Population genetic structure, gene flow and sex-biased dispersal in frillneck lizards (Chlamydosaurus kingii)

By using both mitochondrial and nuclear multiloci markers, we explored population genetic structure, gene flow and sex-specific dispersal of frillneck lizards (Chlamydosaurus kingii) sampled at three locations, separated by 10 to 50 km, in a homogenous savannah woodland in tropical Australia. Apart from a recombinant lizard, the mitochondrial analyses revealed two nonoverlapping haplotypes/populations, while the nuclear markers showed that the frillneck lizards represented three separate clusters/populations. Due to the small population size of the mtDNA, fixation may occur via founder effects and/or drift. We therefore suggest that either of these two processes, or a combination of the two, are the most likely causes of the discordant results obtained from the mitochondrial and the nuclear markers. In contrast to the nonoverlapping mitochondrial haplotypes, in 12 out of 74 lizards, mixed nuclear genotypes were observed, hence revealing a limited nuclear gene flow. Although gene flow should ultimately result in a blending of the populations, we propose that the distinct nuclear population structure is maintained by frequent fires resulting in local bottlenecks, and concomitant spatial separation of the frillneck lizard populations. Limited mark-recapture data and the difference in distribution of the mitochondrial and nuclear markers suggest that the mixed nuclear genotypes were caused by juvenile male-biased dispersal.

Population structure in the highly fragmented range of Tor douronensis (Cyprinidae) in Sarawak, Malaysia revealed by microsatellite DNA markers

1. Understanding the structure of threatened populations, particularly those that exist in degraded or fragmented habitats is crucial for their effective management and conservation. Recently developed methods of individual-based analysis of genetic data provide an unprecedented opportunity to understand the relationships amongst fragmented populations.

2. In the present study, population structure of an important cyprinid species (Tor douronensis), which is indigenous to Sarawak, Malaysia, is investigated as part of an ongoing conservation effort to restore threatened wild populations of the species. The population structure inferred using data from seven autosomal microsatellite loci was generally consistent with geography and habitat fragmentation.

3. The results indicate that there are two well-defined clusters of T. douronensis in Sarawak, namely the 'northeastern' and the 'southwestern' clusters. In addition, a further subdivision was observed in each of the clusters distributed between river systems. Low levels of gene flow were also observed and migrants between habitat fragments were identified, possibly resulting from human-mediated translocations.

4. Implications of the findings for management and conservation of T. douronensis are discussed.

Bovine Muc1 is a highly polymorphic gene encoding an extensively glycosylated mucin that binds bacteria

The bovine Muc1 protein is synthesized by mammary epithelial cells and shed into milk as an integral component of the milk fat globule membrane; however, the structure and functions of this mucin, particularly in relation to lactation, are poorly defined. The objectives of this investigation were to investigate the Muc1 gene and protein structures in the context of lactation and to test the hypothesis that Muc1 has a role in innate immune defense. Polymerase chain reaction analysis of genomic DNA from 630 cattle revealed extensive polymorphism in the variable number of tandem repeats (VNTR) in the bovine Muc1 gene. Nine allelic
variants spanning 7 to 23 VNTR units, each encoding 20 AA, were identified. Three alleles, containing 11, 14, and 16 VNTR units, respectively, were predominant. In addition, a polymorphism in one of the VNTR units has the potential to introduce a unique site for N-linked glycosylation. Statistical analysis indicated weak associations between the VNTR alleles and milk protein and fat percentages in a progeny-tested population of Holstein-Friesian dairy cattle. No association with somatic cell count could be demonstrated. Bovine Muc1 was purified from milk fat globule membranes and characterized. The protein was highly glycosylated, primarily with O-linked sialylated T-antigen [Neu5Ac(α2–3)-Gal(β1–3)-GalNAcα1] and, to a lesser extent, with N-linked oligosaccharides, which together accounted for approximately 60% of the apparent mass of Muc1. Purified bovine Muc1 directly bound fluorescently labeled Escherichia coli BioParticles (Invitrogen, Mount Waverley, Australia) and inhibited their binding to bovine mammary epithelial cells grown in vitro.

Fine-scale effects of habitat loss and fragmentation despite large-scale gene flow for some regionally declining woodland bird species

Habitat loss and associated fragmentation effects are well-recognised threats to biodiversity. Loss of functional connectivity (mobility, gene flow and demographic continuity) could result in population decline in altered habitat, because smaller, isolated populations are more vulnerable to extinction. We tested whether substantial habitat reduction plus fragmentation is associated with reduced gene flow in three 'decliner' woodland-dependent bird species (eastern yellow robin, weebill and spotted pardalote) identified in earlier work to have declined disproportionately in heavily fragmented landscapes in the Box-Ironbark forest region in north-central Victoria, Australia. For these three decliners, and one 'tolerant' species (striated pardalote), we compared patterns of genetic diversity, relatedness, effective population size, sex-ratios and genic (allele frequency) differentiation among landscapes of different total tree cover, identified population subdivision at the regional scale, and explored fine-scale genotypic (individual-based genetic signature) structure. Unexpectedly high genetic connectivity across the study region was detected for 'decliner' and 'tolerant' species. Power analysis simulations suggest that moderate reductions in gene flow should have been detectable. However, there was evidence of local negative effects of reduced habitat extent and structural connectivity: slightly lower effective population sizes, lower genetic diversity, higher within-site relatedness and altered sex-ratios (for weebill and eastern yellow robin) in 10 x 10 km 'landscapes' with low vegetation cover. We conclude that reduced structural connectivity in the Box-Ironbark ecosystem may still allow sufficient gene flow to avoid the harmful effects of inbreeding in our study species. Although there may still be negative consequences of fragmentation for demographic connectivity, the high genetic connectivity of mobile bird species in this system suggests that reconnecting isolated habitat patches may be less important than increasing habitat extent and/or quality if these need to be traded off.

The Bassian Isthmus and the major ocean currents of southeast Australia influence the phylogeography and population structure of a southern Australian intertidal barnacle Catomerus polymerus (Darwin)

Southern Australia is currently divided into three marine biogeographical provinces based on faunal distributions and physical parameters. These regions indicate eastern and western distributions, with an overlap occurring in the Bass Strait in Victoria. However, studies indicate that the boundaries of these provinces vary depending on the species being examined, and in particular on the mode of development employed by that species, be they direct developers or planktonic larvae dispersers. Mitochondrial DNA sequence analysis of the surf barnacle Catomerus polymerus in southern Australia revealed an east–west phylogeographical split involving two highly divergent clades (cytochrome oxidase I 3.5 ± 0.76%, control region 6.7 ± 0.65%), with almost no geographical overlap. Spatial genetic structure was not detected within either clade, indicative of a relatively long-lived planktonic larval phase. Five microsatellite loci indicated that C. polymerus populations exhibit relatively high levels of genetic divergence, and fall into four subregions: eastern Australia, central Victoria, western Victoria and Tasmania, and South Australia. F_ST values between eastern Australia (from the eastern mitochondrial DNA clade) and the remaining three subregions ranged from 0.038 to 0.159, with other analyses indicating isolation by distance between the subregions of western mitochondrial origin. We suggest that the east–west division is indicative of allopatric divergence resulting from the emergence of the Bassian land-bridge during glacial maxima, preventing gene flow between these two lineages. Subsequently, contemporary ecological conditions, namely the East Australian, Leeuwin, and Zeehan currents and the geographical disjunctions at the Coorong and Ninety Mile Beach are most likely responsible for the four subregions indicated by the microsatellite data.

Association of differential gene expression with imatinib mesylate and omacetaxine mepesuccinate toxicity in lymphoblastoid cell lines

Background

Imatinib mesylate is currently the drug of choice to treat chronic myeloid leukemia. However, patient resistance and cytotoxicity make secondary lines of treatment, such as omacetaxine mepesuccinate, a necessity. Given that drug cytotoxicity represents a major problem during treatment, it is essential to understand the biological pathways affected to better predict poor drug response and prioritize a treatment regime.
Methods

We conducted cell viability and gene expression assays to determine heritability and gene expression changes associated with imatinib and omacetaxine treatment of 55 non-cancerous lymphoblastoid cell lines, derived from 17 pedigrees. In total, 48,803 transcripts derived from Illumina Human WG-6 BeadChips were analyzed for each sample using SOLAR, whilst correcting for kinship structure.
Results

Cytotoxicity within cell lines was highly heritable following imatinib treatment (h2 = 0.60-0.73), but not omacetaxine treatment. Cell lines treated with an IC20 dose of imatinib or omacetaxine showed differential gene expression for 956 (1.96%) and 3,892 transcripts (7.97%), respectively; 395 of these (0.8%) were significantly influenced by both imatinib and omacetaxine treatment. k-means clustering and DAVID functional annotation showed expression changes in genes related to kinase binding and vacuole-related functions following imatinib treatment, whilst expression changes in genes related to cell division and apoptosis were evident following treatment with omacetaxine. The enrichment scores for these ontologies were very high (mostly >10).
Conclusions

Induction of gene expression changes related to different pathways following imatinib and omacetaxine treatment suggests that the cytotoxicity of such drugs may be differentially tolerated by individuals based on their genetic background.

Biogeographic models of gene flow in two waterfowl of the Australo-Papuan tropics

There are many large, easy-to-observe anseriform birds (ducks, geese, and swans) in northern Australia and New Guinea and they often gather in large numbers. Yet, the structure of their populations and their regional movements are poorly understood. Lack of understanding of population structure limits our capacity to understand source-sink dynamics relevant to their conservation or assess risks associated with avian-borne pathogens, in particular, avian influenza for which waterfowl are the main reservoir species. We set out to assess present-day genetic connectivity between populations of two widely distributed waterfowl in the Australo-Papuan tropics, magpie goose Anseranas semipalmata (Latham, 1798) and wandering whistling-duck Dendrocygna arcuata (Horsfield, 1824). Microsatellite data were obtained from 237 magpie geese and 64 wandering whistling-duck. Samples were collected across northern Australia, and at one site each in New Guinea and Timor Leste. In the wandering whistling-duck, genetic diversity was significantly apportioned by region and sampling location. For this species, the best model of population structure was New Guinea as the source population for all other populations. One remarkable result for this species was genetic separation of two flocks sampled contemporaneously on Cape York Peninsula only a few kilometers apart. In contrast, evidence for population structure was much weaker in the magpie goose, and Cape York as the source population provided the best fit to the observed structure. The fine scale genetic structure observed in wandering whistling-duck and magpie goose is consistent with earlier suggestions that the west-coast of Cape York Peninsula is a flyway for Australo-Papuan anseriforms between Australia and New Guinea across Torres Strait.

Multilocus phylogeography of Australian teals (Anas spp.) : a case study of the relationship between vagility and genetic structure

Biogeographic barriers potentially restrict gene flow but variation in dispersal or vagility can influence the effectiveness of these barriers among different species and produce characteristic patterns of population genetic structure. The objective of this study was to investigate interspecific and intraspecific genetic structure in two closely related species that differ in several life-history characteristics. The grey teal Anas gracilis is geographically widespread throughout Australia with a distribution that crosses several recognized biogeographic barriers. This species has high vagility as its extensive movements track broad-scale patterns in rainfall. In contrast, the closely related chestnut teal A. castanea is endemic to the mesic southeastern and southwestern regions of Australia and is more sedentary. We hypothesized that these differences in life-history characteristics would result in more pronounced population structuring in the chestnut teal. We sequenced five nuclear loci (nuDNA) for 49 grey teal and 23 chestnut teal and compared results to published mitochondrial DNA (mtDNA) sequences. We used analysis of molecular variance to examine population structure, and applied coalescent based approaches to estimate demographic parameters. As predicted, chestnut teal were more strongly structured at both mtDNA and nuDNA (ΦST= 0.163 and 0.054, respectively) than were grey teal (ΦST < 0.0001 for both sets of loci). Surprisingly, a greater proportion of the total genetic variation was partitioned among populations within species (ΦSC= 0.014 and 0.047 for nuDNA and mtDNA, respectively) than between the two species (ΦCT < 0.0001 for both loci). The ‘Isolation with Migration’ coalescent model suggested a late Pleistocene divergence between the taxa, but remarkably, a deeper divergence between the southeastern and southwestern populations of chestnut teal. We conclude that dispersal potential played a prominent role in the structuring of populations within these species and that divergent selection associated with ecology and life history traits likely contributed to rapid and recent speciation in this pair.

Ocean currents influence the genetic structure of an intertidal mollusc in southeastern Australia – implications for predicting the movement of passive dispersers across a marine biogeographic barrier

Major disjunctions among marine communities in southeastern Australia have been well documented, although explanations for biogeographic structuring remain uncertain. Converging ocean currents, environmental gradients, and habitat discontinuities have been hypothesized as likely drivers of structuring in many species, although the extent to which species are affected appears largely dependent on specific life histories and ecologies. Understanding these relationships is critical to the management of native and invasive species, and the preservation of evolutionary processes that shape biodiversity in this region. In this study we test the direct influence of ocean currents on the genetic structure of a passive disperser across a major biogeographic barrier. Donax deltoides (Veneroida: Donacidae) is an intertidal, soft-sediment mollusc and an ideal surrogate for testing this relationship, given its lack of habitat constraints in this region, and its immense dispersal potential driven by year-long spawning and long-lived planktonic larvae. We assessed allele frequencies at 10 polymorphic microsatellite loci across 11 sample locations spanning the barrier region and identified genetic structure consistent with the major ocean currents of southeastern Australia. Analysis of mitochondrial DNA sequence data indicated no evidence of genetic structuring, but signatures of a species range expansion corresponding with historical inundations of the Bassian Isthmus. Our results indicate that ocean currents are likely to be the most influential factor affecting the genetic structure of D. deltoides and a likely physical barrier for passive dispersing marine fauna generally in southeastern Australia.

Gene flow in east antarctic echinoderms and resilience to climate change

The spatial scales of population genetic structure in three species of Antarctic echinoderm, Sterechinus neumayeri, Abatus nimrodi and Abatus ingens was quantified using mitochondrial sequences and a novel set of microsatellite markers. Reduced fertilisation success in S. neumayeri resulting from increasing temperature and decreasing salinity was also identified.

Association between serotonin transporter genotype, brain structure and adolescent onset major depressive disorder: a longitudinal prospective study

The extent to which brain structural abnormalities might serve as neurobiological endophenotypes that mediate the link between the variation in the promoter of the serotonin transporter gene (5-HTTLPR) and depression is currently unknown. We therefore investigated whether variation in hippocampus, amygdala, orbitofrontal cortex (OFC) and anterior cingulate cortex volumes at age 12 years mediated a putative association between 5-HTTLPR genotype and first onset of major depressive disorder (MDD) between age 13–19 years, in a longitudinal study of 174 adolescents (48% males). Increasing copies of S-alleles were found to predict smaller left hippocampal volume, which in turn was associated with increased risk of experiencing a first onset of MDD. Increasing copies of S-alleles also predicted both smaller left and right medial OFC volumes, although neither left nor right medial OFC volumes were prospectively associated with a first episode of MDD during adolescence. The findings therefore suggest that structural abnormalities in the left hippocampus may be present prior to the onset of depression during adolescence and may be partly responsible for an indirect association between 5-HTTLPR genotype and depressive illness. 5-HTTLPR genotype may also impact upon other regions of the brain, such as the OFC, but structural differences in these regions in early adolescence may not necessarily alter the risk for onset of depression during later adolescence.

Differing impact of a major biogeographic barrier on genetic structure in two large kangaroos from the monsoon tropics of Northern Australia

Tropical savannas cover 20-30% of the world's land surface and exhibit high levels of regional endemism, but the evolutionary histories of their biota remain poorly studied. The most extensive and unmodified tropical savannas occur in Northern Australia, and recent studies suggest this region supports high levels of previously undetected genetic diversity. To examine the importance of barriers to gene flow and the environmental history of Northern Australia in influencing patterns of diversity, we investigated the phylogeography of two closely related, large, vagile macropodid marsupials, the antilopine wallaroo (Macropus antilopinus; n = 78), and the common wallaroo (Macropus robustus; n = 21). Both species are widespread across the tropical savannas of Australia except across the Carpentarian Barrier (CB) where there is a break in the distribution of M. antilopinus. We determined sequence variation in the hypervariable Domain I of the mitochondrial DNA control region and genotyped individuals at 12 polymorphic microsatellite loci to assess the historical and contemporary influence of the CB on these species. Surprisingly, we detected only limited differentiation between the disjunct Northern Territory and QueenslandM. antilopinus populations. In contrast, the continuously distributedM. robustus was highly divergent across the CB. Although unexpected, these contrasting responses appear related to minor differences in species biology. Our results suggest that vicariance may not explain well the phylogeographic patterns in Australia's dynamic monsoonal environments. This is because Quaternary environmental changes in this region have been complex, and diverse individual species' biologies have resulted in less predictable and idiosyncratic responses.

Population genetic structure of the Australian caddisfly Lectrides varians Mosely (Trichoptera: Leptoceridae) and the identification of cryptic species in south-eastern Australia

Lectrides varians (Mosely) is a large, ecologically-important, caddisfly found in perennial and intermittent streams throughout much of eastern Australia. We conducted a population genetic analysis to investigate the dispersal potential of L. varians, building on previous works that have assessed life-history traits associated with drought resistance. Genetic analyses of L. varians from the Grampians region of Victoria, based on mitochondrial DNA sequence data, revealed extensive gene flow and a lack of genetic structure across the sample range (ΦST = 0.04). This suggests that the species is a strong disperser and is likely to be resilient to increased drying and habitat fragmentation under climate change considering other known resistance traits. However, during this study, two divergent genotypes were identified, indicating a potential species complex. A comprehensive phylogenetic analysis of L. varians across its current range was subsequently performed, confirming the species is indeed paraphyletic, consisting of one lineage that is restricted to the Grampians National Park and the other being widespread throughout south-eastern Australia. Further analyses revealed consistent morphological differences between these lineages supporting the notion that L. varians is a species complex. We discuss the implications of these findings with regard to conservation and taxonomy of this important invertebrate group.

Identification of a gene for an ancient cytokine, interleukin 15-like, in mammals; interleukins 2 and 15 co-evolved with this third family member, all sharing binding motifs for IL-15Rα

Interleukins 2 and 15 (IL-2 and IL-15) are highly differentiated but related cytokines with overlapping, yet also distinct functions, and established benefits for medical drug use. The present study identified a gene for an ancient third IL-2/15 family member in reptiles and mammals, interleukin 15-like (IL-15L), which hitherto was only reported in fish. IL-15L genes with intact open reading frames (ORFs) and evidence of transcription, and a recent past of purifying selection, were found for cattle, horse, sheep, pig and rabbit. In human and mouse the IL-15L ORF is incapacitated. Although deduced IL-15L proteins share only ~21 % overall amino acid identity with IL-15, they share many of the IL-15 residues important for binding to receptor chain IL-15Rα, and recombinant bovine IL-15L was shown to interact with IL-15Rα indeed. Comparison of sequence motifs indicates that capacity for binding IL-15Rα is an ancestral characteristic of the IL-2/15/15L family, in accordance with a recent study which showed that in fish both IL-2 and IL-15 can bind IL-15Rα. Evidence reveals that the species lineage leading to mammals started out with three similar cytokines IL-2, IL-15 and IL-15L, and that later in evolution (1) IL-2 and IL-2Rα receptor chain acquired a new and specific binding mode and (2) IL-15L was lost in several but not all groups of mammals. The present study forms an important step forward in understanding this potent family of cytokines, and may help to improve future strategies for their application in veterinarian and human medicine.