Taxonomic Diversification Research Articles

Animal exploitation by the last hunter-gatherers in the Mediterranean Iberia. New data from the Mesolithic groups from Cocina cave (Valencia, Eastern Iberia)

Mesolithic groups in Mediterranean Iberia lived during a period of bioclimatic and cultural changes. Thus, their economic behaviour and the availability of plant and animal resources show some interesting variation compared to previous periods that indicate changes in mobility patterns and social connectivity networks. This paper presents information on patterns of animal exploitation of the last hunter-gatherers in this region through zooarchaeological and taphonomic analyses of faunal remains from one of the key sites of the Iberian Peninsular Mesolithic, Cocina cave. This site is located in a mountainous woodland region with a rich Late Mesolithic archaeological record. Results indicate that Iberian ibex, red deer, and rabbits were the most hunted species, but that a diversity of other taxa were also present. The comparison to other Mediterranean sites suggests that Late Mesolithic foragers had common animal exploitation patterns with an increased taxonomic diversification and a clear connection to coastal areas. We suggest these foragers practiced a logistic pattern of food procurement, combining long-term with short-term camps including hunting spots, and in some cases evidence for broad scale social interactions. We hypothesize that Cocina cave may have served as a nexus of social and subsistence activities.

First report of lepidocystid echinoderm in the Cambrian of North China: Evolutionary and Palaeobiogeographic implications

The diversification of the earliest echinoderms is “explosive” in both space and time. Lepidocystids are the most basal blastozoans and their earliest known occurrences (Cambrian Series 2) provide crucial evidence on the dispersal of early echinoderms. Here we report a new lepidocystid Vyscystis? spinosa sp. nov. based on well-preserved specimens from the Cambrian (Series 2, Stage 4) Mantou Formation in North China. Vyscystis? spinosa sp. nov. is characterized by a long aboral imbricate cup, flattened tessellate oral surface and coiled brachioles. The aboral cup is composed of imbricate plates with nipple-shaped ornamentation. Vyscystis? spinosa sp. nov. documents the first occurrence of lepidocystids in North China Block and thus contributes to increase the taxonomic diversity and global distribution of early blastozoans. Palaeogeographic analysis indicates that there are biogeographic connections among North China, west Gondwana and Laurentia in early Cambrian, and the palaeogeographic expansion in Cambrian eocrinoids precedes the taxonomic diversification.

Cenozoic comparisons of diversity and disparity in the context of tectonic regime: A case study in North American rodents

The tectonic evolution of landscape topography is an important driver of biotic evolution throughout Earth's history. Studies of extant diversity have shown a higher diversity of mammals in topographically complex regions, suggesting that landscape complexity plays a role in generating taxonomic diversity. However, this relationship is poorly understood, especially over geologic time scales. Previous work has posited that heterogeneous topography should lead to increased species diversity as a result of new niche spaces into which lineages may speciate. This is in comparison to homogeneous landscape topography, which offers fewer and less varied niche spaces and thus less ecological opportunities for diversification. It is also thought that barriers to species and individual movement created by mountainous landscapes may divide populations, leading to speciation by restricting gene flow. These two models can be distinguished by their effects on morphological disparity. If niche differentiation is important to the process, we would expect increased morphological disparity in association with heterogeneous landscape topography, whereas the allopatry model predicts no greater morphological disparity over the complex landscape, only taxonomic diversification. We explore these models in the tectonically active and passive regions of North America in rodents from 25 to 0 Ma. We investigate diversity and disparity trends and examine the effects of climate, landscape heterogeneity, and environmental shifts on these patterns. We find that morphological and taxonomic evolution are not impacted by topography in a predictable way, and find that homogeneous landscapes host taxonomic and morphological diversity surpassing that of heterogeneous landscapes for much of the last 19 million years in North America. Furthermore, diversity and disparity trends are both coupled and decoupled during this period, signifiying that taxonomic and morphologic increase and decrease are discordant through time. Our results support the finding that the relationship between landscape heterogeneity and species diversity has not remained constant through geologic time.

Parallel anagenetic patterns in endemic Artemisia species from three Macaronesian archipelagos.

Anagenetic speciation is an important mode of evolution in oceanic islands, yet relatively understudied compared to adaptive radiation. In the Macaronesian region, three closely related species of Artemisia (i.e. A. argentea, A. thuscula and A. gorgonum) are each endemic from a single archipelago (i.e. Madeira, Canary Islands and Cape Verde, respectively), representing a perfect opportunity to study three similar but independent anagenetic speciation processes. By analysing plastid and nuclear DNA sequences, as well as nuclear DNA amount data, generated from a comprehensive sampling in all the islands and archipelagos where these species are currently distributed, we intend to find common evolutionary patterns that help us explain the limited taxonomic diversification experienced by endemic Macaronesian Artemisia. Our time-calibrated phylogenetic reconstruction suggested that divergence among the three lineages occurred in a coincidental short period of time during the Pleistocene. Haplotype and genetic differentiation analyses showed similar diversity values among A. argentea, A. thuscula and A. gorgonum. Clear phylogeographic patterns-showing comparable genetic structuring among groups of islands-were also found within the three archipelagos. Even from the cytogenetic point of view, the three species presented similarly lower genome size values compared to the mainland closely related species A. arborescens. We hypothesize that the limited speciation experienced by the endemic Artemisia in Madeira, Canary Islands and Cape Verde archipelagos could be related to their recent parallel evolutionary histories as independent lineages, combined with certain shared characteristics of seed dispersal, pollen transport and type of habitat.

A switch in jaw form-function coupling during the evolution of mammals.

The evolutionary shift from a single-element ear, multi-element jaw to a multi-element ear, single-element jaw during the transition to crown mammals marks one of the most dramatic structural transformations in vertebrates. Research on this transformation has focused on mammalian middle-ear evolution, but a mandible comprising only the dentary is equally emblematic of this evolutionary radiation. Here, we show that the remarkably diverse jaw shapes of crown mammals are coupled with surprisingly stereotyped jaw stiffness. This strength-based morphofunctional regime has a genetic basis and allowed mammalian jaws to effectively resist deformation as they radiated into highly disparate forms with markedly distinct diets. The main functional consequences for the mandible of decoupling hearing and mastication were a trade-off between higher jaw stiffness versus decreased mechanical efficiency and speed compared with non-mammals. This fundamental and consequential shift in jaw form-function underpins the ecological and taxonomic diversification of crown mammals. This article is part of the theme issue 'The mammalian skull: development, structure and function'.

Cambrian origin but no early burst in functional disparity for Class Bivalvia.

Both the Cambrian explosion, more than half a billion years ago, and its Ordovician aftermath some 35 Myr later, are often framed as episodes of widespread ecological opportunity, but not all clades originating during this interval showed prolific rises in morphological or functional disparity. In a direct analysis of functional disparity, instead of the more commonly used proxy of morphological disparity, we find that ecological functions of Class Bivalvia arose concordantly with and even lagged behind taxonomic diversification, rather than the early-burst pattern expected for clades originating in supposedly open ecological landscapes. Unlike several other clades originating in the Cambrian explosion, the bivalves' belated acquisition of key anatomical novelties imposed a macroevolutionary lag, and even when those novelties evolved in the Early Ordovician, functional disparity never surpassed taxonomic diversity. Beyond this early period of animal evolution, the founding and subsequent diversification of new major clades and their functions might be expected to follow the pattern of the early bivalves-one where interactions between highly dynamic environmental and biotic landscapes and evolutionary contingencies need not promote prolific functional innovation.

Revisiting the Early Cretaceous sauropod Agustinia ligabuei (Dinosauria: Diplodocoidea) from southern Neuquén Basin (Patagonia, Argentina), with implications on the early evolution of rebbachisaurids

ABSTRACT The Lohan Cura Formation (Albian) at the Cerro de los Leones locality (Neuquén Province, Patagonia, Argentina) yielded several fossil materials, especially sauropod specimens. Among these, Agustinia ligabuei includes postcranial elements of a single individual, with widely debated taxonomy and phylogeny. Here, we provide an extended osteological description and illustrations of the axial and appendicular elements of Agustinia, as well as a revised diagnosis. Moreover, the phylogenetic analysis including a new combination of morphological features recognises Agustinia as a basal Rebbachisauridae, closely related with other South American rebbachisaurids. Our results suggest a more diversified sauropod fauna in the Neuquén Basin, where different members of both neosauropod lineages (i.e. Macronaria and Diplodocoidea) survived in the same region during the Albian age. The reassessment of Agustinia as a basal rebbachisaurid improves our knowledge about the early stages of evolutionary history of Rebbachisauridae, adding new information on the morphological and taxonomic diversification of the clade during the Early Cretaceous of southwestern Gondwana.

Monsoon intensification in East Asia triggered the evolution of its flora.

East Asia (EA), which falls within the region of the Asian monsoon that is composed of the East Asia monsoon (EAM) and the Indian monsoon (IM), is known for its high species diversity and endemism. This has been attributed to extreme physiographical heterogeneity in conjunction with climate and sea-level changes during the Pleistocene, this hypothesis has been widely proven by phylogeographic studies. Recently, dated phylogenies have indicated that the origins (stem age) of the flora occurred after the Oligocene-Miocene boundary and are related to the establishment of the EAM. Hence, this study further examined whether the strengthening of the monsoons triggered floral evolution via a meta-analysis of the tempo-spatial pattern of evolutionary radiation dates (crown ages) of 101 endemic seed plant genera. Taxonomic diversification began during the late Eocene, whereas the accumulated number of diversifications did not significantly accelerate until the late Miocene. The distribution of the weighted mean and the average divergence times in the EAM, IM, or transitional regions all fall within the mid-late Miocene. Fossils of the Tertiary relict genera are mostly and widely distributed outside EA and only half of the earliest fossils in the EA region are not older than Miocene, while their divergence times are mostly after the late Miocene. The pattern of divergence time of monotypic and polytypic taxa suggest the climatic changes after the late Pliocene exert more influence on monotypic taxa. The two key stages of floral evolution coincide with the intensifications of the EAM and IM, especially the summer monsoon which brings a humid climate. An integrated review of previous studies concerning flora, genus, and species levels further supports our suggestion that monsoon intensification in EA triggered the evolution of its flora.

Exceptional preservation of nonmineralized biomaterials in Cenozoic fossils of the Mammalia clade

The members of the Mammalia class experienced high ecological, morphological and taxonomic diversification during the Cenozoic Era. With technological advances in molecular paleontology in recent decades, many claims for the exceptional preservation of nonmineralized biomaterials have been made for this clade. However, these data are scattered in the literature and have associated such reports with unique and rare events. This study presents a review of the literature published in the last six decades, aiming to investigate the frequency with which vestigial of nonmineralized biomaterials are found in Mammalia fossils. The results identified 79 published studies describing endogenous biocomponents in Metatheria and Theria members. Of these, protein fragments were more frequent in sedimentary deposits (33.3%), and ancient DNA sequences were more frequent in depositional environments more favorable to exceptional preservation (53.1%), such as ice and cave deposits. The data on organic material for mammalian fossils are geographically and taxonomically comprehensive, with the superordinates Laurasiatheria and Afrotheria presenting the largest number of reports. With the emergence and improvement of new techniques for the recovery of organic material, it is believed that paleomolecular information for fossil mammals should increase, in addition to broadening the understanding of taphonomic factors related to exceptional preservation.

Biogeography and diversification of the freshwater planarian Crenobia alpina sensu lato (Platyhelminthes, Tricladida): A synthetic review

Through an in-depth study of the literature, as well as some other sources of information, geographical distribution maps of the various taxa of the European freshwater planarian genus Crenobia (Platyhelminthes, Tricladida) are provided, which document their records and distributional ranges in a detail that was previously unavailable. The genus Crenobia ranges across Northern, Western, Southern, and Eastern Europe, including several islands in the Mediterranean region, but is absent from a major part of the Iberian Peninsula; it is distributed also in Turkey. The chromosome portrait of Crenobia is complex, as it exhibits chromosome numbers that are multiples of 7, such as 28, 35, 42, 56, and 63. Sexually reproducing populations are tetraploid or hexaploid, while asexually reproducing populations exhibit high chromosome numbers. All taxa of Crenobia are stenothermic, cold-loving species. Although historical biogeographic scenarios interpreting the taxonomic diversification of the genus as being the result of the vicissitudes of the Last Ice Age are still captivating, it may be the case that the genus already diversified 6-20 million years ago. The paper sketches in some detail the anatomy of the copulatory complex of the various taxa. Previously, it went unnoticed that in two of the taxa (Crenobia alpina and C. anophthalma) the two sperm ducts have different, asymmetrical trajectories. Further, it was largely undocumented that in several taxa the sperm ducts exhibit a pronounced recurvature, as well as a dorsal loop before entering the penis papilla. Neither did previous studies document that in C. montenigrina the mouth opening is not located at the most posterior end of the pharyngeal pocket, but has shifted anteriad for some distance. Polypharyngy is a stable, species-specific character, with C. montenigrina usually exhibiting 11-17 pharynges, while C. anophthalma has never more than three pharynges. Different views have been expressed on the taxonomic status of several geographic and anatomical forms of Crenobia. It is shown here that Crenobia comprises five, well-defined full species, viz., C. alpina, C. corsica, C. montenigrina, C. anophthalma, and C. bathycola.

Spatial and taxonomic diversification for conservation investment under uncertainty

SummaryConservation organizations often need to develop risk-diversification strategies that identify not just what species to protect but also where to protect them. The objective of this research is to identify optimal conservation investment allocations for both target sites and species under conditions of uncertainty. We develop a two-step approach using modern portfolio theory (MPT) to estimate percentages of conservation investment (referred to as ‘portfolio weights’) for counties and taxonomic groups in the central and southern Appalachian region under climate and market uncertainties. The portfolio weights across the counties and taxonomic groups from the two steps entail both spatial and taxonomic diversification strategies. Conservation decisions that allow for selecting sites for risk diversification fit the purpose of the first step. Likewise, conservation investments that benefit the biodiversity of particular taxonomic groups for the selected sites are made based on the relative importance of diversifying risk among species in a given area, fitting the purpose of the second step. The two-step MPT approach as a whole allows the greatest flexibility on where and what to protect for conservation investment under uncertainty, and thus would be applicable for the distribution of general conservation funds without predisposition towards protecting either specific sites or species.

Polyploidy, genome size variation and diversification in an autopolyploid complex: the case of Turnera sidoides (Passifloraceae, Turneroideae)

Polyploidy is a major force in plant evolution. The possession of more than two chromosome complements may affect the genetic and genomic constitution and the phenotypes of polyploids, having consequences for their ecology, geography and diversification. Here, we used Turnera sidoides autopolyploid complex to assess the effect of polyploidy on genome size and on the diversification of this species. The remarkable diversity in habitat preferences, ploidy levels and multiple independent origins of polyploids, make this complex a suitable model for disentangling the effects of phylogenetic relationships and environmental conditions on the variation in genome size. We used an integrative approach comprising genome size estimations in 53 (diploid to hexaploid) populations of the different subspecies and morphotypes of T. sidoides, a molecular phylogenetic reconstruction and a biogeographical analysis to identified closely related diploids and polyploids that remained in the same habitat aiming to answer the following questions: 1) does polyploidy per se induce a significant change of the Cx-value?; 2) is the Cx-value variation an adaptive response/consequence to different environmental gradients?; and 3) does polyploidy enable the range expansion of diversified diploid lineages within the same ecoregion?. Comparisons of Cx-values among phylogenetically related diploids–polyploids provided evidence that polyploidy is not the main factor determining the Cx variation. Instead, the Cx-values varied associated with few climatic variables along latitudinal and climatic gradients, suggesting that variation in genome size would have been an adaptive response to different habitats. The analysis of the environmental preferences of diploid and polyploids within each lineage provides evidence that autopolyploidy further promoted the range expansion of the already diversified diploids. These results together with the morphological constancy among different cytotypes within lineages suggest that autopolyploidy per se did not contribute significantly to the morphological and taxonomic diversification, but enabled further range expansion of lineages within the complex.

Chromosome-Level Reference Genome Assembly for the American Pika (Ochotona princeps).

The American pika (Ochotona princeps) is an alpine lagomorph found throughout western North America. Primarily inhabiting talus slopes at higher elevations (>2000 m), American pikas are well adapted to cold, montane environments. Warming climates on both historical and contemporary scales have contributed to population declines in American pikas, positioning them as a focal mammalian species for investigating the ecological effects of climate change. To support and expand ongoing research efforts, here, we present a highly contiguous and annotated reference genome assembly for the American pika (OchPri4.0). This assembly was produced using Dovetail de novo proximity ligation methods and annotated through the NCBI Eukaryotic Genome Annotation pipeline. The resulting assembly was chromosome- scale, with a total length of 2.23 Gb across 9350 scaffolds and a scaffold N50 of 75.8 Mb. The vast majority (>97%) of the total assembly length was found within 36 large scaffolds; 33 of these scaffolds correlated to whole autosomes, while the X chromosome was covered by 3 large scaffolds. Additionally, we identified 17 enriched gene ontology terms among American pika-specific genes putatively related to adaptation to high-elevation environments. This high-quality genome assembly will serve as a springboard for exploring the evolutionary underpinnings of behavioral, ecological, and taxonomic diversification in pikas as well as broader-scale eco-evolutionary questions pertaining to cold-adapted species in general.

Historical biogeography of New World passalid beetles (Coleoptera, Passalidae) reveals Mesoamerican tropical forests as a centre of origin and taxonomic diversification

AbstractAimThe fauna of Mesoamerica is extraordinarily species rich and exhibits a high degree of local, regional and high‐elevation endemism. Traditionally, this area has been seen as a transition zone between the Nearctic and Neotropical regions; in contrast, new data suggest that Mesoamerica is a centre of origin and taxonomic diversification. For example, the diversity of species and genera of Passalidae in Mesoamerica is concentrated in montane environments and there are many locally endemic taxa; thus, Mesoamerica has been suggested as a centre of origin and taxonomic diversification for the group. However, this hypothesis has not been formally tested.LocationNew World tropics, with an emphasis on Mesoamerica.TaxonColeoptera, Passalidae (tribes Passalini and Proculini)MethodsWe studied timing and geographic patterns in the taxonomic diversification of Neotropical Passalidae. We used DNA sequence data from 3 genes (CAD, Wingless, 28S) for 93 species of Passalidae, along with information from the fossil record, to generate a time‐calibrated phylogeny for the group. Additionally, we performed Ancestral Area Estimation and Ancestral State Reconstruction of the altitudinal distribution niche.ResultsThe divergence time analyses recovered a much older estimated timing of origin and diversification events in Passalidae than previously proposed. We recovered the origins of the New World Passalidae in the late Jurassic and the split between Passalini and Proculini during the mid‐Cretaceous. Moreover, we observed congruence between timing and patterns of clade diversification and major paleogeographical events; for example, the origin and crown diversification of montane genera during the uplift and emergence of Mesoamerica from the sea.Main conclusionsOrogenic events throughout the Paleogene and Neogene played a major role in the diversification of New World Passalidae. Moreover, Nuclear and Southern Mesoamerica are centres of origin and taxonomic diversification for Proculini.

Next-Generation Camera Trapping: Systematic Review of Historic Trends Suggests Keys to Expanded Research Applications in Ecology and Conservation

Camera trapping is an effective non-invasive method for collecting data on wildlife species to address questions of ecological and conservation interest. We reviewed 2,167 camera trap (CT) articles from 1994 to 2020. Through the lens of technological diffusion, we assessed trends in: (1) CT adoption measured by published research output, (2) topic, taxonomic, and geographic diversification and composition of CT applications, and (3) sampling effort, spatial extent, and temporal duration of CT studies. Annual publications of CT articles have grown 81-fold since 1994, increasing at a rate of 1.26 (SE = 0.068) per year since 2005, but with decelerating growth since 2017. Topic, taxonomic, and geographic richness of CT studies increased to encompass 100% of topics, 59.4% of ecoregions, and 6.4% of terrestrial vertebrates. However, declines in per article rates of accretion and plateaus in Shannon'sHfor topics and major taxa studied suggest upper limits to further diversification of CT research as currently practiced. Notable compositional changes of topics included a decrease in capture-recapture, recent decrease in spatial-capture-recapture, and increases in occupancy, interspecific interactions, and automated image classification. Mammals were the dominant taxon studied; within mammalian orders carnivores exhibited a unimodal peak whereas primates, rodents and lagomorphs steadily increased. Among biogeographic realms we observed decreases in Oceania and Nearctic, increases in Afrotropic and Palearctic, and unimodal peaks for Indomalayan and Neotropic. Camera days, temporal extent, and area sampled increased, with much greater rates for the 0.90 quantile of CT studies compared to the median. Next-generation CT studies are poised to expand knowledge valuable to wildlife ecology and conservation by posing previously infeasible questions at unprecedented spatiotemporal scales, on a greater array of species, and in a wider variety of environments. Converting potential into broad-based application will require transferable models of automated image classification, and data sharing among users across multiple platforms in a coordinated manner. Further taxonomic diversification likely will require technological modifications that permit more efficient sampling of smaller species and adoption of recent improvements in modeling of unmarked populations. Environmental diversification can benefit from engineering solutions that expand ease of CT sampling in traditionally challenging sites.

Development of qPCR Detection Assay for Potato Pathogen Pectobacterium atrosepticum Based on a Unique Target Sequence.

The recent taxonomic diversification of bacterial genera Pectobacterium and Dickeya, which cause soft rot in plants, focuses attention on the need for improvement of existing methods for the detection and differentiation of these phytopathogens. This research presents a whole genome-based approach to the selection of marker sequences unique to particular species of Pectobacterium. The quantitative real-time PCR assay developed is selective in the context of all tested Pectobacterium atrosepticum strains and is able to detect fewer than 102 copies of target DNA per reaction. The presence of plant DNA extract did not affect the sensitivity of the assay.

Repeated evolution of durophagy during ichthyosaur radiation after mass extinction indicated by hidden dentition

Marine tetrapods quickly diversified and were established as marine top predators after the end-Permian Mass extinction (EPME). Ichthyosaurs were the forerunner of this rapid radiation but the main drivers of the diversification are poorly understood. Cartorhynchus lenticarpus is a basal ichthyosauriform with the least degree of aquatic adaptation, holding a key to identifying such a driver. The unique specimen appeared edentulous based on what was exposed but a CT scanning revealed that the species indeed had rounded teeth that are nearly perpendicular to the jaw rami, and thus completely concealed in lateral view. There are three dental rows per jaw ramus, and the root lacks infoldings of the dentine typical of ichthyopterygians. The well-developed and worn molariform dentition with three tooth rows supports the previous inference that the specimen is not of a juvenile. The premaxilla and the corresponding part of the dentary are edentulous. Molariform dentition evolved three to five times independently within Ichthyosauriformes in the Early and Middle Triassic. Convergent exploitation of hard-shelled invertebrates by different subclades of ichthyosauriforms likely fueled the rapid taxonomic diversification of the group after EPME.

Microphytoplankton from middle palaeolatitudes of the Southern Hemisphere – a record from climate change strata of Baltica’s O/S boundary

In the present study, data on the diversity of acritarch and prasinophyte microphytoplankton were collected from Ordovician–Silurian transitional strata at three different geological localities in Poland: southern part of the Holy Cross Mountains (Malopolska Block, southern Poland), East European Platform (Baltica), and Koszalin–Chojnice Zone (NW Poland). The material represents the mucronata (trilobite) to vesiculosus (graptolite) biozones. The Ordovician microphytoplankton assemblages are characterized by low frequency and low diversity: up to 110 specimens and 12 genera per slide, in contrast to Silurian ones that are more frequent and more diverse – >3000 specimens and 16 genera per slide (diversity at the species level is also higher). Throughout the Ordovician part of the succession, typical Ordovician genera occur, such as Acanthodiacrodium , Ordovicidium , Orthosphaeridium and large Baltisphaeridium , together with isolated occurrences of typical Silurian genera, especially in the upper part of the Hirnantian (e.g., Diexallophasis ). The Silurian assemblages are typified by high frequency of prasinophytes followed by typical Silurian acritarchs: Tylotopalla , Ammonidium , Domasia and Oppilatala . The palynological material from Poland is compared with material known from other localities: the Rapla and Valga boreholes (Estonia) and Anticosti Island (Canada), as well as others placed in different palaeocontinents and different bathymetric zones. Palynological assemblages obtained from Polish material confirm that bathymetry played the key role in taxonomic diversification of the microphytoplankton assemblage. This supports the existing models of distribution: dominance of prasinophytes (leiospheres) and cryptospores is characteristic for shallow-water environments. In deeper water, dominance of acanthomorphs is observed. In the deepest-water zones – mixed assemblages occur. For the Holy Cross Mountains, microphytoplankton frequency is compared with a TOC curve in the same interval.

Transcription Profiles of Age-at-Maturity-Associated Genes Suggest Cell Fate Commitment Regulation as a Key Factor in the Atlantic Salmon Maturation Process.

Despite recent taxonomic diversification in studies linking genotype with phenotype, follow-up studies aimed at understanding the molecular processes of such genotype-phenotype associations remain rare. The age at which an individual reaches sexual maturity is an important fitness trait in many wild species. However, the molecular mechanisms regulating maturation timing processes remain obscure. A recent genome-wide association study in Atlantic salmon (Salmo salar) identified large-effect age-at-maturity-associated chromosomal regions including genes vgll3, akap11 and six6, which have roles in adipogenesis, spermatogenesis and the hypothalamic-pituitary-gonadal (HPG) axis, respectively. Here, we determine expression patterns of these genes during salmon development and their potential molecular partners and pathways. Using Nanostring transcription profiling technology, we show development- and tissue-specific mRNA expression patterns for vgll3, akap11 and six6. Correlated expression levels of vgll3 and akap11, which have adjacent chromosomal location, suggests they may have shared regulation. Further, vgll3 correlating with arhgap6 and yap1, and akap11 with lats1 and yap1 suggests that Vgll3 and Akap11 take part in actin cytoskeleton regulation. Tissue-specific expression results indicate that vgll3 and akap11 paralogs have sex-dependent expression patterns in gonads. Moreover, six6 correlating with slc38a6 and rtn1, and Hippo signaling genes suggests that Six6 could have a broader role in the HPG neuroendrocrine and cell fate commitment regulation, respectively. We conclude that Vgll3, Akap11 and Six6 may influence Atlantic salmon maturation timing via affecting adipogenesis and gametogenesis by regulating cell fate commitment and the HPG axis. These results may help to unravel general molecular mechanisms behind maturation.

Reconstructing the archosaur radiation using a Middle Triassic archosauriform tooth assemblage from Tanzania.

Following the Permo–Triassic mass extinction, Archosauriformes—the clade that includes crocodylians, birds, and their extinct relatives outside crown Archosauria—rapidly diversified into many distinct lineages, became distributed globally, and, by the Late Triassic, filled a wide array of resource zones. Current scenarios of archosauriform evolution are ambiguous with respect to whether their taxonomic diversification in the Early–Middle Triassic coincided with the initial evolution of dietary specializations that were present by the Late Triassic or if their ecological disparity arose sometime after lineage diversification. Late Triassic archosauriform dietary specialization is recorded by morphological divergence from the plesiomorphic archosauriform tooth condition (laterally-compressed crowns with serrated carinae and a generally triangular lateral profile). Unfortunately, the roots of this diversification are poorly documented, with few known Early­–Middle Triassic tooth assemblages, limiting characterizations of morphological diversity during this critical, early period in archosaur evolution. Recent fieldwork (2007–2017) in the Middle Triassic Manda Beds of the Ruhuhu Basin, Tanzania, recovered a tooth assemblage that provides a window into this poorly sampled interval. To investigate the taxonomic composition of that collection, we built a dataset of continuous quantitative and discrete morphological characters based on in situ teeth of known taxonomic status (e.g., Nundasuchus, Parringtonia: N = 65) and a sample of isolated teeth (N = 31). Using crown heights from known taxa to predict tooth base ratio (= base length/width), we created a quantitative morphospace for the tooth assemblage. The majority of isolated, unassigned teeth fall within a region of morphospace shared by several taxa from the Manda Beds (e.g., Nundasuchus, Parringtonia); two isolated teeth fall exclusively within a “Pallisteria” morphospace. A non-metric multidimensional scaling ordination (N = 67) of 11 binary characters reduced overlap between species. The majority of the isolated teeth from the Manda assemblage fall within the Nundasuchus morphospace. This indicates these teeth are plesiomorphic for archosauriforms as Nundasuchus exhibits the predicted plesiomorphic condition of archosauriform teeth. Our model shows that the conservative tooth morphologies of archosauriforms can be differentiated and assigned to species and/or genus, rendering the model useful for identifying isolated teeth. The large overlap in tooth shape among the species present and their overall similarity indicates that dietary specialization lagged behind species diversification in archosauriforms from the Manda Beds, a pattern predicted by Simpson’s “adaptive zones” model. Although applied to a single geographic region, our methods offer a promising means to reconstruct ecological radiations and are readily transferable across a broad range of vertebrate taxa throughout Earth history.