Intraspecific Population Structure Research Articles

Distribution and genomic variation of ammonia-oxidizing archaea in abyssal and hadal surface sediments

Ammonia-oxidizing archaea of the phylum Thaumarchaeota play a central role in the biogeochemical cycling of nitrogen in benthic sediments, at the interface between pelagic and subsurface ecosystems. However, our understanding of their niche separation and of the processes controlling their population structure in hadal and abyssal surface sediments is still limited. Here, we reconstructed 47 AOA metagenome-assembled genomes (MAGs) from surface sediments of the Atacama and Kermadec trench systems. They formed deep-sea-specific groups within the family Nitrosopumilaceae and were assigned to six amoA gene-based clades. MAGs from different clades had distinct distribution patterns along oxygen-ammonium counter gradients in surface sediments. At the species level, MAGs thus seemed to form different ecotypes and follow deterministic niche-based distributions. In contrast, intraspecific population structure, defined by patterns of Single Nucleotide Variants (SNV), seemed to reflect more complex contributions of both deterministic and stochastic processes. Firstly, the bathymetric range had a strong effect on population structure, with distinct populations in abyssal plains and hadal trenches. Then, hadal populations were clearly separated by trench system, suggesting a strong isolation-by-topography effect, whereas abyssal populations were rather controlled by sediment depth or geographic distances, depending on the clade considered. Interestingly, genetic variability between samples was lowest in sediment layers where the mean MAG coverage was highest, highlighting the importance of selective pressure linked with each AOA clade’s ecological niche. Overall, our results show that deep-sea AOA genome distributions seem to follow both deterministic and stochastic processes, depending on the genomic variability scale considered.

Diet Specialization in an Insular Population of Coastal Peregrine Falcons

Individual diet specialization is known to occur in populations of generalist predators, where specific individuals develop specialist feeding strategies. Diet specialization has been reported in many raptor species and it may be an important driver of intraspecific population structure. Here, we quantify the diet of Peregrine Falcons Falco peregrinus from five breeding territories on an island determined from prey remains collected over four breeding seasons. Three prey species accounted for 69.8% of total prey frequency, with Manx Shearwater Puffinus puffinus being the primary prey accounting for 47.3% by frequency and 40.8% by biomass. European Herring Gull Larus argentatus was the second most important prey species by frequency (13.8%) and biomass (29.8%) followed by Feral Pigeon Columba livia (frequency: 8.7%, biomass: 7.0%). Prey frequency on specific prey groups varied substantially between breeding pairs and months. Two pairs specialized on Manx Shearwater, one pair specialized on Herring Gull and Manx Shearwater, with the remaining two pairs having a relatively generalist diet of Manx Shearwaters, Feral Pigeon and small passerines. Prey frequency on Manx Shearwaters increased throughout the breeding season with a peak in total diet frequency of 63.8% in July, with a concurrent decrease in Herring Gull prey frequency. Higher percentage of Manx Shearwater in the diet explained 87% of the variation in a narrower dietary breadth for the Peregrine pairs. Our results suggest individual diet specialization may be one of multiple factors important for understanding population density in insular raptor populations.

Genetic structure of Aedes albopictus (Diptera: Culicidae) populations in China and relationship with the knockdown resistance mutations

BackgroundMosquito control is needed to prevent dengue fever, which is mainly spread by Aedes albopictus in China. Application of insecticides is one of the main mosquito control methods; however, this approach can fail due to the knockdown resistance (kdr) gene mutation that causes decreased sensitivity to insecticides in Ae. albopictus. The kdr mutation patterns among different regions in China differ significantly. However, the underlying mechanism and factors that influence kdr mutation remain unclear. To explore the potential influence of genetic background on the development of insecticide resistance in Ae. albopictus, we analyzed the genetic structure of Ae. albopictus populations in China and its correlation with major kdr mutations.MethodsWe collected Ae. albopictus from 17 sites in 11 provinces (municipalities) across China from 2016 to 2021 and extracted the genomic DNA from individual adult mosquitoes. We selected eight microsatellite loci for genotyping, and based on microsatellite scores, we estimated intraspecific genetic diversity, population structure, and effective population size. The association between the intrapopulation genetic variation and F1534 mutation rate was evaluated by the Pearson correlation coefficient.ResultsBased on variation analysis of the microsatellite loci of 453 mosquitoes representing 17 populations throughout China, more than 90% of the variation occurred within individuals, whereas only about 9% of the variation occurred among populations, indicating that field populations of Ae. albopictus are highly polymorphic. The northern populations tended to belong to gene pool I (BJFT 60.4%, SXXA 58.4%, SDJN 56.1%, SXYC 46.8%), the eastern populations tended to belong to pool III (SH 49.5%, JZHZ 48.1%), and the southern populations tended to belong to three different gene pools. Moreover, we observed that the greater the fixation index (FST), the lower the wild-type frequency of F1534 of VSGC.ConclusionsThe degree of genetic differentiation among Ae. albopictus populations in China was low. These populations were divided into three gene pools, in which the northern and eastern pools are relatively homogeneous, while the southern gene pool is heterogeneous. The possible correlation between its genetic variations and kdr mutations is also noteworthy.Graphical

Genome-wide markers show continental structuring and mitonuclear discordance in the forest tent caterpillar (Malacosoma disstria Hübner) (Lepidoptera: Lasiocampidae)

Abstract The forest tent caterpillar, Malacosoma disstria Hübner (Lepidoptera: Lasiocampidae), is an irruptive forest pest found throughout North America. Widespread species such as M. disstria are exposed to historical and contemporary processes that are not uniform and can generate regionally distinct genomic variation. Previous analyses used a short mitochondrial fragment to infer broad-scale phylogeographic patterns in M. disstria, whereas nuclear markers have been previously applied only in a smaller geographic region. In this study, we quantified M. disstria population variation with genome-wide single nucleotide polymorphisms and cytochrome c oxidase from mitochondrial DNA. Using highly variable genome-wide markers, we resolved clear genomic differences among populations of M. disstria east of the Rocky Mountains that were not detected using mitochondrial variation alone. We also did not detect host-associated divergence in either our genomic or mitochondrial data. Our results highlight the utility of genome-wide markers to resolve intraspecific population structure within a widespread species and support the need for further biogeographic sampling of this forest insect pest.

Geographical distribution, molecular and toxin diversity of the dinoflagellate species Gambierdiscus honu in the Pacific region

An increase in cases of ciguatera poisoning (CP) and expansion of the causative species in the South Pacific region highlight the need for baseline data on toxic microalgal species to help identify new areas of risk and manage known hot spots. Gambierdiscus honu is a toxin producing and potential CP causing dinoflagellate species, first described in 2017. Currently no high-resolution geographical distribution, intraspecific genetic variation or toxin production diversity data is available for G. honu. This research aimed to further characterize G. honu by investigating its distribution using species-specific real-time polymerase chain reaction assays at 25 sites in an area spanning ∼8000 km of the Coral Sea/Pacific Ocean, and assessing intraspecific genetic variation, toxicity and toxin production of isolated strains. Assessment of genetic variation of the partial rRNA operon of isolates demonstrated no significant intraspecific population structure, in addition to a lack of adherence to isolation by distance (IBD) model of evolution. The detected distribution of G. honu in the Pacific region was within the expected tropical to temperate latitudinal ranges of 10° to -30° and extended from Australia to French Polynesia. In the lipophilic fractions, the neuroblastoma cell-based assay (CBA-N2a) showed no ciguatoxin (CTX)-like activity for nine of the 10 isolates, and an atypical pattern for CAWD233 isolate which showed cytotoxic activity in OV- and OV+ conditions. In the same way, liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis confirmed no Pacific-CTXs (CTX-3B, CTX-3C, CTX-4A, CTX-4B) were produced by the ten strains. The CBA-N2a assessment of the hydrophilic fractions showed moderate to high cytotoxicity in both OV- and OV+ condition for all the strains showing a cytotoxic profile similar to that of gambierone. Indeed, this study is the first to show the cytotoxic activity of gambierone on mouse neuroblastoma cells while no cytotoxicity was observed when 44-MG was analysed at the same concentrations using the CBA-N2a. Analysis of the hydrophilic via LC-MS/MS confirmed production of gambierone in all isolates, ranging from 2.1 to 38.1 pg/cell, with 44-methylgambierone (44-MG) also produced by eight of the isolates, ranging from 0.3 to 42.9 pg/cell. No maitotoxin-1 was detected in any of the isolates. Classification of the G. honu strains according to the quantities of gambierone produced aligned with the classification of their cytotoxicity using the CBA-N2a. Finally, no maitotoxin-1 (MTX) was detected in any of the isolates. This study shows G. honu is widely distributed within the Pacific region with no significant intraspecific population structure present. This aligns with the view of microalgal populations as global metapopulations, however more in-depth assessment with other genetic markers could detect further structure. Toxicity diversity across 10 isolates assessed did not display any geographical patterns.

A new set of microsatellite markers for Phoxinus lumaireul senso lato, Phoxinus marsilii and Phoxinus krkae for population and molecular taxonomic studies.

Minnows of the genus Phoxinus are common and an often highly abundant fish species in Palearctic freshwater habitats. Phoxinus species have a complex evolutionary history, phylogenetic relationships are not well understood and there are a number of unresolved taxonomic problems. There are currently 23 different mitochondrial genetic lineages identified in the genus Phoxinus, 13 of which are recognized as valid species. The taxonomic status of these lineages requires resolution, including the degree to which they can interbreed. Suitable nuclear molecular markers for studies of population divergence and interbreeding between morphotypes and mitochondrial lineages are lacking for Phoxinus species. Therefore, the authors developed a set of microsatellite markers using genomic information from Phoxinus lumaireul and tested their suitability for this and two related species, Phoxinus krkae and Phoxinus marsilii. Out of 16 microsatellite candidate loci isolated, 12 were found to be in Hardy-Weinberg equilibrium when tested on two P. lumaireul senso lato populations. Seven loci amplified across the three species, enabling the study of intraspecific genetic diversity and population structure within P. marsilii and P. krkae. The markers were able to clearly resolve differences among the three tested species, including the recently described P. krkae, and are therefore suitable for the detection of introgression and hybridization among populations consisting of mixtures of two or more of P. lumaireul s. l., P. marsilii and P. krkae.

Lack of genetic structure suggests high connectivity of Parnassius phoebus between nearby valleys in the Alps

The spatial scale of intraspecific genetic connectivity and population structure are important aspects of conservation genetics. However, for many species these properties are unknown. Here we used genomic data to assess the genetic structure of the small Apollo butterfly (Parnassius phoebus Fabricius, 1793; Lepidoptera: Papilionidae) across three nearby valleys in the Central Swiss Alps. One of the valleys is currently used for hydropower production with future plans to raise the existing dam wall further. We found no significant genetic structure, suggesting a currently high connectivity of this species in our studied region.

Historical persistence and isolation by distance of

Context Empirical studies of intraspecific genetic diversity and population structure can inform the evolutionary and demographic history of individual species and of landscapes at the bioregional level. Aims We aimed to assess intraspecific genetic variation at macroevolutionary and microevolutionary temporal scales for Mirbelia viminalis, a key species present on the Hamersley Range in the ancient and highly diverse landscape of the Pilbara bioregion of northwest Western Australia. Methods We sampled extant populations and assessed diversity and structure using sequences (chloroplast DNA, 1759 base pairs) and microsatellite markers (nuclear DNA, 15 loci) data. Key results Significant phylogeographic structure and a lack of historical demographic signals of population contraction or expansion suggest historical population persistence. Moderate chloroplast haplotype diversity (h = 15) and moderate divergence among extant haplotypes indicates a degree of historical connectivity via seed dispersal across central populations on the Hamersley Range. Levels of nuclear genetic diversity were low to moderate (allelic richness = 3.554, expected heterozygosity = 0.489, observed heterozygosity = 0.462) and depauperate compared to another member of the Mirbelia genus present further south in the Midwest region. Nuclear diversity revealed a strong signal of isolation by distance with localised admixture among populations and some contemporary genetic clustering along a north-west to south-east transect of the Hamersley Range. Conclusions Low nuclear genetic diversity may be related to recent reductions in population size for M. viminalis. Historical population persistence with few barriers to dispersal other than geographic distance may be common for members of the Fabaceae across the Hamersley Range.

Center of origin and evolutionary history in the high Andean genus Oritrophium (Astereae, Asteraceae)

Páramo, the most species-rich tropical mountain ecosystem, is relatively well-researched in terms of the diversity and evolutionary sources of its flora, yet we know very little about the diversification within this environment. This study aims to unravel the evolutionary history of Oritrophium, an endemic genus of alpine habitats in North and South America, with a disjunct and bi-modal distribution of its species diversity. We aim to disentangle the center of origin and radiation of the genus, and mechanisms structuring its genetic diversity at inter- and intra-specific level. We sampled 19 species (85% from the total) and extended the sampling at population level for the two widely distributed species, O.limnophilum and O.peruvianum, comprising 19 and 24 populations, respectively. Using nuclear ribosomal internal transcribed spacer (ITS) and trnL-trnF chloroplast DNA region, we reconstructed dated phylogenies to test the monophyly of the genus and unravel possible historical forces underlying its diversification. We also performed an ancestral area estimation to reconstruct the biogeographic history of the genus. At the population level, we constructed haplotype networks and run spatial analyses of molecular variance to explore possible mechanisms that operate on structuring the diversity at intraspecific level. Oritrophium resulted polyphyletic, with two species being closely related to Erigeron and three other species ambiguously related to Erigeron, Diplostephium, Linochilus, and/or Hinterhubera. The remaining 14 species formed a clade, Oritrophiums.s., that likely originated during the Early Pliocene in the Andes of northwestern Bolivia to southern Ecuador, the center of the genus' diversity. The group likely diversified with the emergence of the Páramo during the Late Pliocene and further dispersed mainly from South-to-North in the Pleistocene. This migration involved both, long-distance dispersal from the Central Andes to Mexico and gradual migration of the species along the Andes. Accordingly, Oritrophium s.s. appears as the first record of a long-distance dispersal from the Páramo of South America to North America. The dispersal pattern within South America was mirrored by the intraspecific population diversity and structure of the investigated species.

Macroecological trend of increasing values of intraspecific genetic diversity and population structure from temperate to tropical streams

AbstractAimAssuming genetic variants are selectively neutral, estimates of intraspecific genetic diversity and population structure should increase simultaneously in parallel to coalescent time, population size and gene flow. However, other processes, such as genetic drift associated with demographic fluctuations, might cause a loss of genetic diversity while not affecting population structure. In this study, we assess large‐scale patterns of estimates of intraspecific genetic variation across species to determine the roles of dispersal, biogeography, divergence time and demographic fluctuations in decoupling genetic diversity and population structure.LocationPristine first‐order streams distributed in seven regions from Neotropical to boreal climate, covering a gradient of habitat persistence through major biogeographical changes (e.g., Pleistocene glaciations).Time period2008–2010.Major taxa studiedFreshwater insect lineages that differ in dispersal propensity.MethodsIntraspecific nucleotide diversity (π) and population structure (ΦST) were estimated for 33 species using 2,128 sequences of the cox1 gene. The correlation between π and ΦST was tested using linear regression models. The geographical distribution of haplotypes was represented in networks. Phylogenetic trees were time calibrated to determine divergence time.ResultsAt a global scale, a positive relationship between π and ΦST was found. Neotropical species showed the highest values of π and ΦST, probably owing to historical environmental stability. Across Europe, the low estimates of π and the wide array of ΦST values and haplotype networks found across species, lineages and latitude were contrary to the biogeographical and dispersal paradigms.Main conclusionsBeyond the macroecological trend found, genetic trajectories of co‐distributed temperate species were disassociated from their functional traits and probably caused by persistent demographic fluctuations associated with local‐scale habitat instability. Overall, the idiosyncratic relationship between π and ΦST across species prevents the establishment of conclusive global patterns and questions the phylogeographical patterns established when studying a reduced number of co‐distributed species.

How mitonuclear discordance and geographic variation have confounded species boundaries in a widely studied snake

As DNA sequencing technologies and methods for delimiting species with genomic data become more accessible and numerous, researchers have more tools than ever to investigate questions in systematics and phylogeography. However, easy access to sophisticated computational tools is not without its drawbacks. Choosing the right approach for one’s question can be challenging when presented with multitudinous options, some of which fail to distinguish between species and intraspecific population structure. Here, we employ a methodology that emphasizes intensive geographic sampling, particularly at contact zones between populations, with a focus on differentiating intraspecific genetic clusters from species in the Pantherophis guttatus complex, a group of North American ratsnakes. Using a mitochondrial marker as well as ddRADseq data, we find evidence of mitonuclear discordance which has contributed to historical confusion about the relationships within this group. Additionally, we identify geographically and genetically structured populations within the species Pantherophis emoryi that are congruent with previously described morphological variation. Importantly, we find that these structured populations within P. emoryi are highly admixed throughout the range of the species and show no evidence of any reproductive isolation. Our data support a revision of the taxonomy of this group, and we recognize two species within the complex and three subspecies within P. emoryi. This study illustrates the importance of thorough sampling of contact zones and consideration of gene flow when delimiting species in widespread complexes containing parapatric lineages.

The type of substrate does not influence the intraspecific population structure of shrub‐tree species in the Brazilian savanna

AbstractLocal environmental conditions influence the occurrence and abundance of populations, and therefore, the contribution of the same species to the ecological structure and processes of communities can vary in different environments. We investigated the influence of the substrate on the intraspecific population structure of four shrub‐tree species from the Brazilian savanna (Aspidosperma tomentosum, Byrsonima pachyphylla, Davilla elliptica, and Ouratea hexasperma) that occur in adjacent areas, but under different environmental conditions: in shallow soils with rocky outcrops and steep relief in Rupestrian Savanna, and in deep soils and flat relief in Typical savanna. We hypothesized that the relief and physical–chemical conditions of the soil in the Rupestrian Savanna limit the establishment and development of species regarding the abundance of individuals and the horizontal and vertical structure of populations. We found that in the Rupestrian Savanna, the soil has higher levels of total cation exchange capacity and phosphorus, while in Typical Savanna, it is associated with higher pH, base saturation, and clay levels. We show that intraspecific variations do not differ between the two environments in number of individuals, average values of trunk diameter, and total plant height. We observed that the same species contributes in different ways to the structuring of communities in both environments. Our hypothesis was rejected because the population structure was not molded by the substrate type. We conclude that the shrub‐tree species seem to find adaptive alternatives to colonize the different types of substrates, for example, establishing in less stressful microhabitats on the rocky environments.

Phylogenetics of mud snakes (Squamata: Serpentes: Homalopsidae): A paradox of both undescribed diversity and taxonomic inflation

Mud snakes (Serpentes: Homalopsidae) are a family of 55 described, mainly aquatic, species primarily distributed throughout mainland Southeast Asia and the Indo-Australian Archipelago. Although they have been the focus of prior research, the basic relationships amongst genera and species remain poorly known. We used a combined mitochondrial and nuclear gene dataset to infer their phylogenetic relationships, using the highest levels of taxon and geographic sampling for any homalopsid phylogeny to date (62% generic and 62% species coverage; 140 individuals). Our results recover two reciprocally monophyletic groups: the fangless Brachyorrhos and its sister clade comprised of all rear-fanged homalopsids. Most genera and interspecific relationships were monophyletic and strongly supported, but intergeneric relationships and intraspecific population structure lack support. We find evidence of both undescribed diversity as well as cases of taxonomic inflation within several species. Tree-based species delimitation approaches (mPTP) support potential new candidate species as distinct from their conspecifics and also suggest that many named taxa may not be distinct species. Divergence date estimation and lineage-through-time analyses indicate lower levels of speciation in the Eocene, with a subsequent burst in diversification in the Miocene. Homalopsids may have diversified most rapidly during the Pliocene and Pleistocene, possibly in relation to tectonic shifts and sea-level fluctuations that took place in Sundaland and the Sahul Shelf. Our analyses provide new insights on homalopsid taxonomy, a baseline phylogeny for the family, and further biogeographic implications demonstrating how dynamic tectonics and Quaternary sea level changes may have shaped a widespread, diverse family of snakes.

Genetic population structure of the Blackspot seabream (Pagellus bogaraveo): contribution of mtDNA control region to fisheries management

Marine fisheries management models have traditionally considered biological parameters and geopolitical boundaries. The result is the existence of fisheries management units that do not match genetic populations. However, this panorama is changing with the contribution of genetic and genomic data. Pagellus bogaraveo is a commercially important sparid in the northeast Atlantic, with three stock components being considered by ICES: the Celtic Sea and Bay of Biscay, Atlantic Iberian waters and the Azores. The northern stock collapsed (1975–1985) and is essential to characterize the genetic makeup of the species, particularly in the Iberian Peninsula, where it is managed as a single stock. The mitochondrial control region was used to screen the intraspecific diversity and population structure of individuals from six locations across the species range. The genetic diversity found is similar among sites, and there is differentiation between the Azores and the remaining locations.

Multi-Species Phylogeography of Arid-Zone Sminthopsinae (Marsupialia: Dasyuridae) Reveals Evidence of Refugia and Population Expansion in Response to Quaternary Change.

Historical population contraction and expansion events associated with Pleistocene climate change are important drivers of intraspecific population structure in Australian arid-zone species. We compared phylogeographic patterns among arid-adapted Dasyuridae (Sminthopsis and Planigale) with close phylogenetic relationships and similar ecological roles to investigate the drivers of phylogeographic structuring and the importance of historical refugia. We generated haplotype networks for two mitochondrial (control region and cytochrome b) and one nuclear (omega-globin) gene from samples distributed across each species range. We used ΦST to test for a genetic population structure associated with the four Pilbara subregions, and we used expansion statistics and Bayesian coalescent skyline analysis to test for signals of historical population expansion and the timing of such events. Significant population structure associated with the Pilbara and subregions was detected in the mitochondrial data for most species, but not with the nuclear data. Evidence of population expansion was detected for all species, and it likely began during the mid-late Pleistocene. The timing of population expansion suggests that these species responded favorably to the increased availability of arid habitats during the mid-late Pleistocene, which is when previously patchy habitats became more widespread. We interpret our results to indicate that the Pilbara region could have acted as a refugium for small dasyurids.

Extensive cytonuclear discordance in a crested newt from the Balkan Peninsula glacial refugium

Abstract Integration of multilocus data and species distribution modelling into phylogeography allows mitochondrial DNA (mtDNA)-based scenarios to be fine-tuned. We address the question of whether extensive mtDNA substructuring in the crested newt Triturus macedonicus from the Balkan Peninsula is matched in the nuclear genome. We determine the intraspecific population structure based on 52 nuclear DNA markers and project a species distribution model on climate layers for the Last Glacial Maximum. We show that T. macedonicus accumulated nuclear DNA population structure in an area predicted to have been climatically stable during the Pleistocene, with four nuclear DNA groups in the western part of the species range. The distribution of these nuclear DNA groups shows little agreement with that of mtDNA structuring, which shows three highly distinct species-specific clades and a fourth one introgressed from another crested newt species. This cytonuclear discordance conveys that historical biogeographical scenarios based on mtDNA exclusively should be interpreted with caution. Our findings further highlight the important role the Balkan Peninsula has played in the evolution and preservation of European biodiversity.

Impacts of female body size on cannibalism and juvenile abundance in a dominant arctic spider.

Body size influences an individual's physiology and the nature of its intra- and interspecific interactions. Changes in this key functional trait can therefore have important implications for populations as well. For example, among invertebrates, there is typically a positive correlation between female body size and reproductive output. Increasing body size can consequently trigger changes in population density, population structure (e.g. adult to juvenile ratio) and the strength of intraspecific competition. Body size changes have been documented in several species in the Arctic, a region that is warming rapidly. In particular, wolf spiders, one of the most abundant arctic invertebrate predators, are becoming larger and therefore more fecund. Whether these changes are affecting their populations and role within food webs is currently unclear. We investigated the population structure and feeding ecology of the dominant wolf spider species Pardosa lapponica at two tundra sites where adult spiders naturally differ in mean body size. Additionally, we performed a mesocosm experiment to investigate how variation in wolf spider density, which is likely to change as a function of body size, influences feeding ecology and its sensitivity to warming. We found that juvenile abundance is negatively associated with female size and that wolf spiders occupied higher trophic positions where adult females were larger. Because female body size is positively related to fecundity in P. lapponica, the unexpected finding of fewer juveniles with larger females suggests an increase in density-dependent cannibalism as a result of increased intraspecific competition for resources. Higher rates of density-dependent cannibalism are further supported by the results from our mesocosm experiment, in which individuals occupied higher trophic positions in plots with higher wolf spider densities. We observed no changes in wolf spider feeding ecology in association with short-term experimental warming. Our results suggest that body size variation in wolf spiders is associated with variation in intraspecific competition, feeding ecology and population structure. Given the widespread distribution of wolf spiders in arctic ecosystems, body size shifts in these predators as a result of climate change could have implications for lower trophic levels and for ecosystem functioning.

Genetic analysis provides insights into species distribution and population structure in East Atlantic horse mackerel (Trachurus trachurus and T. capensis).

Two sister species of horse mackerel (Trachurus trachurus and T. capensis) are described that are intensively harvested in East Atlantic waters. To address long‐standing uncertainties as to their respective geographical ranges, overlap and intraspecific population structure this study combined genetic (mitochondrial DNA and microsatellite) analysis and targeted sampling of the hitherto understudied West African coast. mtDNA revealed two reciprocally monophyletic clades corresponding to each species with interspecies nuclear differentiation supported by F ST values. The T. trachurus clade was found across the north‐east Atlantic down to Ghana but was absent from Angolan and South African samples. The T. capensis clade was found only in South Africa, Angola and a single Ghanaian individual. This pattern suggests that both species may overlap in the waters around Ghana. The potential for cryptic hybridization and/or indiscriminate harvesting of both species in the region is discussed. For T. capensis mtDNA supports high gene flow across the Benguela upwelling system, which fits with the species' ecology. The data add to evidence of a lack of significant genetic structure throughout the range of T. trachurus though the assumption of demographic panmixia is cautioned against. For both species, resolution of stock recruitment heterogeneity relevant to fishery management, as well as potential hybridization, will require more powerful genomic analyses.

Elucidating the drivers of genetic differentiation in Malaysian torrent frogs (Anura: Ranidae: Amolops): a landscape genomics approach

AbstractThe interplay between environmental attributes and evolutionary processes can provide valuable insights into how biodiversity is generated, partitioned and distributed. This study investigates the role of spatial, environmental and historical factors that could potentially drive diversification and shape genetic variation in Malaysian torrent frogs. Torrent frogs are ecologically conserved, and we hypothesize that this could impose tight constraints on dispersal routes, gene flow and consequently genetic structure. Moreover, levels of gene flow were shown to vary among populations from separate mountain ranges, indicating that genetic differentiation could be influenced by landscape features. Using genome-wide single nucleotide polymorphisms, in conjunction with landscape variables derived from Geographic Information Systems, we performed distance-based redundancy analyses and variance partitioning to disentangle the effects of isolation-by-distance (IBD), isolation-by-resistance (IBR) and isolation-by-colonization (IBC). Our results demonstrated that IBR contributed minimally to genetic variation. Intraspecific population structure can be largely attributed to IBD, whereas interspecific diversification was primarily driven by IBC. We also detected two distinct population bottlenecks, indicating that speciation events were likely driven by vicariance or founder events.

Conservation Genomics in the Sagebrush Sea: Population Divergence, Demographic History, and Local Adaptation in Sage-Grouse (Centrocercus spp.).

Sage-grouse are two closely related iconic species of the North American West, with historically broad distributions across sagebrush-steppe habitat. Both species are dietary specialists on sagebrush during winter, with presumed adaptations to tolerate the high concentrations of toxic secondary metabolites that function as plant chemical defenses. Marked range contraction and declining population sizes since European settlement have motivated efforts to identify distinct population genetic variation, particularly that which might be associated with local genetic adaptation and dietary specialization of sage-grouse. We assembled a reference genome and performed whole-genome sequencing across sage-grouse from six populations, encompassing both species and including several populations on the periphery of the species ranges. Population genomic analyses reaffirmed genome-wide differentiation between greater and Gunnison sage-grouse, revealed pronounced intraspecific population structure, and highlighted important differentiation of a small isolated population of greater sage-grouse in the northwest of the range. Patterns of genome-wide differentiation were largely consistent with a hypothesized role of genetic drift due to limited gene flow among populations. Inferred ancient population demography suggested persistent declines in effective population sizes that have likely contributed to differentiation within and among species. Several genomic regions with single-nucleotide polymorphisms exhibiting extreme population differentiation were associated with candidate genes linked to metabolism of xenobiotic compounds. In vitro activity of enzymes isolated from sage-grouse livers supported a role for these genes in detoxification of sagebrush, suggesting that the observed interpopulation variation may underlie important local dietary adaptations, warranting close consideration for conservation strategies that link sage-grouse to the chemistry of local sagebrush.