Craig Moritz

Australian National University | ANU · Research School of Biology (RSB)

Introgression — the exchange of genetic material through hybridization — is now recognized as common among animal species. The extent of introgression, however, can vary considerably even when it occurs: for example, introgression can be geographically restricted or so pervasive that populations merge. Such variation highlights the importance of un...

Evolutionary lineages at the tip of the tree of life can be genetically diverged yet phenotypically similar and therefore unrecognized by traditional morphology-based taxonomy. Such lineages, spanning the “grey zone of speciation” 1, are increasingly uncovered using genomic analyses. Here we show that incorporating this unrecognized lineage diversi...

Genetic diversity is a fundamental population genetic parameter, and predicts adaptive capacity. Neutral theory predicts a positive correlation between population (or range) size and genetic diversity, but this can be confounded by other demographic processes. To investigate the role of range size, population fluctuation and introgression in determ...

Increased sampling of genomes and populations across closely related species has revealed that levels of genetic exchange during and after speciation are higher than previously thought. One obvious manifestation of such exchange is strong cytonuclear discordance, where the divergence in mitochondrial DNA (mtDNA) differs from that for nuclear genes...

Phylogeographic studies of continental clades, especially when combined with palaeoclimate modelling, provide powerful insight into how environment drives speciation across climatic contexts. Australia, a continent characterized by disparate modern biomes and dynamic climate change, provides diverse opportunity to reconstruct the impact of past and...

Snakes and lizards (Squamata) represent a third of terrestrial vertebrates and exhibit spectacular innovations in locomotion, feeding, and sensory processing. However, the evolutionary drivers of this radiation remain poorly known. We infer potential causes and ultimate consequences of squamate macroevolution by combining individual-based natural h...

Using genetic information to develop and implement conservation programs is vital for maintaining biodiversity and ecosystem resilience. Evaluation of the genetic variability within and among remnant populations can inform management of both natural and translocated populations to maximise species’ adaptive potential, mitigate negative impacts of i...

Translocation programmes are increasingly being informed by genetic data to monitor and enhance conservation outcomes for both natural and established populations. These data provide a window into contemporary patterns of genetic diversity, structure and relatedness that can guide managers in how to best source animals for their translocation progr...

Population isolation and concomitant genetic divergence, resulting in strong phylogeographic structure, is a core aspect of speciation initiation. If and how speciation then proceeds and ultimately completes depends on multiple factors that mediate reproductive isolation, including divergence in genomes, ecology, and mating traits. Here we explored...

The Forest Kingfisher Todiramphus macleayii inhabits eucalypt savannas, rainforests and mangroves across its distribution in Australasia. Two Australian subspecies are consistently recognised but the taxonomic status of resident New Guinean populations is unsettled. Genomic data from populations sampled across the species’ Australian and New Guinea...

Sahul unites the world’s largest and highest tropical island and the oldest and most arid continent on the backdrop of dynamic environmental conditions. Massive geological uplift in New Guinea is predicted to have acted as a species pump from the late Miocene onward, but the impact of this process on biogeography and diversification remains unteste...

The application of high-throughput, short-read sequencing to degraded DNA has greatly increased the feasibility of generating genomic data from historical museum specimens. While many published studies report successful sequencing results from historical specimens; in reality, success and quality of sequence data can be highly variable. To examine...

The environment presents challenges to the transmission and detection of animal signalling systems, resulting in selective pressures that can drive signal divergence amongst populations in disparate environments. For chemical signals, climate is a potentially important selective force because factors such as temperature and moisture influence the p...

Chromosome rearrangements can result in the rapid evolution of hybrid incompatibilities. Robertsonian fusions, particularly those with monobrachial homology, can drive reproductive isolation amongst recently diverged taxa. The recent radiation of rock-wallabies (genus Petrogale) is an important model to explore the role of Robertsonian fusions in s...

Temperature differences over time and space has been hypothesized to cause variation in the rate of molecular evolution of species, but empirical evidence is mixed. To further test this hypothesis, we utilized a large exon-capture sequence data of Australian Eugongylinae skinks, exemplifying a radiation of temperature-sensitive ectotherms spanning...

Differences in the geographic scale and depth of phylogeographic structure across co-distributed taxa can reveal how microevolutionary processes such as population isolation and persistence drive diversification. In turn, environmental heterogeneity, species' traits and historical biogeographic barriers may influence the potential for isolation and...

Significance Native rodents represent 41% of Australian mammal extinctions since European colonization. To determine the scale and timing of their decline, we used museum specimens to generate genome-scale data from eight extinct Australian rodents and their 42 living relatives. Relatively high genetic diversity in extinct species immediately prior...

Global biodiversity loss is a profound consequence of human activity. Disturbingly, biodiversity loss is greater than realized because of the unknown number of undocumented species. Conservation fundamentally relies on taxonomic recognition of species, but only a fraction of biodiversity is described. Here, we provide a new quantitative approach fo...

Lineage differentiation, long-term persistence, and range limitation promote high levels of phylogenetic and phylogeographic endemisms and likely underlie the abundant morphologically cryptic diversity observed in the Brazilian Atlantic Forests (AF). We explore lineage differentiation and range restriction in the AF and ask if genetic divergence an...

Species distribution models (SDMs) are widely used to predict and study distributions of species. Many different modeling methods and associated algorithms are used and continue to emerge. It is important to understand how different approaches perform, particularly when applied to species occurrence records that were not gathered in struc­tured sur...

For over two decades, assessments of geographic variation in mtDNA and small numbers of nuclear loci have revealed morphologically similar, but genetically divergent, intraspecific lineages in lizards from around the world. Subsequent morphological analyses often find subtle corresponding diagnostic characters to support the distinctiveness of line...

Aim Understanding where and why species diversity is geographically concentrated remains a challenge in biogeography and macroevolution. This is true for the Cerrado, the most biodiverse tropical savanna in the world, which has experienced profound biodiversity loss. Previous studies have focused on a single metric (species composition), neglecting...

Disentangling historical, ecological, and abiotic drivers of diversity among closely related species can benefit from morphological diversity being placed in a phylogenetic context. It can also be aided when the species are variously in allopatry, parapatry, and sympatry. We studied a clade of Australian thornbills (Passeriformes: Acanthizidae: Aca...

Climate change is affecting biodiversity and ecosystem function worldwide, and the lowland tropics are of special concern because organisms living in this region experience temperatures that are close to their upper thermal limits. However, it remains unclear how and whether tropical lowland species will be able to cope with the predicted pace of c...

The importance of long-distance dispersal (LDD) in shaping geographical distributions has been debated since the nineteenth century. In terrestrial vertebrates, LDD events across large water bodies are considered highly improbable, but organismal traits affecting dispersal capacity are generally not taken into account. Here, we focus on a recent li...

Many species have experienced dramatic changes in their abundance and distribution during recent climate change, but it is often unclear whether such ecological responses are accompanied by evolutionary change. We used targeted exon sequencing of 294 museum specimens (160 historic, 134 modern) to generate independent temporal genomic contrasts span...

Background: The application of target capture with next-generation sequencing now enables phylogenomic analyses of rapidly radiating clades of species. But such analyses are complicated by extensive incomplete lineage sorting, demanding the use of methods that consider this process explicitly, such as the multispecies coalescent (MSC) model. Howev...

Current approaches to biodiversity conservation are largely based on geographic areas, ecosystems, ecological communities, and species, with less attention on genetic diversity and the evolutionary continuum from populations to species. Conservation management generally rests on discrete categories, such as identified species, and, for threated tax...

A fundamental challenge in resolving evolutionary relationships across the Tree of Life is to account for heterogeneity in the evolutionary signal across loci. Studies of marsupial mammals have demonstrated that this heterogeneity can be substantial, leaving considerable uncertainty in the evolutionary timescale and relationships within the group....

The genus Proablepharus currently contains five species (P. barrylyoni, P. kinghorni, P. naranjicaudus, P. reginae and P. tenuis). Morphologically, these are readily separated into two groups: the small, almost patternless species (P. reginae and P. tenuis) and the larger, striped species (P. kinghorni, P. barrylyoni and P. naranjicaudus). We prese...

Ecological opportunity is a powerful driver of evolutionary diversification, and predicts rapid lineage and phenotypic diversification following colonisation of competitor‐free habitats. Alternatively, topographic or environmental heterogeneity could be key to generating and sustaining diversity. We explore these hypotheses in a widespread lineage...

There is justified concern about the impact of global warming on the persistence of tropical ectotherms. There is also growing evidence for strong selection on climate-relevant physiological traits. Understanding the evolutionary potential of populations is especially important for low dispersal organisms in isolated populations, because these popu...

Recent advances in molecular genetic techniques and increased fine scale sampling in the Australian Monsoonal Tropics (AMT) have provided new impetus to reassess species boundaries in the Gehyra nana species complex, a clade of small-bodied, saxicolous geckos which are widely distributed across northern Australia. A recent phylogenomic analysis re-...

As we collect range-wide genetic data for morphologically-defined species, we increasingly unearth evidence for cryptic diversity. Delimiting this cryptic diversity is challenging, both because the divergences span a continuum and because the lack of overt morphological differentiation suggests divergence has proceeded heterogeneously. Here, we add...

https://www.nccarf.edu.au/sites/default/files/attached_files/NARP_update_Terrestrial_Biodiversity-2017.pdf This document delivers a resource for research providers to identify critical gaps of information needed by sectoral decision-makers; set research priorities based on these gaps, and identify capacity across the network that could be harnesse...

Targeting phylogenetic diversity (PD) in systematic conservation planning is an efficient way to minimize losses across the Tree of Life. Considering representation of genetic diversity below and above species level, also allows robust analyses within systems where taxonomy is in flux. We use dense sampling of phylogeographic diversity for eleven l...

The impact of climate change may be felt most keenly by tropical ectotherms. In these taxa, it is argued, thermal specialisation means a given shift in temperature will have a larger effect on fitness. For species with limited dispersal ability, the impact of climate change depends on the capacity for their climate-relevant traits to shift. Such sh...

Locating and protecting climate change refugia is important to conserving biodiversity with accelerating climate change. Comparative phylogeographic analysis provides an effective tool for locating such refugia, as long-term retention of one or more populations within a refugial landscape will generate unique genetic lineages. The ranges of the wes...

Aim The aim was to examine the links between past biome stability, vegetation dynamics and biodiversity patterns. Location South America. Time period Last 30,000 years. Major taxa studied Plants. Methods We classified South America into major biomes according to their dominant plant functional groups (grasses, trees and shrubs) and ran a random...

Background Different processes determine species’ geographic ranges, including species’ responses to changing climate, habitat, or both simultaneously. Here we ask which combination of factors best predicts shifts in the upper and lower elevation range limits and overall range of small mammal species in Yosemite National Park, California, USA acros...

Climate change refugia, areas buffered from climate change relative to their surroundings, are of increasing interest as natural resource managers seek to prioritize climate adaptation actions. However, evidence that refugia buffer the effects of anthropogenic climate change is largely missing. Focusing on the climate-sensitive Belding’s ground squ...

High throughput sequencing methods promise to improve our ability to infer the evolutionary histories of lineages and to delimit species. These are exciting prospects for the study of Australian vertebrates, a group comprised of many globally unique lineages with a long history of isolation. The evolutionary relationships within many of these linea...

Spatial responses of species to past climate change depend on both intrinsic traits (climatic niche breadth, dispersal rates) and the scale of climatic fluctuations across the landscape. New capabilities in generating and analysing population genomic data, along with spatial modelling, have unleashed our capacity to infer how past climate changes h...

Understanding the joint evolutionary and ecological underpinnings of sympatry among close relatives remains a key challenge in biology. This problem can be addressed through joint phylogenomic and phenotypic analysis of complexes of closely related lineages within, and across, species and hence representing the speciation continuum. For a complex o...

While methods for genetic species delimitation have noticeably improved in the last decade, this remains a work in progress. Ideally, model based approaches should be applied and considered jointly with other lines of evidence, primarily morphology and geography, in an integrative taxonomy framework. Deep phylogeographic divergences have been repor...

Tissue and specimens list Tissue and specimens list with museum origin, mtDNA lineage, for which analysis samples were used (SD, species delimitation, M, morphology), sex information if available and location. ∗ Correspond to the genetically discordant sample with mtDNA of Triacantha B but nuclear of Triacantha A (with no evidence of admixture in A...

Summary of Generalized Linear modelling with a Poisson distribution analyses for relevant meristic variables Summary of Generalized Linear modelling with a Poisson distribution analyses for relevant meristic variables, presenting estimates and respective confidence intervals (C.I.). Bold correspond to significant p-values. After removing samples wi...

Measurements taken from photos (A) Lateral view of specimen with ear aperture length (EAL), eye to ear distance (EED) and palpebral disc length (PDL). (C) Nasal separation (NS) measured in dorsal view. (C) and (D) correspond to forelimb (FLL) and hindlimb length (HLL) measurements in ventral view. Photos by Damien Esquerré.

Dorsal and ventral paratype photos Dorsal and ventral paratype photos for C. insularis sp. nov (A, C) and for C. isostriacantha sp. nov. (B, D). All photos by Damien Esquerré.

Photos with live animals Photos with live animals showing breeding colours of C. insularis sp. nov. (A, photo by Russell Barrett) and a potential diagnostic trait in C. isostriacantha sp. nov. (B, photo by Mark Allen). The white arrow points to the potential white line trait that distinguish this species from C. triacantha.

jModelTest substitution models jModelTest substitution models used with the two StarBeast2 datasets and fragment length of loci. Loci designation based on Anolis carolinensis genome and sequence size that was retrieved for all used samples for each locus.

Priors used for Starbeast2 and SNAPP analyses

Descriptive table with measurements and meristic data for each main lineage within C. johnstonei and C. triacantha

PCA loadings and variables importance of PCA with log transformed data and with size corrected data for both species PCA loadings and variables importance of PCA with log transformed data (A, B) and with size corrected data (C, D) for C. johnstonei and C. triacantha.

Dorsal and ventral view of holotypes Dorsal and ventral view of holotypes of C. insularis sp. nov. (A), specimen WAM R158646, and C. isostriacantha sp. nov. (B), specimen WAM R171420. All photos by Damien Esquerré.

Summary of MANOVA results testing for significant interaction with mtDNA lineage within C. johnstonei The results for testing normality and heteroscedasticity are also presented for both the log-transformed and the log and size-corrected dataset. Bold are significant p-values for the MANOVA results. After removing samples with missing data, analyse...

mtDNA ND4 maximum likelihood phylogenetic tree of Carlia triacantha and Carlia johnstonei mtDNA ND4 maximum likelihood phylogenetic tree of Carlia triacantha and Carlia johnstonei, from Afonso Silva et al. (2017), with specimens that were analysed by morphological analyses. Sample label includes tissue number, original ID and sampling location.

Box plots for all log transformed variables JA, Johnstonei A; JB, Johnstonei B; TA, Triacantha A; TB, Triacantha B.

Summary of MANOVA results testing for significant interaction with mtDNA lineage within C. triacantha The results for testing normality and heteroscedasticity are also presented for both the log-transformed and the log and size-corrected dataset. Bold are significant p-values for the MANOVA results. ∗, non-normal variables with significant support...

Stepping-stone computation of marginal likelihoods for Bayes factor species delimitation This method calculates the marginal likelihoods from the area under the likelihood posterior curve. Two replicate chains were run for each method and dataset. The mean likelihoods are plotted with + symbols for one chain, and × symbols for the other. Segmented...

Box plots for log and size corrected variables JA, Johnstonei A; JB, Johnstonei B; TA, Triacantha A; TB, Triacantha B.

As climate change progresses, there is increasing focus on the possibility of using targeted gene flow (TGF, the movement of pre-adapted individuals into declining populations) as a management tool. Targeted gene flow is a relatively cheap, low-risk management option, and will almost certainly come into increased use over the coming decades. Before...

Species endemic to the tropical regions are expected to be vulnerable to future climate change due in part to their relatively narrow climatic niches. In addition, these species are more likely to have responded strongly to past climatic change, and this can be explored through phylogeographic analyses. To test the hypothesis that tropical speciali...

Climate refugia management has been proposed as a climate adaptation strategy in the face of global change. Key to this strategy is identification of these areas as well as an understanding of how they are connected on the landscape. Focusing on meadows of the Sierra Nevada in California, we examined multiple factors affecting connectivity using ci...

Critical thermal limits are thought to be correlated with the elevational distribution of species living in tropical montane regions, but with upper limits being relatively invariant compared to lower limits. To test this hypothesis, we examined the variation of thermal physiological traits in a group of terrestrial breeding frogs (Craugastoridae)...

The association of chromosome rearrangements (CRs) with speciation is well established, and there is a long history of theory and evidence relating to “chromosomal speciation.” Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced g...