Simon T. Maddock

Context . In the complex balance between the landscapes of energy and fear, human artefacts (e.g., lighting, noise and barriers) affect the routes taken by commuting bats. Those effects result in cumulative impacts on bat fitness by altering nightly calorific burden. Little is known about the movements of urban bats, with mitigation efforts seldom being evidence‐based. Approach and methods . We applied a field protocol (Multi‐Point Activity Survey) combining visual and acoustic observations along riparian corridors in two case studies to quantify and visually represent commuting routes used by Myotis daubentonii in an urban landscape. We hypothesised that MultiPAS data can be used to statistically identify preferred commuting routes along urban canals. Furthermore, we expected that using those data and available aerial imagery can be combined to provide evidence‐based identification of candidate dark corridor sites. In these case studies from the West Midlands, UK, we sought to demonstrate the effective application of the method in two survey methods: a linear study and a canal junction study. Results . The linear method identified important bat ingress and egress points, and a key candidate dark corridor site through a residential area. The junction survey method revealed candidate dark corridors at three junctions and a crossing point for the retention of vegetation. The combined data also allowed us to infer the locations of two major feeding areas for bats. Practical implications . We demonstrate the successful application of the MultiPAS method for identifying commuting routes and crossing points for trawling bats. These data can allow for the selection of corridor sites in effective, evidence‐based, landscape‐scale conservation.

Western Melanesia sits at the junction of three major tectonic plates, characterised by dynamic plate interactions and geological diversity. Tectonic activity in this region has given rise to modern New Guinea, a relatively young island with extreme topographic heterogeneity and evolutionarily complex biota. New Guinea—particularly the East Papuan Composite Terrane (EPCT)—supports exceptional frog diversity; however, evolutionary histories of many frogs of the EPCT are poorly understood. The microhylid frog genus Mantophryne currently includes five described species ( M. axanthogaster , M. insignis , M. louisiadensis , M. menziesi and M. lateralis ), with the first four confined to small portions of the EPCT and the last distributed across the eastern half of New Guinea. The biogeographic history of these frogs remained incompletely resolved at the time of our study. We estimate that Mantophryne diverged from other microhylid genera approximately 14.4 million years ago (MYA) and began to speciate ca. 8.5 MYA. We recover eight distinct lineages within frogs assigned to M. lateralis , which started to diverge ca. 5.5 MYA. Dispersal of Mantophryne out of the EPCT occurred in the late Pliocene, around the time the Central Highlands expanded eastward to connect with the EPCT. Six pairs of sister lineages arose during a time of significant climate reorganisation in the Late Pliocene—Early Pleistocene when it is possible that areas to the north of the Central Highlands experienced increased precipitation, while areas south of the Central Highlands experienced lower rainfall, resulting in contraction of rainforests and expansion of savannahs. We did not identify any significant differences in habitus between lineages, other than M. louisiadensis which is much larger than all other Mantophryne, and has exceptionally high sexual‐size dimorphism. While an interrogation of the putative cryptic species complex within the M. lateralis clade is beyond the scope of our study, we find that a combination of tectonic rearrangement and climatic history are likely responsible for most of the diversity within the genus that we see today.

Target 4 of the Kunming–Montreal Global Biodiversity Framework (KMGBF) calls for urgent management actions to halt human-induced extinctions and enable species recovery. However, most Parties face substantial challenges in determining which species require urgent management actions. Here, we present a transparent, standardised protocol that identifies and ranks species most likely to need urgent management actions at the national level, using globally available data from the IUCN Red List of Threatened Species. The protocol integrates four criteria aligned with Target 4: global extinction risk, rate of decline, population or range restriction, and endemism, to generate a national ranked list of species. Species scoring highly on these four criteria, and therefore most in need of urgent management action, are ranked most highly. We applied this method to all 250 countries and territories listed in the IUCN Red List and pilot-tested national rankings with participants from eight diverse countries. Across pilots, participants reported that the ranked lists were scientifically robust, time-saving, and valuable starting points for national priority-setting, while stating the importance of national context, and the need for additional technical and financial support for implementation. Our results demonstrate that a science-based approach can meaningfully support Parties in identifying species requiring urgent action under Target 4, in a standardised way. With 2030 approaching rapidly, this protocol provides an immediate, practical tool to accelerate progress toward halting extinctions and advancing species recovery.

The clade of blindsnakes historically placed into Ramphotyphlops Fitzinger was divided into several genera in 2014 based on the topology of a molecular phylogeny. We examine the molecular and morphological evidence used for recognizing two of those genera (the diverse Australian Anilios Fitzinger, and the monotypic Lesser Sundan Sundatyphlops Hedges, Marion, Lipp, Marin & Vidal) and find the evidence insufficient to support their distinction. Post hoc attempts at that time to define Anilios and Sundatyphlops using morphological data relied on using among-species averages of within-species means, an arbitrary approach largely driven by pooling species on geographic grounds, which ignored tremendous ranges of overlap in all morphological features claimed to be diagnostic. Three New Guinean species were also arbitrarily assigned to Anilios in the absence of any molecular or morphological evidence. The sole subsequent molecular study that has included the type species of Ramphotyphlops showed it to be sister to but virtually indistinguishable from Anilios. Lastly, all later molecular studies involving these snakes have consistently found the few species of Ramphotyphlops sensu stricto sampled (n = 1–3) to be paraphyletic when Anilios and Sundatyphlops are recognized. Consequently, we find there is no evidentiary basis for recognizing Anilios or Sundatyphlops as valid lineages distinct from Ramphotyphlops, and continuing to do so renders the latter paraphyletic; thus, we synonymize Anilios and Sundatyphlops with Ramphotyphlops. The taxonomic muddling created by recognizing these genera has persisted because consistently poor sampling of non-Australian members of Ramphotyphlops has not allowed for well-supported clarification of relationships among those lineages

The evolutionary history of many species found in Britain has been shaped by a combination of postglacial colonization dynamics and more recent anthropogenic activity. Documenting genetic diversity is important for informing the overall conservation status of given species, and to aid in developing suitable conservation management strategies. In this study we present the first island-wide population genetic study of the toad Bufo bufo in Britain, using two mitochondrial and eight nuclear microsatellite markers which generated data for 823 animals. We found low genetic diversity and low levels of geographical structuring, and possible evidence of a two-wave colonization to Britain from mainland Europe in the mitochondrial loci. Our microsatellite data recovered moderate genetic structuring, with evidence of recent admixture in most sampled sites. Assigned genetic clusters were only loosely associated with geography, suggesting that genetic differentiation is driven primarily by the observed isolation-by-distance rather than discrete barriers to gene flow. Levels of allelic richness decreased significantly with higher latitude and correlated positively with census size based on counts. Other genetic diversity indices and estimates of genetic effective population sizes did not correlate with population census size proxies. Our study identified sites with high genetic distinctiveness or signs of genetic erosion, and will inform the future conservation management of B. bufo across the UK.

Many island archipelagos sit on shallow continental shelves, and during the Pleistocene, these islands were often connected as global sea levels dropped following glaciation. Given a continental shelf only 30–60 m below sea level, the terrestrial biota of the Seychelles Archipelago likely dispersed amongst now isolated islands during the Pleistocene. Hypogeophis rostratus is an egg‐laying, direct‐developing caecilian amphibian found on 10 islands in the granitic Seychelles. Despite the seemingly limited dispersal abilities of this salt‐intolerant amphibian, its distribution on multiple islands suggests likely historic dispersal across now submerged continental shelf corridors. We tested for the genetic signature of these historic corridors using fine‐scale genomic data (ddRADseq). We found that genomic clusters often did not correspond to islands in the archipelago and that isolation‐by‐distance patterns were more consistent with gene flow across a continuous landscape than with isolated island populations. Using effective migration surfaces and ancestral range expansion prediction, we found support for contemporary populations originating near the large southern island of Mahé and dispersing to northern islands via the isolated Frégate island, with additional historic migration across the flat expanse of the Seychelles bank. Collectively, our results suggest that biogeographic patterns can retain signals from Pleistocene ‘palaeo‐islands’ and that present‐day islands can be thought of as hosting bottlenecks or transient refugia rather than discrete genetic units. Thus, the signatures of gene flow associated with palaeo‐islands may be stronger than the isolating effects of contemporary islands in terrestrial species distributed on continental shelf islands.

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium ) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to “leap” to the next level.

New Guinea and surrounding islands are home to some of the richest assemblages of insular biodiversity in the world. The key geological drivers of species richness in this region are largely considered to be mountain uplift and development of offshore archipelagos—some of which have accreted onto New Guinea—with the role of mountain uplift and elevational gradients receiving more attention than the role of isolation on islands. Here, we examine the distribution of lineage richness and body-size diversity in a radiation of Melanesian lizards that is almost entirely absent from montane habitats but closely associated with islands—the geckos of the genus Nactus. Our data indicate that eastern New Guinea—centred on the East Papuan Composite Terrane (EPCT)—shows particularly high levels of endemism and body-size diversity and is also inferred to be a source area for multiple independent colonisations elsewhere in New Guinea, the Pacific and Australia. Two Nactus lineages in Australia have closest relatives occurring to the north of New Guinea’s Central Cordillera, suggesting dispersal through this area in the mid-Miocene, possibly via seaways that would have isolated the islands to the east and west of the proto-Papuan region. Syntopic species tend to differ in body length; however, at a phylogenetic scale, this trait appears to be conservative, with small-sized and large-sized species clustered into separate lineages. These data suggest that species richness in Melanesian Nactus is in part explained by morphological diversification enabling the presence of sympatric communities to exist, but to a greater extent by multiple instances of dispersal and extensive allopatric and parapatric speciation, especially in and around the islands of the EPCT.

Studies in evolution, ecology and conservation are increasingly based on genetic and genomic data. With increased focus on molecular approaches, ethical concerns about destructive or more invasive techniques need to be considered, with a push for minimally invasive sampling to be optimised. Buccal swabs have been increasingly used to collect DNA in a number of taxa, including amphibians. However, DNA yield and purity from swabs are often low, limiting its use. In this study, we compare different types of swabs, preservation method and storage, and DNA extraction techniques in three case studies to assess the optimal approach for recovering DNA in anurans. Out of the five different types of swabs that we tested, Isohelix MS‐02 and Rapidry swabs generated higher DNA yields than other swabs. When comparing storage buffers, ethanol is a better preservative than a non‐alcoholic alternative. Dried samples resulted in similar or better final DNA yields compared to ethanol‐fixed samples if kept cool. DNA extraction via a Qiagen™ DNeasy Blood and Tissue Kit and McHale's salting‐out extraction method resulted in similar DNA yields but the Qiagen™ kit extracts contained less contamination. We also found that samples have better DNA recovery if they are frozen as soon as possible after collection. We provide recommendations for sample collection and extraction under different conditions, including budgetary considerations, size of individual animal sampled, access to cold storage facilities and DNA extraction methodology. Maximising efficacy of all of these factors for better DNA recovery will allow buccal swabs to be used for genetic and genomic studies in a range of vertebrates.

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium ) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to “leap” to the next level.