Possible incipient sympatric ecological speciation in blind mole rats (Spalax)

Conservation status of the blind mole rat populations in Hungary (Rodentia: Spalacinae: Nannospalax) revisited

Regular reviews of long-term research and conservation programs are useful sources of information for future directions in science and for the assessment of current conservation status of taxa. In this paper, we compiled all available data from the last 10 years related to Hungarian blind mole rat populations and assessed this information according to the following main themes: systematics, distribution and threats, and conservation actions. Based on the most recent information, national and global risk assessments are provided for the three species of Nannospalax (N. montanosyrmiensis, N. hungaricus and N. syrmiensis), currently accepted as part of the Hungarian fauna.

Thermal biology in the Upper Galili Mountain blind mole rat (Nannospalax galili) and an overview of spalacine energetics

Several hundred mammalian species thrive in complex burrow systems, which protect them from climatic extremes and predation. At the same time, it is also a stressful environment due to low food supply, high humidity, and, in some cases, a hypoxic and hypercapnic atmosphere. To face such conditions, subterranean rodents have convergently evolved low basal metabolic rate, high minimal thermal conductance and low body temperature. Although these parameters have been intensively studied in the last decades, such information is far from being well-known in one of the most studied groups of subterranean rodents, the blind mole rats of the genus Nannospalax. The lack of information is particularly noticeable for parameters such as the upper critical temperature and the width of the thermoneutral zone. In our study, we analysed the energetics of the Upper Galilee Mountain blind mole rat Nannospalax galili and found its basal metabolic rate of 0.84 ± 0.10 mL O₂×g^-1 × h^-1, thermoneutral zone between 28 and 35 °C, mean T_b within the zone of 36.3 ± 0.6 °C, and minimal thermal conductance equal to 0.082 mL O₂×g^-1 × h^-1 × C^-1. Nannospalax galili is a truly homeothermic rodent well adapted to face lower ambient temperatures, because its T_b was stable down to the lowest temperature measured (10 °C). At the same time, a relatively high basal metabolic rate and relatively low minimal thermal conductance for a subterranean rodent of such body mass, and the difficulty of surviving ambient temperatures slightly above upper critical temperature, indicates problems with sufficient heat dissipation at higher temperatures. This can easily lead to overheating, that is relevant mainly during the hot-dry season. These findings suggest that N. galili can be threatened by ongoing global climate change.

Sympatric Speciation in Mole Rats and Wild Barley and Their Genome Repeatome Evolution: A Commentary

The theories of sympatric speciation (SS) and coding and noncoding (cd and ncd =repeatome)  genome function are still contentious. Studies on SS in our two new models, "Evolution Canyon" and "Evolution Plateau", in Israel, divergent microclimatically and geologically-edaphically, respectively, indicated that in ecologically divergent microsites SS is a common speciation model across life from bacteria to mammals. Genomically, the intergenic ncd repeatome was and is still regarded by many biologists as "selfish," "junk," and non-functional. In contrast, it is considered by the encyclopedia of DNA elements discovery as biochemically functional and regulatory, and the transposable elements were considered earlier by Barbara McClintock as "controlling elements" of genes. Remarkably, it is found that repeated elements can statistically identify significantly, the five species of subterranean mole rats of Spalax ehrenbergi superspecies adapted to increasingly arid climatic trend southward in Israel. Moreover, it is first discovered in the SS studies in two distant taxa, subterranean mole rats and wild barley, and later also in spiny mice in Israel and subterranean zokors in China, that the noncoding repeatome is genomically mirroring the image of the protein-coding genome in divergent ecologies. It is shown that this mirroring image is statistically significant both within and between the ecologically divergent taxa supporting the hypothesis that much of the repeatome might be regulatory and selected as the protein-coding genome by the same ecological stresses.

Host diet shapes functionally differentiated gut microbiomes in sympatric speciation of blind mole rats in Upper Galilee, Israel

The gut microbiome is important for host nutrient metabolism and ecological adaptation. However, how the gut microbiome is affected by host phylogeny, ecology and diet during sympatric speciation remain unclear. Here, we compare and contrast the gut microbiome of two sympatric blind mole rat species and correlate them with their corresponding host phylogeny, ecology soil metagenomes, and diet to determine how these factors may influence their gut microbiome. Our results indicate that within the host microbiome there is no significant difference in community composition, but the functions between the two sympatric species populations vary significantly. No significant correlations were found between the gut microbiome differentiation and their corresponding ecological soil metagenomes and host phylogeny. Functional enrichment analysis suggests that the host diets may account for the functional divergence of the gut microbiome. Our results will help us understand how the gut microbiome changes with corresponding ecological dietary factors in sympatric speciation of blind subterranean mole rats.

Incipient Sympatric Speciation and Evolution of Soil Bacteria Revealed by Metagenomic and Structured Non-Coding RNAs Analysis

Simple Summary

The microevolutionary dynamics of soil bacteria under microclimatic differences are largely unexplored in contrast to our improving knowledge of their vast diversity. In this study, we performed a comparative metagenomic analysis of two sharply divergent rocks and soil types at the Evolution Plateau (EP) in eastern Upper Galilee, Israel. We have identified the significant differences in bacterial taxonomic diversity, functions, and patterns of RNA-based gene regulation between the bacteria from two different soil types. Furthermore, we have identified several species with a significant genetic divergence of the same species between the two soil types, highlighting the soil bacteria’s incipient sympatric speciation.

Abstract

Soil bacteria respond rapidly to changes in new environmental conditions. For adaptation to the new environment, they could mutate their genome, which impacts the alternation of the functional and regulatory landscape. Sometimes, these genetic and ecological changes may drive the bacterial evolution and sympatric speciation. Although sympatric speciation has been controversial since Darwin suggested it in 1859, there are several strong theoretical or empirical evidences to support it. Sympatric speciation associated with soil bacteria remains largely unexplored. Here, we provide potential evidence of sympatric speciation of soil bacteria by comparison of metagenomics from two sharply contrasting abutting divergence rock and soil types (Senonian chalk and its rendzina soil, and abutting Pleistocene basalt rock and basalt soil). We identified several bacterial species with significant genetic differences in the same species between the two soil types and ecologies. We show that the bacterial community composition has significantly diverged between the two soils; correspondingly, their functions were differentiated in order to adapt to the local ecological stresses. The ecologies, such as water availability and pH value, shaped the adaptation and speciation of soil bacteria revealed by the clear-cut genetic divergence. Furthermore, by a novel analysis scheme of riboswitches, we highlight significant differences in structured non-coding RNAs between the soil bacteria from two divergence soil types, which could be an important driver for functional adaptation. Our study provides new insight into the evolutionary divergence and incipient sympatric speciation of soil bacteria under microclimatic ecological differences.

Sympatric speciation of the spiny mouse from Evolution Canyon in Israel substantiated genomically and methylomically

SignificanceWhether sympatric speciation (SS) is rare or common is still debated. Two populations of the spiny mouse, Acomys cahirinus, from Evolution Canyon I (EC I) in Israel have been depicted earlier as speciating sympatrically by molecular markers and transcriptome. Here, we investigated SS both genomically and methylomically, demonstrating that the opposite populations of spiny mice are sister taxa and split from the common ancestor around 20,000 years ago without an allopatric history. Mate choice, olfactory receptors, and speciation genes contributed to prezygotic/postzygotic reproductive isolation. The two populations showed different methylation patterns, facilitating adaptation to their local environment. They cope with abiotic and biotic stresses, due to high solar interslope radiation differences. We conclude that our new genomic and methylomic data substantiated SS.

Adaptation of mammals to hypoxia

Oxygen plays a pivotal role in the metabolism and activities of mammals. However, oxygen is restricted in some environments-subterranean burrow systems or habitats at high altitude or deep in the ocean-and this could exert hypoxic stresses such as oxidative damage on organisms living in these environments. In order to cope with these stresses, organisms have evolved specific strategies to adapt to hypoxia, including changes in physiology, gene expression regulation, and genetic mutations. Here, we review how mammals have adapted to the three high-altitude plateaus of the world, the limited oxygen dissolved in deep water habitats, and underground tunnels, with the aim of better understanding the adaptation of mammals to hypoxia.

Multi-Omics Analysis Reveals the Mechanism Underlying the Edaphic Adaptation in Wild Barley at Evolution Slope (Tabigha)

At the microsite "Evolution Slope", Tabigha, Israel, wild barley (Hordeum spontaneum) populations adapted to dry Terra Rossa soil, and its derivative abutting wild barley population adapted to moist and fungi-rich Basalt soil. However, the mechanisms underlying the edaphic adaptation remain elusive. Accordingly, whole genome bisulfite sequencing, RNA-sequencing, and metabolome analysis are performed on ten wild barley accessions inhabiting Terra Rossa and Basalt soil. A total of 121 433 differentially methylated regions (DMRs) and 10 478 DMR-genes are identified between the two wild barley populations. DMR-genes in CG context (CG-DMR-genes) are enriched in the pathways related with the fundamental processes, and DMR-genes in CHH context (CHH-DMR-genes) are mainly associated with defense response. Transcriptome and metabolome analysis reveal that the primary and secondary metabolisms are more active in Terra Rossa and Basalt wild barley populations, respectively. Multi-omics analysis indicate that sugar metabolism facilitates the adaptation of wild barley to dry Terra Rossa soil, whereas the enhancement of phenylpropanoid/phenolamide biosynthesis is beneficial for wild barley to inhabit moist and fungi pathogen-rich Basalt soil. The current results make a deep insight into edaphic adaptation of wild barley and provide elite genetic and epigenetic resources for developing barley with high abiotic stress tolerance.

Local adaptation of bitter taste and ecological speciation in a wild mammal

Sensory systems are attractive evolutionary models to address how organisms adapt to local environments that can cause ecological speciation. However, tests of these evolutionary models have focused on visual, auditory, and olfactory senses. Here, we show local adaptation of bitter taste receptor genes in two neighboring populations of a wild mammal—the blind mole rat Spalax galili—that show ecological speciation in divergent soil environments. We found that basalt-type bitter receptors showed higher response intensity and sensitivity compared with chalk-type ones using both genetic and cell-based functional analyses. Such functional changes could help animals adapted to basalt soil select plants with less bitterness from diverse local foods, whereas a weaker reception to bitter taste may allow consumption of a greater range of plants for animals inhabiting chalk soil with a scarcity of food supply. Our study shows divergent selection on food resources through local adaptation of bitter receptors, and suggests that taste plays an important yet underappreciated role in speciation.

Resource partitioning is not coupled with assortative mating in sympatrically divergent ricefish in a Wallacean ancient lake

Sympatric speciation is considered to be difficult without the coupling between ecological traits that allow resource partitioning and reproductive traits that allow assortative mating. Such "magic traits" are known to be involved in most of the compelling examples of sympatric speciation. In this study, we report a possible case of sympatric speciation without magic traits. Three species of ricefish (genus Oryzias) are suggested to have diverged sympatrically within Lake Poso, an ancient lake in Sulawesi. An analysis of genome-wide single-nucleotide polymorphisms showed that these three species are reproductively isolated from each other throughout the lake. Stable isotope analyses revealed that the three species use different food resources, which reflect differences in their feeding morphologies (gill rakers and digestive tracts) and feeding sites. Field and laboratory observations showed that O. nebulosus and O. orthognathus share a mating habitat of cobbles, where they scatter fertilized eggs, whereas this site is never used by O. nigrimas, indicating that assortative mating is partly achieved by spatial isolation. The small, less-adhesive eggs of O. nebulosus and O. orthognathus probably reflect their adaptation to spawning on cobble beaches. Laboratory mating experiments showed strong prezygotic isolation between O. nebulosus and O. orthognathus, which is achieved by strong species recognition presumably by both sexes based on species-specific mating dances and nuptial coloration. In summary, the assortative mating of O. nebulosus and O. orthognathus is probably not coupled to resource partitioning. We discussed how sympatric speciation among these species might have been achieved even without magic traits.

Genome evolution of blind subterranean mole rats: Adaptive peripatric versus sympatric speciation

Speciation mechanisms remain controversial. Two speciation models occur in Israeli subterranean mole rats, genus Spalax: a regional speciation cline southward of four peripatric climatic chromosomal species and a local, geologic-edaphic, genic, and sympatric speciation. Here we highlight their genome evolution. The five species were separated into five genetic clusters by single nucleotide polymorphisms, copy number variations (CNVs), repeatome, and methylome in sympatry. The regional interspecific divergence correspond to Pleistocene climatic cycles. Climate warmings caused chromosomal speciation. Triple effective population size, N _e , declines match glacial cold cycles. Adaptive genes evolved under positive selection to underground stresses and to divergent climates, involving interspecies reproductive isolation. Genomic islands evolved mainly due to adaptive evolution involving ancient polymorphisms. Repeatome, including both CNV and LINE1 repetitive elements, separated the five species. Methylation in sympatry identified geologically chalk-basalt species that differentially affect thermoregulation, hypoxia, DNA repair, P53, and other pathways. Genome adaptive evolution highlights climatic and geologic-edaphic stress evolution and the two speciation models, peripatric and sympatric.

Genomic and Phenotypic Divergence in Wild Barley Driven by Microgeographic Adaptation

Microgeographic adaptation is a fundamental driving force of evolution, but the underlying causes remain undetermined. Here, the phenotypic, genomic and transcriptomic variations of two wild barley populations collected from sharply divergent and adjacent micro-geographic sites to identify candidate genes associated with edaphic local adaptation are investigated. Common garden and reciprocal transplant studies show that large phenotypic differentiation and local adaptation to soils occur between these populations. Genetic, phylogenetic and admixture analyses based on population resequencing show that significant genetic divergences occur between basalt and chalk populations. These divergences are consistent with the phenotypic variations observed in the field. Genome sweep analyses reveal 162.7 Mb of selected regions driven by edaphic local adaptation, in which 445 genes identified, including genes associated with root architecture, metal transport/detoxification, and ABA signaling. When the phenotypic, genomic and transcriptomic data are combined, HvMOR, encoding an LBD transcription factor, is determined to be the vital candidate for regulating the root architecture to adapt to edaphic conditions at the microgeographic scale. This study provides new insights into the genetic basis of edaphic adaptation and demonstrates that edaphic factors may contribute to the evolution and speciation of barley.

Vertebrate Chromosome Evolution

The study of chromosome evolution is undergoing a resurgence of interest owing to advances in DNA sequencing technology that facilitate the production of chromosome-scale whole-genome assemblies de novo. This review focuses on the history, methods, discoveries, and current challenges facing the field, with an emphasis on vertebrate genomes. A detailed examination of the literature on the biology of chromosome rearrangements is presented, specifically the relationship between chromosome rearrangements and phenotypic evolution, adaptation, and speciation. A critical review of the methods for identifying, characterizing, and visualizing chromosome rearrangements and computationally reconstructing ancestral karyotypes is presented. We conclude by looking to the future, identifying the enormous technical and scientific challenges presented by the accumulation of hundreds and eventually thousands of chromosome-scale assemblies.

Incipient sympatric speciation in wild barley caused by geological-edaphic divergence

Sympatric speciation is still contentious but here based on genome-wide analysis; we show incipient sympatric speciation of an emerging new wild barley species from Hordeum spontaneum, the progenitor of all cultivated barleys at “Evolution Plateau” (EP), Upper Galilee, Israel.

Sympatric speciation (SS) has been contentious since the idea was suggested by Darwin. Here, we show in wild barley SS due to geologic and edaphic divergence in “Evolution Plateau,” Upper Galilee, Israel. Our whole genome resequencing data showed SS separating between the progenitor old Senonian chalk and abutting derivative young Pleistocene basalt wild barley populations. The basalt wild barley species unfolds larger effective population size, lower recombination rates, and larger genetic diversity. Both species populations show similar descending trend ∼200,000 yr ago associated with the last glacial maximum. Coalescent demography analysis indicates that SS was local, primary, in situ, and not due to a secondary contact from ex situ allopatric population. Adaptive divergent putatively selected genes were identified in both populations. Remarkably, disease resistant genes were selected in the wet basalt population, and genes related to flowering time, leading to temporal reproductive isolation, were selected in the chalk population. The evidence substantiates adaptive ecological SS in wild barley, highlighting the genome landscape during SS with gene flow, due to geologic-edaphic divergence.

Transcriptome-Wide Patterns of the Genetic and Expression Variations in Two Sympatric Schizothoracine Fishes in a Tibetan Plateau Glacier Lake

Sympatric speciation remains a central focus of evolutionary biology. Although some evidence shows speciation occurring in this way, little is known about the gene expression evolution and the characteristics of population genetics as species diverge. Two closely related Gymnocypris fish (Gymnocypris chui and Gymnocypris scleracanthus), which come from a small glacier lake in the Tibetan Plateau, Lake Langcuo, exist a possible incipient sympatric adaptive ecological speciation. We generated large amounts of RNA-Seq data from multiple individuals and tissues from each of the two species and compared gene expression patterns and genetic polymorphisms between them. Ordination analysis separated samples by organ rather than by species. The degree of expression difference between organs within and between species was different. Phylogenetic analyses indicated that the two closely related taxa formed a monophyletic complex. Population structure analysis displayed two distinctly divergent clusters of G. chui and G. scleracanthus populations. By contrast, G. scleracanthus population genetic diversity is higher than that of G. chui. Considerable sites of the two populations were differentiated with a coefficient of F_ST = 0.25–0.50, implying that a small proportion of loci nevertheless exhibited deep divergence in two comparisons. Concomitantly, putatively selected genes during speciation revealed functional categories are enriched in bone morphogenesis, cell growth, neurogenetics, enzyme activity, and binding activity in G. chui population. In contrast, nutrition and localization were highlighted in G. scleracanthus. Collectively, morphological traits and dietary preference combine with genetic variation and expression variation, probably contributed to the incipient speciation of two sympatric populations.

Phylogeny and biogeography of the African Bathyergidae: a review of patterns and processes

Background

We review genealogical relationships, biogeographic patterns and broad historical drivers of speciation within the Bathyergidae, a group of endemic African rodents, as well as identify key taxa which need further research.

Methods

We sourced comparable cytochrome b sequence data (comparable data available for all members for the Family) and geographic information for all six genera of the African subterranean rodent. This information was combined into the most comprehensive and geographically representative evolutionary study for the Bathyergidae to date.

Results

Species richness within the Bathyergidae appears to be underestimated, with undescribed taxa in five of the six genera. Biogeographic patterns suggest large historical distributions, which were repeatedly fragmented by major landscape changes (especially rifting, uplift and drainage evolution) since the Miocene. Aside from vicariant events, other factors (ecological specialization, population-level responses and climatic change) may have been instrumental in driving divergences in the Bathyergidae. As such, adaptive differences may exist among both populations and species across their discrete ranges, driving independent evolutionary trajectories among taxa. In addition, highly fragmented distributions of divergent (and often relict) lineages indicates the possibility of narrow endemics restricted to diminishing suitable habitats. From this, it is clear that a systematic revision of the Bathyergidae is necessary; such a revision should include comprehensive sampling of all putative taxa, the addition of genomic information to assess adaptive differences, as well as ecological information.

Speciation in Howea Palms Occurred in Sympatry, Was Preceded by Ancestral Admixture, and Was Associated with Edaphic and Phenological Adaptation

Howea palms are viewed as one of the most clear-cut cases of speciation in sympatry. The sister species Howea belmoreana and H. forsteriana are endemic to the oceanic Lord Howe Island, Australia, where they have overlapping distributions and are reproductively isolated mainly by flowering time differences. However, the potential role of introgression from Australian mainland relatives had not previously been investigated, a process that has recently put other examples of sympatric speciation into question. Furthermore, the drivers of flowering time-based reproductive isolation remain unclear. We sequenced an RNA-seq data set that comprehensively sampled Howea and their closest mainland relatives (Linospadix, Laccospadix), and collected detailed soil chemistry data on Lord Howe Island to evaluate whether secondary gene flow had taken place and to examine the role of soil preference in speciation. D-statistics analyses strongly support a scenario whereby ancestral Howea hybridized frequently with its mainland relatives, but this only occurred prior to speciation. Expression analysis, population genetic and phylogenetic tests of selection, identified several flowering time genes with evidence of adaptive divergence between the Howea species. We found expression plasticity in flowering time genes in response to soil chemistry as well as adaptive expression and sequence divergence in genes pleiotropically linked to soil adaptation and flowering time. Ancestral hybridization may have provided the genetic diversity that promoted their subsequent adaptive divergence and speciation, a process that may be common for rapid ecological speciation.

Transcriptomes Divergence of Ricotia lunaria Between the Two Micro-Climatic Divergent Slopes at "Evolution Canyon" I, Israel

As one of the hotspot regions for sympatric speciation studies, Evolution Canyon (EC) became an ideal place for its high level of microclimatic divergence interslopes. In this study, to highlight the genetic mechanisms of sympatric speciation, phenotypic variation on flowering time and transcriptomic divergence were investigated between two ecotypes of Ricotia lunaria, which inhabit the opposite temperate and tropical slopes of EC I (Lower Nahal Oren, Mount Carmel, Israel) separated by 100 m at the bottom of the slopes. Growth chamber results showed that flowering time of the ecotype from south-facing slope population # 3 (SFS 3) was significantly 3 months ahead of the north-facing slope population # 5 (NFS 5). At the same floral development stage, transcriptome analysis showed that 1,064 unigenes were differentially expressed between the two ecotypes, which enriched in the four main pathways involved in abiotic and/or biotic stresses responses, including flavonoid biosynthesis, α-linolenic acid metabolism, plant-pathogen interaction and linoleic acid metabolism. Furthermore, based on Ka/Ks analysis, nine genes were suggested to be involved in the ecological divergence between the two ecotypes, whose homologs functioned in RNA editing, ABA signaling, photoprotective response, chloroplasts protein-conducting channel, and carbohydrate metabolism in Arabidopsis thaliana. Among them, four genes, namely, SPDS1, FCLY, Tic21 and BGLU25, also showed adaptive divergence between R. lunaria and A. thaliana, suggesting that these genes could play an important role in plant speciation, at least in Brassicaceae. Based on results of both the phenotype of flowering time and comparative transcriptome, we hypothesize that, after long-time local adaptations to their interslope microclimatic environments, the molecular functions of these nine genes could have been diverged between the two ecotypes. They might differentially regulate the expression of the downstream genes and pathways that are involved in the interslope abiotic stresses, which could further diverge the flowering time between the two ecotypes, and finally induce the reproductive isolation establishment by natural selection overruling interslope gene flow, promoting sympatric speciation.

Steppe rodents at the edge of their range: A case study of Spalax microphthalmus in the north of Ukraine

Based on results obtained during 2000–2018 by field research, polls of colleagues, and OSINT analysis, features of distribution of the greater mole rat Spalax microphthalmus in the eastern forest steppe of Ukraine were considered. The studied part of the species’ range is unique and represents the northern range edge of the entire Spalacidae family and of European steppe faunal assemblages in general. In total, data on 146 record localities were amassed, including 13 localities in the fragmented and 133 in the continuous part of the range. The offshoots of the Central Russian Upland in the valley of the Psel river (east of Sumy Oblast) are the sites with the highest density of settlements, while the species’ type biotopes are steppe balka slopes. The abundance of the greater mole rat decreased from the east to the west, and its colonies are the most fragmented along the Dnipro River. The species occurs in steppe and meadow habitats of an area of at least 20–50 ha. Analysis of the current and former distribution of the greater mole rat revealed that the species range contracts from the west; earlier it was a common species in different regions of the Middle Dnipro Area (including Kyiv city), but the current range edge runs along the line connecting Buryn – Nedryhailiv – Lokhvytsia – Myrhorod – Hadiach – Zinkiv – Zaliznychne. Isolated settlements exist in adjacent territories, particularly in Ichnia Raion of Chernihiv Oblast, and Lubny, Khorol, and Kobeliaky Raions of Poltava Oblast. The study showed that the species’ range contracted by two times to 35,000 km2 for the last 100 years, which includes only 430,000 ha of suitable habitats (15% of the range), allowing the existence here of 86,000–215,000 individuals. In fact, the species remained only in habitats that have been minimally affected by arable farming and other forms of active agricultural use. Besides, the species shows a clear confinement to habitats located near human settlements such as untilled lands, pastures with moderate grazing, waste and neglected lands, which constitute a separate group of transformed and semi-natural habitats. Formally, this allows the greater mole rat to be considered as a synanthropic species, because its inhabited biotopes, beside the zone of offshoots of the Central Russian Upland, have remained only near villages and along roads. The species also has an important biocoenotic role due to its burrowing activity and as prey of predatory birds (e.g., of the long-legged buzzard and Eurasian eagle owl) and mammals. The feeding period of the offspring of these predators generally coincides with the aboveground activity of mole rats, which lasts during May–July with a peak in June. Aboveground activity is mainly related to the resettlement of mole rats to new sites and dispersal of the young, due to which they became victims of predators.

Mito-nuclear discordance across a recent contact zone for California voles

To examine the processes that maintain genetic diversity among closely related taxa, we investigated the dynamics of introgression across a contact zone between two lineages of California voles (Microtus californicus). We tested the prediction that introgression of nuclear loci would be greater than that for mitochondrial loci, assuming ongoing gene flow across the contact zone. We also predicted that genomic markers would show a mosaic pattern of differentiation across this zone, consistent with genomes that are semi-permeable. Using mitochondrial cytochrome b sequences and genome-wide loci developed via ddRAD-seq, we analyzed genetic variation for 10 vole populations distributed along the central California coast; this transect included populations from within the distributions of both parental lineages as well as the putative contact zone. Our analyses revealed that (1) the two lineages examined are relatively young, having diverged ca. 8.5-54 kya, (2) voles from the contact zone in Santa Barbara County did not include F1 or early generation backcrossed individuals, and (3) there appeared to be little to no recurrent gene flow across the contact zone. Introgression patterns for mitochondrial and nuclear markers were not concordant; only mitochondrial markers revealed evidence of introgression, putatively due to historical hybridization. These differences in genetic signatures are intriguing given that the contact zone occurs in a region of continuous vole habitat, with no evidence of past or present physical barriers. Future studies that examine specific isolating mechanisms, such as microhabitat use and mate choice, will facilitate our understanding of how genetic boundaries are maintained in this system.

A phylogenetic test of sympatric speciation in the Hydrobatinae (Aves: Procellariiformes)

Phylogenetic relationships among species can provide insight into how new species arise. For example, careful consideration of both the phylogenetic and geographic distributions of species in a group can reveal the geographic models of speciation within the group. One such model, sympatric speciation, may be more common than previously thought. The Hydrobatinae (Aves: Procellariformes) is a diverse subfamily of Northern Hemisphere storm-petrels for which the taxonomy is unclear. Previous studies showed that Hydrobates (formally Oceanodroma) castro breeding in the Azores during the cool season is sister species to H. monteiroi, a hot season breeder at the same locations, which suggests sympatric speciation by allochrony. To test whether other species within the subfamily arose via sympatric speciation by allochrony, we sequenced the cytochrome b gene and five nuclear introns to estimate a phylogenetic tree using multispecies coalescent methods, and to test whether species breeding in the same geographic area are monophyletic. We found that speciation within the Hydrobatinae appears to have followed several geographic modes of divergence. Sympatric seasonal species in Japan likely did not arise through sympatric speciation, but allochrony may have played a role in the divergence of H. matsudairae, a cool season breeder, and H. monorhis, a hot season breeder. No other potential cases of sympatric speciation were discovered within the subfamily. Despite breeding in the same geographic area, hydrobatine storm-petrels breeding in Baja California (H. microsoma and H. melania) are each sister to a species breeding off the coast of Peru (H. tethys and H. markhami, respectively). In fact, antitropical sister species appear to have diverged at multiple times, suggesting allochronic divergence might be common. In addition, allopatry has likely played a role in divergence of H. furcata, a north Pacific breeder, and H. pelagius, a north Atlantic breeder. This study demonstrates that a variety of mechanisms of divergence have played a role in generating the diversity of the Hydrobatinae and supports the current taxonomy of the subfamily.

Sympatric speciation of spiny mice, Acomys, unfolded transcriptomically at Evolution Canyon, Israel

Spiny mice, Acomys cahirinus, colonized Israel 30,000 y ago from dry tropical Africa and inhabited rocky habitats across Israel. Earlier, we had shown by mtDNA that A. cahirinus incipiently sympatrically speciates at Evolution Canyon I (EC I) in Mount Carmel, Israel because of microclimatic interslope divergence. The EC I microsite consists of a dry and hot savannoid "African" slope (AS) and an abutting humid and cool-forested "European" slope (ES). Here, we substantiate incipient SS in A. cahirinus at EC I based on the entire transcriptome, showing that multiple slope-specific adaptive complexes across the transcriptome result in two divergent clusters. Tajima's D distribution of the abutting Acomys interslope populations shows that the ES population is under stronger positive selection, whereas the AS population is under balancing selection, harboring higher genetic polymorphisms. Considerable sites of the two populations were differentiated with a coefficient of FST = 0.25-0.75. Remarkably, 24 and 37 putatively adaptively selected genes were detected in the AS and ES populations, respectively. The AS genes involved DNA repair, growth arrest, neural cell differentiation, and heat-shock proteins adapting to the local AS stresses of high solar radiation, drought, and high temperature. In contrast, the ES genes involved high ATP associated with energetics stress. The sharp ecological interslope divergence led to strong slope-specific selection overruling the interslope gene flow. Earlier tests suggested slope-specific mate choice. Habitat interslope-adaptive selection across the transcriptome and mate choice substantiate sympatric speciation (SS), suggesting its prevalence at EC I and commonality in nature.

Transcriptome, genetic editing, and microRNA divergence substantiate sympatric speciation of blind mole rat, Spalax

Incipient sympatric speciation in blind mole rat, Spalax galili, in Israel, caused by sharp ecological divergence of abutting chalk-basalt ecologies, has been proposed previously based on mitochondrial and whole-genome nuclear DNA. Here, we present new evidence, including transcriptome, DNA editing, microRNA, and codon usage, substantiating earlier evidence for adaptive divergence in the abutting chalk and basalt populations. Genetic divergence, based on the previous and new evidence, is ongoing despite restricted gene flow between the two populations. The principal component analysis, neighbor-joining tree, and genetic structure analysis of the transcriptome clearly show the clustered divergent two mole rat populations. Gene-expression level analysis indicates that the population transcriptome divergence is displayed not only by soil divergence but also by sex. Gene ontology enrichment of the differentially expressed genes from the two abutting soil populations highlights reproductive isolation. Alternative splicing variation of the two abutting soil populations displays two distinct splicing patterns. L-shaped FST distribution indicates that the two populations have undergone divergence with gene flow. Transcriptome divergent genes highlight neurogenetics and nutrition characterizing the chalk population, and energetics, metabolism, musculature, and sensory perception characterizing the abutting basalt population. Remarkably, microRNAs also display divergence between the two populations. The GC content is significantly higher in chalk than in basalt, and stress-response genes mostly prefer nonoptimal codons. The multiple lines of evidence of ecological-genomic and genetic divergence highlight that natural selection overrules the gene flow between the two abutting populations, substantiating the sharp ecological chalk-basalt divergence driving sympatric speciation.

Adaptive methylation regulation of p53 pathway in sympatric speciation of blind mole rats, Spalax

Epigenetic modifications play significant roles in adaptive evolution. The tumor suppressor p53, well known for controlling cell fate and maintaining genomic stability, is much less known as a master gene in environmental adaptation involving methylation modifications. The blind subterranean mole rat Spalax eherenbergi superspecies in Israel consists of four species that speciated peripatrically. Remarkably, the northern Galilee species Spalax galili (2n = 52) underwent adaptive ecological sympatric speciation, caused by the sharply divergent chalk and basalt ecologies. This was demonstrated by mitochondrial and nuclear genomic evidence. Here we show that the expression patterns of the p53 regulatory pathway diversified between the abutting sympatric populations of S. galili in sharply divergent chalk-basalt ecologies. We identified higher methylation on several sites of the p53 promoter in the population living in chalk soil (chalk population). Site mutagenesis showed that methylation on these sites linked to the transcriptional repression of p53 involving Cut-Like Homeobox 1 (Cux1), paired box 4 (Pax 4), Pax 6, and activator protein 1 (AP-1). Diverse expression levels of p53 between the incipiently sympatrically speciating chalk-basalt abutting populations of S. galili selectively affected cell-cycle arrest but not apoptosis. We hypothesize that methylation modification of p53 has adaptively shifted in supervising its target genes during sympatric speciation of S. galili to cope with the contrasting environmental stresses of the abutting divergent chalk-basalt ecologies.

Strictly conserved tri-nucleotide motif "CAT" is associated with TAS DNA protein-binding sites in human mitochondrial DNA control region

The mitochondrial DNA (mtDNA) control region is a highly variable segment that contains functional elements that control mtDNA transcription and replication. By analysis of the polymorphic nucleotide spectrum of that segment, we aimed to identify the most conserved sites that should be associated with these elements. For that aim, we analyzed 50 033 human mtDNA control region sequences (mtDNA positions 16 066-16 374). We identified 10 conserved tri-nucleotides, one conserved tetra-nucleotide, and one conserved penta-nucleotide, containing six repetitions of the motif CAT, and two of its complement motif ATG (p value < 2 × 10 ^- 4). Three other appearances of the tri-nucleotide CAT were almost perfectly preserved. The positions of the preserved CAT elements are associated with the location of previously identified termination-associated sequences (TAS) which are the binding locations for proteins involved in mtDNA replication. We, therefore, hypothesize that the CAT tri-nucleotide elements within the control region may be the binding sites for TAS proteins and are directly involved in mtDNA transcription and replication.

Sympatric speciation revealed by genome-wide divergence in the blind mole rat Spalax

Sympatric speciation (SS), i.e., speciation within a freely breeding population or in contiguous populations, was first proposed by Darwin [Darwin C (1859) On the Origins of Species by Means of Natural Selection] and is still controversial despite theoretical support [Gavrilets S (2004) Fitness Landscapes and the Origin of Species (MPB-41)] and mounting empirical evidence. Speciation of subterranean mammals generally, including the genus Spalax, was considered hitherto allopatric, whereby new species arise primarily through geographic isolation. Here we show in Spalax a case of genome-wide divergence analysis in mammals, demonstrating that SS in continuous populations, with gene flow, encompasses multiple widespread genomic adaptive complexes, associated with the sharply divergent ecologies. The two abutting soil populations of S. galili in northern Israel habituate the ancestral Senonian chalk population and abutting derivative Plio-Pleistocene basalt population. Population divergence originated ∼0.2-0.4 Mya based on both nuclear and mitochondrial genome analyses. Population structure analysis displayed two distinctly divergent clusters of chalk and basalt populations. Natural selection has acted on 300+ genes across the genome, diverging Spalax chalk and basalt soil populations. Gene ontology enrichment analysis highlights strong but differential soil population adaptive complexes: in basalt, sensory perception, musculature, metabolism, and energetics, and in chalk, nutrition and neurogenetics are outstanding. Population differentiation of chemoreceptor genes suggests intersoil population's mate and habitat choice substantiating SS. Importantly, distinctions in protein degradation may also contribute to SS. Natural selection and natural genetic engineering [Shapiro JA (2011) Evolution: A View From the 21st Century] overrule gene flow, evolving divergent ecological adaptive complexes. Sharp ecological divergences abound in nature; therefore, SS appears to be an important mode of speciation as first envisaged by Darwin [Darwin C (1859) On the Origins of Species by Means of Natural Selection].

Habitat and Burrow System Characteristics of the Blind Mole Rat Spalax galili in an Area of Supposed Sympatric Speciation

A costly search for food in subterranean rodents resulted in various adaptations improving their foraging success under given ecological conditions. In Spalax ehrenbergi superspecies, adaptations to local ecological conditions can promote speciation, which was recently supposed to occur even in sympatry at sites where two soil types of contrasting characteristics abut each other. Quantitative description of ecological conditions in such a site has been, nevertheless, missing. We measured characteristics of food supply and soil within 16 home ranges of blind mole rats Spalax galili in an area subdivided into two parts formed by basaltic soil and pale rendzina. We also mapped nine complete mole rat burrow systems to compare burrowing patterns between the soil types. Basaltic soil had a higher food supply and was harder than rendzina even under higher moisture content and lower bulk density. Population density of mole rats was five-times lower in rendzina, possibly due to the lower food supply and higher cover of Sarcopoterium shrubs which seem to be avoided by mole rats. A combination of food supply and soil parameters probably influences burrowing patterns resulting in shorter and more complex burrow systems in basaltic soil.

Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation

One of the most celebrated examples of sympatric speciation in nature are monophyletic radiations of cichlid fishes endemic to Cameroon crater lakes. However, phylogenetic inference of monophyly may not detect complex colonization histories involving some allopatric isolation, such as double invasions obscured by genome-wide gene flow. Population genomic approaches are better suited to test hypotheses of sympatric speciation in these cases. Here, we use comprehensive sampling from all four sympatric crater lake cichlid radiations in Cameroon and outgroups across Africa combined with next-generation sequencing to genotype tens of thousands of SNPs. We find considerable evidence of gene flow between all four radiations and neighboring riverine populations after initial colonization. In a few cases, some sympatric species are more closely related to outgroups than others, consistent with secondary gene flow facilitating their speciation. Our results do not rule out sympatric speciation in Cameroon cichlids, but rather reveal a complex history of speciation with gene flow, including allopatric and sympatric phases, resulting in both reproductively isolated species and incipient species complexes. The best remaining non-cichlid examples of sympatric speciation all involve assortative mating within microhabitats. We speculate that this feature may be necessary to complete the process of sympatric speciation in nature.

p53 gene discriminates two ecologically divergent sister species of pine voles

Genes with relevant roles in the differentiation of closely-related species are likely to have diverged simultaneously with the species and more accurately reproduce the species tree. The Lusitanian (Microtus lusitanicus) and Mediterranean (M. duodecimcostatus) pine voles are two recently separated sister species with fossorial lifestyles whose different ecological, physiological and morphological phenotypes reflect the better adaptation of M. duodecimcostatus to the underground habitat. Here we asked whether the differentiation of M. lusitanicus and M. duodecimcostatus involved genetic variations within the tumour suppressor p53 gene, given its role in stress-associated responses. We performed a population-genetic analysis through sequencing of exons and introns of p53 in individuals from sympatric and allopatric populations of both the species in the Iberian Peninsula in which a unidirectional introgression of mitochondrial DNA was previously observed. We were able to discriminate the two species to a large extent. We show that M. duodecimcostatus is composed of one genetically unstructured group of populations sharing a P53 protein that carries a mutation in the DNA-binding region not observed in M. lusitanicus, raising the possibility that this mutation may have been central in the evolutionary history of M. duodecimcostatus. Our results provide suggestive evidence for the involvement of a master transcription factor in the separation of M. lusitanicus and M. duodecimcostatus during Microtus radiation in the Quaternary presumably via a differential adaptive role of the novel p53 in M. duodecimcostatus.

Social and Environmental Influences on Daily Activity Pattern in Free-Living Subterranean Rodents

Predictable daily activity patterns have been detected repeatedly even in mammals living in stable environments, as is the case for subterranean rodents. Whereas studies on activity of these rodents under laboratory conditions almost exclusively have concerned themselves with the influence of light, many field studies have revealed signs of an association between the activity pattern and daily fluctuations of temperature under the ground. This would assume that behavioral thermoregulation is probably involved. The only exceptions to the relationship between temperature and activity are 2 eusocial mole-rats of the genus Fukomys (Bathyergidae, Rodentia), which indicates that activity patterns could be affected also by social cues. To better understand how social and environmental factors influence the activity pattern in a eusocial mole-rat, we monitored the outside-nest activity in another species of this genus, the Ansell’s mole-rat ( Fukomys anselli), which has a relatively small body mass, high conductance, and more superficially situated burrows. Its daily activity had 1 prominent peak (around 1400 h), and it was tightly correlated with the temperature measured at depth of foraging burrows. Since F. anselli has high thermoregulatory requirements to maintain stable body temperature below the lower critical temperature, we conclude that the observed pattern is probably the result of minimizing the cost of thermoregulation. There were no significant differences in the daily activity patterns of breeding males and females and nonbreeders. Members of the same family group tended to have more similar activity patterns, but consistent activity synchronization between individuals was not proven. From the comparison of available data on all subterranean rodents, we assume that social cues in communally nesting mole-rats may disrupt (mask) temperature-related daily activity rhythms but probably only if the additional cost of thermoregulation is not too high, as it likely is in the Ansell’s mole-rat.

Evolution in action: adaptation and incipient sympatric speciation with gene flow across life at “Evolution Canyon”, Israel

Various major evolutionary problems are still open, controversial or unsettled. These include even the basic evolutionary processes of adaptation and speciation. The “Evolution Canyon” model is a microscale natural laboratory that can highlight some of the basic problems requiring clarification (Nevo list of “Evolution Canyon” publications at http://evolution.haifa.ac.il). This is especially true if an interdisciplinary approach is practiced including ecological functional genomics, transcriptomics, proteomics, metabolomics and phenomics. Here I overview and reanalyze the incipient sympatric adaptive ecological speciation of five model organisms at “Evolution Canyon”, across life: the soil bacterium, Bacillus simplex; wild barley, the progenitor of cultivated barley, Hordeum spontaneum; the tiny beetle Oryzaephilus surinamensis; the cosmopolitan fruit-fly, Drosophila melanogaster, and the Africa-originated spiny mouse, Acomys cahirinus. All five models of organisms display evolution in action of microclimatic adaptation and incipient sympatric adaptive ecological speciation on the tropical and temperate abutting slopes, separated on average by only 250 meters. Some distant species converge in their micro-climatic adaptations to the hot and dry “African”, south-facing slope (SFS or AS) and to the cool and humid “European”, north-facing slope (NSF or ES). Natural selection overrules ongoing inter-slope gene-flow between the free interbreeding populations within and between slopes, and leads to adaptive incipient sympatric ecological speciation on the dramatically opposite abutting xeric savannoid and mesic forested slopes.

Sympatric incipient speciation of spiny mice Acomys at "Evolution Canyon," Israel

Does the paucity of empirical evidence of sympatric speciation in nature reflect reality, despite theoretical support? Or is it due to inappropriate searches in nature with overly restrictive assumptions and an incorrect null hypothesis? Spiny mice, Acomys, described here at Evolution Canyon (EC) incipiently and sympatrically speciate owing to microclimatic interslope divergence. The opposite slopes at EC vary dramatically, physically and biotically, representing the dry and hot south-facing slope savannoid-African continent ["African" slope (AS)], abutting with the north-facing slope forested south-European continent ["European" slope (ES)]. African-originated spiny mice, of the Acomys cahirinus complex, colonized Israel 30,000 y ago based on fossils. Genotypically, we showed significantly higher genetic diversity of mtDNA and amplified fragment length polymorphism of Acomys on the AS compared with the ES. This is also true regionally across Israel. In complete mtDNA, 25% of the haplotypes at EC were slope-biased. Phenotypically, the opposite slope's populations also showed adaptive morphology, physiology, and behavior divergence paralleling regional populations across Israel. Preliminary tests indicate slope-specific mate choices. Colonization of Acomys at the EC first occurred on the AS and then moved to the ES. Strong slope-specific natural selection (both positive and negative) overrules low interslope gene flow. Both habitat slope selection and mate choices suggest ongoing incipient sympatric speciation. We conclude that Acomys at the EC is ecologically and genetically adaptively, incipiently, sympatrically speciating on the ES owing to adaptive microclimatic natural selection.