Disentangling the contemporary and historical effects of landscape on the population genomic variation of two bird species restricted to the highland forest enclaves of northeastern Brazil

Investigating the impact of landscape features on patterns of genetic variation is crucial to understand spatially dependent evolutionary processes. Here, we assess the population genomic variation of two bird species (Conopophaga cearae and Sclerurus cearensis) through the Caatinga moist forest enclaves in northeastern Brazil. To infer the evolutionary dynamics of bird populations through the Late Quaternary, we used genome-wide polymorphism data obtained from double-digestion restriction-site-associated DNA sequencing (ddRADseq), and integrated population structure analyses, historical demography models, paleodistribution modeling, and landscape genetics analyses. We found the population differentiation among enclaves to be significantly related to the geographic distance and historical resistance across the rugged landscape. The climate changes at the end of the Pleistocene to the Holocene likely triggered synchronic population decline in all enclaves for both species. Our findings revealed that both geographic distance and historical connectivity through highlands are important factors that can explain the current patterns of genetic variation. Our results further suggest that levels of population differentiation and connectivity cannot be explained purely on the basis of contemporary environmental conditions. By combining historical demographic analyses and niche modeling predictions in a historical framework, we provide strong evidence that climate fluctuations of the Quaternary promoted population differentiation and a high degree of temporal synchrony among population size changes in both species.

Draft genome and multi-tissue transcriptome assemblies of the Neotropical leaf-frog Phyllomedusa bahiana

Amphibians are increasingly threatened worldwide, but the availability of genomic resources that could be crucial for implementing informed conservation practices lags well behind that for other vertebrate groups. Here, we describe draft de novo genome, mitogenome, and transcriptome assemblies for the Neotropical leaf-frog Phyllomedusa bahiana native to the Brazilian Atlantic Forest and Caatinga. We used a combination of PacBio long reads and Illumina sequencing to produce a 4.74-Gbp contig-level genome assembly, which has a contiguity comparable to other recent nonchromosome level assemblies. The assembled mitogenome comprises 16,239 bp and the gene content and arrangement are similar to other Neobratrachia. RNA-sequencing from 8 tissues resulted in a highly complete (86.3%) reference transcriptome. We further use whole-genome resequencing data from P. bahiana and from its sister species Phyllomedusa burmeisteri, to demonstrate how our assembly can be used as a backbone for population genomics studies within the P. burmeisteri species group. Our assemblies thus represent important additions to the catalog of genomic resources available from amphibians.

P-661 dydrogesterone as an alternative to supress LH surge in single stimulus protocols with follitropin delta

Study question

Is oral dydrogesterone (DYG) 30 mg daily efficient on prevention of premature luteinizing hormone (LH) surge in ART cycles?

Summary answer

Oral dydrogesterone demonstrated to be as safe and effective as GnRH-ant in IVF/ICSI cycles intended to freeze-all / PGT-A, oocyte preservation and embryo banking programs

What is known already

The use of progesterone (PG) to inhibit pituitary LH surge during ovarian stimulation have been described over the last decades. Due to its harmful effect on the endometrium, PG suppression is mainly reserved for freeze-all cycles. Dydrogesterone (DYG), a known and safe synthetic progesterone, has been tested for this purpose based on the concept of its more selective PG receptors activity, which could reduce the inconveniences of side effects with less relevant androgenic, estrogenic, glyco or mineralocorticoid activity. Accordind to some recent work, DYG would be an effective tool both in cycles intended to freeze-all or in oocyte preservation strategies.

Study design, size, duration

Observational, comparative single center study, comparing the effect of DYG and gonadotropin releasing hormone (GnRH) antagonists on prevention of premature luteinizing hormone (LH) surge as well as to evaluate the number of metaphase II oocytes. From January 2019 to January 2020, 143 no age restrictions patients underwent both IVF/ICSI or oocyte preservation, all of them receiving the same single stimulus protocol with follitropin delta (Rekovelle).

Participants/materials, setting, methods

92 IVF/ICSI plus 51 oocyte cryopreservation cycles underwent deltafollitropin (Rekovelle®, Ferring Pharmaceuticals) in a fixed daily and individualized SC-dose. Clinical decision led to a GnRH-antagonist (CTA-Cetrorelix acetate, Cetrotide®, Merck) 0,25 mg/d initiated in a flexible schedule in presence of one follicle ≥14 mm and continued throughout the stimulation period (48 cycles) or dydrogesterone (DYG), 10mg 8/8 hours (Duphaston®, Abbott) combined to gonadotrophin from the beginning of stimulation until the day after the trigger (95 cycles).

Main results and the role of chance

DYG-group had a mean age significantly higher (37.8 x 35.8-p 0.002) but there were no differences in mean parameters of BMI (24.08 x 24.81), days of stimulation (9.95 x 10.08), AMH (2.30 x 2.52), AFC (14.6 x 16.2). In the same way, no differences were observed between follicles 15 mm to 18 mm (3.06 x 3.68) and ≥ 18 mm (4.56 x 3.9), with a tendency for a greater number of larger follicles in the DYG-group. Metaphase II oocytes (7.48 x 7.33) was similar in both groups. One patient from each group experienced a premature LH surge (3.54 x 3.06) and one case in the DYG-group had no oocyte in a single 20mm aspirated follicle. There happened no cancelling. No patients experienced moderate to severe ovarian hyper stimulation syndrome, even when AMH>3 ng/mL. Cancelling criteria: no follicles with a diameter 17 mm by day 15. Oocyte retrieval took place 36 hours after trigging. Primary outcome was the incidence of premature LH surge. Secondary outcomes included follicles ≥ 15 mm and < 18 mm and ≥ 18 mm on hCG day, metaphase II oocytes, number of cancelled cycles and OHSS symptoms. Statistics were performed by Mann-Whitney test.

Limitations, reasons for caution

The main limitation point is the small number of patients. Despite having relative experience with the use of DYG, in this work we limited the sample to consider only one type of stimulus protocol, making the groups more homogeneous for the analysis.

Wider implications of the findings

Dydrogesterone is as effective as GnRH-ant in reducing premature LH surge. It can be considered for IVF/ICSI cycles intended to freeze-all / PGT-A, oocyte preservation and for embryo banking strategies, representing lower costs in these cases.

Trial registration number

not applicable

Genetic traces of hybrid zone movement across a fragmented habitat

Theoretical and empirical studies suggest that the structure and position of hybrid zones can change over time. Evidence for moving hybrid zones has been directly inferred by repeated sampling over time, or indirectly through the detection of genetic footprints left by the receding species and the resulting asymmetric patterns of introgression across markers. We here investigate a hybrid zone formed by two subspecies of the Iberian golden-striped salamander, Chioglossa lusitanica, using a panel of 35 nuclear loci (31 SNPs and 4 allozymes) and one mitochondrial locus in a transect in central Portugal. We found concordant and coincident clines for most of the nuclear loci (n=22, 63%), defining a narrow hybrid zone of ca. 6 km wide, with the centre positioned ca. 15 km south of the Mondego river. Asymmetric introgression was observed at another 14 loci. Their clines are displaced towards the north, with positions located either close to the Mondego river (n=6), or further northwards (n=8). We interpret these profiles as genetic traces of the southward displacement of C. lusitanica lusitanica by C. l. longipes over the wider Mondego river valley. We noted the absence of significant linkage disequilibrium and we inferred low levels of effective selection per locus against hybrids, suggesting that introgression in the area of species replacement occurred under a neutral diffusion process. A species distribution model suggests that the C. lusitanica hybrid zone coincides with a narrow corridor of fragmented habitat. From the position of the displaced clines, we infer that patches of locally suitable habitat trapped some genetic variants that became disassociated from the southward moving hybrid zone. This study highlights the influence of habitat availability on hybrid zone movement.

Evaluating surrogates of genetic diversity for conservation planning

Protected-area systems should conserve intraspecific genetic diversity. Because genetic data require resources to obtain, several approaches have been proposed for generating plans for protected-area systems (prioritizations) when genetic data are not available. Yet such surrogate-based approaches remain poorly tested. We evaluated the effectiveness of potential surrogate-based approaches based on microsatellite genetic data collected across the Iberian Peninsula for 7 amphibian and 3 reptilian species. Long-term environmental suitability did not effectively represent sites containing high genetic diversity (allelic richness). Prioritizations based on long-term environmental suitability had similar performance to random prioritizations. Geographic distances and resistance distances based on contemporary environmental suitability were not always effective surrogates for identification of combinations of sites that contain individuals with different genetic compositions. Our results demonstrate that population genetic data based on commonly used neutral markers can inform prioritizations, and we could not find an adequate substitute. Conservation planners need to weigh the potential benefits of genetic data against their acquisition costs.

Living in a tiny world: reproductive biology and population ecology of the Neotropical miniature frog Euparkerella aff. brasiliensis (Terraranae, Strabomantidae)

Miniaturisation is an important evolutionary trend for amphibians and has occurred several times in independent anuran lineages. Most miniaturised frogs live in the leaf litter of tropical forests and have terrestrial reproductive modes. They are expected to have reduced fecundity in number of eggs than larger-bodied related species, but little is known about reproductive cycles and proportion of reproductive females. Lower vagility is also assumed, however, as they are difficult to observe, there is little empirical evidence about their dispersal. We studied the reproductive biology (sex ratio, sexual size dimorphism and fecundity parameters) and population ecology (growth, dispersal, and phenology) of the miniature Guanabara Frog Euparkerella aff. brasiliensis (⩽ 20 mm). We collected and analysed 75 specimens of E. aff. brasiliensis, of which 27 were adult females with vitellogenic oocytes in their ovaries. Fecundity was low for number of eggs (average number = 9.7), but only one adult female had no vitellogenic oocytes. Sex ratio was relatively balanced among sexes, being female-biased (0.92) for all individuals and male-biased (1.17) for adults. Juveniles and ovigerous females were observed throughout the year during the two years of mark-recapture study, which indicates continuous breeding. We captured 121 individuals, of which 12% were recaptured in their original collection sites, suggesting low vagility. We discuss our findings considering the current knowledge about the ecology of miniaturised frogs and other Terraranae and suggest future directions for ecological studies and conservation planning.

The roles of vicariance and dispersal in the differentiation of two species of the Rhinella marina species complex

The high levels of Neotropical biodiversity are commonly associated with the intense Neogene-Quaternary geological events and climate dynamics. Here, we investigate the evolutionary history of two species of Neotropical closely related amphibians (R. horribilis and R. marina). We combine published data with new mitochondrial DNA sequences and multiple nuclear markers, including 12 microsatellites. The phylogenetic analyses showed support for grouping the samples in two main clades; R. horribilis (Central America and Mexico) and R. marina (South America east of the Andes). However, the phylogenetic inferences also show an evident mito-nuclear discordance. We use Approximate Bayesian Computation (ABC) to test the role of different events in the diversification between the two groups recovered. We found that both species were affected primarily by a recent Pleistocene divergence, which was similar to the divergence estimate revealed by the Isolation-with-Migration model, under persistent bidirectional gene flow through time. We provide the first evidence that R. horribilis is differentiated from the South American R. marina at the nuclear level supporting the taxonomic status of R. horribilis, which has been controversial for more than a century.

Discordant patterns of introgression across a narrow hybrid zone between two cryptic lineages of an Iberian endemic newt

The study of natural hybrid zones can illuminate aspects of lineage divergence and speciation in morphologically cryptic taxa. We studied a hybrid zone between two highly divergent but morphologically similar lineages (south-western and south-eastern) of the Iberian endemic Bosca's newt (Lissotriton boscai) in SW Iberia with a multilocus dataset (microsatellites, nuclear and mitochondrial genes). STRUCTURE and NEWHYBRIDS analyses retrieved few admixed individuals, which classified as backcrosses involving parental individuals of the south-western lineage. Our results show asymmetric introgression of mtDNA beyond the contact from this lineage into the south-eastern lineage. Analysis of nongeographic introgression patterns revealed asymmetries in the direction of introgression, but except for mtDNA, we did not find evidence for nonconcordant introgression patterns across nuclear loci. Analysis of a 150-km transect across the hybrid zone showed broadly coincident cline widths (ca. 3.2-27.9 km), and concordant cline centres across all markers, except for mtDNA that is displaced ca. 60 km northward. Results from ecological niche modelling show that the hybrid zone is in a climatically homogenous area with suitable habitat for the species, suggesting that contact between the two lineages is unlikely to occur further south as their distributions are currently separated by an extensive area of unfavourable habitat. Taken together, our findings suggest the genetic structure of this hybrid zone results from the interplay of historical (biogeographic) and population-level processes. The narrowness and coincidence of genetic clines can be explained by weak selection against hybrids and reflect a degree of reproductive isolation that is consistent with cryptic speciation.

A dynamic continental moisture gradient drove Amazonian bird diversification

The Amazon is the primary source of Neotropical diversity and a nexus for discussions on processes that drive biotic diversification. Biogeographers have focused on the roles of rivers and Pleistocene climate change in explaining high rates of speciation. We combine phylogeographic and niche-based paleodistributional projections for 23 upland terra firme forest bird lineages from across the Amazon to derive a new model of regional biological diversification. We found that climate-driven refugial dynamics interact with dynamic riverine barriers to produce a dominant pattern: Older lineages in the wetter western and northern parts of the Amazon gave rise to lineages in the drier southern and eastern parts. This climate/drainage basin evolution interaction links landscape dynamics with biotic diversification and explains the east-west diversity gradients across the Amazon.

Improving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader

Background

Cane toads (Rhinella marina) are an iconic invasive species introduced to 4 continents and well utilized for studies of rapid evolution in introduced environments. Despite the long introduction history of this species, its profound ecological impacts, and its utility for demonstrating evolutionary principles, genetic information is sparse. Here we produce a de novo transcriptome spanning multiple tissues and life stages to enable investigation of the genetic basis of previously identified rapid phenotypic change over the introduced range.

Findings

Using approximately 1.9 billion reads from developing tadpoles and 6 adult tissue-specific cDNA libraries, as well as a transcriptome assembly pipeline encompassing 100 separate de novo assemblies, we constructed 62 202 transcripts, of which we functionally annotated ∼50%. Our transcriptome assembly exhibits 90% full-length completeness of the Benchmarking Universal Single-Copy Orthologs data set. Robust assembly metrics and comparisons with several available anuran transcriptomes and genomes indicate that our cane toad assembly is one of the most complete anuran genomic resources available.

Conclusions

This comprehensive anuran transcriptome will provide a valuable resource for investigation of genes under selection during invasion in cane toads, but will also greatly expand our general knowledge of anuran genomes, which are underrepresented in the literature. The data set is publically available in NCBI and GigaDB to serve as a resource for other researchers.

Draft genome assembly of the invasive cane toad, Rhinella marina

Background

The cane toad (Rhinella marina formerly Bufo marinus) is a species native to Central and South America that has spread across many regions of the globe. Cane toads are known for their rapid adaptation and deleterious impacts on native fauna in invaded regions. However, despite an iconic status, there are major gaps in our understanding of cane toad genetics. The availability of a genome would help to close these gaps and accelerate cane toad research.

Findings

We report a draft genome assembly for R. marina, the first of its kind for the Bufonidae family. We used a combination of long-read Pacific Biosciences RS II and short-read Illumina HiSeq X sequencing to generate 359.5 Gb of raw sequence data. The final hybrid assembly of 31,392 scaffolds was 2.55 Gb in length with a scaffold N50 of 168 kb. BUSCO analysis revealed that the assembly included full length or partial fragments of 90.6% of tetrapod universal single-copy orthologs (n = 3950), illustrating that the gene-containing regions have been well assembled. Annotation predicted 25,846 protein coding genes with similarity to known proteins in Swiss-Prot. Repeat sequences were estimated to account for 63.9% of the assembly.

Conclusions

The R. marina draft genome assembly will be an invaluable resource that can be used to further probe the biology of this invasive species. Future analysis of the genome will provide insights into cane toad evolution and enrich our understanding of their interplay with the ecosystem at large.

De novo transcriptome assembly and polymorphism detection in two highly divergent evolutionary units of Bosca's newt (Lissotriton boscai) endemic to the Iberian Peninsula

This article reports the de novo transcriptome assemblies of two highly divergent evolutionary units of the Iberian endemic Bosca's newt, Lissotriton boscai. These two units are distributed mostly allopatrically but overlap in the central-southwestern coastal region of Portugal. The resources we provide include the raw sequence reads, the assembled transcripts, the annotation and SNPs called for both lineages.

Concerted evolution in the mitochondrial control region of the Amazon small-bodied frog Pseudopaludicola canga (Anura, Leiuperidae)

This study presents evidence of concerted evolution in the mitochondrial control region of the frog Pseudopaludicola canga. Four repeat units of 88 bp (as well as a fifth, incomplete unit) were observed in the 5' domain, with the duplicated segments of the same specimen being more related to one another than to the equivalent regions in other specimens, as a result of concerted evolution. We highlight that drawing conclusions from phylogeographical analysis using the control region containing VNTRs must be interpreted with caution, because it violated a basic assumption of phylogeny, since the regions cannot be treated as independent characters.

Patterns of Genetic Variability in Island Populations of the Cane Toad (Rhinella marina) from the Mouth of the Amazon

The Amazonian coast has several unique geological characteristics resulting from the interaction between drainage pattern of the Amazon River and the Atlantic Ocean. It is one of the most extensive and sedimentologically dynamic regions of the world, with a large number of continental islands mostly formed less than 10,000 years ago. The natural distribution of the cane toad (Rhinella marina), one of the world's most successful invasive species, in this complex Amazonian system provides an intriguing model for the investigation of the effects of isolation or the combined effects of isolation and habitat dynamic changes on patterns of genetic variability and population differentiation. We used nine fast-evolving microsatellite loci to contrast patterns of genetic variability in six coastal (three mainlands and three islands) populations of the cane toad near the mouth of the Amazon River. Results from Bayesian multilocus clustering approach and Discriminant Analyses of Principal Component were congruent in showing that each island population was genetically differentiated from the mainland populations. All FST values obtained from all pairwise comparisons were significant, ranging from 0.048 to 0.186. Estimates of both recent and historical gene flow were not significantly different from zero across all population pairs, except the two mainland populations inhabiting continuous habitats. Patterns of population differentiation, with a high level of population substructure and absence/restricted gene flow, suggested that island populations of R. marina are likely isolated since the Holocene sea-level rise. However, considering the similar levels of genetic variability found in both island and mainland populations, it is reliable to assume that they were also isolated for longer periods. Given the genetic uniqueness of each cane toad population, together with the high natural vulnerability of the coastal regions and intense human pressures, we suggest that these populations should be treated as discrete units for conservation management purposes.

Patients With Anorexia Nervosa: Outcome Inpatient Care

Introduction

Anorexia nervosa (AN) is characterized by self-induced starvation coupled with fear of gaining weight and a distorted body image. Its treatment is complex and challenging, and sometimes hospitalization is needed.

Santa Maria Hospital's Eating Disorders Unit (SMH-EDU) is a multidisciplinary team, formed in 1989, that provides both outpatient and inpatient treatment.

Objective

To present and discuss SMH-EDU's AN treatment and its results.

Methods

Revision and statistical analysis of all hospitalized AN’ patients’ clinical files, from 1 January 2014 to 31 December 2014. Treatment outcome was assessed by BMI variation.

Results

A total of 45 admissions (41 patients) were analysed: 75.65% had AN restricting type and 24.45% had AN purging type. All patient were females, with median age of 27 years old (range 12–57 years). Average admission BMI was 14.51 kg/m2 (ranging from 11.19 to 17.77 kg/m2). The mean lengths of stay were 39 days. Thirty-six percent of the patients had at least one previous hospitalization. Only 2 patients were readmitted at SMH-EDU: triple readmissions. The mean time between the beginning of the disorder and the admission was 111 months (ranging 2 to 408 months). Average discharged BMI was 16.32 kg/m2 (ranging from 13.24 to 19.11 kg/m2).

Conclusion

Inpatient treatment for AN at SMH-EDU is considered only for those patients whose disorder has not improved with appropriate outpatient treatment. Therefore, most inpatients at SMH-EDU have disorders of high severity, as demonstrated in our results.

Disclosure of interest

The authors have not supplied their declaration of competing interest.

Multilocus phylogeography of the common midwife toad, Alytes obstetricans (Anura, Alytidae): Contrasting patterns of lineage diversification and genetic structure in the Iberian refugium

Recent investigations on the evolutionary history of the common midwife toad (Alytes obstetricans) revealed high levels of geographically structured genetic diversity but also a situation where delineation of major historical lineages and resolution of their relationships are much more complex than previously thought. We studied sequence variation in one mitochondrial and four nuclear genes throughout the entire distribution range of all recognized A. obstetricans subspecies to infer the evolutionary processes that shaped current patterns of genetic diversity and population subdivision. We found six divergent, geographically structured mtDNA haplogroups diagnosing population lineages, and varying levels of admixture in nuclear markers. Given the timeframe inferred for the splits between major lineages, the climatic and environmental changes that occurred during the Pleistocene seem to have shaped the diversification history of A. obstetricans. Survival of populations in allopatric refugia through the Ice Ages supports the generality of the "refugia-within-refugia" scenario for the Iberian Peninsula. However, lineages corresponding to subspecies A. o. almogavarii, A. o. pertinax, A. o. obstetricans, and A. o. boscai responded differently to Pleistocene climatic oscillations after diverging from a common ancestor. Alytes o. obstetricans expanded northward from a northern Iberian refugium through the western Pyrenees, leaving a signal of contrasting patterns of genetic diversity, with a single mtDNA haplotype north of the Pyrenees from SW France to Germany. Both A. o. pertinax and A. o. boscai are widespread and genetically diverse in Iberia, the latter comprising two divergent lineages with a long independent history. Finally, A. o. almogavarii is mostly restricted to the north-eastern corner of Iberia north of the Ebro river, with additional populations in a small region in south-eastern France. This taxon exhibits unparalleled levels of genetic diversity and little haplotype sharing with other lineages, suggesting a process of incipient speciation.

Cryptic genetic diversity is paramount in small-bodied amphibians of the genus Euparkerella (Anura: Craugastoridae) endemic to the Brazilian Atlantic forest

Morphological similarity associated to restricted distributions and low dispersal abilities make the direct developing “Terrarana” frogs of the genus Euparkerella a good model for examining diversification processes. We here infer phylogenetic relationships within the genus Euparkerella, using DNA sequence data from one mitochondrial and four nuclear genes coupled with traditional Bayesian phylogenetic reconstruction approaches and more recent coalescent methods of species tree inference. We also used Bayesian clustering analysis and a recent Bayesian coalescent-based approach specifically to infer species delimitation. The analysis of 39 individuals from the four known Euparkerella species uncovered high levels of genetic diversity, especially within the two previously morphologically-defined E. cochranae and E. brasiliensis. Within these species, the gene trees at five independent loci and trees from combined data (concatenated dataset and the species tree) uncovered six deeply diverged and geographically coherent evolutionary units, which may have diverged between the Miocene and the Pleistocene. These six units were also uncovered in the Bayesian clustering analysis, and supported by the Bayesian coalescent-based species delimitation (BPP), and Genealogical Sorting Index (GSI), providing thus strong evidence for underestimation of the current levels of diversity within Euparkerella. The cryptic diversity now uncovered opens new opportunities to examine the origins and maintenance of microendemism in the context of spatial heterogeneity and/or human induced fragmentation of the highly threatened Brazilian Atlantic forest hotspot.

Development of microsatellite markers for the Neotropical endemic Brazilian Guanabara frog, Euparkerella brasiliensis, through 454 shotgun pyrosequencing

The new-generation 454 GS-FLX Titanium pyrosequencing was used to isolate microsatellite markers for the Brazilian Guanabara frog, Euparkerella brasiliensis, an Atlantic forest endemic species. Three multiplex polymerase chain reaction sets were optimized for genotyping of 11 polymorphic (di- and tetranucleotide) microsatellite markers. Genetic diversity was assessed in 21 individuals from a population (Reserva Ecológica de Guapiaçu, REGUA) located in the central region of the Rio de Janeiro State, in Brazil. The mean number of alleles per locus ranged from 3 to 12. Observed and expected heterozygosities ranged from 0.095 to 0.905 and from 0.094 to 0.904, respectively. After using the Bonferroni correction for multiple tests, there was no evidence of linkage disequilibrium between pairs of loci but deviations for Hardy-Weinberg equilibrium were found in 4 loci. We found no evidence for allele dropouts or stuttering, but we detected the presence of null alleles at loci Eb10 and Eb36. These markers will be useful for analyses of fine-scale population structure and determination of relative effects of habitat loss and fragmentation on population genetic variability within species.

Hybridization and massive mtDNA unidirectional introgression between the closely related Neotropical toads Rhinella marina and R. schneideri inferred from mtDNA and nuclear markers

Background

The classical perspective that interspecific hybridization in animals is rare has been changing due to a growing list of empirical examples showing the occurrence of gene flow between closely related species. Using sequence data from cyt b mitochondrial gene and three intron nuclear genes (RPL9, c-myc, and RPL3) we investigated patterns of nucleotide polymorphism and divergence between two closely related toad species R. marina and R. schneideri. By comparing levels of differentiation at nuclear and mtDNA levels we were able to describe patterns of introgression and infer the history of hybridization between these species.

Results

All nuclear loci are essentially concordant in revealing two well differentiated groups of haplotypes, corresponding to the morphologically-defined species R. marina and R. schneideri. Mitochondrial DNA analysis also revealed two well-differentiated groups of haplotypes but, in stark contrast with the nuclear genealogies, all R. schneideri sequences are clustered with sequences of R. marina from the right Amazon bank (RAB), while R. marina sequences from the left Amazon bank (LAB) are monophyletic. An Isolation-with-Migration (IM) analysis using nuclear data showed that R. marina and R. schneideri diverged at ≈ 1.69 Myr (early Pleistocene), while R. marina populations from LAB and RAB diverged at ≈ 0.33 Myr (middle Pleistocene). This time of divergence is not consistent with the split between LAB and RAB populations obtained with mtDNA data (≈ 1.59 Myr), which is notably similar to the estimate obtained with nuclear genes between R. marina and R. schneideri. Coalescent simulations of mtDNA phylogeny under the speciation history inferred from nuclear genes rejected the hypothesis of incomplete lineage sorting to explain the conflicting signal between mtDNA and nuclear-based phylogenies.

Conclusions

The cytonuclear discordance seems to reflect the occurrence of interspecific hybridization between these two closely related toad species. Overall, our results suggest a phenomenon of extensive mtDNA unidirectional introgression from the previously occurring R. schneideri into the invading R. marina. We hypothesize that climatic-induced range shifts during the Pleistocene/Holocene may have played an important role in the observed patterns of introgression.

Novel C1q assay reveals a clinically relevant subset of human leukocyte antigen antibodies independent of immunoglobulin G strength on single antigen beads

It has been known for 40 years that cytotoxic human leukocyte antigen (HLA) antibodies are associated with graft rejection. However, the complement-dependent cytotoxicity assay (CDC) used to define these clinically deleterious antibodies suffers from a lack of sensitivity and specificity. Recently, methods exploiting immunoglobulin G (IgG) antibody binding to HLA single antigen beads (SAB) have overcome sensitivity and specificity drawbacks but introduced a new dilemma: which of the much broader set of antibodies defined by these methods are clinically relevant. To address this, we developed a complement-fixing C1q assay on the HLA SAB that combines sensitivity, specificity, and functional potential into one assay. We compared the CDC, IgG, and C1q assays on 96 sera having 2,118 defined antibodies and determined that CDC detects only 19% of complement-fixing antibodies detected by C1q, whereas C1q detects only 47% of antibodies detected by IgG. In the same patient, there is no predictability by IgG mean fluorescence intensity (MFI) as to which of the antibodies will bind C1q because fixation is independent of MFI values. In 3 clinical studies, C1q(+) antibodies appear to be more highly correlated than those detected by IgG alone for antibody-mediated rejection in hearts as well as for kidney transplant glomerulopathy and graft failure.

On the edge of Bantu expansions: mtDNA, Y chromosome and lactase persistence genetic variation in southwestern Angola

Background

Current information about the expansion of Bantu-speaking peoples is hampered by the scarcity of genetic data from well identified populations from southern Africa. Here, we fill an important gap in the analysis of the western edge of the Bantu migrations by studying for the first time the patterns of Y-chromosome, mtDNA and lactase persistence genetic variation in four representative groups living around the Namib Desert in southwestern Angola (Ovimbundu, Ganguela, Nyaneka-Nkumbi and Kuvale). We assessed the differentiation between these populations and their levels of admixture with Khoe-San groups, and examined their relationship with other sub-Saharan populations. We further combined our dataset with previously published data on Y-chromosome and mtDNA variation to explore a general isolation with migration model and infer the demographic parameters underlying current genetic diversity in Bantu populations.

Results

Correspondence analysis, lineage sharing patterns and admixture estimates indicate that the gene pool from southwestern Angola is predominantly derived from West-Central Africa. The pastoralist Herero-speaking Kuvale people were additionally characterized by relatively high frequencies of Y-chromosome (12%) and mtDNA (22%) Khoe-San lineages, as well as by the presence of the -14010C lactase persistence mutation (6%), which likely originated in non-Bantu pastoralists from East Africa. Inferred demographic parameters show that both male and female populations underwent significant size growth after the split between the western and eastern branches of Bantu expansions occurring 4000 years ago. However, males had lower population sizes and migration rates than females throughout the Bantu dispersals.

Conclusion

Genetic variation in southwestern Angola essentially results from the encounter of an offshoot of West-Central Africa with autochthonous Khoisan-speaking peoples from the south. Interactions between the Bantus and the Khoe-San likely involved cattle herders from the two groups sharing common aspects of their social organization. The presence of the -14010C mutation in southwestern Angola provides a link between the East and Southwest African pastoral scenes that might have been established indirectly, through migrations of Khoe herders across southern Africa. Differences in patterns of mtDNA and Y-chromosome intrapopulation diversity and interpopulation differentiation may be explained by contrasting demographic histories underlying the current female and male genetic variation.

Assessing the phylogenetic signal of the nuclear β-Fibrinogen intron 7 in salamandrids (Amphibia: Salamandridae)

Abstract

The potential of the seventh intron of the β-subunit of the fibrinogen gene (β-fibint 7) for phylogenetic analysis within the Salamandridae family was explored, comparing the topologies of trees based on this marker to those based on mitochondrial 12S rRNA gene previously published. Using primers designed specifically for amphibians, we amplified 25 sequences of β-fibint 7 corresponding to 15 species of salamandrids and one plethodontid species. There was considerable length variation among the β-fibint 7 sequences examined, ranging from 1123 bp in S. atra to 400 bp in P. waltl. Many aspects of the phylogenetic relationships estimated by the two independent loci were congruent and corroborate current taxonomic hypothesis. Although the number of taxa analysed is small, the data obtained in this work suggested that β-fibint 7 is a useful marker for assessing phylogenetic relationships within the Salamandridae family, and is probably appropriate for phylogenetic studies among closely related salamanders that have diverged over the last 20 Myr.

Genetic exchange across a hybrid zone within the Iberian endemic golden-striped salamander, Chioglossa lusitanica

The study of hybrid zones resulting from Pleistocene vicariance is central in examining the potential of genetically diverged evolutionary units either to introgress and merge or to proceed with further isolation. The hybrid zone between two mitochondrial lineages of Chioglossa lusitanica is located near the Mondego River in Central Portugal. We used mitochondrial and nuclear diagnostic markers to conduct a formal statistical analysis of the Chioglossa hybrid zone in the context of tension zone theory. Key results are: (i) cline centres are not coincident for all markers, with average widths of ca. 2-15 km; (ii) heterozygote deficit was not observed across loci near the transect centre; (iii) associations of parental allele combinations ('linkage disequilibrium'R) were not detected either across loci or across the transect. These observations suggest that the Chioglossa hybrid zone is not a tension zone with strong selection against hybrids but instead one shaped mostly by neutral mixing. The patterns uncovered suggest a complex history of populations over a small scale that may be common in southern Pleistocene refugia.