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1. Life in the “dead heart” of Australia: The geohistory of the Australian deserts and its impact on genetic diversity of arid zone lizards

Author:
J Scott Keogh,   et al.   ; Mitzy Pepper;     Show all 2 Author
Source:
Journal of biogeography 2021 v.48 no.4 pp. 716-746
ISSN:
0305-0270
Subject:
Pleistocene epoch; arid zones; biogeography; ecosystems; fossils; gene flow; genetic structure; genetic variation; geographical distribution; landscapes; life history; topography; Australia
Abstract:
... AIM: The Australian deserts are home to a remarkable diversity of taxa that might appear to have evolved in the absence of topographic and physical barriers to dispersal. In fact this is a biogeographical illusion, as the dunefields of the modern arid zone obscure the fossil landscapes of the wet desert that existed for much of the Cenozoic. As the geohistory of Australia's arid zone is not widely ...
DOI:
10.1111/jbi.14063

2. Between a rock and a dry place: phylogenomics, biogeography, and systematics of ridge-tailed monitors (Squamata: Varanidae: Varanus acanthurus complex)

Author:
J. Scott Keogh,   et al.   ; Carlos J. Pavón-Vázquez; Damien Esquerré; Alison J. Fitch; Brad Maryan; Paul Doughty; Stephen C. Donnellan;     Show all 7 Authors
Source:
Molecular phylogenetics and evolution 2022 v.173 pp. 107516
ISSN:
1055-7903
Subject:
Acanthurus; Cenozoic era; Varanus; biogeography; data collection; genetic structure; genomics; geographical distribution; indigenous species; mitochondria; new species; phylogeny; refuge habitats; Australia
Abstract:
... 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 sequen ...
DOI:
10.1016/j.ympev.2022.107516

3. Phylogeography, historical demography and systematics of the world’s smallest pythons (Pythonidae, Antaresia)

Author:
J. Scott Keogh,   et al.   ; Damien Esquerré; Stephen C. Donnellan; Carlos J. Pavón-Vázquez; Jéssica Fenker;     Show all 5 Authors
Source:
Molecular phylogenetics and evolution 2021 v.161 pp. 107181
ISSN:
1055-7903
Subject:
Antaresia childreni; demography; gene flow; genomics; geometry; mitochondrial DNA; morphometry; new species; phylogeny; phylogeography; population structure; species diversity; Australia; New Guinea
Abstract:
... Advances from empirical studies in phylogeography, systematics and species delimitation highlight the importance of integrative approaches for quantifying taxonomic diversity. Genomic data have greatly improved our ability to discern both systematic diversity and evolutionary history. Here we combine analyses of mitochondrial DNA sequences, thousands of genome-wide SNPs and linear and geometric mo ...
DOI:
10.1016/j.ympev.2021.107181

4. Sexual selection on performance traits in an Australian lizard with alternative reproductive tactics

Author:
J. Scott Keogh,   et al.   ; Daniel W. A. Noble; Fonti Kar; Shinichi Nakagawa; Martin J. Whiting;     Show all 5 Authors
Source:
Journal of evolutionary biology 2021 v.34 no.3 pp. 451-464
ISSN:
1010-061X
Subject:
lizards; reproductive success; sexual selection
Abstract:
... Sexual selection shapes the adaptive landscape in complex ways that lead to trait integration. Much of our understanding of selection comes from studies of morphological traits. However, few studies attempt to quantify the form and direction of selection on performance even though it is predicted to be a more direct target of selection in nature. We measured sexual selection on performance traits ...
DOI:
10.1111/jeb.13752

5. Disease influences male advertisement and mating outcomes in a critically endangered amphibian

Author:
J. Scott Keogh,   et al.   ; Shannon R. Kelleher; Ben C. Scheele; Aimee J. Silla; David A. Hunter; John A. Endler; Phillip G. Byrne;     Show all 7 Authors
Source:
Animal behaviour 2021 v.173 pp. 145-157
ISSN:
0003-3472
Subject:
Batrachochytrium dendrobatidis; Pseudophryne; body size; color; frogs; fungi; genomics; infectious diseases; males; nests; parentage; pathogens; phenotype; probability; progeny; reproductive behavior; sexual selection; soil water; virulence; water potential; Australia
Abstract:
... The sublethal effects of infectious disease on reproductive behaviour and mating success are not well understood. Here, we investigated predictors of male mating success in one of Australia's most critically endangered vertebrates: the northern corroboree frog, Pseudophryne pengilleyi. Using a genomic approach to assign parentage, we explored whether infection with the amphibian chytrid fungus Bat ...
DOI:
10.1016/j.anbehav.2021.01.007

6. Phylogenomics, biogeography and taxonomic revision of New Guinean pythons (Pythonidae, Leiopython) harvested for international trade

Author:
J. Scott Keogh,   et al.   ; Daniel J.D. Natusch; Damien Esquerré; Jessica A. Lyons; Amir Hamidy; Alan R. Lemmon; Emily Moriarty Lemmon; Awal Riyanto; Stephen Donnellan;     Show all 9 Authors
Source:
Molecular phylogenetics and evolution 2021 v.158 pp. 106960
ISSN:
1055-7903
Subject:
Pythonidae; geographical distribution; international trade; loci; mitochondrial genome; mountains; pets; phylogeny; species diversity; sympatry; taxonomic revisions; New Guinea
Abstract:
... The large and enigmatic New Guinean pythons in the genus Leiopython are harvested from the wild to supply the international trade in pets. Six species are currently recognized (albertisii, biakensis, fredparkeri, huonensis, meridionalis, montanus) but the taxonomy of this group has been controversial. We combined analysis of 421 nuclear loci and complete mitochondrial genomes with morphological da ...
DOI:
10.1016/j.ympev.2020.106960

7. Parallel selective pressures drive convergent diversification of phenotypes in pythons and boas

Author:
J. Scott Keogh,   et al.   ; Damien Esquerré;     Show all 2 Author
Source:
Ecology letters 2016 v.19 no.7 pp. 800-809
ISSN:
1461-023X
Subject:
Pythonidae; adaptive radiation; head; morphometry; niches; phenotype; snakes
Abstract:
... Pythons and boas are globally distributed and distantly related radiations with remarkable phenotypic and ecological diversity. We tested whether pythons, boas and their relatives have evolved convergent phenotypes when they display similar ecology. We collected geometric morphometric data on head shape for 1073 specimens representing over 80% of species. We show that these two groups display stro ...
DOI:
10.1111/ele.12620

8. Aridification drove repeated episodes of diversification between Australian biomes: Evidence from a multi-locus phylogeny of Australian toadlets (Uperoleia: Myobatrachidae)

Author:
J. Scott Keogh,   et al.   ; Renee A. Catullo;     Show all 2 Author
Source:
Molecular phylogenetics and evolution 2014 v.79 pp. 106-117
ISSN:
1055-7903
Subject:
Myobatrachidae; arid zones; climate change; deserts; ecosystems; frogs; introgression; landscapes; loci; mitochondria; monsoon season; phylogeny; taxonomy; topology; tropical rain forests; Australia
Abstract:
... Australia is a large and complex landmass that comprises diverse biomes ranging from tropical rainforests to harsh deserts. While Australian biotic diversity has evolved in response to landscape and climate changes, evidence of Miocene or later biome shifts are few. The Australo-Papuan endemic frog genus Uperoleia is widely distributed across mesic, monsoonal tropic and arid regions of Australia. ...
DOI:
10.1016/j.ympev.2014.06.012

9. The unexpected genetic mating system of the red‐backed toadlet (Pseudophryne coriacea): A species with prolonged terrestrial breeding and cryptic reproductive behaviour

Author:
J. Scott Keogh,   et al.   ; Daniel M. O'Brien; Aimee J. Silla; Phillip G. Byrne;     Show all 4 Authors
Source:
Molecular ecology 2018 v.27 no.14 pp. 3001-3015
ISSN:
0962-1083
Subject:
Pseudophryne; amphibians; eggs; females; genetic analysis; introgression; males; mating systems; nesting sites; nests; paternity; polyandry; reproductive behavior; reproductive success; single nucleotide polymorphism; sires
Abstract:
... Molecular technologies have revolutionized our classification of animal mating systems, yet we still know very little about the genetic mating systems of many vertebrate groups. It is widely believed that anuran amphibians have the highest reproductive diversity of all vertebrates, yet genetic mating systems have been studied in <1% of all described species. Here, we use single nucleotide polymorp ...
DOI:
10.1111/mec.14737

10. Biogeography of the Kimberley, Western Australia: a review of landscape evolution and biotic response in an ancient refugium

Author:
J. Scott Keogh,   et al.   ; Mitzy Pepper; Malte Ebach;     Show all 3 Authors
Source:
Journal of biogeography 2014 v.41 no.8 pp. 1443-1455
ISSN:
0305-0270
Subject:
arid zones; biogeography; deformation; deserts; drainage; ecosystems; genetic variation; indigenous species; landscapes; monsoon season; paleoecology; phylogeny; plateaus; refuge habitats; rivers; sandstone; Western Australia
Abstract:
... AIM: We review the biogeography of the Kimberley, with a particular focus on the geological and landscape history of the region. We identified broad geological and biogeographical discontinuities across the Kimberley, and propose a number of testable hypotheses concerning how the evolution of these land‐forms may have harboured and structured genetic diversity across the region. LOCATION: The Kimb ...
DOI:
10.1111/jbi.12324

11. Experimental evidence for sexual selection against inbred males

Author:
J. Scott Keogh,   et al.   ; Regina Vega‐Trejo; Megan L. Head; Michael D. Jennions;     Show all 4 Authors
Source:
journal of animal ecology 2017 v.86 no.2 pp. 394-404
ISSN:
0021-8790
Subject:
Gambusia holbrooki; adults; artificial insemination; diet; eggs; embryonic mortality; fecundity; females; heterozygosity; inbreeding; inbreeding depression; juveniles; males; mortality; paternity; phenotype; progeny; rearing; reproductive success; sexual selection; single nucleotide polymorphism; sires; spermatozoa
Abstract:
... The detrimental effects of matings between relatives are well known. However, few studies determine the extent to which inbreeding depression in males is due to natural or sexual selection. Importantly, measuring fitness or key fitness components, rather than phenotypic traits allows more accurate estimation of inbreeding depression. We investigate how differences in inbreeding and juvenile diet ( ...
DOI:
10.1111/1365-2656.12615

12. Speciation across mountains: Phylogenomics, species delimitation and taxonomy of the Liolaemus leopardinus clade (Squamata, Liolaemidae)

Author:
J. Scott Keogh,   et al.   ; Damien Esquerré; Diego Ramírez-Álvarez; Carlos J. Pavón-Vázquez; Jaime Troncoso-Palacios; Carlos F. Garín; Adam D. Leaché;     Show all 7 Authors
Source:
Molecular phylogenetics and evolution 2019 v.139 pp. 106524
ISSN:
1055-7903
Subject:
Liolaemus; allopatry; altitude; introgression; lizards; mitochondria; mitochondrial DNA; mountains; nuclear genome; phylogeny; population structure; single nucleotide polymorphism; taxonomy; Andes region; Chile
Abstract:
... Organisms rapidly diversifying across unstable environments such as mountain tops provide substantial challenges for resolving evolutionary histories and delimiting species. The Liolaemus leopardinus clade is a group of five species of lizards adapted to high altitudes in central Chile, with most species found in the Andes, but one species, L. frassinettii is found in the independent Costa Cordill ...
DOI:
10.1016/j.ympev.2019.106524

13. Species delimitation and systematics of the green pythons (Morelia viridis complex) of Melanesia and Australia

Author:
J. Scott Keogh,   et al.   ; Daniel J.D. Natusch; Damien Esquerré; Jessica A. Lyons; Amir Hamidy; Alan R. Lemmon; Emily Moriarty Lemmon; Awal Riyanto; Stephen Donnellan;     Show all 9 Authors
Source:
Molecular phylogenetics and evolution 2019 pp. -
ISSN:
1055-7903
Subject:
Morelia viridis; biogeography; data collection; exons; fauna; mitochondrial genome; mountains; pets; taxonomy; Australia; Melanesia; New Guinea
Abstract:
... Molecular data sets and the increasing use of integrative systematics is revealing cryptic diversity in a range of taxa – particularly in remote and poorly sampled landscapes like the island of New Guinea. Green pythons (Morelia viridis complex) are one of the most conspicuous elements of this island’s fauna, with large numbers taken from the wild to supply international demand for exotic pets. We ...
DOI:
10.1016/j.ympev.2019.106640

14. Multiple mating in a lizard increases fecundity but provides no evidence for genetic benefits

Author:
J. Scott Keogh,   et al.   ; Daniel W.A. Noble; Martin J. Whiting;     Show all 3 Authors
Source:
Behavioral ecology 2013 v.24 no.5 pp. 1128-1137
ISSN:
1045-2249
Subject:
Scincidae; eggs; fecundity; females; genes; lizards; males; progeny; reproductive success; spermatozoa
Abstract:
... Lay summaryFemale lizards get a ‘boost’ in reproductive success by mating with many males. In Water Skinks females engage in multiple mating to elevate their reproductive success rather than trying to obtain ‘good’ genes, which increase their offspring’s survival. Females may increase their reproductive success by mating with multiple males simply because their eggs are more likely to be fertilize ...
DOI:
10.1093/beheco/art040

15. Sexual selection on male body size, genital length and heterozygosity: Consistency across habitats and social settings

Author:
J. Scott Keogh,   et al.   ; Megan L. Head; Andrew T. Kahn; Jonathan M. Henshaw; Michael D. Jennions;     Show all 5 Authors
Source:
journal of animal ecology 2017 v.86 no.6 pp. 1458-1468
ISSN:
0021-8790
Subject:
Gambusia holbrooki; body size; environmental factors; females; genetic variation; genome; habitats; heterozygosity; males; mating competitiveness; paternity; reproductive success; sex ratio; sexual selection; single nucleotide polymorphism; temporal variation
Abstract:
... Spatial and temporal variation in environmental factors and the social setting can help to maintain genetic variation in sexually selected traits if it affects the strength of directional selection. A key social parameter which affects the intensity of, and sometimes predicts the response to, mating competition is the operational sex ratio (OSR; ratio of receptive males to females). How the OSR af ...
DOI:
10.1111/1365-2656.12742

16. Maternal and additive genetic effects contribute to variation in offspring traits in a lizard

Author:
J. Scott Keogh,   et al.   ; Daniel W.A. Noble; S. Eryn McFarlane; Martin J. Whiting;     Show all 4 Authors
Source:
Behavioral ecology 2014 v.25 no.3 pp. 633-640
ISSN:
1045-2249
Subject:
additive gene effects; early development; genes; lizards; maternal effect; mothers; phenotype; progeny
Abstract:
... Lay SummaryMothers are more important than genes in directing the early development of lizards. Genes, maternal effects, and the environment encountered during development govern offspring phenotype. Yet, we know little about their relative contributions in explaining variation in lizard phenotypes. We found that mothers strongly influenced the traits of their offspring and only one trait showed v ...
DOI:
10.1093/beheco/aru032

17. New approaches to cataloguing and understanding evolutionary diversity: a perspective from Australian herpetology

Author:
J. Scott Keogh,   et al.   ; Paul Oliver; Craig Moritz;     Show all 3 Authors
Source:
Australian journal of zoology 2014 v.62 no.6 pp. 417-430
ISSN:
0004-959X
Subject:
analytical methods; biodiversity; herpetology; planning
Abstract:
... Species are a fundamental unit for all fields of biology but conceptual and practical limitations have hampered the process of identifying and describing species in many organismal groups. One outcome of these challenges is the accumulation of genetically divergent lineages and morphologically distinctive populations that are ‘known’, but remain of uncertain taxonomic status and evolutionary signi ...
DOI:
10.1071/ZO14091

18. The biogeographical boundaries of northern Australia: evidence from ecological niche models and a multi‐locus phylogeny of Uperoleia toadlets (Anura: Myobatrachidae)

Author:
J. Scott Keogh,   et al.   ; Renee A. Catullo; Robert Lanfear; Paul Doughty; W. Daniel Kissling;     Show all 5 Authors
Source:
Journal of biogeography 2014 v.41 no.4 pp. 659-672
ISSN:
0305-0270
Subject:
Anura; allopatry; deserts; frogs; models; phylogeny; plateaus; refuge habitats; sandstone; sandy soils; savannas; statistical analysis; tropics; woodlands; Northern Territory
Abstract:
... AIM: Our aim was to test hypothesized biogeographical barriers using small‐bodied terrestrial Uperoleia frogs, to identify Pleistocene refugia and to define biogeographical units. LOCATION: The Australian Monsoonal Tropics, defined as the open woodlands and savanna north of the inland arid and eastern winter‐rainfall zones. METHODS: A multi‐locus molecular phylogeny of the Uperoleia lithomoda, U.  ...
DOI:
10.1111/jbi.12230

19. Direct effects of incubation temperature on morphology, thermoregulatory behaviour and locomotor performance in jacky dragons (Amphibolurus muricatus)

Author:
J. Scott Keogh,   et al.   ; Damien Esquerré; Lisa E. Schwanz;     Show all 3 Authors
Source:
Journal of thermal biology 2014 v.43 pp. 33-39
ISSN:
0306-4565
Subject:
body temperature; hatching; lizards; mortality; phenotypic plasticity; thermoregulation
Abstract:
... Incubation temperature is one of the most studied factors driving phenotypic plasticity in oviparous reptiles. We examined how incubation temperature influenced hatchling morphology, thermal preference and temperature-dependent running speed in the small Australian agamid lizard Amphibolurus muricatus. Hatchlings incubated at 32°C grew more slowly than those incubated at 25 and 28°C during their f ...
DOI:
10.1016/j.jtherbio.2014.04.007

20. The first complete mitochondrial genome of Pygopodidae (Aprasia parapulchella Kluge)

Author:
J. Scott Keogh,   et al.   ; Anna J. MacDonald; Theresa Knopp; Mitzy Pepper; Stephen D. Sarre;     Show all 5 Authors
Source:
Australian journal of zoology 2015 v.63 no.2 pp. 111-114
ISSN:
0004-959X
Subject:
genes; lizards; mitochondrial genome; nucleotide sequences; ribosomal RNA; transfer RNA; Australia
Abstract:
... The Pygopodidae comprise an enigmatic group of legless lizards endemic to the Australo-Papuan region. Here we present the first complete mitochondrial genome for a member of this family, Aprasia parapulchella, from Australia. The mitochondrial genome of A. parapulchella is 16528 base pairs long and contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes and the control region, conforming t ...
DOI:
10.1071/ZO14092