The roles of hybridization and habitat fragmentation in the evolution of Brazil's enigmatic longwing butterflies, Heliconius nattereri and H. hermathena

BACKGROUND

Heliconius butterflies are widely distributed across the Neotropics and have evolved a stunning array of wing color patterns that mediate Müllerian mimicry and mating behavior. Their rapid radiation has been strongly influenced by hybridization, which has created new species and allowed sharing of color patterning alleles between mimetic species pairs. While these processes have frequently been observed in widespread species with contiguous distributions, many Heliconius species inhabit patchy or rare habitats that may strongly influence the origin and spread of species and color patterns. Here, we assess the effects of historical population fragmentation and unique biology on the origins, genetic health, and color pattern evolution of two rare and sparsely distributed Brazilian butterflies, Heliconius hermathena and Heliconius nattereri.

RESULTS

We assembled genomes and re-sequenced whole genomes of eight H. nattereri and 71 H. hermathena individuals. These species harbor little genetic diversity, skewed site frequency spectra, and high deleterious mutation loads consistent with recent population bottlenecks. Heliconius hermathena consists of discrete, strongly isolated populations that likely arose from a single population that dispersed after the last glacial maximum. Despite having a unique color pattern combination that suggested a hybrid origin, we found no genome-wide evidence that H. hermathena is a hybrid species. However, H. hermathena mimicry evolved via introgression, from co-mimetic Heliconius erato, of a small genomic region upstream of the color patterning gene cortex.

CONCLUSIONS

Heliconius hermathena and H. nattereri population fragmentation, potentially driven by historical climate change and recent deforestation, has significantly reduced the genetic health of these rare species. Our results contribute to a growing body of evidence that introgression of color patterning alleles between co-mimetic species appears to be a general feature of Heliconius evolution.

BRAZIL ROAD-KILL: a data set of wildlife terrestrial vertebrate road-kills

Mortality from collision with vehicles is the most visible impact of road traffic on wildlife. Mortality due to roads (hereafter road-kill) can affect the dynamic of populations of many species and can, therefore, increase the risk of local decline or extinction. This is especially true in Brazil, where plans for road network upgrading and expansion overlaps biodiversity hotspot areas, which are of high importance for global conservation. Researchers, conservationists and road planners face the challenge to define a national strategy for road mitigation and wildlife conservation. The main goal of this dataset is a compilation of geo-referenced road-kill data from published and unpublished road surveys. This is the first Data Paper in the BRAZIL series (see ATLANTIC, NEOTROPICAL, and BRAZIL collections of Data Papers published in Ecology), which aims make public road-kill data for species in the Brazilian Regions. The dataset encompasses road-kill records from 45 personal communications and 26 studies published in peer-reviewed journals, theses and reports. The road-kill dataset comprises 21,512 records, 83% of which are identified to the species level (n = 450 species). The dataset includes records of 31 amphibian species, 90 reptile species, 229 bird species, and 99 mammal species. One species is classified as Endangered, eight as Vulnerable and twelve as Near Threatened. The species with the highest number of records are: Didelphis albiventris (n = 1,549), Volatinia jacarina (n = 1,238), Cerdocyon thous (n = 1,135), Helicops infrataeniatus (n = 802), and Rhinella icterica (n = 692). Most of the records came from southern Brazil. However, observations of the road-kill incidence for non-Least Concern species are more spread across the country. This dataset can be used to identify which taxa seems to be vulnerable to traffic, analyze temporal and spatial patterns of road-kill at local, regional and national scales and also used to understand the effects of road-kill on population persistence. It may also contribute to studies that aims to understand the influence of landscape and environmental influences on road-kills, improve our knowledge on road-related strategies on biodiversity conservation and be used as complementary information on large-scale and macroecological studies. No copyright or proprietary restrictions are associated with the use of this data set other than citation of this Data Paper.

DNA barcoding meets molecular scatology: short mtDNA sequences for standardized species assignment of carnivore noninvasive samples

Although species assignment of scats is important to study carnivore biology, there is still no standardized assay for the identification of carnivores worldwide, which would allow large-scale routine assessments and reliable cross-comparison of results. Here, we evaluate the potential of two short mtDNA fragments [ATP6 (126 bp) and cytochrome oxidase I gene (COI) (187 bp)] to serve as standard markers for the Carnivora. Samples of 66 species were sequenced for one or both of these segments. Alignments were complemented with archival sequences and analysed with three approaches (tree-based, distance-based and character-based). Intraspecific genetic distances were generally lower than between-species distances, resulting in diagnosable clusters for 86% (ATP6) and 85% (COI) of the species. Notable exceptions were recently diverged species, most of which could still be identified using diagnostic characters and uniqueness of haplotypes or by reducing the geographic scope of the comparison. In silico analyses were also performed for a 110-bp cytochrome b (cytb) segment, whose identification success was lower (70%), possibly due to the smaller number of informative sites and/or the influence of misidentified sequences obtained from GenBank. Finally, we performed case studies with faecal samples, which supported the suitability of our two focal markers for poor-quality DNA and allowed an assessment of prey DNA co-amplification. No evidence of prey DNA contamination was found for ATP6, while some cases were observed for COI and subsequently eliminated by the design of more specific primers. Overall, our results indicate that these segments hold good potential as standard markers for accurate species-level identification in the Carnivora.

A large scale analysis of resistance gene homologues in Arachis

Arachis hypogaea L., commonly known as the peanut or groundnut, is an important and widespread food legume. Because the crop has a narrow genetic base, genetic diversity in A. hypogaea is low and it lacks sources of resistance to many pests and diseases. In contrast, wild diploid Arachis species are genetically diverse and are rich sources of disease resistance genes. The majority of known plant disease resistance genes encode proteins with a nucleotide binding site domain (NBS). In this study, degenerate PCR primers designed to bind to DNA regions encoding conserved motifs within this domain were used to amplify NBS-encoding regions from Arachis spp. The Arachis spp. used were A. hypogaea var. Tatu and wild species that are known to be sources of disease resistance: A. cardenasii, A. duranensis, A. stenosperma and A. simpsonii. A total of 78 complete NBS-encoding regions were isolated, of which 63 had uninterrupted ORFs. Phylogenetic analysis of the Arachis NBS sequences derived in this study and other NBS sequences from Arabidopsis thaliana, Medicago trunculata, Glycine max, Lotus japonicus and Phaseolus vulgaris that are available in public databases This analysis indicates that most Arachis NBS sequences fall within legume-specific clades, some of which appear to have undergone extensive copy number expansions in the legumes. In addition, NBS motifs from A. thaliana and legumes were characterized. Differences in the TIR and non-TIR motifs were identified. The likely effect of these differences on the amplification of NBS-encoding sequences by PCR is discussed.