Multilocus Coalescent Analyses Research Articles

Phylogenetic and morphological analysis of Gloydius himalayanus (Serpentes, Viperidae, Crotalinae), with the description of a new species

Gloydius is a widespread pitviper group occurring from Eastern Europe to Korea and Siberia, with only one known species, G. himalayanus (Günther, 1864), found south of the Himalayas. We provide combined genetic and morphological data for G. himalayanus from specimens collected from Himachal Pradesh, India. Bayesian Inference and Maximum Likelihood phylogenetic analysis were performed on four concatenated mitochondrial genes, along with a multi-locus coalescent analysis of these and five additional nuclear genes. Our results indicate that G. himalayanus from the Chamba Valley, in western Himachal Pradesh, are highly distinct from the remaining studied populations. Haplotype networks of each nuclear locus showed that G. himalayanus contains high haplotype diversity with low haplotype sharing between the Chamba Valley population and populations from further west. Principal component analysis and canonical variate analysis conducted on morphological data of live and museum specimens also highlight the morphological distinctiveness of the Chamba population and we herein describe this population as a new species, Gloydius chambensis sp. nov. Recent descriptions of other new species of snakes from this valley underscores its isolation and suggests that further herpetological investigation of the highly dissected landscapes of the western Himalayas is needed to assess the true diversity of the region.

Pleistocene-dated biogeographic barriers drove divergence within the Australo-Papuan region in a sex-specific manner: an example in a widespread Australian songbird

Understanding how environmental change has shaped species evolution can inform predictions of how future climate change might continue to do so. Research of widespread biological systems spanning multiple climates that have been subject to environmental change can yield generalizable inferences about the neutral and adaptive processes driving lineage divergence during periods of environmental change. We contribute to the growing body of multi-locus phylogeographic studies investigating the effect of Pleistocene climate change on species evolution by focusing on a widespread Australo-Papuan songbird with several mitochondrial lineages that diverged during the Pleistocene, the grey shrike-thrush (Colluricincla harmonica). We employed multi-locus phylogenetic, population genetic and coalescent analyses to (1) assess whether nuclear genetic diversity suggests a history congruent with that based on phenotypically defined subspecies ranges, mitochondrial clade boundaries and putative biogeographical barriers, (2) estimate genetic diversity within and genetic differentiation and gene flow among regional populations and (3) estimate population divergence times. The five currently recognized subspecies of grey shrike-thrush are genetically differentiated in nuclear and mitochondrial genomes, but connected by low levels of gene flow. Divergences among these populations are concordant with recognized historical biogeographical barriers and date to the Pleistocene. Discordance in the order of population divergence events based on mitochondrial and nuclear genomes suggests a history of sex-biased gene flow and/or mitochondrial introgression at secondary contacts. This study demonstrates that climate change can impact sexes with different dispersal biology in different ways. Incongruence between population and mitochondrial trees calls for a genome-wide investigation into dispersal, mitochondrial introgression and mitonuclear evolution.

Speciation Generates Mosaic Genomes in Kangaroos.

The iconic Australasian kangaroos and wallabies represent a successful marsupial radiation. However, the evolutionary relationship within the two genera, Macropus and Wallabia, is controversial: mitochondrial and nuclear genes, and morphological data have produced conflicting scenarios regarding the phylogenetic relationships, which in turn impact the classification and taxonomy. We sequenced and analyzed the genomes of 11 kangaroos to investigate the evolutionary cause of the observed phylogenetic conflict. A multilocus coalescent analysis using ∼14,900 genome fragments, each 10 kb long, significantly resolved the species relationships between and among the sister-genera Macropus and Wallabia. The phylogenomic approach reconstructed the swamp wallaby (Wallabia) as nested inside Macropus, making this genus paraphyletic. However, the phylogenomic analyses indicate multiple conflicting phylogenetic signals in the swamp wallaby genome. This is interpreted as at least one introgression event between the ancestor of the genus Wallabia and a now extinct ghost lineage outside the genus Macropus. Additional phylogenetic signals must therefore be caused by incomplete lineage sorting and/or introgression, but available statistical methods cannot convincingly disentangle the two processes. In addition, the relationships inside the Macropus subgenus M. (Notamacropus) represent a hard polytomy. Thus, the relationships between tammar, red-necked, agile, and parma wallabies remain unresolvable even with whole-genome data. Even if most methods resolve bifurcating trees from genomic data, hard polytomies, incomplete lineage sorting, and introgression complicate the interpretation of the phylogeny and thus taxonomy.

Conspicuous morphological differentiation without speciation in Anemonia viridis (Cnidaria, Actiniaria)

Anemonia viridis is a model species for studies of physiological and transcriptomic response to symbiosis and environmental stress (temperature, light, symbiosis breakdown). Five morphs are described in this species, based on morphology, pigment protein content, and major mode of reproduction. Up to now, the taxonomic status of these morphs remains unclear, without clear knowledge of whether the morphological variation amongst the morphs is due to phenotypic plasticity or adaptation. In the present study, we assess the species status of the three most commonly found morphs by coalescent analyses. For this purpose, five markers were designed for genes whose expression is modified under stress (ca2m, duf140, RNAbinding5, tyrK, sym32) and analysed in 34 individuals representing the morphs A. viridis var rufescens, rustica and smaragdina from eight geographic sites (two in the English Channel and six in the Mediterranean Sea). Phylogenetic analyses of individual gene trees showed no clear separation of the morphs. Furthermore, multilocus coalescent analyses using SpedeSTEM and BPP regrouped all the morphs into one species, showing very few genetic differences amongst them. In a further analysis, we checked for clonality amongst 80 individuals of A. viridis var. smaragdina from one geographic site using three microsatellite loci. This morph proved to be as clonal as var. rustica, indicating a similar potential for asexual reproduction.

Mechanisms of global diversification in the marine species Madeiran Storm-petrel Oceanodroma castro and Monteiro’s Storm-petrel O. monteiroi: Insights from a multi-locus approach

The evolutionary mechanisms underlying the geographic distribution of gene lineages in the marine environment are not as well understood as those affecting terrestrial groups. The continuous nature of the pelagic marine environment may limit opportunities for divergence to occur and lineages to spatially segregate, particularly in highly mobile species. Here, we studied the phylogeography and historical demography of two tropically distributed, pelagic seabirds, the Madeiran Storm-petrel Oceanodroma castro, sampled in the Azores, Madeira, Galapagos and Japan, and its sister species Monteiro’s Storm-petrel O. monteiroi (endemic to the Azores), using a multi-locus dataset consisting of 12 anonymous nuclear loci and the mitochondrial locus control region. Both marker types support the existence of four significantly differentiated genetic clusters, including the sampled O. monteiroi population and three populations within O. castro, although only the mitochondrial locus suggests complete lineage sorting. Multi-locus coalescent analyses suggest that most divergence events occurred within the last 200,000years. The proximity in divergence times precluded robust inferences of the species tree, in particular of the evolutionary relationships of the Pacific populations. Despite the great potential for dispersal, divergence among populations apparently proceeded in the absence of gene flow, emphasizing the effect of non-physical barriers, such as those driven by the paleo-oceanographical environments, philopatry and local adaptation, as important mechanisms of population divergence and speciation in highly mobile marine species. In view of the predicted climate change impacts, future changes in the demography and evolutionary dynamics of marine populations might be expected.

Molecular phylogenetics and species delimitation of leaf-toed geckos (Phyllodactylidae: Phyllodactylus) throughout the Mexican tropical dry forest

Methods and approaches for accurate species delimitation continue to be a highly controversial subject in the systematics community. Inaccurate assessment of species’ limits precludes accurate inference of historical evolutionary processes. Recent evidence suggests that multilocus coalescent methods show promise in delimiting species in cryptic clades. We combine multilocus sequence data with coalescence-based phylogenetics in a hypothesis-testing framework to assess species limits and elucidate the timing of diversification in leaf-toed geckos (Phyllodactylus) of Mexico’s dry forests. Tropical deciduous forests (TDF) of the Neotropics are among the planet’s most diverse ecosystems. However, in comparison to moist tropical forests, little is known about the mode and tempo of biotic evolution throughout this threatened biome. We find increased speciation and substantial, cryptic molecular diversity originating following the formation of Mexican TDF 30–20million years ago due to orogenesis of the Sierra Madre Occidental and Mexican Volcanic Belt. Phylogenetic results suggest that the Mexican Volcanic Belt, the Rio Fuerte, and Isthmus of Tehuantepec may be important biogeographic barriers. Single- and multilocus coalescent analyses suggest that nearly every sampling locality may be a distinct species. These results suggest unprecedented levels of diversity, a complex evolutionary history, and that the formation and expansion of TDF vegetation in the Miocene may have influenced subsequent cladogenesis of leaf-toed geckos throughout western Mexico.

Species, ESUs or populations? Delimiting and describing morphologically cryptic diversity in Australian desert spring amphipods

Cryptic species are frequently being discovered in refugial habitats, such as desert springs and groundwater systems. Unfortunately, many of these taxa remain as unnamed entities years after their initial discovery. Recent advances in the use of molecular data and coalescent analyses allow DNA-based delimitation of species to move from single locus, tree-based methods to multilocus coalescent analyses. This study compares two DNA-based approaches to delimit species of putatively cryptic freshwater amphipods (Chiltoniidae) from desert springs in central Australia. In addition, a morphometric analysis of 11 characters was undertaken to determine whether the DNA-delimited species were morphologically distinguishable. The single locus method results in identification of lineages that are not supported as species under the multilocus coalescent analyses. We conclude that Wangiannachiltonia guzikae King, 2009, as currently circumscribed, represents six genetically distinct amphipod species, and we describe and name these species despite no clear diagnosable morphological differences. Critically, all of these newly recognised species have extremely limited distributions, which increases the biodiversity significance of their desert spring habitat.

Divergence history of the Rufous-tailed Tailorbird (Orthotomus sericeus) of Sundaland: Implications for the biogeography of Palawan and the taxonomy of island species in general

ABSTRACT The Rufous-tailed Tailorbird (Orthotomus sericeus)—a Sunda endemic—is divided into 3 morphologically based subspecies: one in western Sundaland (Malay Peninsula, Sumatra, and associated islands), one from the Natuna Islands in the South China Sea, and one on Borneo, Palawan, and smaller islands of the Sunda continental shelf east of Borneo. Previous study, however, suggested that these subspecies do not conform to molecular genetic subdivisions of the species. We reexamined the morphology and performed molecular phylogeographic and multi-locus coalescent analysis of two subspecies of Rufous-tailed Tailorbird comprising populations on the Malay Peninsula, Sumatra, Borneo, and Palawan. We found (1) little morphological difference among the two subspecies, (2) no substantial genetic differences between the Borneo and western Sunda populations, but (3) marked genetic divergence between the Palawan and other populations. We conclude that the Bornean and western Sunda populations interbred extensively ...

Genetic species delineation among branching Caribbean Porites corals

Coral species are difficult to discern because of their morphological plasticity, long generation times, and slow rates of mitochondrial DNA evolution. Among Caribbean representatives of the genus Porites are three named species (P. divaricata, P. furcata, and P. porites) with branching colony morphologies whose validity as genetically isolated species has been debated. We present sequence data from the mitochondrial control region, nuclear ITS, and nine single-copy nuclear loci for the Caribbean Porites and a related eastern Pacific species. mtDNA sequences were nearly invariant among the three branching species and their crustose sister P. branneri, and ITS sequences from these four were intermingled. An information theoretic analysis provided no support for upholding the three named Caribbean branching species. Both a clustering analysis and an analysis of molecular variance showed that sequence variation from the three branching forms is partitioned more by geography than by taxonomy. Multi-locus coalescent phylogenetic analysis provided a calibrated estimate for the nuclear DNA substitution rate (0.14 % Ma−1) close to that for other corals. Because no generalities have emerged from genetic investigations of the validity of morphologically defined coral species, the use of single-copy nuclear data is likely to be important in testing problematic species designations.

Integrating phylogeography and morphometrics to assess conservation merits and inform conservation strategies for an endangered subspecies of a common bird species

Understanding the evolutionary history of threatened populations can improve their conservation management. Re-establishment of past but recent gene flow could re-invigorate threatened populations and replenish genetic diversity, necessary for population persistence. One of the four nominal subspecies of the common yellow-tufted honeyeater, Lichenostomus melanops cassidix, is critically endangered despite substantial conservation efforts over 55years. Using a combination of morphometric, genetic and modeling approaches we tested for its evolutionary distinctiveness and conservation merit. We confirmed that cassidix has at least one morphometric distinction. It also differs genetically from the other subspecies in allele frequencies but not phylogenetically, implying that its evolution was recent. Modeling historical distribution supported a lack of vicariance and suggested possible gene flow among subspecies at least since the late Pleistocene. Multi-locus coalescent analyses indicated that cassidix diverged from its common ancestor with neighboring subspecies gippslandicus sometime from the mid-Pleistocene to the Holocene, and that it has the smallest historical effective population size of all subspecies. It appears that cassidix diverged from its ancestor with gippslandicus through a combination of drift and local selection. From patterns of genetic subdivision on two spatial scales and morphological variation we concluded that cassidix, gippslandicus and (melanops+meltoni) are diagnosable as subspecies. Low genetic diversity and effective population size of cassidix may translate to low genetic fitness and evolutionary potential, accordingly we recommend managed gene flow from gippslandicus (with which it can be inferred to have recently experienced natural gene flow) to favor recovery of cassidix.

Multilocus coalescent analyses reveal the demographic history and speciation patterns of mouse lemur sister species

BackgroundDebate continues as to whether allopatric speciation or peripatric speciation through a founder effect is the predominant force driving evolution in vertebrates. The mouse lemurs of Madagascar are a system in which evolution has generated a large number of species over a relatively recent time frame. Here, we examine speciation patterns in a pair of sister species of mouse lemur, Microcebus murinus and M. griseorufus. These two species have ranges that are disparately proportioned in size, with M. murinus showing a much more extensive range that marginally overlaps that of M. griseorufus. Given that these two species are sister taxa, the asymmetric but overlapping geographic ranges are consistent with a model of peripatric speciation. To test this hypothesis, we analyze DNA sequence data from four molecular markers using coalescent methods. If the peripatric speciation model is supported, we predict substantially greater genetic diversity in M. murinus, relative to M. griseorufus. Further, we expect a larger effective population size in M. murinus and in the common ancestor of the two species than in M. griseorufus, with a concomitant decrease in gene tree/species tree incongruence in the latter and weak signs of demographic expansion in M. murinus.ResultsOur results reject a model of peripatric divergence. Coalescent effective population size estimates were similar for both extant species and larger than that estimated for their most recent common ancestor. Gene tree results show similar levels of incomplete lineage sorting within species with respect to the species tree, and locus-specific estimates of genetic diversity are concordant for both species. Multilocus demographic analyses suggest range expansions for M. murinus, with this species also experiencing more recent population declines over the past 160 thousand years.ConclusionsResults suggest that speciation occurred in allopatry from a common ancestor narrowly distributed throughout southwest Madagascar, with subsequent range expansion for M. murinus. Population decline in M. murinus is likely related to patterns of climate change in Madagascar throughout the Pleistocene, potentially exacerbated by continual anthropogenic perturbation. Genome-level data are needed to quantify the role of niche specialization and adaptation in shaping the current ranges of these species.

Late Pleistocene colonization of South Georgia by yellow-billed pintails pre-dates the Last Glacial Maximum

Aim Glacial cycles had a major influence on the distribution of high-latitude species, and while genetic consequences of these cycles have been well studied in the Circumpolar North, notably fewer studies have been undertaken in the Antarctic. Here, we use multilocus genetic data from the South Georgia pintail (Anas georgica georgica) as a proxy to study the presence and timing of ice-free refugia on South Georgia, a glaciated subantarctic island in the South Atlantic Ocean that has been the subject of intense geomorphological and palaeoenvironmental study. Location South Georgia. Methods Multilocus DNA sequence data from five nuclear loci and the mitochondrial DNA control region were analysed for South Georgia pintails (n = 60) and the neighbouring population of yellow-billed pintails (A. georgica spinicauda) in Argentina (n = 64). Population genetic structure and gene flow were examined using ΦST, assignment tests, and multilocus coalescent analyses. Results Isolation-with-migration (IM) analysis revealed that the South Georgia pintail population was founded by pintails dispersing from South America. Although the confidence intervals on divergence dates inferred from genetic data are generally wide and there may be time-dependency in rate calibrations, our analysis suggests that this founding event probably occurred c. 34,000 years ago, prior to the Last Glacial Maximum (LGM). Our findings further suggest that South Georgia pintails might have experienced a bottleneck coinciding with complete replacement of mitochondrial DNA prior to 8700 years ago following the final advance of glaciers. Main conclusions These findings suggest that ice-free refugia existed earlier in the chronology of deglaciation in contrast with earlier studies, but in agreement with observations that the plant community was also established on South Georgia prior to the end of the Pleistocene. Like other recent studies that have utilized genetic data to date dispersal and vicariance events in the Antarctic, our results provide a constraint on the extent of ice sheets, suggesting that past ice coverage on South Georgia through the LGM was overestimated.

A multilocus coalescent analysis of the speciational history of the Australo-Papuan butcherbirds and their allies

Changes in geology, sea-level and climate are hypothesised to have been major driving processes of evolutionary diversification (speciation and extinction) in the Australo-Papuan region. Here we use complete species-level sampling and multilocus (one mitochondrial gene, five nuclear loci) coalescent analyses to estimate evolutionary relationships and test hypotheses about the role of changes in climate and landscape in the diversification of the Australo-Papuan butcherbirds and allies (Cracticinae: Cracticus, Strepera, Peltops). Multilocus species trees supported the current classification of the morphologically, ecologically and behaviourally divergent Australian Magpie (Cracticus tibicen (previously Gymnorhina tibicen)) as a member of an expanded genus Cracticus, which includes seven other species with ‘butcherbird’ morphology and behaviour. Non-monophyly of currently recognised species within Peltops and the white-throated butcherbird species-group (C.argenteus, C.mentalis, C. torquatus) at both mtDNA and nuclear loci suggest that a comprehensive taxonomic revision is warranted for both of these groups. The time-calibrated multilocus species tree revealed an early divergence between the New Guinean rainforest-restricted Peltops lineage and the largely open-habitat inhabiting Cracticus (butcherbirds and magpies) plus Strepera (currawongs) lineage around 17–28Ma, as well as a relatively recent radiation of lineages within Cracticus over the past 8Ma. Overall, patterns and timings of speciation were consistent with the hypothesis that both the expansion of open sclerophyllous woodlands 25–30Ma and the formation of extensive grassland-dominated woodlands 6–8Ma allowed the radiation of lineages adapted to open woodland habitats.

Genetic divergence and population demography of the Hainan endemic Black-throated Laughingthrush (Aves: Timaliidae, Garrulax chinensis monachus) and adjacent mainland subspecies

Geographic variation in the Black-throated Laughingthrush (Garrulax chinensis) is examined to infer the influence of Pleistocene glacial oscillations on the genetic diversity of its subspecies. Mitochondrial evidence suggests that the endemic Hainan Island taxon, G. c. monachus, is monophyletic, whereas its closest continental relatives, G. c. chinensis and G. c. lochmius, are not. Multilocus coalescent analysis based on two mitochondrial and two nuclear intron loci indicates inter-subspecific genetic differentiation during the Pleistocene and substantial post-divergence genetic introgression from G. c. chinensis into G. c. lochmius. In contrast, G. c. monachus experienced no post-divergence gene flow despite occasional land-bridge contact with its continental relatives, suggesting its isolation may have been imposed by ecology as well as geography. It is probably reproductively isolated and should be treated as a distinct species.

Multilocus coalescent analysis of haemoglobin differentiation between low‐ and high‐altitude populations of crested ducks (Lophonetta specularioides)

Hypoxia is a key factor determining survival, and haemoglobins are targets of selection in species native to high-altitude regions. We studied population genetic structure and evaluated evidence for local adaptation in the crested duck (Lophonetta specularioides). Differentiation, gene flow and time since divergence between highland and lowland populations were assessed for three haemoglobin genes (α(A) , α(D) , β(A) ) and compared to seven reference loci (six autosomal introns and mtDNA). Four derived amino acid replacements were found in the globin genes that had elevated Φ(ST) values between the Andean highlands and Patagonian lowlands. A single β(A) -globin polymorphism at a site known to influence O(2) affinity was fixed for different alleles in the two populations, whereas three α(A) - and α(D) -globin polymorphisms exhibited high heterozygosity in the highlands but not in the lowlands. Coalescent analyses supported restricted gene flow for haemoglobin alleles and mitochondrial DNA but nonzero gene flow for the introns. Simulating genetic data under a drift-migration model of selective neutrality, the β(A) -globin fell outside the 95% confidence limit of simulated data, suggesting that directional selection is maintaining different variants in the contrasting elevational environments, thereby restricting migration of β(A) -globin alleles. The α(A) - and α(D) -globins, by contrast, did not differ from the simulated values, suggesting that variants in these genes are either selectively neutral, or that the effects of selection could not be differentiated from background levels of population structure and linkage disequilibrium. This study illustrates the combined effects of selection and population history on inferring levels of population divergence for a species distributed across an altitudinal gradient in which selection for hypoxia resistance has likely played an important role.

Multilocus phylogeography and population structure of common eiders breeding in North America and Scandinavia

Aim Glacial refugia during the Pleistocene had major impacts on the levels and spatial apportionment of genetic diversity of species in northern latitude ecosystems. We characterized patterns of population subdivision, and tested hypotheses associated with locations of potential Pleistocene refugia and the relative contribution of these refugia to the post-glacial colonization of North America and Scandinavia by common eiders (Somateria mollissima). Specifically, we evaluated localities hypothesized as ice-free areas or glacial refugia for other Arctic vertebrates, including Beringia, the High Arctic Canadian Archipelago, Newfoundland Bank, Spitsbergen Bank and north-west Norway. Location Alaska, Canada, Norway and Sweden. Methods Molecular data from 12 microsatellite loci, the mitochondrial DNA (mtDNA) control region, and two nuclear introns were collected and analysed for 15 populations of common eiders (n = 716) breeding throughout North America and Scandinavia. Population genetic structure, historical population fluctuations and gene flow were inferred using F-statistics, analyses of molecular variance, and multilocus coalescent analyses. Results Significant inter-population variation in allelic and haplotypic frequencies were observed (nuclear DNA FST = 0.004‐0.290; mtDNA FST = 0.051‐0.927). Whereas spatial differentiation in nuclear genes was concordant with subspecific designations, geographic proximity was more predictive of inter-population variance in mitochondrial DNA haplotype frequency. Inferences of historical population demography were consistent with restriction of common eiders to four geographic areas during the Last Glacial Maximum: Belcher Islands, Newfoundland Bank, northern Alaska and Svalbard. Three of these areas coincide with previously identified glacial refugia: Newfoundland Bank, Beringia and Spitsbergen Bank. Gene-flow and clustering analyses indicated that the Beringian refugium contributed little to common eider post-glacial colonization of North America, whereas Canadian, Scandinavian and southern Alaskan post-glacial colonization is likely to have occurred in a stepwise fashion from the same glacial refugium. Main conclusions Concordance of proposed glacial refugia used by common eiders and other Arctic species indicates that Arctic and subarctic refugia were important reservoirs of genetic diversity during the Pleistocene. Furthermore, suture zones identified at MacKenzie River, western Alaska/Aleutians and Scandinavia coincide with those identified for other Arctic vertebrates, suggesting that these regions were strong geographic barriers limiting dispersal from Pleistocene refugia.

Recombination and lineage‐specific gene loss in the aflatoxin gene cluster of Aspergillus flavus

Aflatoxins produced by Aspergillus flavus are potent carcinogens that contaminate agricultural crops. Recent efforts to reduce aflatoxin concentrations in crops have focused on biological control using nonaflatoxigenic A. flavus strains AF36 (=NRRL 18543) and NRRL 21882 (the active component of afla-guard. However, the evolutionary potential of these strains to remain nonaflatoxigenic in nature is unknown. To elucidate the underlying population processes that influence aflatoxigenicity, we examined patterns of linkage disequilibrium (LD) spanning 21 regions in the aflatoxin gene cluster of A. flavus. We show that recombination events are unevenly distributed across the cluster in A. flavus. Six distinct LD blocks separate late pathway genes aflE, aflM, aflN, aflG, aflL, aflI and aflO, and there is no discernable evidence of recombination among early pathway genes aflA, aflB, aflC, aflD, aflR and aflS. The discordance in phylogenies inferred for the aflW/aflX intergenic region and two noncluster regions, tryptophan synthase and acetamidase, is indicative of trans-species evolution in the cluster. Additionally, polymorphisms in aflW/aflX divide A. flavus strains into two distinct clades, each harbouring only one of the two approved biocontrol strains. The clade with AF36 includes both aflatoxigenic and nonaflatoxigenic strains, whereas the clade with NRRL 21882 comprises only nonaflatoxigenic strains and includes all strains of A. flavus missing the entire gene cluster or with partial gene clusters. Our detection of LD blocks in partial clusters indicates that recombination may have played an important role in cluster disassembly, and multilocus coalescent analyses of cluster and noncluster regions indicate lineage-specific gene loss in A. flavus. These results have important implications in assessing the stability of biocontrol strains in nature.

Evidence for Differential Assortative Female Preference in Association with Refugial Isolation of Rainbow Skinks in Australia's Tropical Rainforests

BackgroundDivergence driven by female preference can give rise to pre-mating isolation more rapidly than post-mating isolation can evolve through the accumulation of allelic incompatibilities. Moreover pre-mating isolation may be more effective at maintaining morphological differentiation between divergent populations. In the context of Australian rainforest endemic skinks that were historically subjected to refugial isolation, this study examined the following predictions: 1) that assortative female preference is associated with more recent divergence of southern C. rubrigularis (S-RED) and C. rhomboidalis (BLUE), but not with deeply divergent S-RED and northern C. rubrigularis (N-RED); and 2) that upon secondary contact, morphological differentiation is maintained between S-RED and BLUE, whereas N-RED and S-RED remain morphogically indistinguishable.Principal FindingsFemale preference trials found no evidence for assortative female preference between N-RED and S-RED, supporting a previous genetic hybrid zone study which inferred post-mating but no pre-mating isolation. In contrast there is evidence for assortative female preference between S-RED and BLUE, with BLUE females preferring to associate with BLUE males, but S-RED females showing no preference. Multi-locus coalescent analyses, used to estimate post-divergence gene-flow between proximally located S-RED and BLUE populations, rejected zero gene-flow from BLUE to S-RED and thus RED and BLUE have maintained morphological differentiation despite secondary contact. Morphometric analyses confirmed a lack of morphological divergence between N-RED and S-RED and established that BLUE is morphologically divergent from RED in traits other than throat colour.Conclusions/SignificanceLong-term isolation has been sufficient to generate post-mating isolation but no morphological divergence between N-RED and S-RED. In contrast, greater morphological differentiation is associated with evidence for assortative female preference between more recently diverged S-RED and BLUE. Combined with previous estimates of lineage-wide gene flow, these results are consistent with the suggestion that assortative female preference is more effective than post-mating isolation in maintaining morphological differentiation between divergent populations.

DIVERGENCE ACROSS AUSTRALIA'S CARPENTARIAN BARRIER: STATISTICAL PHYLOGEOGRAPHY OF THE RED-BACKED FAIRY WREN (MALURUS MELANOCEPHALUS)

Multilocus analysis of phylogeography and population history is a powerful tool for understanding the origin, dispersal, and geographic structure of species over time and space. Using 36 genetic markers (29 newly developed anonymous nuclear loci, six introns and one from mitochondrial DNA, amounting to over 15 kb per individual), we studied population structure and demographic history of the red-backed fairy wren Malurus melanocephalus, a small passerine distributed in the northern and eastern part of Australia across the Carpentarian barrier. Analysis of anonymous loci markers revealed large amounts of genetic diversity (pi= 0.016 +/- 0.01; average number of SNPs per locus = 48; total number of SNPs = 1395), and neither nuclear nor mitochondrial gene trees showed evidence of reciprocal monophyly among Cape York (CY), Eastern Forest (EF), and Top End (TE) populations. Despite traditional taxonomy linking TE and CY populations to the exclusion of EF, we found that the CY population is genetically closer to the EF population, consistent with predicted area cladograms in this region. Multilocus coalescent analysis suggests that the CY population was separated from the other two regions approximately 0.27 million years ago, and that significant gene flow between the ER and the CY populations ( approximately 2 migrants per generation) suggests geographic continuity in eastern Australia. By contrast, gene flow between the CY and the TE populations has been dampened by divergence across the Carpentarian barrier.

Pleistocene speciation of sister taxa in a North Pacific clade of brooding sea stars (Leptasterias)

Although numerous coastal marine species show intra-specific lineage splitting and population divergence times that date to the period of glacial cycles during the Pleistocene epoch, reported instances of recent speciation in the coastal marine environment are relatively rare. Marine organisms with brood-protection and other reproductive modes with limited dispersal potential have been suggested to experience more frequent speciation and extinction events than related species with higher dispersal rates, but few studies have actually estimated divergence times of sister species in these organisms. Here, two mitochondrial gene regions (cytochrome oxidase subunit I, putative control region and upstream tRNAs) and a nuclear gene region (Elongation factor 1α subunit intron 4) provide evidence of recent (0.5–1.2 Mya) cladogenetic events in four pairs of putative sister taxa in a predominantly North Pacific brooding subgenus of sea stars (Leptasterias subgenus Hexasterias). Calibration is obtained from a trans-arctic migration in a related clade of sea stars (Leptasterias subgenera Hexasterias and Nesasterias) that is timed to the opening of the Bering Strait at 3.5 ± 0.25 Mya, and uncertainty in the calibration point is accommodated with a normally-distributed Bayesian prior probability. Similar estimates of population splitting times for two of the pairs of putative sister taxa were obtained by a multilocus coalescent analysis. Estimates of mitochondrial mutation rates (0.01/My) were approximately 50% of the values calibrated for sister species pairs in tropical sea stars and sea urchins.