexity is evident, and this will influence assessments of tropical biodiversity and species conservation. This study supports the need for taxonomic studies of freshwater fishes to underpin management in areas subject to significant environmental change.

The complete mitogenome of Caridina indistincta 'sp. A' (Decapoda: Atyidae)

A complete mitochondrial genome sequence was determined for a member of the Caridina indistincta species complex known as C. indistincta 'sp. A'. The 15,461 bp sequence (GenBank: MH189850) was obtained via genome skimming, and contains 13 protein coding genes, 22 tRNA genes, 2 rRNA genes, and a 646 bp control region arranged in the pancrustacean ground pattern. Caridina indistincta sp. A is a freshwater macroinvertebrate important for ecosystem health monitoring in Australia and this reference will be a useful resource for metabarcoding and eDNA studies.

Patterns of genetic structuring at the northern limits of the Australian smelt (Retropinna semoni) cryptic species complex

Freshwater fishes often exhibit high genetic population structure due to the prevalence of dispersal barriers (e.g., waterfalls) whereas population structure in diadromous fishes tends to be weaker and driven by natal homing behaviour and/or isolation by distance. The Australian smelt (Retropinnidae: Retropinna semoni) is a native fish with a broad distribution spanning inland and coastal drainages of south-eastern Australia. Previous studies have demonstrated variability in population genetic structure and movement behaviour (potamodromy, facultative diadromy, estuarine residence) across the southern part of its geographic range. Some of this variability may be explained by the existence of multiple cryptic species. Here, we examined genetic structure of populations towards the northern extent of the species’ distribution, using ten microsatellite loci and sequences of the mitochondrial cyt b gene. We tested the hypothesis that genetic connectivity among rivers should be low due to a lack of dispersal via the marine environment, but high within rivers due to dispersal. We investigated populations corresponding with two putative cryptic species, SEQ-North (SEQ-N), and SEQ-South (SEQ-S) lineages occurring in south east Queensland drainages. These two groups formed monophyletic clades in the mtDNA gene tree and among river phylogeographic structure was also evident within each clade. In agreement with our hypothesis, highly significant overall F_ST values suggested that both groups exhibit very low dispersal among rivers (SEQ-S F_ST = 0.13; SEQ-N F_ST= 0.27). Microsatellite data indicated that connectivity among sites within rivers was also limited, suggesting dispersal may not homogenise populations at the within-river scale. Northern groups in the Australian smelt cryptic species complex exhibit comparatively higher among-river population structure and smaller geographic ranges than southern groups. These properties make northern Australian smelt populations potentially susceptible to future conservation threats, and we define eight genetically distinct management units along south east Queensland to guide future conservation management. The present findings at least can assist managers to plan for effective conservation and management of different fish species along coastal drainages of south east Queensland, Australia.

Multiple molecular markers reinforce the systematic framework of unique Australian cave fishes (Milyeringa : Gobioidei)

Australia was once thought to be a biodiversity desert when considering the subterranean world; however, recent work has revealed a fascinating collection of cave creatures, many with surprising biogeographic histories. This has especially been so in the karstic regions of north-western Australia (Cape Range peninsula, Barrow Island, Pilbara), which is home not only to a diverse collection of subterranean invertebrates, but also to the continent’s only known underworld-adapted vertebrates, which includes the cave fish in the genus Milyeringa. These cave gudgeons have recently been in a state of taxonomic flux, with species being both split and lumped, but this was done with limited data (incomplete geographic sampling and no nuclear DNA sequence data). Therefore, we have revisited the systematic status of Milyeringa in a total-evidence molecular approach by integrating all existing data (mitochondrial, allozymes) with new DNA sequences from nuclear and mitochondrial loci and new multilocus allozyme data. Our conclusion, that there are two species, matches the most recent taxonomic treatment, with Milyeringa veritas present on both the eastern and western sides of the Cape Range peninsula, and Milyeringa justitia on Barrow Island. This has implications for future research in the linked fields of biogeography and conservation.

Complete mitogenomes for two lineages of the Australian smelt, Retropinna semoni (Osmeriformes: Retropinnidae)

Complete mitochondrial genome sequences were determined for two lineages (“CEQ” and “SEQ”) of the Australian smelt, Retropinna semoni. Both mitogenomes contain the typical vertebrate arrangement of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and control region. A conventional start codon for ND2 was not present in either lineage; instead CTG (Leucine) was present at this position. These sequences will be a useful resource for evolutionary studies of a significant species complex in the Australian freshwater fish fauna.

Phylogeographic concordance factors quantify phylogeographic congruence among co-distributed species in the Sarracenia alata pitcher plant system

Comparative phylogeographic investigations have identified congruent phylogeographic breaks in co-distributed species in nearly every region of the world. The qualitative assessments of phylogeographic patterns traditionally used to identify such breaks, however, are limited because they rely on identifying monophyletic groups across species and do not account for coalescent stochasticity. Only long-standing phylogeographic breaks are likely to be obvious; many species could have had a concerted response to more recent landscape events, yet possess subtle signs of phylogeographic congruence because ancestral polymorphism has not completely sorted. Here, we introduce Phylogeographic Concordance Factors (PCFs), a novel method for quantifying phylogeographic congruence across species. We apply this method to the Sarracenia alata pitcher plant system, a carnivorous plant with a diverse array of commensal organisms. We explore whether a group of ecologically associated arthropods have co-diversified with the host pitcher plant, and identify if there is a positive correlation between ecological interaction and PCFs. Results demonstrate that multiple arthropods share congruent phylogeographic breaks with S. alata, and provide evidence that the level of ecological association can be used to predict the degree of similarity in the phylogeographic pattern. This study outlines an approach for quantifying phylogeographic congruence, a central concept in biogeographic research.

Human effects on ecological connectivity in aquatic ecosystems: Integrating scientific approaches to support management and mitigation

Understanding the drivers and implications of anthropogenic disturbance of ecological connectivity is a key concern for the conservation of biodiversity and ecosystem processes. Here, we review human activities that affect the movements and dispersal of aquatic organisms, including damming of rivers, river regulation, habitat loss and alteration, human-assisted dispersal of organisms and climate change. Using a series of case studies, we show that the insight needed to understand the nature and implications of connectivity, and to underpin conservation and management, is best achieved via data synthesis from multiple analytical approaches. We identify four key knowledge requirements for progressing our understanding of the effects of anthropogenic impacts on ecological connectivity: autecology; population structure; movement characteristics; and environmental tolerance/phenotypic plasticity. Structuring empirical research around these four broad data requirements, and using this information to parameterise appropriate models and develop management approaches, will allow for mitigation of the effects of anthropogenic disturbance on ecological connectivity in aquatic ecosystems.