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"Thompson, Michael B"
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Patterns of niche filling and expansion across the invaded ranges of an Australian lizard
Studies of realized niche shifts in alien species typically ignore the potential effects of intraspecific niche variation and different invaded‐range environments on niche lability. We incorporate our detailed knowledge of the native‐range source populations and global introduction history of the delicate skink Lampropholis delicata to examine intraspecific variation in realized niche expansion and unfilling, and investigate how alternative niche modelling approaches are affected by that variation. We analyzed the realized niche dynamics of L. delicata using an ordination method, ecological niche models (ENMs), and occurrence records from 1) Australia (native range), 2) New Zealand, 3) Hawaii, 4) the two distinct native‐range clades that were the sources for the New Zealand and Hawaii introductions, and 5) the species’ global range (including Lord Howe Island, Australia). We found a gradient of realized niche change across the invaded ranges of L. delicata: niche stasis on Lord Howe Island, niche unfilling in New Zealand (16%), and niche unfilling (87%) and expansion (14%) in Hawaii. ENMs fitted to native‐range data generally identified suitable climatic conditions at sites where the species has established non‐native populations, whereas ENMs based on native‐range source clades and non‐native populations had lower spatial transferability. Our results suggest that the extent to which realized niches are maintained during invasion does not depend on species‐level traits. When realized niche shifts are predominately due to niche unfilling, fully capturing species’ responses along climatic gradients by basing ENMs on native distributions may be more important for accurate invasion forecasts than incorporating phylogenetic differentiation, or integrating niche changes in the invaded range.
Journal Article
A framework for the development of a global standardised marine taxon reference image database (SMarTaR-ID) to support image-based analyses
Video and image data are regularly used in the field of benthic ecology to document biodiversity. However, their use is subject to a number of challenges, principally the identification of taxa within the images without associated physical specimens. The challenge of applying traditional taxonomic keys to the identification of fauna from images has led to the development of personal, group, or institution level reference image catalogues of operational taxonomic units (OTUs) or morphospecies. Lack of standardisation among these reference catalogues has led to problems with observer bias and the inability to combine datasets across studies. In addition, lack of a common reference standard is stifling efforts in the application of artificial intelligence to taxon identification. Using the North Atlantic deep sea as a case study, we propose a database structure to facilitate standardisation of morphospecies image catalogues between research groups and support future use in multiple front-end applications. We also propose a framework for coordination of international efforts to develop reference guides for the identification of marine species from images. The proposed structure maps to the Darwin Core standard to allow integration with existing databases. We suggest a management framework where high-level taxonomic groups are curated by a regional team, consisting of both end users and taxonomic experts. We identify a mechanism by which overall quality of data within a common reference guide could be raised over the next decade. Finally, we discuss the role of a common reference standard in advancing marine ecology and supporting sustainable use of this ecosystem.
Journal Article
Different Genes are Recruited During Convergent Evolution of Pregnancy and the Placenta
Abstract
The repeated evolution of the same traits in distantly related groups (convergent evolution) raises a key question in evolutionary biology: do the same genes underpin convergent phenotypes? Here, we explore one such trait, viviparity (live birth), which, qualitative studies suggest, may indeed have evolved via genetic convergence. There are >150 independent origins of live birth in vertebrates, providing a uniquely powerful system to test the mechanisms underpinning convergence in morphology, physiology, and/or gene recruitment during pregnancy. We compared transcriptomic data from eight vertebrates (lizards, mammals, sharks) that gestate embryos within the uterus. Since many previous studies detected qualitative similarities in gene use during independent origins of pregnancy, we expected to find significant overlap in gene use in viviparous taxa. However, we found no more overlap in uterine gene expression associated with viviparity than we would expect by chance alone. Each viviparous lineage exhibits the same core set of uterine physiological functions. Yet, contrary to prevailing assumptions about this trait, we find that none of the same genes are differentially expressed in all viviparous lineages, or even in all viviparous amniote lineages. Therefore, across distantly related vertebrates, different genes have been recruited to support the morphological and physiological changes required for successful pregnancy. We conclude that redundancies in gene function have enabled the repeated evolution of viviparity through recruitment of different genes from genomic “toolboxes”, which are uniquely constrained by the ancestries of each lineage.
Journal Article
Uterine cellular changes during mammalian pregnancy and the evolution of placentation
There are many different forms of nutrient provision in viviparous (live-bearing) species. The formation of a placenta is one method where the placenta functions to transfer nutrients from mother to fetus (placentotrophy), to transfer waste from the fetus to the mother, and to perform respiratory gas exchange. Despite having the same overarching function, there are different types of placentation within placentotrophic vertebrates, and many morphological changes occur in the uterus during pregnancy to facilitate formation of the placenta. These changes are regulated in complex ways but are controlled by similar hormonal mechanisms across species. This review describes current knowledge of the morphological and molecular changes to the uterine epithelium preceding implantation among mammals. Our aim is to identify the commonalities and constraints of these cellular changes to understand the evolution of placentation in mammals and to propose directions for future research. We compare and discuss the complex modifications to the ultrastructure of uterine epithelial cells (UEC) and show that there are similarities in the changes to the cytoskeleton and gross morphology of the UEC, especially of the apical and lateral plasma membrane of the cells during the formation of a placenta in all eutherians and marsupials studied to date. We conclude that further research is needed to understand the evolution of placentation among viviparous mammals, particularly concerning the level of placental invasiveness, hormonal control, and genetic underpinnings of pregnancy in marsupial taxa. Summary sentence There are many complex modifications to the ultrastructure of uterine epithelial cells during pregnancy with similarities in the changes to their gross morphology during the formation of a placenta in eutherians and marsupials studied to date. Graphical Abstract
Journal Article
Changes in participant behaviour and attitudes are associated with knowledge and skills gained by using a turtle conservation citizen science app
Citizen science has become a popular way to collect biodiversity data and engage the wider public in scientific research. It has the potential to improve the knowledge and skills of participants, and positively change their behaviour and attitude towards the environment. Citizen science outcomes are particularly valuable for wildlife conservation, as they could help alleviate human impacts on the environment. We used an online questionnaire to investigate the consequences of participating in an Australian turtle mapping app, TurtleSAT, on skills and knowledge gain, and test for any association between these gains and behavioural or attitudinal changes reported by the participants. One hundred and forty‐eight citizen scientists completed our questionnaire, mostly from the states of New South Wales and Victoria. TurtleSAT was the third most common source of correct answers about turtle ecology and conservation, after a talk about turtles and personal observations/research. Citizen scientists who participated more often were more knowledgeable about turtles than infrequent users. Self‐reported gains in knowledge and skills were positively linked to attitudinal and behavioural changes, such as being more aware of turtles on roads. However, behaviour and attitude changes were not related to participation rate. Respondents also reported that after learning about the current decline in turtle populations, they adopted several turtle‐friendly practices, such as habitat restoration or moving turtles out of harm's way, underlining the importance of increasing people's awareness on species declines. The reported changes in attitudes and behaviours are likely to positively impact the conservation of Australian freshwater turtles. Engagement with citizen science projects like TurtleSAT may result in participants being more interested in the natural world, by learning more about it and being more exposed to it, and therefore contributing more actively to its protection. A free Plain Language Summary can be found within the Supporting Information of this article. A free Plain Language Summary can be found within the Supporting Information of this article.
Journal Article
Transcriptomic changes in the pre-implantation uterus highlight histotrophic nutrition of the developing marsupial embryo
Early pregnancy is a critical time for successful reproduction; up to half of human pregnancies fail before the development of the definitive chorioallantoic placenta. Unlike the situation in eutherian mammals, marsupial pregnancy is characterised by a long pre-implantation period prior to the development of the short-lived placenta, making them ideal models for study of the uterine environment promoting embryonic survival pre-implantation. Here we present a transcriptomic study of pre-implantation marsupial pregnancy, and identify differentially expressed genes in the
Sminthopsis crassicaudata
uterus involved in metabolism and biosynthesis, transport, immunity, tissue remodelling, and uterine receptivity. Interestingly, almost one quarter of the top 50 genes that are differentially upregulated in early pregnancy are putatively involved in histotrophy, highlighting the importance of nutrient transport to the conceptus prior to the development of the placenta. This work furthers our understanding of the mechanisms underlying survival of pre-implantation embryos in the earliest live bearing ancestors of mammals.
Journal Article
Phylogeographic divergence in the widespread delicate skink (Lampropholis delicata) corresponds to dry habitat barriers in eastern Australia
Background
The mesic habitats of eastern Australia harbour a highly diverse fauna. We examined the impact of climatic oscillations and recognised biogeographic barriers on the evolutionary history of the delicate skink (
Lampropholis delicata
), a species that occurs in moist habitats throughout eastern Australia. The delicate skink is a common and widespread species whose distribution spans 26° of latitude and nine major biogeographic barriers in eastern Australia. Sequence data were obtained from four mitochondrial genes (
ND2, ND4, 12SrRNA, 16SrRNA
) for 238 individuals from 120 populations across the entire native distribution of the species. The evolutionary history and diversification of the delicate skink was investigated using a range of phylogenetic (Maximum Likelihood, Bayesian) and phylogeographic analyses (genetic diversity, Φ
ST
, AMOVA, Tajima's
D
, Fu's
F
statistic).
Results
Nine geographically structured, genetically divergent clades were identified within the delicate skink. The main clades diverged during the late Miocene-Pliocene, coinciding with the decline and fragmentation of rainforest and other wet forest habitats in eastern Australia. Most of the phylogeographic breaks within the delicate skink were concordant with dry habitat or high elevation barriers, including several recognised biogeographic barriers in eastern Australia (Burdekin Gap, St Lawrence Gap, McPherson Range, Hunter Valley, southern New South Wales). Genetically divergent populations were also located in high elevation topographic isolates inland from the main range of
L. delicata
(Kroombit Tops, Blackdown Tablelands, Coolah Tops). The species colonised South Australia from southern New South Wales via an inland route, possibly along the Murray River system. There is evidence for recent expansion of the species range across eastern Victoria and into Tasmania, via the Bassian Isthmus, during the late Pleistocene.
Conclusions
The delicate skink is a single widespread, but genetically variable, species. This study provides the first detailed phylogeographic investigation of a widespread species whose distribution spans virtually all of the major biogeographic barriers in eastern Australia.
Journal Article
Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards
Background
High-throughput sequencing using targeted enrichment and transcriptomic methods enables rapid construction of phylogenomic data sets incorporating hundreds to thousands of loci. These advances have enabled access to an unprecedented amount of nucleotide sequence data, but they also pose new questions. Given that the loci targeted for enrichment are often highly conserved, how informative are they at different taxonomic scales, especially at the intraspecific/phylogeographic scale? We investigate this question using Australian scincid lizards in the
Eugongylus
group (Squamata: Scincidae). We sequenced 415 anchored hybrid enriched (AHE) loci for 43 individuals and mined 1650 exons (1648 loci) from transcriptomes (transcriptome mining) from 11 individuals, including multiple phylogeographic lineages within several species of
Carlia
,
Lampropholis
, and
Saproscincus
skinks. We assessed the phylogenetic information content of these loci at the intergeneric, interspecific, and phylogeographic scales. As a further test of the utility at the phylogeographic scale, we used the anchor hybrid enriched loci to infer lineage divergence parameters using coalescent models of isolation with migration.
Results
Phylogenetic analyses of both data sets inferred very strongly supported trees at all taxonomic levels. Further, AHE loci yielded estimates of divergence times between closely related lineages that were broadly consistent with previous population-level analyses.
Conclusions
Anchored-enriched loci are useful at the deep phylogeny and phylogeographic scales. Although overall phylogenetic support was high throughout the Australian
Eugongylus
group phylogeny, there were nonetheless some conflicting or unresolved relationships, especially regarding the placement of
Pseudemoia
,
Cryptoblepharus
, and the relationships amongst closely-related species of Tasmanian
Niveoscincus
skinks.
Journal Article
A review of the evolution of viviparity in squamate reptiles: the past, present and future role of molecular biology and genomics
Squamate reptiles (lizards and snakes) offer a unique model system for testing hypotheses about the evolutionary transition from oviparity (egg-laying) to viviparity (live-bearing) in amniote vertebrates. The evolution of squamate viviparity has occurred remarkably frequently (>108 times) and has resulted in major changes in reproductive physiology. Such frequent changes in reproductive strategy pose two questions: (1) what are the molecular mechanisms responsible for the evolution of squamate viviparity? (2) Are these molecular mechanisms the same for separate origins of viviparity? Molecular approaches, such as RT-PCR, in situ hybridisation, Western blotting and immunofluorescence, have been invaluable for identifying genes and proteins that are involved in squamate placental development, materno-foetal immunotolerance, placental transport, placental angiogenesis, hormone synthesis and hormone receptor expression. However, the candidate-gene or -protein approach that has been used until now does not allow for de novo gene/protein discovery; results to date suggest that the reproductive physiologies of mammals and squamate reptiles are very similar, but this conclusion may simply be due to a limited capacity to study the subset of genes and proteins that are unique to reptiles. Progress has also been slowed by the lack of appropriate molecular and genomic resources for squamate reptiles. The advent of next-generation sequencing provides a relatively inexpensive way to conduct rapid high-throughput sequencing of genomes and transcriptomes. We discuss the potential use of next-generation sequencing technologies to analyse differences in gene expression between oviparous and viviparous squamates, provide important sequence information for reptiles, and generate testable hypotheses for the evolution of viviparity.
Journal Article