Speciation Process Research Articles

Impact of the climatic changes in the Pliocene-Pleistocene transition on Irano-Turanian species. The radiation of genus Jurinea (Compositae)

The Irano-Turanian region is one of the world’s richest floristic regions and the centre of diversity for numerous xerophytic plant lineages. However, we still have limited knowledge on the timing of evolution and biogeographic history of its flora, and potential drivers of diversification remain underexplored. To fill this knowledge gap, we focus on the Eurasian genus Jurinea (ca. 200 species), one of the largest plant radiations that diversified in the region. We applied a macroevolutionary integrative approach to explicitly test diversification hypotheses and investigate the relative roles of geography vs. ecology and niche conservatism vs. niche lability in speciation processes. To do so, we gathered a sample comprising 77% of total genus richness and obtained data about (1) its phylogenetic history, recovering 502 nuclear loci sequences; (2) growth forms; (3) ecological niche, compiling data of 21 variables for more than 2500 occurrences; and (4) paleoclimatic conditions, to estimate climatic stability. Our results revealed that climate was a key factor in the evolutionary dynamics of Jurinea. The main diversification and biogeographic events that occurred during past climate changes, which led to colder and drier conditions, are the following: (1) the origin of the genus (10.7 Ma); (2) long-distance dispersals from the Iranian Plateau to adjacent regions (∼7–4 Ma); and (3) the diversification shift during Pliocene-Pleistocene Transition (ca. 3 Ma), when net diversification rate almost doubled. Our results supported the pre-adaptation hypothesis, i.e., the evolutionary success of Jurinea was linked to the retention of the ancestral niche adapted to aridity. Interestingly, the paleoclimatic analyses revealed that in the Iranian Plateau long-term climatic stability favoured old-lineage persistence, resulting in current high species richness of semi-arid and cold adapted clades; whereas moderate climate oscillations stimulated allopatric diversification in the lineages distributed in the Circumboreal region. In contrast, growth form lability and high niche disparity among closely related species in the Central Asian clade suggest adaptive radiation to mountain habitats. In sum, the radiation of Jurinea is the result of both adaptive and non-adaptive processes influenced by climatic, orogenic and ecological factors.

Mechanisms of Intrinsic Postzygotic Isolation: From Traditional Genic and Chromosomal Views to Genomic and Epigenetic Perspectives.

Intrinsic postzygotic isolation typically appears as reduced viability or fertility of interspecific hybrids caused by genetic incompatibilities between diverged parental genomes. Dobzhansky-Muller interactions among individual genes, and chromosomal rearrangements causing problems with chromosome synapsis and recombination in meiosis, have both long been considered as major mechanisms behind intrinsic postzygotic isolation. Recent research has, however, suggested that the genetic basis of intrinsic postzygotic isolation can be more complex and involves, for example, overall divergence of the DNA sequence or epigenetic changes. Here, we review the mechanisms of intrinsic postzygotic isolation from genic, chromosomal, genomic, and epigenetic perspectives across diverse taxa. We provide empirical evidence for these mechanisms, discuss their importance in the speciation process, and highlight questions that remain unanswered.

Mortality in Interspecific Hybrids of Nasonia vitripennis and Nasonia giraulti (Hymenoptera: Pteromalidae)

Abstract Barriers to gene flow can result in populations evolving into separate species, and understanding how these barriers evolve is a key step in understanding the process of speciation. This study investigates a major barrier to gene flow, mortality during development, of two parasitoid wasp species, Nasonia vitripennis Walker and N. giraulti Darling. Previous work has demonstrated high mortality in haploid hybrid males of these species and has shown potential rescue from this mortality in diploid hybrid females through backcrossing. However, this previous work did not directly measure egg clutch sizes in hybrids and also did not account for male eggs in these clutches. Here, we measure female-only egg and adult clutch sizes of both parent species and F2 hybrids, as well as F2 male egg and adult clutch sizes, in order to determine the impact of backcrossing on mortality in these hybrids. We find significant egg-to-adult mortality in diploid F2 hybrid females with a N. giraulti cytotype when backcrossed to N. vitripennis males; yet, these hybrids also experience less mortality than haploid F2 males. These results confirm the mortality and rescue in these F2 hybrid females and indicate that there is likely a combination of nuclear-cytoplasmic and nuclear-nuclear incompatibilities in these hybrids that lead to this mortality. This work provides a foundation for future studies to investigate the genetic basis of this mortality.

Thermal niche breadth and their relationship with sturnira bat species diversification

The interaction between climatic conditions and the ability of organisms to maintain homeostasis regulates the distribution of species on the planet. However, its influence on macroevolutionary dynamics is not well understood. It has been suggested that diversification rates will be different in lineages with narrow thermal niches (specialists) to diversification rates in generalist lineages, but the evidence for this is elusive. Here, we tested this hypothesis by using the most diverse (in species richness and geographic range variation) tropical bat genus within the Phyllostomidae family. We estimated the realized thermal niche breadth of Sturnira species from their geographic range and categorized them as generalists, cold specialists, or warm specialists. We compared dynamic evolutionary models that differ in 1) niche breadth evolution, 2) parental niche breadth inheritance, and 3) whether niche breadth evolution is associated with shifts in diversification rates. Our best-performing model indicates that most Sturnira species arose as specialists in warm climates and that over time, their niche breadth broadens, and just a subset of those species becomes specialists in cold environments. We found that the evolution of realized thermal niche breadth causes fluctuations in per-lineage rates of diversification, where warm specialists boast the highest speciation rates. However, we found no evidence of these changes in niche neither triggering nor being a result of speciation events themselves; this suggests that diversification events in Sturnira could instead depend on allopatric speciation processes such as the development of geographic barriers.

Model of phylomorphogeny of P1 elements of the Tournaisian (Mississippian) siphonodellids

Conodonts are a group of extinct marine organisms widely used in Paleozoic and Triassic biostratigraphy. The genus Siphonodella comprises ozarkodinid conodonts from the latest Famennian to the middle Tournaisian. The phylogenetic model of this genus plays an important role in biostratigraphy. This study is based on the authors' and published data on 31 species of siphonodellids of cosmopolitan and East European groups. A new phylomorphogeny of Siphonodella is proposed on the basis of known mechanisms of morphological transformations of siphonodellid P1 elements during speciation processes, presence of interspecies transitional forms, and data on ontogeny. The main morphogenetic pathways in the evolution of siphonodellids are the following: formation and transformation of the rostrum, transformation of the platform outline, transformation of the platform ornamentation, transformation of the keel, and histological transformations. In the process of modeling the phylomorphogeny of Siphonodella, some taxonomic problems are solved: a new species S. thompfelli is described, a new variant of the division of S. lobata (Branson and Mehl) into morphotypes is proposed, the validity of S. plana (Huddle), S. praeplana Bardasheva, Bardashev, Weddige and Ziegler, and S. gladia Zhuravlev and Plotitsyn is clarified, and the knowledge of the morphospace of most representatives of the genus is extended. The phylogeny of siphonodellids provides a basis for the new phylogenetic zonal sequences based on the conodont phylogenetic-zone concept.

New species based on the biological species concept within the complex of Lariophagus distinguendus (Hymenoptera, Chalcidoidea, Pteromalidae), a parasitoid of household pests.

The pteromalid parasitoid Lariophagus distinguendus (Foerster) belongs to the Hymenoptera, a megadiverse insect order with high cryptic diversity. It attacks stored product pest beetles in human storage facilities. Recently, it has been shown to consist of two separate species. To further study its cryptic diversity, strains were collected to compare their relatedness using barcoding and nuclear genes. Nuclear genes identified two clusters which agree with the known two species, whereas the barcode fragment determined an additional third Clade. Total reproductive isolation (RI) according to the biological species concept (BSC) was investigated in crossing experiments within and between clusters using representative strains. Sexual isolation exists between all studied pairs, increasing from slight to strong with genetic distance. Postzygotic barriers mostly affected hybrid males, pointing to Haldane's rule. Hybrid females were only affected by unidirectional Spiroplasma-induced cytoplasmic incompatibility and behavioural sterility, each in one specific strain combination. RI was virtually absent between strains separated by up to 2.8% COI difference, but strong or complete in three pairs from one Clade each, separated by at least 7.2%. Apparently, each of these clusters represents one separate species according to the BSC, highlighting cryptic diversity in direct vicinity to humans. In addition, these results challenge the recent 'turbo-taxonomy' practice of using 2% COI differences to delimitate species, especially within parasitic Hymenoptera. The gradual increase in number and strength of reproductive barriers between strains with increasing genetic distance also sheds light on the emergence of barriers during the speciation process in L. distinguendus.

Across mountains and ocean: species delimitation and historical connectivity in Holarctic and Arctic-Alpine wolf spiders (Lycosidae, Pardosa)

Abstract Holarctic species offer great opportunities to study biogeography, phylogenetics, taxonomy, and local adaptation. Species that are considered conspecific between the Palearctic and the Nearctic realms are often split into 2 or more species when denser sampling and molecular markers are applied. Similar in complexity but at a finer geographical scale are species groups having Arctic-Alpine distributions where lineages have complicated demographic histories due to glacial dynamics. In both cases, allopatric speciation might not result in fast differentiation of morphological characters if environmental conditions in isolated areas are similar and the main driver of variability is genetic drift. Here, we study the Holarctic Pardosa hyperborea (Thorell, 1872) and its closest European relatives to assess their taxonomic status and patterns of genetic variability. Based on DNA barcodes and genomic data from double-digest restriction site associated sequencing, we propose that the North American populations should be regarded as a distinct species (P. luteola Emerton,1894, stat. resurr.), possibly consisting of several independent lineages. With the help of D-statistics, population genetic simulations and phylogenetic networks analysis, we demonstrate historical introgression among European species of the group and a likely explanation for shared DNA barcodes among allopatric and fully differentiated species. Our study exposes a promising model for studying speciation processes and demographic history in parallel on both sides of the Atlantic Ocean and demonstrates the usefulness of genomic tools in elucidating the taxonomy and biogeography of taxa across broad geographic scales.

Can demographic histories explain long-term isolation and recent pulses of asymmetric gene flow between highly divergent grey fox lineages?

Secondary contact zones between deeply divergent, yet interfertile, lineages provide windows into the speciation process. North American grey foxes (Urocyon cinereoargenteus) are divided into western and eastern lineages that diverged approximately 1 million years ago. These ancient lineages currently hybridize in a relatively narrow zone of contact in the southern Great Plains, a pattern more commonly observed in smaller-bodied taxa, which suggests relatively recent contact after a long period of allopatry. Based on local ancestry inference with whole-genome sequencing (n = 43), we identified two distinct Holocene pulses of admixture. The older pulse (500-3500 YBP) reflected unidirectional gene flow from east to west, whereas the more recent pulse (70-200 YBP) of admixture was bi-directional. Augmented with genotyping-by-sequencing data from 216 additional foxes, demographic analyses indicated that the eastern lineage declined precipitously after divergence, remaining small throughout most of the late Pleistocene, and expanding only during the Holocene. Genetic diversity in the eastern lineage was highest in the southeast and lowest near the contact zone, consistent with a westward expansion. Concordantly, distribution modelling indicated that during their isolation, the most suitable habitat occurred far east of today's contact zone or west of the Great Plains. Thus, long-term isolation was likely caused by the small, distant location of the eastern refugium, with recent contact reflecting a large increase in suitable habitat and corresponding demographic expansion from the eastern refugium. Ultimately, long-term isolation in grey foxes may reflect their specialized bio-climatic niche. This system presents an opportunity for future investigation of potential pre- and post-zygotic isolating mechanisms.

Genomic diversity, evolutionary history, and species limits of the endemic Ethiopian laminate-toothed rats (genus Otomys, Rodentia: Muridae)

Abstract The Ethiopian Highlands represent one of the most important centres of endemism on Earth. Six endemic species of laminate-toothed rats have been reported from Ethiopia in a previous study based mostly on morphological analyses. Largely missing genetic data for some of the species, insufficient sampling across Ethiopia, and presence of a pseudogene on cytochrome b created knowledge gaps in basic taxonomy, distribution, and phylogenetic position of the Ethiopian taxa. Here we perform an integrative taxonomic revision of the group by using the largest available sets of genomic and morphological data. We first reconstructed the mitochondrial phylogeny of the whole genus, delimited major clades, and evidenced two independent colonization events of Otomys to Ethiopia. By using genome-scale SNPs, we delimited putative Ethiopian species and analysed their phylogenetic relationships. In genetically characterized specimens we assessed morphological variation of skulls. We confirmed the presence of six previously reported species and significantly extended the known distributional range for some of them. Furthermore, we discovered a genetically and morphologically distinct lineage in northern Ethiopia, probably representing a new species. The speciation processes are similar to other Afromontane Ethiopian endemic rodent clades, with prevailing allopatric diversification combined with reticulate processes.

Patterns of phylogenetic diversification in the Dollarbird (Eurystomus orientalis) and Azure Roller (Eurystomus azureus) complex

Genetic isolation and morphological differentiation are two important factors in the speciation process that not always act in concert. A rapid morphological change in a lineage can hide its close relationship to another lineage, while slight morphological differentiation between two taxa can give the appearance of a closer relationship than is actually the case. The Dollarbird (Eurystomus orientalis) and the Azure Roller (Eurystomus azureus) is such an example. Today the Dollarbird and the Azure Roller are unanimously considered to constitute two distinct species, but in a recent genetic study it has been shown that the latter taxon, despite being larger and having a distinctly different coloration, is phylogenetically nested within the former. Its precise placement within this complex has not been determined, however.In this study, we investigate the phylogenetic relationships within the Dollarbird/Azure Roller complex. We estimate divergence times and infer phylogenetic relationships using sequence data from 6,475 genome-wide intronic regions, as well as complete mitochondrial genomes, using both concatenation and multispecies coalescence approaches.We find that within the Dollarbird/Azure Roller complex there are several examples of discrepancies between genetic and morphological differentiation. The Dollarbird is currently divided into between nine to twelve subspecies. Some of these subspecies are poorly differentiated, whereas others are morphologically more clearly discernable. Our data suggest that the complex consist of at least seven distinct genetic lineages that do not entirely match the morphological variation within the group.For instance, our results show that the subspecies solomonensis from the Solomon Islands, despite being morphologically very similar to its geographically closest neighbors, in fact is a highly distinct lineage that became isolated more than 700,000 years ago. In contrast, the morphologically distinct Azure Roller, which is currently treated as a distinct species, is nested within the Dollarbird and forms a slightly younger lineage than solomonensis and is the sister group to a clade with Australian and New Guinean Dollarbirds. Our results also show a deep genetic split within the Dollarbirds on the Asian mainland. This stands in contrast to the apparent clinal morphological variation reported for the birds on the Asian mainland.We also find support for the presence of a genetically distinct clade in the Wallacea region. The birds from the Wallacea region has previously been recognized as a distinct subspecies, connectens, but is currently placed in synonymy of other subspecies.Our results are thus at odds with the current division of the Dollarbird/Azure Roller complex into two species. Given that the species status of azureus is undisputed, the apparent genetic isolation of solomonensis and its clear separation from the other lineages suggests that this taxon also warrants species status. Based on the genetic and morphological variation observed within the Dollarbird/Azure Roller complex there is little doubt that even more taxa should regarded as species, but this require further examination.

Surf-diatoms from sandy beaches on the Eastern Coast of South America (Brazil): the identification ofAnaulusEhrenberg andAsterionellopsisRound

Abstract“Surf diatoms” can form high biomass in the surf zone of sandy beaches around the world,AsterionellopsisandAnaulusbeing the main genera of this group in Brazil.Asterionellopsis glacialiswas considered a cosmopolitan species, and taxonomic studies using molecular and morphological tools showed thatA. glacialisis a complex with cryptic and semicryptic species. So, it would be plausible to suppose thatAnaulus australis, another surf zone patch-forming diatom with wide latitudinal occurrence could also be part of a species complex. We collected and identifiedAnaulusandAsterionellopsisstrains from tropical, subtropical and warm temperate sandy beaches on the east coast of South America (Brazil) based on genetic divergence, phylogeny, single-locus automated species delimitation methods (both genera), and frustule ultrastructure (Anaulus).AnaulusandAsterionellopsisshowed contrasting diversity patterns and spatial distribution: a single species ofAnaulus australiswas registered in tropical and subtropical beaches, while at least three species ofAsterionellopsis:A. tropicalis,A. thurstoniiandA. guyunusaewere observed at different latitudes, indicating thatAsterionellopsisspecies have distinct ecological requirements.Asterionellopsis thurstoniiwas previously reported in Europe and it is documented here for the first time in the Southern Hemisphere. The different diversity patterns between these two surf diatom genera suggest that they are likely to have distinct ages, and dispersion and/or speciation processes.

First insight into molecular diversity of interstitial water mites (Acari: Hydrachnidia): a case study from the upper Neretva River in Bosnia and Herzegovina

ABSTRACT Water mites are a diverse but neglected meiofaunal group in interstitial habitats. In this study, water mites were sampled from the hyporheic zone of the upper Neretva river catchment in Bosnia and Herzegovina. In total, 10 obligate subterranean (hyporheobiontic) species were detected. Seven of them, i.e. Atractidespumilus (Szalay, 1946), Frontipodopsis reticulatifrons Szalay, 1945, Lethaxona pygmaea K. Viets, 1932, Paraxonopsis inferorum (Motaş and Tanasachi, 1947), P. vietsi (Motaş and Tanasachi, 1947), Erebaxonopsis brevipes Motaş and Tanasachi, 1947, and one halacarid species, Parasoldanellonyx typhlops K. Viets, 1933, were recorded for the first time for the fauna of Bosnia and Herzegovina. The first DNA barcoding data are provided for three families (Frontipodopsidae, Lethaxonidae, and Hungarohydracaridae), one subfamily (Stygomomoniinae), and 10 species, providing the first basis for a DNA barcode reference library of water mites from the interstitial habitats in South-Eastern Europe. In each of the four species, considered to have a wide Western Palaearctic distribution, i.e., A. pumilus, F. reticulatifrons, Hungarohydracarus subterraneaus, and Stygomomonia latipes, two separate lineages were distinguished. Fossil-calibrated modelling revealed that the diversification and speciation processes within the above-mentioned species started in the Late Miocene (7.3–11.8 Ma).

Geographical and ecological drivers of coexistence dynamics in squamate reptiles

AbstractAimSpecies richness varies widely across space and is determined by underlying factors that drive species coexistence. Such factors include the speciation process (sympatric vs. allopatric), time since divergence, geographic context and intrinsic properties of the organisms. We model for the first time the coexistence dynamics of lizards and snakes across broad temporal and spatial scales, investigating whether an increase in niche divergence, dispersal abilities and inhabiting islands or continents affect their probability of coexistence.LocationGlobal.Time periodCenozoic.Major taxa studiedSquamata.MethodsWe used 447 sister species pairs, their age since divergence, their level of spatial (sympatric or allopatric) and niche overlap and geographical setting (islands or continents) to fit probabilistic models of species coexistence. We measured morphological traits to quantify niche divergence and used range and body size as proxies for dispersal ability. We applied a model‐comparison framework in lizards and snakes separately to evaluate which factors best explained their coexistence dynamics.ResultsAllopatric speciation is the main speciation mode in snakes but we did not find evidence to favour one speciation mode in lizards. In snakes, sympatric pairs tend to occur on islands and to be more different in body size. On the contrary, dispersal ability shaped the coexistence of lizards, where species were more likely to coexist when they have higher dispersal abilities.Main conclusionsDistinct patterns and mechanisms underlie species coexistence within the order Squamata. Snake coexistence is preferentially produced by secondary sympatry favoured by niche divergence and is more likely to occur in more restricted geographical settings (islands vs. continents). Coexistence in lizards is strongly influenced only by dispersal abilities, but the high heterogeneity of processes simultaneously shaping the distribution of different lizard lineages might have masked specific coexistence signals, and future work should compare coexistence dynamics between clades (e.g. families).

Extensive introgression among strongylocentrotid sea urchins revealed by phylogenomics.

Gametic isolation is thought to play an important role in the evolution of reproductive isolation in broadcast-spawning marine invertebrates. However, it is unclear whether gametic isolation commonly evolves early in the speciation process or only accumulates after other reproductive barriers are already in place. It is also unknown whether gametic isolation is an effective barrier to introgression following speciation. Here, we used whole-genome sequencing data and multiple complementary phylogenomic approaches to test whether the well-documented gametic incompatibilities among the strongylocentrotid sea urchins have limited introgression. We quantified phylogenetic discordance, inferred reticulate phylogenetic networks, and applied the Δ statistic using gene tree topologies reconstructed from multiple sequence alignments of protein-coding single-copy orthologs. In addition, we conducted ABBA-BABA tests on genome-wide single nucleotide variants and reconstructed a phylogeny of mitochondrial genomes. Our results revealed strong mito-nuclear discordance and considerable nonrandom gene tree discordance that cannot be explained by incomplete lineage sorting alone. Eight of the nine species examined demonstrated a history of introgression with at least one other species or ancestral lineage, indicating that introgression was common during the diversification of the strongylocentrotid urchins. There was strong support for introgression between four extant species pairs (Strongylocentrotus pallidus ⇔ S. droebachiensis, S. intermedius ⇔ S. pallidus, S. purpuratus ⇔ S. fragilis, and Mesocentrotus franciscanus ⇔ Pseudocentrotus depressus) and additional evidence for introgression on internal branches of the phylogeny. Our results suggest that the existing gametic incompatibilities among the strongylocentrotid urchin species have not been a complete barrier to hybridization and introgression following speciation. Their continued divergence in the face of widespread introgression indicates that other reproductive isolating barriers likely exist and may have been more critical in establishing reproductive isolation early in speciation.

Phosphorus speciation, transformation and benthic processes with implications for environmental impacts in the aquaculture area of Rushan Bay

Phosphorus speciation, transformation and benthic processes with implications for environmental impacts in the aquaculture area of Rushan Bay

Chromosomal-level reference genome of a wild North American mallard (Anas platyrhynchos).

The mallard (Anas platyrhynchos) is one of the most common, economically, and socially important birds around the world. Mallards were not only an important food source for early humans but eventually becoming intimately linked with people as they were domesticated over the last 2,000 years. To date, mallard genomes are largely reconstructed from samples of domestic or unknown genetic heritage. Here, we report the first high-quality genome assembly and annotation of a genetically vetted wild mallard from North America (NAwild_v1.0). The genome was assembled using a combination of shotgun libraries, proximity ligation Chicago, and Dovetail Hi-C libraries. The final assembly is ∼1.04 Gb in size, with 98.3% of the sequence located in 30 full or nearly full chromosome-level scaffolds, and with a N50/L50 of 79.1 Mb/4 scaffolds. We used a combination of gene prediction and similarity approaches to annotate a total of 23,584 functional genes, of which 19,242 were associated to GO terms. The genome assembly and the set of annotated genes yielded a 95.4% completeness score when compared with the BUSCO aves_odb10 dataset. Next, we aligned 3 previously published mallard genomes to ours, and demonstrate how runs of homozygosity and nucleotide diversity are substantially higher and lower, respectively, to ours and how these artificially changed genomes resulted in profoundly different and biased demographic histories. Our wild mallard assembly not only provides a valuable resource to shed light onto genome evolution, speciation, and other adaptive processes, but also helping with identifying functional genes that have been significantly altered during the domestication process.

Species delimitation and integrative taxonomy of the Reithrodontomys mexicanus (Rodentia: Cricetidae) cryptic complex.

Species boundaries are difficult to establish in groups with very similar morphology. As an alternative, it has been suggested to integrate multiple sources of data to clarify taxonomic problems in taxa where cryptic speciation processes have been reported. This is the case of the harvest mouse Reithrodontomys mexicanus, which has a problematic taxonomy history as it is considered a complex species. Here, we evaluate the cryptic diversity of R. mexicanus using an integrative taxonomy approach in order to detect candidate lineages at the species level. The molecular analysis used one mitochondrial (cytb) and two nuclear (Fgb-I7 and IRBP) genes. Species hypotheses were suggested based on three molecular delimitation methods (mPTP, bGMYC, and STACEY) and cytb genetic distance values. Skull and environmental space differences between the delimited species were also tested to complement the discrimination of candidate species. Based on the consensus across the delimitation methods and genetic distance values, four species were proposed, which were mostly supported by morphometric and ecological data: R. mexicanus clade I, R. mexicanus clade IIA, R. mexicanus clade IIIA, and R. mexicanus clade IIIB. In addition, the evolutionary relationships between the species that comprise the R. mexicanus group were discussed from a phylogenetic approach. Our findings present important taxonomic implications for Reithrodontomys, as the number of known species for this genus increases. Furthermore, we highlight the importance of the use of multiple sources of data in systematic studies to establish robust delimitations between species considered taxonomically complex.

A Reference Genome Assembly for the Spotted Flycatcher (Muscicapa striata).

The spotted flycatcher (Muscicapa striata) forms with the Mediterranean flycatcher (Muscicapa tyrrhenica) a newly recognized species pair of trans-Saharan migratory passerines. These flycatchers present a nested peripatric distribution, a pattern especially unusual among high dispersal species that questions the eco-evolutionary factors involved during the speciation process. Here, we present a genome assembly for M. striata assembled using a combination of Nanopore and Illumina sequences. The final assembly is 1.08 Gb long and consists of 4,779 contigs with an N50 of 3.2 Mb. The completeness of our M. striata genome assembly is supported by the number of BUSCO (95%) and ultraconserved element (UCE) (4889/5041; 97.0%) loci retrieved. This assembly showed high synteny with the Ficedula albicollis reference genome, the closest species for which a chromosome-scale reference genome is available. Several inversions were identified and will need to be investigated at the family level.

A melting-pot for Pterodroma petrels on Rapa Nui: ecological divergence and reproductive isolation in a contact zone

Speciation is thought to depend on general ecological segregation rather than on strict allopatry in species with planetary-scale foraging ranges, such as Pterodroma petrels. Separation in both breeding islands and foraging grounds are generally considered to be the conditions for prezygotic isolation. However, it is unclear how both can be maintained in a context of ongoing distributional range shifts due to global change, with range contractions and expansions caused by changing land use in breeding territories and oceanographic conditions impacting productivity areas. In this context, we expect that wherever the fragile balance of allopatric segregation breaks down, gene flow may be re-established across the borders of what is currently considered separated species. In these “melting pot” areas, fine-scale ecological differentiation is likely the only force opposing panmixia in otherwise highly similar organisms. In this study, we focus on six Polynesian Pterodroma species currently found on Motu Nui, a protected islet offshore of Rapa Nui (Easter Island), four of which have likely extended their breeding range to that island recently. To understand the fine-scale interaction between these closely-related species in their new contact zone, we used an integrative approach combining ecological and genetic methods, including morphometric, bioacoustics, stable isotope niche reconstruction, breeding site characterisation, phenology traits, and both nuclear and mitochondrial DNA markers. We found that significant amounts of gene flow occur across what is currently considered species boundaries, sometimes questioning the relevance of the accepted species classification. Interestingly, our results indicate that multivariate ecological distance between individuals in a group of closely related species (P. alba, P. atrata, P. heraldica, and P. neglecta) is a relevant predictor of gene flow intensity, while more distant species such as P. ultima and P. nigripennis seem to maintain reproductive isolation. Thus, the case of Pterodroma petrels supports the idea that incomplete allopatric speciation processes may be halted or even reversed on a secondary contact zone. Beyond their direct taxonomical relevance, our results underline the importance of considering fine ecological structures for biodiversity mapping and conservation policies.

Microbiome specificity and fluxes between two distant plant taxa in Iberian forests

BackgroundPlant-associated microbial communities play important roles in host nutrition, development and defence. In particular, the microbes living within internal plant tissues can affect plant metabolism in a more intimate way. Understanding the factors that shape plant microbial composition and discovering enriched microbes within endophytic compartments would thus be valuable to gain knowledge on potential plant–microbial coevolutions. However, these interactions are usually studied through reductionist approaches (in vitro models or crop controlled systems). Here, we investigate these ecological factors in wild forest niches using proximally located plants from two distant taxa (blueberry and blackberry) as a model.ResultsAlthough the microbial communities were quite similar in both plants, we found that sampling site had a high influence on them; specifically, its impact on the rhizosphere communities was higher than that on the roots. Plant species and sample type (root vs. rhizosphere) affected the bacterial communities more than the fungal communities. For instance, Xanthobacteraceae and Helotiales taxa were more enriched in roots, while the abundance of Gemmatimonadetes was higher in rhizospheres. Acidobacteria abundance within the endosphere of blueberry was similar to that in soil. Several taxa were significantly associated with either blackberry or blueberry samples regardless of the sampling site. For instance, we found a significant endospheric enrichment of Nevskia in blueberry and of Sphingobium, Novosphingobium and Steroidobacter in blackberry.ConclusionsThere are selective enrichment and exclusion processes in the roots of plants that shapes a differential composition between plant species and sample types (root endosphere—rhizosphere). The special enrichment of some microbial taxa in each plant species might suggest the presence of ancient selection and/or speciation processes and might imply specific symbiosis. The selection of fungi by the host is more pronounced when considering the fungal trait rather than the taxonomy. This work helps to understand plant–microbial interactions in natural ecosystems and the microbiome features of plants.