Low levels of realized seed and pollen gene flow and strong spatial genetic structure in a small,isolated and fragmented population of the tropical tree Copaifera langsdorffii Desf

Over the past century, the Brazilian Atlantic forest has been reduced to small, isolated fragments of forest. Reproductive isolation theories predict a loss of genetic diversity and increases in inbreeding and spatial genetic structure (SGS) in such populations. We analysed eight microsatellite loci to investigate the pollen and seed dispersal patterns, genetic diversity, inbreeding and SGS of the tropical tree Copaifera langsdorffii in a small (4.8 ha), isolated population. All 112 adult trees and 128 seedlings found in the stand were sampled, mapped and genotyped. Seedlings had significantly lower levels of genetic diversity (A=16.5±0.45, mean±95% s.e.; H_e=0.838±0.006) than did adult trees (A=23.2±0.81; H_e=0.893±0.030). Parentage analysis did not indicate any seed immigration (m_seeds=0) and the pollen immigration rate was very low (m_pollen=0.047). The average distance of realized pollen dispersal within the stand was 94 m, with 81% of the pollen travelling <150 m. A significant negative correlation was found between the frequency and distance of pollen dispersal (r=−0.79, P<0.01), indicating that short-distance pollinations were more frequent. A significant SGS for both adults (∼50 m) and seedlings (∼20 m) was also found, indicating that most of the seeds were dispersed over short distances. The results suggested that the spatial isolation of populations by habitat fragmentation can restrict seed and pollen gene flow, increase SGS and affect the genetic diversity of future generations.     

Fine-scale spatial genetic structure of Dalbergia nigra (Fabaceae), a threatened and endemic tree of the Brazilian Atlantic Forest

The Atlantic Forest is one of the most diverse ecosystems in the world and considered a hotspot of biodiversity conservation. Dalbergia nigra (Fabaceae) is a tree endemic to the Brazilian Atlantic Forest, and has become threatened due to overexploitation of its valuable timber. In the present study, we analyzed the genetic diversity and fine-scale spatial genetic structure of D. nigra in an area of primary forest of a large reserve. All adult individuals (N = 112) were sampled in a 9.3 ha plot, and genotyped for microsatellite loci. Our results indicated high diversity with a mean of 8.6 alleles per locus, and expected heterozygosity equal to 0.74. The co-ancestry coefficients were significant for distances among trees up to 80 m. The Sp value was equal to 0.017 and indirect estimates of gene dispersal distances ranged from 89 to 144 m. No strong evidence of bottleneck or effects of human-disturbance was found. This study highlights that long-term efforts to protect a large area of Atlantic Forest have been effective towards maintaining the genetic diversity of D. nigra. The results of this study are important towards providing a guide for seed collection for ex-situ conservation and reforestation programmes of this threatened species.     

High molecular diversity in the true service tree (Sorbus domestica) despite rareness: data from Europe with special reference to the Austrian occurrence

Background and Aims Sorbus domestica (Rosaceae) is one of the rarest deciduous tree species in Europe and is characterized by a scattered distribution. To date, no large-scale geographic studies on population genetics have been carried out. Therefore, the aims of this study were to infer levels of molecular diversity across the major part of the European distribution of S. domestica and to determine its population differentiation and structure. In addition, spatial genetic structure was examined together with the patterns of historic and recent gene flow between two adjacent populations.Methods Leaf or cambium samples were collected from 17 populations covering major parts of the European native range from north-west France to south-east Bulgaria. Seven nuclear microsatellites and one chloroplast minisatellite were examined and analysed using a variety of methods.Key Results Allelic richness was unexpectedly high for both markers within populations (mean per locus: 3·868 for nSSR and 1·647 for chloroplast minisatellite). Moreover, there was no evidence of inbreeding (mean F_is = –0·047). The Italian Peninsula was characterized as a geographic region with comparatively high genetic diversity for both genomes. Overall population differentiation was moderate (F_ST = 0·138) and it was clear that populations formed three groups in Europe, namely France, Mediterranean/Balkan and Austria. Historic gene flow between two local Austrian populations was high and asymmetric, while recent gene flow seemed to be disrupted.Conclusions It is concluded that molecular mechanisms such as self-incompatibility and high gene flow distances are responsible for the observed level of allelic richness as well as for population differentiation. However, human influence could have contributed to the present genetic pattern, especially in the Mediterranean region. Comparison of historic and recent gene flow may mirror the progress of habitat fragmentation in eastern Austria.     

Molecular phylogeography of Carapichea ipecacuanha,an amphitropical shrub that occurs in the understory of both semideciduous and evergreen forests

The medicinal shrub Carapichea ipecacuanha (ipecac) is an amphitropic species with three disjunct areas of distribution. In the Brazilian Atlantic and Amazonian ranges, the species was associated mostly with the understory of seasonal semideciduous forests, whereas in the Central American–Colombian range, the species occurred in the understory of moist evergreen forests. We examined the phylogeographic structure of ipecac using chloroplast trnT‐trnL and nuclear internal transcribed spacer (ITS) sequences from 120 and 46 specimens, respectively. To complement existing data on root alkaloid profiles, we used high‐performance liquid chromatography to assess the levels of emetine and cephaeline in 33 specimens from the two Brazilian ranges. The three ranges shared neither nuclear nor chloroplast haplotypes. The phylogeographic structures showed an uneven distribution of genetic diversity, sharp breaks and high levels of genetic differentiation among ranges. Our results suggest that the extant populations are descendents of at least four distinct ancestral lineages. The Atlantic ipecacs showed higher levels of genetic diversity than ipecacs from the other two ranges; it is likely that they derive from two ancestral lineages, with long‐term persistence in that region. The Amazonian ipecacs were monomorphic with respect to the ITS and cpDNA sequences, which supports the view that there was a recent expansion from a single parental source after a strong genetic bottleneck. The existence of a fourth distinct lineage is apparent from the high levels of genetic and chemical differentiation that we identified in the Central American–Columbian ipecacs.     

Natural or Naturalized? Phylogeography Suggests That the Abundant Sea Urchin Arbacia lixula Is a Recent Colonizer of the Mediterranean

We present the global phylogeography of the black sea urchin Arbacia lixula, an amphi-Atlantic echinoid with potential to strongly impact shallow rocky ecosystems. Sequences of the mitochondrial cytochrome c oxidase gene of 604 specimens from 24 localities were obtained, covering most of the distribution area of the species, including the Mediterranean and both shores of the Atlantic. Genetic diversity measures, phylogeographic patterns, demographic parameters and population differentiation were analysed. We found high haplotype diversity but relatively low nucleotide diversity, with 176 haplotypes grouped within three haplogroups: one is shared between Eastern Atlantic (including Mediterranean) and Brazilian populations, the second is found in Eastern Atlantic and the Mediterranean and the third is exclusively from Brazil. Significant genetic differentiation was found between Brazilian, Eastern Atlantic and Mediterranean regions, but no differentiation was found among Mediterranean sub-basins or among Eastern Atlantic sub-regions. The star-shaped topology of the haplotype network and the unimodal mismatch distributions of Mediterranean and Eastern Atlantic samples suggest that these populations have suffered very recent demographic expansions. These expansions could be dated 94–205 kya in the Mediterranean, and 31–67 kya in the Eastern Atlantic. In contrast, Brazilian populations did not show any signature of population expansion. Our results indicate that all populations of A. lixula constitute a single species. The Brazilian populations probably diverged from an Eastern Atlantic stock. The present-day genetic structure of the species in Eastern Atlantic and the Mediterranean is shaped by very recent demographic processes. Our results support the view (backed by the lack of fossil record) that A. lixula is a recent thermophilous colonizer which spread throughout the Mediterranean during a warm period of the Pleistocene, probably during the last interglacial. Implications for the possible future impact of A. lixula on shallow Mediterranean ecosystems in the context of global warming trends must be considered.     

Diversity and relationships of Crocus sativus and its relatives analysed by inter-retroelement amplified polymorphism (IRAP)

Background and Aims: Saffron (Crocus sativus) is a sterile triploid (2n = 3x = 24) cultivated species, of unknown origin from other diploid and polyploid species in the genus Crocus (Iridaceae). Species in the genus have high morphological diversity, with no clear phylogenetic patterns below the level of section Crocus series Crocus. Using DNA markers, this study aimed to examine the diversity and relationships within and between species of Crocus series Crocus.Methods: Eleven inter-retroelement amplified polymorphism (IRAP) primers were used in 63 different combinations with 35 single-plant accessions of C. sativus and related Crocus species in order to determine genetic variability and to conduct phylogenetic analysis.Key Results: A total of 4521 distinct polymorphic bands from 100 bp to approx. 4 kb were amplified; no fragment specific to all accessions of a single species was amplified. The polymorphic information content (PIC) values varied from approx. 0·37 to approx. 0·05 (mean 0·17 ± 0·1) and the major allele frequency had a mean of 0·87. High levels of polymorphism were identified between accessions of the six species of Crocus series Crocus related to C. sativus, with further variation between the species. In contrast, no polymorphisms were seen among 17 C. sativus accessions obtained in the region from Kashmir through Iran to Spain.Conclusions In contrast to the intraspecific variability seen in other Crocus species, C. sativus has minimal genetic variation, and it is concluded that the triploid hybrid species has most probably arisen only once. The data show that saffron is an allotriploid species, with the IRAP analysis indicating that the most likely ancestors are C. cartwrightianus and C. pallasii subsp. pallasii (or close relatives). The results may facilitate resynthesizing saffron with improved characteristics, and show the need for conservation and collection of wild Crocus.     

The ancient tropical rainforest tree Symphonia globulifera L. f. (Clusiaceae) was not restricted to postulated Pleistocene refugia in Atlantic Equatorial Africa

Understanding the history of forests and their species'' demographic responses to past disturbances is important for predicting impacts of future environmental changes. Tropical rainforests of the Guineo-Congolian region in Central Africa are believed to have survived the Pleistocene glacial periods in a few major refugia, essentially centred on mountainous regions close to the Atlantic Ocean. We tested this hypothesis by investigating the phylogeographic structure of a widespread, ancient rainforest tree species, Symphonia globulifera L. f. (Clusiaceae), using plastid DNA sequences (chloroplast DNA [cpDNA], psbA-trnH intergenic spacer) and nuclear microsatellites (simple sequence repeats, SSRs). SSRs identified four gene pools located in Benin, West Cameroon, South Cameroon and Gabon, and São Tomé. This structure was also apparent at cpDNA. Approximate Bayesian Computation detected recent bottlenecks approximately dated to the last glacial maximum in Benin, West Cameroon and São Tomé, and an older bottleneck in South Cameroon and Gabon, suggesting a genetic effect of Pleistocene cycles of forest contraction. CpDNA haplotype distribution indicated wide-ranging long-term persistence of S. globulifera both inside and outside of postulated forest refugia. Pollen flow was four times greater than that of seed in South Cameroon and Gabon, which probably enabled rapid population recovery after bottlenecks. Furthermore, our study suggested ecotypic differentiation—coastal or swamp vs terra firme—in S. globulifera. Comparison with other tree phylogeographic studies in Central Africa highlighted the relevance of species-specific responses to environmental change in forest trees.     

The importance of Anatolian mountains as the cradle of global diversity in Arabis alpina, a key arctic-alpine species

Background and Aims

Anatolia is a biologically diverse, but phylogeographically under-explored region. It is described as either a centre of origin and long-term Pleistocene refugium, or as a centre for genetic amalgamation, fed from distinct neighbouring refugia. These contrasting hypotheses are tested through a global phylogeographic analysis of the arctic–alpine herb, Arabis alpina.

Methods

Herbarium and field collections were used to sample comprehensively the entire global range, with special focus on Anatolia and Levant. Sequence variation in the chloroplast DNA trnL-trnF region was examined in 483 accessions. A haplotype genealogy was constructed and phylogeographic methods, demographic analysis and divergence time estimations were used to identify the centres of diversity and to infer colonization history.

Key Results

Fifty-seven haplotypes were recovered, belonging to three haplogroups with non-overlapping distributions in (1) North America/Europe/northern Africa, (2) the Caucuses/Iranian Plateau/Arabian Peninsula and (3) Ethiopia–eastern Africa. All haplogroups occur within Anatolia, and all intermediate haplotypes linking the three haplogroups are endemic to central Anatolia and Levant, where haplotypic and nucleotide diversities exceeded all other regions. The local pattern of haplotype distribution strongly resembles the global pattern, and the haplotypes began to diverge approx. 2·7 Mya, coinciding with the climate cooling of the early Middle Pleistocene.

Conclusions

The phylogeographic structure of Arabis alpina is consistent with Anatolia being the cradle of origin for global genetic diversification. The highly structured landscape in combination with the Pleistocene climate fluctuations has created a network of mountain refugia and the accumulation of spatially arranged genotypes. This local Pleistocene population history has subsequently left a genetic imprint at the global scale, through four range expansions from the Anatolian diversity centre into Europe, the Near East, Arabia and Africa. Hence this study also illustrates the importance of sampling and scaling effects when translating global from local diversity patterns during phylogeographic analyses.     

Leaf shape evolution has a similar genetic architecture in three edaphic specialists within the Mimulus guttatus species complex

Background and Aims The genetic basis of leaf shape has long interested botanists because leaf shape varies extensively across the plant kingdom and this variation is probably adaptive. However, knowledge of the genetic architecture of leaf shape variation in natural populations remains limited. This study examined the genetic architecture of leaf shape diversification among three edaphic specialists in the Mimulus guttatus species complex. Lobed and narrow leaves have evolved from the entire, round leaves of M. guttatus in M. laciniatus, M. nudatus and a polymorphic serpentine M. guttatus population (M2L).Methods Bulk segregant analysis and next-generation sequencing were used to map quantitative trait loci (QTLs) that underlie leaf shape in an M. laciniatus × M. guttatus F₂ population. To determine whether the same QTLs contribute to leaf shape variation in M. nudatus and M2L, F₂s from M. guttatus × M. nudatus and lobed M2L × unlobed M. guttatus crosses were genotyped at QTLs from the bulk segregant analysis.Key Results Narrow and lobed leaf shapes in M. laciniatus, M. nudatus and M. guttatus are controlled by overlapping genetic regions. Several promising leaf shape candidate genes were found under each QTL.Conclusions The evolution of divergent leaf shape has taken place multiple times in the M. guttatus species complex and is associated with the occupation of dry, rocky environments. The genetic architecture of elongated and lobed leaves is similar across three species in this group. This may indicate that parallel genetic evolution from standing variation or new mutations is responsible for the putatively adaptive leaf shape variation in Mimulus.     

Life in the desert: The impact of geographic and environmental gradients on genetic diversity and population structure of Ivesia webberi

For range‐restricted species with disjunct populations, it is critical to characterize population genetic structure, gene flow, and factors that influence functional connectivity among populations in order to design effective conservation programs. In this study, we genotyped 314 individuals from 16 extant populations of Ivesia webberi, a United States federally threatened Great Basin Desert using six microsatellite loci. We assessed the effects of Euclidean distance, landscape features, and ecological dissimilarity on the pairwise genetic distance of the sampled populations, while also testing for a potential relationship between I. webberi genetic diversity and diversity in the vegetative communities. The results show low levels of genetic diversity overall (H _e = 0.200–0.441; H _o = 0.192–0.605) and high genetic differentiation among populations. Genetic diversity was structured along a geographic gradient, congruent with patterns of isolation by distance. Populations near the species’ range core have relatively high genetic diversity, supporting in part a central‐marginal pattern, while also showing some evidence for a metapopulation dynamic. Peripheral populations have lower genetic diversity, significantly higher genetic distances, and higher relatedness. Genotype cluster admixture results suggest a complex dispersal pattern among populations with dispersal direction and distance varying on the landscape. Pairwise genetic distance strongly correlates with elevation, actual evapotranspiration, and summer seasonal precipitation, indicating a role for isolation by environment, which the observed phenological mismatches among the populations also support. The significant correlation between pairwise genetic distance and floristic dissimilarity in the germinated soil seed bank suggests that annual regeneration in the plant communities contribute to the maintenance of genetic diversity in I. webberi.     

Genetic diversity and population dynamic of Ziziphus jujuba var. spinosa (Bunge) Hu ex H. F. Chow in Central China

Phylogeographic research concerning Central China has been rarely conducted. Population genetic and phylogeography of Ziziphus jujuba var. spinosa (also called sour jujube) were investigated to improve our understanding of plant phylogeographic patterns in Central China. Single‐copy nuclear gene markers and complete chloroplast genome data were applied to 328 individuals collected from 21 natural populations of sour jujube in China. Nucleotide variation of sour jujube was relatively high (π = 0.00720, θ _w = 0.00925), which resulted from the mating system and complex population dynamics. Analysis of molecular variation analysis revealed that most of the total variation was attributed to variation within populations, and a high level of genetic differentiation among populations was detected (F _st = 0.197). Relatively low long‐distance dispersal capability and vitality of pollen contributed to high genetic differentiation among populations. Differences in the environmental conditions and long distance among populations further restricted gene flow. Structure clustering analysis uncovered intraspecific divergence between central and marginal populations. Migrate analysis found a high level of gene flow between these two intraspecific groups. Bayesian skyline plot detected population expansion of these two intraspecific groups. Network and phylogeny analysis of chloroplast haplotypes also found intraspecific divergence, and the divergence time was estimated to occur at about 55.86 Ma. Haplotype native to the Loess Plateau was more ancient, and multiple glacial refugia of sour jujube were found to locate at the Loess Plateau, areas adjacent to the Qinling Mountains and Tianmu Mountains. Species distribution model analysis found a typical contraction‐expansion model corresponding to the Quaternary climatic oscillations. In the future, the distribution of sour jujube may shift to high‐latitude areas. This study provides new insights for phylogeographic research of temperate plant species distributed in Central China and sets a solid foundation for the application of the scientific management strategy of Z. jujuba var. spinosa.     

Hawksbill turtle terra incognita: conservation genetics of?eastern Pacific rookeries

Prior to 2008 and the discovery of several important hawksbill turtle (Eretmochelys imbricata) nesting colonies in the EP (Eastern Pacific), the species was considered virtually absent from the region. Research since that time has yielded new insights into EP hawksbills, salient among them being the use of mangrove estuaries for nesting. These recent revelations have raised interest in the genetic characterization of hawksbills in the EP, studies of which have remained lacking to date. Between 2008 and 2014, we collected tissue samples from 269 nesting hawksbills at nine rookeries across the EP and used mitochondrial DNA sequences (766 bp) to generate the first genetic characterization of rookeries in the region. Our results inform genetic diversity, population differentiation, and phylogeography of the species. Hawksbills in the EP demonstrate low genetic diversity: We identified a total of only seven haplotypes across the region, including five new and two previously identified nesting haplotypes (pooled frequencies of 58.4% and 41.6%, respectively), the former only evident in Central American rookeries. Despite low genetic diversity, we found strong stock structure between the four principal rookeries, suggesting the existence of multiple populations and warranting their recognition as distinct management units. Furthermore, haplotypes EiIP106 and EiIP108 are unique to hawksbills that nest in mangrove estuaries, a behavior found only in hawksbills along Pacific Central America. The detected genetic differentiation supports the existence of a novel mangrove estuary “reproductive ecotype” that may warrant additional conservation attention. From a phylogeographic perspective, our research indicates hawksbills colonized the EP via the Indo‐Pacific, and do not represent relict populations isolated from the Atlantic by the rising of the Panama Isthmus. Low overall genetic diversity in the EP is likely the combined result of few rookeries, extremely small reproductive populations and evolutionarily recent colonization events. Additional research with larger sample sizes and variable markers will help further genetic understanding of hawksbill turtles in the EP.     

Molecular data reveal a complex population genetic structure for Psalidodon scabripinnis (Teleostei: Characidae) in the Atlantic Rainforest,Brazil

Recently renamed, Psalidodon scabripinnis populations of Serra da Mantiqueira, previously known as Astyanax scabripinnis have been deeply studied in the last years. These populations are small and isolated and occur very close to the watershed between Paraíba do Sul River basin and Upper Paraná River basin, in Serra da Mantiqueira region in the Atlantic Rainforest. These conditions arouse the interest in knowing theor genetic conservation status and how they responded to the separation between the two rivers basins. Therefore, we accessed the genetic diversity of five P. scabripinnis populations of this region with microsatellites and mitochondrial data. The results showed a complex structure pattern that doesn’t match the simple basin separation and a reasonably conservation status when compared with other populations of the same family or with similar natural history.     

Genetic and palaeo-climatic evidence for widespread persistence of the coastal tree species Eucalyptus gomphocephala (Myrtaceae) during the Last Glacial Maximum

Background and Aims

Few phylogeographic studies have been undertaken of species confined to narrow, linear coastal systems where past sea level and geomorphological changes may have had a profound effect on species population sizes and distributions. In this study, a phylogeographic analysis was conducted of Eucalyptus gomphocephala (tuart), a tree species restricted to a 400 × 10 km band of coastal sand-plain in south west Australia. Here, there is little known about the response of coastal vegetation to glacial/interglacial climate change, and a test was made as to whether this species was likely to have persisted widely through the Last Glacial Maximum (LGM), or conforms to a post-LGM dispersal model of recovery from few refugia.

Methods

The genetic structure over the entire range of tuart was assessed using seven nuclear (21 populations; n = 595) and four chloroplast (24 populations; n = 238) microsatellite markers designed for eucalypt species. Correlative palaeodistribution modelling was also conducted based on five climatic variables, within two LGM models.

Key Results

The chloroplast markers generated six haplotypes, which were strongly geographically structured (G_ST = 0·86 and R_ST = 0·75). Nuclear microsatellite diversity was high (overall mean H_E 0·75) and uniformly distributed (F_ST = 0·05), with a strong pattern of isolation by distance (r² = 0·362, P = 0·001). Distribution models of E. gomphocephala during the LGM showed a wide distribution that extended at least 30 km westward from the current distribution to the palaeo-coastline.

Conclusions

The chloroplast and nuclear data suggest wide persistence of E. gomphocephala during the LGM. Palaeodistribution modelling supports the conclusions drawn from genetic data and indicates a widespread westward shift of E. gomphocephala onto the exposed continental shelf during the LGM. This study highlights the importance of the inclusion of complementary, non-genetic data (information on geomorphology and palaeoclimate) to interpret phylogeographic patterns.     

Signature of mid‐Pleistocene lineages in the European silver fir (Abies alba Mill.) at its geographic distribution margin

In a conservation and sustainable management perspective, we identify the ecological, climatic, and demographic factors responsible for the genetic diversity patterns of the European silver fir (Abies alba Mill.) at its southwestern range margin (Pyrenees Mountains, France, Europe). We sampled 45 populations throughout the French Pyrenees and eight neighboring reference populations in the Massif Central, Alps, and Corsica. We genotyped 1,620 individuals at three chloroplast and ten nuclear microsatellite loci. We analyzed within‐ and among‐population genetic diversity using phylogeographic reconstructions, tests of isolation‐by‐distance, Bayesian population structure inference, modeling of demographic scenarios, and regression analyses of genetic variables with current and past environmental variables. Genetic diversity decreased from east to west suggesting isolation‐by‐distance from the Alps to the Pyrenees and from the Eastern to the Western Pyrenees. We identified two Pyrenean lineages that diverged from a third Alpine–Corsica–Massif Central lineage 0.8 to 1.1 M years ago and subsequently formed a secondary contact zone in the Central Pyrenees. Population sizes underwent contrasted changes, with a contraction in the west and an expansion in the east. Glacial climate affected the genetic composition of the populations, with the western genetic cluster only observed in locations corresponding to the coldest past climate and highest elevations. The eastern cluster was observed over a larger range of temperatures and elevations. All demographic events shaping the current spatial structure of genetic diversity took place during the Mid‐Pleistocene Transition, long before the onset of the Holocene. The Western Pyrenees lineage may require additional conservation efforts, whereas the eastern lineage is well protected in in situ gene conservation units. Due to past climate oscillations and the likely emergence of independent refugia, east–west oriented mountain ranges may be important reservoir of genetic diversity in a context of past and ongoing climate change in Europe.     

Genomic Consequences of Long-Term Population Decline in Brown Eared Pheasant

Population genetic theory and empirical evidence indicate that deleterious alleles can be purged in small populations. However, this viewpoint remains controversial. It is unclear whether natural selection is powerful enough to purge deleterious mutations when wild populations continue to decline. Pheasants are terrestrial birds facing a long-term risk of extinction as a result of anthropogenic perturbations and exploitation. Nevertheless, there are scant genomics resources available for conservation management and planning. Here, we analyzed comparative population genomic data for the three extant isolated populations of Brown eared pheasant (Crossoptilon mantchuricum) in China. We showed that C. mantchuricum has low genome-wide diversity and a contracting effective population size because of persistent declines over the past 100,000 years. We compared genome-wide variation in C. mantchuricum with that of its closely related sister species, the Blue eared pheasant (C. auritum) for which the conservation concern is low. There were detrimental genetic consequences across all C. mantchuricum genomes including extended runs of homozygous sequences, slow rates of linkage disequilibrium decay, excessive loss-of-function mutations, and loss of adaptive genetic diversity at the major histocompatibility complex region. To the best of our knowledge, this study is the first to perform a comprehensive conservation genomic analysis on this threatened pheasant species. Moreover, we demonstrated that natural selection may not suffice to purge deleterious mutations in wild populations undergoing long-term decline. The findings of this study could facilitate conservation planning for threatened species and help recover their population size.     

Phylogeography and genetic diversity of the widespread katydid Ducetia japonica (Thunberg, 1815) across China

Habitat fragmentation can lower migration rates and genetic connectivity among remaining populations of native species. Ducetia japonica is one of the most widespread katydids in China, but little is known about its genetic structure and phylogeographic distribution. We combined the five‐prime region of cytochrome c oxidase subunit I (COI‐5P), 11 newly developed microsatellite loci coupled with an ecological niche model (ENM) to examine the genetic diversity and population structure of D. japonica in China and beyond to Laos and Singapore. Both Bayesian inference (BI) and haplotype network methods revealed six mitochondrial COI‐5P lineages. The distribution of COI‐5P haplotypes may not demonstrate significant phylogeographic structure (N _ST > G _ST, p > .05). The STRUCTURE analysis based on microsatellite data also revealed six genetic clusters, but discordant with those obtained from COI‐5P haplotypes. For both COI‐5P and microsatellite data, Mantel tests revealed a significant positive correlation between geographic and genetic distances in mainland China. Bayesian skyline plot (BSP) analyses indicated that the population size of D. japonica''s three major mitochondrial COI‐5P lineages were seemingly not affected by last glacial maximum (LGM, 0.015–0.025 Mya). The ecological niche models showed that the current distribution of D. japonica was similar to the species’ distribution during the LGM period and only slightly extended in northern China. Further phylogeographic studies based on more extensive sampling are needed to identify specific locations of glacial refugia in northern China.     

Unraveling the plant diversity of the Amazonian canga through DNA barcoding

The canga of the Serra dos Carajás, in Eastern Amazon, is home to a unique open plant community, harboring several endemic and rare species. Although a complete flora survey has been recently published, scarce to no genetic information is available for most plant species of the ironstone outcrops of the Serra dos Carajás. In this scenario, DNA barcoding appears as a fast and effective approach to assess the genetic diversity of the Serra dos Carajás flora, considering the growing need for robust biodiversity conservation planning in such an area with industrial mining activities. Thus, after testing eight different DNA barcode markers (matK, rbcL, rpoB, rpoC1, atpF‐atpH, psbK‐psbI, trnH‐psbA, and ITS2), we chose rbcL and ITS2 as the most suitable markers for a broad application in the regional flora. Here we describe DNA barcodes for 1,130 specimens of 538 species, 323 genera, and 115 families of vascular plants from a highly diverse flora in the Amazon basin, with a total of 344 species being barcoded for the first time. In addition, we assessed the potential of using DNA metabarcoding of bulk samples for surveying plant diversity in the canga. Upon achieving the first comprehensive DNA barcoding effort directed to a complete flora in the Brazilian Amazon, we discuss the relevance of our results to guide future conservation measures in the Serra dos Carajás.     

Novel Clostridium populations involved in the anaerobic degradation of Microcystis blooms

Understanding the microbial degradation of Microcystis biomass is crucial for determining the ecological consequences of Microcystis blooms in freshwater lakes. The purpose of this study was to identify bacteria involved in the anaerobic degradation of Microcystis blooms. Microcystis scum was anaerobically incubated for 90 days at three temperatures (15 °C, 25 °C and 35 °C). We used terminal restriction fragment length polymorphism (T-RFLP) analysis of bacterial 16S rRNA genes, followed by cloning and sequencing of selected samples, to reveal the community composition of bacteria and their dynamics during decomposition. Clostridium spp. were found to be the most dominant bacteria in the incubations, accounting for 72% of the sequenced clones. Eight new clusters or subclusters (designated CLOS.1–8) were identified in the Clostridium phylogenetic tree. The bacterial populations displayed distinct successions during Microcystis decomposition. Temperature had a strong effect on the dynamics of the bacterial populations. At 15 °C, the initial dominance of a 207-bp T-RF (Betaproteobacteria) was largely substituted by a 227-bp T-RF (Clostridium, new cluster CLOS.2) at 30 days. In contrast, at 25 °C and 35 °C, we observed an alternating succession of the 227-bp T-RF and a 231-bp T-RF (Clostridium, new cluster CLOS.1) that occurred more than four times; no one species dominated the flora for the entire experiment. Our study shows that novel Clostridium clusters and their diverse consortiums dominate the bacterial communities during anaerobic degradation of Microcystis, suggesting that these microbes'' function in the degradation process.     

Genetic diversity of Cedrela fissilis (Meliaceae) in the Brazilian Atlantic Forest reveals a complex phylogeographic history driven by Quaternary climatic fluctuations

Quaternary climatic fluctuations have shaped the geographic distribution of lineages, potentially affecting the demography, genetic structure, and patterns of genetic diversity of extant species. Different phylogeographic scenarios have been proposed for plants in neotropical cloud forests during the Last Glacial Maximum based on paleoecological data: the dry refugia hypothesis (DRH) and the moist forest hypothesis. We specifically focus on the Brazilian Atlantic Forest (BAF) range of Cedrela fissilis (Meliaceae), sampling 410 specimens from 50 localities. Our study combines analyses of the genetic diversity, phylogeographic patterns, and past geographic distributions with a particular focus on highland populations. We identified 283 alleles across the 11 microsatellite loci, ranging from 18 to 33 alleles per locus, distributed across five genetic groups. Most populations of C. fissilis from the BAF exhibited a diffuse genetic structure, reflected in low pairwise F_ST values, which could be the consequence of high gene flow. In addition, the plastid data showed a connection between the western, southern, and eastern populations in the North‐East of Brazil, but no association between genetic data and elevation was observed. Habitat suitability projections over the past 140 000 years showed less fragmentation relative to the present, indicating a higher connectivity and gene flow. Our results provide support for both the moist forest as well as the DRH, suggesting that most likely, a mixture of these processes has acted through space and time.