Craig Moritz

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

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648
Publications
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Publications

Publications (648)
Article
Full-text available
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...
Article
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...
Article
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...
Article
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...
Article
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...
Article
Australia has the highest historically recorded rate of mammalian extinction in the world, with 34 terrestrial species declared extinct since European colonization in 1788. Among Australian mammals, rodents have been the most severely affected by these recent extinctions ; however, given a sparse historical record, the scale and timing of their dec...
Article
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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...
Article
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...
Article
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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...
Article
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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...
Article
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 the...
Article
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...
Article
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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...
Article
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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...
Article
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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...
Article
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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...
Article
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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...
Article
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....
Article
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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...
Article
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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...
Article
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...
Article
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-...
Article
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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...
Technical Report
Full-text available
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...
Article
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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...
Article
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...
Article
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...
Article
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The aim was to examine the links between past biome stability, vegetation dynamics and biodiversity patterns. South America. Last 30,000 years. Plants. We classified South America into major biomes according to their dominant plant functional groups (grasses, trees and shrubs) and ran a random forest (RF) classification with data on current climate...
Article
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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...
Article
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...
Article
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...
Article
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...
Article
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...
Article
Full-text available
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...
Data
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...
Data
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...
Data
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.
Data
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.
Data
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.
Data
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.
Data
Priors used for Starbeast2 and SNAPP analyses
Data
Descriptive table with measurements and meristic data for each main lineage within C. johnstonei and C. triacantha
Data
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.
Data
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.
Data
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...
Data
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.
Data
Box plots for all log transformed variables JA, Johnstonei A; JB, Johnstonei B; TA, Triacantha A; TB, Triacantha B.
Data
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...
Data
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...
Data
Box plots for log and size corrected variables JA, Johnstonei A; JB, Johnstonei B; TA, Triacantha A; TB, Triacantha B.
Article
Full-text available
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...
Article
Full-text available
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...
Article
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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...
Article
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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)...
Article
Full-text available
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...
Article
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The tropical savannah landscapes of Australia’s north, though previously overshadowed by the biodiverse rainforests of the Wet Tropics, are themselves now attracting interest for their biological significance and uniqueness. The Einasleigh Uplands region of north-east Queensland is home to a diverse group of mammals and reptiles and was previously...
Article
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In the midst of global species loss, Indigenous languages and culture are experiencing similar declines. Current international policies and programs advocate the involvement of local and Indigenous people in sustaining biodiversity and culture, but the anticipated benefits are not always realized or assessed. This paper draws on three objectives of...