Contributors: Francois, Olivier, Martins, Helena, Caye, Kevin, Schoville, Sean
... Population differentiation (PD) and ecological association (EA) tests have recently emerged as prominent statistical methods to investigate signatures of local adaptation using population genomic data. Based on statistical models, these genome-wide testing procedures have attracted considerable attention as tools to identify loci potentially targeted by natural selection. An important issue with PD and EA tests is that incorrect model specification can generate large numbers of false positive associations. Spurious association may indeed arise when shared demographic history, patterns of isolation by distance, cryptic relatedness or genetic background are ignored. Recent works on PD and EA tests have widely focused on improvements of test corrections for those confounding effects. Despite significant algorithmic improvements, there is still a number of open questions on how to check that false discoveries are under control and implement test corrections, or how to combine statistical tests from multiple genome scan methods. This tutorial paper provides a detailed answer to these questions. It clarifies the relationships between traditional methods based on allele frequency differentiation and EA methods, and provides a unified framework for their underlying statistical tests. We demonstrate how techniques developed in the area of genome-wide association studies, such as inflation factors and linear mixed models, benefit genome scan methods, and provide guidelines for good practice while conducting statistical tests in landscape and population genomic applications. Finally, we highlight how the combination of several well-calibrated statistical tests can increase the power to reject neutrality, improving our ability to infer patterns of local adaptation in large population genomic datasets.
Contributors: Lee, Michael S. Y., Sanders, Kate L., King, Benedict, Palci, Alessandro
... The relationship between rates of diversification and of body size change (a common proxy for phenotypic evolution) was investigated across Elapidae, the largest radiation of highly venomous snakes. Time-calibrated phylogenetic trees for 175 species of elapids (more than 50% of known taxa) were constructed using seven mitochondrial and nuclear genes. Analyses using these trees revealed no evidence for a link between speciation rates and changes in body size. Two clades (Hydrophis, Micrurus) show anomalously high rates of diversification within Elapidae, yet exhibit rates of body size evolution almost identical to the general elapid ‘background’ rate. Although correlations between speciation rates and rates of body size change exist in certain groups (e.g. ray-finned fishes, passerine birds), the two processes appear to be uncoupled in elapid snakes. There is also no detectable shift in diversification dynamics associated with the colonization of Australasia, which is surprising given that elapids appear to be the first clade of venomous snakes to reach the continent.
Data from: Cryptic species or inadequate taxonomy? implementation of 2D geometric morphometrics based on integumental organs as landmarks for delimitation and description of copepod taxa
Contributors: Karanovic, Tomislav, Djurakic, Marko, Eberhard, Stefan M.
... Discovery of cryptic species using molecular tools has become common in many animal groups but it is rarely accompanied by morphological revision, creating ongoing problems in taxonomy and conservation. In copepods, cryptic species have been discovered in most groups where fast-evolving molecular markers were employed. In this study at Yeelirrie in Western Australia we investigate a subterranean species complex belonging to the harpacticoid genus Schizopera Sars, 1905, using both the barcoding mitochondrial COI gene and landmark-based two-dimensional geometric morphometrics. Integumental organs (sensilla and pores) are used as landmarks for the first time in any crustacean group. Complete congruence between DNA-based species delimitation and relative position of integumental organs in two independent morphological structures suggests the existence of three distinct evolutionary units. We describe two of them as new species, employing a condensed taxonomic format appropriate for cryptic species. We argue that many supposedly cryptic species might not be cryptic if researchers focus on analyzing morphological structures with multivariate tools that explicitly take into account geometry of the phenotype. A perceived supremacy of molecular methods in detecting cryptic species is in our view a consequence of disparity of investment and unexploited recent advancements in morphometrics among taxonomists. Our study shows that morphometric data alone could be used to find diagnostic morphological traits and gives hope to anyone studying small animals with a hard integument or shell, especially opening the door to assessing fossil diversity and rich museum collections. We expect that simultaneous use of molecular tools with geometry-oriented morphometrics may yield faster formal description of species. Decrypted species in this study are a good example for urgency of formal descriptions, as they display short-range endemism in small groundwater calcrete aquifers in a paleochannel, where their conservation may be threatened by proposed mining.
Contributors: Halliday, Thomas John Dixon, Goswami, Anjali
... In the aftermaths of mass extinction events, during radiations of clades, and in several other evolutionary scenarios, there is often a decoupling of taxonomic diversity and morphological disparity. The placental mammal radiation after the end-Cretaceous mass extinction is one of the archetypal adaptive radiations, but the change in morphological disparity of the entire skeleton has never been quantified across this important boundary. We reconstruct ancestral morphologies of 680 discrete morphological characters onto dated phylogenies of 177 mostly Cretaceous and Palaeogene eutherians (placental mammals and their stem relatives). Using a new approach to incorporate morphologies representing ghost lineages, we assess three measures of morphological disparity (sum of ranges, sum of variances and mean pairwise dissimilarity) across stage-level time bins within the Cretaceous and Palaeogene. We find that the range-based metric suggests that eutherian disparity increased immediately after the end-Cretaceous mass extinction, while both variance-based metrics declined from the Campanian to the Maastrichtian, but showed no change in disparity from the Maastrichtian to the Puercan – the first North American Land Mammal Age of the Paleocene. Increases in variance-based metrics lag behind the range-based metric and per-lineage accumulation rate, suggesting that the response of mammals to the Cretaceous–Palaeogene event was characterized by an early radiation that increased overall morphospace occupation, followed later by specialization that resulted in increased dissimilarity.
Data from: Inferring speciation history in the Andes with reduced-representation sequence data: an example in the bay-backed antpittas (Aves; Grallariidae; Grallaria hypoleuca s. l.)
Contributors: Winger, Benjamin M., Hosner, Peter A., Bravo, Gustavo A., Cuervo, Andrés M., Aristizábal, Natalia, Cueto, Luis E., Bates, John M.
... In the Andes, humid-forest organisms frequently exhibit pronounced genetic structure and geographic variation in phenotype, often coincident with physical barriers to dispersal. However, phylogenetic relationships of clades have often been difficult to resolve due to short internodes. Consequently, even in taxa with well-defined genetic structure, the temporal and geographic sequences of dispersal and vicariance events that led to this differentiation have remained opaque, hindering efforts to test the association between diversification and earth history and to understand the assembly of species rich communities on Andean slopes. Here, we use mitochondrial DNA and thousands of short-read sequences generated with Genotyping-by-Sequencing (GBS) to examine the geographic history of speciation in a lineage of passerine birds found in the humid forest of the Andes, the “bay-backed” antpitta complex (Grallaria hypoleuca s. l). Mitochondrial DNA genealogies documented genetic structure among clades, but were poorly resolved at nodes relevant for biogeographic inference. By contrast, relationships inferred from GBS loci were highly resolved and suggested a biogeographic history in which the ancestor originated in the northern Andes and dispersed south. Our results are consistent with a scenario of vicariant speciation wherein the range of a widespread ancestor was fragmented as a result of geologic or climatic change, rather than a stepping-stone series of dispersal events across pre-existing barriers. However, our study also highlights challenges of distinguishing dispersal-mediated speciation from static vicariance. Our results further demonstrate the substantial evolutionary timescale over which the diverse biota of the Andes was assembled.
Data from: Testing classical species properties with contemporary data: how 'bad species' in the brassy ringlets (Erebia tyndarus complex, Lepidoptera) turned good
Contributors: Gratton, Paolo, Trucchi, Emiliano, Trasatti, Alessandra, Riccarducci, Giorgio, Marta, Silvio, Allegrucci, Giuliana, Cesaroni, Donatella, Sbordoni, Valerio
... All species concepts are rooted in reproductive, and ultimately genealogical, relations. Genetic data are thus the most important source of information for species delimitation. Current ease of access to genomic data and recent computational advances are blooming a plethora of coalescent-based species delimitation methods. Despite their utility as objective approaches to identify species boundaries, coalescent-based methods i) rely on simplified demographic models that may fail to capture some attributes of biological species, ii) do not make explicit use of the geographic information contained in the data, and iii) are often computationally intensive. In this paper we present a case of species delimitation in the Erebia tyndarus species complex, a taxon regarded as a classic example of problematic taxonomic resolution. Our approach to species delimitation used genomic data to test predictions rooted in the biological species concept and in the criterion of coexistence in sympatry. We 1) obtained RAD sequencing data from a carefully designed sample, 2) applied two genotype clustering algorithms to identify genetic clusters and 3) performed within-clusters and between-clusters analyses of isolation by distance (IBD) as a test for intrinsic reproductive barriers. Comparison of our results with those from a Bayes Factor Delimitation (BFD*) coalescent-based analysis, showed that coalescent-based approaches may lead to overconfident splitting of allopatric populations, and indicated that incorrect species delimitation is likely to be inferred when an incomplete geographic sample is analysed. While we acknowledge the theoretical justification and practical usefulness of coalescent-based species delimitation methods, our results stress that, even in the phylogenomic era, the toolkit for species delimitation should not dismiss more traditional, biologically grounded, approaches coupling genomic data with geographic information.
Data from: Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments
Contributors: Jansen, Michael Andrew, Franz, Nico M.
... This contribution adopts the taxonomic concept annotation and alignment approach. Accordingly, and where indicated, previous and newly inferred meanings of taxonomic names are individuated according to one specific source. Articulations among these concepts and pairwise, logically consistent alignments of original and revisionary classifications are also provided, in addition to conventional nomenclatural provenance information. A phylogenetic revision of the broad-nosed weevil genera Minyomerus Horn, 1876 sec. O’Brien & Wibmer (1982), and Piscatopus Sleeper, 1960 sec. O’Brien & Wibmer (1982) (Curculionidae [non-focal]: Entiminae [non-focal]: Tanymecini [non-focal]) is presented. Prior to this study, Minyomerus sec. O’Brien & Wibmer (1982) contained seven species, whereas the monotypic Piscatopus sec. O’Brien & Wibmer (1982) was comprised solely of P. griseus Sleeper, 1960 sec. O’Brien & Wibmer (1982). We thoroughly redescribe these recognized species-level entities and furthermore describe ten species as new to science: M. bulbifrons sec. Jansen & Franz (2015) (henceforth: [JF2015]), sp. n., M. aeriballux [JF2015], sp. n., M. cracens [JF2015], sp. n., M. gravivultus [JF2015], sp. n., M. imberbus [JF2015], sp. n., M. reburrus [JF2015], sp. n., M. politus [JF2015], sp. n., M. puticulatus [JF2015], sp. n., M. rutellirostris [JF2015], sp. n., and M. trisetosus [JF2015], sp. n. A cladistic analysis using 46 morphological characters of 22 terminal taxa (5/17 outgroup/ingroup) yielded a single most-parsimonious cladogram (L = 82, CI = 65, RI = 82). The analysis strongly supports the monophyly of Minyomerus [JF2015] with eight unreversed synapomorphies, and places P. griseus sec. O’Brien & Wibmer (1982) within the genus as sister to M. rutellirostris [JF2015]. Accordingly, Piscatopus sec. Sleeper (1960), syn. n. is changed to junior synonymy of Minyomerus [JF2015], and its sole member P. griseus sec. Sleeper (1960) is moved to Minyomerus [JF2015] as M. griseus [JF2015], comb. n. In addition, the formerly designated type M. innocuus Horn, 1876 sec. Pierce (1913), syn. n. is changed to junior synonymy of M. microps (Say, 1831) [JF2015] which has priority. The genus is widespread throughout western North America, ranging from Canada to Mexico and Baja California. Apparent patterns of interspecific diversity of exterior and genitalic morphology, varying host plant ranges, overlapping and widely extending species distributions, suggest an early origin for Minyomerus [JF2015], with a diversification that likely followed the development of North American desert biomes. Three species in the genus – i.e., M. languidus Horn, 1876 [JF2015], M. microps [JF2015], and M. trisetosus [JF2015] – are putatively considered parthenogenetic.
Data from: The diverse fossil chelonians from Milia (Late Pliocene, Grevena, Greece) with a new species of Testudo Linnaeus, 1758 (Testudines: Testudinidae)
Contributors: Vlachos, Evangelos, Tsoukala, Evangelia
... The late Pliocene (early Villafranchian, MN 16a) locality of Milia (Grevena, Greece) has yielded numerous remains of mammals, such as zygodons, mastodons, rhinocerotids, hipparions, bovids, cervids, suids, carnivorans and tapirs. Several specimens of chelonians have also been discovered and comprise a small testudinid, a geoemydid and a giant tortoise. The presence of a giant tortoise and the presence of a geoemydid with large dimensions are further examples of the trend towards gigantism evidenced by the diverse fauna of Milia. In terms of taxonomic abundance of extinct turtles, this is the richest locality in Greece. The small testudinid is of particular importance because it preserves a posteriorly flared carapace, as in the extant Testudo marginata, but the posterior carapace is much taller and anteroposteriorly shorter. These characters allow us to erect a new species, Testudo brevitesta sp. nov., and to discuss the presence of the marginated tortoise and closely related forms in Greece. The new taxon is analysed in a phylogenetic context within other extant and extinct testudinids, providing new information on the clade Testudona.
Data from: Processes driving the adaptive radiation of a tropical tree (Diospyros, Ebenaceae) in New Caledonia, a biodiversity hotspot
Contributors: Paun, Ovidiu, Turner, Barbara, Trucchi, Emiliano, Munzinger, Jérôme, Chase, Mark W., Samuel, Rosabelle
... Due to its special geological history, the New Caledonian Archipelago is a mosaic of soil types, and in combination with climatic conditions this results in a heterogeneous environment across relatively small distances. A group of over 20 endemic species of Diospyros (Ebenaceae) has rapidly and recently radiated on the archipelago after a single long-distance dispersal event. Most of the Diospyros species in the radiating group are morphologically and ecologically well differentiated, but they exhibit low levels of DNA variability. To investigate the processes that shaped the diversification of this group we employed restriction site associated DNA sequencing (RADseq). Over 8,400 filtered SNPs generally confirm species delimitations and produce a well-supported phylogenetic tree. Our analyses document local introgression, but only a limited potential for gene flow over longer distances. The phylogenetic relationships point to an early regional clustering among populations and species, indicating that allopatric speciation with respect to macrohabitat (i.e., climatic conditions) may have had a role in the initial differentiation within the group. A later, more rapid radiation involved divergence with respect to microhabitat (i.e., soil preference). Several sister species in the group show a parallel divergence in edaphic preference. Searches for genomic regions that are systematically differentiated in this replicated phenotypic divergence pointed to loci potentially involved in ion binding and cellular transport. These loci appear meaningful in the context of adaptations to soil types that differ in heavy-metal and mineral content. Identical nucleotide changes affected only two of these loci, indicating that introgression may have played a limited role in their evolution. Our results suggest that both allopatric diversification and (parapatric) ecological divergence shaped successive rounds of speciation in the Diospyros radiation on New Caledonia.
Data from: The dipnoan buccal pump reconstructed in 3D and implications for air breathing in Devonian lungfishes
Contributors: Clement, Alice M., Long, John A., Tafforeau, Paul, Ahlberg, Per E.
... Lungfishes are known for, and indeed take their name from, their bimodal respiratory abilities. All three extant genera can use their lungs to extract oxygen from the atmosphere, although their reliance upon this capability differs among taxa. Lungs are considered primitive for the Osteichthyes, however the distinctive buccal pump mode of air gulping exhibited by extant lungfishes appears to be a specialization. It is associated with a number of derived skeletal characters (cranial ribs, long parasphenoid stalk, midline gap between palatal tooth plates) that first appeared during the Devonian. These have been described individually, but in no Devonian lungfish has their three-dimensional (3D) spatial relationship been reconstructed and analyzed. Here we present the 3D morphology of Rhinodipterus, a Mid-Late Devonian lungfish from Australia and Europe, based on synchrotron tomography and conventional microtomography scans. Unlike less crownward contemporaneous lungfishes such as Griphognathus and Chirodipterus, Rhinodipterus has a full set of skeletal buccal pump components that can be directly compared to those of extant lungfishes, suggesting that it made more extensive use of air breathing than other Gogo or Bergisch Gladbach genera. This is interesting in relation to the environmental context as Gogo and Bergisch Gladbach are both marine, contrasting with the frequently hypoxic tropical to subtropical fresh water environments inhabited by modern lungfishes. The evolution of buccal pump-supported lung ventilation was evidently not necessarily associated with a transition to non-marine habitats.