Genetic diversity hotspots of trematodes (Platyhelminthes) in Mexico and their overlap with protected natural areas

AimSpecies diversity in the region of the Qinghai–Tibet Plateau has been extensively explored, whereas the distribution of genetic diversity remains poorly understood in this species‐rich area, parts of which are listed as biodiversity hotspots. In this study, we aimed to map the patterns of genetic diversity and divergence of plant species in this region, and to identify potential evolutionary hotspots for conservation planning.LocationRegion of the Qinghai–Tibet Plateau (QTP).MethodsWe compiled published molecular data for 60 plant species, and calculated intra‐population genetic diversity and inter‐population genetic divergence using haplotype sequences (chloroplast or mitochondrial DNA). We analysed the relationships between genetic diversity and longitude, latitude and elevation. We mapped the landscapes of genetic diversity and divergence for each species in GIS, and combined the resulting landscapes in order to identify hotspots of high genetic diversity and divergence.ResultsThere were no significant relationships between genetic diversity and longitude, latitude and elevation. For most species, areas characterized by high genetic diversity and divergence were located across the Hengduan Mountains. Nine evolutionary hotspots across the region of the QTP were identified.Main conclusionsThe Hengduan Mountains are a remarkable hotspot of all three dimensions of biodiversity (genes, species and ecosystems), yet patterns of genetic diversity were partially incongruent with the distribution of species diversity. For example, several hotspots of genetic diversity were located on the QTP proper, which is relatively species poor. This partial geographic mismatch between species and genetic diversity highlights the need to consider both aspects in conservation programs. Our study suggests that more protected areas in the region of the QTP need to be established in order to protect genetic diversity and thus adaptive potential.

Understanding the genetic diversity and distribution patterns of seaweeds species is crucial for evaluating key regions of high genetic diversity. Identifying hotspots of high intraspecific diversity is an important step for developing conservation strategies. Grateloupia is a diverse genus of Rhodophyta, many of which are resource of numerous useful bioactive compounds; therefore, the genus is valuable target for conservation. The aim of this study is to examine the genetic diversity and population structure of two Grateloupia species, Grateloupia asiatica and Grateloupia jejuensis, with the understanding of the phylogeography of the Korean genetic diversity hotspot for two species. Plastid rbcL gene sequences of 134 specimens of G. asiatica and 112 specimens of G. jejuensis collected from the Korean coast were analyzed. We evaluated the number of haplotypes, genetic diversity (haplotype and nucleotide diversity), and haplotype networks of two species. Historical demographic was inferred by calculating neutrality tests and genetic differentiation was estimated using the fixation index, FST. Our results show that both species are generally similar in geographical distribution patterns, that is, relatively homogeneous with few haplotypes derived from the most frequent haplotype. The east coast of Korea is identified as a 'hotspot' with the highest genetic diversity for both species, whereas Jeju Island is identified as a 'cold spot' with the lowest genetic diversity for G. jejuensis. Analyses across most distribution ranges of the two species in Korea reveal low genetic and haplotype diversities, which could indicate that these two Grateloupia species have either experienced a historical lack of diversity or a recent reduction in diversity due to high gene flow. The low genetic diversity values found in the present study raise considerable concern about the conservation status of these two Grateloupia species and highlight the need to locate further hotspots of genetic diversity to strengthen their resilience against further decline.

AimWe explored lineage diversification within desert‐dwelling fauna. Our goals were (1) to determine whether phylogenetic lineages and population expansions were consistent with younger Pleistocene climate fluctuation hypotheses or much older events predicted by pre‐Pleistocene vicariance hypotheses, (2) to assess concordance in spatial patterns of genetic divergence and diversity among species and (3) to identify regional evolutionary hotspots of divergence and diversity and assess their conservation status.LocationMojave, Colorado, and Sonoran Deserts, USA.MethodsWe analysed previously published gene sequence data for twelve species. We used Bayesian gene tree methods to estimate lineages and divergence times. Within each lineage, we tested for population expansion and age of expansion using coalescent approaches. We mapped interpopulation genetic divergence and intra‐population genetic diversity in a GIS to identify hotspots of highest genetic divergence and diversity and to assess whether protected lands overlapped with evolutionary hotspots.ResultsIn seven of the 12 species, lineage divergence substantially predated the Pleistocene. Historical population expansion was found in eight species, but expansion events postdated the Last Glacial Maximum (LGM) in only four. For all species assessed, six hotspots of high genetic divergence and diversity were concentrated in the Colorado Desert, along the Colorado River and in the Mojave/Sonoran ecotone. At least some proportion of the land within each recovered hotspot was categorized as protected, yet four of the six also overlapped with major areas of human development.Main conclusionsMost of the species studied here diversified into distinct Mojave and Sonoran lineages prior to the LGM – supporting older diversification hypotheses. Several evolutionary hotspots were recovered but are not strategically paired with areas of protected land. Long‐term preservation of species‐level biodiversity would entail selecting areas for protection in Mojave and Sonoran Deserts to retain divergent genetic diversity and ensure connectedness across environmental gradients.

AimThe Irano‐Anatolian biodiversity hotspot is among the least‐known biodiversity hotspots on earth. In this study, we aim to map the richness and genetic divergence of lizards in the biodiversity hotspot and its surrounding areas and identify the most important determinants of the richness and genetic divergence patterns.LocationIran and Turkey (Irano‐Anatolian biodiversity hotspot).MethodsHere, we mapped the distribution of 211 lizard species in Iran and Turkey using existing occurrence data and generated the first genetic divergence pattern map of the lizard species in the two countries to identify areas of high species diversity and genetic divergence in the Irano‐Anatolian biodiversity hotspot. We also identified determinants of lizard richness and genetic divergence patterns.ResultsResults showed that the Zagros Mountains, Central Iranian Plateau and the northern Persian Gulf have the highest lizard richness. The Zagros Mountains, Central Iranian Plateau, the northern Persian Gulf and the regions around the Lut Desert and Jazmourian Plain have the highest total genetic divergence in Iran. Alborz and Kopet Dag mountains and south western parts of Turkey have the highest average genetic divergence. The annual temperature was the most important predictor of lizard richness, and temperature change velocity was the most influential determinant of genetic divergence pattern. Much to our surprise, species diversity and most areas with high genetic divergence are located outside of Irano‐Anatolian biodiversity hotspot.Main conclusionsThis study showed that lizard richness and genetic divergence patterns are associated with current and past climate. In particular, this study highlights the legacy of past climate changes on lizard genetic divergence distribution patterns. We showed that most of the species‐rich and genetically diverse regions are located outside of the biodiversity hotspot. So conservation efforts that are concentrated inside the biodiversity hotspot may not benefit lizard biodiversity conservation. Thus, future studies and conservation programs on the biodiversity hotspot should also consider its surrounding areas.

Pyropia yezoensis and Py. suborbiculata have been traditionally important for marine aquaculture as food resources in the northwest Pacific region. We conducted molecular analyses using plastid rbcL and mitochondrial COI-5P markers to identify their genetic diversity hotspot using samples collected from various locations of the northwest Pacific region as well as genetic information obtained from a public repository, representing specimens around the world. In the rbcL result, Py. yezoensis was separated into 19 haplotypes, and Py. suborbiculata was separated into 26 haplotypes. In COI-5P, 5 and 14 haplotypes were revealed in Py. yezoensis and Py. suborbiculata, respectively. We discovered a large number of haplotypes of Py. yezoensis in Hokkaido of Japan and high genetic diversity of Py. suborbiculata in the East Sea. Interestingly, Py. yezoensis and Py. suborbiculata showed unique haplotypes in the eastern coast of Korea. The distinction of haplotype composition between the East Sea and those of other regions in the northwest Pacific could be due to the divergence from environmental isolation of the East Sea during the Last Glacial Maximum. Our results show that the East Sea including Hokkaido of Japan is an important genetic diversity hotspot of Py. yezoensis and Py. suborbiculata and needs to be further monitored for conservation.

Genetic diversity across geographical scales in marine coastal ecosystems: Holothuria arguinensis a model species

Genetic diversity feeds the evolutionary process and allows populations to adapt to environmental changes. However, we still lack a thorough understanding of why hotspots of genetic diversity are so 'hot'. Here, we analysed the relative contribution of bioclimatic stability and genetic admixture between divergent lineages in shaping spatial patterns of genetic diversity in the common toad Bufo bufo along the Italian peninsula. We combined population genetic, phylogeographic and species distribution modelling (SDM) approaches to map ancestral areas, glacial refugia, and secondary contact zones. We consistently identified three phylogeographic lineages, distributed in northern, central and southern Italy. These lineages expanded from their ancestral areas and established secondary contact zones, before the last interglacial. SDM identified widespread glacial refugia in peninsular Italy, sometimes located under the present-day sea-level. Generalized linear models indicated genetic admixture as the only significant predictor of the levels of population genetic diversity. Our results show that glacial refugia contributed to preserving both levels and patterns of genetic diversity across glacial-interglacial cycles, but not to their formation, and highlight a general principle emerging in Mediterranean species: higher levels of genetic diversity mark populations with substantial contributions from multiple genetic lineages, irrespective of the location of glacial refugia.

Quercus castaneifolia C.A. Mey., a dominant and ecologically important oak species in the Hyrcanian forests of northern Iran, is experiencing rapid decline due to climate change, anthropogenic pressures, and severe habitat fragmentation. This study aims to delineate genetic diversity patterns and identify key conservation areas for Q. castaneifolia across its entire range within Iran. We integrated population genetic analyses with landscape connectivity modeling to identify regions of high evolutionary and ecological importance. Using 14 polymorphic nuclear microsatellite (nSSR) and four chloroplast microsatellite (cpSSR) loci, we assessed 235 individuals across the species' geographical distribution. Nuclear markers revealed high genetic diversity (H e = 0.54) and weak differentiation (F ST = 0.019), suggesting extensive pollen flow, while cpSSRs showed strong spatial structure and restricted seed dispersal. Seven distinct chloroplast haplotypes were identified, with the Talesh-Mardab hydro-region exhibiting the highest haplotype diversity and harboring four private haplotypes. Habitat connectivity analysis using UNICOR revealed two main core areas located in the western (Talesh-Mardab) and eastern (Qarasu-Gorgan) Hyrcanian regions, connected by a central corridor through Lahijan-Nur and Haraz-Naka. These spatial patterns closely overlapped with areas of haplotype diversity, highlighting them as conservation hotspots. Our nuclear SSR results are consistent with previous findings showing low differentiation and extensive pollen flow, whereas cpDNA markers provided additional insights into seed dispersal and spatially structured haplotype variation. Our integrated approach provides a valuable framework for identifying core populations and genetic diversity hotspots, as well as for preserving gene flow pathways essential to the species' long-term persistence and its dynamic gene conservation.

The Cerrado, the largest Neotropical savanna, and the Brazilian Atlantic Forest form large ecotonal areas where savanna and forest habitats occupy adjacent patches with closely related species occurring side by side, providing opportunities for hybridization. Here, we investigated the evolutionary divergence between the savanna and forest ecotypes of the widely distributed tree Plathymenia reticulata (n = 233 individuals). Genetic structure analysis of P. reticulata was congruent with the recognition of two ecotypes, whose divergence captured the largest proportion of genetic variance in the data (F CT = 0.222 and F ST = 0.307). The ecotonal areas between the Cerrado and the Atlantic Forest constitute a hybrid zone in which a diversity of hybrid classes was observed, most of them corresponding to second‐generation hybrids (F2) or backcrosses. Gene flow occurred mainly toward the forest ecotype. The genetic structure was congruent with isolation by environment, and environmental correlates of divergence were identified. The observed pattern of high genetic divergence between ecotypes may reflect an incipient speciation process in P. reticulata. The low genetic diversity of the P. reticulata forest ecotype indicate that it is threatened in areas with high habitat loss on Atlantic Forest. In addition, the high divergence from the savanna ecotype suggests it should be treated as a different unit of management. The high genetic diversity found in the ecotonal hybrid zone supports the view of ecotones as important areas for the origin and conservation of biodiversity in the Neotropics.

SummaryThe Qinghai-Tibet Plateau (QTP) is a global biodiversity hotspot, yet the distribution of genetic diversity hotspots in co-distributed species remains poorly understood. Here, we integrate genomic data from three co-distributed endemic species (plateau pika and two snowfinches) on the QTP, with ecological niche models (ENMs) based on paleoclimate data to identify shared genetic diversity hotspots. Our results reveal a consistent northeast-to-southwest decline in genetic diversity, with a shared hotspot located in the northeastern QTP. ENMs further suggest that these species shared glacial refugia in this region during the last glacial maximum, followed by post-glacial expansions into the central plateau, resulting in similar spatial patterns of genetic diversity. Differences in genetic differentiation, demographic history, inbreeding depression, and genetic load suggest species-specific evolutionary responses to historical climate fluctuations. Overall, our study highlights the importance of protecting hotspots of shared genetic diversity across multiple species to preserve their evolutionary potential.

BackgroundHotspots of intraspecific genetic diversity represent invaluable resources for species to cope with environmental changes, and their identification is increasingly recognized as a major goal of conservation ecology research. However, even for iconic and endangered species, conservation strategies are often planned without thorough information on the geographic patterns of genetic variation. Here, we investigated the spatial patterns of genetic variation of the endangered Hermann’s tortoise Testudo hermanni in the Italian Peninsula by genotyping 174 individuals at 7 microsatellite loci, with the aim to contribute to planning effective conservation strategies.ResultsOrdination-based and Bayesian clustering analyses consistently identified three main genetic clusters, one spread in the central and northern part of the peninsula, and two restricted to southern Italy and Sicily, respectively. The highest levels of genetic diversity were found in populations of the southern cluster and, in particular, at the northern edges of its distribution (He > 0.6, Ar > 2.8 ), that correspond to areas of putative secondary contact and admixture between distinct lineages. Our results clearly identify a hotspot of genetic diversity for the Hermann’s tortoise in southern Italy.ConclusionWe inferred the evolutionary history and the spatial patterns of genetic variation of the Hermann’s tortoise in the Italian Peninsula. We identified three main genetic clusters along the peninsula and a hotspot of intraspecific diversity in southern Italy. Our results underline the urgent need for conservation actions to warrant the long-term persistence of viable tortoise populations in this area. Furthrmore, these data add further evidence to the role of southern Italy as a biodiversity hotspot for temperate fauna, claiming for higher consideration of this area in large scale conservation programs.

AimEmpirical studies have often reported parallel patterns of genetic and species diversity, but the strength and generality of this association, as well as its origin, are still debated. Particularly in human‐dominated landscapes with complex histories of land use histories, more complicated and partly diverging patterns have been observed. In this study, we examine whether species and genetic diversity correlate across grasslands with different levels of land use pressure and spatial differentiation in habitat quality and heterogeneity.LocationWe selected eight extensively used (grazed, unfertilized) dry grasslands and eight intensively used (mown, fertilized) hay meadows in southeastern Germany.MethodsWe used vegetation surveys and molecular markers of six widespread dry grassland and six hay meadow plant species to compare species and genetic alpha and beta diversity between the two grassland types.ResultsSpecies diversity patterns expectedly showed higher alpha diversity, stronger spatial structure and less turnover in dry grasslands than in hay meadows. Neither of the corresponding genetic diversity patterns showed the same significant trends.Main conclusionOur results question the idea that species and genetic diversity patterns will always show similar patterns. Likely, genetic and species diversity emerge partly from shared, partly from different processes, including the regional species pool, environmental heterogeneity, fragmentation and land use history. The practical conservation implication is that species and genetic diversity are not generally interchangeable. Looking at species and genetic patterns together, however, may eventually lead to a better understanding of the complex processes that shape the structure and dynamics of ecological communities.

BackgroundBrachypodium distachyon (Poaceae), an annual Mediterranean Aluminum (Al)-sensitive grass, is currently being used as a model species to provide new information on cereals and biofuel crops. The plant has a short life cycle and one of the smallest genomes in the grasses being well suited to experimental manipulation. Its genome has been fully sequenced and several genomic resources are being developed to elucidate key traits and gene functions. A reliable germplasm collection that reflects the natural diversity of this species is therefore needed for all these genomic resources. However, despite being a model plant, we still know very little about its genetic diversity. As a first step to overcome this gap, we used nuclear Simple Sequence Repeats (nSSR) to study the patterns of genetic diversity and population structure of B. distachyon in 14 populations sampled across the Iberian Peninsula (Spain), one of its best known areas.ResultsWe found very low levels of genetic diversity, allelic number and heterozygosity in B. distachyon, congruent with a highly selfing system. Our results indicate the existence of at least three genetic clusters providing additional evidence for the existence of a significant genetic structure in the Iberian Peninsula and supporting this geographical area as an important genetic reservoir. Several hotspots of genetic diversity were detected and populations growing on basic soils were significantly more diverse than those growing in acidic soils. A partial Mantel test confirmed a statistically significant Isolation-By-Distance (IBD) among all studied populations, as well as a statistically significant Isolation-By-Environment (IBE) revealing the presence of environmental-driven isolation as one explanation for the genetic patterns found in the Iberian Peninsula.ConclusionsThe finding of higher genetic diversity in eastern Iberian populations occurring in basic soils suggests that these populations can be better adapted than those occurring in western areas of the Iberian Peninsula where the soils are more acidic and accumulate toxic Al ions. This suggests that the western Iberian acidic soils might prevent the establishment of Al-sensitive B. distachyon populations, potentially causing the existence of more genetically depauperated individuals.

A set of 107 hulless barley (Hordeum vulgare L. subsp. vulgare) landraces originally collected from the highlands of Nepal along the Annapurna and Manaslu Himalaya range were studied for genetic relatedness and population differentiation using simple sequence repeats (SSRs). The 44 genome covering barley SSRs applied in this study revealed a high level of genetic diversity among the landraces (diversity index, DI = 0.536) tested. The genetic similarity (GS) based UPGMA clustering and Bayesian Model-based (MB) structure analysis revealed a complex genetic structure of the landraces. Eight genetically distinct populations were identified, of which seven were further studied for diversity and differentiation. The genetic diversity estimated for all and each population separately revealed a hot spot of genetic diversity at Pisang (DI = 0.559). The populations are fairly differentiated (theta = 0.433, R(ST) = 0.445) accounting for > 40% of the genetic variation among the populations. The pairwise population differentiation test confirmed that many of the geographic populations significantly differ from each other but that the differentiation is independent of the geographic distance (r = 0.224, P > 0.05). The high level of genetic diversity and complex population structure detected in Himalayan hulless barley landraces and the relevance of the findings are discussed.

Complex parasite life cycles frequently require trophic transfer of parasites from an intermediate host prey to a definitive host predator. This results in aggregated distributions of parasites in predator host populations, which are subsequently expected to host more genetically diverse parasite infrapopulations than lower trophic level hosts. Host dispersal and seasonal population dynamics, particularly in the case of first-intermediate hosts, are also expected to drive population genetic patterns within and across populations. To examine how parasite life history and host ecology influence parasite genetic patterns, we characterized the genetic diversity of within-host infrapopulations, as well as overall population genetic structure, of sympatric tongueworm (Halipegus occidualis) and lungworm (Haematoloechus complexus) freshwater trematode parasite populations. Parasites were collected across three host stages (snail, odonate insect, and frog) and sequenced at the cytochrome oxidase I (COI) mitochondrial region (519 bp for lungworms; 526 bp for tongueworms) to characterize genetic variation within and across hosts. Infection abundance per host and genetic diversity of within-host parasite infrapopulations generally increased with host trophic level, as expected. Additionally, tongueworm assemblages in odonate hosts were essentially equally as genetically diverse (depending on the index used) as those in definitive host frogs; tongueworms have an additional trophic transfer in their life cycle before the odonate stage, which highlights how trophic transmission and multi-host life cycle structure can benefit parasites by increasing genetic diversity of sexually reproducing adult assemblages. We also found that tongueworm populations, which infect a long-lived snail as a first-intermediate host, had higher population genetic diversity than lungworms, which infect a much shorter-lived snail with highly unstable population dynamics. Thus, we expect that first-intermediate host dynamics and dispersal ability played a large role in predicting population-level parasite genetic diversity and genetic structure in this system. This study investigates the effects of small- and large-scale processes on parasite genetic population structure and diversity and provides critical genetic data for future studies on these genera.