Genetic factors associated with population size may increase extinction risks and decrease colonization potential in a keystone tropical pine

Habitat remediation followed by managed connectivity reduces unwanted changes in evolutionary trajectory of high extirpation risk populations

As we continue to convert green spaces into roadways and buildings, connectivity between populations and biodiversity will continue to decline. In threatened and endangered species, this trend is particularly concerning because the cessation of immigration can cause increased inbreeding and loss of genetic diversity, leading to lower adaptability and higher extirpation probabilities in these populations. Unfortunately, monitoring changes in genetic diversity from management actions such as assisted migration and predicting the extent of introduced genetic variation that is needed to prevent extirpation is difficult and costly in situ. Therefore, we designed an agent-based model to link population-wide genetic variability and the influx of unique alleles via immigration to population stability and extirpation outcomes. These models showed that management of connectivity can be critical in restoring at-risk populations and reducing the effects of inbreeding depression. However, the rescued populations were more similar to the migrant source population (average FST range 0.05-0.10) compared to the historical recipient population (average FST range 0.23-0.37). This means that these management actions not only recovered the populations from the effects of inbreeding depression, but they did so in a way that changed the evolutionary trajectory that was predicted and expected for these populations prior to the population crash. This change was most extreme in populations with the smallest population sizes, which are representative of critically endangered species that could reasonably be considered candidates for restored connectivity or translocation strategies. Understanding how these at-risk populations change in response to varying management interventions has broad implications for the long-term adaptability of these populations and can improve future efforts for protecting locally adapted allele complexes when connectivity is restored.

Overcoming taxonomic challenges in DNA barcoding for improvement of identification and preservation of clariid catfish species

DNA barcoding without assessing reliability and validity causes taxonomic errors of species identification, which is responsible for disruptions of their conservation and aquaculture industry. Although DNA barcoding facilitates molecular identification and phylogenetic analysis of species, its availability in clariid catfish lineage remains uncertain. In this study, DNA barcoding was developed and validated for clariid catfish. 2,970 barcode sequences from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes and D-loop sequences were analyzed for 37 clariid catfish species. The highest intraspecific nearest neighbor distances were 85.47%, 98.03%, and 89.10% for COI, Cytb, and D-loop sequences, respectively. This suggests that the Cytb gene is the most appropriate for identifying clariid catfish and can serve as a standard region for DNA barcoding. A positive barcoding gap between interspecific and intraspecific sequence divergence was observed in the Cytb dataset but not in the COI and D-loop datasets. Intraspecific variation was typically less than 4.4%, whereas interspecific variation was generally more than 66.9%. However, a species complex was detected in walking catfish and significant intraspecific sequence divergence was observed in North African catfish. These findings suggest the need to focus on developing a DNA barcoding system for classifying clariid catfish properly and to validate its efficacy for a wider range of clariid catfish. With an enriched database of multiple sequences from a target species and its genus, species identification can be more accurate and biodiversity assessment of the species can be facilitated.

Mating System in a Native Norway Spruce (Picea abies [L.] KARST.) Stand-Relatedness and Effective Pollen Population Size Show an Association with the Germination Percentage of Single Tree Progenies

Norway spruce differs little in neutral genetic markers among populations and provenances often reported, but in terms of putative adaptive traits and their candidate genes, some clear differences have been observed. This has previously been shown for crown morphotypes. Stands with mostly narrow crown shapes are adapted to high elevation conditions, but these stands are scattered, and the forest area is often occupied by planted stands with predominantly broad crowned morphotypes. This raises questions on whether this differentiation can remain despite gene flow, and on the level of gene flow between natural and planted stands growing in close neighbourhood. The locally adapted stands are a valuable seed source, the progeny of which is expected to have high genetic quality and germination ability. The presented case study is useful for spruce plantation by demonstrating evaluation of these expectations. Immigrant pollen and seeds from planted trees could be maladaptive and may alter the genetic composition of the progeny. This motivated us to study single tree progenies in a locally adapted stand with narrow crowned trees in a partial mast year at nuclear genomic simple sequence repeat (SSR) markers. Spruce is a typical open-pollinated conifer tree species with very low selfing rates, which were also observed in our study (s = 0.3–2.1%) and could be explained by efficient cross-pollination and postzygotic early embryo abortion, common in conifers. The estimated high amount of immigrant pollen found in the pooled seed lot (70.2–91.5%) is likely to influence the genetic composition of the seedlings. Notably, for individual mother trees located in the centre of the stand, up to 50% of the pollen was characterised as local. Seeds from these trees are therefore considered to retain most of the adaptive variance of the stand. Germination percentage varied greatly between half-sib families (3.6–61.9%) and was negatively correlated with relatedness and positively with effective pollen population size of the respective families. As pollen mostly originated from outside the stand and no family structures in the stand itself were found, germination differences can likely be explained by diversity differences in the individual pollen cloud.

Performance in a novel environment subject to ghost competition

Background

A central tenet of the evolutionary theory of communities is that competition impacts evolutionary processes such as local adaptation. Species in a community exert a selection pressure on other species and may drive them to extinction. We know, however, very little about the influence of unsuccessful or ghost species on the evolutionary dynamics within the community.

Methods

Here we report the long-term influence of a ghost competitor on the performance of a more successful species using experimental evolution. We transferred the spider mite Tetranychus urticae onto a novel host plant under initial presence or absence of a competing species, the congeneric mite T. ludeni.

Results

The competitor species, T. ludeni, unintentionally went extinct soon after the start of the experiment, but we nevertheless completed the experiment and found that the early competitive pressure of this ghost competitor positively affected the performance (i.e., fecundity) of the surviving species, T. urticae. This effect on T. urticae lasted for at least 25 generations.

Discussion

Our study suggests that early experienced selection pressures can exert a persistent evolutionary signal on species’ performance in novel environments.

Genome-scale data reveal that endemic Poecilia populations from small sulphidic springs display no evidence of inbreeding

Populations with limited ranges can be highly vulnerable to changes in their environment and are, thus, of high conservation concern. Populations that experience human-induced range reductions are often highly inbred and lack genetic diversity, but it is unknown whether this is also the case for populations with naturally small ranges. The fishes Poecilia sulphuraria (listed as critically endangered) and Poecilia thermalis, which are endemic to small hydrogen sulphide-rich springs in southern Mexico, are examples of such populations with inherently small habitats. We used geometric morphometrics and population genetics to quantify phenotypic and genetic variation within and among two populations of P. sulphuraria and one population of P. thermalis. Principal component analyses revealed phenotypic and genetic differences among the populations. Evidence for inbreeding was low compared to populations that have undergone habitat reduction. The genetic data were also used to infer the demographic history of these populations to obtain estimates for effective population sizes and migration rates. Effective population sizes were large given the small habitats of these populations. Our results imply that these three endemic extremophile populations should each be considered separately for conservation purposes. Additionally, this study suggests that populations in naturally small habitats may have lower rates of inbreeding and higher genetic diversity than expected, and therefore may be better equipped to handle environmental perturbations than anticipated. We caution, however, that the inferred lack of inbreeding and the large effective population sizes could potentially be a result of colonization by genetically diverse ancestors.

A systematic review of ecological attributes that confer resilience to climate change in environmental restoration

Ecological restoration is widely practiced as a means of rehabilitating ecosystems and habitats that have been degraded or impaired through human use or other causes. Restoration practices now are confronted by climate change, which has the potential to influence long-term restoration outcomes. Concepts and attributes from the resilience literature can help improve restoration and monitoring efforts under changing climate conditions. We systematically examined the published literature on ecological resilience to identify biological, chemical, and physical attributes that confer resilience to climate change. We identified 45 attributes explicitly related to climate change and classified them as individual- (9), population- (6), community- (7), ecosystem- (7), or process-level attributes (16). Individual studies defined resilience as resistance to change or recovery from disturbance, and only a few studies explicitly included both concepts in their definition of resilience. We found that individual and population attributes generally are suited to species- or habitat-specific restoration actions and applicable at the population scale. Community attributes are better suited to habitat-specific restoration at the site scale, or system-wide restoration at the ecosystem scale. Ecosystem and process attributes vary considerably in their type and applicability. We summarize these relationships in a decision support table and provide three example applications to illustrate how these classifications can be used to prioritize climate change resilience attributes for specific restoration actions. We suggest that (1) including resilience as an explicit planning objective could increase the success of restoration projects, (2) considering the ecological context and focal scale of a restoration action is essential in choosing appropriate resilience attributes, and (3) certain ecological attributes, such as diversity and connectivity, are more commonly considered to confer resilience because they apply to a wide variety of species and ecosystems. We propose that identifying sources of ecological resilience is a critical step in restoring ecosystems in a changing climate.

A conceptual framework to describe the ecology of fragmented landscapes and implications for conservation and management

The study of the ecology of fragmented landscapes has been dominated by two assumptions: the unique unidirectional path from larger to smaller fragments and the negligible role of fragment species on fragment properties. An accurate conceptualization of fragmented landscapes requires consideration of the age and origin of the fragments, i.e., direct fragmentation or reverse fragmentation (generation or increase of vegetated fragments by colonization), and the habitat modifications of fragment species (autogenic processes). Colonization and autogenic processes alter the fragments' composition and function. Fragment metrics affect colonization. Autogenic processes are antagonized by disturbances and modulated by abiotic inputs. Fragment alterations by autogenic processes may explain the continuous species substitution detected in some fragments or the species persistence in others. Reverse fragmentation, a natural process in commonly disturbed landscapes, challenges the avoidance-of-habitat disturbance as the ultimate strategy for biodiversity conservation and stresses the importance of pioneer species that promote succession as resilience elements in fragmented landscapes. Among-fragment diversity, generated by local disturbances, can be essential for the resilience of fragmented landscapes, suggesting that conservation and habitat utilization can be complementary processes. Traditional agroforestry systems that depend on disturbance, fragmentation, colonization, and autogenic processes may provide important insights into fragmentation ecology.

The status of evolutionary medicine education in North American medical schools

BACKGROUND

Medical and public health scientists are using evolution to devise new strategies to solve major health problems. But based on a 2003 survey, medical curricula may not adequately prepare physicians to evaluate and extend these advances. This study assessed the change in coverage of evolution in North American medical schools since 2003 and identified opportunities for enriching medical education.

METHODS

In 2013, curriculum deans for all North American medical schools were invited to rate curricular coverage and perceived importance of 12 core principles, the extent of anticipated controversy from adding evolution, and the usefulness of 13 teaching resources. Differences between schools were assessed by Pearson's chi-square test, Student's t-test, and Spearman's correlation. Open-ended questions sought insight into perceived barriers and benefits.

RESULTS

Despite repeated follow-up, 60 schools (39%) responded to the survey. There was no evidence of sample bias. The three evolutionary principles rated most important were antibiotic resistance, environmental mismatch, and somatic selection in cancer. While importance and coverage of principles were correlated (r = 0.76, P < 0.01), coverage (at least moderate) lagged behind importance (at least moderate) by an average of 21% (SD = 6%). Compared to 2003, a range of evolutionary principles were covered by 4 to 74% more schools. Nearly half (48%) of responders anticipated igniting controversy at their medical school if they added evolution to their curriculum. The teaching resources ranked most useful were model test questions and answers, case studies, and model curricula for existing courses/rotations. Limited resources (faculty expertise) were cited as the major barrier to adding more evolution, but benefits included a deeper understanding and improved patient care.

CONCLUSION

North American medical schools have increased the evolution content in their curricula over the past decade. However, coverage is not commensurate with importance. At a few medical schools, anticipated controversy impedes teaching more evolution. Efforts to improve evolution education in medical schools should be directed toward boosting faculty expertise and crafting resources that can be easily integrated into existing curricula.

Possible combined effects of climate change, deforestation, and harvesting on the epiphyte Catopsis compacta: a multidisciplinary approach

Climate change, habitat loss, and harvesting are potential drivers of species extinction. These factors are unlikely to act on isolation, but their combined effects are poorly understood. We explored these effects in Catopsis compacta, an epiphytic bromeliad commercially harvested in Oaxaca, Mexico. We analyzed local climate change projections, the dynamics of the vegetation patches, the distribution of Catopsis in the patches, together with population genetics and demographic information. A drying and warming climate trend projected by most climate change models may contribute to explain the poor forest regeneration. Catopsis shows a positive mean stochastic population growth. A PVA reveals that quasi-extinction probabilities are not significantly affected by the current levels of harvesting or by a high drop in the frequency of wet years (2%) but increase sharply when harvesting intensity duplicates. Genetic analyses show a high population genetic diversity, and no evidences of population subdivision or a past bottleneck. Colonization mostly takes place on hosts at the edges of the fragments. Over the last 27 years, the vegetation cover has being lost at a 0.028 years(-1) rate, but fragment perimeter has increased 0.076 years(-1). The increases in fragment perimeter and vegetation openness, likely caused by climate change and logging, appear to increase the habitat of Catopsis, enhance gene flow, and maintain a growing and highly genetically diverse population, in spite of harvesting. Our study evidences conflicting requirements between the epiphytes and their hosts and antagonistic effects of climate change and fragmentation with harvesting on a species that can exploit open spaces in the forest. A full understanding of the consequences of potential threatening factors on species persistence or extinction requires the inspection of the interactions of these factors among each other and their effects on both the focus species and the species on which this species depends.

Forest fragmentation and edge effects on the genetic structure ofClusia sphaerocarpaandC. lechleri(Clusiaceae) in tropical montane forests

Fragmentation of tropical forests influences abiotic and biotic processes that affect the genetic structure of plant populations. In forest fragments, edge effects, i.e. changes of abiotic and biotic factors at forest edges, may be prevalent. In two forest fragments (c. 200 ha atc. 2450 m asl) of tropical montane forest in Bolivia, sympatric populations of the dioecious tree speciesClusia sphaerocarpaandC. lechleriwere used as case study species to compare genetic diversity and small-scale genetic structure (SGS) between edge and interior habitats. Eight microsatellite markers were employed to genotype 343 individuals including adults, juveniles and seedlings ofC. sphaerocarpaand 196 ofC. lechleri. Genetic differentiation was found between habitats in both species (ΦRT= 0.071 forC. sphaerocarpaand ΦRT= 0.028 forC. lechleri) and among ages inC. sphaerocarpa(ΦRT= 0.016). Overall, SGS was weak but significant with more pronounced SGS inC. lechleri(Sp= 0.0128) than inC. sphaerocarpa(Sp= 0.0073). However, positive spatial genetic autocorrelation extended only up to 10 m. ForC. sphaerocarpa, SGS was stronger in seedling and juvenile stages than in adults and in the forest interior than at forest edges. Our results show that edge effects can extend to the genetic level by breaking-up local genetic structures, probably due to increased gene flow and enhanced pollination and seed-dispersal interactions at forest edges.