Broad Taxonomic Scales Research Articles

Physiological trait coordination and variability across and within three Pinus species.

Studies have explored how traits separate plants ecologically and the trade-offs that underpin this separation. However, uncertainty remains as to the taxonomic scale at which traits can predictably separate species. We studied how physiological traits separated three Pinus (Pinus banksiana, Pinus resinosa, and Pinus strobus) species across three sites. We collected traits from four common leaf and branch measurements (light-response curves, CO2-response curves, pressure-volume curves, and hydraulic vulnerability curves) across each species and site. While common, these measurements are not typically measured together due to logistical constraints. Few traits varied across species and sites as expected given the ecological preferences of the species and environmental site characteristics. Some trait trade-offs present at broad taxonomic scales were observed across the three species, but most were absent within species. Certain trade-offs contrasted expectations observed at broader scales but followed expectations given the species' ecological preferences. We emphasize the need to both clarify why certain traits are being studied, as variation in unexpected but ecologically meaningful ways often occurs and certain traits might not vary substantially within a given lineage (e.g. hydraulic vulnerability in Pinus), highlighting the role a trait selection in trait ecology.

Comprehensive Genomic and Evolutionary Analysis of Biofilm Matrix Clusters and Proteins in the Vibrio Genus.

Vibrio cholerae pathogens cause cholera, an acute diarrheal disease resulting in significant morbidity and mortality worldwide. Biofilm formation by V. cholerae enhances its survival in natural ecosystems and facilitates transmission during cholera outbreaks. Critical components of the biofilm matrix are the Vibrio polysaccharide (VPS) produced by the vps-1 and vps-2 gene clusters, and biofilm matrix proteins encoded in the rbm cluster. However, the biofilm matrix clusters and associated matrix proteins in other Vibrio species remain under investigated, and their evolutionary patterns are largely unknown. In this study, we systematically annotated the biofilm matrix clusters across 6,121 Vibrio genomes, revealing their distribution, diversity, and evolution. We found that biofilm matrix clusters not only exist in V. cholerae but also in phylogenetically distant Vibrio species. Additionally, vps-1 clusters tend to co-locate with rbmABC genes, while vps-2 clusters are often adjacent to rbmDEF genes in various Vibrio species, which helps explain the separation of these clusters by the rbm cluster in well-characterized V. cholerae strains. Evolutionary analysis of RbmC and Bap1 reveals that these two major biofilm matrix proteins are sequentially and structurally related and have undergone domain/modular alterations during their evolution. RbmC genes are more prevalent, while bap1 likely resulted from an ancient duplication event of rbmC and is only present in a major clade of species containing rbmC counterparts. Notably, a novel loop-less Bap1 variant, identified in two subspecies clades of V. cholerae, was found to be associated with altered biofilm formation and the loss of antibiotic efflux pumps and chemotaxis. Another rbm cluster gene, rbmB, involved in biofilm dispersal, was found to share a common ancestor with Vibrio prophage pectin lyase-like tail proteins, indicating its functional and evolutionary linkages to Vibriophage proteins. In summary, our findings establish a foundational understanding of the proteins and gene clusters that contribute to Vibrio biofilm formation from an evolutionary perspective across a broad taxonomic scale. This knowledge paves the way for future strategies aimed at engineering and controlling biofilms through genetic modification.

De novo transcriptome assembly of a lipoxygenase knock-down strain in the diatom Pseudo-nitzschia arenysensis

Diatoms are microalgae that live in marine and freshwater environments and are responsible for about 20% of the world’s carbon fixation. Population dynamics of these cells is finely regulated by intricate signal transduction systems, in which oxylipins are thought to play a relevant role. These are oxygenated fatty acids whose biosynthesis is initiated by a lipoxygenase enzyme (LOX) and are widely distributed in all phyla, including diatoms. Here, we present a de novo transcriptome obtained from the RNA-seq performed in the diatom species Pseudo-nitzschia arenysensis, using both a wild-type and a LOX-silenced strain, which will represent a reliable reference for comparative analyses within the Pseudo-nitzschia genus and at a broader taxonomic scale. Moreover, the RNA-seq data can be interrogated to go deeper into the oxylipins metabolic pathways.

Fusion/fission protein family identification in Archaea.

The majority of newly discovered archaeal lineages remain without a cultivated representative, but scarce experimental data from the cultivated organisms show that they harbor distinct functional repertoires. To unveil the ecological as well as evolutionary impact of Archaea from metagenomics, new computational methods need to be developed, followed by in-depth analysis. Among them is the genome-wide protein fusion screening performed here. Natural fusions and fissions of genes not only contribute to microbial evolution but also complicate the correct identification and functional annotation of sequences. The products of these processes can be defined as fusion (or composite) proteins, the ones consisting of two or more domains originally encoded by different genes and split proteins, and the ones originating from the separation of a gene in two (fission). Fusion identifications are required for proper phylogenetic reconstructions and metabolic pathway completeness assessments, while mappings between fused and unfused proteins can fill some of the existing gaps in metabolic models. In the archaeal genome-wide screening, more than 1,900 fusion/fission protein clusters were identified, belonging to both newly sequenced and well-studied lineages. These protein families are mainly associated with different types of metabolism, genetic, and cellular processes. Moreover, 162 of the identified fusion/fission protein families are archaeal specific, having no identified fused homolog within the bacterial domain. Our approach was validated by the identification of experimentally characterized fusion/fission cases. However, around 25% of the identified fusion/fission families lack functional annotations for both composite and split states, showing the need for experimental characterization in Archaea.IMPORTANCEGenome-wide fusion screening has never been performed in Archaea on a broad taxonomic scale. The overlay of multiple computational techniques allows the detection of a fine-grained set of predicted fusion/fission families, instead of rough estimations based on conserved domain annotations only. The exhaustive mapping of fused proteins to bacterial organisms allows us to capture fusion/fission families that are specific to archaeal biology, as well as to identify links between bacterial and archaeal lineages based on cooccurrence of taxonomically restricted proteins and their sequence features. Furthermore, the identification of poorly characterized lineage-specific fusion proteins opens up possibilities for future experimental and computational investigations. This approach enhances our understanding of Archaea in general and provides potential candidates for in-depth studies in the future.

Using a Handful of Transcriptomes to Detect Sex-Linked Markers and Develop Molecular Sexing Assays in a Species with Homomorphic Sex Chromosomes.

To understand the biology of a species, it is often crucial to be able to differentiate males and females. However, many species lack easily identifiable sexually dimorphic traits. In those that possess sex chromosomes, molecular sexing offers a good alternative, and molecular sexing assays can be developed through the comparison of male and female genomic sequences. However, in many nonmodel species, sex chromosomes are poorly differentiated, and identifying sex-linked sequences and developing sexing assays can be challenging. In this study, we highlight a simple transcriptome-based procedure for the detection of sex-linked markers suitable for the development of sexing assays that circumvents limitations of more commonly used approaches. We apply it to the spotted snow skink Carinascincus ocellatus, a viviparous lizard with homomorphic XY chromosomes that has environmentally induced sex reversal. With transcriptomes from three males and three females alone, we identify thousands of putative Y-linked sequences. We confirm linkage through alignment of assembled transcripts to a distantly related lizard genome and readily design multiple single locus polymerase chain reaction primers to sex C. ocellatus and related species. Our approach also facilitates valuable comparisons of sex determining systems on a broad taxonomic scale.

Phylogeny, Ecology, and Gene Families Covariation Shaped the Olfactory Subgenome of Rodents.

Olfactory receptor (OR) genes represent the largest multigenic family in mammalian genomes and encode proteins that bind environmental odorant molecules. The OR repertoire is extremely variable among species and is subject to many gene duplications and losses, which have been linked to ecological adaptations in mammals. Although they have been studied on a broad taxonomic scale (i.e., placental), finer sampling has rarely been explored in order to better capture the mechanisms that drove the evolution of the OR repertoire. Among placental mammals, rodents are well-suited for this task, as they exhibit diverse life history traits, and genomic data are available for most major families and a diverse array of lifestyles. In this study, 53 rodent published genomes were mined for their OR subgenomes. We retrieved more than 85,000 functional and pseudogene OR sequences that were subsequently classified into phylogenetic clusters. Copy number variation among rodents is similar to that of other mammals. Using our OR counts along with comparative phylogenetic approaches, we demonstrated that ecological niches such as diet, period of activity, and a fossorial lifestyle strongly impacted the proportion of OR pseudogenes. Within the OR subgenome, phylogenetic inertia was the main factor explaining the relative variations of the 13 OR gene families. However, a striking exception was a convergent 10-fold expansion of the OR family 14 among the phylogenetically divergent subterranean mole-rat lineages belonging to Bathyergidae and Spalacidae families. This study illustrates how the diversity of the OR repertoire has evolved among rodents, both shaped by selective forces stemming from species life history traits and neutral evolution along the rodent phylogeny.

Island biogeography of birds in the South West Pacific: Direct and indirect effects of physical geography and co‐occurring vegetation

AbstractAimThe distribution of birds among islands is thought to be regulated by island physical geography (i.e. island area, isolation and latitude). In contrast, work on continents indicates that bird diversity is often regulated by plant diversity. Consequently, the (statistical) direct and indirect effects of physical geography on island bird distribution are poorly understood. We investigated the relative roles of physical geography and vegetation in determining island bird diversity in the South West Pacific at two taxonomic scales of resolution: total bird diversity and bird diversity within functional guilds.LocationEleven archipelagos in the South West Pacific.TaxonLand birds.MethodsWe created a dataset characterising total and functional guild diversity for land birds and seed plants (i.e. Spermatophytes) among archipelagos. We then used mediation analysis to disentangle the direct and indirect (i.e. mediated) effects of physical geography and vegetation on bird diversity.ResultsOn a broad taxonomic scale, total bird diversity was directly determined by total plant diversity, not the area, isolation or latitude of islands. On a fine taxonomic scale results differed between functional guilds. The diversity of herbivorous and frugivorous birds was directly determined by physical geography rather than plant total and trait diversity. Woody and herbaceous plant species diversity mediated the effect of physical geography on forest‐dwelling, above ground nesting and ground nesting bird diversity. Granivorous, nectarivorous and grassland‐dwelling bird diversities were unrelated to both physical geography and herbaceous plant diversity.Main ConclusionsPhysical geography and vegetation can have both direct and indirect effects on island bird diversity. Furthermore, relationships between physical geography, vegetation and bird diversity can vary markedly among functional guilds.

Tracking life cycles of parasites across a broad taxonomic scale in a marine ecosystem

Parasitic helminths exhibit remarkable diversity in their life cycles, although few parasite species have their whole life cycles resolved. Owing to the fact that parasite life stages within hosts are often not comparable using morphological data, genetic data provides convincing evidence of transmission pathways between intermediate and definitive hosts. We took this approach to an ecosystem level, genetically matching parasite (acanthocephalan, cestode, nematode and trematode) life stages across a broad taxonomic range of intermediate and definitive hosts (invertebrates, seabirds, elasmobranchs and teleost fish) in Otago’s (New Zealand) coastal marine ecosystem. We identified which transmission routes are utilized by the most parasite species and assessed which intermediate hosts are most important in facilitating the transmission of parasites in this ecosystem. Our findings reveal 59 new records of larval parasites infecting their respective intermediate hosts and 289 transmission pathways utilized by 35 helminth species to complete their life cycles. Sprat, triplefin and arrow squid all hosted the highest number of larval parasite species, suggesting they play important roles as intermediate hosts. We then used the new life cycle data to provide a synthetic overview of the life cycles known for various parasite groups in New Zealand. This study highlights how studying parasite life cycles can enhance our understanding of the ecology and evolution of parasites and hosts in natural systems, beyond simply resolving life cycles.

A high-throughput multispectral imaging system for museum specimens

We present an economical imaging system with integrated hardware and software to capture multispectral images of Lepidoptera with high efficiency. This method facilitates the comparison of colors and shapes among species at fine and broad taxonomic scales and may be adapted for other insect orders with greater three-dimensionality. Our system can image both the dorsal and ventral sides of pinned specimens. Together with our processing pipeline, the descriptive data can be used to systematically investigate multispectral colors and shapes based on full-wing reconstruction and a universally applicable ground plan that objectively quantifies wing patterns for species with different wing shapes (including tails) and venation systems. Basic morphological measurements, such as body length, thorax width, and antenna size are automatically generated. This system can increase exponentially the amount and quality of trait data extracted from museum specimens.

Heterogeneity across Neotropical aquatic environments affects prokaryotic and eukaryotic biodiversity based on environmental DNA

AbstractCharacterizing biological communities and knowledge on the distribution of biodiversity allows the assessment of ecological quality. This provides valuable information for conservation biology and monitoring purposes. While obtaining such data has been challenging in the past, environmental DNA (eDNA) sampling represents a promising tool to describe biodiversity on a broad taxonomic scale. In this study, we provide the first broad‐scale biodiversity assessment for ten Neotropical water bodies in Nicaragua (a major river, two great lakes, and seven relatively young and small crater lakes) using eDNA sampling to determine how abiotic factors structure the distribution of prokaryotic and eukaryotic biodiversity across these environments. Further, we explored to what extent levels of biodiversity are associated across different taxonomic groups and environments. We found that prokaryotic and eukaryotic α‐diversity was consistently higher in the great lakes (i.e., Lakes Nicaragua and Managua) as well as in Río San Juan compared with the young and small crater lakes. Differences of prokaryotic and eukaryotic communities (β‐diversity) were significantly correlated, indicating that biological communities are similarly structured across environments. Accordingly, differences in salinity were correlated with prokaryotic and eukaryotic communities, whereas differences in dissolved oxygen were only correlated with prokaryotic communities (β‐diversity). Yet, salinity and dissolved oxygen only affected prokaryotic α‐diversity, suggesting different effects of these two abiotic factors on biodiversity within aquatic environments. Moreover, α‐diversity of different phyla was positively correlated, although more strongly in prokaryotes, showing that biodiversity patterns are congruent across a broad range of lineages, particularly in prokaryotes.

Assessing candidate DNA barcodes for Chinese and internationally traded timber species.

Accurate identification of species from timber is an essential step to help control illegal logging and forest loss. However, current approaches to timber identification based on morphological and anatomical characteristics have limited species resolution. DNA barcoding is a proven tool for plant species identification, but there is a need to build reliable reference data across broad taxonomic and spatial scales. Here, we construct a species barcoding library consisting of 1550 taxonomically diverse timber species from 656 genera and 124 families, representing a comprehensive genetic reference data set for Chinese timber species and international commercial traded timber species, using four barcodes (rbcL, matK, trnH-psbA, and ITS2). The ITS2 fragment was found to be the most efficient locus for Chinese timber species identification among the four barcodes tested, both at the species and genus level, despite its low recovery rate. Nevertheless, the barcode combination matK+trnH-psbA+ITS2 was required as a complementary barcode to distinguish closely related species in complex data sets involving internationally traded timber species. Comparative analyses of family-level discrimination and species/genus ratios indicated that the inclusion of closely related species is an important factor affecting the resolution ability of barcodes for timber species verification. Our study indicates that although nuclear ITS2 is the most efficient single barcode for timber species authentication in China, complementary combinations like matK+trnH-psbA+ITS2 are required to provide broader discrimination power. These newly-generated sequences enrich the existing publicly available databases, especially for tropical and subtropical evergreen timber trees and this current timber species barcode reference library can serve as an important genetic resource for forestry monitoring, illegal logging prosecution and biodiversity projects.

Elastic Moduli of Avian Eggshell.

Simple SummaryBirds have existed on Earth for over one hundred million years, and the eggshell is one of the main factors in them having survived for such a long period of time. The avian eggshell is a multifunctional thin-shelled structure that protects the developing embryo from damage and excessive water loss, provides the embryo with calcium for its skeleton, and sustains the weight of incubating birds. It must also be breakable for the hatchling to emerge. Elastic modulus (Young’s modulus) is the most fundamental mechanical property for such a load-bearing structure. Despite extensive studies on avian eggs, our understanding of the elastic moduli and structure–function relationship of avian eggshells remains incomplete—most previous works have focused on chicken or only a few species. One challenge is the availability and collection of freshly-laid egg samples. The present study is based on 700 freshly-laid eggs collected over a period of seven years from 2015 to 2021, covering a wide taxonomic scale and egg mass (from 1 g to 1459 g). With this large dataset, we may obtain a bird’s-eye view of the elasticity and structure–function relationships of the avian eggshell.We analyze 700 freshly-laid eggs from 58 species (22 families and 13 orders) across three orders of magnitude in egg mass. We study the elastic moduli using three metrics: (i) effective Young’s modulus, EFEM, by a combined experimental and numerical method; (ii) elastic modulus, Enano, by nanoindentation, and (iii) theoretical Young’s modulus, Etheory. We measure the mineral content by acid-base titration, and crystallographic characteristics by electron backscatter diffraction (EBSD), on representative species. We find that the mineral content ranges between 83.1% (Zebra finch) and 96.5% (ostrich) and is positively correlated with EFEM—23.28 GPa (Zebra finch) and 47.76 GPa (ostrich). The EBSD shows that eggshell is anisotropic and non-homogeneous, and different species have different degrees of crystal orientation and texture. Ostrich eggshell exhibits strong texture in the thickness direction, whereas chicken eggshell has little. Such anisotropy and inhomogeneity are consistent with the nanoindentation tests. However, the crystal characteristics do not appear to correlate with EFEM, as EFEM represents an overall “average” elasticity of the entire shell. The experimental results are consistent with the theoretical prediction of linear elasticity. Our comprehensive investigation into the elastic moduli of avian eggshell over broad taxonomic scales provides a useful dataset for those who work on avian reproduction.

Identifying co-phylogenetic hotspots for zoonotic disease.

The incidence of zoonotic diseases is increasing worldwide, which makes identifying parasites likely to become zoonotic and hosts likely to harbour zoonotic parasites a critical concern. Prior work indicates that there is a higher risk of zoonotic spillover accruing from closely related hosts and from hosts that are infected with a high phylogenetic diversity of parasites. This suggests that host and parasite evolutionary history may be important drivers of spillover, but identifying whether host-parasite associations are more strongly structured by the host, parasite or both requires co-phylogenetic analyses that combine host-parasite association data with host and parasite phylogenies. Here, we use host-parasite datasets containing associations between helminth taxa and free-range mammals in combination with phylogenetic models to explore whether host, parasite, or both host and parasite evolutionary history influences host-parasite associations. We find that host phylogenetic history is most important for driving patterns of helminth-mammal association, indicating that zoonoses are most likely to come from a host's close relatives. More broadly, our results suggest that co-phylogenetic analyses across broad taxonomic scales can provide a novel perspective for surveying potential emerging infectious diseases. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.

Host phylogeny and host ecology structure the mammalian gut microbiota at different taxonomic scales

The gut microbiota is critical for host function. Among mammals, host phylogenetic relatedness and diet are strong drivers of gut microbiota structure, but one factor may be more influential than the other. Here, we used 16S rRNA gene sequencing to determine the relative contributions of host phylogeny and host diet in structuring the gut microbiotas of 11 herbivore species from 5 families living sympatrically in southwest Kenya. Herbivore species were classified as grazers, browsers, or mixed-feeders and dietary data (% C4 grasses in diet) were compiled from previously published sources. We found that herbivore gut microbiotas were highly species-specific, and that host taxonomy accounted for more variation in the gut microbiota (30%) than did host dietary guild (10%) or sample month (8%). Overall, similarity in the gut microbiota increased with host phylogenetic relatedness (r = 0.74) across the 11 species of herbivores, but among 7 closely related Bovid species, dietary %C4 grass values more strongly predicted gut microbiota structure (r = 0.64). Additionally, within bovids, host dietary guild explained more of the variation in the gut microbiota (17%) than did host species (12%). Lastly, while we found that the gut microbiotas of herbivores residing in southwest Kenya converge with those of distinct populations of conspecifics from central Kenya, fine-scale differences in the abundances of bacterial amplicon sequence variants (ASVs) between individuals from the two regions were also observed. Overall, our findings suggest that host phylogeny and taxonomy strongly structure the gut microbiota across broad host taxonomic scales, but these gut microbiotas can be further modified by host ecology (i.e., diet, geography), especially among closely related host species.

Animals, protists and bacteria share marine biogeographic patterns.

Over millennia, ecological and evolutionary mechanisms have shaped macroecological patterns across the tree of life. Research describing these patterns at both regional and global scales has traditionally focused on the study of metazoan species. Consequently, there is a limited understanding of cross-phylum biogeographic structuring and an escalating need to understand the macroecology of both microscopic and macroscopic organisms. Here we used environmental DNA (eDNA) metabarcoding to explore the biodiversity of marine metazoans, protists and bacteria along an extensive and highly heterogeneous coastline. Our results showed remarkably consistent biogeographic structure across the kingdoms of life despite billions of years of evolution. Analyses investigating the drivers of these patterns for each taxonomic kingdom found that environmental conditions (such as temperature) and, to a lesser extent, anthropogenic stressors (such as fishing pressure and pollution) explained some of the observed variation. Additionally, metazoans displayed biogeographic patterns that suggested regional biotic homogenization. Against the backdrop of global pervasive anthropogenic environmental change, our work highlights the importance of considering multiple domains of life to understand the maintenance and drivers of biodiversity patterns across broad taxonomic, ecological and geographical scales.

Metabarcoding reveals hidden species and improves identification of marine zooplankton communities in the North Sea

Abstract Although easily collected in large numbers, the subsequent processing and identification of zooplankton have usually been a barrier to large-scale biodiversity assessments. Therefore, DNA barcoding has been increasingly used by non-taxonomists to identify specimens. Here, we studied the community composition of zooplankton in the Belgian part of the North Sea over the course of 1 year. We identified zooplankton using both a traditional approach based on morphological characteristics and by metabarcoding of a 650 bp fragment of the V4-V5 region of the 18S rRNA gene using nanopore sequencing. Using long rDNA sequences, we were able to identify several taxa at the species level, across a broad taxonomic scale. Using both methods, we compared community composition and obtained diversity metrics. Diversity indices were not significantly correlated. Metabarcoding allowed for comparisons of diversity and community composition, but not all groups were successfully sequenced. Additionally, some disparities existed between relative abundances of the most abundant taxa based on traditional counts and those based on sequence reads. Overall, we conclude that for zooplankton samples, metabarcoding is capable of detecting taxa with a higher resolution, regardless of developmental stage of the organism. Combination of molecular and morphological methods results in the highest detection and identification levels of zooplankton.

Functional redundancy in local spatial scale microbial communities suggests stochastic processes at an urban wilderness preserve in Austin, TX, USA.

Empirical evidence supports selection of soil microbial communities by edaphic properties across large spatial scales; however, less is known at smaller spatial scales. The goal of this research was to evaluate relationships between ecosystem characteristics and bacterial community structure/function at broad taxonomic resolutions in soils across small spatial scales. We employed 16S rRNA gene sequencing, community-level physiological profiling and soil chemical analysis to address this goal. We found weak relationships between gradients in soil characteristics and community structure/function. Specific operational taxonomic units did not respond to edaphic variation, but Acidobacteria, Bacteroidetes and Nitrospirae shifted their relative abundances. High metabolic diversity within the bacterial communities was observed despite general preference of Tween 40/80. Carbon metabolism patterns suggest dominance of functional specialists at our times of measurement. Pairwise comparison of carbon metabolism patterns indicates high levels of functional redundancy. Lastly, at broad taxonomic scales, community structure and function weakly covary with edaphic properties. This evidence suggests that stochasticity or unmeasured environmental gradients may be influential in bacterial community assembly in soils at small spatial scales.

A test of the lateral semicircular canal correlation to head posture, diet and other biological traits in \u201cungulate\u201d mammals

For over a century, researchers have assumed that the plane of the lateral semicircular canal of the inner ear lies parallel to the horizon when the head is at rest, and used this assumption to reconstruct head posture in extinct species. Although this hypothesis has been repeatedly questioned, it has never been tested on a large sample size and at a broad taxonomic scale in mammals. This study presents a comprehensive test of this hypothesis in over one hundred “ungulate” species. Using CT scanning and manual segmentation, the orientation of the skull was reconstructed as if the lateral semicircular canal of the bony labyrinth was aligned horizontally. This reconstructed cranial orientation was statistically compared to the actual head posture of the corresponding species using a dataset of 10,000 photographs and phylogenetic regression analysis. A statistically significant correlation between the reconstructed cranial orientation and head posture is found, although the plane of the lateral semicircular canal departs significantly from horizontal. We thus caution against the use of the lateral semicircular canal as a proxy to infer precisely the horizontal plane on dry skulls and in extinct species. Diet (browsing or grazing) and head-butting behaviour are significantly correlated to the orientation of the lateral semicircular canal, but not to the actual head posture. Head posture and the orientation of the lateral semicircular canal are both strongly correlated with phylogenetic history.

Latitudinal gradients in genetic diversity and natural selection at a highly adaptive gene in terrestrial mammals

Identifying where high genetic diversity is located across our planet and what factors affect the geographical patterns of genetic variation not only provides important insights into distributions of biodiversity but is also crucial for human health, animal and plant breeding and biodiversity conservation. Recent studies show that genetic diversity at nearly neutral genes decreases from the tropics to the poles in different taxa, mirroring the oldest recognized latitudinal gradient of species richness, yet functional genetic diversity has received little attention at such broad spatial or taxonomic scales. Here, we investigated latitudinal gradients in genetic diversity at a polymorphic exon 2 (MHC II DRB gene, 1515 sequences) of the major histocompatibility complex that confers resistance to parasites in 93 terrestrial mammal species at the global scale. We also estimated the effects of species traits, positive selection and anthropogenic biomes on genetic diversity. We found clear latitudinal gradients in genetic diversity and the presence of positive selection at exon 2. Absolute latitude, the presence of positive selection and body mass are important predictors of within‐species genetic diversity. A higher occurrence of positive selection, faster evolutionary speed or slower drift at low latitudes may shape the latitudinal gradient in the within‐species genetic diversity of the gene. Our results contribute to a greater understanding of how species traits, selection and drift geographically shape functional genetic diversity, broadening the generality of latitudinal biodiversity gradient. The results highlight the importance of conservation at low latitudes.

A global test of Allen’s rule in rodents

AbstractAimWe test whether geographical variation in the length of appendages in rodent species follows predictions of Allen's rule (a positive relationship between appendage length and temperature) at a broad taxonomic scale (order Rodentia). We also test whether the applicability of this rule varies based on the unit of analysis (species or assemblage), the appendage examined (tail, hind foot, ear), body size, occupied habitat, geographical range size, life mode and saltatorial ability.LocationWorld‐wide.Time periodCurrent.Major taxa studiedRodents (order Rodentia).MethodsWe assembled data on the morphology, ecology and phylogeny for ≤ 2,212 rodent species, representing c. 86% of all the described rodent species and c. 95% of the described genera. We tested the predicted Allen's rule associations among size‐corrected appendage lengths and both latitudinal and climatic variables (temperature and precipitation). We applied a cross‐species approach based on phylogenetic regressions and a cross‐assemblage approach based on spatial regressions in equal‐area 1.5° grid cells.ResultsSupport for Allen's rule was greatest for the tail and was stronger across assemblages than across species. We detected a negative relationship between tail length and (absolute) latitude, which was accounted for by a positive association between tail length and temperature of the coldest month. This association was greatest in desert species. In addition, we observed a negative relationship between ear length and precipitation.Main conclusionsIn rodents, Allen's rule is confirmed only for tails, and this association seems to be driven by adaptation to the cold, rather than warm temperatures. Habitat type seems to influence conformity to this rule. Conformity to Allen's rule is likely to be the result of complex evolutionary trade‐offs between temperature regulation and other essential species traits.