Asymmetric habitat isolation and sexual isolation predicted by the cost of migration and hybridization generate novel signatures of reinforcing selection

Reinforcement is an evolutionary process whereby increased prezygotic reproductive isolation evolves in response to the cost of hybridization. Despite theory predicting that multiple prezygotic barriers can evolve via reinforcement, most empirical studies examine a single barrier. We test novel predictions for the reinforcement of both habitat isolation and sexual isolation between ecologically divergent lineages under asymmetric migration: the lineage that emigrates more should evolve stronger habitat isolation due to the lower fitness of immigrants in the alternative habitat, while the lineage that receives more immigrants should exhibit stronger sexual isolation due to the lower fitness of hybrids. We found both signatures of reinforcement in two sympatric sister species of gall wasps that are host specific to the southern live oaks, Quercus virginiana and Q. geminata, respectively. Specifically, we observed stronger habitat isolation in the species with higher emigration rates, Belonocnema treatae, and stronger sexual isolation in the species facing more immigrants, B. fossoria. In contrast, comparisons of both species to a third, allopatric, species showed that B. kinseyi exhibited both lower habitat isolation and sexual isolation than the sympatric species, consistent with the classic predictions of reinforcement. Our study provides a rare examination of the interplay of ecology and geography in the evolution of multiple reproductive barriers to gene flow. Given that asymmetric migration between ecologically divergent lineages increasingly appears to be the rule rather than the exception, concomitant asymmetries in the strength of habitat and sexual isolation could be more widespread than currently understood.

Patterns of regulatory divergence and gene expression in hybrids are associated with molecular evolution in species undergoing gene flow

The extent to which hybridization disrupts a gene's pattern of expression likely governs its propensity for introgression, while its extent of molecular divergence can itself underlie such disruption. Together, these phenomena shape the landscape of sequence and transcriptional divergence across the genome as species diverge. To understand this process, we examine gene expression inheritance, regulatory and molecular divergences in the reproductive transcriptomes of species linked by gene flow. The fruit flies Anastrepha fraterculus and A. obliqua show evidence of gene flow despite clear evolutionary divergence and incomplete reproductive isolation. We find that their transcriptional patterns are a mosaic between those typically observed within and between allopatric species. Genes showing transgressive expression in hybrids or cis-regulatory divergence between species are associated with greater molecular divergence. This may reflect pleiotropic constraints that make them more resistant to gene flow or they may be more likely to experience divergent selection. However, while these highly divergent genes are likely to be important contributors to species differences, they are relatively rare. Instead, most differentially regulated genes, including those linked to reproduction, show high degrees of dominance in hybrids and trans-regulated divergence between species, suggesting widespread genetic compatibility that allowed for the identified introgression. These findings provide insights into how postzygotic isolating mechanisms might evolve in the presence of gene flow: regions showing cis-regulatory divergence or transgressive expression contribute to reproductive isolation, while regions with dominant expression and trans-regulatory divergence act as a buffer of hybrid breakdown, facilitating introgression, and leading to a genomic mosaic of expression and sequence divergence.

Intraspecific structure of the Coregonus lavaretus complex in water bodies of Siberia: a case of postglacial allopatric origin of Yukagirian whitefish

The results of morphological and genetic analyses of forms/species of the Coregonus lavaretus pidschian (Gmelin, 1789) complex from the Indigirka and Kolyma river basins are presented in the context of there being recent postglacial speciation events. It has been found that the studied whitefishes belong to the sparsely rakered and low lateral-line forms and have previously been described as Coregonus lavaretus pidschian n. jucagiricus Drjagin (Berg), 1932. Based on these characters, this whitefish does not differ from most Arctic whitefish populations (in particular from Coregonus lavaretus glacialis Kirillov, 1972). Analysis of variability of the ND1 gene (mtDNA) showed that whitefishes from the Indigirka and Kolyma basins belong to a distant phylogenetic lineage, which is significantly different from all previously studied whitefish lineages from the Ob, Yenisei, Lena, Anadyr, and Amur river basins. Analysis of variability of the ITS1 fragment (nDNA) showed that all studied forms/species (from Ob River to Amur River basins), including C. l. pidschian n. jucagiricus, have a tandem arrangement of two identical nucleotide fragments and very similar nucleotide composition of the ITS1 region. Based on contemporary data, this phylogenetic lineage of the C. pidschian complex could be considered a young postglacial allopatric species.

The Genealogical Divergence Index Across a Speciation Continuum in Hercules Beetles

The genealogical divergence index (gdi) was developed to aid in molecular species delimitation under the multispecies coalescent model, which has been shown to delimit genetic structures but not necessarily species. Although previous studies have used meta-analyses to show that gdi could be informative for distinguishing taxonomically good species, the biological and evolutionary implications of divergences showing different gdi values have yet to be studied. I showed that an increase in gdi value was correlated with later stages of divergence further along a speciation continuum in an Amazonian Hercules beetle system. Specifically, a gdi value of 0.7 or higher was associated with diverge between biological species that can coexist in geographic proximity while maintaining their evolutionary independence. Divergences between allopatric species that were conventionally given subspecific status, such as geographic taxa that may or may not be morphologically divergent, had gdi values that fell within the species delimitation ambiguous zone (0.2 < gdi < 0.7). However, the results could be drastically affected by the sampling design, i.e., the choice of different geographic populations and the lumping of distinct genetic groups when running the analyses. Different gdi values may prove to be biologically and evolutionarily informative should additional speciation continua from different empirical systems be investigated, and the results obtained may help with objectively delimiting species in the era of integrative taxonomy.

Population genetics meets phylogenetics: new insights into the relationships among members of the genus Euthynnus (family Scombridae)

Euthynnus (family Scombridae) is a genus of marine pelagic fish species with a worldwide distribution that comprises three allopatric species: E. alletteratus, E. affinis and E. lineatus. All of them targeted by artisanal and commercial fisheries. We analyzed 263 individuals from Atlantic and Pacific Oceans using two genetic markers, the mtDNA Control Region (350 bp) and nuclear calmodulin (341 bp). The results obtained challenge the phylogeny of this group. We found a deep genetic divergence, probably at species level, within E. alletteratus, between the North Atlantic-Mediterranean and the Tropical East Atlantic. This deep genetic divergence was tested with several species delimitation methods. This complete phylogeographic association between the North Atlantic and the Tropical East Atlantic support the hypothesis of two cryptic species. In addition, population genetic heterogeneity was detected between the North East Atlantic–Mediterranean and North West Atlantic regions. Our results indicate two scales of differentiation in what is currently considered a single population. Accordingly, for management purposes, the populations of E. alletteratus, should be divided into a minimum of three management units. On the other hand, the high level of differentiation found in E. alletteratus contrasts with the shallow genetic divergence of E. affinis and E. lineatus.

Multilocus phylogeography and ecological niche modeling suggest speciation with gene flow between the two Bamboo Partridges

BackgroundUnderstanding how species diversify is a long-standing question in biology. The allopatric speciation model is a classic hypothesis to explain the speciation process. This model supposes that there is no gene flow during the divergence process of geographically isolated populations. On the contrary, the speciation with gene flow model supposes that gene flow does occur during the speciation process. Whether allopatric species have gene flow during the speciation process is still an open question.MethodsWe used the genetic information from 31 loci of 24 Chinese Bamboo Partridges (Bambusicola thoracicus) and 23 Taiwan Bamboo Partridges (B. sonorivox) to infer the gene flow model of the two species, using the approximate Bayesian computation (ABC) model. The ecological niche model was used to infer the paleo-distribution during the glacial period. We also tested whether the two species had a conserved ecological niche by means of a background similarity test.ResultsThe genetic data suggested that the post-divergence gene flow between the two species was terminated before the mid-Pleistocene. Furthermore, our ecological niche modeling suggested that their ecological niches were highly conserved, and that they shared an overlapping potential distribution range in the last glacial maximum.ConclusionsThe allopatric speciation model cannot explain the speciation process of the two Bamboo Partridges. The results of this study supported a scenario in which speciation with gene flow occurring between the allopatric species and have contributed to our understanding of the speciation process.

Phylogeography and distribution of the freshwater razor clams Novaculina myanmarensis and N. gangetica in Myanmar, with notes on two doubtful nominal taxa described as Novaculina members (Bivalvia: Pharidae)

The razor clam genus Novaculina Benson, 1830 (Bivalvia: Pharidae: Pharellinae) is a group of secondary freshwater bivalves. Four allopatric species in this genus are distributed throughout Asian freshwater drainages from the Ganges River in India to the Yangtze River in China. Here, we present several new occurrences of Novaculina myanmarensis and N. gangetica from Myanmar that were confirmed by means of a molecular approach. These occurrences expand our knowledge on the ranges of both species. Furthermore, we compiled an updated distribution map for all the species in this genus. Our phylogeographic research suggests that Novaculina myanmarensis colonized the Ayeyarwady Basin from rivers of the Salween Estuary (Donthami and Ataran rivers) during the Late Pleistocene. Conversely, Novaculina gangetica populations from Myanmar does not demonstrate any clear phylogeographic structure. At first glance, this pattern can also be caused by a (sub)recent (Pleistocene) immigration into coastal rivers of western Myanmar from the Ganges Basin, although this preliminary hypothesis is yet to be confirmed using DNA sequences of samples from India and Bangladesh. Finally, the taxonomic status of two doubtful nominal taxa initially described as Novaculina members is discussed, i.e. N. gangetica theobaldi Hanley & Theobald, 1874 and N. andamanensis Preston, 1908. These taxa are considered junior subjective synonyms of the estuarine bivalve species Cultellus maximus (Gmelin, 1791) (Pharidae) and Azorinus coarctatus (Gmelin, 1791) (Solecurtidae), respectively.

Genetic insights into the globally invasive and taxonomically problematic tree genus Prosopis

Accurate taxonomic identification of alien species is crucial to detect new incursions, prevent or reduce the arrival of new invaders and implement management options such as biological control. Globally, the taxonomy of non-native Prosopis species is problematic due to misidentification and extensive hybridization. We performed a genetic analysis on several Prosopis species, and their putative hybrids, including both native and non-native populations, with a special focus on Prosopis invasions in Eastern Africa (Ethiopia, Kenya and Tanzania). We aimed to clarify the taxonomic placement of non-native populations and to infer the introduction histories of Prosopis in Eastern Africa. DNA sequencing data from nuclear and chloroplast markers showed high homology (almost 100%) between most species analysed. Analyses based on seven nuclear microsatellites confirmed weak population genetic structure among Prosopis species. Hybrids and polyploid individuals were recorded in both native and non-native populations. Invasive genotypes of P. juliflora in Kenya and Ethiopia could have a similar native Mexican origin, while Tanzanian genotypes likely are from a different source. Native Peruvian Prosopis pallida genotypes showed high similarity with non-invasive genotypes from Kenya. Levels of introduced genetic diversity, relative to native populations, suggest that multiple introductions of P. juliflora and P. pallida occurred to Eastern Africa. Polyploidy may explain the successful invasion of P. juliflora in Eastern Africa. The polyploid Prosopis juliflora was highly differentiated from the rest of the (diploid) species within the genus. The lack of genetic differentiation between most diploid species in their native ranges supports the notion that hybridization between allopatric species may occur frequently when they are co-introduced into non-native areas. For regulatory purposes, we propose to treat diploid Prosopis taxa from the Americas as a single taxonomic unit in non-native ranges.

High cryptic diversity in the kleptoparasitic genus Hyalorisia Dall, 1889 (Littorinimorpha: Capulidae) with the description of nine new species from the Indo-West Pacific

ABSTRACT Species in the family Capulidae (Littorinimorpha: Capuloidea) display a wide range of shell morphologies. Several species are known to live in association with other benthic invertebrates—mostly bivalves and sabellid worms, but also other gastropods—and are believed to be kleptoparasitic filter feeders that take advantage of the water current produced by the host. This peculiar trophic ecology, implying a sedentary lifestyle, has resulted in highly convergent shell forms. This is particularly true for the genus Hyalorisia Dall, 1889, which occurs in deep water in the Caribbean and Indo-West Pacific provinces, with two nominal species recognized so far. Combining morphological, ecological and molecular data, we assessed the diversity of the genus, its phylogenetic position inside the family and its association with its bivalve host, the genus Propeamussium de Gregorio, 1884 (Pectinoidea), resulting in the description of nine new cryptic species. When sympatric, species of Hyalorisia are associated with different host species, but the same species of Propeamussium may be the host of several allopatric species of Hyalorisia.

Immunoreactivity and neutralization capacity of Philippine cobra antivenom against Naja philippinensis and Naja samarensis venoms

Background The Philippine cobra (Naja philippinensis) and Samar cobra (Naja samarensis) are two WHO Category 1 medically important venomous snakes in the Philippines. Philippine cobra antivenom (PCAV) is the only antivenom available in the country, but its neutralization capacity against the venoms of N. philippinensis and hetero-specific N. samarensis has not been reported. This knowledge gap greatly hinders the optimization of antivenom use in the region. Methods This study examined the immunological binding and neutralization capacity of PCAV against the two cobra venoms using WHO-recommended protocols. Results In mice, both venoms were highly neurotoxic and lethal with a median lethal dose of 0.18 and 0.20 µg/g, respectively. PCAV exhibited strong and comparable immunoreactivity toward the venoms, indicating conserved venom antigenicity between the two allopatric species. In in vivo assay, PCAV was only moderately effective in neutralizing the toxicity of both venoms. Its potency was even lower against the hetero-specific N. samarensis venom by approximately two-fold compared with its potency against N. philippinensis venom. Conclusion The results indicated that PCAV could be used to treat N. samarensis envenomation but at a higher dose, which might increase the risk of hypersensitivity and worsen the shortage of antivenom supply in the field. Antivenom manufacturing should be improved by developing a low-dose, high-efficacy product against cobra envenomation.