Restricted Gene Flow Research Articles

Whole genome sequencing reveals stepping-stone dispersal buffered against founder effects in a range expanding seabird.

Many species are shifting their ranges in response to climate-driven environmental changes, particularly in high-latitude regions. However, the patterns of dispersal and colonization during range shifting events are not always clear. Understanding how populations are connected through space and time can reveal how species navigate a changing environment. Here, we present a fine-scale population genomics study of gentoo penguins (Pygoscelis papua), a presumed site-faithful colonial nesting species that has increased in population size and expanded its range south along the Western Antarctic Peninsula. Using whole genome sequencing, we analysed 129 gentoo penguin individuals across 12 colonies located at or near the southern range edge. Through a detailed examination of fine-scale population structure, admixture, and population divergence, we inferred that gentoo penguins historically dispersed rapidly in a stepping-stone pattern from the South Shetland Islands leading to the colonization of Anvers Island, and then the adjacent mainland Western Antarctica Peninsula. Recent southward expansion along the Western Antarctic Peninsula also followed a stepping-stone dispersal pattern coupled with limited post-divergence gene flow from colonies on Anvers Island. Genetic diversity appeared to be maintained across colonies during the historical dispersal process, and range-edge populations are still growing. This suggests large numbers of migrants may provide a buffer against founder effects at the beginning of colonization events to maintain genetic diversity similar to that of the source populations before migration ceases post-divergence. These results coupled with a continued increase in effective population size since approximately 500-800 years ago distinguish gentoo penguins as a robust species that is highly adaptable and resilient to changing climate.

Genetic consequences of Last Glacial-Holocene changes in snowfall regime in Arnica mallotopus populations: A plant confined to heavy-snow areas of Japan.

Snow is an important environmental factor affecting plant distribution. Past changes in snowfall regimes may have controlled the demographies of snow-dependent plants. However, our knowledge of changes in the distribution and demographies of such plants is limited because of the lack of fossil records. Population genetic and landscape genetic analyses were used to investigate the response of population dynamics of Arnica mallotopus (Asteraceae)-a plant confined to heavy-snow areas of Japan-to changes in snowfall regimes from the Last Glacial Period to the Holocene. The population genetic analysis suggested that the four geographic lineages diverged during the Last Glacial Period. The interaction between reduced snowfall and lower temperatures during this period likely triggered population isolation in separate refugia. Subpopulation differentiation in the northern group was lower than in the southern group. Our ecological niche model predicted that the current distribution was patchy in the southern region; that is, the populations were isolated by topologically flat and climatically unsuitable lowlands. The landscape genetic analysis suggested that areas with little snowfall acted as barriers to the Holocene expansion of species distribution and continued limiting gene flow between local populations. These findings indicate that postglacial population responses vary among regions and are controlled by environmental and geographic factors. Thus, changes in snowfall regime played a major role in shaping the distribution and genetic structure of the snow-dependent plant.

The geno-geo-climate nexus: contributions of geographic and ecological factors in shaping the genomic divergence of two closely related threatened rainforest species of Fontainea Heckel (Euphorbiaceae)

ContextProcesses that shape genomic and ecological divergence can reveal important evolutionary dynamics to inform the conservation of threatened species. Fontainea is a genus of rainforest shrubs and small trees including critically endangered and threatened species restricted to narrow, but complex geographic and ecological regions. Several species of Fontainea are subject to spatially explicit conditions and experience limited intra-specific gene flow, likely generating genetic differentiation and local adaptation.ObjectivesHere, we explored the genetic and ecological mechanisms underlying patterns of diversification in two, closely related threatened Fontainea species. Our aim was to compare spatial patterns of genetic variation between the vulnerable Fontainea australis (Southern Fontainea) and critically endangered F. oraria (Coastal Fontainea), endemic to the heterogeneous subtropical region of central, eastern Australia, where large-scale clearing has severely reduced rainforest habitat to a fraction (< 1%) of its pre-European settlement extent.MethodsWe used a set of 10,000 reduced-representation markers to infer genetic relationships and the drivers of spatial genetic variation across the two species. In addition, we employed a combination of univariate and multivariate genome-environment association analysis using a set of topo-climatic variables to explore potential patterns of local adaptation as a factor impacting genomic divergence.ResultsOur study revealed that Coastal Fontainea have a close genetic relationship with Southern Fontainea. We showed that isolation by distance has played a key role in their genetic variation, indicating that vicariance can explain the spatial genetic distribution of the two species. Genotype-environment analyses showed a strong association with temperature and topographic features, suggesting adaptation to localised thermal environments. We used a multivariate redundancy analysis to identify a range of putatively adapted loci associated with local environmental conditions.ConclusionsDivergent selection at the local-habitat scale as a result of dispersal limitations and environmental heterogeneity (including physical barriers) are likely contributors to adaptive divergence between the two Fontainea species. Our findings have presented evidence to indicate that Southern and Coastal Fontainea were comprised of distinct genetic groups and ecotypes, that together may form a single species continuum, with further phenotype research suggested to confirm the current species boundaries. Proactive conservation actions, including assisted migration to enhance the resilience of populations lacking stress-tolerant single nucleotide polymorphisms (SNPs) may be required to secure the long-term future of both taxa. This is especially vital for the critically endangered Coastal Fontainea given projections of habitat decline for the species under future climate scenarios.

Towards a genomic resolution of the Phengaris alcon species complex

AbstractTaxonomic entities below the species level often pose difficulties for conservation practice, especially when they are ecologically distinct from the nominal species. Genomic tools provide the opportunity to study and potentially resolve such cryptic diversity. The Alcon blue butterfly Phengaris alcon species complex is such a cryptic example, comprising different ecotypes or even subspecies, one of them is the high elevation taxon P. rebeli from the European Alps. We sequenced a first reference genome for Phengaris alcon. Furthermore, we generated whole genome resequence data for individuals of three Swiss ecotypes, i.e., the low elevation P. alcon, the mid elevation and high elevation alpine P. rebeli and integrated genomic data from across Europe to study the relationship among these ecotypes. At a European scale, our results suggest that for the P. alcon complex, biogeography and the evolutionary context of diversification is more multifaceted than previously suggested, falling in the range of more recent ecological speciation. In Switzerland, the three ecotypes were genetically isolated with only limited current gene flow between them. Past gene flow, however, could have given rise to the mid elevation ecotype. Our findings emphasise that high elevation P. rebeli in the Alps should be treated as a distinct species. Our study highlights how the availability of reference genome assemblies allows to address so far open taxonomic questions in conservation research and that broadscale studies are needed to understand the biogeographic history of apparent diversification.

Anti-predator defences are linked with high levels of genetic differentiation in frogs.

Predator-prey interactions have been suggested as drivers of diversity in different lineages, and the presence of anti-predator defences in some clades is linked to higher rates of diversification. Warning signals are some of the most widespread defences in the animal world, and there is evidence of higher diversification rates in aposematic lineages. The mechanisms behind such species richness, however, are still unclear. Here, we test whether lineages that use aposematism as anti-predator defence exhibit higher levels of genetic differentiation between populations, leading to increased opportunities for divergence. We collated from the literature more than 3000 pairwise genetic differentiation values across more than 700 populations from over 60 amphibian species. We find evidence that over short geographical distances, populations of species of aposematic lineages exhibit greater genetic divergence relative to species that are not aposematic. Our results support a scenario where the use of warning signals could restrict gene flow, and suggest that anti-predator defences could impact divergence between populations and potentially have effects at a macro-evolutionary scale.

Genetic variation reveals complex population structuring of Tomicus piniperda L. (Coleoptera, Scolytidae) in the UK: Implications for management of this important pest

Abstract Tomicus piniperda is a common pest of pine trees responsible for significant economic damage. Although the impact of T. piniperda on forestry is likely to increase in the future due to climate change, little is known about its dispersal within the United Kingdom (UK) or between continental Europe and the UK. This study addressed these knowledge gaps using mitochondrial and microsatellite DNA markers. Mitochondrial DNA revealed high levels of genetic diversity as previously reported for this species across Europe. Nuclear DNA diversity revealed two geographically incoherent groups (Scotland, Wales, Belgium and the Netherlands vs. England and Switzerland). These genetic patterns likely reflect a combination of historical gene flow, anthropogenic introduction and restricted contemporary gene flow between the UK and Europe. Significant structure was found among UK samples suggesting T. piniperda might not disperse extensively between pine stands. This differs from widespread gene flow across continental Europe and may be due to the low percentage of land covered by forests in the UK in addition to the high fragmentation of its forest cover. Genetic variation was higher among the Scottish samples compared to those from more southern clines, suggesting the potential proximity of Scotland to a Pleistocene glacial refuge for T. piniperda.

Population genetic structure of the provincially endangered mainland Eastern Moose (&lt;i&gt;Alces americanus americanus&lt;/i&gt;) in Nova Scotia, Canada

Eastern Moose (Alces americanus americanus (Clinton, 1822)) on mainland Nova Scotia (MNS) are declining and experience limited immigration across the Isthmus of Chignecto from the larger population in neighbouring New Brunswick. Provincially Endangered, the recovery strategy for MNS Moose involves mitigating various threats that may lead to local extirpation. We examine genetic diversity of MNS Moose using microsatellite markers and mitochondrial (mtDNA) control region sequences. Genetic similarities with the Alces a. americana population in New Brunswick and the introduced Northwestern Moose (Alces americanus andersoni (= Alces alces andersoni) Peterson, 1952) population on Cape Breton Island are also analysed. Observed heterozygosity for microsatellites for MNS Moose was low and there was also evidence of limited gene flow between Nova Scotia and New Brunswick across the narrow Isthmus of Chignecto that connects these provinces. Consistent with relatively recent colonization of North America by Moose dispersing across the Bering Land Bridge &lt;15 000 years ago, mtDNA haplotypes of MNS Moose were identical or extremely similar to haplotypes found across North America. However, mtDNA diversity was lower in Nova Scotia and New Brunswick than in more central regions of the species’ range. Active measures to maintain habitat that promote connectivity across the Isthmus of Chignecto would likely be valuable for Moose in terms of maintaining genetic variation in the region and reducing inbreeding.

Cenozoic comparisons of diversity and disparity in the context of tectonic regime: A case study in North American rodents

The tectonic evolution of landscape topography is an important driver of biotic evolution throughout Earth's history. Studies of extant diversity have shown a higher diversity of mammals in topographically complex regions, suggesting that landscape complexity plays a role in generating taxonomic diversity. However, this relationship is poorly understood, especially over geologic time scales. Previous work has posited that heterogeneous topography should lead to increased species diversity as a result of new niche spaces into which lineages may speciate. This is in comparison to homogeneous landscape topography, which offers fewer and less varied niche spaces and thus less ecological opportunities for diversification. It is also thought that barriers to species and individual movement created by mountainous landscapes may divide populations, leading to speciation by restricting gene flow. These two models can be distinguished by their effects on morphological disparity. If niche differentiation is important to the process, we would expect increased morphological disparity in association with heterogeneous landscape topography, whereas the allopatry model predicts no greater morphological disparity over the complex landscape, only taxonomic diversification. We explore these models in the tectonically active and passive regions of North America in rodents from 25 to 0 Ma. We investigate diversity and disparity trends and examine the effects of climate, landscape heterogeneity, and environmental shifts on these patterns. We find that morphological and taxonomic evolution are not impacted by topography in a predictable way, and find that homogeneous landscapes host taxonomic and morphological diversity surpassing that of heterogeneous landscapes for much of the last 19 million years in North America. Furthermore, diversity and disparity trends are both coupled and decoupled during this period, signifiying that taxonomic and morphologic increase and decrease are discordant through time. Our results support the finding that the relationship between landscape heterogeneity and species diversity has not remained constant through geologic time.

Structure, diversity, and genetic delimitation of two Magnolia species endemic to eastern Mexico

Abstract In Mexico, Magnolia species of the section Macrophylla have been segregated based on phenotypic characteristics. However, the wide environmental variation throughout their distribution area in the eastern region of the country could be the main cause of the high degree of morphological variation among the taxa of this section. Therefore, it is necessary to carry out studies at the genetic level to confirm the taxonomic identity of these species. In the present study, the diversity and genetic structure of the populations of Magnolia rzedowskiana and M. zotictla were estimated using simple sequence repeat markers. We evaluated whether the taxonomic delimitation as independent species is consistent with their degree of genetic differentiation, comparing three regions of chloroplast DNA: trnH-psbA, ORF350, and rpl32-trnL. The DNA was obtained from four populations of the two species, which are distributed in the states of Hidalgo, Querétaro and San Luis Potosí. The populations presented intermediate–high genetic diversity (He = 0.52–0.60), limited gene flow (Nm = 0.62) and high genetic differentiation (Fst = 0.288), which may be related to their low density and strong geographic isolation, caused by the high degree of fragmentation of their habitat. The phylogenetic analysis and the genetic differentiation values indicate that each of the populations of the two Magnolia species analyzed behaves as an independent evolutionary unit, so the taxonomic delimitation of the three M. rzedowskiana populations must be reconsidered. The results obtained could be very useful for implementing management and conservation strategies for these populations in the short term.

Genetic Differentiation of the Bloodsucking Midge Forcipomyia taiwana (Diptera: Ceratopogonidae): Implication of the Geographic Isolation by the Central Mountain Ranges in Taiwan.

Forcipomyia (Lasiohelea) taiwana, a small bloodsucking midge, thrives in moderately moist habitats and is commonly found in grassy and bushy areas at an elevation below 250 m. This species exhibits a diurnal biting pattern and shows a marked preference for human blood. Although not known to transmit arthropod-borne diseases, the bites of F. taiwana can induce severe allergic reactions in some individuals. As a significant nuisance in Taiwan, affecting both daily life and the tourism industry, comprehensive studies on its population genetics across different geographical regions remain scarce. The central mountain ranges in Taiwan, comprising more than two hundred peaks above 3000 m in elevation, extend from the north to the south of the island, creating distinct eastern and western geographical divisions. This study utilizes microsatellite markers to explore the genetic differentiation of F. taiwana populations located in the eastern and western regions of the mountain ranges. Our findings reveal substantial genetic differentiation among populations inhabiting Taiwan's western region compared to those in the eastern region. This indicates that the topographical barriers presented by the mountain ranges significantly restrict gene flow, particularly given the species' limited active flight ability and habitat preferences. Although passive dispersal mechanisms, like wind or human activity, could contribute, this study concludes that the gene flow of F. taiwana between the western and eastern regions is primarily influenced by topographical constraints.

Limited gene flow in adjacent valleys and genetic introgression in a mountain hybrid zone between &lt;i&gt;Aconitum&lt;/i&gt; (Ranunculaceae) species

The number of polyploid plants in angiosperms is estimated at about 30-80%, depending on the study, but hybridization between diploids and tetraploids is not a common phenomenon. In this study, our aim was to determine the extent of hybridization and introgression between &lt;i&gt;Aconitum&lt;/i&gt; species in a mountainous hybrid zone in the Tatra Mountains (Western Carpathians). We hypothesized that topography would affect their populations’ genetic structure. For this purpose, inter simple sequence repeat (ISSR) molecular markers and chloroplast DNA (cpDNA, region &lt;i&gt;trn&lt;/i&gt;L(UAG)–&lt;i&gt;ndh&lt;/i&gt;F) sequencing were used. The results revealed that diploid and tetraploid &lt;i&gt;Aconitum&lt;/i&gt; species had specific cpDNA haplotypes, while the spontaneous hybrid species harbored a cpDNA haplotype typical for tetraploids. Bayesian STRUCTURE analysis showed that introgression occurred between diploid and tetraploid species above the tree line, where a spontaneous hybrid, a putative triploid &lt;i&gt;A. ×berdaui&lt;/i&gt;, originated, probably via the triploid bridge mechanism. Molecular analysis of variance, principal coordinate analysis, and neighbor-net clustering revealed different genetic profiles of the diploids between neighboring mountain valleys. Hence, mountain topography, ridges, and valleys can form an effective geographical barrier, preventing gene flow over longer distances. Introgression happens near or above the tree line, where the hybridization zone is formed. In the introgressants, however, no morphological alterations were discernible.

A systematic review of the Iberian springsnail subgenus Alzoniella (Navarriella) (Caenogastropoda: Hydrobiidae), with the description of a new potentially relict subfamily

Abstract The threatened springsnail subgenus Alzoniella (Navarriella) in the Iberian Peninsula has been suggested to be an old and relict lineage of the family Hydrobiidae. The subgenus is represented by two morphological species, both endemic to the Pyrenees and their southern foothills. We conducted phylogenetic analyses based on mitochondrial and nuclear gene fragments of topotypes and other populations, four molecular species delimitation methods, and morphological examinations to clarify the uncertain systematic position of the subgenus within the family, assess its species diversity, and understand the population genetic structure of the two geographically restricted species. Our phylogenetic results revealed that Alzoniella (Navarriella) is distantly related to all other species of Alzoniella, even belonging to an independent subfamily-level clade, for which we introduce the new genus Navarriella and the new subfamily Navarriellinae subfam. nov. Molecular methods and geometric morphometric analysis of shell shape identified a single species in the new genus. The significant phylogenetic distance from other hydrobiid taxa, narrow distribution, and limited gene flow among its populations (estimated from mitochondrial cytochrome c oxidase subunit I sequences) highlight Navarriella as an isolated lineage within the family that requires urgent conservation attention. Furthermore, our results cast a new light on the northern Iberian Mountains as a dispersal barrier for ancient spring lineages.

Mapping restricted introgression across the genomes of admixed indigenous African cattle breeds

BackgroundThe genomes of indigenous African cattle are composed of components with Middle Eastern (taurine) and South Asian (indicine) origins, providing a valuable model to study hybridization and to identify genetic barriers to gene flow. In this study, we analysed indigenous African cattle breeds as models of hybrid zones, considering taurine and indicine samples as ancestors. In a genomic cline analysis of whole-genome sequence data, we considered over 8 million variants from 144 animals, which allows for fine-mapping of potential genomic incompatibilities at high resolution across the genome.ResultsWe identified several thousand variants that had significantly steep clines (‘SCV’) across the whole genome, indicating restricted introgression. Some of the SCV were clustered into extended regions, with the longest on chromosome 7, spanning 725 kb and including 27 genes. We found that variants with a high phenotypic impact (e.g. indels, intra-genic and missense variants) likely represent greater genetic barriers to gene flow. Furthermore, our findings provide evidence that a large proportion of breed differentiation in African cattle could be linked to genomic incompatibilities and reproductive isolation. Functional evaluation of genes with SCV suggest that mitonuclear incompatibilities and genes associated with fitness (e.g. resistance to paratuberculosis) could account for restricted gene flow in indigenous African cattle.ConclusionsTo our knowledge, this is the first time genomic cline analysis has been applied to identify restricted introgression in the genomes of indigenous African cattle and the results provide extended insights into mechanisms (e.g. genomic incompatibilities) contributing to hybrid differentiation. These results have important implications for our understanding of genetic incompatibilities and reproductive isolation and provide important insights into the impact of cross-breeding cattle with the aim of producing offspring that are both hardy and productive.

Mito‐nuclear discordance and phylogeography of the surf clam Mesodesma donacium along the Southeast Pacific coast

AbstractMesodesma donacium is a surf clam endemic to the southeast Pacific coast, and it is an important resource species of the sandy beach artisanal fishery in Peru and Chile. Over time, the species has shown high variability in population dynamics (presence and abundance), which has been attributed to overfishing and environmental events. In this study, we assess the phylogeography of seven natural beds of M. donacium (17 to 42° S), to reveal the geographic distribution of the genetic diversity through the analysis of 278 sequences of the mitochondrial gene COI. Sequences of the nuclear genes 18S and 28S were used to evaluate the divergence of COI haplogroups. Two divergent parapatric mitochondrial haplogroups were found, which lacked divergence at nuclear markers (18S and 28S); this mito‐nuclear discordance allows inferring that there is no reproductive isolation of mitochondrial haplogroups. The North haplogroup is the only one present at the northernmost site, while only the South haplogroup was present in Cucao in the south. Between 28° and 32° S, coincident with a coastal biogeographic break at 30° S, both haplogroups are in sympatry. Haplogroups differed in their genetic structure, with the North haplogroup representing a single, highly diverse population and the South haplogroup with genetic differentiation and more restricted genetic diversity and gene flow. The divergence in mitochondrial haplogroups without nuclear divergence suggests a past scenario of geographic isolation in the northern and southern areas, without developing reproductive isolation, followed by secondary contact. Given the phylogeography, genetic information should be considered in restocking and management activities.

Influence of climate and landscape on genetic differentiation of aardvarks (Orycteropus afer)

AbstractAimAs climate change accelerates, assessing how climate shapes gene flow and neutral and adaptive genetic differentiation on landscapes is increasingly important. Aardvarks (Orycteropus afer) are ecologically important in sub‐Saharan Africa but are sensitive to human pressures and increasing aridity. We used individual, population and landscape genetic approaches to infer the influence of landscape, climate and potential adaptive differences on gene flow.LocationWe surveyed 8 protected and 4 privately owned areas in South Africa, 2 protected areas in Eswatini and one location in Kenya during 2016–2018.MethodsWe developed microsatellite markers and methods for DNA extraction from faeces, collected and genotyped faecal samples from focal areas and estimated genetic structure. We inferred space use from individual redetections, tested for close relatives and estimated genetic neighbourhood distance. We applied individual‐based landscape genetic analyses at multiple scales to test hypotheses about genetic differentiation by landscape resistance and potential adaptive differences.ResultsWe developed 19 variable microsatellite loci and collected 253 faecal samples from 13 focal areas. We genotyped 104 samples successfully at ≥8 loci as needed for individual identification. The genetic structure suggested 3 regional divisions in South Africa. We detected individuals at locations ≤7.3 km distant and closely related individuals at ≤44 km; genetic neighbourhood distance was &lt;55 km. Lower precipitation increased landscape resistance and strongly predicted genetic differentiation at most spatial scales. Temperature differences at sampling sites also influenced structure, suggesting climate‐associated adaptive differences.Main ConclusionsThe genetic structure of aardvarks is strongly shaped by climate, with arid areas limiting gene flow and reflects apparent isolation by adaptation associated with temperature. Dispersal distances likely are &lt;55 km. The markers we developed will facilitate studies of space use, dispersal, population density or survival. Aridification will increase fragmentation and we recommend monitoring aardvark presence as an indicator of ecosystem change associated with aridification.

How Veeries vary: Whole genome sequencing resolves genetic structure in a long-distance migratory bird

Abstract In high-latitude species with high dispersal ability, such as long-distance migratory birds, populations are often assumed to exhibit little genetic structure due to high gene flow or recent postglacial expansion. We sequenced over 120 low-coverage whole genomes from across the breeding range of a long-distance migratory bird, the Veery (Catharus fuscescens), revealing strong evidence for isolation by distance. Additionally, we found distinct genetic structure between boreal, western montane U.S., and southern Appalachian sampling regions. We suggest that population genetic structure in this highly migratory species is detectable with the high resolution afforded by whole-genomic data because, similar to many migratory birds, the Veery exhibits high breeding-site fidelity, which likely limits gene flow. Resolution of isolation by distance across the breeding range was sufficient to assign likely breeding origins of individuals sampled in this species’ poorly understood South American nonbreeding range, demonstrating the potential to assess migratory connectivity in this species using genomic data. As the Veery’s breeding range extends across both historically glaciated and unglaciated regions in North America, we also evaluated whether contemporary patterns of structure and genetic diversity are consistent with historical population isolation in glacial refugia. We found that patterns of genetic diversity did not support southern montane regions (southern Appalachians or western U.S. mountains) as glacial refugia. Overall, our findings suggest that isolation by distance yields subtle associations between genetic structure and geography across the breeding range of this highly vagile species even in the absence of obvious historical vicariance or contemporary barriers to dispersal.

Microgeographic speciation in a complex of Anatolian bush crickets facilitated by fast evolution of reproductive isolation.

Identifying the drivers of microgeographic speciation (i.e., speciation over small, local geographic scales) is key to understand the origin of speciose groups. Here, we use genomic data to infer the demographic processes underlying diversification in Poecilimon luschani (Orthoptera: Tettigoniidae), a species complex belonging to the most diverse genus of bush crickets from the Mediterranean region (>170 taxa) that comprises three recognized subspecies with small allopatric distributions in the topographically complex Teke Peninsula, southwestern Anatolia. Phylogenomic reconstructions that include all other taxa within the species group confirmed that subspecies of P. luschani originated from a common ancestor during the Pleistocene, supporting recent (<1 Ma) diversification within a small geographical area (ca. 120 × 80 km). Genetic clustering analyses corroborated the distinctiveness of each subspecies and the cohesiveness of their respective populations, with abrupt genetic discontinuities coinciding with contemporary range boundaries. Indeed, our analyses uncovered the presence of two sympatric cryptic sister lineages that diverged <300 ka ago and do not admix despite being co-distributed. Collectively, these results support that all lineages within the complex represent independently evolving entities corresponding to full-fledged species. Statistical evaluation of alternative models of speciation strongly supports a scenario of divergence in isolation followed by a period of limited gene flow during the last glacial period, when all lineages experienced marked expansions according to demographic reconstructions. Our study exemplifies how localized allopatric divergence and fast evolution of reproductive isolation can promote microgeographic speciation and explain the high rates of endemism characterizing biodiversity hotspots.

Bayesian hybrid index and genomic cline estimation with the R package gghybrid.

Admixture, the interbreeding of individuals from differentiated source populations, is now known to be a widespread phenomenon. Genomic studies of natural hybridisation can help to answer many questions on the impacts of admixture on adaptive evolution, reproductive isolation, and speciation. When a large variety of admixture proportions between two source populations exist, both geographic and genomic cline analysis are suitable methods for inferring biased, restricted or excessive gene flow at individual loci into the foreign genomic background, providing evidence for reproductive isolation, selection across an environmental transition, balancing selection, and adaptive introgression. Genomic cline analysis replaces geographic location with genome-wide hybrid index and is therefore useable in circumstances that violate geographic cline assumptions. Here, I introduce gghybrid, an R package for simple and flexible Bayesian estimation of Buerkle's hybrid index and Fitzpatrick's logit-logistic genomic clines using bi-allelic data, suitable for both small and large datasets. gghybrid allows any ploidy and uses Structure input file format. It has separate functions for hybrid index and cline estimation, treating each individual and locus respectively as an independent analysis, making it highly parallelisable. Admixture proportions from other software can alternatively be used in cline analysis, alongside parental allele frequencies. Parameters can be fixed and samples pooled for statistical model comparison with AIC or waic. Here, I describe the functions, pipeline, and statistical properties of gghybrid. Simulations reveal that model comparison with waic is preferred, and use of Bayesian posterior distributions and p values to select candidate non-null loci is problematic and should be avoided.

Morphological and Genetic Diversity of Mangrove Species Ceriops tagal (Perr.) C.B. Rob. Around Java Island

Ceriops tagal (Perr.) C.B. Rob can be found in Baluran National Park, Kepulauan Seribu National Park, Karimunjawa National Park, and Segara Anakan Cilacap in Java and its surrounding areas. These locations have different demographics and environmental conditions. Plant species found in different geographical areas have varied genetic structures and morphological traits as a result of their adaptability to their environment. The goal of this study is to evaluate the morphological and genetic differences between the four populations of C. tagal in Java and its surroundings. Internode length, leaf length, leaf width, petiole length, and leaf area were the morphological characters used. The Internal Transcribed Spacer (ITS) region is used as a molecular marker. The UPGMA dendogram was used to analyze the morphological similarity, and multidimensional unfolding analysis was used to determine which character most determined the grouping. Mega X software was used to analyze genetic variation using the neighbor-joining approach, while Arlequin 3.5 software was used to estimate genetic variation within and among populations. The results of this study showed that the population of Baluran National Park has features or is distinct from the other three populations based on morphological and genetic characters; this could be because of variations in geographic conditions, and that population diversification was aided by a combination of genetic and physical divergence, restricted gene flow, and local adaptation.

Three systems of molecular markers reveal genetic differences between varieties sabina and balkanensis in the Juniperus sabina L. range

Key messageJ. sabina var. balkanensis, that is of hybrid origin, and its maternal progenitor J. sabina var. sabina are genetically distinct with respect to cpDNA, SNP, and SilicoDArT loci. Mostly non-overlapping distributions of the sabina and balkanensis varieties are the result of their different climatic requirements.ContextJuniperus sabina L. is present in the Eurasian mountains, but its range is severely fragmented. In Europe, two varieties of J. sabina occur: var. sabina and var. balkanensis, the latter being an allotetraploid hybrid between the diploid var. sabina and a tetraploid ancestor of Juniperus thurifera L. The distribution of the two varieties is mostly disjunct.AimsAssess the taxonomic affiliation and genetic differentiation of the populations of var. sabina and var. balkanensis in Europe and Asia using cpDNA, SilicoDArT, and SNP markers. Identify climatic niches of both juniper varieties in Europe.MethodsAltogether, 21,134 SilicoDArT, 8,579 SNP, and four cpDNA loci were used. Seven climatic variables were compared in sites inhabited by var. balkanensis and the two parental species.ResultsThe SilicoDArTs and SNPs revealed a pattern of population differentiation that was congruent with the cpDNA analysis. The hybrid var. balkanensis occupies habitats with higher temperatures and intermediate levels of precipitation compared to both parental taxa.ConclusionThe low genetic variation and significant genetic differentiation among J. sabina populations likely result from the restriction of gene flow imposed by the mountain ranges. The balkanensis variety is able to cope with hot and dry climates probably thanks to the admixture of J. thurifera genes.