Centro de Investigação em Biodiversidade e Recursos Genéticos

Abstract Geometric morphometric (GM) tools are essential for meaningfully quantifying and understanding patterns of variation in complex traits like shape. In this field, the breadth of answerable questions has grown dramatically in recent years through the development of new analyses and increased computational efficiency. In this note, we describe the ways in which geomorph , a widely used R package for quantifying and analysing GM data, has grown with the field. We present geomorph v4.0 and describe the ways in which this version has dramatically improved upon previous versions. We also present a new graphical user interface for easy implementation, gmShiny . These contributions position geomorph to be the primary tool for GM analyses, particularly those employing a phylogenetic comparative approach.

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.

MOTIVATION: TCS is a widely used haplotype network reconstruction software, but lacks the capability of overlapping genetic with geographic structure, which is often a first step in phylogeographic analysis. RESULTS: tcsBU is a web-based program that extends the capabilities of TCS, by implementing haplotype classification into an arbitrary user-defined scheme, which is displayed as pie-chart like graphs embedded into the network. Taking advantage of modern graphic libraries, tcsBU also improves the speed at which the final network layout is reached. Networks can be saved as a Scalable Vector Graphics format. AVAILABILITY AND IMPLEMENTATION: tcsBU is available on-line at http://cibio.up.pt/software/tcsBU/. The source code is freely available from https://github.com/sairum/tcsbu/ under a standard MIT license.

Abstract Well‐documented changes in species abundances and distributions coinciding with global warming have been increasing during recent years. A trend of raising sea‐surface temperature has also been observed along the Portuguese coast which could affect intertidal species' ranges. The present study aimed at evaluating the direction and intensity of distribution changes of macroalgae in the area. The last 50‐year trend of coastal air and sea temperature was reassessed, providing an accurate estimate of the warming process. Information on species' range shifts was obtained by comparing data from recent resurveys with historical records of algal distributions collected during the 1950s and 1960s. Although a prevalence of northward migrations was anticipated, this work showed a marked difference in the average direction of changes between cold‐ and warm‐water species. Cold‐water species, when considered together, showed no particular shifting trend, because the number of species that shifted north or south was the same. Contrarily, all shifting warm‐water species expanded their range northwards. Therefore, generalizations about poleward range shifts due to increasing temperature should be made with caution.

It is an open question how animals find food in dynamic natural environments where they possess little or no knowledge of where resources are located. Foraging theory predicts that in environments with sparsely distributed target resources, where forager knowledge about resources' locations is incomplete, Lévy flight movements optimize the success of random searches. However, the putative success of Lévy foraging has been demonstrated only in model simulations. Here, we use high-temporal-resolution Global Positioning System (GPS) tracking of wandering (Diomedea exulans) and black-browed albatrosses (Thalassarche melanophrys) with simultaneous recording of prey captures, to show that both species exhibit Lévy and Brownian movement patterns. We find that total prey masses captured by wandering albatrosses during Lévy movements exceed daily energy requirements by nearly fourfold, and approached yields by Brownian movements in other habitats. These results, together with our reanalysis of previously published albatross data, overturn the notion that albatrosses do not exhibit Lévy patterns during foraging, and demonstrate that Lévy flights of predators in dynamic natural environments present a beneficial alternative strategy to simple, spatially intensive behaviors. Our findings add support to the possibility that biological Lévy flight may have naturally evolved as a search strategy in response to sparse resources and scant information.

Abstract There has been considerable recent interest concerning the impact of climate change on a wide range of taxa. However, little is known about how the biogeographic affinities of taxa may affect their responses to these impacts. Our main aim was to study how predicted climate change will affect the distribution of 28 European bat species grouped by their biogeographic patterns as determined by a spatial Principal Component Analysis. Using presence‐only modelling techniques and climatic data (minimum temperature, average temperature, precipitation, humidity and daily temperature range) for four different climate change scenarios (IPCC scenarios ranging from the most extreme A1FI, A2, B2 to the least severe, B1), we predict the potential geographic distribution of bat species in Europe grouped according to their biogeographic patterns for the years 2020–2030, 2050–2060 and 2090–2100. Biogeographic patterns exert a great influence on a species' response to climate change. Bat species more associated with colder climates, hence northern latitudes, could be more severely affected with some extinctions predicted by the end of the century. The Mediterranean and Temperate groups seem to be more tolerant of temperature increases, however, their projections varied considerably under different climate change scenarios. Scenario A1FI was clearly the most detrimental for European bat diversity, with several extinctions and declines in occupied area predicted for several species. The B scenarios were less damaging and even predicted that some species could increase their geographical ranges. However, all models only took into account climatic envelopes whereas available habitat and species interactions will also probably play an important role in delimiting future distribution patterns. The models may therefore generate ‘best case’ predictions about future changes in the distribution of European bats.

1. We evaluated the accuracy of presence-only modelling for predicting the distribution of rare species, when data are scarce and usually collected with sampling biases. We modelled the potential distribution in Portugal of one of the rarest European bats Barbastella barbastellus and subsequently ground-validated predictions by using acoustic transects. 2. We used ecological niche factor analysis (ENFA) and maximum entropy (Maxent) modelling to build distribution models of B. barbastellus, and determined which ecological factors were more relevant for each model. As ENFA only accepts continuous variables, we built one Maxent model using the same variables as ENFA and another using land cover as a categorical variable. 3. Ecological niche factor analysis and both Maxent models predicted similar areas of occurrence in central and northern regions of Portugal, although ENFA predicted suitable habitat over a wider range. Conversely, there was substantial disagreement on the location of high-suitability areas in the south. This could be a consequence of a different choice of important variables made by each model. Native woodland and average temperature were the most relevant variables for Maxent, while in ENFA B. barbastellus was linked to higher altitudes although avoiding production forests and infrastructures. 4. Threshold-independent and -dependent statistics showed that Maxent models outperformed ENFA, probably as a consequence of divergent predictions in the new areas of occurrence. Overall, 15 new B. barbastellus sites were discovered and known distribution was extended c. 100 km to the south. 5. Synthesis and applications. Our results support the use of presence-only modelling as an indispensible tool for survey design as shown by the discovery of B. barbastellus populations outside of the previously known range. ENFA seems to be more suited to determining a species’ potential distribution, although failing to extrapolate it. In contrast, Maxent is better suited to determining a species’ realized distribution. It was successful in predicting occurrence in previously unsurveyed areas and can be recommended as a technique for determination of a conservative distribution for a species. Maxent modelling would greatly aid biodiversity conservation, especially when it is necessary to develop survey plans or first assessments of a species’ distribution.

Adaptive modifications of heteromeric proteins may involve genetically based changes in single subunit polypeptides or parallel changes in multiple genes that encode distinct, interacting subunits. Here we investigate these possibilities by conducting a combined evolutionary and functional analysis of duplicated globin genes in natural populations of deer mice (Peromyscus maniculatus) that are adapted to different elevational zones. A multilocus analysis of nucleotide polymorphism and linkage disequilibrium revealed that high-altitude adaptation of deer mouse hemoglobin involves parallel functional differentiation at multiple unlinked gene duplicates: two alpha-globin paralogs on chromosome 8 and two beta-globin paralogs on chromosome 1. Differences in O(2)-binding affinity of the alternative beta-chain hemoglobin isoforms were entirely attributable to allelic differences in sensitivity to 2,3-diphosphoglycerate (DPG), an allosteric cofactor that stabilizes the low-affinity, deoxygenated conformation of the hemoglobin tetramer. The two-locus beta-globin haplotype that predominates at high altitude is associated with suppressed DPG-sensitivity (and hence, increased hemoglobin-O(2) affinity), which enhances pulmonary O(2) loading under hypoxia. The discovery that allelic differences in DPG-sensitivity contribute to adaptive variation in hemoglobin-O(2) affinity illustrates the value of integrating evolutionary analyses of sequence variation with mechanistic appraisals of protein function. Investigation into the functional significance of the deer mouse beta-globin polymorphism was motivated by the results of population genetic analyses which revealed evidence for a history of divergent selection between elevational zones. The experimental measures of O(2)-binding properties corroborated the tests of selection by demonstrating a functional difference between the products of alternative alleles.

The newts Triturus vulgaris and Triturus montandoni are sister species that exhibit contrasting levels of intraspecific morphological variation. Triturus vulgaris has a broad Eurasiatic distribution encompassing both formerly glaciated and unglaciated areas and shows substantial morphological differentiation in the southern part of its range, while T. montandoni, confined to the Carpathians, is morphologically uniform. We analysed sequence variation of two mtDNA fragments of the total length of c. 1850 bp in 285 individuals of both species collected from 103 localities. Phylogenetic analysis of 200 unique haplotypes defined 12 major clades, their age estimated at c. 4.5-1.0 million years (Myr). Most of the older clades were found in the southern part of the range, and also in central Europe, mainly in Romania. The distribution of mtDNA clades points to the existence of several glacial refugia, located in the Caucasus region, Anatolia, the Balkan Peninsula, Italy, and more to the north in central Europe. The concordance between mtDNA based phylogeny and the distribution of T. vulgaris subspecies was weak. Triturus montandoni haplotypes did not form a monophyletic group. Instead they were found in six clades, in five of them mixed with T. vulgaris haplotypes, most likely as a result of past or ongoing hybridization and multiple introgression of mtDNA from T. vulgaris to T. montandoni. Patterns of sequence variation within clades suggested long-term demographic stability in the southern groups, moderate and relatively old demographic growth in the populations inhabiting central Europe, and high growth in some of the groups that colonized northern parts of Europe after the last glacial maximum.

Abstract Aim We tested whether the contraction of the equatorward boundary of an intertidal organism, the blue mussel, Mytilus edulis , was due to high summer temperatures limiting mortality. Location The Atlantic coast of the United States. Methods Field transplant experiments were conducted at three locations along the US Atlantic coast. Survival and heat shock protein 70 expression were determined at biweekly intervals. Air and water temperature profiles were used to model current and historical patterns of mortality, and to determine rates of temperature change. Results High levels of mortality and expression of the inducible heat shock protein 70 were observed after multiple consecutive aerial exposures of 32 °C or greater. Since 1960, seasonal air and water temperatures have increased along the eastern US seaboard, and south of Lewes, DE (38.8° N) summer sea surface temperature increases have exceeded the upper lethal limits of this organism. Main conclusions Along the southern portion of its range, intertidal populations of M. edulis have experienced catastrophic mortality directly associated with summer high temperatures. Over the past 50 years, a geographic contraction of the southern, equatorward range edge of M. edulis has occurred, shifting the range edge approximately 350 km north of the previous limit at Cape Hatteras, NC (35.2° N).

The protection, preservation and restoration of aquatic ecosystems and their functions are of global importance. For European states it became legally binding mainly through the EUWater Framework Directive (WFD). In order to assess the ecological status of a given water body, aquatic biodiversity data are obtained and compared to a reference water body. The quantified mismatch obtained determines the extent of potential management actions. The current approach to biodiversity assessment is based on morpho-taxonomy. This approach has many drawbacks such as being time consuming, limited in temporal and spatial resolution, and error-prone due to the varying individual taxonomic expertise of the analysts. Novel genomic tools can overcome many of the aforementioned problems and could complement or even replace traditional bioassessment. Yet, a plethora of approaches are independently developed in different institutions, thereby hampering any concerted routine application. The goal of this Action is to nucleate a group of researchers across disciplines with the task to identify gold-standard genomic tools and novel ecogenomic indices for routine application in biodiversity assessments of European fresh- and marine water bodies. Furthermore, DNAqua-Net will provide a platform for training of the next generation of European researchers preparing them for the new technologies. Jointly with water managers, politicians, and other stakeholders, the group will develop a DNAqua-Net: Developing new genetic tools for bioassessment and monitoring ... 3 conceptual framework for the standard application of eco-genomic tools as part of legally binding assessments.

Abstract Individual identification is a crucial step to answer many questions in evolutionary biology and is mostly performed by marking animals with tags. Such methods are well‐established, but often make data collection and analyses time‐consuming, or limit the contexts in which data can be collected. Recent computational advances, specifically deep learning, can help overcome the limitations of collecting large‐scale data across contexts. However, one of the bottlenecks preventing the application of deep learning for individual identification is the need to collect and identify hundreds to thousands of individually labelled pictures to train convolutional neural networks (CNNs). Here we describe procedures for automating the collection of training data, generating training datasets, and training CNNs to allow identification of individual birds. We apply our procedures to three small bird species, the sociable weaver Philetairus socius, the great tit Parus major and the zebra finch Taeniopygia guttata , representing both wild and captive contexts. We first show how the collection of individually labelled images can be automated, allowing the construction of training datasets consisting of hundreds of images per individual. Second, we describe how to train a CNN to uniquely re‐identify each individual in new images. Third, we illustrate the general applicability of CNNs for studies in animal biology by showing that trained CNNs can re‐identify individual birds in images collected in contexts that differ from the ones originally used to train the CNNs. Finally, we present a potential solution to solve the issues of new incoming individuals. Overall, our work demonstrates the feasibility of applying state‐of‐the‐art deep learning tools for individual identification of birds, both in the laboratory and in the wild. These techniques are made possible by our approaches that allow efficient collection of training data. The ability to conduct individual recognition of birds without requiring external markers that can be visually identified by human observers represents a major advance over current methods.

Abstract Co‐extinctions are increasingly recognized as one of the major processes leading to the global biodiversity crisis, but there is still limited scientific evidence on the magnitude of potential impacts and causal mechanisms responsible for the decline of affiliate (dependent) species. Freshwater mussels (Bivalvia, Unionida), one of the most threatened faunal groups on Earth, need to pass through a parasitic larval (glochidia) phase using fishes as hosts to complete their life cycle. Here, we provide a synthesis of published evidence on the fish–mussel relationship to explore possible patterns in co‐extinction risk and discuss the main threats affecting this interaction. We retrieved 205 publications until December 2015, most of which were performed in North America, completed under laboratory conditions and were aimed at characterizing the life cycle and/or determining the suitable fish hosts for freshwater mussels. Mussel species were reported to infest between one and 53 fish species, with some fish families (e.g., Cyprinidae and Percidae) being used more often as hosts than others. No relationship was found between the breadth of host use and the extinction risk of freshwater mussels. Very few studies focused on threats affecting the fish–mussel relationship, a knowledge gap that may impair the application of future conservation measures. Here, we identify a variety of threats that may negatively affect fish species, document and discuss the concomitant impacts on freshwater mussels, and suggest directions for future studies.

In animals, the population genomic literature is dominated by two taxa, namely mammals and drosophilids, in which fully sequenced, well-annotated genomes have been available for years. Data from other metazoan phyla are scarce, probably because the vast majority of living species still lack a closely related reference genome. Here we achieve de novo, reference-free population genomic analysis from wild samples in five non-model animal species, based on next-generation sequencing transcriptome data. We introduce a pipe-line for cDNA assembly, read mapping, SNP/genotype calling, and data cleaning, with specific focus on the issue of hidden paralogy detection. In two species for which a reference genome is available, similar results were obtained whether the reference was used or not, demonstrating the robustness of our de novo inferences. The population genomic profile of a hare, a turtle, an oyster, a tunicate, and a termite were found to be intermediate between those of human and Drosophila, indicating that the discordant genomic diversity patterns that have been reported between these two species do not reflect a generalized vertebrate versus invertebrate gap. The genomic average diversity was generally higher in invertebrates than in vertebrates (with the notable exception of termite), in agreement with the notion that population size tends to be larger in the former than in the latter. The non-synonymous to synonymous ratio, however, did not differ significantly between vertebrates and invertebrates, even though it was negatively correlated with genetic diversity within each of the two groups. This study opens promising perspective regarding genome-wide population analyses of non-model organisms and the influence of population size on non-synonymous versus synonymous diversity.

BACKGROUND: Current information about the expansion of Bantu-speaking peoples is hampered by the scarcity of genetic data from well identified populations from southern Africa. Here, we fill an important gap in the analysis of the western edge of the Bantu migrations by studying for the first time the patterns of Y-chromosome, mtDNA and lactase persistence genetic variation in four representative groups living around the Namib Desert in southwestern Angola (Ovimbundu, Ganguela, Nyaneka-Nkumbi and Kuvale). We assessed the differentiation between these populations and their levels of admixture with Khoe-San groups, and examined their relationship with other sub-Saharan populations. We further combined our dataset with previously published data on Y-chromosome and mtDNA variation to explore a general isolation with migration model and infer the demographic parameters underlying current genetic diversity in Bantu populations. RESULTS: Correspondence analysis, lineage sharing patterns and admixture estimates indicate that the gene pool from southwestern Angola is predominantly derived from West-Central Africa. The pastoralist Herero-speaking Kuvale people were additionally characterized by relatively high frequencies of Y-chromosome (12%) and mtDNA (22%) Khoe-San lineages, as well as by the presence of the -14010C lactase persistence mutation (6%), which likely originated in non-Bantu pastoralists from East Africa. Inferred demographic parameters show that both male and female populations underwent significant size growth after the split between the western and eastern branches of Bantu expansions occurring 4000 years ago. However, males had lower population sizes and migration rates than females throughout the Bantu dispersals. CONCLUSION: Genetic variation in southwestern Angola essentially results from the encounter of an offshoot of West-Central Africa with autochthonous Khoisan-speaking peoples from the south. Interactions between the Bantus and the Khoe-San likely involved cattle herders from the two groups sharing common aspects of their social organization. The presence of the -14010C mutation in southwestern Angola provides a link between the East and Southwest African pastoral scenes that might have been established indirectly, through migrations of Khoe herders across southern Africa. Differences in patterns of mtDNA and Y-chromosome intrapopulation diversity and interpopulation differentiation may be explained by contrasting demographic histories underlying the current female and male genetic variation.

Variation in human skin and eye color is substantial and especially apparent in admixed populations, yet the underlying genetic architecture is poorly understood because most genome-wide studies are based on individuals of European ancestry. We study pigmentary variation in 699 individuals from Cape Verde, where extensive West African/European admixture has given rise to a broad range in trait values and genomic ancestry proportions. We develop and apply a new approach for measuring eye color, and identify two major loci (HERC2[OCA2] P = 2.3 × 10(-62), SLC24A5 P = 9.6 × 10(-9)) that account for both blue versus brown eye color and varying intensities of brown eye color. We identify four major loci (SLC24A5 P = 5.4 × 10(-27), TYR P = 1.1 × 10(-9), APBA2[OCA2] P = 1.5 × 10(-8), SLC45A2 P = 6 × 10(-9)) for skin color that together account for 35% of the total variance, but the genetic component with the largest effect (~44%) is average genomic ancestry. Our results suggest that adjacent cis-acting regulatory loci for OCA2 explain the relationship between skin and eye color, and point to an underlying genetic architecture in which several genes of moderate effect act together with many genes of small effect to explain ~70% of the estimated heritability.

Although invasive alien species have long been recognized as a major threat to nature and people, until now there has been no comprehensive global review of the status, trends, drivers, impacts, management and governance challenges of biological invasions. The Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) Thematic Assessment Report on Invasive Alien Species and Their Control (hereafter ‘IPBES invasive alien species assessment’) drew on more than 13,000 scientific publications and reports in 15 languages as well as Indigenous and local knowledge on all taxa, ecosystems and regions across the globe. Therefore, it provides unequivocal evidence of the major and growing threat of invasive alien species alongside ambitious but realistic approaches to manage biological invasions. The extent of the threat and impacts has been recognized by the 143 member states of IPBES who approved the summary for policymakers of this assessment. Here, the authors of the IPBES assessment outline the main findings of the IPBES invasive alien species assessment and highlight the urgency to act now. This Perspective highlights the global consensus on the urgency and growing threat of invasive alien species, and management needs, as found by the 2023 report on invasive alien species conducted by the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES).

Abstract Aim Cryptoblepharus is a genus of small arboreal or rock‐dwelling scincid lizards, widespread through the Indo‐Pacific and Australian regions, with a disjunct outlier in the Malagasy region. The taxonomy within this genus is controversial, with different authors ranking the different forms (now some 36) at various levels, from different species to subspecies of a single species, Cryptoblepharus boutonii . We investigated the biogeography and genetic differentiation of the Cryptoblepharus from the Western Indian Ocean region, in order to understand their origin and history. Location Western Indian Ocean region. Methods We analysed sequences of mitochondrial DNA (partial 12s and 16s rRNA genes, 766 bp) from 48 specimens collected in Madagascar, Mauritius, the four Comoros islands and East Africa, and also in New Caledonia, representing the Australo‐Pacific unit of the distribution. Results Pairwise sequence divergences of c. 3.1% were found between the New Caledonian forms and the ones from the Western Indian Ocean. Two clades were identified in Madagascar, probably corresponding to the recognized forms cognatus and voeltzkowi , and two clades were identified in the Comoro islands, where each island population formed a distinct haplotype clade. The East African samples form a monophyletic unit, with some variation existing between Pemba, Zanzibar and continental Tanzania populations. Individuals from Mauritius form a divergent group, more related to populations from Moheli and Grand Comore (Comoros islands) than to the others. Main conclusions The level of divergence between the populations from the Western Indian Ocean and Australian regions and the geographic coherence of the variation within the Western Indian Ocean group are concordant with the hypothesis of a colonization of this region by a natural transoceanic dispersal (from Australia or Indonesia). The group then may have diversified in Madagascar, from where it separately colonized the East African coast, the Comoros islands (twice), and Mauritius. The genetic divergence found is congruent with the known morphological variation, but its degree is much lower than typically seen between distinct species of reptiles.

Domestication has led to similar changes in morphology and behavior in several animal species, raising the question whether similarities between different domestication events also exist at the molecular level. We used mRNA sequencing to analyze genome-wide gene expression patterns in brain frontal cortex in three pairs of domesticated and wild species (dogs and wolves, pigs and wild boars, and domesticated and wild rabbits). We compared the expression differences with those between domesticated guinea pigs and a distant wild relative (Cavia aperea) as well as between two lines of rats selected for tameness or aggression towards humans. There were few gene expression differences between domesticated and wild dogs, pigs, and rabbits (30-75 genes (less than 1%) of expressed genes were differentially expressed), while guinea pigs and C. aperea differed more strongly. Almost no overlap was found between the genes with differential expression in the different domestication events. In addition, joint analyses of all domesticated and wild samples provided only suggestive evidence for the existence of a small group of genes that changed their expression in a similar fashion in different domesticated species. The most extreme of these shared expression changes include up-regulation in domesticates of SOX6 and PROM1, two modulators of brain development. There was almost no overlap between gene expression in domesticated animals and the tame and aggressive rats. However, two of the genes with the strongest expression differences between the rats (DLL3 and DHDH) were located in a genomic region associated with tameness and aggression, suggesting a role in influencing tameness. In summary, the majority of brain gene expression changes in domesticated animals are specific to the given domestication event, suggesting that the causative variants of behavioral domestication traits may likewise be different.

Diagnoses that are both timely and accurate are critically important for patients with life-threatening or drug resistant infections. Technological improvements in High-Throughput Sequencing (HTS) have led to its use in pathogen detection and its application in clinical diagnoses of infectious diseases. The present study compares two HTS methods, 16S rRNA marker gene sequencing (metataxonomics) and whole metagenomic shotgun sequencing (metagenomics), in their respective abilities to match the same diagnosis as traditional culture methods (culture inference) for patients with ventilator associated pneumonia (VAP). The metagenomic analysis was able to produce the same diagnosis as culture methods at the species-level for five of the six samples, while the metataxonomic analysis was only able to produce results with the same species-level identification as culture for two of the six samples. These results indicate that metagenomic analyses have the accuracy needed for a clinical diagnostic tool, but full integration in diagnostic protocols is contingent on technological improvements to decrease turnaround time and lower costs.