A phylogeographic investigation of the hybrid origin of a species of swordtail fish from Mexico

Hybrid speciation may contribute significantly to generating biodiversity, but only a few well‐documented examples for it exist so far that do not involve polyploidization as a mechanism. The swordtail fish, Xiphophorus clemenciae, shows common hallmarks of a hybrid origin and still overlaps in its current geographic distribution with its putative ancestral species (Xiphophorus hellerii and Xiphophorus maculatus). Xiphophorus clemenciae provides an ideal system for investigating the possible continued genetic interactions between a hybrid and its parental species. Here, we use microsatellite and mitochondrial markers to investigate the population structure of these species of swordtails and search for signs of recent hybridization. Individuals were sampled from 21 localities across the known range of X. clemenciae– the Isthmus of Tehuantepec (IT) Mexico, and several environmental parameters that might represent barriers to dispersal were recorded. The hybridization event that gave rise to X. clemenciae appears to be rather ancient, and a single origin is likely. We find negligible evidence for ongoing hybridization and introgression between the putative ancestral species, because they now occupy distinct ecological niches, and a common haplotype is shared by most populations of X. clemenciae. The population structure within these species shows an isolation‐by‐distance (IBD) pattern and genetic differentiation between most populations is significant and high. We infer that tectonic evolution in the Isthmus has greatly restricted gene flow between the southern and central IT populations of X. clemenciae and X. helleriii and provide preliminary information to aid in conservation management of this geographically restricted hybrid species, X. clemenciae.     

Rapid formation of distinct hybrid lineages after secondary contact of two fish species (Cottus sp.)

Homoploid hybridization after secondary contact between related species can lead to mixtures of genotypes which have the potential for rapid adaptation to new environmental conditions. Here, we focus on a case where anthropogenic changes within the past 200 years have allowed the hybridization between two fish species (Cottus rhenanus and Cottus perifretum) in the Netherlands. Specifically, we address the question of the dynamics of the emergence of these hybrids and invasion of the river systems. Using a set of 81 mostly ancestry-informative SNP markers, as well as broad sample coverage in and around the area of the initial contact, we find a structured hybrid swarm with at least three distinct hybrid lineages that have emerged out of this secondary contact situation. We show that genetically coherent groups can occur at geographically distant locations, while geographically adjacent groups can be genetically different, indicating that some form of reproductive isolation between the lineages is already effective. Using a newly developed modelling approach, we test the relative influence of founding admixture, drift and migration on the allele compositions of the sampling sites. We find that the allele frequency distributions can best be explained if continued gene flow between the parental species and the hybrid lineages is invoked. Genome mapping of the invasive lineage in the Rhine shows that major chromosomal rearrangements were not involved in creating this distinct lineage. Our results show that hybridization after secondary contact can quickly lead to multiple independent new lineages that have the capacity to form hybrid species.     

A hybrid zone and bidirectional introgression between two catadromous species: Australian bass Macquaria novemaculeata and estuary perch Macquaria colonorum

The presence and distribution of hybrid individuals and the existence of a hybrid zone between the catadromous Australian bass Macquaria novemaculeata and estuary perch Macquaria colonorum were investigated throughout the range of both species in Australia. Bayesian analyses and genotypic simulations identified 140 putative hybrids (11·5% of the total sample) with varying levels of introgression. Most hybrids were observed in an area extending from the Snowy River to the Albert River suggesting a hybrid zone in the eastern Bass Strait region. Sixteen hybrids, however, were found outside this zone, possibly reflecting the movement of hybrid offspring between estuaries or their inadvertent release during fish stocking programmes. Biparental backcrossing was found to occur suggesting that hybrids were fertile. These results have implications for the management of the extensive stocking programme in M. novemaculeata and for understanding the potential role of habitat degradation and reduced water flow in facilitating hybridization in species with migratory life histories.     

Population structure in two sympatric species of the Lake Tanganyika cichlid tribe Eretmodini: evidence for introgression

Patterns of genetic differentiation were analysed and compared in two sympatric species of the endemic Lake Tanganyika cichlid tribe Eretmodini by means of mitochondrial DNA (mtDNA) sequences of the control region and six microsatellite DNA loci. The sample area covers a total of 138 km of mostly uninterrupted rocky shoreline in the Democratic Republic of Congo and includes the entire distribution range of Tanganicodus cf. irsacae that stretches over a distance of 35 km. Both markers detected significant genetic differentiation within and between the two species. T. cf. irsacae contained lower overall genetic variation than Eretmoduscyanostictus, possibly due to its more restricted range of distribution and its smaller effective population sizes. Complete fixation of Tanganicodus mtDNA haplotypes was observed in Eretmodus at two localities, while at two other localities some Tanganicodus individuals possessed Eretmodus mtDNA haplotypes. Taking into account the relatively large average sequence divergence of 6.2% between the two species, as well as the geographical distribution of mtDNA haplotypes in the lake, the observed pattern is more likely to be a consequence of asymmetric introgression than of shared ancestral polymorphism. As there is significant population differentiation between sympatric Tanganicodus and Eretmodus populations, the events of introgressions may have happened after secondary contact, but our data provide no evidence for ongoing gene flow and suggest that both species are reproductively isolated at present time.     

TreeGOER: A database with globally observed environmental ranges for 48,129 tree species

The TreeGOER (Tree Globally Observed Environmental Ranges) database provides information for most known tree species of their environmental ranges for 38 bioclimatic, eight soil and three topographic variables. It is based on species distribution modelling analyses of more than 44 million occurrences. The database can be accessed from https://doi.org/10.5281/zenodo.7922927 . Statistics that include 5% and 95% quantiles were estimated for a cleaned and taxonomically standardized occurrence data set with different methods of outlier detection, with estimates for roughly 45% of species being based on 20 or more observation records. Where sufficient representative observations are available, the ranges provide useful preliminary estimates of suitable conditions particularly for lesser-known species under climate change. Inferred core bioclimatic ranges of species along global temperature and moisture index gradients and across continents follow the known global distribution of tree diversity such as its highest levels in moist tropical forests and the ‘odd man out’ pattern of lower levels in Africa. To demonstrate how global analyses for large numbers of tree species can easily be done in R with TreeGOER , here I present two case studies. The first case study investigated latitudinal trends of tree vulnerability and compared these with previous results obtained for urban trees. The second case study focused on tropical areas, compared trends in different longitudinal zones and investigated patterns for the moisture index. TreeGOER is expected to benefit researchers conducting biogeographical and climate change research for a wide range of tree species at a variety of spatial and temporal scales.     

Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae)

Microsatellites are often considered ideal markers to investigate ecological processes in animal populations. They are regularly used as genetic barcodes to identify species, individuals, and infer familial relationships. However, such applications are highly sensitive the number and diversity of microsatellite markers, which are also prone to error. Here, we propose a novel framework to assess the suitability of microsatellite datasets for parentage analysis and species discrimination in two closely related species of coral reef fish, Plectropomus leopardus and P. maculatus (Serranidae). Coral trout are important fisheries species throughout the Indo‐Pacific region and have been shown to hybridize in parts of the Great Barrier Reef, Australia. We first describe the development of 25 microsatellite loci and their integration to three multiplex PCRs that co‐amplify in both species. Using simulations, we demonstrate that the complete suite of markers provides appropriate power to discriminate between species, detect hybrid individuals, and resolve parent–offspring relationships in natural populations, with over 99.6% accuracy in parent–offspring assignments. The markers were also tested on seven additional species within the Plectropomus genus with polymorphism in 28–96% of loci. The multiplex PCRs developed here provide a reliable and cost‐effective strategy to investigate evolutionary and ecological dynamics and will be broadly applicable in studies of wild populations and aquaculture brood stocks for these closely related fish species.     

Evidence for broadscale introgressive hybridization between two redfish (genus Sebastes) in the North-west Atlantic: a rare marine example

The evolutionary importance of introgressive hybridization has long been recognized by plant evolutionists, and there is now a growing recognition for its potential role in animals as well. Detailed empirical investigations of this evolutionary process, however, are still lacking in many animal groups, particularly in the marine environment. Using integrated microsatellite DNA data (eight loci analysed over 803 individuals representing 17 sampling locations) and multivariate statistical procedures (principal component, factorial correspondence and admixture proportion analyses), we: (i) provide a detailed dissection of the dynamics of introgressive hybridization between Sebastes fasciatus and S. mentella, two economically important redfishes from the North-west Atlantic; and (ii) infer the factors potentially involved in the maintenance of the hybrid zone observed in the gulf of St. Lawrence and south of Newfoundland. This study provided one of the rare examples of extensive introgressive hybridization in the ocean, and highlighted the predominant role of this process in shaping the extent of genetic diversity, interspecific differences and population structuring among redfishes from the North-west Atlantic. The extensive (average rate of introgression = 15%) but geographically circumscribed and asymmetrical pattern of introgressive hybridization, the sympatric persistence of two reproductively isolated introgressed groups, the differential patterns of linkage disequilibrium among samples, and the maintenance of genetic integrity of both species outside the defined zone of introgression despite high potential for gene flow, all implicated selection in promoting and maintaining the observed pattern of introgression.     

Growth and temperature relationships for juvenile fish species in seagrass beds: implications of climate change

The effect of water temperature on growth responses of three common seagrass fish species that co‐occur as juveniles in the estuaries in Sydney (34° S) but have differing latitudinal ranges was measured: Pelates sexlineatus (subtropical to warm temperate: 27–35° S), Centropogon australis (primarily subtropical to warm temperate: 24–37° S) and Acanthaluteres spilomelanurus (warm to cool temperate: below 32° S). Replicate individuals of each species were acclimated over a 7 day period in one of three temperature treatments (control: 22° C, low: 18° C and high: 26° C) and their somatic growth was assessed within treatments over 10 days. Growth of all three species was affected by water temperature, with the highest growth of both northern species (P. sexlineatus and C. australis) at 22 and 26° C, whereas growth of the southern ranging species (A. spilomelanurus) was reduced at temperatures higher than 18° C, suggesting that predicted increase in estuarine water temperatures through climate change may change relative performance of seagrass fish assemblages.     

Niche divergence of two closely related Carbula species (Insecta: Hemiptera: Pentatomidae) despite the presence of a hybrid zone

1. The extent to which ecologically divergent selection acts to maintain species boundaries in the presence of hybridisation and gene flow is not well understood. Two parapatric taxa, Carbula humerigera (Uhler) and Carbula putoni (Jakovlev), were used to test the extent to which niche differentiation might sustain divergence of related taxa despite ongoing gene flow. 2. Mitochondrial [cytochrome c oxidase subunit I (COI), cytochrome c oxidase subunit II (COII) and cytochrome b (Cytb)] and nuclear [elongation factor 1‐alpha (EF‐1α)] markers were sequenced from 383 individuals. Clusters of morphological variations were estimated and visualised using principal component analysis (PCA). Haplotype networks were constructed using median‐joining and neighbour‐net algorithm methods. Gene flows were estimated using migrate‐n analyses. Suitable habitats for each species and their sympatric distribution were predicted with ecological niche modelling (ENM). Niche comparisons were conducted using Schoener's D and Warren's I. In addition, PCA, multivariate analysis of variance (manova ) and discriminant function analysis were used to test ecological differentiation. 3. Morphological clusters and network analysis indicated that samples were generally divided into three groups (C. humerigera, C. putoni and hybrids). Ongoing gene flow was detected among the three groups, with abundant magnitudes in the sympatric region. Niche comparison and statistical analysis showed ecological differentiation between C. humerigera and C. putoni. Two potential hybrid zones were predicted in the ENM reconstruction, located along the Yanshan‐Taihang‐Qinling and Taishan mountains. 4. These results reveal a geographically delineated hybrid zone between C. humerigera and C. putoni. These two closely related Carbula species still live in different ecological niches despite hybridisation and ongoing gene flow.     

A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification

Whole genome duplication (WGD) is often considered to be mechanistically associated with species diversification. Such ideas have been anecdotally attached to a WGD at the stem of the salmonid fish family, but remain untested. Here, we characterized an extensive set of gene paralogues retained from the salmonid WGD, in species covering the major lineages (subfamilies Salmoninae, Thymallinae and Coregoninae). By combining the data in calibrated relaxed molecular clock analyses, we provide the first well-constrained and direct estimate for the timing of the salmonid WGD. Our results suggest that the event occurred no later in time than 88 Ma and that 40–50 Myr passed subsequently until the subfamilies diverged. We also recovered a Thymallinae–Coregoninae sister relationship with maximal support. Comparative phylogenetic tests demonstrated that salmonid diversification patterns are closely allied in time with the continuous climatic cooling that followed the Eocene–Oligocene transition, with the highest diversification rates coinciding with recent ice ages. Further tests revealed considerably higher speciation rates in lineages that evolved anadromy—the physiological capacity to migrate between fresh and seawater—than in sister groups that retained the ancestral state of freshwater residency. Anadromy, which probably evolved in response to climatic cooling, is an established catalyst of genetic isolation, particularly during environmental perturbations (for example, glaciation cycles). We thus conclude that climate-linked ecophysiological factors, rather than WGD, were the primary drivers of salmonid diversification.     

A hybrid zone dominated by fertile F1s of two alpine shrub species, Phyllodoce caerulea and Phyllodoce aleutica, along a snowmelt gradient

In alpine ecosystems, the steep environmental gradients produced by the difference in snowmelt timing create a dynamic selective regime for alpine plants. As these gradients directly alter flowering phenology, they can affect pollen-mediated gene flow among populations of single and related species. In northern Japan, we found a hybrid zone dominated by fertile F(1)s of two alpine shrub species, Phyllodoce caerulea and P. aleutica, along a snowmelt gradient. Seed germination confirmed the fertility of F(1) hybrid, making the rarity and absence of backcross and F(2) plants puzzling. The long-term clonal perpetuation of F(1) hybrids (at least a few thousand years ago) contributes the maintenance of this unique hybrid zone. The distribution patterns of chloroplast DNA haplotypes suggest that F(1) formation might be caused by directional pollen flow between parental species along the snowmelt gradient. Based on these results, we discuss the ecological and evolutionary significance of this unique hybrid zone.     

Genetic polymorphism of a haemoglobin chain and adenosine deaminase in European shads: evidence for the existence of two distinct genetic entities with natural hybridization

The degree of genetic differentiation between European shads, Alosa alosa and A. fallax , was studied in populations from different Portuguese hydrographic basins. Using isoelectric focusing, polymorphic variation was detected in a haemoglobin (HB) chain and in adenosine deaminase (ADA). These polymorphisms are shared by the two species but show significant differences in their gene frequency distributions. Individuals with intermediate morphological characteristics were found to exhibit intermediate allele frequencies. While not completely excluding introgression, our results strongly support the existence of two distinct species that can hybridize.     

A decline in primary production in the North Sea over 25 years,associated with reductions in zooplankton abundance and fish stock recruitment

Phytoplankton primary production is at the base of the marine food web; changes in primary production have direct or indirect effects on higher trophic levels, from zooplankton organisms to marine mammals and seabirds. Here, we present a new time‐series on gross primary production in the North Sea, from 1988 to 2013, estimated using in situ measurements of chlorophyll and underwater light. This shows that recent decades have seen a significant decline in primary production in the North Sea. Moreover, primary production differs in magnitude between six hydrodynamic regions within the North Sea. Sea surface warming and reduced riverine nutrient inputs are found to be likely contributors to the declining levels of primary production. In turn, significant correlations are found between observed changes in primary production and the dynamics of higher trophic levels including (small) copepods and a standardized index of fish recruitment, averaged over seven stocks of high commercial significance in the North Sea. Given positive (bottom‐up) associations between primary production, zooplankton abundance and fish stock recruitment, this study provides strong evidence that if the decline in primary production continues, knock‐on effects upon the productivity of fisheries are to be expected unless these fisheries are managed effectively and cautiously.     

The carbon fertilization effect over a century of anthropogenic CO2 emissions: higher intracellular CO2 and more drought resistance among invasive and native grass species contrasts with increased water use efficiency for woody plants in the US Southwest

From 1890 to 2015, anthropogenic carbon dioxide emissions have increased atmospheric CO₂ concentrations from 270 to 400 mol mol^?1. The effect of increased carbon emissions on plant growth and reproduction has been the subject of study of free‐air CO₂ enrichment (FACE) experiments. These experiments have found (i) an increase in internal CO₂ partial pressure (c_i) alongside acclimation of photosynthetic capacity, (ii) variable decreases in stomatal conductance, and (iii) that increases in yield do not increase commensurate with CO₂ concentrations. Our data set, which includes a 115‐year‐long selection of grasses collected in New Mexico since 1892, is consistent with an increased c_i as a response to historical CO₂ increase in the atmosphere, with invasive species showing the largest increase. Comparison with Palmer Drought Sensitivity Index (PDSI) for New Mexico indicates a moderate correlation with Δ¹³C (r² = 0.32, P < 0.01) before 1950, with no correlation (r² = 0.00, P = 0.91) after 1950. These results indicate that increased c_i may have conferred some drought resistance to these grasses through increased availability of CO₂ in the event of reduced stomatal conductance in response to short‐term water shortage. Comparison with C₃ trees from arid environments (Pinus longaeva and Pinus edulis in the US Southwest) as well as from wetter environments (Bromus and Poa grasses in New Mexico) suggests differing responses based on environment; arid environments in New Mexico see increased intrinsic water use efficiency (WUE) in response to historic elevated CO₂ while wetter environments see increased c_i. This study suggests that (i) the observed increases in c_i in FACE experiments are consistent with historical CO₂ increases and (ii) the CO₂ increase influences plant sensitivity to water shortage, through either increased WUE or c_i in arid and wet environments, respectively.