Evolutionary Units Research Articles

Assessing evolutionary history and species boundaries in a polymorphic tropical lizard, the Aspidoscelis lineattissimus species complex (Squamata, Teiidae)

Identification of species boundaries within the genus Aspidoscelis is one of the most complex tasks in herpetological systematics due to the extensive morphological variation and complex evolutionary history involved. The whiptail lizard Aspidoscelis lineattissimus is a polymorphic species that inhabits tropical ecosystems over a wide region of western Mexico and is currently classified into four subspecies, A. l. exoristus, A. l. lineattissimus, A. l. lividus and A. l. duodecemlineatus. In this study, we used phylogenetic and coalescent-based approaches to disentangle the phylogenetic relationships among the subspecies of A. lineattissimus and to assess the level of differentiation between these subspecific taxa. We also inferred the divergence times and historical biogeography to reconstruct the evolutionary history of the A. lineattissimus complex. Three mitochondrial genes (ND4, 12S and 16S) and one nuclear exon (BACH1) were used, along with comprehensive sampling that included individuals representing the four subspecies. Coalescence analyses supported three well-differentiated lineages as independent evolutionary units, corresponding to A. l. exoristus, A. l. lineattissimus + A. l. lividus and A. l. duodecemlineatus, partially recovering the previous classification. Furthermore, phylogenetic analyses support three additional discrete lineages within A. l. duodecemlineatus. Finally, divergence time estimates and reconstructions of ancestral areas indicated that the origin and diversification of the five differentiated lineages within the A. lineattissimus complex was strongly associated with oscillations in sea level due to glacial/interglacial climatic fluctuations beginning in the Mid-Pliocene. Our research highlights the importance of phylogenetic studies within the genus Aspidoscelis to disentangle their evolutionary history and reveal hitherto underestimated diversity.

Phylogeography and evolutionary history of the Panamic Clingfish Gobiesox adustus in the Tropical Eastern Pacific

The Panamic Clingfish Gobiesox adustus is widely distributed in the Tropical Eastern Pacific (TEP), from the central Gulf of California, Mexico to Ecuador, including the oceanic Revillagigedo Archipelago, and Isla del Coco. This cryptobenthic species is restricted to very shallow rocky-reef habitats. Here, we used one mitochondrial and three nuclear DNA markers from 155 individuals collected across the distribution range of the species in order to evaluate if geographically structured populations exist and to elucidate its evolutionary history. Phylogenetic analyses recovered a monophyletic group, with four well-supported, allopatric subgroups. Each subgroup corresponded to one of the following well-known biogeographic regions/provinces: 1) the Revillagigedo Archipelago, 2) the Cortez + Mexican provinces (Mexico), 3) the Panamic province (from El Salvador to Ecuador), and 4) Isla del Coco. A molecular-clock analysis showed a mean date for the divergence between clade I (the Revillagigedos and Cortez + Mexican provinces) and clade II (Panamic province and Isla del Coco) in the Pliocene, at ca. 5.33 Mya. Within clade I, the segregation between the Revillagigedos and Cortez + Mexican province populations was dated at ca. 1.18 Mya, during the Pleistocene. Within clade II, the segregation between samples of Isla del Coco and the Panamic province samples was dated at ca. 0.77 Mya, during the Pleistocene. The species tree, Bayesian species delimitation tests (BPP and STACEY), the ΦST, AMOVA, and the substantial genetic distances that exist between those four subgroups, indicate that they are independent evolutionary units. These cladogenetic events seem to be related to habitat discontinuities, and oceanographic and geological processes that produce barriers to gene flow for G. adustus, effects of which are enhanced by the intrinsic ecological characteristics of this species.

The common bottlenose dolphin (Tursiops truncatus) ecotypes of the western North Atlantic revisited: an integrative taxonomic investigation supports the presence of distinct species

Abstract Integrative taxonomy can help us to gain a better understanding of the degree of evolutionary divergence between taxa. In the western North Atlantic (wNA), two ecotypes (coastal and offshore) of common bottlenose dolphin, Tursiops truncatus, exhibit some external morphological differences, and previous genetic findings suggested that they could be different species. However, their taxonomy remains unsettled. Using an integrative approach comparing traditional and geometric morphometrics, mitochondrial and nuclear DNA, we evaluated evolutionary relationships between these ecotypes. We observed congruence among these lines of evidence, strongly indicating that the wNA ecotypes are following distinct evolutionary trajectories. Based on mitochondrial DNA analyses, we detected significant divergence (Nei’s dA = 0.027), unshared haplotypes and one fixed difference leading to complete diagnosability (percentage diagnosable = 100%) of the wNA coastal ecotype. We found morphological diagnosability and negligible nuclear gene flow between the wNA ecotypes. Integration of these multiple lines of evidence revealed that the wNA coastal ecotype is an independent evolutionary unit, appearing to be more closely related to coastal dolphins in the Gulf of Mexico and Caribbean Sea than to their parapatric offshore neighbours, while the offshore dolphins form a relatively cohesive worldwide unit, T. truncatus. We propose that this coastal ecotype is recognized as a distinct species, resurrecting the name Tursiops erebennus.

Reassessing the systematics of Leptodeira (Serpentes, Dipsadidae) with emphasis in the South American species

AbstractWithin the diverse subfamily Dipsadinae, Imantodini represents one of the few groups distributed in North, Central and South America. The tribe comprises the genera Leptodeira and Imantodes, from which Leptodeira is the most diverse, including 15 species and 11 subspecies, distributed from southern USA to central Argentina. Taxonomy and affinities among these taxa are poorly resolved, and the phylogenetic relationships among the South American diversity were never properly assessed before. Here, we investigate the phylogenetic relationships and the taxonomic status of Leptodeira spp. based on a comprehensive multilocus dataset with emphasis in the South American radiation. Besides assessing the phylogenetic relationship and species cohesion, we also evaluate the morphological variation among the South American diversity of Leptodeira. Our results support the monophyly of Imatodini and Leptodeira, while indicating that several individuals classified as Leptodeira annulata and L. septentrionalis do not cluster together within their respective species. Moreover, specimens identified as belonging to the subspecies L. a. annulata, L. a. cussiliris, L. s. ornata and L. s. polysticta do not group together suggesting the current classification includes non‐natural groups. The analysis of morphological evidence also supports the phylogenetics results, indicating that several clades can be recognized as evolutionary units presenting distinct phenotypes. To equate the taxonomy to our results, we propose a new taxonomic arrangement for Leptodeira in which we are: (1) redefining the composition of L. annulata and L. septentrionalis; (2) elevating five subspecies to species level; (3) revalidating one species; (4) recognizing four species complexes; and (5) indicating the presence of hidden diversity (probably four undescribed species). Finally, we describe a new species (Leptodeira tarairiu sp. nov.) from the open formations of South America (Cerrado and Caatinga), and we provide detailed redescriptions for all South American species of Leptodeira.

Deep Optimisation: Transitioning the Scale of Evolutionary Search by Inducing and Searching in Deep Representations

We investigate the optimisation capabilities of an algorithm inspired by the Evolutionary Transitions in Individuality. In these transitions, the natural evolutionary process is repeatedly rescaled through successive levels of biological organisation. Each transition creates new higher-level evolutionary units that combine multiple units from the level below. We call the algorithm Deep Optimisation (DO) to recognise both its use of deep learning methods and the multi-level rescaling of biological evolutionary processes. The evolutionary model used in DO is a simple hill-climber, but, as higher-level representations are learned, the hill-climbing process is repeatedly rescaled to operate in successively higher-level representations. The transition process is based on a deep learning neural network (NN), specifically a deep auto-encoder. Our experiments with DO start with a study using the NP-hard problem, multiple knapsack (MKP). Comparing with state-of-the-art model-building optimisation algorithms (MBOAs), we show that DO finds better solutions to MKP instances and does so without using a problem-specific repair operator. A second, much more in-depth investigation uses a class of configurable problems to understand more precisely the distinct problem characteristics that DO can solve that other MBOAs cannot. Specifically, we observe a polynomial vs exponential scaling distinction where DO is the only algorithm to show polynomial scaling for all problems. We also demonstrate that some problem characteristics need a deep network in DO. In sum, our findings suggest that the use of deep learning principles have significant untapped potential in combinatorial optimisation. Moreover, we argue that natural evolution could be implementing something like DO, and the evolutionary transitions in individuality are the observable result.

As fast as a hare: Did intraspecific morphological change bring the Hallands Väderö Island population of Lepus timidus close to interspecific differences in less than 150 years?

The study of insular variation has fascinated generations of biologists and has been central to evolutionary biology at least since the time of Wallace and Darwin. In this context, using 3D geometric morphometrics, I investigate whether the population of mountain hares (Lepus timidus Linnaeus, 1758) introduced in 1857 on the Swedish island of Hallands Väderö shows distinctive traits in cranial size and shape. I find that size divergence follows the island rule, but is very small. In contrast, shape differences, compared to the mainland population, are almost as large as interspecific differences among lineages separated by hundreds of thousands of years of a largely independent evolutionary history. Even if, contrary to what is documented in the scientific literature, mountain hares were present in HV before 1857, the evolutionary history of this population could not have start earlier than the end of the last glaciation (i.e., at least one order of magnitude more recently than the separation of L. timidus from other hare species in this study). My results, thus, suggest that the insular population is a significant evolutionary unit and a potentially important component of the diversity of Swedish mountain hares. This is interesting for evolutionary biologists, but even more relevant for conservationists trying to protect the disappearing population of southern Swedish L. timidus, threatened by changes in climate and the environment, as well as by disease and the introduced European hare (Lepus europaeus Pallas, 1778). Island populations of mountain hares, thus, represent a potential source for future reintroductions on the mainland and, as my research shows, an important component of variability to maximize the preservation of the evolutionary potential in a species facing huge environmental changes.

The Evolution of Microbial Facilitation: Sociogenesis, Symbiogenesis, and Transition in Individuality

Metabolic cooperation is widespread, and it seems to be a ubiquitous and easily evolvable interaction in the microbial domain. Mutual metabolic cooperation, like syntrophy, is thought to have a crucial role in stabilizing interactions and communities, for example biofilms. Furthermore, cooperation is expected to feed back positively to the community under higher-level selection. In certain cases, cooperation can lead to a transition in individuality, when freely reproducing, unrelated entities (genes, microbes, etc.) irreversibly integrate to form a new evolutionary unit. The textbook example is endosymbiosis, prevalent among eukaryotes but virtually lacking among prokaryotes. Concerning the ubiquity of syntrophic microbial communities, it is intriguing why evolution has not lead to more transitions in individuality in the microbial domain. We set out to distinguish syntrophy-specific aspects of major transitions, to investigate why a transition in individuality within a syntrophic pair or community is so rare. We review the field of metabolic communities to identify potential evolutionary trajectories that may lead to a transition. Community properties, like joint metabolic capacity, functional profile, guild composition, assembly and interaction patterns are important concepts that may not only persist stably but according to thought-provoking theories, may provide the heritable information at a higher level of selection. We explore these ideas, relating to concepts of multilevel selection and of informational replication, to assess their relevance in the debate whether microbial communities may inherit community-level information or not.

The Italian Alpine and Subalpine trouts: Taxonomy, Evolution, and Conservation.

Simple SummaryIn a great part of the world, trout fishing has long inspired human spiritual ideals of immersion into nature and recreation, far removed from the fast-encroaching urbanization. Concurrently, these values and emotions fueled a white-hot business, establishing a florid market of outdoor recreation. Since the 20th century, the trout-culture industry strived to provide anglers with fishing entertainment by stocking massive amounts of non-native trouts in dozens of countries, irrespective of the lakes’ and rivers’ carrying capacity. This had dire consequences on the structural and functional diversity of these ecosystems. “Trout wars” sparked throughout the world between the promoters of stocking activities and the promoters of “wild trout management” and ethics. The “Italian trout war” has been fought on the harsh battleground of trout taxonomy, ecology, distribution, and native vs. non-native interfertile species. Northern Italy, home to the Italian Alpine and subalpine trouts and economic center of the national trout-culture and stocking industry, was particularly affected by this clash. We review here the state of art of this ongoing debate, outlining our scientific view of the taxonomy, evolution, distribution, and sustainable management of the native Italian trouts of northern Italy.During the last 150 years, the trout-culture industry focused on enhancing trout populations by stocking, in response to the growing anglers’ demand and the habitat degradation associated to the rapid urbanization and hydropower development. The industrialized north of Italy, home to the Italian Alpine and subalpine trout populations, is the source of most of the revenues of the national trout-culture industry. Its rapid growth, and the massive introduction of non-native interfertile trouts eroded the genetic diversity of native lineages, leading to harsh confrontations between scientists, institutions, and sportfishing associations. We review here the state of the art of the taxonomy and distribution of the northern Italian native trouts, presenting both scientific results and historical documentation. We think the only native trouts in this region are Salmo marmoratus, widespread in this region, plus small and fragmented populations of S. ghigii, present only in the South-western Alps. We strongly recommend the interruption of stocking of domesticated interfertile non-native trouts in this area, and recommend the adoption of Evolutionary Significant Units for salmonid fishery management. We further propose future research directions for a sustainable approach to the conservation and ecosystem management of the fishery resources and inland waters of northern Italy.

The right tool for the right question: contrasting biogeographic patterns in the notothenioid fish Harpagifer spp. along the Magellan Province

Molecular-based analysis has become a fundamental tool to understand the role of Quaternary glacial episodes. In the Magellan Province in southern South America, ice covering during the last glacial maximum (20 ka) radically altered the landscape/seascape, speciation rates and distribution of species. For the notothenioid fishes of the genus Harpagifer, in the area are described two nominal species. Nevertheless, this genus recently colonized South America from Antarctica, providing a short time for speciation processes. Combining DNA sequences and genotyping-by-sequencing SNPs, we evaluated the role of Quaternary glaciations over the patterns of genetic structure in Harpagifer across its distribution in the Magellan Province. DNA sequences showed low phylogeographic structure, with shared and dominant haplotypes between nominal species, suggesting a single evolutionary unit. SNPs identified contrastingly two groups in Patagonia and a third well-differentiated group in the Falkland/Malvinas Islands with limited and asymmetric gene flow. Linking the information of different markers allowed us to infer the relevance of postglacial colonization mediated by the general oceanographic circulation patterns. Contrasting rough- and fine-scale genetic patterns highlights the relevance of combined methodologies for species delimitation, which, depending on the question to be addressed, allows discrimination among phylogeographic structure, discarding incipient speciation, and contemporary spatial differentiation processes.

Design for an Individual: Connectionist Approaches to the Evolutionary Transitions in Individuality

The truly surprising thing about evolution is not how it makes individuals better adapted to their environment, but how it makes individuals. All individuals are made of parts that used to be individuals themselves, e.g., multicellular organisms from unicellular organisms. In such evolutionary transitions in individuality, the organised structure of relationships between component parts causes them to work together, creating a new organismic entity and a new evolutionary unit on which selection can act. However, the principles of these transitions remain poorly understood. In particular, the process of transition must be explained by “bottom-up” selection, i.e., on the existing lower-level evolutionary units, without presupposing the higher-level evolutionary unit we are trying to explain. In this hypothesis and theory manuscript we address the conditions for evolutionary transitions in individuality by exploiting adaptive principles already known in learning systems.Connectionistlearning models, well-studied in neural networks, demonstrate how networks of organised functional relationships between components, sufficient to exhibit information integration and collective action, can be produced via fully-distributed and unsupervised learning principles, i.e., without centralised control or an external teacher. Evolutionary connectionism translates these distributed learning principles into the domain of natural selection, and suggests how relationships among evolutionary units could become adaptively organised by selection from below without presupposing genetic relatedness or selection on collectives. In this manuscript, we address how connectionist models with a particular interaction structure might explain transitions in individuality. We explore the relationship between the interaction structures necessary for (a) evolutionary individuality (where the evolution of the whole is a non-decomposable function of the evolution of the parts), (b) organismic individuality (where the development and behaviour of the whole is a non-decomposable function of the behaviour of component parts) and (c) non-linearly separable functions, familiar in connectionist models (where the output of the network is a non-decomposable function of the inputs). Specifically, we hypothesise that the conditions necessary to evolve a new level of individuality are described by the conditions necessary to learn non-decomposable functions of this type (or deep model induction) familiar in connectionist models of cognition and learning.

Phylogeographical Analyses of a Relict Fern of Palaeotropical Flora (Vandenboschia speciosa): Distribution and Diversity Model in Relation to the Geological and Climate Events of the Late Miocene and Early Pliocene.

Fern phylogeographic studies have mostly focused on the influence of the Pleistocene climate on fern distributions and the prevalence of long-distance dispersal. The effect of pre-Pleistocene events on the distributions of fern species is largely unexplored. Here, we elucidate a hypothetical scenario for the evolutionary history of Vandenboschia speciosa, hypothesised to be of Tertiary palaeotropical flora with a peculiar perennial gametophyte. We sequenced 40 populations across the species range in one plastid region and two variants of the nuclear gapCp gene and conducted time-calibrated phylogenetic, phylogeographical, and species distribution modelling analyses. Vandenboschia speciosa is an allopolyploid and had a Tertiary origin. Late Miocene aridification possibly caused the long persistence in independent refugia on the Eurosiberian Atlantic and Mediterranean coasts, with the independent evolution of gene pools resulting in two evolutionary units. The Cantabrian Cornice, a major refugium, could also be a secondary contact zone during Quaternary glacial cycles. Central European populations resulted from multiple post-glacial, long-distance dispersals. Vandenboschia speciosa reached Macaronesia during the Pliocene–Pleistocene, with a phylogeographical link between the Canary Islands, Madeira, and southern Iberia, and between the Azores and northwestern Europe. Our results support the idea that the geological and climate events of the Late Miocene/Early Pliocene shifted Tertiary fern distribution patterns in Europe.

Teacher Institute for Evolutionary Science

While evolution is widely and confidently taught in high schools across the country, there are some educators who struggle with the topic. There are a variety of reasons for this. Some states prohibit the teaching of evolution in public schools, and sometimes teachers lack the background knowledge on the topic, while others simply choose not to contend with the possibility of pushback from the community. Middle and elementary school teachers are the most likely to lack coursework and training to teach evolution.The Teacher Institute for Evolutionary Science (TIES) is a teacher-led organization that was started for the sole purpose of creating and curating quality, free resources to teachers who are teaching evolution. Their mission is to provide elementary and middle school teachers the tools they need to effectively teach evolution and answer its critics based on the Next Generation Science Standards. There is a team of over 80 teachers who contribute to TIES, testing, writing, and recommending educational materials, as well as conducting professional development workshops to help support science teachers at all levels.The website is organized with nine pages: About, Teacher Materials, Workshops, Online Workshops, TIES book, Webinars, TIES TiPs, Contribute Resources, and Join TIES. The Teacher Materials page contains dozens of resources of all varieties. There are complete evolutionary biology units for middle school and high school (in both English and Spanish) that can be delivered in person or completely virtually. The Ready-To-Go evolution units have a collection of activities and notes that any science teacher can use to effectively address all the NGSS middle and high school evolution standards. Answer keys are provided on request.The Ready-To-Go unit for grades 6–8 includes three bell-ringer activities, classroom presentation with all essential vocabulary, background on the work of Charles Darwin, evidence of evolution and natural selection, and links to extension activities. There is also an assortment of hands-on investigations that provide notes and support for teachers, regardless of their expertise, to facilitate hands-on evolution simulations. These include lab activities where students simulate the natural selection of bird beaks and coloration of peppered moths. There are also online games that have been vetted by experienced life science teachers along with general online resources for teaching evolution.The site also has Ready-To-Go units for high school and elementary grades (3–5) that address all the NGSS LS4-Biological Evolution: Unity and Diversity standards.On the workshop page, users will find upcoming and past TIES workshops. There is a recorded workshop that walks the viewer through how to use the entire Ready-To-Go unit with all the supplemental materials linked on the online workshops page. The TIES book with all of its resources can be found on the TIES book page. Additionally, there are recorded and upcoming webinars from presentations by classroom teachers, scientists, and authors. These webinars would be helpful to teachers who are looking to refresh their content knowledge or to learn more about current research in the field of evolutionary science.From complete units to individual activities and professional learning, the Teacher Institute for Evolutionary Science has something for every biology, middle school, and elementary teacher to make sure their students have a deep and comprehensive understanding of evolution.

Revisiting taxonomic disparities in the genus Naemorhedus: new insights from Indian Himalayan Region

Abstract Gorals are distributed in varied ranges of habitats in South and South–East Asia, and the existence of the number of species in the genus Naemorhedus has been greatly debated from time to time. A school of thought supports the presence of three species, while a recent genetic study recognizes five species of goral throughout their distribution range. However, the unavailability of DNA sequences of gorals from India left a gap in understanding the species occurrence in Indian Himalayan Region (IHR). We revisited goral taxonomy by sequencing mitochondrial Cytochrome b gene (∼404 bp) and control region (∼225 bp) of 75 Himalayan gorals from Western and Central Himalayas in India. Based on various species delineating methods, we suggest that Himalayan goral (N. goral) is a highly diverged species and possibly exists into two subspecies, i.e. N. g. bedfordi in Western Himalayas and N. g. goral in the Central Himalayas. We validate the presence of plausibly six species of gorals across the distribution and recognize N. griseus and N. goral are two distinct species considering the observed discrepancy in the available sequences. We also propose that goral populations distributed in Western and Central Himalayas may be considered as two evolutionary significant units (ESUs). This recognition will bring concentrated efforts in further exploring the natural populations and ecological information required for prioritizing conservation and management of Himalayan goral.

Implications on the Use of the Phylogenetic Species Concept in the Risk Categories Assignment: The Case of the Birds of Mexico

Background and Aims Conservation efforts require a rational basis for taxa prioritization; it is essential to recognize the evolutionary independence of units, typically recognized as species. Because different criteria on species limits lead to different conservation assessment priorities, conceptual problems limit the possibility to accurately assess the conservation status that species are undergoing to protect them effectively. Methods We analyze the implications of using the phylogenetic species concept (PSC) in the risk categories determination, based on the analysis of the Mexican endemic avifauna. We modeled the potential distribution areas with the MaxEnt algorithm for those species that have had or could be susceptible to taxonomic updates based on the PSC. Results Of the 93 studied species, 68 were highly restricted, and 23 have high scores according to the evaluation of the Partners In Flight conservation status, so they can be considered species with high vulnerability or risk of extinction. Additionally, based on the recognition of several allopatric populations as independent phylogenetic species, 45% are susceptible to reconsideration of their risk categories due to a decrease in the extent of areas where they are potentially distributed. Implications for Conservation The use of a taxonomic perspective focused on the phylogenetic relationship of the different populations would directly impact the definition of risk categories, particularly for those endemic or restricted distribution evolutionary units for which there is usually very little information available and which, undoubtedly, are the ones that most need to be studied and, particularly, protected.

An Integrated Taxonomic Approach Points towards a Single-Species Hypothesis for Santolina (Asteraceae) in Corsica and Sardinia.

Simple SummarySystematics is the branch of biology that studies the relationships among organisms and their evolution, while taxonomy is the science of classification. In this work, a systematic and taxonomic investigation about three plant species of Santolina, commonly known as lavender-cotton, is presented. Two of these species occur exclusively in Corsica and Sardinia, two of the main islands of the Mediterranean Sea, while a third one is a common ornamental plant, known only as cultivated. By integrating several approaches, we find out that the two putative species from Corsica and Sardinia are actually very similar from many points of view. A two-species hypothesis is no longer supported according to our results, so that these plants should be reclassified as a single species. This study demonstrates the importance of integrating different sources of information to produce reliable classifications (i.e. taxonomic hypotheses). In addition, our study is useful to better understand plant evolution in the context of the Mediterranean Basin, one of the world’s biodiversity hotspots.Santolina is a plant genus of dwarf aromatic shrubs that includes about 26 species native to the western Mediterranean Basin. In Corsica and Sardinia, two of the main islands of the Mediterranean, Santolina corsica (tetraploid) and S. insularis (hexaploid) are reported. Along with the cultivated pentaploid S. chamaecyparissus, these species form a group of taxa that is hard to distinguish only by morphology. Molecular (using ITS, trnH-psbA, trnL-trnF, trnQ-rps16, rps15-ycf1, psbM-trnD, and trnS-trnG), cypsela morpho-colorimetric, morphometric, and niche similarity analyses were conducted to investigate the diversity of plants belonging to this species group. Our results confute the current taxonomic hypothesis and suggest considering S. corsica and S. insularis as a single species. Moreover, molecular and morphometric results highlight the strong affinity between S. chamaecyparissus and the Santolina populations endemic to Corsica and Sardinia. Finally, the populations from south-western Sardinia, due to their high differentiation in the studied plastid markers and the different climatic niche with respect to all the other populations, could be considered as an evolutionary significant unit.

Deciphering the morphological variation and its ontogenetic dynamics in the Late Devonian conodont Icriodus alternatus

Identification of relevant taxonomic and evolutionary units is a recurrent issue in the fossil record, and all the more for ancient fossils devoid of modern equivalents such as conodonts. Extensive morphological variation has often led to the description of numerous species, subspecies or morphotypes, which may correspond to end-member morphologies reached through ontogeny. The platform elements of the Late Devonian conodont speciesIcriodus alternatuswere characterized by rows of denticles coming into occlusion between opposite elements; each element grew by the incremental addition of lamellae and by the addition of successive triads during ontogeny. During the late Frasnian and the early Famennian, the important morphological variation within this species led to the description of three subspecies. An extensive sample of early FamennianIcriodus alternatuswas quantified using 2D biometric measurements and denticle counts on 2D pictures, showing that the subspecies mainly differed in their size range but not in their general morphology. A 3D morphometric analysis was further performed on a subsample to characterize the shape of the ontogenetically older part of the elements. During ontogeny, early valleys between denticles tended to be filled, and the asymmetry between the inner and outer side of the element increased. These ontogenetic trends are responsible for the morphologies formerly described as the subspeciesIc. alt. mawsonaeandIc. alt. helmsi. Slight discrepancies between temporal ranges of the subspecies may be achieved through variations in range of size reached by the elements as a response to environmental changes. Disparity along ontogeny seems to follow an “hourglass model” suggesting a shift from relatively loose developmental constraints to a pattern of growth modulated by functional constraints during occlusion.

Defining Management Units for Wild Nile Tilapia Oreochromis niloticus from Nine River Basins in Ghana

Despite the global importance of the Nile tilapia Oreochromis niloticus, especially to aquaculture, knowledge of genetic variability within native populations is still limited. While several studies have assessed genetic differentiation across the major drainage basins of Africa, relatively little effort has focused on characterizing genetic differentiation at finer scales. We assessed genetic variation in O. niloticus within and among nine drainage basins in Ghana using nuclear microsatellite DNA markers as the basis for identifying potential units of conservation among wild populations. We screened 312 wild individuals using eight nuclear microsatellite DNA markers. We found moderate genetic diversity within and differentiation among all wild populations studied, with strong signals of recent demographic bottlenecks in several populations. Genetic structure among 11 populations suggested the presence of up to ten management units (MUs). In particular, the Black Volta and the Tano–Asuhyea populations, which were the most genetically distinct and geographically isolated and may be most at risk of loss of genetic diversity over time, may well represent evolutionary significant units. Therefore, at the minimum, the Black Volta and Tano–Asuhyea populations should be prioritized for conservation actions to sustain them over the long-term.

Uncovering Hidden Diversity: Three New Species of the Keratella Genus (Rotifera, Monogononta, Brachionidae) of High Altitude Water Systems from Central Mexico

The correct identification of species is an essential step before any study on biodiversity, ecology or genetics. Keratella is a genus with a predominantly temperate distribution and with several species being endemics or restricted geographically. Its diversity may be underestimated considering the confusing taxonomy of species complexes such as K. cochlearis. In this study, we examined genetic diversity and morphology among some Keratella populations from Mexico in order to determine if these populations represent different species. We analyzed a dataset of previously published and newly generated sequences of the mitochondrial COI gene and the nuclear ITS1 marker. We conducted phylogenetic analyses and applied three methods of species delimitation (ABGD, PTP and GMYC) to identify evolutionary significant units (ESUs) equivalent to species. Morphological analyses were conducted through scanning electron microscope (SEM) and morphometry under a compound microscope. In the present study, three new species Keratella cuitzeiensis sp. nov., Keratella huapanguensis sp. nov., and Keratella albertae sp. nov., are formally described. These species were collected in high-altitude water bodies located in the Central Plateau of Mexico. Combining DNA results through COI and ITS1 molecular markers and morphology it was possible to confirm the identity of the new species.

The mitochondrial genome of the endangered Spiny Butterfly Ray Gymnura altavela (Linnaeus 1758) (Myliobatiformes: Gymnuridae) provides insights into cryptic lineages

The Spiny Butterfly Ray, Gymnura altavela, is found in tropical and temperate coastal waters with a discontinuous distribution: it occurs along the east coast of the United States of America, Brazil, and Uruguay in the western Atlantic Ocean, from Portugal to Angola in the eastern Atlantic, and also in the Mediterranean Sea. Globally, Gymnura altavela is considered endangered by the International Union for Conservation of Nature (IUCN). Our study analyzed the complete mitochondrial genome of G. altavela sequenced from an individual captured in the western Atlantic and compared it with a mitochondrial genome from a conspecific collected in the Mediterranean to explore if G. altavela comprises cryptic species. The newly assembled mitochondrial genome of G. altavela is 19,361bp in length and has 13 protein-coding genes (PCGs), two ribosomal RNA genes (12s ribosomal RNA and 16s ribosomal RNA), 22 transfer RNA (tRNA) genes, and a 3,659 bp control region. The gene order is identical to that reported for the specimen collected in the Mediterranean and that of the congeneric Long-tailed Butterfly Ray, G. poecilura. A phylomitogenomic analysis based on translated PCGs supported the monophyly of the genus Gymnura and indicated that genetic dissimilarity between G. altavela from the western Atlantic Ocean and the Mediterranean Sea was greater than that calculated among congeneric species belonging to the genera Mobula and Neotrygon, similar to that calculated among congeneric stingrays in the genus Hemitrygon, but lower than that calculated among congeneric species in the genera Pateobatis and Urogymnus. Overall, our comparisons suggest that G. altavela comprises cryptic species or at least indicates considerable genetic structure between populations in the western Atlantic and Mediterranean. We present these findings in a phylomitogenomic analysis of other Myliobatiformes and Rhinopristiformes. Additional phylogeographic and taxonomic studies of G. altavela are needed to support conservation efforts for this endangered ray that may comprise cryptic evolutionary units.

Phylogeographic advances in midwife toads ( Alytes ) support the existence of a novel taxon endemic to the Central Pyrenees

Although necessary to promote conservation, defining evolutionary units and naming biodiversity remain a difficult task, especially in problematic species groups that experienced a dynamic biogeographic history. In this article, we undertake such task for midwife toads of the Alytes obstetricans complex by integrating recent molecular studies altogether—multilocus phylogenies and population genetic barcoding. Despite a partly unresolved phylogeny underlain by deep cyto-nuclear discordances, nuclear and mitochondrial evidence support the validity of six genuine lineages assigned to two different species (A. obstetricans and A. almogavarii), which could be accurately mapped across most of their ranges. In particular, we demonstrate the existence for an overlooked yet genetically distinct lineage previously confounded with A. almogavarii, confined to the northern part of Huesca Province in the Spanish Central Pyrenees. We describe this micro-endemic as the subspecies Alytes almogavarii inigoi ssp. nov., with reports on the mating call and the larvae. Conservation genetics of eight populations of this new taxon revealed two independent conservation units, separated by topographic barriers. In the wait for upcoming genomic analyses to unravel many elusive aspects of the evolution, diversity and systematics of Alytes, the present paper offers an integrative phylogeographic overview to guide future investigations and generally illustrates how multiple lines of molecular evidence can be combined to clarify the confusing taxonomy of complex species groups.