The gut bacterial microbiome of Nile tilapia (Oreochromis niloticus) from lakes across an altitudinal gradient.

BACKGROUND: Microorganisms inhabiting the gut play a significant role in supporting fundamental physiological processes of the host, which contributes to their survival in varied environments. Several studies have shown that altitude affects the composition and diversity of intestinal microbial communities in terrestrial animals. However, little is known about the impact of altitude on the gut microbiota of aquatic animals. The current study examined the variations in the gut microbiota of Nile tilapia (Oreochromis niloticus) from four lakes along an altitudinal gradient in Ethiopia by using 16S rDNA Illumina MiSeq high-throughput sequencing. RESULTS: The results indicated that low-altitude samples typically displayed greater alpha diversity. The results of principal coordinate analysis (PCoA) showed significant differences across samples from different lakes. Firmicutes was the most abundant phylum in the Lake Awassa and Lake Chamo samples whereas Fusobacteriota was the dominant phylum in samples from Lake Hashengie and Lake Tana. The ratio of Firmicutes to Bacteroidota in the high-altitude sample (Lake Hashengie, altitude 2440 m) was much higher than the ratio of Firmicutes to Bacteroidota in the low altitude population (Lake Chamo, altitude 1235 m). We found that the relative abundances of Actinobacteriota, Chloroflexi, Cyanobacteria, and Firmicutes were negatively correlated with altitude, while Fusobacteriota showed a positive association with altitude. Despite variability in the abundance of the gut microbiota across the lakes, some shared bacterial communities were detected. CONCLUSIONS: In summary, this study showed the indirect influence of altitude on gut microbiota. Altitude has the potential to modulate the gut microbiota composition and diversity of Nile tilapia. Future work will be needed to elucidate the functional significance of gut microbiota variations based on the geographical environment. SIGNIFICANCE AND IMPACT OF THE STUDY: Our study determined the composition and diversity of the gut microbiota in Nile tilapia collected from lakes across an altitude gradient. Our findings greatly extend the baseline knowledge of fish gut microbiota in Ethiopian lakes that plays an important role in this species sustainable aquaculture activities and conservation.

Molecular genetic diversity and differentiation of Nile tilapia (Oreochromis niloticus, L. 1758) in East African natural and stocked populations.

BACKGROUND: The need for enhancing the productivity of fisheries in Africa triggered the introduction of non-native fish, causing dramatic changes to local species. In East Africa, the extensive translocation of Nile tilapia (Oreochromis niloticus) is one of the major factors in this respect. Using 40 microsatellite loci with SSR-GBS techniques, we amplified a total of 664 individuals to investigate the genetic structure of O. niloticus from East Africa in comparison to Ethiopian and Burkina Faso populations. RESULTS: All three African regions were characterized by independent gene-pools, however, the Ethiopian population from Lake Tana was genetically more divergent (Fst = 2.1) than expected suggesting that it might be a different sub-species. In East Africa, the genetic structure was congruent with both geographical location and anthropogenic activities (Isolation By Distance for East Africa, R2 = 0.67 and Uganda, R2 = 0.24). O. niloticus from Lake Turkana (Kenya) was isolated, while in Uganda, despite populations being rather similar to each other, two main natural catchments were able to be defined. We show that these two groups contributed to the gene-pool of different non-native populations. Moreover, admixture and possible hybridization with other tilapiine species may have contributed to the genetic divergence found in some populations such as Lake Victoria. We detected other factors that might be affecting Nile tilapia genetic variation. For example, most of the populations have gone through a reduction in genetic diversity, which can be a consequence of bottleneck (G-W, < 0.5) caused by overfishing, genetic erosion due to fragmentation or founder effect resulting from stocking activities. CONCLUSIONS: The anthropogenic activities particularly in the East African O. niloticus translocations, promoted artificial admixture among Nile Tilapia populations. Translocations may also have triggered hybridization with the native congenerics, which needs to be further studied. These events may contribute to outbreeding depression and hence compromising the sustainability of the species in the region.

Using a new RAD-sequencing approach to study the evolution of Micromeria in the Canary islands.

As found in other oceanic islands, the Canary Islands include a large number of single island endemic species, some of which form clades that are broadly distributed within the archipelago. The genus Micromeria (Lamiaceae), for instance, includes groups of morphologically similar but ecologically diverse species on each island, representing a great model to investigate niche shifts and adaptation within the Canary Archipelago. Previous attempts to reconstruct phylogenetic relationships within the genus did not lead to robust phylogenies, presumably due to introgression and/or incomplete lineage sorting. In this study, we use a newly developed RAD-sequencing method to improve phylogenetic resolution and to better understand relationships among the Canary Island endemic Micromeria. Overall, we obtained 3571 loci that were genotyped for a total of 46 individuals of Micromeria. Our data reconstructed a highly resolved phylogeny, and corroborated the latest species reclassification of the M. varia s.l. species complex, the taxonomically most complicated group within the genus. Furthermore, taxa occupying similar ecological conditions in different islands, were shown to be closely related. This is the case of taxa from the laurel forest from La Gomera and Gran Canaria, suggesting that the laurel forest likely worked as a filter, only allowing the establishment of colonizers already pre-adapted to these conditions. We also found introgression between these species so it is also possible that the genes that facilitated the adaptation to laurel forest were swapped between Gran Canaria and La Gomera. The observations obtained in this study also allowed us to explain the role of introgression in the origin of M. varia s.l. species complex.

Phylogeography of the wild and cultivated stimulant plant qat (Catha edulis, Celastraceae) in areas of historical cultivation.

PREMISE OF THE STUDY: Qat (Catha edulis, Celastraceae) is a woody plant species cultivated for its stimulant alkaloids. Qat is important to the economy and culture in large regions of Ethiopia, Kenya, and Yemen. Despite the importance of this species, the wild origins and dispersal of cultivars have only been described in often contradictory historical documents. We examined the wild origins, human-mediated dispersal, and genetic divergence of cultivated qat compared to wild qat. METHODS: We sampled 17 SSR markers and 1561 wild and cultivated individuals across the historical areas of qat cultivation. KEY RESULTS: On the basis of genetic structure inferred using Bayesian and nonparametric methods, two centers of origin in Kenya and one in Ethiopia were found for cultivated qat. The centers of origin in Ethiopia and northeast of Mt. Kenya are the primary sources of cultivated qat genotypes. Qat cultivated in Yemen is derived from Ethiopian genotypes rather than Yemeni wild populations. Cultivated qat with a wild Kenyan origin has not spread to Ethiopia or Yemen, whereas a small minority of qat cultivated in Kenya originated in Ethiopia. Hybrid genotypes with both Ethiopian and Kenyan parentage are present in northern Kenya. CONCLUSIONS: Ethiopian cultivars have diverged from their wild relatives, whereas Kenyan qat has diverged less. This pattern of divergence could be caused by the extinction of the wild-source qat populations in Ethiopia due to deforestation, undersampling, and/or artificial selection for agronomically important traits.

Climate structures genetic variation across a species' elevation range: a test of range limits hypotheses.

Gene flow may influence the formation of species range limits, and yet little is known about the patterns of gene flow with respect to environmental gradients or proximity to range limits. With rapid environmental change, it is especially important to understand patterns of gene flow to inform conservation efforts. Here we investigate the species range of the selfing, annual plant, Mimulus laciniatus, in the California Sierra Nevada. We assessed genetic variation, gene flow, and population abundance across the entire elevation-based climate range. Contrary to expectations, within-population plant density increased towards both climate limits. Mean genetic diversity of edge populations was equivalent to central populations; however, all edge populations exhibited less genetic diversity than neighbouring interior populations. Genetic differentiation was fairly consistent and moderate among all populations, and no directional signals of contemporary gene flow were detected between central and peripheral elevations. Elevation-driven gene flow (isolation by environment), but not isolation by distance, was found across the species range. These findings were the same towards high- and low-elevation range limits and were inconsistent with two common centre-edge hypotheses invoked for the formation of species range limits: (i) decreasing habitat quality and population size; (ii) swamping gene flow from large, central populations. This pattern demonstrates that climate, but not centre-edge dynamics, is an important range-wide factor structuring M. laciniatus populations. To our knowledge, this is the first empirical study to relate environmental patterns of gene flow to range limits hypotheses. Similar investigations across a wide variety of taxa and life histories are needed.

A new amplicon based approach of whole mitogenome sequencing for phylogenetic and phylogeographic analysis: An example of East African white-eyes (Aves, Zosteropidae).

Classical Sanger sequencing is still frequently used to generate sequence data for phylogenetic and phylogeographic inference. In this contribution we present a novel approach to genotype whole mitogenomic haplotypes using Illumina MiSeq reads from indexed amplicons. Our new approach reduces preparation time by multiplexing loci within a single or few PCR reactions and by plate format library construction. The use of paired-end reads allows covering amplicons of about 0.5kb and thus no nebulisation and assembly are necessary. We tested the power and effectiveness of this technique by analysing the mitogenomic diversity of East African white-eye bird species (Zosteropidae), a taxonomically highly diverse and complex species flock found in various ecosystems spread across major parts of Africa. We compare the newly generated mitogenomic data set with published data of three mitochondrial genes for a similar set of populations and taxa. The comparison demonstrates that our new procedure represents a cost effective use of NGS for medium throughput phylogenetic analyses. Using this method, we were able to increase the amount of phylogenetic information significantly, while reducing the costs and effort in the laboratory. The mitogenomic data show a higher resolution than previous studies providing higher support and new insights in the relationships of Zosterops species. Our data suggest to split Z. poliogaster into four distinct species, three of which had previously been proposed: Z. silvanus, Z. mbulensis, Z. kikyuensis and Z. kulalensis. Our approach allows the genotyping of whole mitogenomes for a large number of individuals and thus allows more reliable reconstruction of phylogenetic and phylogeographic relationships - also for non-model organisms.

Molecular phylogenetics of Micromeria (Lamiaceae) in the Canary Islands, diversification and inter-island colonization patterns inferred from nuclear genes.

Here we reconstruct the evolutionary history of Micromeria in the Canary Islands using eight nuclear markers. Our results show two centers of diversification for Micromeria, one in the eastern islands Gran Canaria and Lanzarote, the other in the western islands, Tenerife, La Palma and El Hierro. Suggested directions of inter-island colonization are the following: Gran Canaria to Lanzarote and La Gomera; Tenerife to La Palma (from the paleoisland of Teno), to El Hierro (from the younger, central part), and to La Gomera and Madeira (from the paleoislands). Colonization of La Gomera probably occurred several times from Gran Canaria and Tenerife. The taxonomic implications of these results are discussed. Incongruence among the different markers was evaluated and, using next generation sequencing, we investigated if this incongruence is due to gene duplication.

Patterns of genetic diversity in Hepatozoon spp. infecting snakes from North Africa and the Mediterranean Basin.

Species of Hepatozoon Miller, 1908 are blood parasites most commonly found in snakes but some have been described from all tetrapod groups and a wide variety of hematophagous invertebrates. Previous studies have suggested possible associations between Hepatozoon spp. found in predators and prey. Particularly, some saurophagous snakes from North Africa and the Mediterranean region have been found to be infected with Hepatozoon spp. similar to those of various sympatric lizard hosts. In this study, we have screened tissue samples of 111 North African and Mediterranean snakes, using specific primers for the 18S rRNA gene. In the phylogenetic analysis, the newly-generated Hepatozoon spp. sequences grouped separately into five main clusters. Three of these clusters were composed by Hepatozoon spp. also found in snakes and other reptiles from the Mediterranean Basin and North Africa. In the other two clusters, the new sequences were not closely related to geographically proximate known sequences. The phylogeny of Hepatozoon spp. inferred here was not associated with intermediate host taxonomy or geographical distribution. From the other factors that could explain these evolutionary patterns, the most likely seems series of intermediate hosts providing similar ribotypes of Hepatozoon and a high prevalence of host shifts for Hepatozoon spp. This is indicated by ribotypes of high similarity found in different reptile families, as well as by divergent ribotypes found in the same host species. This potentially low host specificity has profound implications for the systematics of Hepatozoon spp.

Small-scale metapopulation structure of a limnophilic fish species in a natural river system investigated using microsatellite genotyping by amplicon sequencing (SSR-GBAS).

Habitat niches of fish species can exert a strong influence on population structure, even on a small geographical scale. In this scope, Pelasgus thesproticus is a great model species to study connectivity in riverine environments owing to its naturally patchy habitat distribution. Furthermore, it is important to conduct such studies in near-natural systems to avoid the impact of human disturbances on the river, such as fragmentation, morphological changes and habitat degradation. In this sense, the Vjosa in Albania is an excellent study area. A total of 204 individuals were sampled from five locations in the lower Vjosa and two tributaries and genotyped with 33 newly designed microsatellites loci using high throughput sequencing. The application of microsatellite genotyping by sequencing revealed genetic structure and some differentiation, even at a small spatial scale (< 65 river km). A total of 500 alleles were found with an average of 0.93 private alleles among sites with rather low FST values (< 0.04). The extent of admixture observed in some populations indicate that the genetic structure is mainly influenced by upstream populations, either from the main river itself or from tributaries. In addition, the connection between a tributary and the other sites is disrupted by the flow regime, which is reflected in a high degree of divergence from the other populations. Our results indicate that hydrological conditions of the flowing river present strong barriers to gene flow, particularly in the upstream direction, but at the same time act as dispersal corridors in the downstream direction and exhibit source-sink dynamics in which upstream populations contribute disproportionately to downstream populations for this habitat specialist along the river. It is suggested that processes of colonization and reinforcement may play an important role in shaping the genetic structure of patchily distributed fish species in natural river systems. Future studies should increase the knowledge of dispersal factors, habitat heterogeneity, consequence of source-sink dynamics, and gene flow within the system, which will help to understand and maintain important processes related to metapopulation theory and the potential evolutionary consequences of habitat loss and fragmentation.

Microsatellites reveal divergence in population genetic diversity, and structure of osyris lanceolata (santalaceae) in Uganda and Kenya.

BACKGROUND: Osyris lanceolata (Hochst. & Steud.) (Santalaceae) is a multipurpose plant highly valued culturally and economically in Africa. However, O. lanceolata populations have rapidly dwindled in East Africa due to overexploitation and this is believed to cause further consequences on the species' genetic diversity and structure within the region. Information regarding a species' genetic diversity and structure is necessary for conservation but this is currently lacking for O. lanceolata in Uganda and Kenya. Lack of adequate scientific data hinders conservation efforts hence threatening the species survival and livelihoods. This study investigated patterns in genetic diversity and structure of O. lanceolata in Uganda and Kenya. Ten polymorphic microsatellite loci were used to genotype 210 individuals: 96 from Ugandan and 114 from Kenyan populations. RESULTS: All populations were highly polymorphic (80-100% polymorphism). A genetic differentiation was found between Kenyan and Ugandan populations. The highest genetic differentiation was among individuals and the least among populations. The Kenyan populations showed higher genetic diversity than Ugandan populations. The Ugandan populations showed more marker deviations from Hardy-Weinberg equilibrium and inbreeding coefficient. Two populations showed evidence of going through a recent bottleneck. There was significant genetic differentiation and structuring at higher K values into larger clusters and observed admixture between populations. The populations were significantly isolated by altitude as opposed to distance and climatic variables. Main barriers were associated with altitude differences. The data supports the idea of long-distance gene-flow between high altitude populations in both countries. CONCLUSION: The divergence in genetic structure suggests unrecognised taxonomic units within O. lanceolata which are characteristic to lower altitudes and higher altitudes including most Kenyan populations with divergent evolutionary patterns. Geographical barriers and environmental gradients could have influenced this genetic divergence, and such patterns may escalate the species microevolutionary processes into full allopatric speciation. Further investigations into the species' genetic admixture and emerging taxonomic units are necessary to guide conservation strategies in the region.

Changes in Community Composition and Functional Traits of Bumblebees in an Alpine Ecosystem Relate to Climate Warming.

Climate warming has been observed as the main cause of changes in diversity, community composition, and spatial distribution of different plant and invertebrate species. Due to even stronger warming compared to the global mean, bumblebees in alpine ecosystems are particularly exposed to these changes. To investigate the effects of climate warming, we sampled bumblebees along an elevational gradient, compared the records with data from 1935 and 1936, and related our results to climate models. We found that bumblebee community composition differed significantly between sampling periods and that increasing temperatures in spring were the most plausible factor explaining these range shifts. In addition, species diversity estimates were significantly lower compared to historical records. The number of socio-parasitic species was significantly higher in the historical communities, while recent communities showed increases in climate generalists and forest species at lower elevations. Nevertheless, no significant changes in community-weighted means of a species temperature index (STI) or the number of cold-adapted species were detected, likely due to the historical data resolution. We conclude that the composition and functionality of bumblebee communities in the study area have been significantly affected by climate warming, with changes in land use and vegetation cover likely playing an additional important role.

Exploring the morphological dynamics of Nile tilapia (Oreochromis niloticus Linn. 1758) in Victoria Nile as depicted from geometric morphometrics.

BACKGROUND: Various anthropogenic activities continue to threaten the fish biodiversity of the East African water bodies such as the Victoria Nile. Although the Victoria Nile is a significant source of livelihood for human populations, the biology and ecology of Nile tilapia in this ecosystem remain understudied with little or no information on the morphology of the fish given varying and immense anthropogenic activities. Here, we use geometric morphometrics to examine the morphology/shape variations of Nile tilapia populations in Victoria Nile to gain insights into their current ecological state. RESULTS: Our results indicate unexpectedly smaller Nile tilapia body weights in Victoria Nile than in L. Victoria. Despite this, nearly all the populations displayed a relative condition factor (Kn) of greater ≥1 suggesting a healthy stock. However, two populations, LMF and VN_Bukeeka demonstrated Kn values of less than one (< 1). We also report that some Upper and Lower Victoria Nile populations display morphological similarities. Apart from L. Albert, Nile tilapia populations from Lakes Victoria and Kyoga are morphologically divergent from the riverine ones. We note that Nile tilapia from Nalubale Dam Reservoir is morphologically distinct from the close neighbouring Victoria Nile populations which are likely allied to the influence of the Nalubale Hydroelectric power dam as a barrier. CONCLUSION: Nile tilapia's morphological variation appears to be influenced by various anthropogenic disturbances notably, overfishing, hydroelectric power dams, and fish translocational history in Uganda. Management should enforce regulatory frameworks to avert human-mediated activities as these are likely to compromise the sustainability of the fisheries. Further studies are required to follow these populations with molecular genetics and environmental data to gain a deeper understanding of the fish species for informed sustainable management and conservation options.

Development of phylogenetic markers from single-copy nuclear genes for multi locus, species level analyses in the mint family (Lamiaceae).

The use of single copy nuclear markers is of increasing importance in plant phylogenetics. The generally higher level of variability compared to chloroplast DNA and the ability to use incongruence in a multilocus analysis to determine reticulation patterns makes these kinds of sequence based markers especially useful for species level investigations. However, the prevalence of gene duplication that results from the high frequency of polyploidization events during the evolution of higher plants can impede marker development especially for groups lacking model organisms. Here, we present the strategy and results of marker development for phylogenetic analysis in Micromeria, using publicly available DNA sequences and ESTs from related genera from Lamiaceae, subfamily Nepetoideae. By eliminating markers with signatures of duplication during four steps of marker development, we were able to select 19 primer pairs that resulted in orthologous products for all the species studied. This corresponds to 23% of the initial 84 primer pairs designed. Using an initial sampling of eight individuals, we tested the markers for support of phylogenetic hypotheses related to the evolution of Micromeria on the Canary Islands. While some hypotheses were supported by all markers, an east west split, with a closer relationship between the species of Tenerife and Madeira on one hand and the ones from Gran Canaria and the eastern islands on the other is supported by 12 markers but contradicted by the remaining seven. This indicates that reticulation and inter-island gene flow played a role in the evolution of Micromeria.

Morphospecies and molecular diversity of 'lace corals': the genus Reteporella (Bryozoa: Cheilostomatida) in the central North Atlantic Azores Archipelago.

BACKGROUND: As in most bryozoans, taxonomy and systematics of species in the genus Reteporella Busk, 1884 (family Phidoloporidae) has hitherto almost exclusively been based on morphological characters. From the central North Atlantic Azores Archipelago, nine Reteporella species have historically been reported, none of which have as yet been revised. Aiming to characterise the diversity and biogeographic distribution of Azorean Reteporella species, phylogenetic reconstructions were conducted on a dataset of 103 Azorean Reteporella specimens, based on the markers cytochrome C oxidase subunit 1, small and large ribosomal RNA subunits. Morphological identification was based on scanning electron microscopy and complemented the molecular inferences. RESULTS: Our results reveal two genetically distinct Azorean Reteporella clades, paraphyletic to eastern Atlantic and Mediterranean taxa. Moreover, an overall concordance between morphological and molecular species can be shown, and the actual bryozoan diversity in the Azores is greater than previously acknowledged as the dataset comprises three historically reported species and four putative new taxa, all of which are likely to be endemic. The inclusion of Mediterranean Reteporella specimens also revealed new species in the Adriatic and Ligurian Sea, whilst the inclusion of additional phidoloporid taxa hints at the non-monophyly of the genus Reteporella. CONCLUSION: Being the first detailed genetic study on the genus Reteporella, the high divergence levels inferred within the genus Reteporella and family Phidoloporidae calls for the need of further revision. Nevertheless, the overall concordance between morphospecies and COI data suggest the potential adequacy of a 3% cut-off to distinguish Reteporella species. The discovery of new species in the remote Azores Archipelago as well as in the well-studied Mediterranean Sea indicates a general underestimation of bryozoan diversity. This study constitutes yet another example of the importance of integrative taxonomical approaches on understudied taxa, contributing to cataloguing genetic and morphological diversity.

On the road: Anthropogenic factors drive the invasion risk of a wild solitary bee species.

Complex biotic networks of invaders and their new environments pose immense challenges for researchers aiming to predict current and future occupancy of introduced species. This might be especially true for invasive bees, as they enter novel trophic interactions. Little attention has been paid to solitary, invasive wild bees, despite their increasing recognition as a potential global threat to biodiversity. Here, we present the first comprehensive species distribution modelling approach targeting the invasive bee Megachile sculpturalis, which is currently undergoing parallel range expansion in North America and Europe. While the species has largely colonised the most highly suitable areas of North America over the past decades, its invasion of Europe seems to be in its early stages. We showed that its current distribution is largely explained by anthropogenic factors, suggesting that its spread is facilitated by road and maritime traffic, largely beyond its intrinsic dispersal ability. Our results suggest that M. sculpturalis is likely to be negatively affected by future climate change in North America, while in Europe the potential suitable areas at-risk of invasion remain equally large. Based on our study, we emphasise the role of expert knowledge for evaluation of ecologically meaningful variables implemented and interpreted for species distribution modelling. We strongly recommend that the monitoring of this and other invasive pollinator species should be prioritised in areas identified as at-risk, alongside development of effective management strategies.

Development of microsatellites in the Hawaiian endemic palm Pritchardia martii (Arecaceae) and their utility in congeners.

PREMISE OF THE STUDY: Pritchardia (loulu palm) is the seventh largest flowering plant genus in the Hawaiian archipelago, and many species are of high conservation concern. The island radiation has produced many cryptic species complexes across fine ecological gradients. Microsatellite primers were optimized to investigate genetic diversity of Pritchardia martii (Gaudich.) H. Wendl. and species boundaries among the Hawaiian Pritchardia. METHODS AND RESULTS: Six new loci and three previously described loci for a closely related genus, Phoenix, were optimized and tested. Five loci were polymorphic, and 72 alleles were detected across loci within P. martii. The five loci were also polymorphic across the other 27 currently recognized Pritchardia species. • CONCLUSIONS: These results indicate the utility of these microsatellite markers for understanding the conservation genetics of P. martii and species delimitation and hybridization across the genus.

Genetic variability and differentiation among populations of the Azorean endemic gymnosperm Juniperus brevifolia: baseline information for a conservation and restoration perspective.

The Azorean endemic gymnosperm Juniperus brevifolia (Seub.) Antoine is a top priority species for conservation in Macaronesia, based on its ecological significance in natural plant communities. To evaluate genetic variability and differentiation among J. brevifolia populations from the Azorean archipelago, we studied 15 ISSR and 15 RAPD markers in 178 individuals from 18 populations. The average number of polymorphic bands per population was 65 for both ISSR and RAPD. The majority of genetic variability was found within populations and among populations within islands, and this partitioning of variability was confirmed by AMOVA. The large majority of population pairwise F(ST) values were above 0.3 and below 0.6. The degree of population genetic differentiation in J. brevifolia was relatively high compared with other species, including Juniperus spp. The genetic differentiation among populations suggests that provenance should be considered when formulating augmentation or reintroduction strategies.

Investigating Explanatory Factors of Machine Learning Models for Plant Classification.

Recent progress in machine learning and deep learning has enabled the implementation of plant and crop detection using systematic inspection of the leaf shapes and other morphological characters for identification systems for precision farming. However, the models used for this approach tend to become black-box models, in the sense that it is difficult to trace characters that are the base for the classification. The interpretability is therefore limited and the explanatory factors may not be based on reasonable visible characters. We investigate the explanatory factors of recent machine learning and deep learning models for plant classification tasks. Based on a Daucus carota and a Beta vulgaris image data set, we implement plant classification models and compare those models by their predictive performance as well as explainability. For comparison we implemented a feed forward convolutional neuronal network as a default model. To evaluate the performance, we trained an unsupervised Bayesian Gaussian process latent variable model as well as a convolutional autoencoder for feature extraction and rely on a support vector machine for classification. The explanatory factors of all models were extracted and analyzed. The experiments show, that feed forward convolutional neuronal networks (98.24% and 96.10% mean accuracy) outperforms the Bayesian Gaussian process latent variable pipeline (92.08% and 94.31% mean accuracy) as well as the convolutional autoenceoder pipeline (92.38% and 93.28% mean accuracy) based approaches in terms of classification accuracy, even though not significant for Beta vulgaris images. Additionally, we found that the neuronal network used biological uninterpretable image regions for the plant classification task. In contrast to that, the unsupervised learning models rely on explainable visual characters. We conclude that supervised convolutional neuronal networks must be used carefully to ensure biological interpretability. We recommend unsupervised machine learning, careful feature investigation, and statistical feature analysis for biological applications.

Evidence for multiple introductions of an invasive wild bee species currently under rapid range expansion in Europe.

BACKGROUND: Invasive species are increasingly driving biodiversity decline, and knowledge of colonization dynamics, including both drivers and dispersal modes, are important to prevent future invasions. The bee species Megachile sculpturalis (Hymenoptera: Megachilidae), native to East-Asia, was first recognized in Southeast-France in 2008, and has since spread throughout much of Europe. The spread is very fast, and colonization may result from multiple fronts. RESULT: To track the history of this invasion, codominant markers were genotyped using Illumina sequencing and the invasion history and degree of connectivity between populations across the European invasion axis were investigated. Distinctive genetic clusters were detected with east-west differentiations in Middle-Europe. CONCLUSION: We hypothesize that the observed cluster formation resulted from multiple, independent introductions of the species to the European continent. This study draws a first picture of an early invasion stage of this wild bee and forms a foundation for further investigations, including studies of the species in their native Asian range and in the invaded range in North America.