In reptile taxonomy, many subspecies have been described based on subtle variation in morphological traits like colour pattern and scalation. However, the subspecific rank itself has received increasing scrutiny on both conceptual and operational grounds. The species-rich (~100 species) and morphologically diverse Australian lizard genus Lerista Bell, 1833 provides opportunities to assess the evolutionary significance of subspecies taxa, given that subspecies throughout the genus were described before the widespread use of genetic-based assessments of divergence in taxonomy. Based on a combined analysis of patterns of genetic and morphological variation in Leristaplaniventralis (Lucas & Frost, 1902), we found that partitioning of populations into subspecies, namely L. p. planiventralis (Lucas & Frost, 1902), L. p. decora Storr, 1978 and L. p. maryani Storr, 1991, is unwarranted. We found negligible molecular or phenotypic divergence corresponding to those names, revealing continuous, overlapping clinal variation rather than discrete, diagnosable units. Consequently, we synonymise all three subspecies under a single, morphologically variable L. planiventralis and present its revised species-level diagnosis.

Whole-genome duplication can be adaptive in the long term but in the short term can impair chromosome segregation and fertility, obstacles polyploids must overcome to regain fitness. To investigate how animals adapt to polyploidy, we focused on Australian burrowing frogs (genus Neobatrachus), three species of which are polyploid: N. aquilonius, N. kunapalari and N. sudellae. We assembled a reference genome for diploid N. pictus and sequenced 96 individuals from all nine Neobatrachus species, finding tetraploid-specific selection on genes with meiotic roles in synaptonemal complex and crossover distribution (SYCE2, PRR19), or chromosome and spindle size (Condensin-2, KifC1). These changes may represent a genetic adaptation in vertebrate polyploids with tetrasomic and mixed inheritance that raises crossover interference and scales chromosome and spindle size to ensure successful chromosomal segregation. Finally, we show that adaptive alleles are shared between the tetraploids via interspecific introgression.

The Common House Gecko, Hemidactylus frenatus, also known as the Asian House Gecko (AHG), is the most significant invasive gecko globally. Detecting this species can be challenging because it closely resembles other geckos, and is often not directly observed, being cryptic and nocturnal. Traces such as scats, however, are more readily observed than the animal itself. Here, we developed and tested a new diagnostic mitochondrial ND2 LAMP (Loop-mediated isothermal amplification) assay to detect and distinguish AHG from other geckos. Testing DNA from twenty-five non-target gecko and skink species present in Western Australia demonstrated the species-specificity of the assay. This new molecular assay showed amplification in under 15 minutes from AHG DNA. Intraspecific variation did not adversely affect the LAMP assay, with all AHG tissue samples successfully amplifying. This included samples from the Cocos (Keeling) Islands territory of Australia which were >6% genetically divergent from mainland Australian samples, representing a genetic group that was previously unknown, referred to here as AHG "clade E". The assay was found to be highly sensitive, capable of amplifying AHG DNA at very low levels, down to 0.0001 ng/µL of AHG DNA, within 25 minutes. The new LAMP assay has been fully optimised for in-field use, including development and testing of a non-destructive DNA extraction method for in-field extractions from both AHG tissue and scat samples, as well as a gBlock gene fragment for use as a synthetic positive control. The in-field protocols were tested on 100 field collected scats, from multiple lizard species in Western Australia, demonstrating the AHG specificity of the assay, with amplification successful on 79% of AHG scats tested in-field. While the assay was highly effective, scat DNA degradation and inhibitors limited detection in 21% of AHG samples, highlighting preservation challenges. This new assay has already been applied operationally in the field, providing early detection of AHG, and preventing potential introduction of this species into new areas.

The accurate characterization of species diversity is a vital prerequisite for ecological and evolutionary research, as well as conservation. Thus, it is necessary to generate robust hypotheses of species limits based on the inference of evolutionary processes. Integrative species delimitation, the inference of species limits based on multiple sources of evidence, can provide unique insight into species diversity and the processes behind it. Here, we show how community observations can be integrated with standard molecular and phenotypic data sets under an integrative framework to identify the processes generating genetic and phenotypic variation. We implement this approach in Varanus tristis, a widespread and variable complex of Australian monitor lizards. Using genomic, phenotypic (linear and geometric morphometrics, coloration), spatial, and environmental data, we show that disparity in this complex is inconsistent with intraspecific variation and instead suggests that speciation has occurred. Based on our results, we provide an updated taxonomy for this complex and identify the processes that may have been responsible for the geographic sorting of variation. Our workflow provides a guideline for the integrative analysis of several types of data to identify the occurrence and causes of speciation. Furthermore, our study highlights the benefits and caveats associated with community science and machine learning-two tools used here-in taxonomic research.

AI-based solutions offer the potential for rapid taxonomic identification of species of biosecurity concern, enhanced global accessibility and time-saving in contrast to traditional taxonomic identification by humans. This study provides a systematic approach to the application of deep learning for biosecurity surveillance, using the Asian House Gecko (AHG), Hemidactylus frenatus, Schlegel, 1836, as a case study. An effective triage tool for rapid initial identification of this invasive species was developed using machine learning, achieving high accuracy. This demonstrates the efficacy of deep learning for identifying complex morphological characteristics. The AI model used the AHG's head as a key identifying feature, highlighting the importance of specific morphological features for effective identification of target species. A structured approach for the use of machine learning was developed, which included the collation of source images, cataloguing, tagging, naming and storing images, validating and uploading images, labelling images, creating, training and deploying the model, testing model accuracy and retraining the model. This procedure allows for more rapid application of the methodology in biosecurity surveillance. The structured methodology developed can be applied to similar AI-based projects. Outcomes of this research have the potential to reduce the time delays associated with taxonomic identification of invasive species, allowing follow-up action to occur sooner. Reducing time delays is critical to implementing effective biosecurity measures.

The Litoria rubella species complex (L. capitula and L. rubella) is distributed across much of continental Australia, southern New Guinea, and the Tanimbar Islands of Indonesia, in habitats ranging from deserts to tropical forests. We carried out an appraisal of molecular genetics, advertisement calls, and morphological variation in the species complex. Analyses of thousands of nuclear gene SNPs and nucleotide sequences from the mitochondrial ND4 gene identified four reciprocally monophyletic lineages in both marker types, two exclusively in Australia, one in Australia/New Guinea and one from the Tanimbar Islands. The advertisement calls of the three lineages on continental Australia have overlapping but significant differences in the number of pulses in the notes, dominant frequency, and call duration, particularly where the lineages come into contact. The Tanimbar Islands lineage is genetically and morphologically distinct and represents L. capitula. Molecular and advertisement call data together support the recognition of three species in Australia: a widespread central arid and northern tropics lineage, a western arid zone lineage, and an eastern mesic lineage. Litoria rubella sensu stricto is widespread across the tropical Kimberley and Top End regions, southern New Guinea, the central arid zone, and the Murray Darling Basin, making it an extreme climate-generalist. SNP data indicates that L. rubella has gene flow to the north of the Lake Eyre Basin but not the south, making it a possible ring species. The western arid zone lineage does not differ in appearance or advertisement call from L. rubella but is geographically disjunct and phylogenetically distinct. The eastern lineage is primarily distributed to the east of the Great Dividing Range and Cape York in Queensland. We redescribe L. rubella sensu stricto, describe the eastern lineage and western arid lineage as new species, L. pyrina sp. nov. and L. larisonans sp. nov. respectively. Although L. rubella and L. larisonans sp. nov. are morphologically similar, they do not overlap in distribution, making identification non-problematic. Litoria pyrina sp. nov. can be distinguished from L. rubella at contact zones by having advertisement calls with a higher dominant frequency. We investigated the history and morphology of the type for L. mystacina and designate it a nomen dubium. The three Australian species are likely to have a conservation status of Least Concern as they are widespread and abundant, with no significant threats. Little is known about L. capitula from the Tanimbar Islands outside of the few existing museum specimens.

The subspecies rank has been widely applied by taxonomists to capture infraspecific variation within the Linnaean classification system. Many subspecies described throughout the 20th century were recognised largely based on perceived variation in single morphological characters yet have since been found not to correspond to separately evolving population lineages, thus requiring synonymy or elevation to full species under lineage-based views of species. These modern lineage-based taxonomic resolutions have resulted from a combination of new molecular genetic techniques, improved geographical sampling of specimens, and more sophisticated analyses of morphological variation (e.g., statistical assessments rather than solely univariate descriptive ones). Here, we revisit the current taxonomic arrangement of species-level and subspecific taxa in the Lerista microtis (Gray) group, which is distributed along a narrow ~2000 km strip on the southern coast of Australia. From specimens of the L. microtis group, an additional species (Lerista arenicola) and two additional subspecies (L. m. intermedia and L. m. schwaneri) were described. We collected data on mensural, meristic, and colour pattern characters to explore morpho-spatial relationships among these taxa. Although our morphological analyses revealed some distinctiveness among specimens from locations assigned to each taxon, this variation is continuous along Australia’s southern coastline, assuming the form of a geographic cline rather than discrete forms. For many characters, however, spatial patterns were inconsistent with the original descriptions, particularly of the subspecies. Moreover, analysis of genome wide restriction-associated DNA loci revealed multiple instances of paraphyly among taxa, with phylogenetic clustering of specimens assigned to distinct species and subspecies. These emerging patterns provide no support for L. arenicola as a species evolving separately from L. microtis. Additionally, our findings challenge the presumed distinctiveness and coherence of the three subspecies of L. microtis. We thus synonymise L. arenicola and the L. microtis subspecies with L. microtis and provide a redescription of a single yet morphologically variable species—an arrangement that best reflects evolutionary history and the continuous nature of morphological variation across space.

Environmental factors, such as temperature, precipitation, and elevation, explain most of the variation in species richness at the global scale. Nevertheless, richness patterns may have different drivers across taxa and regions. To date, a comprehensive global examination of how various factors such as climate or topography drive patterns of species richness across all terrestrial vertebrates, using the same methods and predictors, has been lacking. Recent advances in species-distribution data allowed us to model and examine the richness pattern of all terrestrial tetrapods comprehensively. We tested the relationship between environmental and biogeographical variables and richness of amphibians (5983 species), birds (9630), mammals (5004), reptiles (8939), and tetrapods as a whole, globally, and across biogeographical realms. We studied the effects of climatic, ecological, and biogeographic drivers using generalized additive models. Richness patterns and their environmental associations varied among taxa and realms. Overall precipitation was the predominant richness predictor. However, temperature was more important in realms where both cold and warm conditions exist. In the Indomalayan realm, elevational range was very important. Richness patterns of mammals, birds, and amphibians were strongly related to precipitation whereas reptile richness was mostly associated with temperature. Our results support the universal importance of precipitation but also suggest that future global-scaled research should incorporate other relevant variables other than climate, such as elevational range, to gain a better understanding of the richness-environment relationship. By doing so, we can further advance our knowledge of the complex relationships between biodiversity and the environment. In this study we tested the relationship between environmental and biogeographical variables and richness of amphibians, birds, mammals, reptiles, and all tetrapods, globally, and across biogeographical realms, using the most up-to-date richness dataset. We found taxonomic and spatial variations, but about a common theme. Precipitation is largely the most influential predictor with the exception of the Nearctic (and the Palearctic to some extent) and reptiles. Elevational range is usually less important than climate, but it is highly influential in the Indomalaya realm.*image

The Lesser Sunda Archipelago is one of the world's most tectonically complex regions and hosts a unique assemblage of amphibian species.Paddy frogs (genus Fejervarya) occur throughout the region, but the systematic position and distribution of each constituent species remains unclear.We present a set of comprehensive mtDNA and morphometric data on the three paddy frog species in the Lesser Sundas: F. cancrivora, F. iskandari and F. verruculosa.We clarify the phylogenetic position of F. verruculosa, placing it as the sister species of F. cancrivora.We also confirm that F. iskandari occur in the Lesser Sundas.Molecular data suggests that F. cancrivora is panmictic across Java and the Sunda Arc, while F. verruculosa and F. iskandari comprise multiple highly divergent populations within the Lesser Sundas.Phylogeographic results appear to support at least two natural colonisations of Fejervarya in the Lesser Sunda Archipelago, one by F. iskandari and one by F. verruculosa, whereas contemporary F. cancrivora populations likely arose from humanmediated movement.Our results demonstrate the biogeographic complexity of the Lesser Sunda Archipelago and identify key knowledge gaps in Lesser Sunda Fejervarya.

Many subspecies were described to capture phenotypic variation in wide-ranging taxa, with some later being found to correspond to divergent genetic lineages. We investigate whether currently recognized subspecies correspond to distinctive and coherent evolutionary lineages in the widespread Australian lizard Ctenotus pantherinus based on morphological, mitochondrial and genome-wide nuclear variation. We find weak and inconsistent correspondence between morphological patterns and the presumed subspecies ranges, with character polymorphism within regions and broad morphological overlap across regions. Phylogenetic analyses suggest paraphyly of populations assignable to each subspecies, mitonuclear discordance and little congruence between subspecies ranges and the distribution of inferred clades. Genotypic clustering supports admixture across regions. These results undermine the presumed phenotypic and genotypic coherence and distinctiveness of C. pantherinus subspecies. Based on our findings, we comment on the operational and conceptual shortcomings of morphologically defined subspecies and discuss practical challenges in applying the general notion of subspecies as incompletely separated population lineages. We conclude by highlighting a historical asymmetry that has implications for ecology, evolution and conservation: subspecies proposed in the past are difficult to falsify even in the face of new data that challenge their coherence and distinctiveness, whereas modern researchers appear hesitant to propose new subspecies.

Litoria rothii is a widespread pelodryadid frog with a charismatic “laughing” advertisement call, distributed across the Australian Monsoon Tropics and southern New Guinea. Given its large distribution spanning well-known biogeographic barriers, variation in male advertisement calls and the prevalence of unresolved species complexes in the Australian frog fauna, we examine the genetic, morphological and acoustic diversity in the species from across its range. Our analyses reveal the presence of a previously unrecognised species in western parts of the range of L. rothii sensu lato, which we describe herein as a new species. Litoria ridibunda sp. nov. is distinguished from L. rothii on the basis of paraphyly of nuclear gene trees with L. everetti from Indonesia, colour patterns on the posterior thigh and male advertisement calls. Compared to L. rothii, the new species has a less contrasting pattern on the posterior thigh and a male advertisement call with a greater number of notes per call and a greater call duration. In particular, the magnitude of call differences between the species is highest where the ranges of the two species are in proximity in north-western Queensland. Our study further emphasises the undiagnosed diversity that remains in Australian frogs, even in relatively large, charismatic, frequently encountered species that often share human dwellings.

—The accurate characterization of species diversity is a vital prerequisite for ecological and evolutionary research, as well as conservation. Thus, it is necessary to generate robust hypotheses of species limits based on the inference of evolutionary processes. Integrative species delimitation, the inference of species limits based on multiple sources of evidence, can provide unique insight into species diversity and the processes behind it. However, the application of integrative approaches in non-model organisms is often limited by the amount of data that is available. Here, we show how data relevant for species delimitation can be bolstered by incorporating information from tissue collections, museum specimens, and observations made by the wider community. We show how to integrate these data under a hypothesis-driven, integrative framework by identifying the processes generating genetic and phenotypic variation in Varanus tristis , a widespread and variable complex of Australian monitor lizards. Using genomic, morphometric (linear and geometric), coloration, spatial, and environmental data we show that disparity in this complex is inconsistent with intraspecific variation and instead suggests that speciation has occurred. Based on our results, we identify the environmental factors that may have been responsible for the geographic sorting of variation. Our workflow provides a guideline for the integrative analysis of several types of data to identify the occurrence and causes of speciation. Furthermore, our study highlights how community science and machine learning—two tools used here—can be used to accelerate taxonomic research.

When closely related species come into contact via range expansion, both may experience reduced fitness as a result of the interaction. Selection is expected to favour traits that minimize costly interspecies reproductive interactions (such as mismating) via a phenomenon called reproductive character displacement (RCD). Research on RCD frequently assumes secondary contact between species, but the geographical history of species interactions is often unknown. Population genomic data permit tests of geographical hypotheses about species origins and secondary contact through range expansion. We used population genomic data from single nucleotide polymorphisms (SNPs), mitochondrial sequence data, advertisement call data and morphological data to investigate a species complex of toadlets (Uperoleia borealis, U. crassa, U. inundata) from northern Australia. Although the three species of frogs were morphologically indistinguishable in our analysis, we determined that U. crassa and U. inundata form a single species (synonymized here) based on an absence of genomic divergence. SNP data identified the phylogeographical origin of U. crassa as the Top End, with subsequent westward invasion into the range of U. borealis in the Kimberley. We identified six F1 hybrids, all of which had the U. borealis mitochondrial haplotype, suggesting unidirectional hybridization. Consistent with the RCD hypothesis, U. borealis and U. crassa sexual signals differ more in sympatry than in allopatry. Hybrid males have intermediate calls, which probably reduces attractiveness to females. Integrating population genomic data, mitochondrial sequencing, morphology and behavioural approaches provides an unusually detailed collection of evidence for reproductive character displacement following range expansion and secondary contact.

Genomic data are a powerful tool for the elucidation of evolutionary patterns at the population level and above. The combined analysis of genomic and morphological data can result in species delimitation hypotheses that reflect evolutionary history better than traditional taxonomy or any individual source of evidence. Here, we used thousands of single nucleotide polymorphisms, mitochondrial sequences, and comprehensive morphological data to characterize the evolutionary history of the ridge-tailed monitors in the Varanus acanthurus complex (V. acanthurus, V. baritji, and V. storri), a group of saxicolous lizards with a wide distribution in Australia, the driest vegetated continent. We found substantial genetic structure in the group and identify nine geographically clustered populations. Based on admixture patterns and species delimitation analyses we propose a taxonomic scheme that differs from current taxonomy. We consider V. acanthurus as monotypic, synonymize V. baritji with V. a. insulanicus (as a redefined V. insulanicus), elevate the subspecies of V. storri to full species (V. storri and V. ocreatus), and describe a new species from a previously identified center of endemism. The relationships among the species remain unresolved, likely as a result of fast speciation. Our study highlights the capability of large datasets to illuminate admixture patterns, biogeographic history, and species limits, even when phylogeny is not completely resolved. Furthermore, our results highlight the impact that the Cenozoic aridification of Australia had on saxicolous taxa and the role of mesic rocky escarpments as refugia. These habitats apparently allowed the persistence of lineages that became sources of colonization for arid environments.

Genomic data are a powerful tool for the elucidation of evolutionary patterns at the population level and above. The combined analysis of genomic and morphological data can result in species delimitation hypotheses that reflect evolutionary history better than traditional taxonomy or any individual source of evidence. Here, we used thousands of single nucleotide polymorphisms, mitochondrial sequences, and comprehensive morphological data to characterize the evolutionary history of the ridge-tailed monitors in the Varanus acanthurus complex (V. acanthurus, V. baritji, and V. storri), a group of saxicolous lizards with a wide distribution in Australia, the driest vegetated continent. We found substantial genetic structure in the group and identify nine geographically clustered populations. Based on admixture patterns and species delimitation analyses we propose a taxonomic scheme that differs from current taxonomy. We consider V. acanthurus as monotypic, synonymize V. baritji with V. a. insulanicus (as a redefined V. insulanicus), elevate the subspecies of V. storri to full species (V. storri and V. ocreatus), and describe a new species from a previously identified center of endemism. The relationships among the species remain unresolved, likely as a result of fast speciation. Our study highlights the capability of large datasets to illuminate admixture patterns, biogeographic history, and species limits, even when phylogeny is not completely resolved. Furthermore, our results highlight the impact that the Cenozoic aridification of Australia had on saxicolous taxa and the role of mesic rocky escarpments as refugia. These habitats apparently allowed the persistence of lineages that became sources of colonization for arid environments.

•We used single nucleotide polymorphisms mitochondrial sequences, and morphological data to infer the evolutionary history of ridge-tailed monitor lizards.•We identified nine populations which we propose belong to four species.•The geographic distribution of the populations and admixture patterns reflect the aridification of Australia and highlight the importance of rocky escarpments as mesic refugia.•We identified and described a new species from a region that has been recognized as a historical refugium in northern Australia.

Genomic data are a powerful tool for the elucidation of evolutionary patterns at the population level and above. The combined analysis of genomic and morphological data can result in species delimitation hypotheses that reflect evolutionary history better than traditional taxonomy or any individual source of evidence. Here, we used thousands of single nucleotide polymorphisms, mitochondrial sequences, and comprehensive morphological data to characterize the evolutionary history of the ridge-tailed monitors in the Varanus acanthurus complex (V. acanthurus, V. baritji, and V. storri), a group of saxicolous lizards with a wide distribution in Australia, the driest vegetated continent. We found substantial genetic structure in the group and identify nine geographically clustered populations. Based on admixture patterns and species delimitation analyses we propose a taxonomic scheme that differs from current taxonomy. We consider V. acanthurus as monotypic, synonymize V. baritji with V. a. insulanicus (as a redefined V. insulanicus), elevate the subspecies of V. storri to full species (V. storri and V. ocreatus), and describe a new species from a previously identified center of endemism. The relationships among the species remain unresolved, likely as a result of fast speciation. Our study highlights the capability of large datasets to illuminate admixture patterns, biogeographic history, and species limits, even when phylogeny is not completely resolved. Furthermore, our results highlight the impact that the Cenozoic aridification of Australia had on saxicolous taxa and the role of mesic rocky escarpments as refugia. These habitats apparently allowed the persistence of lineages that became sources of colonization for arid environments.