Systematics Research Research Articles

Characterization of the plastid and mitochondrial genomes of Aeschynomene indica (Fabaceae)

The current study undertook a detailed analysis of both the plastid and mitochondrial genomes (plastome and mitogenome) of Aeschynomene indica (Fabaceae), a plant notable both as a problematic weed in global rice cultivation and for its medicinal properties. The primary goal was to furnish comprehensive organelle genome resources and explore genomic characteristics. A sample of A. indica was collected and sequenced using a next-generation sequencing technique. The resulting plastome is 160,502 base pairs (bp) long and includes 128 genes—comprising 83 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The plastome displays a typical quadripartite structure consisting of a large single-copy region (89,347 bp), a small single-copy region (19,803 bp), and two inverted repeat regions (each 25,676 bp). The mitogenome spans 388,249 bp and contains 57 genes, which include 34 protein-coding genes, 20 tRNA genes, and four rRNA genes. Phylogenetic analyses leveraging these organelle genome sequences produced well-resolved trees, elucidating the phylogenetic position of A. indica within the Fabaceae. The organelle genomes of A. indica presented in this study offer valuable genomic resources that will facilitate further research in plant systematics and biotechnology.

Complete Chloroplast Genome of Krascheninnikovia ewersmanniana: Comparative and Phylogenetic Analysis.

Krascheninnikovia ewersmanniana is a dominant desert shrub in Xinjiang, China, with high economic and ecological value. However, molecular systematics research on K. ewersmanniana is lacking. To resolve the genetic composition of K. ewersmanniana within Amaranthaceae and its systematic relationship with related genera, we used a second-generation Illumina sequencing system to detect the chloroplast genome of K. ewersmanniana and analyze its assembly, annotation, and phylogenetics. Total length of the chloroplast genome of K. ewersmanniana reached 152,287 bp, with 84 protein-coding genes, 36 tRNAs, and eight rRNAs. Codon usage analysis showed the majority of codons ending with base A/U. Mononucleotide repeats were the most common (85.42%) of the four identified simple sequence repeats. A comparison with chloroplast genomes of six other Amaranthaceae species indicated contraction and expansion of the inverted repeat boundary region in K. ewersmanniana, with some genes (rps19, ndhF, ycf1) differing in length and distribution. Among the seven species, the variation in non-coding regions was greater. Phylogenetic analysis revealed Krascheninnikovia ceratoides, Dysphania ambrosioides, Dysphania pumilio, and Dysphania botrys to have a close monophyletic relationship. By sequencing the K. ewersmanniana chloroplast genome, this research resolves the relatedness among 35 Amaranthaceae species, providing molecular insights for germplasm utilization, and theoretical support for studying evolutionary relationships.

From Galls to Cecidological Herbaria: The Role of Gall Collections in Modern Life Sciences.

Galls (also known as cecidia) have been studied by botanists, zoologists and microbiologists over the last century. Indeed, galls can be induced by different animals, bacteria, viruses and fungi, so that their presence simultaneously attested the presence of specific host plants and gall-inducing species. Consequently, gall collections, also known as cecidological herbaria or cecidological collections, can be interesting to study biodiversity changes over time. This review describes the main cecidological collections currently available in different European museums in order to stimulate their future study. The present analysis suggests that well-organized and preserved cecidological collections have great potential to guide research in taxonomy and systematics. Furthermore, this review aims to encourage future research on the conservation and digitisation standards of gall specimens in order to make cecidological data more accessible to researchers.

Chondrichthyan systematics in Brazil depicted: historical overview, research trends and future perspectives

Abstract Brazil comprises one of the world’s biodiversity hotspots of the chondrichthyan fauna, currently with 12 orders, 44 families, 90 genera and over 200 species of sharks, batoids, and chimaeras. These species inhabit marine, estuarine and freshwater realms of coastal and oceanic zones from the North equatorial central to the South-western Atlantic Ocean. Reporting on species occurrence in Brazil goes back to the pre-Linnaean Period. The golden era of the European Zoological studies put in place the knowledge on the local fauna with many Brazilian endemic and native species being officially described. The birth of Ichthyology in Brazil in the early 20th century, however, represents the milestone for the Chondrichthyan Systematics in the country when national scientists published the first list of species. This study provides an historical overview of the Chondrichthyan Systematics research in Brazil through a literature review of peer-reviewed publications in shark taxonomy, phylogenetics and morphology. Scientific trends of over 120-year period of dedicated investigations are herein pointed out regarding research scope and subject area, methodology, target study taxa, and gender diversity. Research recommendations and priorities are further given to assist researchers and interested stakeholders on future efforts in shark science and conservation in the country.

Ecology, evolution, and conservation of Ethiopia’s biodiversity

Ethiopia is home to one of the richest and most unique assemblages of fauna and flora on the African continent. Contained within its borders are two major centers of endemism, the mesic Roof of Africa (also known as the Ethiopian Highlands) and the arid Horn of Africa, resulting from the country’s varied topography and consequent geographic isolation. These centers of endemism are crucial to global conservation as evidenced by their classification within the Eastern Afromontane and Horn of Africa biodiversity hotspots, respectively. Ethiopia’s diverse ecosystems and the biodiversity they contain are increasingly threatened by climate change and the growing impacts of Africa’s second largest human and largest livestock populations. In this paper, we focus on several key areas of recent and ongoing research on Ethiopian biodiversity that have broadened our understanding of nature and its conservation in Africa. Topics explored include the behavioral ecology of Ethiopia’s large social mammals, the ecology and conservation of its unique coffee forests, and Ethiopian approaches to community conservation, fortress conservation, and nature-based solutions. We also highlight the increasing prominence of Ethiopian scientists in studies of the country’s biodiversity in recent decades. We suggest promising avenues for future research in evolutionary biology, ecology, systematics, and conservation in Ethiopia and discuss how recent and ongoing work in Ethiopia is helping us better understand and conserve nature in the human-dominated landscapes of Africa and other tropical regions today.

The seven grand challenges in arachnid science

This perspective identifies the grand challenges in arachnid science: 1. Grasp the arachnid species diversity. There is a need to accelerate taxonomic research to obtain a sense of arachnid species diversity, however, at the same time, taxonomy needs to increase its quality, rigor, and repeatability. 2. Standardize arachnid systematics research. A solid phylogenetic definition and morphological diagnosis of Arachnida and its composing subgroups, usually treated at the rank of order, are needed. Studies should aim to stabilize and standardize phylogenetic efforts at all levels of hierarchy, and systematists should adopt criteria for higher level ranks in arachnid classification. 3. Interpret arachnid trait evolution through omics approaches. Among the field’s grand challenges is to define the genetic diversity encoding for the diverse arachnid traits, including developmental, morphological and ecological characteristics, biomaterials such as silks, venoms, digestive fluids, or allergens and bioproducts that cause diseases. Comparative genomics, transcriptomics, and proteomics will provide the empirical basis for biotechnology to modify arachnid genomes to fit numerous applications. 4. Facilitate biotechnological applications of arachnid molecules and biomaterials. Among the grand field challenges is to define potential applications of arachnid bioproducts from therapeutics to industry. New natural and biodegradable products, e.g. from spider silks, should ease our burden on ecosystems. 5. Utilize arachnids as models in ecological and biogeographic research. Biodiversity inventory sampling and analytical techniques should be extended from spiders to other arachnid groups. Spiders and their webs could be used as environmental DNA samplers, measuring or monitoring ecosystems’ overall biodiversity. Arachnids are excellent models to address biogeographical questions at the global to local scales. 6. Disentangle evolutionary drivers of arachnid diversity. Among the field grand challenges is a more precise evaluation to what extent the emergence of arachnid phenotypes is shaped by classical selection processes, and under what conditions, if any, sexual conflict needs to be invoked. 7. Define effective conservation measures for arachnids in the light of global changes. Effective conservation measures in arachnology should integrate the data from phylogenetic diversity, physiology, ecology, biogeography, and global change biology.

An open and continuously updated fern tree of life.

Ferns, with about 12,000 species, are the second most diverse lineage of vascular plants after angiosperms. They have been the subject of numerous molecular phylogenetic studies, resulting in the publication of trees for every major clade and DNA sequences from nearly half of all species. Global fern phylogenies have been published periodically, but as molecular systematics research continues at a rapid pace, these become quickly outdated. Here, we develop a mostly automated, reproducible, open pipeline to generate a continuously updated fern tree of life (FTOL) from DNA sequence data available in GenBank. Our tailored sampling strategy combines whole plastomes (few taxa, many loci) with commonly sequenced plastid regions (many taxa, few loci) to obtain a global, species-level fern phylogeny with high resolution along the backbone and maximal sampling across the tips. We use a curated reference taxonomy to resolve synonyms in general compliance with the community-driven Pteridophyte Phylogeny Group I classification. The current FTOL includes 5,582 species, an increase of ca. 40% relative to the most recently published global fern phylogeny. Using an updated and expanded list of 51 fern fossil constraints, we find estimated ages for most families and deeper clades to be considerably older than earlier studies. FTOL and its accompanying datasets, including the fossil list and taxonomic database, will be updated on a regular basis and are available via a web portal (https://fernphy.github.io) and R packages, enabling immediate access to the most up-to-date, comprehensively sampled fern phylogeny. FTOL will be useful for anyone studying this important group of plants over a wide range of taxonomic scales, from smaller clades to the entire tree. We anticipate FTOL will be particularly relevant for macroecological studies at regional to global scales and will inform future taxonomic systems with the most recent hypothesis of fern phylogeny.

The Bricolage of Pig Genomics

The history of genomic research on the pig (Sus scrofa)—as uncovered through archival research, oral histories, and the analysis of a quantitative dataset and co-authorship network—demonstrates the importance of two distinct genealogies. These consist of research programs focused on agriculturally oriented genetics, on the one hand, and systematics research concerned with evolution and diversity, on the other. The relative weight of these two modes of research shifted following the production of a reference genome for the species from 2006 to 2011. Before this inflection point, the research captured in our networks mainly involved intensive sequencing that concentrated primarily on increasing the resolution of genomic data both in particular regions and more widely across the genome. Sequencing practices later became more extensive, with greater focus on the generation and comparison of sequence data across and between populations. We explain these shifts in research modes as a function of the availability, circulation, distribution, and exchange of genomic tools and resources—including data and materials—concerning the pig in general, and increasingly for particular populations. Consequently, we describe the history of pig genomics as constituting a kind of bricolage, in which geneticists cobbled together resources to which they had access—often ones produced by them for other purposes—in pursuit of their research aims. The concept of bricolage adds to the thicker vision of genomics that we have shown throughout the special issue and further highlights the singularity of the dominant, thin narrative focused on the production of the human reference sequence at large-scale genome centers. This essay is part of a special issue entitled The Sequences and the Sequencers: A New Approach to Investigating the Emergence of Yeast, Human, and Pig Genomics, edited by Miguel García-Sancho and James Lowe.

About the Authors

About the Authors

Evolution in the Model Genus Antirrhinum Based on Phylogenomics of Topotypic Material.

Researchers in phylogenetic systematics typically choose a few individual representatives of every species for sequencing based on convenience (neighboring populations, herbarium specimens, samples provided by experts, garden plants). However, few studies are based on original material, type material or topotypic material (living specimens from the locality where the type material was collected). The use of type or topotypic material in phylogenetic studies is paramount particularly when taxonomy is complex, such as that of Antirrhinum (Plantaginaceae). In this paper, we used topotypic materials of Antirrhinum at the species level (34 species proposed by previous authors), 87 specimens representing the species distributions and >50,000 informative nucleotide characters (from ∼4,000 loci) generated by the genotyping-by-sequencing (GBS) technique: (i) to test two explicit taxonomic hypotheses widely followed by local taxonomic treatments; (ii) to robustly estimate phylogenetic relationships; (iii) to investigate the evolution of key morphological characters and biogeographic centers of differentiation. Two GBS phylogenies based on two datasets (87 localities and 34 topotypic specimens) revealed that: (1) Sutton’s (1988) taxonomic account is the most congruent with phylogenetic results, whereas division of Antirrhinum into three major clades disagrees with Rothmaler’s (1956) infrageneric classification; (2) monophyly of populations currently included in the same species is primarily supported; (3) the historically recognized Antirrhinum majus group is not monophyletic; (4) sister-group relationships are robust for eight species pairs; (5) the evolutionary radiation of 26 species since the Pliocene is underpinned given a high rate of diversification (0.54 spp. Myr–1); (6) a geographic pattern of speciation is reconstructed, with northern Iberia as the center of early diversification followed by more recent speciation in southeastern Iberia; and (7) multiple acquisitions of key taxonomic characters in the course of Antirrhinum diversification are strongly supported, with no evidence of hybridization between major clades. Our results also suggest incipient speciation in some geographic areas and point to future avenues of research in evolution and systematics of Antirrhinum.

Updated Checklist of the Benthic Marine Macroalgae of the Philippines

Records of taxa of benthic marine macroalgae in the Philippines continue to increase as molecularbased biodiversity and systematics research involving seaweed specimens collected from various localities in the country continue to grow. Several molecular systematics studies on seaweeds within the last decade also resulted in taxonomic, nomenclatural, and classification changes, consequently affecting our knowledge and understanding of the biodiversity of the Philippine seaweed flora. Moreover, global efforts to make biodiversity resources that are deposited in various herbaria openly available through online databases provide a good opportunity to reassess our current foundational biodiversity knowledge on these ecologically and economically important marine resources. Herein, we provide an updated checklist of Philippine seaweeds by integrating results of recent biodiversity and systematics studies and by perusing open-access records of seaweeds collected from the Philippines that are deposited in foreign herbaria and/or found in online databases. We report a total of 1,065 seaweed taxa in the Philippines; this is composed primarily of 600 red seaweed taxa (Florideophyceae and Bangiophyceae, Rhodophyta), followed by 272 green seaweed taxa (Ulvophyceae, Chlorophyta), and by 193 brown seaweed taxa (Phaeophyceae, Ochrophyta). We added a total of 104 new records (including recently described species) to the latest checklist on Philippine seaweeds in 2013, more than half of which were derived from records of the collections deposited in foreign herbaria. The latter highlights the need to make herbarium collection records accessible and underscores the important role of herbaria (and museums in general) in documenting and preserving biodiversity resources of biodiversity hotspot areas such as the Philippines. We also reiterate here the call to increase support in building local expertise and funding on marine (seaweed) biodiversity and systematics research as these are crucial not only in documenting and conserving our marine biodiversity resources but also in developing them for their socio-economic values.

The geography of follicle pubescence in the Physocarpus opulifolius (Rosaceae) complex1,2

Taxonomic circumscription is a critical prerequisite for ecological, taxonomic, and systematics research but can be complicated by undetected patterns in morphological variation. Cryptic variation has long confounded the taxonomy of Physocarpus (Cambess.) Raf., with conflicting circumscriptions especially prevalent in the Physocarpus opulifolius (L.) Maxim. complex, which comprises P. opulifolius sensu stricto and Physocarpus intermedius (Rydb.) C.K.Schneid. Here, we assess variation for carpel and follicle pubescence, a key diagnostic character for the P. opulifolius s.l. complex. Data were collected from 748 herbarium accessions obtained from across the range of this complex in North America. We then assessed the statistical and geographic distribution of this variation. As suggested by Rydberg and others, follicle pubescence is bimodally distributed and exhibits a strong geographic signal. An eastern, glabrous (or nearly so) form occurs in temperate forests from the St. Lawrence River valley of Quebec west to the Upper Great Lakes region and south to the southern Appalachians (i.e., P. opulifolius s.s.), while a more western, densely pubescent form occurs from the Interior Highlands north to the Driftless Area, with disjunct populations in the Southeastern Plains of Alabama, Sand Hills of Nebraska, Black Hills of South Dakota, Front Range of Colorado, and Sierra Madre Oriental of northeastern Mexico (i.e., P. intermedius). We conclude that taxonomic recognition is warranted based on variation in follicle pubescence, which also has implications for downstream research (e.g., floristics, phylogenetics, and ecological niche modeling).

Molecular systematics, species limits, and diversification of the genus Dendrocolaptes (Aves: Furnariidae): Insights on biotic exchanges between dry and humid forest types in the Neotropics

The true diversity and interspecific limits in the Neotropical endemic avian genus Dendrocolaptes (Furnariidae) remain a highly controversial subject, with previous genus-wide assessments, based mostly on morphological characters, producing poorly resolved phylogenies. The lack of well-resolved, robust, and taxonomically densely sampled phylogenies for Dendrocolaptes prevents reliable inferences on the genus’ actual species diversity and evolutionary history. Here, we analyzed 2,741 base pairs of mitochondrial and nuclear genes from 43 specimens belonging to all species and the majority of subspecies described for Dendrocolaptes to evaluate species limits and reconstruct its diversification through time. Our phylogenies recovered a monophyletic Dendrocolaptes, with two main highly supported internal clades corresponding to the D. certhia and D. picumnus species complexes. Also, our analyses supported the monophyly of most Dendrocolaptes species recognized today, except D. picumnus, which was consistently recovered as paraphyletic with respect to D. hoffmannsi. A coalescent-based test supported a total of 15 different lineages in Dendrocolaptes and indicated that the number of currently accepted species within the genus may be greatly underestimated. Particularly relevant, when combined with previous analyses based on plumage characters, comparative high levels of genetic differentiation and coalescent analyses support the recognition of D. picumnus transfasciatus as a full species that is already under threat. Ancestral area reconstructions suggest that diversification in Dendrocolaptes was centered in lowland Amazonia, with several independent dispersal events leading to differentiation into different adjacent dry and high elevation forest types throughout the Neotropics, mainly during the Middle and Late Pleistocene. © 2020 The Authors. Journal of Zoological Systematics and Evolutionary Research published by Blackwell Verlag GmbH

Scientific achievements of the last 60 years: From a single to a multispecies concept of the genus Trichinella

The scientific basis that led to the development of a multispecies concept within the Trichinella genus originated in the 1950s, when scientists began reporting an increasing number of host-specific peculiarities among different geographic isolates. This led to speculation that important geographic variability existed within Trichinella spiralis, the only species in the genus at that time. Comparative infection results sparked great interest among investigators and led to similar studies using various geographic isolates of the parasite. In 1972, the Russian scientists V.A. Britov, S.N. Boev and B.L. Garkavi, described three new species: Trichinella nativa, Trichinella nelsoni and Trichinella pseudospiralis. This shattered the concept that the genus Trichinella was monospecific and widened the host range to include birds. The description of these new species generated an intense debate over their taxonomic validity because there were no clear morphological differences among them and because the concept of sibling species had not yet been accepted by parasitologists. The resolution of the taxonomic issues was facilitated by the adoption of new biochemical and molecular techniques for systematics research. In 1992, the first study comparing 152 isolates from various host species and geographical regions identified eight distinct taxa, coded T1 through T8; four of these represented the previously proposed species and included one new species, Trichinella britovi (T3). During the past 27 years, an increasing number of investigations in different geographical regions and hosts coupled with the availability of new and highly sensitive molecular techniques have allowed the description of four new species; Trichinella murrelli (T5), Trichinella papuae (T10), Trichinella zimbabwensis (T11) and Trichinella patagoniensis (T12), and two new genotypes Trichinella T9 and T13. Thus, the taxonomic status of Trichinella T6, T8, T9 and T13 remain unresolved. These new technologies have also advanced a more complete phylogenetic, zoogeographical and epidemiological knowledge base for future work.

Host Genotypic Effect on Algal Symbiosis Establishment in the Coral Model, the Anemone Exaiptasia diaphana, From the Great Barrier Reef

This research was funded by the Australian Government through the Australian Research Council Discovery Project DP160101539. GT thanks the Botany Foundation at the University of Melbourne for awarding the Protist Systematics research fund that supported Symbiodiniaceae ITS2 sequencing.

Complete plastome sequence of Croton laevigatus Vahl (Euphorbiaceae): an endemic species in Hainan, China

Croton laevigatus grows as an evergreen tree or shrub with 15 meters height. It is distributed in the dense or open forests of Hainan province, China. Here, we report and characterize the complete plastome of C. laevigatus in an effort to provide genomic resources useful for promoting its systematics research. The plastome of C. laevigatus is found to possess a total length 162,515 bp with the typical quadripartite structure of angiosperms, contains two Inverted Repeats (IRs) of 26,866 bp, a Large Single-Copy (LSC) region of 90,234 bp and a Small Single-Copy (SSC) region of 18,549 bp. The plastome contains 113 genes, consisting of 79 unique protein-coding genes, 30 unique tRNA genes and four unique rRNA genes. The overall A/T content in the plastome of C. laevigatus is 64.10%. The phylogenetic analysis indicated that C. laevigatus is close to C. tiglium within Euphorbiaceae in this study. The complete plastome sequence of C. laevigatus will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies of Euphorbiaceae.

Target Capture Sequencing Unravels Rubus Evolution.

Rubus (Rosaceae) comprises more than 500 species with additional commercially cultivated raspberries and blackberries. The most recent (> 100 years old) global taxonomic treatment of the genus defined 12 subgenera; two subgenera were subsequently described and some species were rearranged. Intra- and interspecific ploidy levels and hybridization make phylogenetic estimation of Rubus challenging. Our objectives were to estimate the phylogeny of 94 taxonomically and geographically diverse species and three cultivars using chloroplast DNA sequences and target capture of approximately 1,000 low copy nuclear genes; estimate divergence times between major Rubus clades; and examine the historical biogeography of species diversification. Target capture sequencing identified eight major groups within Rubus. Subgenus Orobatus and Subg. Anoplobatus were monophyletic, while other recognized subgenera were para- or polyphyletic. Multiple hybridization events likely occurred across the phylogeny at subgeneric levels, e.g., Subg. Rubus (blackberries) × Subg. Idaeobatus (raspberries) and Subg. Idaeobatus × Subg. Cylactis (Arctic berries) hybrids. The raspberry heritage within known cultivated blackberry hybrids was confirmed. The most recent common ancestor of the genus was most likely distributed in North America. Multiple distribution events occurred during the Miocene (about 20 Ma) from North America into Asia and Europe across the Bering land bridge and southward crossing the Panamanian Isthmus. Rubus species diversified greatly in Asia during the Miocene. Rubus taxonomy does not reflect phylogenetic relationships and subgeneric revision is warranted. The most recent common ancestor migrated from North America towards Asia, Europe, and Central and South America early in the Miocene then diversified. Ancestors of the genus Rubus may have migrated to Oceania by long distance bird dispersal. This phylogeny presents a roadmap for further Rubus systematics research. In conclusion, the target capture dataset provides high resolution between species though it also gave evidence of gene tree/species tree and cytonuclear discordance. Discordance may be due to hybridization or incomplete lineage sorting, rather than a lack of phylogenetic signal. This study illustrates the importance of using multiple phylogenetic methods when examining complex groups and the utility of software programs that estimate signal conflict within datasets.

A new species of Sigmodontinae (Rodentia) from the late Hemphillian of central Mexico, and comments on the possible radiation of this group

The Sigmodontinae subfamily represents one of the most diverse groups of mammals in the world; this rodent group evolved in the open and arid ecosystems of the Miocene of North America and was the most successful legion of mammals in the Great American Biotic Interchange. Part of its diversification occurred in the Mexican Pliocene, in the Hemphillian-Blancan boundary, where Prosigmodon and Sigmodon species are very common. Recent molecular phylogenetic systematics research propose that Sigmodon is related to South American sigmodontines, while studies of classical morphometry in isolated molar teeth consider Prosigmodon as synonymy of Sigmodon, which modifies the biogeographic and chronostratigraphic interpretations of this group in America. In this paper, we describe a new species of Prosigmodon from the late Hemphillian (~4.89 Ma) of central Mexico based on jaws, maxillary, and complete isolated teeth. This is the most complete and austral record of the genus in North America. This species was compared with North American species of the Sigmodontinae and Neotominae subfamilies and we defined it as a new Prosigmodon species characterized by having a consistently present minute mesoloph in M1 and M2, in addition, there is an isolated metaconid from the protoconid in the m1 of young individuals. We performed a phylogenetic model focused on understanding the relationship between Prosigmodon (four species) and Sigmodon (eight species), where we included Baiomys (two species), Neotoma (two species), Peromyscus (two species), and Reithrodontomys (two species). Our results indicate that Prosigmodon is a monophyletic group if Sigmodon minor is included within the genus and P. chihuahuensis is excluded. The Mexican Prosigmodon species have more apomorphic characters with respect to S. minor and P. holocuspis. The species of Prosigmodon and Sigmodon are not closely related, Sigmodon is more related to the Neotoma species than the species of Baiomys, Prosigmodon, Reitrhodontomys, and Peromyscus. Based on the topology of our cladogram and the stratigraphic ranges of the species Sigmodontinae and Neotominae, we discuss that Baiomys, Prosigmodon, Reitrhodontomys, and Peromyscus probably diversified in the early Hemphillian, while Sigmodon and Neotoma did so during the late Pliocene.

Toward Phylomics in Entomology: Current Systematic and Evolutionary Morphology

Abstract Morphology, encompassing the study of phenotypic form and function, is one of the ancient branches of human knowledge and is foundational for organismal classification. Two decades into the current century, the specialized biological knowledge of the history and pattern of evolution has been revolutionized by genome-scale sequencing technologies, and cryptic variation within and among species is quantifiable even with a few genetic markers. The application of statistical phylogenetic models of nucleotide and amino acid substitution to sequence data has enabled revised interpretations of morphological identities—be they population-level generalizations, such as species diagnoses, or the definition and homology of specific anatomical entities—and evolutionary transformation across the tree of life (e.g., insect genitalia, ancestral morphology of Polyneoptera). These models are also being adapted for phylogenetic analysis of morphological data, allowing explicit incorporation of fossil terminals and their stratigraphic information. In this special collection of research in Insect Systematics & Diversity (ISD), we present six papers on the topic of Current Techniques in Morphology. These papers span an arc from integrated methods of phenotype observation and visualization to methods and background for phylogenetic modeling of morphological characters. In this editorial, I review the central role of anatomical classification and anatomical terminology in systematic by way of outlining the special collection. I argue ultimately for a reconceptualization of phylogenetic morphology.

Towards a New Legume Systematics Portal

The need for scientists to exchange, share, and organise data has resulted in a proliferation of research data portals in the past decades. These cyberinfrastructures have had a major impact on taxonomy and helped to revitalise the discipline, by allowing quick access to bibliographic information, biological and nomenclatural data, and specimen information. In addition, several specialised portals aggregate particular data types for a large number of species and can be queried to extract information for a particular taxonomic group. Because of their ecological and economic importance, several early initiatives to develop and deploy information technologies for capturing, sharing, and disseminating information focused specifically on the plant family Leguminosae (Fabaceae). Initiatives such as ILDIS (International Legume Database and Information Service), which was created in 1985, led the way in developing methods and thinking with regard to taxonomic data management more generally. More recently, the Legume Phylogeny Working Group (LPWG) was founded in 2010 with the objective of facilitating collaboration amongst systematists working on the plant family Leguminosae (Fabaceae). As part of this endeavour, the LPWG has explored whether it would be desirable and pertinent to develop a new portal focused on the legume family. We argue that, despite access to numerous data aggregation portals, a taxon-focussed portal curated by a community of researchers specialised on a particular taxonomic group, such as the LPWG, have the interest, commitment, existing collaborative links, and knowledge necessary to verify data quality, thereby providing a valuable resource and actively contributing to other more general data providers. We consider that a new portal focused on Leguminosae would thus serve a useful function in parallel to and different from large international data-aggregation portals. We explored best practices for developing a legume-focused portal that will enable long-term sustainability, data sharing, a better understanding of what data are available, missing, or erroneous, and ultimately facilitate cross analyses and development of novel research. We surveyed existing data portals to see what features are of interest to our goal and we present a general way forward for developing a legume-focused portal that would respond to the needs of the legume systematics research community as well as to the broader user community. We propose to take full advantage of existing data sources, informatics tools, and protocols to develop an easily manageable, scalable, and interactive portal that will be used, contributed to, and fully endorsed and supported by the legume systematics community.