Genome assembly, structural variants, and genetic differentiation between Lake Whitefish young species pairs (Coregonus sp.) with long and short reads

The parallel evolution of nascent pairs of ecologically differentiated species offers an opportunity to get a better glimpse at the genetic architecture of speciation. Of particular interest is our recent ability to consider a wider range of genomic variants, not only single-nucleotide polymorphisms (SNPs), thanks to long-read sequencing technology. We can now identify structural variants (SVs) like insertions, deletions, and other structural rearrangements, allowing further insights into the genetic architecture of speciation and how different variants are involved in species differentiation. Here, we investigated genomic patterns of differentiation between sympatric species pairs (Dwarf and Normal) belonging to the Lake Whitefish (Coregonus clupeaformis) species complex. We assembled the first reference genomes for both Dwarf and Normal Lake Whitefish, annotated the transposable elements, and analysed the genome in the light of related coregonid species. Next, we used a combination of long-read and short-read sequencing to characterize SVs and genotype them at population-scale using genome-graph approaches, showing that SVs cover five times more of the genome than SNPs. We then integrated both SNPs and SVs to investigate the genetic architecture of species differentiation in two different lakes and highlighted an excess of shared outliers of differentiation. In particular, a large fraction of SVs differentiating the two species was driven by transposable elements (TEs), suggesting that TE accumulation during a period of allopatry predating secondary contact may have been a key process in the speciation of the Dwarf and Normal Whitefish. Altogether, our results suggest that SVs play an important role in speciation and that by combining second and third generation sequencing we now have the ability to integrate SVs into speciation genomics.

The island rule and its application to multiple plant traits

<p>The Island Rule refers to a continuum of body size changes where large mainland species evolve to become smaller and small species evolve to become larger on islands. Previous work focuses almost solely on animals, with virtually no previous tests of its predictions on plants. I tested for (1) reduced floral size diversity on islands, a logical corollary of the island rule and (2) evidence of the Island Rule in plant stature, leaf size and petiole length. Endemic island plants originated from small islands surrounding New Zealand; Antipodes, Auckland, Bounty, Campbell, Chatham, Kermadec, Lord Howe, Macquarie, Norfolk, Snares, Stewart and the Three Kings. I compared the morphology of 65 island endemics and their closest ‘mainland’ relative. Species pairs were identified. Differences between archipelagos located at various latitudes were also assessed. Floral sizes were reduced on islands relative to the ‘mainland’, consistent with predictions of the Island Rule. Plant stature, leaf size and petiole length conformed to the Island Rule, with smaller plants increasing in size, and larger plants decreasing in size. Results indicate that the conceptual umbrella of the Island Rule can be expanded to plants, accelerating understanding of how plant traits evolve on isolated islands.</p>

The island rule and its application to multiple plant traits

<p>The Island Rule refers to a continuum of body size changes where large mainland species evolve to become smaller and small species evolve to become larger on islands. Previous work focuses almost solely on animals, with virtually no previous tests of its predictions on plants. I tested for (1) reduced floral size diversity on islands, a logical corollary of the island rule and (2) evidence of the Island Rule in plant stature, leaf size and petiole length. Endemic island plants originated from small islands surrounding New Zealand; Antipodes, Auckland, Bounty, Campbell, Chatham, Kermadec, Lord Howe, Macquarie, Norfolk, Snares, Stewart and the Three Kings. I compared the morphology of 65 island endemics and their closest ‘mainland’ relative. Species pairs were identified. Differences between archipelagos located at various latitudes were also assessed. Floral sizes were reduced on islands relative to the ‘mainland’, consistent with predictions of the Island Rule. Plant stature, leaf size and petiole length conformed to the Island Rule, with smaller plants increasing in size, and larger plants decreasing in size. Results indicate that the conceptual umbrella of the Island Rule can be expanded to plants, accelerating understanding of how plant traits evolve on isolated islands.</p>

Multitrophic higher-order interactions modulate species persistence

There is growing recognition that interactions between species pairs are modified in a multispecies context by the density of a third species. However, how these higher-order interactions (HOIs) affect species persistence remains poorly understood. To explore the effect of HOIs steaming from multiple trophic layers on plant persistence, we experimentally built a mutualistic system containing three plants and three pollinators species with two contrasting network structures. For both structures, we first estimated the statistically supported HOIs on plant species, in addition to the pairwise interactions among plants and plant-pollinators. Following a structuralist approach, we then assessed the effects of the supported HOIs on the persistence probability of each of the three competing plant species and their combinations. HOIs produced substantial effects on the strength and sign of per capita interactions between plant species to such an extent that predictions of species persistence differ from a non-HOIs scenario. Changes in network structure due to removing a plant-pollinator link further modulated the species persistence probabilities by reorganizing per capita interaction strengths of both pairwise interactions and HOIs. Our study provides empirical evidence of the joint importance of HOIs and network structure for determining the probability of species to persist within diverse communities.

Niche difference determines coexistence and similar underlying processes in four ecological groups

Understanding how species interactions affect community composition is an important objective in ecology. Yet, the multitude of methods to study coexistence has hampered cross-community comparisons. Here, we standardized niche and fitness differences across 1018 species pairs to compare the processes driving composition and outcomes, among four community types (annual plant, perennial plant, phytoplankton, and bacteria/yeast). First, we show that niche differences are more important drivers of coexistence than fitness differences. Second, in all community types negative frequency dependence is the most frequent process. Finally, the outcome of species interactions differs among community types. Coexistence was the most frequent outcome for perennial plants and phytoplankton, while competitive exclusion was the most prevalent outcome in annual plants and bacteria/yeasts. Overall, our results show that niche and fitness differences can be used as a common currency that allow cross community comparisons to understand species coexistence.

Extensive sympatry and frequent hybridization of ecologically divergent aquatic plants on the Qinghai-Tibetan Plateau

Hybridization has fascinated biologists in recent centuries for its evolutionary importance, especially in plants. Hybrid zones are commonly located in regions across environmental gradients due to more opportunities to contact and ecological heterogeneity. For aquatic taxa, intrazonal character makes broad overlapping regions in intermediate environments between related species. However, we have limited information on the hybridization pattern of aquatic taxa across an altitudinal gradient. In this study, we aimed to test the hypotheses that niche overlap and hybridization might be extensive in related aquatic plants in alpines. We evaluated the niche overlap in three related species pairs on the Qinghai-Tibetan Plateau and assessed the spatial pattern of hybrid populations. Obvious niche overlap and common hybridization were revealed in all three pairs of related aquatic plants. The plateau edge and river basins were broad areas for the sympatry of divergent taxa, where a large proportion of hybrid populations occurred. Hybrids are also discretely distributed in diverse habitats on the plateau. Differences in the extent of niche overlap, genetic incompatibility and phylogeographic history might lead to inconsistences in hybridization patterns among the three species pairs. Our results suggested that plateau areas are a hotspot for ecologically divergent aquatic species to contact and mate and implied that hybridization may be important for the freshwater biodiversity of highlands.

Exclusion of the fittest predicts microbial community diversity in fluctuating environments

Microorganisms live in environments that inevitably fluctuate between mild and harsh conditions. As harsh conditions may cause extinctions, the rate at which fluctuations occur can shape microbial communities and their diversity, but we still lack an intuition on how. Here, we build a mathematical model describing two microbial species living in an environment where substrate supplies randomly switch between abundant and scarce. We then vary the rate of switching as well as different properties of the interacting species, and measure the probability of the weaker species driving the stronger one extinct. We find that this probability increases with the strength of demographic noise under harsh conditions and peaks at either low, high, or intermediate switching rates depending on both species’ ability to withstand the harsh environment. This complex relationship shows why finding patterns between environmental fluctuations and diversity has historically been difficult. In parameter ranges where the fittest species was most likely to be excluded, however, the beta diversity in larger communities also peaked. In sum, how environmental fluctuations affect interactions between a few species pairs predicts their effect on the beta diversity of the whole community.

Breeding biology of two sympatric Nesospiza finches at Nightingale Island, Tristan da Cunha

Nesospiza finches are a classic example of a simple adaptive radiation, with two ecologically distinct forms confined to the Tristan da Cunha Archipelago, South Atlantic Ocean: an abundant, small-billed dietary generalist, and a scarce, large-billed specialist. These have segregated into two species at Nightingale Island, but there is still local introgression between the two forms at Inaccessible Island. We describe the phenology and breeding behaviour of the two sympatric species at Nightingale Island (2.6 km2): Wilkins’s Finch Nesospiza wilkinsi (Endangered) and Nightingale Island Finch N. questi (Vulnerable). The finch breeding season starts in late October-November but the onset of breeding varies by 4–5 weeks among years. The small-billed Nightingale Island Finch typically (two of three study seasons) starts breeding 1–3 weeks earlier than the large-billed Wilkins’s Finch, unlike at Inaccessible Island where the Wilkins’s Finches start breeding first. Laying of initial clutches was quite well synchronised, peaking 1–2 weeks after the first nests were found. Females constructed the nests, which were mostly (>90%) in dense Spartina arundinacea tussock grass stands and occasionally in ferns or sedge grasses. Clutches comprised one or two eggs, with no difference between Wilkins’s (1.66 ± 0.48) or Nightingale Island finch clutches (1.71 ± 0.46). Incubation periods averaged longer for Wilkins’s Finch (18.3 ± 0.5 d) than Nightingale Island Finch (17.7 ± 0.5 d), but this difference was not statistically significant. Females incubated the eggs, and were fed by the males. The difference in egg volume within two-egg clutches was 2–13% for Wilkins’s Finches (mean 5.9 ± 3.3%) and 1–19% for Nightingale Island Finches (mean 8.4 ± 5.3%). At least 31% of pairs re -laid after their first breeding attempt failed but there was no evidence of double brooding. Repeat nests were 0–20 m (mean 5.6 ± 4.9 m) from the initial nest site and inter-seasonal nest sites for 38 known pairs were 0–33 m apart (mean 12 ± 9 m). No inter-species pairs or hybrid birds were seen, but two instances of inter-species fledgling provisioning were observed.

Revision of the ‘dragon-head’ cusk eels of the genus Porogadus (Teleostei: Ophidiidae), with description of eight new species and one new genus

The ophidiid genus Porogadus occurs between 800 and 5300 m in the tropical and subtropical world oceans. Fifteen nominal species have been described since 1878 and most of them until 1902. The genus has been highlighted as needing revision in recent compilations about ophidiiforms and here we present the first comprehensive review. Twelve of the previously described species are here accepted as valid with two being moved to the newly established genus Tenuicephalus n. gen. that encompasses fishes differing from those of Porogadus in the extremely weak ossification, the stout head, absence of head spines and absence of the “triple” lateral line system considered typical for Porogadus and a reduced dentition. In addition, eight new species are described: Porogadus caboverdensis, P. dracocephalus, P. lacrimatus, P. mendax, P. solomonensis, P. turgidus, Tenuicephalus multitrabs and T. squamilabrus. The species of Porogadus show a distinctive depth segregation with the majority of species having a demersal bathyal life-style between 800 and 3500 m and other species being more or less exclusively restricted to abyssal depths below 3000 m. The biogeographic distribution pattern of bathyal groups shows putative species pairs in the Atlantic versus the eastern Pacific and a clear separation of eastern Pacific from Indo-West Pacific species. The geographic effects and timing are being discussed that may have led to this speciation events. Generally, we found widely distributed species that are found far away from continental masses and others restrained to continental slopes and sometimes exhibiting regionalism. In abyssal depth, the Cabo Verde and Canary basins off NW-Africa have yielded three exclusive species, but it is uncertain at this stage whether this could represent a sampling bias with this area being extensively sampled by the Discovery research vessel (BMNH) over the years from 1970–1998. Another instance of a potentially endemic abyssal species is that of Porogadus melanocephalus in the Bay of Bengal. The latter has been caught with 45 specimens in a single trawl, representing the highest number of Porogadus specimens collected in any trawl and indicating that these fishes may actually not be as rare as one might assume from the literature.