Evolutionary history of the European free-tailed bat,a tropical affinity species spanning across the Mediterranean Basin

The Mediterranean Basin is a global biodiversity hotspot, hosting a number of native species belonging to families that are found almost exclusively in tropical climates. Yet, whether or not these taxa were able to survive in the Mediterranean region during the Quaternary climatic oscillations remains unknown. Focusing on the European free-tailed bat (Tadarida teniotis), we aimed to (a) identify potential ancient populations and glacial refugia; (b) determine the post-glacial colonization routes across the Mediterranean; and (c) evaluate current population structure and demography. Mitochondrial and nuclear markers were used to understand T. teniotis evolutionary and demographic history. We show that T. teniotis is likely restricted to the Western Palearctic, with mitochondrial phylogeny suggesting a split between an Anatolian/Middle East clade and a European clade. Nuclear data pointed to three genetic populations, one of which is an isolated and highly differentiated group in the Canary Islands, another distributed across Iberia, Morocco, and France, and a third stretching from Italy to the east, with admixture following a pattern of isolation by distance. Evolutionary and demographic reconstruction supports a pre-Last Glacial Maximum (LGM) colonization of Italy and the Anatolian/Middle East, while the remaining populations were colonized from Italy after the Younger Dryas. We also found support for demographic expansion following the Iberian colonization. The results show that during the LGM T. teniotis persisted in Mediterranean refugia and has subsequently expanded to its current circum-Mediterranean range. Our findings raise questions regarding the physiological and ecological traits that enabled species with tropical affinities to survive in colder climates.     

Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species

C₄ photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C₄ and non-C₄ populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during and after photosynthetic divergence in A. semialata. We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C₄ lineage after dispersal to warmer areas of lower elevation. Nuclear genome analyses highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C₄ phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple intraspecific allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C₄ physiology away from its region of origin.     

The toad’s warts: Discordance creates bumpy expectations of mitochondrial‐nuclear evolution between species

Discordance between the mitochondrial and nuclear genomes is a prevalent phenomenon in nature, in which the underlying processes responsible are considered to be important in shaping genetic variation in natural populations. Among the evolutionary processes that best explain such genomic mismatches incomplete lineage sorting and introgression are commonly identified, however, many studies are unable to distinguish between these hypotheses, which has become a major challenge in the field. In this issue of Molecular Ecology, Firneno et al. (2020) present an elegant exploration of mitochondrial‐nuclear discordance in Mesoamerican toads. Integrating genome‐scale and spatial data to test between these hypotheses within an empirical model testing framework, they find strong support that incomplete lineage sorting explains the observed discordance. Their work, along with many previous articles in Molecular Ecology, highlights the commonality of mito‐nuclear discordance among species despite the expectations of tightly concerted mitochondrial and nuclear genome evolution. It is increasingly clear that the nuclear genomes of many species are (at least for short periods of evolutionary time) functionally compatible with multiple, divergent mitochondrial haplotypes. As such, we suggest future research not only seeks to understand the processes causing spatial mito‐nuclear discordance (e.g. incomplete lineage sorting, introgression), but also explores those that maintain discordance through time and space (e.g. relaxed selection on mito‐nuclear interactions, heterozygosity, population demographics). We also discuss the vital role that taxonomy plays in interpreting patterns of mito‐nuclear discordance when data‐consistent yet differing taxonomies are used, such as treating allopatrically distributed taxa as multiple isolated populations versus multiple micro‐endemic species.     

Fungal communities living within leaves of native Hawaiian dicots are structured by landscape‐scale variables as well as by host plants

A phylogenetically diverse array of fungi live within healthy leaf tissue of dicotyledonous plants. Many studies have examined these endophytes within a single plant species and/or at small spatial scales, but landscape‐scale variables that determine their community composition are not well understood, either across geographic space, across climatic conditions, or in the context of host plant phylogeny. Here, we evaluate the contributions of these variables to endophyte beta diversity using a survey of foliar endophytic fungi in native Hawaiian dicots sampled across the Hawaiian archipelago. We used Illumina technology to sequence fungal ITS1 amplicons to characterize foliar endophyte communities across five islands and 80 host plant genera. We found that communities of foliar endophytic fungi showed strong geographic structuring between distances of 7 and 36 km. Endophyte community structure was most strongly associated with host plant phylogeny and evapotranspiration, and was also significantly associated with NDVI, elevation and solar radiation. Additionally, our bipartite network analysis revealed that the five islands we sampled each harboured significantly specialized endophyte communities. These results demonstrate how the interaction of factors at large and small spatial and phylogenetic scales shapes fungal symbiont communities.     

Genotyping‐by‐sequencing and ecological niche modeling illuminate phylogeography,admixture, and Pleistocene range dynamics in quaking aspen (Populus tremuloides)

Populus tremuloides is the widest‐ranging tree species in North America and an ecologically important component of mesic forest ecosystems displaced by the Pleistocene glaciations. Using phylogeographic analyses of genome‐wide SNPs (34,796 SNPs, 183 individuals) and ecological niche modeling, we inferred population structure, ploidy levels, admixture, and Pleistocene range dynamics of P. tremuloides, and tested several historical biogeographical hypotheses. We found three genetic lineages located mainly in coastal–Cascades (cluster 1), east‐slope Cascades–Sierra Nevadas–Northern Rockies (cluster 2), and U.S. Rocky Mountains through southern Canadian (cluster 3) regions of the P. tremuloides range, with tree graph relationships of the form ((cluster 1, cluster 2), cluster 3). Populations consisted mainly of diploids (86%) but also small numbers of triploids (12%) and tetraploids (1%), and ploidy did not adversely affect our genetic inferences. The main vector of admixture was from cluster 3 into cluster 2, with the admixture zone trending northwest through the Rocky Mountains along a recognized phenotypic cline (Utah to Idaho). Clusters 1 and 2 provided strong support for the “stable‐edge hypothesis” that unglaciated southwestern populations persisted in situ since the last glaciation. By contrast, despite a lack of clinal genetic variation, cluster 3 exhibited “trailing‐edge” dynamics from niche suitability predictions signifying complete northward postglacial expansion. Results were also consistent with the “inland dispersal hypothesis” predicting postglacial assembly of Pacific Northwestern forest ecosystems, but rejected the hypothesis that Pacific‐coastal populations were colonized during outburst flooding from glacial Lake Missoula. Overall, congruent patterns between our phylogeographic and ecological niche modeling results and fossil pollen data demonstrate complex mixtures of stable‐edge, refugial locations, and postglacial expansion within P. tremuloides. These findings confirm and refine previous genetic studies, while strongly supporting a distinct Pacific‐coastal genetic lineage of quaking aspen.     

Is population subdivision different from speciation? From phylogeography to species delimitation

Species‐level diversity and the underlying mechanisms that lead to the formation of new species, that is, speciation, have often been confounded with intraspecific diversity and population subdivision. The delineation between intraspecific and interspecific divergence processes has received much less attention than species delimitation. The ramifications of confounding speciation and population subdivision are that the term speciation has been used to describe many different biological divergence processes, rendering the results, or inferences, between studies incomparable. Phylogeographic studies have advanced our understanding of how spatial variation in the pattern of biodiversity can begin, become structured, and persist through time. Studies of species delimitation have further provided statistical and model‐based approaches to determine the phylogeographic entities that merit species status. However, without a proper understanding and delineation between the processes that generate and maintain intraspecific and interspecific diversity in a study system, the delimitation of species may still not be biologically and evolutionarily relevant. I argue that variation in the continuity of the divergence process among biological systems could be a key factor leading to the enduring contention in delineating divergence patterns, or species delimitation, meriting future comparative studies to help us better understand the nature of biological species.     

Land masses and oceanic currents drive population structure of Heritiera littoralis,a widespread mangrove in the Indo‐West Pacific

Phylogeographic forces driving evolution of sea‐dispersed plants are often influenced by regional and species characteristics, although not yet deciphered at a large spatial scale for many taxa like the mangrove species Heritiera littoralis. This study aimed to assess geographic distribution of genetic variation of this widespread mangrove in the Indo‐West Pacific region and identify the phylogeographic factors influencing its present‐day distribution. Analysis of five chloroplast DNA fragments’ sequences from 37 populations revealed low genetic diversity at the population level and strong genetic structure of H. littoralis in this region. The estimated divergence times between the major genetic lineages indicated that glacial level changes during the Pleistocene epoch induced strong genetic differentiation across the Indian and Pacific Oceans. In comparison to the strong genetic break imposed by the Sunda Shelf toward splitting the lineages of the Indian and Pacific Oceans, the genetic differentiation between Indo‐Malesia and Australasia was not so prominent. Long‐distance dispersal ability of H. littoralis propagules helped the species to attain transoceanic distribution not only across South East Asia and Australia, but also across the Indian Ocean to East Africa. However, oceanic circulation pattern in the South China Sea was found to act as a barrier creating further intraoceanic genetic differentiation. Overall, phylogeographic analysis in this study revealed that glacial vicariance had profound influence on population differentiation in H. littoralis and caused low genetic diversity except for the refugia populations near the equator which might have persisted through glacial maxima. With increasing loss of suitable habitats due to anthropogenic activities, these findings therefore emphasize the urgent need for conservation actions for all populations throughout the distribution range of H. littoralis.     

Sampling and distribution pattern of Trioza erytreae Del Guercio, 1918 (Hemiptera: Triozidae) in citrus orchard

Developing efficient sampling protocols is essential to monitor crop pests. One vector of the citrus disease HLB, the African citrus psyllid Trioza erytreae Del Guercio, 1918 (Hemiptera: Triozidae), currently threatens the lemon industry throughout the Mediterranean region. In this work, a pool of sampling methods devoted to monitoring the population of T. erytreae was compared, its spatial distribution in the orchard was assessed, and the minimum sampling effort for the best sampling method was estimated. Three lemon orchards in North-western Portugal were sampled for one year using two types of yellow sticky traps (standard yellow and fluorescent Saturn yellow), B-vac sampling and sweep net sampling. The method that best performed, in terms of cost-efficiency, was the yellow sticky traps. The two colours of the sticky traps tested did not yield a significantly different number of catches. The spatial distribution throughout the orchards was found to be aggregated towards the borders. A minimum of three sticky traps per hectare was found to be enough to estimate the population at 90% accuracy for the mean during the outbreak. These results should help to monitor and anticipate outbreaks that may even colonize neighbour orchards. Studies on the local dispersion patterns of T. erytreae throughout the orchard are mandatory to further refine and optimize efficient monitoring protocols.