Restricted Gene Flow Research Articles

What Predicts Gene Flow During Speciation? The Relative Roles of Time, Space, Morphology and Climate.

The processes that restrict gene flow between populations are fundamental to speciation. Here, we develop a simple framework for studying whether divergence in morphology, climatic niche, time and space contribute to reduced gene flow among populations and species. We apply this framework to a model system involving a clade of spiny lizards (Sceloporus) occurring mostly in northeastern Mexico, which show striking variation in morphology and habitat among closely related species and populations. We developed a new time-calibrated phylogeny for the group using RADseq data from 152 individuals. This phylogeny identified 12 putative species-level clades, including at least two undescribed species. We then estimated levels of gene flow among 21 geographically adjacent pairs of species and populations. We also estimated divergence in morphological and climatic niche variables among these same pairs, along with divergence times and geographic distances. Using Bayesian generalised linear models, we found that gene flow between pairs of lineages is negatively related to divergence time and morphological divergence among them (which are uncorrelated), and not to geographic distance or climatic divergence. The framework used here can be applied to study speciation in many other organisms having genomic data but lacking direct data on reproductive isolation. We also found several other intriguing patterns in this system, including the parallel evolution of a strikingly similar montane blue-red morph from more dull-coloured desert ancestors within two different, nonsister species.

Population Expansion but Limited Gene Flow in Kuhl's Blue‐Spotted Maskray Along the Tanzanian Coast

Population Expansion but Limited Gene Flow in Kuhl's Blue‐Spotted Maskray Along the Tanzanian Coast

Genetic and Phenotypic Divergence in a Dung Beetle 50 Years After Its Introduction to Australia.

Species translocations are increasingly being used in conservation and for biological control. The success of a translocation can be strongly influenced by the evolutionary processes occurring during the early phase of the introduction and the subsequent spread to new regions. In this study, morphological variation and population genetic structure were assessed in the African dung beetle Digitonthophagus gazella, a species that was intentionally introduced to Australia for biological control in 1968 and subsequently spread widely across the northern part of the continent. A dataset based on 1594 neutral single nucleotide polymorphism (SNP) loci that were genotyped in 187 individuals from 12 sites revealed significant genetic divergences between sites (global F ST = 0.118) and provides evidence of restricted gene flow among established populations at small to moderate spatial scales (74-500 km). Geometric morphometric analyses revealed significant divergence among populations in the shape of the foretibia, a trait ecologically important for tunnelling in soil and dung. Moreover, phenotypic divergence in this trait for both sexes was significantly higher than genetic differentiation at selectively neutral loci (P ST > F ST), suggesting that directional selection is contributing to the phenotypic divergences among populations. Our study shows how population structure can establish quickly in an introduced species and highlights the importance of considering local adaptation when performing translocations on established populations.

Conservation biology of three threatened Limonium species endemic to Zakynthos Island (Ionian Islands, Greece)

Abstract Knowledge of the life history traits, reproductive biology and demography of rare species is fundamental for their conservation, yet plant population monitoring is uncommon. The restricted ranges of the Limonium species endemic to the Mediterranean area, combined with the vulnerability of their specialized littoral habitats, indicate the need for appropriate conservation measures. We evaluate the conservation status and estimate the future extinction risk of three Limonium species endemic to Zakynthos Island in the Ionian Islands, Greece (Limonium korakonisicum, Limonium phitosianum and Limonium zacynthium) using 5 years of monitoring data. We compile information on their geographical distribution, population dynamics, reproductive biology and genetic diversity. Population sizes and survival rates of seedlings exhibited marked annual fluctuations, although fecundity and relative reproductive success remained high throughout the monitoring period. We observed a dominance of mature individuals in all three species, indicating their increased tolerance to salinity. Three subpopulations each of L. phitosianum and L. zacynthium were genotyped using five microsatellite loci. The observed number of alleles and the low gene flow value potentially indicate reduced genetic diversity, inbreeding, and limited gene flow within and among subpopulations of both species. Based on the IUCN categories and criteria, we assess L. korakonisicum as Critically Endangered, L. phitosianum as Near Threatened and L. zacynthium as Endangered. Population viability analyses predict that, among the three species, L. zacynthium will face the highest risk of extinction within the next 50 years. Knowledge of the biology of these species provides data essential for identifying critical factors for their survival and for proposing targeted conservation measures.

Using eDNA to Supplement Population Genetic Analyses for Cryptic Marine Species: Identifying Population Boundaries for Alaska Harbour Porpoises.

Isolation by distance and biogeographical boundaries define patterns of population genetic structure for harbour porpoise along the Pacific coast from California to British Columbia. Until recently, inadequate sample sizes in many regions constrained efforts to characterise population genetic structure throughout the coastal waters of Alaska. Here, tissue samples from beachcast strandings and fisheries bycatch were supplemented with targeted environmental DNA (eDNA) samples in key regions of Alaska coastal and inland waters. Using a geographically explicit, hierarchical approach, we examined the genetic structure of Alaska harbour porpoises, using both mitochondrial DNA (mtDNA) sequence data and multilocus SNP genotypes. Despite a lack of evidence of genetic differentiation from nuclear SNP loci, patterns of relatedness and genetic differentiation from mtDNA suggest natal philopatry at multiple geographic scales, with limited gene flow among sites possibly mediated by male dispersal. A priori clustering of sampled areas at an intermediate scale (eastern and western Bering Sea, Gulf of Alaska and Southeast Alaska) best explained the genetic variance (12.37%) among regions. In addition, mtDNA differentiation between the Gulf of Alaska and eastern Bering Sea, and among regions within the Gulf of Alaska, indicated significant genetic structuring of harbour porpoise populations in Southeast Alaska. The targeted collection of eDNA samples from strata within Southeast Alaska was key for elevating the statistical power of our mtDNA dataset, and findings indicate limited dispersal between neighbouring strata within coastal and inland waters. These results provide evidence supporting a population boundary within the currently recognised Southeast Alaska Stock. Together, these findings will prove useful for ongoing management efforts to reduce fisheries conflict and conserve genetic diversity in this iconic coastal species.

Mitochondrial genome insights into the spatio-temporal distribution and genetic diversity of Dendrobium hancockii Rolfe (Orchidaceae).

With its distinctive evolutionary rate and inheritance patterns separate from the nuclear genome, mitochondrial genome analysis has become a prominent focus of current research. Dendrobium hancockii Rolfe, a species of orchid with both medicinal and horticultural value, will benefit from the application of the fully assembled and annotated mitochondrial genome. This will aid in elucidating its phylogenetic relationships, comparative genomics, and population genetic diversity. Based on sequencing results from Illumina combined with PacBio and Nanopore, the mitochondrial genome map of D. hancockii was constructed. Comparative analysis was conducted from the perspectives of phylogeny across multiple species, selection pressure on protein-coding genes, and homologous segments. The population diversity of D. hancockii was analyzed using single nucleotide polymorphism (SNP) data from the mitochondrial genome and single-copy nuclear genes. This research constructed a circular mitochondrial map for D. hancockii, spanning 523,952 bp, containing 40 unique protein-coding genes, 37 transfer RNA genes, and 4 ribosomal RNA genes. Comparative analysis of mitochondrial genes from 26 land plants revealed a conserved gene cluster, "rpl16-ccmFn-rps3-rps19," particularly within the Dendrobium genus. The mitochondrial genome of D. hancockii exhibits a lower point mutation rate but significant structural variation. Analysis of 103 resequencing samples identified 19,101 SNP sites, dividing D. hancockii into two major groups with limited gene flow between them, as supported by population diversity, genetic structure analysis, principal component analysis, and phylogenetic trees. The geographical distribution and genetic differentiation of D. hancockii into two major groups suggest a clear phytogeographical division, likely driven by ancient geological or climatic events. The close alignment of mitochondrial data with nuclear gene data highlights the potential of the mitochondrial genome for future studies on genetic evolution in this species.

Increased Evolutionary Rate in the Z chromosome of Sympatric and Allopatric Species of Morpho Butterflies.

Divergent evolution of genomes among closely related species is shaped by both neutral processes and ecological forces, such as local adaptation and reinforcement. These factors can drive accelerated evolution of sex chromosomes relative to autosomes. Comparative genomic analyses between allopatric and sympatric species with overlapping or divergent ecological niches offer insights into reinforcement and ecological specialization on genome evolution. In the butterfly genus Morpho, several species coexist in sympatry, with specialization across forest strata and temporal niches. We analyzed the genomes of eight Morpho species, along with previously published genomes of three others, to compare chromosomal rearrangements and signs of positive selection in the Z chromosome vs. autosomes. We found extensive chromosomal rearrangements in Z chromosome, particularly in sympatric species with similar ecological niches, suggesting a role for inversions in restricting gene flow at a postzygotic level. Z-linked genes also exhibited significantly higher dN/dS ratios than autosomal genes across the genus, with pronounced differences in closely related species living in sympatry. Additionally, we examined the evolution of eight circadian clock genes, detecting positive selection in Period, located on the Z chromosome. Our findings suggest that the Z chromosome evolves more rapidly than autosomes, particularly among closely related species, raising questions about its role in prezygotic and postzygotic isolation mechanisms.

Monitoring spatiotemporal patterns in the genetic diversity of a European butterfly species

Abstract The importance of genetic diversity has been recognised by the Convention on Biological Diversity but attempts at monitoring or improving the genetic diversity of populations have been minimal. Here, we investigate changes over time in the genetic diversity of a wild insect species, Maniola jurtina (Lepidoptera: Nymphalidae) and present a large‐scale investigation into contemporary spatial genetic diversity. Using microsatellite markers, we calculate multiple measures of genetic diversity and divergence for M. jurtina populations over 8 years in the UK and compare these findings with long‐term abundance trends. We also conduct a large‐scale spatial analysis into the genetic diversity and population structuring of M. jurtina across Europe. All UK populations sampled have high levels of gene flow and genetic diversity, with genetic diversity stable over time. Across Europe, we find some population structuring between populations in the UK and the European mainland, suggesting restricted geneflow between the two regions. The monitoring of a wild species' genetic diversity is an achievable aim, and one that could be carried out for many species, particularly Lepidoptera. Future approaches may aim to develop higher resolution genetic markers and cover a wider range of species. The use of abundance data offers additional insight, and we find that concurrent, dedicated genetic monitoring can provide effective tracking of biodiversity trends.

Population connectivity and size reductions in the Anthropocene: the consequence of landscapes and historical bottlenecks in white forsythia fragmented habitats

BackgroundWhite forsythia (Abeliophyllum distichum) is an endangered Korean Peninsula endemic that has been subjected to recent population genomics studies using SNPs via RAD sequencing. Here, we primarily employed the often underutilized haplotype information from RAD loci to further describe the species’ previously uninvestigated haplotype-based genomic variation and structure, and genetic-geographic characteristics and gene flow patterns among its five earlier identified genetic groups. We also inferred the time of past events that may have impacted the effective population size of these groups, as well as the species’ potential future distribution amidst the warming climate and anthropogenic threats.ResultsOur findings emphasized the recognition of the species’ regional patterns of genetic structure, and the role of topography and its associated gene flow patterns as some of the possible factors that may have influenced the species’ present-day fragmented population distribution. The inferred bottleneck events during the Anthropocene, some of which aligned with the time of historical catastrophic events on the Peninsula (e.g., the Korean War), were revealed to have contributed to the generally low effective population size of its five lineages, particularly those with marginal distributional range. Future distribution under both optimistic and pessimistic climatic scenarios suggests unlikely suitable habitats for these populations to expand from their current range limits, at least in the next 80 years.ConclusionsThe small effective population size and landscape-driven limited gene flow among white forsythia populations will remain a big challenge for the conservation management of the species’ already fragmented population distribution. To help mitigate these impacts, the merging of various research approaches and the use of genomic data to their full potential is recommended to provide the optimized knowledge-based tools for the conservation of this endangered species, and other similar plants under pressure.

Do Sex Ratio Distorting Microbes Inhibit the Evolution of Pesticide Resistance? An Experimental Test.

We are still largely reliant on pesticides for the suppression of arthropod pests which threaten human health and food production, but the recent rise of evolved resistance among important pest species has reduced pesticide efficacy. Despite this, our understanding of strategies that effectively limit the evolution of resistance remains weak. Male-killing sex ratio distorting microbes (SRDMs), such as Wolbachia and Spiroplasma, are common among arthropod species. Previous theoretical work has suggested that they could limit adaptive potential in two ways: first, because by distorting sex ratios they reduce the effective population size, and second, because infected females produce no male offspring which restricts gene flow. Here we present the results of a novel experiment in which we test the extent by which these two mechanisms limit the adaptive response of arthropods to pesticide. Using a fully factorial design, we manipulated the adult sex ratio of laboratory populations of Drosophila melanogaster, both in the presence and absence of SRDMs, and exposed these populations to six generations of pesticide poisoning. This design allows the effects of SRDMs on sex ratio and their effects on gene flow to be estimated separately. After six generations, individuals from populations with even sex ratios displayed a higher resistance to pesticide relative to individuals from female-biased populations. By contrast, we found no effect of the presence of SRDMs in host populations on pesticide resistance independent of sex ratio. In addition, males were more susceptible to pesticide than females-this was true of flies from both naïve and previously exposed populations. These findings provide the first empirical proof of concept that sex ratio distortion arising from SRDMs can limit adaptation to pesticides, but cast doubt on the theoretical effect of male-killers limiting adaptation by disrupting gene flow.

Seascape Genetics and Distinct Intraspecific Diversification of the Decapod Nephrops norvegicus in the Adriatic Sea.

Norway lobster Nephrops norvegicus, a prized decapod crustacean species, is found at different depths across the East Atlantic Ocean and Mediterranean Sea. Despite management efforts, the stocks are globally characterised as overexploited. In the present study, the impact of biogeographical boundaries on the phylogeographical and demographic population status was investigated within the Adriatic Sea, addressing important genetic indices for decapod functional conservation management. Central Mediterranean, Adriatic Sea A total of 482 individuals of Nephrops divided into the 12 samples were collected across biogeographical range of the Adriatic Sea. Using the mtDNA D-loop and microsatellite markers, methods of phylogeography and seascape genetics were applied to infer offshore versus coastal population divergence, demography and structure. Significant findings include genetic differentiation between offshore and coastal samples, with higher diversity indices in open waters. The limited gene flow observed between these two areas emphasises the self-sustained nature of coastal populations. Recent demographic changes in coastal populations reflect geographical constraints, fishing pressures and fluctuations in self-recruitment success. Additionally, the study reveals historical biogeographic events shaping the Adriatic populations, with evidence suggesting lineage divergence during the upper Pleistocene and postglacial recolonisation from southern Adriatic refugia. The role of biogeographical conditions in shaping genetic structure and limited gene flow between inshore and offshore areas underscore the need for improved management strategies, emphasising the importance of marine protected areas in conserving coastal populations and maintaining overall genetic diversity of the Norway lobster in the Adriatic Sea. Genomic monitoring within current management practices is recommended.

Limited Migration From Physiological Refugia Constrains the Rescue of Native Gastropods Facing an Invasive Predator.

Biological invasions have caused the loss of freshwater biodiversity worldwide. The interplay between adaptive responses and demographic characteristics of populations impacted by invasions is expected to be important for their resilience, but the interaction between these factors is poorly understood. The freshwater gastropod Amnicola limosus is native to the Upper St. Lawrence River and distributed along a water calcium concentration gradient within which high-calcium habitats are impacted by an invasive predator fish (Neogobius melanostomus, round goby), whereas low-calcium habitats provide refuges for the gastropods from the invasive predator. Our objectives were to (1) test for adaptation of A. limosus to the invasive predator and the low-calcium habitats, and (2) investigate if migrant gastropods could move from refuge populations to declining invaded populations (i.e., demographic rescue), which could also help maintain genetic diversity through gene flow (i.e., genetic rescue). We conducted a laboratory reciprocal transplant of wild F0 A. limosus sourced from the two habitat types (high calcium/invaded and low calcium/refuge) to measure adult survival and fecundity in home and transplant treatments of water calcium concentration (low/high) and round goby cue (present/absent). We then applied pooled whole-genome sequencing of 12 gastropod populations from across the calcium/invasion gradient. We identified patterns of life-history traits and genetic differentiation across the habitats that are consistent with local adaptation to low-calcium concentrations in refuge populations and to round goby predation in invaded populations. We also detected restricted gene flow from the low-calcium refugia towards high-calcium invaded populations, implying that the potential for demographic and genetic rescue is limited by natural dispersal. Our study highlights the importance of considering the potentially conflicting effects of local adaptation and gene flow for the resilience of populations coping with invasive predators.

Genetic Attributes and Conservation of an Endangered Giant Water Bug Species, Diplonychus esakii Miyamoto and Lee, 1966 (Hemiptera: Belostomatidae).

Diplonychus esakii, a water bug from the family Belostomatidae, plays an important role in freshwater ecosystems as one of the top predators. In this study, we investigated the genetic diversity and population structure of D. esakii by analyzing 318 specimens across 27 sites in South Korea. We found that the populations of D. esakii possess 11 haplotypes with a haplotype diversity of 0.623. This represents a relatively low level of genetic diversity compared to other known belostomatids and endangered species. AMOVA and FST analyses revealed significant genetic differentiation among populations, with most populations harboring only 1-2 haplotypes, suggesting restricted gene flow between populations and a low level of genetic diversity. This low genetic diversity and limited gene flow suggest a potential vulnerability to environmental changes and an increased risk of extinction, indicating that D. esakii should be designated as a protected species in South Korea as part of future conservation efforts. Based on the results of this study, Upo Wetland, which maintains relatively high levels of genetic diversity and Jeju Island, which, despite its lower genetic diversity compared to the mainland, does not share haplotypes with other regions, should be considered key conservation units for this species. This study highlights the importance of incorporating genetic information into conservation status assessments under the Red List Categories and Criteria and also emphasizes the need to evaluate this species on the Korean Red List. The data provided here will serve as essential baseline information and valuable resources for the development of effective conservation strategies.

Host-driven phenotypic and phenological differentiation in sympatric races of a parasitic plant

Host specificity is a key factor influencing the ecology and evolutionary diversification of parasitic organisms. Host specialisation and geographic isolation are known to lead to the genetic differentiation of allopatric races in parasitic plants. However, how divergence can co-occur in sympatry remains largely unknown. We investigated phenological and phenotypic differentiation and potential reproductive isolation among three sympatric genetic races of Cytinus hypocistis (Cytinaceae) - an extreme endophytic holoparasite with a high degree of host specialisation. We compared spatio-temporal variations in flowering phenology, flower production, floral longevity, floral rewards, and morphology, and conducted inter-race pollinations among three races parasitising Cistus ladanifer, C. salviifolius, and Halimium halimifolium (Cistaceae) in six co-occurring populations. We found that host-defined genetic races differed significantly across multiple phenotypic and phenological aspects – a phenomenon previously overlooked due to the plants’ cryptic morphology. The race parasitising H. halimifolium showed earlier blooming, higher floral display, longer flowers, and higher pollen production and nectar concentration; the race on C. salviifolius showed later flowering, significantly lower floral display and smaller flowers with lower floral rewards; the race on C. ladanifer had intermediate characteristics. Genetic races were interfertile yet may remain differentiated by restricted gene flow and host-driven selection pressures. Together, our data point to a rare case of sympatric divergent evolution hiding in plain sight: apparently morphologically similar co-occurring parasite races can be genetically, phenotypically, and phenologically distinct. This hitherto unreported example of host-driven sympatric diversification challenges how species concepts are applied to cryptic parasitic plant races.

Population genetics analysis of Diospyrosmun A.Chev. ex Lecomte (Ebenaceae) based on EST-SSR markers derived from a novel transcriptome.

Diospyrosmun A.Chev. ex Lecomte (Ebenaceae), a native evergreen tree in Vietnam, has important economic and ecological values. The absence of effective and reliable molecular markers has hampered the study of D.mun's genetic diversity and population structure, even though it is an endemic and endangered species. Therefore, significant enrichment of genomic resources is urgently needed to uncover and better understand the genetic architecture of D.mun. This study aims to demonstrate an efficient and reliable tool to explore the polymorphism within D.mun germplasm. It provides a valuable platform for the breeding and conservation of this species and other endangered species worldwide. The Illumina HiSeq™ 4000 sequencing technology was applied for the transcriptomic analysis, genetic differentiation and population structure of D.mun in Vietnam. In this study, the transcriptomes of D.mun were analysed using the Illumina HiSeqTM 4000 sequencing system and a total of 5,588,615,700 base pairs were generated. De novo assembly indicated that 91,134 unigenes were generated (average length = 645.55 bp, N50 = 957 bp, Q20 = 98.08% and Q30 = 94.51%). A total of 92,798 and 21,134 unigenes had significant similarities amongst Nr and Swiss-Prot, respectively. In the GO database, 19,929 unigenes were annotated and these genes were divided into three major categories and 50 subcategories. In the KOG analysis, 18,499 unigenes were annotated and divided into 25 gene function categories. In the KEGG analysis, 12,017 unigenes were annotated. According to the related pathways involved, they could be classified into 56 subclasses. In this study, we have identified a total of 9,391 EST-SSR markers. Ten microsatellite loci were employed to assess the genetic diversity and structure of 82 adult D.mun trees across three populations in Vietnam. The results indicated moderate levels of genetic diversity with PIC = 0.77, NA = 3.9, NE = 2.8, Ho = 0.56 and HE = 0.58 and the fixation index value was recorded as positive for three populations (NS, NH and CP). Genetic differentiation among populations was low (FST = 0.045), suggesting limited gene flow (Nm = 5.34). This result indicates gene exchange between the populations of ancient D.mun from different geographical areas and regions. The analysis of molecular variance (AMOVA) showed that high genetic variation existed within individuals (91%) compared to amongst populations (4%). Genetic structure analysis, DAPC and the NJ tree indicated that the three populations were divided into three main clusters. With this study, we provide a molecular resoureces for the breeding and conservation of D.mun.

Genetic rescue often leads to higher fitness as a result of increased heterozygosity across animal taxa.

Biodiversity loss has reached critical levels partly due to anthropogenic habitat loss and degradation. These landscape changes are damaging as they can fragment species distributions into small, isolated populations, resulting in limited gene flow, population declines and reduced adaptive potential. Genetic rescue, the translocation of individuals to increase genetic diversity and ultimately fitness, has produced promising results for fragmented populations but remains underutilized due to a lack of long-term data and monitoring. To promote a better understanding of genetic rescue and its potential risks and benefits over the short-term, we reviewed and analysed published genetic rescue attempts to identify whether genetic diversity increases following translocation, and if this change is associated with increased fitness. Our review identified 19 studies that provided genetic and fitness data from before and after the translocation; the majority of these were on mammals, and included experimental, natural and conservation-motivated translocations. Using a Bayesian meta-analytical approach, we found that on average, genetic diversity and fitness increased in populations post translocations, although there were some exceptions to this trend. Overall, genetic diversity was a positive predictor of population fitness, and in some cases this relationship extended three generations post-rescue. These data suggest a single translocation can have lasting fitness benefits, and support translocation as another tool to facilitate conservation success. Given the limited number of studies with long-term data, we echo the need for genetic monitoring of populations post-translocation to understand whether genetic rescue can also limit the loss of adaptive potential in the long-term.

Assessment of Population Genetic Diversity of Medicinal Meconopsis integrifolia (Maxim.) Franch. Using Newly Developed SSR Markers.

Meconopsis integrifolia is an endangered Tibetan medicinal plant with significant medicinal and ornamental value. Understanding its genetic diversity and structure is crucial for its sustainable utilization and effective conservation. Here, we develop a set of SSR markers based on transcriptome data to analyze the genetic diversity and structure of 185 individuals from 16 populations of M. integrifolia. The results indicate that M. integrifolia exhibits relatively high genetic diversity at the species level (the percentage of polymorphic bands PPB = 91.67%, Nei's genetic diversity index He = 0.2989, Shannon's information index I = 0.4514) but limited genetic variation within populations (PPB = 12.08%, He = 0.0399, I = 0.0610). The genetic differentiation among populations is relatively high (the coefficient of gene differentiation GST = 0.6902), and AMOVA analysis indicates that 63.39% of the total variation occurs among populations. This suggests that maintaining a limited number of populations is insufficient to preserve the overall diversity of M. integrifolia. Different populations are categorized into four representative subclusters, but they do not cluster strictly according to geographical distribution. Limited gene flow (Nm = 0.2244) is likely the main reason for the high differentiation among these populations. Limited seed and pollen dispersal abilities, along with habitat fragmentation, may explain the restricted gene flow among populations, highlighting the necessity of conserving as many populations in the wild as possible.

Habitat fragmentation strongly restricts gene flow in endangered ectomycorrhizal fungal populations: Evidence from Rhizopogon togasawarius, specific to Pseudotsuga japonica, across the entire distribution range.

Habitat fragmentation reduces gene flow, causing genetic differentiation and diversity loss in endangered species through genetic drift and inbreeding. However, the impact of habitat fragmentation on ectomycorrhizal (ECM) fungi remains unexplored, despite their critical roles in forest ecosystems. Here, we investigated the population genetic structure and the demographic history of Rhizopogon togasawarius, the ECM fungus specifically colonizing the host tree Pseudotsuga japonica, across its entire distribution range (>200 km). These two species are designated as endangered species on the IUCN Red List since they are found only in small, fragmented forests in Japan. We analysed 236 R. togasawarius individuals from five remaining populations across the Kii Peninsula and the Shikoku Island, separated by a sea channel. Simple sequence repeat analyses using 20 loci revealed strong genetic differentiation among populations (FST = 0.255), even significant in the nearest population pair separated by a distance of only 8 km (FST = 0.075), indicating extremely limited gene flow between populations. DIYABC-RF analyses implied that population divergence occurred approximately 6000 generations ago between the two regions, and nearly 1500 generations ago between the nearest populations within Shikoku Island, related to past climate events. Because of prolonged genetic isolation, significant inbreeding was confirmed in four of five populations, where effective population sizes became very small (Ne = 9.0-58.0). Although evaluation of extinction risks for microorganisms is challenging, our conservation genetic results indicated that habitat fragmentation increases extinction risk through population genetic mechanisms, and therefore should not be overlooked in biodiversity conservation efforts.

The Limits of the Metapopulation: Lineage Fragmentation in a Widespread Terrestrial Salamander (Plethodon cinereus)

Abstract In vicariant species formation, divergence results primarily from periods of allopatry and restricted gene flow. Widespread species harboring differentiated, geographically distinct sublineages offer a window into what may be a common mode of species formation, whereby a species originates, spreads across the landscape, then fragments into multiple units. However, incipient lineages usually lack reproductive barriers that prevent their fusion upon secondary contact, blurring the boundaries between a single, large metapopulation-level lineage and multiple independent species. Here, we explore this model of species formation in the Eastern Red-backed Salamander (Plethodon cinereus), a widespread terrestrial vertebrate with at least 6 divergent mitochondrial clades throughout its range. Using anchored hybrid enrichment data, we applied phylogenomic and population genomic approaches to investigate patterns of divergence, gene flow, and secondary contact. Genomic data broadly match most mitochondrial groups but reveal mitochondrial introgression and extensive admixture at several contact zones. While species delimitation analyses in Bayesian Phylogenetics and Phylogeography supported 5 lineages of P. cinereus, genealogical divergence indices (gdi) were highly sensitive to the inclusion of admixed samples and the geographic representation of candidate species, with increasing support for multiple species when removing admixed samples or limiting sampling to a single locality per group. An analysis of morphometric data revealed differences in body size and limb proportions among groups, with a reduction of forelimb length among warmer and drier localities consistent with increased fossoriality. We conclude that P. cinereus is a single species, but one with highly structured component lineages of various degrees of independence.

Does rafting promote contemporary gene flow? Global and regional patterns of population genetic diversity and structure on the false limpet Siphonaria lateralis in the Southern Ocean

Rafting has been proposed as an effective mechanism for species without free-living pelagic larvae to achieve long-distance dispersal, theoretically preventing population differentiation over wide distributional ranges. Moreover, rafting has been advocated as a main dispersal mechanism for marine invertebrates with sub-Antarctic distributions, because of abundant buoyant kelps, driven by the Antarctic Circumpolar Current. Nonetheless, little attention has been given to the role of rafting to establish regular gene flow across the sub-Antarctic, and the geographic and temporal scales at which it occurs. Aiming to unravel these major questions about the extent of genetic connectivity across the Southern Ocean (SO), we studied the pulmonate limpet Siphonaria lateralis, a benthic species with encapsulated larvae, found on the rocky intertidal of sub-Antarctic islands and southern South America. Since S. lateralis is closely associated with D. antarctica, dispersal by rafting is plausible, as revealed by the absence of phylogeographic structure across the sub-Antarctic. We sampled 116 individuals from eight localities across the SO, and used 5,515 SNPs obtained through Genotyping-by-Sequencing, to determine contemporary genetic diversity, structure, and gene flow at two spatial scales; global, across the SO, and regional, within Kerguelen. Results identified substantial genetic structure, differentiating Patagonia, Falklands/Malvinas Islands, South Georgia and the Kerguelen archipelago, and low levels of contemporary gene flow. The most notable genetic differentiation was found between Patagonia/Falklands and South Georgia/Kerguelen. Structure was also significant between Patagonia and the Falkland/Malvinas Islands. Conversely, South Georgia and Kerguelen exhibited closer genetic affinity, and indications of recent but limited gene flow. Moreover, historical gene flow estimates between the four populations were low. At regional scale, noteworthy genetic structure persisted, and gene flow was insufficient to prevent genetic differentiation within Kerguelen. Consequently, rafting’s potential may be overestimated as a contemporary mechanism promoting gene flow across the SO, as these events may be sporadic, irregular, and unpredictable for marine invertebrates lacking a larval dispersal stage, since contemporary dispersal events don’t seem to facilitate high gene flow at both scales. Accordingly, other oceanographic factors or processes may hinder the establishment of species associated with macroalgae, and as consequence, contemporary genetic connectivity in the sub-Antarctic.