Speciation with gene flow: Evidence from a complex of alpine butterflies (Coenonympha, Satyridae)

Gene flow throughout the evolutionary history of a colour polymorphic and generalist clownfish

Even seemingly homogeneous on the surface, the oceans display high environmental heterogeneity across space and time. Indeed, different soft barriers structure the marine environment, which offers an appealing opportunity to study various evolutionary processes such as population differentiation and speciation. Here, we focus on Amphiprion clarkii (Actinopterygii; Perciformes), the most widespread of clownfishes that exhibits the highest colour polymorphism. Clownfishes can only disperse during a short pelagic larval phase before their sedentary adult lifestyle, which might limit connectivity among populations, thus facilitating speciation events. Consequently, the taxonomic status of A. clarkii has been under debate. We used whole-genome resequencing data of 67 A. clarkii specimens spread across the Indian and Pacific Oceans to characterize the species' population structure, demographic history and colour polymorphism. We found that A. clarkii spread from the Indo-Pacific Ocean to the Pacific and Indian Oceans following a stepping-stone dispersal and that gene flow was pervasive throughout its demographic history. Interestingly, colour patterns differed noticeably among the Indonesian populations and the two populations at the extreme of the sampling distribution (i.e. Maldives and New Caledonia), which exhibited more comparable colour patterns despite their geographic and genetic distances. Our study emphasizes how whole-genome studies can uncover the intricate evolutionary past of wide-ranging species with diverse phenotypes, shedding light on the complex nature of the species concept paradigm.

Spatiotemporal dynamics in butterfly hybrid zones

Evaluating whether hybrid zones are stable or mobile can provide novel insights for evolution and conservation biology. Butterflies exhibit high sensitivity to environmental changes and represent an important model system for the study of hybrid zone origins and maintenance. Here, we review the literature exploring butterfly hybrid zones, with a special focus on their spatiotemporal dynamics and the potential mechanisms that could lead to their movement or stability. We then compare different lines of evidence used to investigate hybrid zone dynamics and discuss the strengths and weaknesses of each approach. Our goal with this review is to reveal general conditions associated with the stability or mobility of butterfly hybrid zones by synthesizing evidence obtained using different types of data sampled across multiple regions and spatial scales. Finally, we discuss spatiotemporal dynamics in the context of a speciation/divergence continuum, the relevance of hybrid zones for conservation biology, and recommend key topics for future investigation.

Chromosome-Level Assembly and Annotation of the Pearly Heath Coenonympha arcania Butterfly Genome

We present the first chromosome-level genome assembly and annotation of the pearly heath Coenonympha arcania, generated with a PacBio HiFi sequencing approach and complemented with Hi-C data. We additionally compare synteny, gene, and repeat content between C. arcania and other Lepidopteran genomes. This reference genome will enable future population genomics studies with Coenonympha butterflies, a species-rich genus that encompasses some of the most highly endangered butterfly taxa in Europe.

Signals of differential introgression in the genome of natural hybrids of Caribbean anoles

Hybridization facilitates recombination between divergent genetic lineages and can be shaped by both neutral and selective processes. Upon hybridization, loci with no net fitness effects introgress randomly from parental species into the genomes of hybrid individuals. Conversely, alleles from one parental species at some loci may provide a selective advantage to hybrids, resulting in patterns of introgression that do not conform to random expectations. We investigated genomic patterns of differential introgression in natural hybrids of two species of Caribbean anoles, Anolis pulchellus and A. krugi in Puerto Rico. Hybrids exhibit A. pulchellus phenotypes but possess A. krugi mitochondrial DNA, originated from multiple, independent hybridization events, and appear to have replaced pure A. pulchellus across a large area in western Puerto Rico. Combining genome-wide SNP datasets with bioinformatic methods to identify signals of differential introgression in hybrids, we demonstrate that the genomes of hybrids are dominated by pulchellus-derived alleles and show only 10%-20% A. krugi ancestry. The majority of A. krugi loci in hybrids exhibit a signal of non-random differential introgression and include loci linked to genes involved in development and immune function. Three of these genes (delta like canonical notch ligand 1, jagged1 and notch receptor 1) affect cell differentiation and growth and interact with mitochondrial function. Our results suggest that differential non-random introgression for a subset of loci may be driven by selection favouring the inheritance of compatible mitochondrial and nuclear-encoded genes in hybrids.

The hybridization origin of the Chinese endemic herb genus Notopterygium (Apiaceae): Evidence from population genomics and ecological niche analysis

Hybridization is recognized as a major force in species evolution and biodiversity formation, generally leading to the origin and differentiation of new species. Multiple hybridization events cannot easily be reconstructed, yet they offer the potential to study a number of evolutionary processes. Here, we used nuclear expressed sequence tag-simple sequence repeat and large-scale single nucleotide polymorphism variation data, combined with niche analysis, to investigate the putative independent hybridization events in Notopterygium, a group of perennial herb plants endemic to China. Population genomic analysis indicated that the four studied species are genetically well-delimited and that N. forrestii and N. oviforme have originated by hybridization. According to Approximate Bayesian Computation, the best-fit model involved the formation of N. forrestii from the crossing of N. franchetii and N. incisum, with N. forrestii further backcrossing to N. franchetii to form N. oviforme. The niche analyses indicated that niche divergence [likely triggered by the regional climate changes, particularly the intensification of East Asian winter monsoon, and tectonic movements (affecting both Qinghai-Tibetan Plateau and Qinling Mountains)] may have promoted and maintained the reproductive isolation among hybrid species. N. forrestii shows ecological specialization with respect to their parental species, whereas N. oviforme has completely shifted its niche. These results suggested that the climate and environmental factors together triggered the two-step hybridization of the East Asia herb plants. Our study also emphasizes the power of genome-wide SNPs for investigating suspected cases of hybridization, particularly unravelling old hybridization events.

Species delimitation and mitonuclear discordance within a species complex of biting midges

The inability to distinguish between species can be a serious problem in groups responsible for pathogen transmission. Culicoides biting midges transmit many pathogenic agents infecting wildlife and livestock. In North America, the C. variipennis species complex contains three currently recognized species, only one of which is a known vector, but limited species-specific characters have hindered vector surveillance. Here, genomic data were used to investigate population structure and genetic differentiation within this species complex. Single nucleotide polymorphism data were generated for 206 individuals originating from 17 locations throughout the United States and Canada. Clustering analyses suggest the occurrence of two additional cryptic species within this complex. All five species were significantly differentiated in both sympatry and allopatry. Evidence of hybridization was detected in three different species pairings indicating incomplete reproductive isolation. Additionally, COI sequences were used to identify the hybrid parentage of these individuals, which illuminated discordance between the divergence of the mitochondrial and nuclear datasets.

Demographic inferences and climatic niche modelling shed light on the evolutionary history of the emblematic cold-adapted Apollo butterfly at regional scale

Cold-adapted species escape climate warming by latitudinal and/or altitudinal range shifts, and currently occur in Southern Europe in isolated mountain ranges within "sky islands". Here, we studied the genetic structure of the Apollo butterfly in five such sky islands (above 1,000 m) in France, and infer its demographic history since the last interglacial, using single nucleotide polymorphisms (ddRADseq SNPs). The Auvergne and Alps populations show strong genetic differentiation but not alpine massifs, although separated by deep valleys. Combining three complementary demographic inference methods and species distribution models (SDMs) we show that the LIG period was highly unfavourable for Apollo that probably survived in small population in the highest summits of Auvergne. The population shifted downslope and expanded eastward between LIG and LGM throughout the large climatically suitable Rhône valley between the glaciated summits of Auvergne and Alps. The Auvergne and Alps populations started diverging before the LGM but remained largely connected till the mid-Holocene. Population decline in Auvergne was more gradual but started before (~7 kya vs. 800 ya), and was much stronger with current population size ten times lower than in the Alps. In the Alps, the low genetic structure and limited evidence for isolation by distance suggest a nonequilibrium metapopulation functioning. The core Apollo population experienced cycles of contraction-expansion with climate fluctuations with largely interconnected populations overtime according to a "metapopulation-pulsar" functioning. This study demonstrates the power of combining demographic inferences and SDMs to determine past and future evolutionary trajectories of an endangered species at a regional scale.

Whole-genome re-sequencing data to infer historical demography and speciation processes in land snails: the study of two Candidula sister species

Despite the global biodiversity of terrestrial gastropods and their ecological and economic importance, the genomic basis of ecological adaptation and speciation in land snail taxa is still largely unknown. Here, we combined whole-genome re-sequencing with population genomics to evaluate the historical demography and the speciation process of two closely related species of land snails from western Europe, Candidula unifasciata and C. rugosiuscula. Historical demographic analysis indicated fluctuations in the size of ancestral populations, probably driven by Pleistocene climatic fluctuations. Although the current population distributions of both species do not overlap, our approximate Bayesian computation model selection approach on several speciation scenarios suggested that gene flow has occurred throughout the divergence process until recently. Positively selected genes diverging early in the process were associated with intragenomic and cyto-nuclear incompatibilities, respectively, potentially fostering reproductive isolation as well as ecological divergence. Our results suggested that the speciation between species entails complex processes involving both gene flow and ecological speciation, and that further research based on whole-genome data can provide valuable understanding on species divergence. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.

Double-digest RAD-sequencing: do pre- and post-sequencing protocol parameters impact biological results?

Next-generation sequencing technologies have opened a new era of research in population genetics. Following these new sequencing opportunities, the use of restriction enzyme-based genotyping techniques, such as restriction site-associated DNA sequencing (RAD-seq) or double-digest RAD-sequencing (ddRAD-seq), has dramatically increased in the last decade. From DNA sampling to SNP calling, the laboratory and bioinformatic parameters of enzyme-based techniques have been investigated in the literature. However, the impact of those parameters on downstream analyses and biological results remains less documented. In this study, we investigated the effects of sevral pre- and post-sequencing settings on ddRAD-seq results for two biological systems: a complex of butterfly species (Coenonympha sp.) and several populations of common beech (Fagus sylvatica). Our results suggest that pre-sequencing parameters (i.e., DNA quantity, number of PCR cycles during library preparation) have a significant impact on the number of recovered reads and SNPs, on the number of unique alleles and on individual heterozygosity. In the same way, we found that post-sequencing settings (i.e., clustering and minimum coverage thresholds) influenced loci reconstruction (e.g., number of loci, mean coverage) and SNP calling (e.g., number of SNPs; heterozygosity) but had only a marginal impact on downstream analyses (e.g., measure of genetic differentiation, estimation of individual admixture, and demographic inferences). In addition, replication analyses confirmed the reproducibility of the ddRAD-seq procedure. Overall, this study assesses the degree of sensitivity of ddRAD-seq data to pre- and post-sequencing protocols, and illustrates its robustness when studying population genetics.

Hybrid Speciation and Introgression Both Underlie the Genetic Structures and Evolutionary Relationships of Three Morphologically Distinct Species of Lilium (Liliaceae) Forming a Hybrid Zone Along an Elevational Gradient

We studied hybrid interactions of Lilium meleagrinum, Lilium gongshanense, and Lilium saluenense using an integrative approach combining population genetics, fieldwork, and phenological research. These three species occur along an elevational gradient, with L. meleagrinum occurring at lower elevations, L. saluenense at higher elevations, and L. gongshanense between them. The species show strong morphological differentiation despite there being no clear environmental barriers to gene flow among them. Lilium gongshanense is likely to have a hybrid origin based on our prior work, but its progenitors remain uncertain. We sought to determine whether gene flow occurs among these three parapatric species, and, if so, whether L. gongshanense is a hybrid of L. meleagrinum and/or L. saluenense. We analyzed data from multiple chloroplast genes and spacers, nuclear internal transcribed spacer (ITS), and 18 nuclear Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR) microsatellites for accessions of the three species representing dense population-level sampling. We also inferred phenology by examining species in the field and using herbarium specimens. We found that there are only two types of chloroplast genomes shared among the three species and that L. gongshanense forms two distinct groups with closest links to other species of Lilium based on ITS. Taken together, L. gongshanense is unlikely to be a hybrid species resulting from a cross between L. meleagrinum and L. saluenense, but gene flow is occurring among the three species. The gene flow is likely to be rare according to evidence from all molecular datasets, and this is corroborated by detection of only one putative hybrid individual in the field and asynchronous phenology. We suspect that the rarity of hybridization events among the species facilitates their continued genetic separation.

Genetic, morphological and ecological variation across a sharp hybrid zone between two alpine butterfly species

Identifying the mechanisms involved in the formation and maintenance of species is a central question in evolutionary biology, and distinguishing the selective drivers of populations' divergence from demographic processes is of particular interest to better understand the speciation process. Hybrid zones are recognized to provide ideal places to investigate the genetic architecture of speciation and to identify the mechanisms allowing diverging species to maintain their integrity in the face of gene flow. Here, we studied two alpine butterfly species, Coenonympha macromma and C. gardetta, which can be found flying together and hybridizing in narrow contact zones in the southern French Alps. We characterized the genomic composition of individuals, their morphology and their local habitat requirements, within and around a hybrid zone. Genetic diversity analysis at 794 SNPs revealed that all individuals within the hybrid zone were highly admixed, which was not the case outside the hybrid zone. Cline analysis showed that, despite ongoing hybridization, 56 out of 122 loci differentially fixed or nearly so between the two species were impermeable to introgression across the sharp hybrid zone (9 km wide). We also found concordance in cline position and width among genetic, morphological and environmental variation, suggesting a coupling of different reproductive barriers. Habitat characteristics such as the presence of trees and shrubs and the start of the growing season were strongly associated with the genetic variation, and we found evidence of divergence at genetic markers associated with morphology and physiology, putatively involved in visual or environmental reproductive isolation. We discuss the various behavioural and ecological factors that might interplay to maintain current levels of divergence and gene flow between this species pair.

Are you more than the sum of your parents' genes? Phenotypic plasticity in a clonal vertebrate and F1 hybrids of its parental species

All known vertebrate clones have originated from hybridization events and some have produced distinct evolutionary lineages via hybrid speciation. Amazon mollies (Poecilia formosa) present an excellent study system to investigate how clonal species have adapted to heterogeneous environments because they are the product of a single hybridization event between male sailfin mollies (Poecilia latipinna) and female Atlantic mollies (Poecilia mexicana). Here, we ask whether the hybrid species differs from the combination of its parental species' genes in its plastic response to different environments. Using a three-way factorial design, we exposed neonates produced by Amazon mollies and reciprocal F1 hybrid crosses to different thermal (24°C and 29°C) and salinity (0/2, 12, and 20 ppt) regimes. We measured various ontogenetic and life history characteristics across the life span of females. Our major results were as follows: (1) Reaction norms of growth and maturation to temperature and salinity are quite similar between the two hybrid crosses; (2) Amazon molly reaction norms were qualitatively different than the P. latipinna male and P. mexicana female (L×M) hybrids for the ontogenetic variables; (3) Amazon molly reaction norms in reproductive traits were also quite different from L×M hybrids; and (4) The reaction norms of net fertility were very different between Amazon mollies and L×M hybrids. We conclude that best locale for Amazon mollies is not the best locale for hybrids, which suggests that Amazon mollies are not just an unmodified mix of parental genes but instead have adapted to the variable environments in which they are found. Hybridization resulting in asexuality may represent an underappreciated mechanism of speciation because the unlikely events required to produce such hybrids rarely occur and is dependent upon the genetic distance between parental species.

One, two or more species? Mitonuclear discordance and species delimitation

Delimiting species boundaries is central to understand ecological and evolutionary processes, and to monitor biodiversity patterns over time and space. Yet, most of our current knowledge on animal diversity and phylogeny relies on morphological and mitochondrial (mt) DNA variation, a popular molecular marker also used as a barcode to assign samples to species. For morphologically undistinguishable sympatric species (cryptic species), the congruence of several independent markers is necessary to define separate species. Nuclear markers are becoming more accessible, and have confirmed that cryptic species are widespread in all animal phyla (Fišer, Robinson, & Malard, 2018). However, striking differences between the mitochondrial and nuclear variation patterns are also commonly found within single species. Mitonuclear discordance can result from incomplete lineage sorting, sex-biased dispersal, asymmetrical introgression, natural selection or Wolbachia-mediated genetic sweeps. But more generally, the distinct mode of transmission of these two types of markers (maternal vs. biparental) is sufficient to explain their distinct sensitivity to purely demographic events such as spatial range and population size fluctuations over time. In a From the Cover manuscript in this issue of Molecular Ecology, Hijonosa et al. (2019) show that highly divergent mtDNA lineages coexist in a widespread European butterfly (Figure 1). None of the hundreds of nuclear markers analyzed was associated with mt lineages, nor was Wolbachia variation. These findings rule out the presence of cryptic species but shed light on complex demographic history of lineage divergence/fusion during the Pleistocene climatic fluctuations, and pave the way to a better integration of both mt and nuclear information in demographic models.