Introduced or glacial relict? Phylogeography of the cryptogenic tunicate Molgula manhattensis (Ascidiacea, Pleurogona)

Local environment-driven adaptive evolution in a marine invasive ascidian (Molgula manhattensis)

Elucidating molecular mechanisms of environment-driven adaptive evolution in marine invaders is crucial for understanding invasion success and further predicting their future invasions. Although increasing evidence suggests that adaptive evolution could contribute to organisms' adaptation to varied environments, there remain knowledge gaps regarding how environments influence genomic variation in invaded habitats and genetic bases underlying local adaptation for most marine invaders. Here, we performed restriction-site-associated DNA sequencing (RADseq) to assess population genetic diversity and further investigate genomic signatures of local adaptation in the marine invasive ascidian, Molgula manhattensis. We revealed that most invasive populations exhibited significant genetic differentiation, low recent gene flow, and no signal of significant population bottleneck. Based on three genome scan approaches, we identified 109 candidate loci potentially under environmental selection. Redundancy analysis and variance partitioning analysis suggest that local environmental factors, particularly the salinity-related variables, represent crucial evolutionary forces in driving adaptive divergence. Using the newly developed transcriptome as a reference, 14 functional genes were finally obtained with potential roles in salinity adaptation, including SLC5A1 and SLC9C1 genes from the solute carrier gene (SLC) superfamily. Our findings confirm that differed local environments could rapidly drive adaptive divergence among invasive populations and leave detectable genomic signatures in marine invaders.

Speciation across the Tree of Life

Much of what we know about speciation comes from detailed studies of well-known model systems. Although there have been several important syntheses on speciation, few (if any) have explicitly compared speciation among major groups across the Tree of Life. Here, we synthesize and compare what is known about key aspects of speciation across taxa, including bacteria, protists, fungi, plants, and major animal groups. We focus on three main questions. Is allopatric speciation predominant across groups? How common is ecological divergence of sister species (a requirement for ecological speciation), and on what niche axes do species diverge in each group? What are the reproductive isolating barriers in each group? Our review suggests the following patterns. (i) Based on our survey and projected species numbers, the most frequent speciation process across the Tree of Life may be co-speciation between endosymbiotic bacteria and their insect hosts. (ii) Allopatric speciation appears to be present in all major groups, and may be the most common mode in both animals and plants, based on non-overlapping ranges of sister species. (iii) Full sympatry of sister species is also widespread, and may be more common in fungi than allopatry. (iv) Full sympatry of sister species is more common in some marine animals than in terrestrial and freshwater ones. (v) Ecological divergence of sister species is widespread in all groups, including ~70% of surveyed species pairs of plants and insects. (vi) Major axes of ecological divergence involve species interactions (e.g. host-switching) and habitat divergence. (vii) Prezygotic isolation appears to be generally more widespread and important than postzygotic isolation. (viii) Rates of diversification (and presumably speciation) are strikingly different across groups, with the fastest rates in plants, and successively slower rates in animals, fungi, and protists, with the slowest rates in prokaryotes. Overall, our study represents an initial step towards understanding general patterns in speciation across all organisms.

An elongated COI fragment to discriminate botryllid species and as an improved ascidian DNA barcode

Botryllids are colonial ascidians widely studied for their potential invasiveness and as model organisms, however the morphological description and discrimination of these species is very problematic, leading to frequent specimen misidentifications. To facilitate species discrimination and detection of cryptic/new species, we developed new barcoding primers for the amplification of a COI fragment of about 860 bp (860-COI), which is an extension of the common Folmer's barcode region. Our 860-COI was successfully amplified in 177 worldwide-sampled botryllid colonies. Combined with morphological analyses, 860-COI allowed not only discriminating known species, but also identifying undescribed and cryptic species, resurrecting old species currently in synonymy, and proposing the assignment of clade D of the model organism Botryllus schlosseri to Botryllus renierii. Importantly, within clade A of B. schlosseri, 860-COI recognized at least two candidate species against only one recognized by the Folmer's fragment, underlining the need of further genetic investigations on this clade. This result also suggests that the 860-COI could have a greater ability to diagnose cryptic/new species than the Folmer's fragment at very short evolutionary distances, such as those observed within clade A. Finally, our new primers simplify the amplification of 860-COI even in non-botryllid ascidians, suggesting their wider usefulness in ascidians.

Impacts of climate change on geographical distributions of invasive ascidians

Ocean warming associated with global climate change renders marine ecosystems susceptible to biological invasions. Here, we used species distribution models to project habitat suitability for eight invasive ascidians under present-day and future climate scenarios. Distance to shore and maximum sea surface temperature were identified as the most important variables affecting species distributions. Results showed that eight ascidians might respond differently to future climate change. Alarmingly, currently colonized areas are much smaller than predicted, suggesting ascidians may expand their invasive ranges. Areas such as Americas, Europe and Western Pacific have high risks of receiving new invasions. In contrast, African coasts, excluding the Mediterranean side, are not prone to new invasions, likely due to the high sea surface temperature there. Our results highlight the importance of climate change impacts on future invasions and the need for accurate modelling of invasion risks, which can be used as guides to develop management strategies.

Unravelling the origin and introduction pattern of the tropical species Paracaprella pusilla Mayer, 1890 (Crustacea, Amphipoda, Caprellidae) in temperate European waters: first molecular insights from a spatial and temporal perspective

Paracaprellapusilla Mayer, 1890 is a tropical caprellid species recently introduced to the Eastern Atlantic coast of the Iberian Peninsula and the Mediterranean Sea. In this study, we used direct sequencing of mitochondrial (COI and 16S) and nuclear (28S and ITS) genes to compare genetic differences in presumed native and introduced populations in order to infer its introduction pattern and to shed light on the native range of this species. The temporal pattern of genetic diversity at the westernmost limit of the geographic range of P.pusilla in Europe (the Atlantic coast of southern Spain) over an eight-year period was also investigated. Our results confirm P.pusilla as a neocosmopolitan species and suggest that the species is native to the Atlantic coast of Central and South America. Paracaprellapusilla seems to have been introduced into European waters from multiple introduction pathways and source populations, which are likely to include populations from coastal waters of Brazil. Multiple introduction pathways may have been involved, with the most important being commercial shipping through the Strait of Gibraltar. While this tropical species appears to be expanding in the Mediterranean, populations from the westernmost limit of its geographic range in Europe showed a temporal instability. This study constitutes the first molecular approach focused on this species, but it is also the first study of temporal change in genetic diversity of any introduced marine amphipod. Additional intensive sampling of this species, including both native and non-native populations, and detailed temporal studies are still necessary to properly understand how genetic diversity influences the introduction and survival of P.pusilla in invaded areas.

A Framework for Understanding Marine Cosmopolitanism in the Anthropocene

Recent years have witnessed growing appreciation for the ways in which human-mediated species introductions have reshaped marine biogeography. Despite this we have yet to grapple fully with the scale and impact of anthropogenic dispersal in both creating and determining contemporary distributions of marine taxa. In particular, the past several decades of research on marine biological invasions have revealed that broad geographic distributions of coastal marine organisms-historically referred to simply as "cosmopolitanism"-may belie complex interplay of both natural and anthropogenic processes. Here we describe a framework for understanding contemporary cosmopolitanism, informed by a synthesis of the marine bioinvasion literature. Our framework defines several novel categories in an attempt to provide a unified terminology for discussing cosmopolitan distributions in the world's oceans. We reserve the term eucosmopolitan to refer to those species for which data exist to support a true, natural, and prehistorically global (or extremely broad) distribution. While in the past this has been the default assumption for species observed to exhibit contemporary cosmopolitan distributions, we argue that given recent advances in marine invasion science this assignment should require positive evidence. In contrast, neocosmopolitan describes those species that have demonstrably achieved extensive geographic ranges only through historical anthropogenic dispersal, often facilitated over centuries of human maritime traffic. We discuss the history and human geography underpinning these neocosmopolitan distributions, and illustrate the extent to which these factors may have altered natural biogeographic patterns. We define the category pseudocosmopolitan to encompass taxa for which a broad distribution is determined (typically after molecular investigation) to reflect multiple, sometimes regionally endemic, lineages with uncertain taxonomic status; such species may remain cosmopolitan only so long as taxonomic uncertainty persists, after which they may splinter into multiple geographically restricted species. We discuss the methods employed to identify such species and to resolve both their taxonomic status and their biogeographic histories. We argue that recognizing these different types of cosmopolitanism, and the important role that invasion science has played in understanding them, is critically important for the future study of both historical and modern marine biogeography, ecology, and biodiversity.

Contrasting global genetic patterns in two biologically similar, widespread and invasive Ciona species (Tunicata, Ascidiacea)

Human-mediated dispersal interplays with natural processes and complicates understanding of the biogeographical history of species. This is exemplified by two invasive tunicates, Ciona robusta (formerly Ciona intestinalis type A) and C. intestinalis (formerly Ciona intestinalis type B), globally distributed and sympatric in Europe. By gathering new mitochondrial sequences that were merged with published datasets, we analysed genetic patterns in different regions, with a focus on 1) their sympatric range and 2) allopatric populations in N and S America and southern Europe. In the sympatric range, the two species display contrasting genetic diversity patterns, with low polymorphism in C. robusta supporting the prevalent view of its recent introduction. In the E Pacific, several genetic traits support the non-native status of C. robusta. However, in the NE Pacific, this appraisal requires a complex scenario of introduction and should be further examined supported by extensive sampling efforts in the NW Pacific (putative native range). For C. intestinalis, Bayesian analysis suggested a natural amphi-North Atlantic distribution, casting doubt on its non-native status in the NW Atlantic. This study shows that both natural and human-mediated dispersal have influenced genetic patterns at broad scales; this interaction lessens our ability to confidently ascertain native vs. non-native status of populations, particularly of those species that are globally distributed.

The more we search, the more we find: discovery of a new lineage and a new species complex in the genus Asparagopsis

In the past few decades, in the marine realm in particular, the use of molecular tools has led to the discovery of hidden taxonomic diversity, revealing complexes of sister species. A good example is the red algal genus Asparagopsis. The two species (A. armata and A. taxiformis) recognized in this genus have been introduced in many places around the world. Within the nominal species A. taxiformis, previous molecular analyses have uncovered several lineages, suggesting the existence of sister species or subspecies. Although the genus has been well studied in some regions (e.g., the Mediterranean Sea and Hawaii), it remains poorly investigated in others (e.g., South Pacific). Our study mainly focused on these latter areas to clarify lineages and better determine lineage status (i.e., native vs. introduced). A total of 188 specimens were collected from 61 sites, 58 of which had never been sampled before. We sequenced the DNA from samples for three markers and obtained 112 sequences for the chloroplastic RuBisCo spacer, 118 sequences for the nuclear LSU rRNA gene, and 174 for the mitochondrial spacer cox2-3. Phylogenetic analyses using all three markers suggested the existence of two cryptic sister species with the discovery of a new clade within A. armata. This clade was found only in Western Australia, Tasmania and New Zealand, and is thus restricted to a subregional biogeographic unit. We also discovered a new, fifth lineage for A. taxiformis restricted to the South Pacific and Western Australia. Except for this newly described lineage, all other lineages showed a global distribution influenced by introduction events. These results illustrate the difficulty in accurately defining cosmopolitan species. Our findings also highlight the need for targeted (i.e., in poorly studied areas) and geographically extensive sampling efforts when studying taxa that have been introduced globally and that are likely to hide species complexes.

Can novel genetic analyses help to identify low-dispersal marine invasive species?

Genetic methods can be a powerful tool to resolve the native versus introduced status of populations whose taxonomy and biogeography are poorly understood. The genetic study of introduced species is presently dominated by analyses that identify signatures of recent colonization by means of summary statistics. Unfortunately, such approaches cannot be used in low-dispersal species, in which recently established populations originating from elsewhere in the species' native range also experience periods of low population size because they are founded by few individuals. We tested whether coalescent-based molecular analyses that provide detailed information about demographic history supported the hypothesis that a sea squirt whose distribution is centered on Tasmania was recently introduced to mainland Australia and New Zealand through human activities. Methods comparing trends in population size (Bayesian Skyline Plots and Approximate Bayesian Computation) were no more informative than summary statistics, likely because of recent intra-Tasmanian dispersal. However, IMa2 estimates of divergence between putatively native and introduced populations provided information at a temporal scale suitable to differentiate between recent (potentially anthropogenic) introductions and ancient divergence, and indicated that all three non-Tasmanian populations were founded during the period of European settlement. While this approach can be affected by inaccurate molecular dating, it has considerable (albeit largely unexplored) potential to corroborate nongenetic information in species with limited dispersal capabilities.