Genomic Traces of the Fruit Fly Anastrepha obliqua Associated with Its Polyphagous Nature

Anastrepha obliqua (Macquart) (Diptera: Tephritidae) is an important pest in the neotropical region. It is considered a polyphagous insect, meaning it infests plants of different taxonomic families and readily colonizes new host plants. The change to new hosts can lead to diversification and the formation of host races. Previous studies investigating the effect of host plants on population structure and selection in Anastrepha obliqua have focused on the use of data from the mitochondrial DNA sequence and microsatellite markers of nuclear DNA, and there are no analyses at the genomic level. To better understand this issue, we used a pooled restriction site-associated DNA sequencing (pooled RAD-seq) approach to assess genomic differentiation and population structure across sympatric populations of Anastrepha obliqua that infest three host plants—Spondias purpurea (red mombin), Mangifera indica (mango) of the family Anacardiaceae and Averrhoa carambola (carambola) of the family Oxalidaceae—in sympatric populations of the species Anastrepha obliqua of Inter-Andean Valley of the Cauca River in southwestern Colombia. Our results show genomic differentiation of populations from carambola compared to mango and red mombin populations, but the genetic structure was mainly established by geography rather than by the host plant. On the other hand, we identified 54 SNPs in 23 sequences significantly associated with the use of the host plant. Of these 23 sequences, we identified 17 candidate genes and nine protein families, of which four protein families are involved in the nutrition of these flies. Future studies should investigate the adaptive processes undergone by phytophagous insects in the Neotropics, using fruit flies as a model and state-of-the-art molecular tools.

Mapping and monitoring genetic diversity of an alpine freshwater top predator by applying newly proposed indicators

Genetic diversity is the basis for population adaptation and long-term survival, yet rarely considered in biodiversity monitoring. One key issue is the need for useful and straightforward indicators of genetic diversity. To test newly proposed indicators, we monitored genetic diversity over 40 years (1970-2010) in metapopulations of brown trout inhabiting 27 small mountain lakes representing 10 water systems in central Sweden. Three of the indicators were previously proposed for broad, international use for the Convention on Biological Diversity (CBD) context, while three others were recently elaborated for national use by a Swedish science-management effort and applied for the first time here. The Swedish indicators use molecular genetic data to monitor genetic diversity within and between populations and assess the effective population size (Ne). We used a panel of 96 SNPs and identified 29 discrete populations retained over time. Over 40 percent of the lakes harbored more than one population indicating that brown trout biodiversity hidden as cryptic, sympatric populations are more common than recognized. The Ne indicator showed values below the threshold (Ne≤500) in 20 populations with five showing Ne<100. Although statistically significant genetic diversity reductions occurred in several populations, they were mostly within proposed threshold limits. Metapopulation structure appears to buffer against diversity loss; when applying the indicators to metapopulations most indicators suggest an acceptable genetic status in all but one system. The CBD indicators agreed with the national ones but provided less detail. We propose that all indicators applied here are appropriate for monitoring genetic diversity within species.

Behavioural responses to con- and heterospecific alarm cues by an alien and a coexisting native fish

The monkey goby Neogobius fluviatilis is an invasive Ponto-Caspian fish that enters habitats of the native gudgeon Gobio gobio in European freshwaters, likely belonging to the same prey guild. Their abilities to detect and avoid predation have been poorly understood, although these traits may contribute to the competitive advantage and drive the invasion success of the goby. We tested intra- and interspecific responses of fish from sympatric populations to damage-released alarm cues (skin extract) in laboratory. Both species of fish responded to conspecific and heterospecific cues, but their responses to conspecifics were more diverse (changed social distancing among individuals, reduced vertical and horizontal movement) than those elicited by heterospecifics (changed social distancing only). Moreover, the fish differed in their anti-predation behaviour: the gudgeon increased whilst the monkey goby decreased inter-individual distances and only the gudgeon exhibited thigmotaxis and reduced mobility in response to the conspecific cues. Interspecific differences show that the species exhibit distant anti-predation strategies. This might be associated with their phylogenetic distance and/or higher differentiation of their ecological niches than commonly assumed. Besides, our results suggest that alien species be included in the interspecific exchange of information in local fish assemblages.

Recovery of vulture population in roosting and scavenging areas of Bastar and Bijapur, Chhattisgarh, India

Chhattisgarh is home to seven of the nine vulture species in India. One reason for this high vulture diversity is the presence of large herds of bovines numbering over 11 million individuals (ratio of human to bovine population is approximately 0.38), from which carcasses are disposed off in the open for scavengers. The late 1990s saw large scale decimation of vulture population, and since then there have been few studies with no sighting estimates available. In this study, concurrent sighting records were collected from different locations of southern Chhattisgarh and corroborated to develop conservative sighting estimates for sympatric populations of Gyps bengalensis and Gyps indicus. We present the first report on population recovery, with an estimated 30–35 Gyps bengalensis & 20–25 Gyps indicus in/ around Rudraram of Bijapur and 18 Gyps bengalensis & five Gyps indicus at Jamguda village of Bastar. Krishna Swami Gutta hill is identified as a nesting-roosting habitat for both species, for which six scavenging areas were identified in Bastar and Bijapur districts. The human/bovine population ratio for Bastar is 0.4, similar to the state ratio, while in Bijapur the ratio is 1.07, which justifies considering Bijapur as a conservation refuge. The few vultures that survived the diclofenac catastrophe in wild habitats most likely consumed wildlife carcasses that sustained a residual population. In these areas, the age-old practise of disposing off dead domesticated bovines away from settlements near reserve forests may also have supported the recovery of vulture population.

The role of sexual isolation during rapid ecological divergence: evidence for a new dimension of isolation in Rhagoletis pomonella

The pace of divergence and likelihood of complete speciation may depend how and when different types of reproductive barriers evolve. After initial reproductive barriers evolve, questions remain about how subsequently evolving barriers may facilitate additional divergence and potential speciation. We tested for the presence of sexual isolation (reduced mating between populations due to divergent mating preferences and traits) in Rhagoletis pomonella flies, a model system for incipient ecological speciation. We measured the strength of sexual isolation between two very recently diverged (~170 years) sympatric populations, adapted to different host fruits. We found that sexual isolation was significantly stronger than expectations of random mating. Thus, sexual isolation may play an important role in reducing gene flow allowed by earlier-acting ecological barriers. We also found that sexual isolation was markedly asymmetric between the sexes of each population. Lastly, we tested how warmer temperatures predicted under climate change could alter sexual isolation and found that mating interactions were sensitive to temperature experienced during development. Our findings provide a window into the early divergence process and the role of sexual isolation after initial ecological divergence, in addition to examining multiple factors that could shape the likelihood of further divergence.

Allochronic isolation on a latitudinal gradient in the polyphagous moth Hyphantria cunea

Allochronic speciation, where reproductive isolation between populations of a species is facilitated by a difference in reproductive timing, depends on the existence of seasonality. Seasonality is strongly driven by latitude, so there may be a relationship between latitude and divergence among populations separated by life history timing. Here we explore the relationship between allochronic speciation and latitude using Hyphantria cunea (the fall webworm), a Lepidopteran defoliator with red and black colour morphs that may be undergoing an incipient allochronic speciation. We annotated >9000 community science observations of fall webworm to model colour morph phenology and differences in phenotype across North America. We also examined the physiology of two sympatric populations to determine differences in diapause intensity. We found the fall webworm is multivoltine with differing numbers of generations between colour morphs at lower latitudes, and univoltine at latitudes higher than 41°. This shift to univoltism correlated with a decline in morphological differentiation. This shows that conditions at lower latitudes facilitate greater divergence in an incipient allochronic speciation potentially due to longer reproductive seasons allowing for greater mismatches in generations. Our results demonstrate how latitude affects allochronic speciation, and how sympatric speciation along latitudinal gradients contributes to trends in global biodiversity.

Floral Trait and Mycorrhizal Similarity between an Endangered Orchid and Its Natural Hybrid

Hybridization can often lead to the formation of novel taxa which can have traits that resemble either or both parental species. Determining the similarity of hybrid traits to parental taxa is particularly important in plant conservation, as hybrids that form between rare and common taxa may more closely resemble a rare parental species, thereby putting the rare parental taxon at further risk of extinction via increased backcrossing and introgression. We investigated the floral (morphological and chemical) traits and orchid mycorrhizal (OrM) fungal associations of the endangered orchid Orchis patens, its more common sister species O. provincialis, and their natural hybrid O. × fallax in natural sympatric populations. We found that both morphological and chemical floral traits of O. × fallax are shared by the parents but are more similar to O. patens than O. provincialis. OrM fungi were shared among all three taxa, indicating that the availability of OrM fungi should not represent a barrier to establishment of individuals of any of these taxa. These results suggest that O. × fallax may be able to expand its distribution within a similar niche to O. patens. This highlights the importance of quantifying differences between hybrids and parental taxon in species conservation planning.

Selective sorting of ancestral introgression in maize and teosinte along an elevational cline

While often deleterious, hybridization can also be a key source of genetic variation and pre-adapted haplotypes, enabling rapid evolution and niche expansion. Here we evaluate these opposing selection forces on introgressed ancestry between maize (Zea mays ssp. mays) and its wild teosinte relative, mexicana (Zea mays ssp. mexicana). Introgression from ecologically diverse teosinte may have facilitated maize’s global range expansion, in particular to challenging high elevation regions (> 1500 m). We generated low-coverage genome sequencing data for 348 maize and mexicana individuals to evaluate patterns of introgression in 14 sympatric population pairs, spanning the elevational range of mexicana, a teosinte endemic to the mountains of Mexico. While recent hybrids are commonly observed in sympatric populations and mexicana demonstrates fine-scale local adaptation, we find that the majority of mexicana ancestry tracts introgressed into maize over 1000 generations ago. This mexicana ancestry seems to have maintained much of its diversity and likely came from a common ancestral source, rather than contemporary sympatric populations, resulting in relatively low FST between mexicana ancestry tracts sampled from geographically distant maize populations. Introgressed mexicana ancestry in maize is reduced in lower-recombination rate quintiles of the genome and around domestication genes, consistent with pervasive selection against introgression. However, we also find mexicana ancestry increases across the sampled elevational gradient and that high introgression peaks are most commonly shared among high-elevation maize populations, consistent with introgression from mexicana facilitating adaptation to the highland environment. In the other direction, we find patterns consistent with adaptive and clinal introgression of maize ancestry into sympatric mexicana at many loci across the genome, suggesting that maize also contributes to adaptation in mexicana, especially at the lower end of its elevational range. In sympatric maize, in addition to high introgression regions we find many genomic regions where selection for local adaptation maintains steep gradients in introgressed mexicana ancestry across elevation, including at least two inversions: the well-characterized 14 Mb Inv4m on chromosome 4 and a novel 3 Mb inversion Inv9f surrounding the macrohairless1 locus on chromosome 9. Most outlier loci with high mexicana introgression show no signals of sweeps or local sourcing from sympatric populations and so likely represent ancestral introgression sorted by selection, resulting in correlated but distinct outcomes of introgression in different contemporary maize populations.

Genomic signals of admixture and reinforcement between two closely related species of European sepsid flies

Interspecific gene flow by hybridization may weaken species barriers and adaptive divergence, but can also initiate reinforcement of reproductive isolation trough natural and sexual selection. The extent of interspecific gene flow and its consequences for the initiation and maintenance of species barriers in natural systems remain poorly understood, however. To assess genome-wide patterns of gene flow between the two closely related European dung fly species Sepsis cynipsea and Sepsis neocynipsea (Diptera: Sepsidae), we tested for historical gene flow with the aid of ABBA-BABA test using whole-genome resequencing data from pooled DNA of male specimens originating from natural and laboratory populations. We contrasted genome-wide variation in DNA sequence differences between samples from sympatric populations of the two species in France and Switzerland with that of interspecific differences between pairs of samples involving allopatric populations from Estonia and Italy. In the French Cevennes, we detected a relative excess of DNA sequence identity, suggesting interspecific gene flow in sympatry. In contrast, at two sites in Switzerland, we observed a relative depletion of DNA sequence identity compatible with reinforcement of species boundaries in sympatry. Our results suggest that the species boundaries between S. cynipsea and S. neocynipsea in Europe depend on the eco-geographic context.

Are members of the Anopheles fluviatilis complex conspecific?

Anopheles fluviatilis sensu lato, a primary malaria vector in India, was identified to be comprised of four cryptic species, provisionally designated as species S, T, U and V. However, Kumar et al. (Mol Ecol Resour, 2013;13:354-61) considered all of the then known three members of this species complex (S, T and U) conspecific. The specific status of species S and T was refuted based on the lack of sufficient barcode gap in mitochondrial-CO1 and the perceived presence of heterozygotes in populations as detected through one of the two species-specific PCR assays employed for the cryptic species identification. The existence of species U was refuted claiming that earlier investigations have already refuted their existence. This conclusion is concerning because of the differential public health implications of members of the Fluviatilis Complex. Here we discuss problems associated with the CO1-based barcode approach for delimitation of cryptic species, the perceived heterozygosity between species S and T based on a species-specific PCR assay, and interpretation of published reports. We demonstrated that fixed differences do exist in the ITS2-rDNA sequence of species S and T with no evidence of heterozygotes in sympatric populations and, that the observed heterozygosity by Kumar et al. in the ITS2-based species diagnostic PCR is due to the high mispriming tendency of the T-specific primer with species S. We infer that mitochondrial DNA-based barcoding-gap, an arbitrary threshold recommended for species delimitation, alone, is inadequate to delimit the members of An. fluviatilis complex.