Eight anonymous nuclear loci for the squamate antbird (Myrmeciza squamosa), cross-amplifiable in other species of typical antbirds (Aves, Thamnophilidae)

Typical antbirds (similar to 209 species) represent a diverse radiation of Neotropical birds that includes many species of conservation concern. Here we present eight anonymous nuclear loci designed for the squamate antbird Myrmeciza squamosa, a species endemic to the Atlantic Forest of Brazil. We also show that those anonymous nuclear loci are amplifiable in a number of other typical antbird species from related genera (Myrmeciza, Percnostola, Gymnocichla, Myrmoborus, Pyriglena and Formicivora), including three threatened species (Myrmeciza ruficauda, Formicivora littoralis, and Pyriglena atra). Those markers will be useful not only to help management of threatened species of typical antbirds, but also to explore their evolutionary histories, both at intra and interspecific levels.

New primers for the amplification and sequencing of nuclear loci in a taxonomically wide set of reptiles and amphibians

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Philopatry of male marine turtles inferred from mitochondrial DNA markers

Recent studies of mitochondrial DNA (mtDNA) variation among marine turtle populations are consistent with the hypothesis that females return to beaches in their natal region to nest as adults. In contrast, less is known about breeding migrations of male marine turtles and whether they too are philopatric to natal regions. Studies of geographic structuring of restriction fragment and microsatellite polymorphisms at anonymous nuclear loci in green turtle (Chelonia mydas) populations indicate that nuclear gene flow is higher than estimates from mtDNA analyses. Regional populations from the northern and southern Great Barrier Reef were distinct for mtDNA but indistinguishable at nuclear loci, whereas the Gulf of Carpentaria (northern Australia) population was distinct for both types of marker. To assess whether this result was due to reduced philopatry of males across the Great Barrier Reef, we determined the mtDNA haplotypes of breeding males at courtship areas for comparison with breeding females from the same three locations. We used a PCR-restriction fragment length polymorphism approach to determine control region haplotypes and designed mismatch primers for the identification of specific haplotypes. The mtDNA haplotype frequencies were not significantly different between males and females at any of the three areas and estimates of Fst among the regions were similar for males and females (Fst = 0.78 and 0.73, respectively). We conclude that breeding males, like females, are philopatric to courtship areas within their natal region. Nuclear gene flow between populations is most likely occurring through matings during migrations of both males and females through nonnatal courtship areas.

Distinctively variable sequence-based nuclear DNA markers for multilocus phylogeography of the soybean- and rice-infecting fungal pathogen Rhizoctonia solani AG-1 IA

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The evolutionary history of ferns inferred from 25 low-copy nuclear genes.

UNLABELLED: • PREMISE OF THE STUDY: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data.• METHODS: Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35877 bp), along with rigorous alignment, orthology inference and model selection.• KEY RESULTS: Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to ∼200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data.• CONCLUSIONS: Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.

Postglacial dispersal, rather than in situ glacial survival, best explains the disjunct distribution of the Lusitanian plant species Daboecia cantabrica (Ericaceae)

Aim:

The distribution of the Lusitanian flora and fauna, species which are found only in southern and western Ireland and in northern Spain and Portugal but which are absent from intervening countries, represents one of the classic conundrums of biogeography. The aim of the present study was to determine whether the distribution of the Lusitanian plant species Daboecia cantabrica was due to persistence in separate Irish and Iberian refugia, or has resulted from post-glacial recolonization followed by subsequent extinction of intervening populations.

Location:

Northern Spain and Co. Galway, western Ireland.

Methods:

Palaeodistribution modelling using Maxent was employed to identify putative refugial areas for D. cantabrica at the Last Glacial Maximum (LGM). Phylogeographical analysis of samples from 64 locations in Ireland and Spain were carried out using a chloroplast marker (atpB–rbcL), the nuclear ITS region, and an anonymous nuclear single-copy locus.

Results:

The palaeodistribution model indicated areas with a high probability of survival for D. cantabrica at the LGM off the western coast of Galicia in Spain, and in the Bay of Biscay. Spanish populations exhibited substantially higher genetic diversity than Irish populations at all three loci, as well as geographical structuring of haplotypes within Spain consistent with divergence in separate refugia. Spanish populations also exhibited far more endemic haplotypes. Divergence time between Irish and Spanish populations associated with the putative Biscay refugium was estimated as 3.333–32 ka.

Main conclusions:

Our data indicate persistence by D. cantabrica throughout the LGM in two separate southern refugia: one in western Galicia and one in the area off the coast of western France which now lies in the Bay of Biscay. Spain was recolonized from both refugia, whilst Ireland was most likely recolonized from the Biscay refugium. On the balance of evidence across the three marker types and the palaeodistribution modelling, our findings do not support the idea of in situ survival of D. cantabrica in Ireland, contrary to earlier suggestions. The fact that we cannot conclusively rule out the existence of a small, more northerly refugium, however, highlights the need for further analysis of Lusitanian plant species.

Amplifiability of mitochondrial, microsatellite and amelogenin DNA loci from fecal samples of red brocket deer Mazama americana (Cetartiodactyla, Cervidae)

We tried to amplify mitochondrial, microsatellite and amelogenin loci in DNA from fecal samples of a wild Mazama americana population. Fifty-two deer fecal samples were collected from a 600-ha seasonal semideciduous forest fragment in a subtropical region of Brazil (21°20′, 47°17′W), with the help of a detection dog; then, stored in ethanol and georeferenced. Among these samples 16 were classified as fresh and 36 as non-fresh. DNA was extracted using the QIAamp® DNA Stool Mini Kit. Mitochondrial loci were amplified in 49 of the 52 samples. Five microsatellite loci were amplified by PCR; success in amplification varied according to locus size and sample age. Successful amplifications were achieved in 10/16 of the fresh and in 13/36 of the non-fresh samples; a negative correlation (R = -0.82) was found between successful amplification and locus size. Amplification of the amelogenin locus was successful in 22 of the 52 samples. The difficulty of amplifying nuclear loci in DNA samples extractedfrom feces collected in the field was evident. Some methodological improvements, including collecting fresh samples, selecting primers for shorter loci and quantifying the extracted DNA by real-time PCR, are suggested to increase amplification success in future studies. © FUNPEC-RP.

In silico identification and characterisation of 17 polymorphic anonymous non-coding sequence markers (ANMs) for red grouse (Lagopus lagopus scotica)

Peer reviewed

Single copy nuclear DNA markers characterized for comparative phylogeography in Australian wet tropics rainforest skinks

In order to investigate population history and demography in skinks endemic to the wet tropics of Australia, multiple nuclear DNA markers were sought. The utility of 72 primers (including 63 published intron-spanning 'CATS' primers) was tested.. Seven loci were characterized and shown to be single copy by single-strand conformation polymorphism analysis. Primers to five nuclear loci were developed, four with utility in skinks and three with utility in frogs. These observations extend the available information on intron-spanning primers for amphibians and reptiles.

Soral synapomorphies are significant for the systematics of the Ustilago-Sporisorium-Macalpinomyces complex (Ustilaginaceae)

The genera Ustilago, Sporisorium and Macalpinomyces are a polyphyletic complex of plant pathogenic fungi. The four main morphological characters used to define these genera have been considered homoplasious and not useful for resolving the complex. This study re-evaluates character homology and discusses the use of these characters for defining monophyletic groups recovered from a reconstructed phylogeny using four nuclear loci. Generic delimitation of smut fungi based on their hosts is also discussed as a means for identifying genera within this group. Morphological characters and host specificity can be used to circumscribe genera within the Ustilago-Sporisorium-Macalpinomyces complex.

Molecular phylogeny, biogeography, and habitat preference evolution of marsupials

Marsupials exhibit great diversity in ecology and morphology. However, compared to their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species. This tree allows us to analyze the evolution of habitat preference and geographic distributions of marsupial species through time. We found a pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change. However, contrary to the general trend, several lineages subsequently appear to have reverted from drier to more mesic habitats. Biogeographic reconstructions suggest that current views on the connectivity between Australia and New Guinea/Wallacea during the Miocene and Pliocene need to be revised. The antiquity of several endemic New Guinean clades strongly suggests a substantially older period of connection stretching back to the Middle Miocene, and implies that New Guinea was colonized by multiple clades almost immediately after its principal formation.

Rapid Global Expansion of the Fungal Disease Chytridiomycosis into Declining and Healthy Amphibian Populations.

The fungal disease chytridiomycosis, caused by Batrachochytrium dendrobatidis, is enigmatic because it occurs globally in both declining and apparently healthy (non-declining) amphibian populations. This distribution has fueled debate concerning whether, in sites where it has recently been found, the pathogen was introduced or is endemic. In this study, we addressed the molecular population genetics of a global collection of fungal strains from both declining and healthy amphibian populations using DNA sequence variation from 17 nuclear loci and a large fragment from the mitochondrial genome. We found a low rate of DNA polymorphism, with only two sequence alleles detected at each locus, but a high diversity of diploid genotypes. Half of the loci displayed an excess of heterozygous genotypes, consistent with a primarily clonal mode of reproduction. Despite the absence of obvious sex, genotypic diversity was high (44 unique genotypes out of 59 strains). We provide evidence that the observed genotypic variation can be generated by loss of heterozygosity through mitotic recombination. One strain isolated from a bullfrog possessed as much allelic diversity as the entire global sample, suggesting the current epidemic can be traced back to the outbreak of a single clonal lineage. These data are consistent with the current chytridiomycosis epidemic resulting from a novel pathogen undergoing a rapid and recent range expansion. The widespread occurrence of the same lineage in both healthy and declining populations suggests that the outcome of the disease is contingent on environmental factors and host resistance.

Soral synapomorphies are significant for the systematics of the Ustilago-Sporisorium-Macalpinomyces complex (Ustilaginaceae)

The genera Ustilago, Sporisorium and Macalpinomyces are a polyphyletic complex of plant pathogenic fungi. The four main morphological characters used to define these genera have been considered homoplasious and not useful for resolving the complex. This study re-evaluates character homology and discusses the use of these characters for defining monophyletic groups recovered from a reconstructed phylogeny using four nuclear loci. Generic delimitation of smut fungi based on their hosts is also discussed as a means for identifying genera within this group. Morphological characters and host specificity can be used to circumscribe genera within the Ustilago-Sporisorium-Macalpinomyces complex.

Hybridization between two serranids, the coney (Cephalopholis fulva) and the creole-fish (Paranthias furcifer), at Bermuda

Intergeneric hybridization between the epinepheline serranids Cephalopholis fulva and Paranthias furcifer in waters off Bermuda was investigated by using morphological and molecular characters. Putative hybrids, as well as members of each presumed parent species, were analyzed for 44 morphological characters and screened for genetic variation at 16 nuclear allozyme loci, two nuclear (n)DNA loci, and three mitochondrial (mt)DNA gene regions. Four of 16 allozyme loci, creatine kinase (CK-B*), fumarase (FH*), isocitrate dehydrogenase (ICDH-S*), and lactate dehydrogenase (LDH-B*), were unique in C. fulva and P. furcifer. Restriction fragments of two nuclear DNA intron regions, an actin gene intron and the second intron in the S7 ribosomal protein gene, also exhibited consistent differences between the two presumed parent species. Restriction fragments of three mtDNA regions—ND4, ATPase 6, and 12S/16S ribosomal RNA—were analyzed to identify maternal parentage of putative hybrids. Both morphological data and nuclear genetic data were found to be consistent with the hypothesis that the putative hybrids were the result of interbreeding between C. fulva and P. furcifer. Mean values of 38 morphological characters were different between presumed parent species, and putative hybrids were intermediate to presumed parent species for 33 of these characters. A principal component analysis of the morphological and meristic data was also consistent with hybridization between C. fulva and P. furcifer. Thirteen of 15 putative hybrids were heterozygous at all diagnostic nuclear loci, consistent with F1 hybrids. Two putative hybrids were identified as post-F1 hybrids based on homozygosity at one nuclear locus each. Mitochondrial DNA analysis showed that the maternal parent of all putative hybrid individuals was C. fulva. A survey of nuclear and mitochondrial loci of 57 C. fulva and 37 P. furcifer from Bermuda revealed no evidence of introgression between the parent species mediated by hybridization.

An examination of spatial and temporal genetic variation in walleye pollock (Theragra chalcogramma) using allozyme, mitochondrial DNA, and microsatellite data

We used allozyme, microsatellite, and mitochondrial DNA (mtDNA) data to test for spatial and interannual genetic diversity in wall-eye pollock (Theragra chalcogramma) from six spawning aggregations representing three geographic regions: Gulf of Alaska, eastern Bering Sea, and eastern Kamchatka. Interpopulation genetic diversity was evident primarily from the mtDNA and two allozyme loci (SOD-2*, MPI*). Permutation tests ˆindicated that FST values for most allozyme and microsatellite loci were not significantly greater than zero. The microsatellite results suggested that high locus polymorphism may not be a reliable indicator of power for detecting population differentiation in walleye pollock. The fact that mtDNA revealed population structure and most nuclear loci did not suggests that the effective size of most walleye pollock populations is large (genetic drift is weak) and migration is a relatively strong homogenizing force. The allozymes and mtDNA provided mostly concordant estimates of patterns of spatial genetic variation. These data showed significant genetic variation between North American and Asian populations. In addition, two spawning aggregations in the Gulf of Alaska, in Prince William Sound, and off Middleton Island, appeared genetically distinct from walleye pollock spawning in the Shelikof Strait and may merit management as a distinct stock. Finally, we found evidence of interannual genetic variation in two of three North American spawning aggregations, similar in magnitude to the spatial variation among North American walleye pol-lock. We suggest that interannual genetic variation in walleye pollock may be indicative of one or more of the following factors: highly variable reproductive success, adult philopatry, source-sink metapopulation structure, and intraannual variation (days) in spawning timing among genetically distinct but spatially identical spawning aggregates.