Complete mitochondrial genomes of the New World jacanas: Jacana spinosa and Jacana jacana

Mitochondrial genome of bronze-winged jacana (Metopidius indicus, Latham 1790)

We reported the mitochondrial genome (mitogenome) of bronze-winged jacana (Metopidius indicus, Latham 1790). The circular mitogenome was 17,208 base pairs (bp) in length, containing 13 protein-coding genes, two rRNAs, 22 tRNAs, and a non-coding control region. A DNA spacer 109 bp long was also detected between ND5 and Cytb. Phylogenetic analysis indicated that M. indicus was more closely related with the genera Himantopus, Jacana and Hydrophasianus. This annotated mitogenome reference can be utilized as a data resource for comparative mitogenomics of waders or shorebirds, with possible use in ecological and evolutionary studies.

Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data

The advent of Next Generation Sequencing has reduced sequencing costs and increased genomic projects from a huge amount of organismal taxa, generating an unprecedented amount of genomic datasets publicly available. Often, only a tiny fraction of outstanding relevance of the genomic data produced by researchers is used in their works. This fact allows the data generated to be recycled in further projects worldwide. The assembly of complete mitogenomes is frequently overlooked though it is useful to understand evolutionary relationships among taxa, especially those presenting poor mtDNA sampling at the level of genera and families. This is exactly the case for ants (Hymenoptera:Formicidae) and more specifically for the subfamily Pseudomyrmecinae, a group of arboreal ants with several cases of convergent coevolution without any complete mitochondrial sequence available. In this work, we assembled, annotated and performed comparative genomics analyses of 14 new complete mitochondria from Pseudomyrmecinae species relying solely on public datasets available from the Sequence Read Archive (SRA). We used all complete mitogenomes available for ants to study the gene order conservation and also to generate two phylogenetic trees using both (i) concatenated set of 13 mitochondrial genes and (ii) the whole mitochondrial sequences. Even though the tree topologies diverged subtly from each other (and from previous studies), our results confirm several known relationships and generate new evidences for sister clade classification inside Pseudomyrmecinae clade. We also performed a synteny analysis for Formicidae and identified possible sites in which nucleotidic insertions happened in mitogenomes of pseudomyrmecine ants. Using a data mining/bioinformatics approach, the current work increased the number of complete mitochondrial genomes available for ants from 15 to 29, demonstrating the unique potential of public databases for mitogenomics studies. The wide applications of mitogenomes in research and presence of mitochondrial data in different public dataset types makes the "no budget mitogenomics" approach ideal for comprehensive molecular studies, especially for subsampled taxa.

Ultraconserved Elements Sequencing as a Low-Cost Source of Complete Mitochondrial Genomes and Microsatellite Markers in Non-Model Amniotes

Sequence capture of ultraconserved elements (UCEs) associated with massively parallel sequencing has become a common source of nuclear data for studies of animal systematics and phylogeography. However, mitochondrial and microsatellite variation are still commonly used in various kinds of molecular studies, and probably will complement genomic data in years to come. Here we show that besides providing abundant genomic data, UCE sequencing is an excellent source of both sequences for microsatellite loci design and complete mitochondrial genomes with high sequencing depth. Identification of dozens of microsatellite loci and assembly of complete mitogenomes is exemplified here using three species of Poospiza warbling finches from southern and southeastern Brazil. This strategy opens exciting opportunities to simultaneously analyze genome-wide nuclear datasets and traditionally used mtDNA and microsatellite markers in non-model amniotes at no additional cost.

Extreme mitogenomic divergence between two syntopic specimens of Arremon aurantiirostris (Aves: Emberizidae) in central Panama suggests possible cryptic species

We report the complete mitochondrial genome of two specimens of Orange-billed Sparrow Arremon aurantiirostris from Colón Province, in central Panama. The two specimens were collected on the same day, and at the same locality; however, they showed substantial divergence (6.3% average pairwise divergence among coding genes). A survey of ND2 sequence variation across Panama suggests that this divergence is the result of geographic differentiation and secondary contact. This high level of mitochondrial divergence among co-occurring individuals raises the possibility of multiple biological species in Orange-billed Sparrows. Our results are yet another demonstration that much remains to be discovered regarding avian biodiversity in Panama and throughout the Neotropics.

Genetic and phenotypic characterization of a hybrid zone between polyandrous Northern and Wattled Jacanas in Western Panama

Background

Hybridization provides a unique perspective into the ecological, genetic and behavioral context of speciation. Hybridization is common in birds, but has not yet been reported among bird species with a simultaneously polyandrous mating system; a mating system where a single female defends a harem of males who provide nearly all parental care. Unlike simple polyandry, polyandrous mating is extremely rare in birds, with only 1% of bird species employing this mating system. Although it is classically held that females are “choosy” in avian hybrid systems, nearly-exclusive male parental care raises the possibility that female selection against heterospecific matings might be reduced compared to birds with other mating systems.

Results

We describe a narrow hybrid zone in southwestern Panama between two polyandrous freshwater waders: Northern Jacana, Jacana spinosa and Wattled Jacana, J. jacana. We document coincident cline centers for three phenotypic traits, mtDNA, and one of two autosomal introns. Cline widths for these six markers varied from seven to 142 km, with mtDNA being the narrowest, and five of the six markers having widths less than 100 km. Cline tails were asymmetrical, with greater introgression of J. jacana traits extending westward into the range of J. spinosa. Likewise, within the hybrid zone, the average hybrid index of phenotypic hybrids was significantly biased towards J. spinosa. Species distribution models indicate that the hybrid zone is located at the edge of a roughly 100 km wide overlap where habitat is predicted to be suitable for both species, with more westerly areas suitable only for spinosa and eastward habitats suitable only for J. jacana.

Conclusion

The two species of New World jacanas maintain a narrow, and persistent hybrid zone in western Panama. The hybrid zone may be maintained by the behavioral dominance of J. spinosa counterbalanced by unsuitable habitat for J. spinosa east of the contact zone. Although the two parental species are relatively young, mitochondrial cline width was extremely narrow. This result suggests strong selection against maternally-inherited markers, which may indicate either mitonuclear incompatibilities and/or female choice against heterospecific matings typical of avian hybrid systems, despite jacana sex role reversal.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-014-0227-7) contains supplementary material, which is available to authorized users.

Extreme sequence divergence between mitochondrial genomes of two subspecies of White-breasted Wood-wren (Henicorhina leucosticta, Cabanis, 1847) from western and central Panamá

Prior studies of mitochondrial variation in White-breasted Wood-Wrens (Henicorhina leucosticta) have suggested that populations in South American and Mesoamerica might represent multiple species. Here we report the complete mitochondrial genomes from two individuals of H. leucosticta, representing the Panamanian subspecies pittieri and alexandri. The two sequences were 16,721 and 16,726 base pairs in size with both genomes comprised of the usual 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes, and one displacement loop region in the standard avian order. Uncorrected pairwise divergence between mitogenome features was high, with the highest divergence occurring in protein-coding genes (average = 8.2%), followed by control region (6.7%). RNA features had lower pairwise divergences (average tRNA = 4.3%, average rRNA = 2.3%). The protein-coding ATPase 6 gene had a different stop codon between these two specimens. The high level of sequence variation between these subspecies suggests that Mesoamerican H. leucosticta might be comprised of multiple species. We urge a full phylogeographic survey of this widespread Neotropical forest bird.