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We provide an example of ecological vicariance among two epilithic, high mountain taxa of mosses. Phylogenetic analyses using plastid (rps4-trnS, atpB-rbcL, trnL-trnF) and nuclear (EST-115, EST-317, ITS region) markers and morphological data revealed the distinctiveness of the neglected Orthotrichum killiasii, here resurrected from the synonymy of Lewinskya speciosa and newly combined in Lewinskya. Furthermore, our data indicate a speciation process within O. killiasii related to the rock type inhabited (silicate vs. carbonate). We translate this into the recognition of two subspecies, corresponding to O. killiasii s.s. and the recently described O. simonyi. The incongruence between nuclear and plastid markers in some accessions and the partial but rare incongruence between ITS ribotypes and the morphological manifestation in phenotypes indicate incomplete lineage sorting with respect to rather recent segregation and possible gene flow between the two entities.

Eumops floridanus (Allen, 1932) is a molossid commonly called the Florida bonneted bat or the Florida mastiff bat. Eumops floridanus is the largest species of bat in Florida and is one of 16 species in the genus Eumops. With one of the smallest distributions of any bat in the United States, it is endemic to southern peninsular Florida where it roosts in cavities of live and dead trees and man-made structures. Eumops floridanus was formerly classified as a subspecies of E. glaucinus but has been elevated to species level based on morphology. Due primarily to its restricted distribution, small population size, and the continued loss of habitat, E. floridanus is federally listed as “Endangered” (EN) by the United States Fish and Wildlife Service.

Integrative taxonomy is central to modern taxonomy and systematic biology, including behavior, niche preference, distribution, morphological analysis, and DNA barcoding. However, decades of use demonstrate that these methods can face challenges when used in isolation, for instance, potential misidentifications due to phenotypic plasticity for morphological methods, and incorrect identifications because of introgression, incomplete lineage sorting, and horizontal gene transfer for DNA barcoding. Although researchers have advocated the use of integrative taxonomy, few detailed algorithms have been proposed. Here, we develop a convolutional neural network method (morphology-molecule network [MMNet]) that integrates morphological and molecular data for species identification. The newly proposed method (MMNet) worked better than four currently available alternative methods when tested with 10 independent data sets representing varying genetic diversity from different taxa. High accuracies were achieved for all groups, including beetles (98.1% of 123 species), butterflies (98.8% of 24 species), fishes (96.3% of 214 species), and moths (96.4% of 150 total species). Further, MMNet demonstrated a high degree of accuracy ($>$98%) in four data sets including closely related species from the same genus. The average accuracy of two modest subgenomic (single nucleotide polymorphism) data sets, comprising eight putative subspecies respectively, is 90%. Additional tests show that the success rate of species identification under this method most strongly depends on the amount of training data, and is robust to sequence length and image size. Analyses on the contribution of different data types (image vs. gene) indicate that both morphological and genetic data are important to the model, and that genetic data contribute slightly more. The approaches developed here serve as a foundation for the future integration of multimodal information for integrative taxonomy, such as image, audio, video, 3D scanning, and biosensor data, to characterize organisms more comprehensively as a basis for improved investigation, monitoring, and conservation of biodiversity. [Convolutional neural network; deep learning; integrative taxonomy; single nucleotide polymorphism; species identification.]

Recently diverged taxa often exhibit heterogeneous landscapes of genomic differentiation, characterized by regions of elevated differentiation on an otherwise homogeneous background. While divergence peaks are generally interpreted as regions responsible for reproductive isolation, they can also arise due to background selection, selective sweeps unrelated to speciation, and variation in recombination and mutation rates. To investigate the association between patterns of recombination and landscapes of genomic differentiation during the early stages of speciation, we generated fine-scale recombination maps for six southern capuchino seedeaters (Sporophila) and two subspecies of White Wagtail (Motacilla alba), two recent avian radiations in which divergent selection on pigmentation genes has likely generated peaks of differentiation. We compared these recombination maps to those of Collared (Ficedula albicollis) and Pied Flycatchers (Ficedula hypoleuca), non-sister taxa characterized by moderate genomic divergence and a heterogenous landscape of genomic differentiation shaped in part by background selection. Although recombination landscapes were conserved within all three systems, we documented a weaker negative correlation between recombination rate and genomic differentiation in the recent radiations. All divergence peaks between capuchinos, wagtails, and flycatchers were located in regions with lower-than-average recombination rates, and most divergence peaks in capuchinos and flycatchers fell in regions of exceptionally reduced recombination. Thus, co-adapted allelic combinations in these regions may have been protected early in divergence, facilitating rapid diversification. Despite largely conserved recombination landscapes, divergence peaks are specific to each focal comparison in capuchinos, suggesting that regions of elevated differentiation have not been generated by variation in recombination rate alone.

Climate has a significant influence on species distribution and the expression of functional traits in different plant species. However, it is unknown if subspecies with different climate envelopes also show differences in their expression of plant functional traits or if they respond differently to drought stress. We measured functional traits and drought responses of five subspecies of a widely distributed, cosmopolitan polymorphic shrub, Dodonaea viscosa (L.) Jacq., in an experiment with 1-year-old plants. Functional traits, such as leaf size, specific leaf area, turgor loss point (ΨTLP), maximum stomatal conductance and maximum plant hydraulic conductance, differed among the five subspecies. However, while the were some differences among traits, these were not related to their climate of origin, as measured by mean annual temperature, mean annual precipitation and mean annual aridity index. Drought response was also not related to climate of origin, and all subspecies showed a combination of drought avoiding and drought tolerance responses. All subspecies closed their stomata at very high water potentials (between −1.0 and −1.3 MPa) and had large hydraulic safety margins (drought avoidance). All subspecies adjusted their ΨTLP via osmotic adjustment, and subspecies with inherently lower ΨTLP showed greater osmotic adjustment (drought tolerance). All subspecies adjusted their midday water potentials in response to drought but subspecies from more arid environments did not show greater adjustments. The results indicated that climate niche was not related to plant trait expression or response to drought. The combination of drought avoidance and drought tolerance behavior seems to be a successful strategy for this widely distributed species that occupies many different climate zones and ecosystems. Hence, the wide distribution of D. viscosa seems to be related to plasticity of trait expression and drought response rather than long-term genetic adaptations to different environmental conditions.

The distribution of the iridescent dung beetle Bolbites onitoides can be divided, based on dorsal colouration, into a blue western-half and a red eastern-half. This has raised the question, in 1959, of whether the two colour variants could represent distinct subspecies. Having examined ~1200 specimens and evaluated the proposal under both an ontological and an operational subspecies concept, we conclude that B. onitoides should continue to be treated as a single monotypic species because: (1) two kinds of colour intermediates were found living among populations of the two main variants; (2) the distribution of the variants overlaps; (3) no other characters were seen to vary consistently in accordance with the colour variants; (4) the overall geographical pattern can be explained by phenomena other than (incipient) speciation, such as phenotypic plasticity and distinct selective regimes; and (5) colour has been extensively shown not to be a reliable indicator of speciation processes among dung beetles. By comparing our findings with other cases of polychromatism among scarabaeines, we discuss publications proposing subspecies taxa relying uniquely upon colour variants. We contend that, due to the often continuous, populational, polytopic and, several times, clinal nature of the intraspecific geographical variation, subspecies classification schemes should not be established simply to classify variation across a species range without a commitment to the reality as evolutionary entities of the taxa being proposed. The alternative stance championed by many contemporary authors to give trinomina to conspecific (meta)population lineages, in turn, may eventually prove to be adequate, but we express some of our concerns as to the feasibility of this practice. Whether these intraspecific taxa should be ranked in a Linnaean hierarchy – e.g. as subspecies – is equally an open question. We also elaborate on an evolutionary scenario where the role of the iridescence in sexual selection, as hypothesized in a previous work, may be an exaptation, not an adaptation, among the horned Phanaeina.

The Large Treeshrew, Tupaia tana Raffles, 1821, is a small mammal (~205 g) from Southeast Asia with a complicated taxonomic history. Currently, 15 subspecies are recognized from Borneo, Sumatra, and smaller islands, and many were originally differentiated based on minor pelage differences and small sample sizes. We explored intraspecific variation in T. tana using quantitative osteological data obtained from the hands and skulls of museum specimens. Multivariate analyses reveal extensive overlap among T. tana populations in morphospace, indicating that the majority of currently recognized subspecies are not morphometrically distinct. In contrast, the separation between Bornean and Sumatran populations of T. tana is sufficient to recognize them as different subspecies. Comparisons of Bornean specimens to those on small, offshore islands reveal that the latter average smaller body size. This pattern is inconsistent with Foster’s island rule, which predicts that island populations of small mammals (< 5 kg) will average larger body size relative to mainland forms. A similar lack of support for ecogeographic rules has been noted in T. glis (Diard, 1820), suggesting that these “rules” are poor predictors of geographic variation in treeshrews.

Secondary contact zones have been formed between several pairs of avian species and subspecies in northern and north-eastern Iran during the post-Pleistocene and Holocene periods. Three subspecies groups out of the four in the great tit (Parus major), major, bokharensis and cinereus, are believed to have come into local or regional secondary contact in north-eastern Iran. Parus major intermedius is also known from this region and has long been suggested to have a hybrid origin from hybridization between the yellow western (major) subspecies group and the grey-coloured eastern (bokharensis or cinereus) subspecies group based on its intermediate plumage coloration. Here, we investigated the evidence of intergradation between subspecies groups and the evolutionary origin of P. m. intermedius using mitochondrial DNA sequences and microsatellites, and approximate Bayesian computation to test competing scenarios for the demographic history of the populations. Our analyses indicate a divergence origin for intermedius that resulted from expansion of the major subspecies group. Low mitochondrial diversity and high genetic differentiation in comparison with central populations suggest that intermedius is a peripheral population. Microsatellite data show no signs of nuclear admixture between the bokharensis and major subspecies groups. However, one phenotypically intermedius specimen had bokharensis mtDNA and major nuclear DNA in the assumed hybrid zone (Lotf Abad), supporting past introgression.

Cyclic climatic and glacial fluctuations of the Late Quaternary produced a dynamic biogeographic history for high latitudes. To refine our understanding of this history in northwestern North America, we explored geographic structure in a wide-ranging carnivore, the wolverine (Gulo gulo). We examined genetic variation in populations across mainland Alaska, coastal Southeast Alaska, and mainland western Canada using nuclear microsatellite genotypes and sequence data from the mitochondrial DNA (mtDNA) control region and Cytochrome b (Cytb) gene. Data from maternally inherited mtDNA reflect stable populations in Northwest Alaska, suggesting the region harbored wolverine populations since at least the Last Glacial Maximum (LGM; 21 Kya), consistent with their persistence in the fossil record of Beringia. Populations in Southeast Alaska are characterized by minimal divergence, with no genetic signature of long-term refugial persistence (consistent with the lack of pre-Holocene fossil records there). The Kenai Peninsula population exhibits mixed signatures depending on marker type: mtDNA data indicate stability (i.e., historical persistence) and include a private haplotype, whereas biparentally inherited microsatellites exhibit relatively low variation and a lack of private alleles consistent with a more recent Holocene colonization of the peninsula. Our genetic work is largely consistent with the early 20th century taxonomic hypothesis that wolverines on the Kenai Peninsula belong to a distinct subspecies. Our finding of significant genetic differentiation of wolverines inhabiting the Kenai Peninsula, coupled with the peninsula’s burgeoning human population and the wolverine’s known sensitivity to anthropogenic impacts, provides valuable foundational data that can be used to inform conservation and management prescriptions for wolverines inhabiting these landscapes.

Taxonomic analysis of microbial communities is well supported at the level of species and strains. However, species can contain significant phenotypic diversity and strains are rarely widely shared across global populations. Stratifying the diversity between species and strains can identify ‘subspecies’, which are a useful intermediary. High-throughput identification and profiling of subspecies is not yet supported in the microbiome field. Here, we use an operational definition of subspecies based on single nucleotide variant (SNV) patterns within species to identify and profile subspecies in metagenomes, along with their distinctive SNVs and genes. We incorporate this method into metaSNV v2, which extends existing SNV-calling software to support further SNV interpretation for population genetics. These new features support microbiome analyses to link SNV profiles with host phenotype or environment and niche-specificity. We demonstrate subspecies identification in marine and fecal metagenomes. In the latter, we analyze 70 species in 7524 adult and infant subjects, supporting a common subspecies population structure in the human gut microbiome and illustrating some limits in subspecies calling., Bioinformatics, 38 (4), ISSN:1367-4803, ISSN:1460-2059

Aims Existing methods for the identification of the subspecies of Xylella fastidiosa are time-consuming which can lead to delays in diagnosis and the associated plant health response to outbreaks and interceptions. Methods and results Diagnostic markers were identified using a comparative genomics approach to allow fine differentiation of the very closely related subspecies. Five qPCR assays were designed to allow specific detection of X. fastidiosa subsp. fastidiosa, X. fastidiosa subsp. multiplex, X. fastidiosa subsp. pauca, X. fastidiosa subsp. morus and X. fastidiosa subsp. sandyi. All assays were validated according to the European and Mediterranean Plant Protection Organisation (EPPO) standard PM7/98(2). Conclusions All of the assays were shown to be specific to the target subspecies and all the assays could be used to detect femtogram quantities of X. fastidiosa DNA. Significance and impact of the study At present, diagnosing the subspecies of X. fastidiosa requires multiple conventional PCR assays (although only available for three of the five subspecies) or multi-locus sequence typing which takes several days. By comparison, the new assays provide a substantial reduction in the turnaround time for direct identification to the subspecies level in as little as 75 min.

[EN] Aims: The survival and ecological distribution of plants in arid habitats are mainly conditioned by water availability and physiological adaptations to withstand drought. In the present study, we have compared the physiological responses to drought of two Retama raetam (retama) subspecies from Tunisia, one of them living under the desert climate (subsp. raetam) and the other one growing on the coast (subsp. bovei). Methods: To physiologically characterize the two R. raetam subspecies, and to elucidate their main mechanisms underlying their tolerance to drought stress, parameters related to seed germination, growth, photosynthesis (net photosynthetic rate, intracellular CO2 concentration, transpiration rate, stomatal conductance and water-use efficiency) and accumulation of osmolytes (proline, glycine betaine [GB] and soluble sugars) were determined in 4-month-old plants subjected to stress for up to 1 month. Important Findings: Drought significantly inhibited germination, growth and all the evaluated photosynthetic parameters. Plants of R. raetam subsp. bovei were severely affected by drought after 3 weeks of treatment when photosynthesis rates were up to 7-fold lower than in the controls. At the same time, proline and GB significantly accumulated compared with the irrigated controls, but much less than in R. raetam subsp. raetam; in the latter subspecies, proline and GB increased to levels 24- and 6-fold higher, respectively, than in the corresponding controls. In summary, the population living in the desert region exhibited stronger tolerance to drought stress than that adapted to the semiarid littoral climate, suggesting that tolerance in R. raetam is dependent on accumulation of osmolytes., Dhikra Zayoud's stay in Valencia was supported by a grant from the Tunisian Ministry of Higher Education and Scientific Research.

Climates around the world are rapidly turning warmer and often drier. Agricultural approaches must change accordingly. One important global practice is commercial use of cryptic species of the Chrysoperla carnea-group of green lacewings to control arthropod pests. Recently, one highly drought-tolerant species, originally present only in the Old World, is suspected of expanding its range to some of the driest habitats in the New World. Here we examine putative specimens of this species, Chrysoperla zastrowi (Esben-Petersen, 1928), collected in the desert southwest of the United States, the parched northwest of Mexico, and Guatemala. Using species-specific vibrational duetting-song phenotypes, subtle morphological character states, and mitochondrial DNA sequences, we confirm that C. zastrowi is now a naturalized part of the lacewing fauna of the Americas, making it the only species of the carnea-group to have a truly global range. As such, we encourage its broader commercial use for pest control on irrigated agricultural systems in the hotter, drier regions of the world to which it is best adapted and within which it now appears to be fully naturalized. We briefly consider future range expansion of both subspecies of C. zastrowi, C. z. zastrowi, and C. z. sillemi, in response to continued global warming.

Northern yellow bats (Dasypterus intermedius) are tree-roosting bats in the family Vespertilionidae comprised of two subspecies: D. intermedius intermedius and D. intermedius floridanus. The two subspecies are thought to be geographically separated. Due to their cryptic morphology, this hypothesis has never been tested and can benefit from being examined within a molecular framework. In this study, mitochondrial sequence data from 38 D. intermedius and nuclear sequence data from 14 D. intermedius from across their range were used to test the hypothesis that genetically defined groups correspond geographically with the two morphologically defined subspecies. Although high levels of divergence of the mitochondrial sequence (11.6%) suggest genetically distinct clusters sympatric in southern Texas, no genetic structure was recovered with the nuclear marker. Moreover, the mitochondrial sequence data recovered a paraphyletic relationship between the two subspecies of D. intermedius with the Cuban yellow bat (D. insularis), whereas no such paraphyly was recovered from analysis of the nuclear marker. Divergence time based on analyses of mitochondrial sequence for the two subspecies was approximately 5.5 Ma. The patterns observed are hypothesized to be the result of past isolation of lineages and secondary contact that is currently contributing to gene flow.

Phenotypic variation is often used to delineate species and subspecies boundaries. Statistical analysis of phenotypic variation within a species is helpful both for understanding biodiversity and for its conservation. At least three named subspecies of barn swallows (Hirundo rustica) have distributions that span China, yet, to date, no systematic study of phenotypic differentiation has been applied to understand the delineation of these subspecies. In this study, we collected 510 samples of barn swallow from 23 populations in China, including two recognized subspecies, H. r. rustica and H. r. gutturalis, and one potential subspecies, H. r. mandschurica. With these samples, we examined and found morphometric and colour differences among different populations. Western Chinese barn swallows (H. r. rustica) have larger body size and could be clearly differentiated from eastern H. r. gutturalis and H. r. mandschurica, while north-eastern populations (named H. r. mandschurica) have darker, redder ventral plumage than H. r. rustica and H. r. gutturalis. However, we inferred that although there were phenotypic differences between H. r. mandschurica and H. r. gutturalis, they were not sufficiently distinct to assign them to separate subspecies based on the 75% rule for defining subspecies.

OCBIL theory provides a basis for understanding of the evolution and ecology of biota on old, climatically buffered, infertile landscapes (OCBILs) worldwide. Here, we test a genetic hypothesis presented in OCBIL theory that predicts highly differentiated intraspecific population systems on OCBILs vs. more limited differentiation on young, often disturbed, fertile landscapes (YODFELs). We examined patterns of genomic and morphological divergence in Banksia seminuda across OCBILs and YODFELs in south-western Australia. We also used these data to determine whether these OCBIL and YODFEL populations represent distinct subspecific lineages, a point of previous contention among taxonomists. As hypothesized, genomic analyses based on 3466 SNP loci revealed strong structuring within B. seminuda, with high differentiation across narrow geographic scales among OCBIL populations vs. lower differentiation across much larger geographic scales among YODFEL populations. In addition, genomic and morphological divergence was found between OCBIL and YODFEL populations, providing comprehensive quantitative evidence for two subspecies. These findings have taxonomic implications for the species and provide support for OCBIL theory and its insights into the evolution, ecology and conservation of biota on ancient landscapes.

Made available in DSpace on 2021-06-25T12:33:18Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-11-01 SELVA Society for the Study of Evolution American Ornithology Society Graduate Research Award Provost's Graduate Research Award from the University of Illinois at Chicago Field Museum's H. B. Conover Fund Society of Integrative and Comparative Biology Field Museum Armour Graduate Student Fellowship Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET-Argentina) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) University of Buenos Aires Sonations are sounds that animals produce with structures other than the vocal apparatus for communication. In birds, many sonations are usually produced with modified flight feathers through diverse kinematic mechanisms. For instance, aeroelastic fluttering of feathers produces tonal sound when airflow exceeds a threshold velocity and induces flight feathers to oscillate at a constant frequency. The Fork-tailed flycatcher (Tyrannus savana) is a Neotropical bird with both migratory and year-round resident subspecies that differ in the shape of the outer primary feathers of their wings. By integrating behavioral observations, audio recordings, and high-speed videos, we find that male Fork-tailed flycatchers produce sonations with their outer primary feathers P8-10, and possibly P7. These sounds are produced during different behavioral contexts including: the pre-dawn display, intraspecific territorial disputes, when attacking potential nest predators, and when escaping. By placing feathers in a wind tunnel, we elicited flutter at frequencies that matched the acoustic signature of sounds recorded in the wild, indicating that the kinematic mechanism responsible for sound production is aeroelastic flutter. Video of wild birds indicated that sonations were produced during the downstroke. Finally, the feathers of migratory (T.s.savana) and year-round resident (T.s.monachus) Fork-tailed flycatchers flutter in feather locations that differ in shape between the subspecies, and these shape differences between the subspecies result in sounds produced at different frequencies. Univ Illinois, Dept Biol Sci, 845 West Taylor St,MC066, Chicago, IL 60607 USA SELVA Invest Conservac Neotrop, Diagonal 42a 20-37, Bogota, Colombia Field Museum Nat Hist, Negaunee Integrat Res Ctr, 1400 South Lake Shore Dr, Chicago, IL 60605 USA Univ Buenos Aires, Dept Ecol Genet & Evoluc, Fac Ciencias Exactas & Nat, Inst IEGEBA CONICET UBA, Ciudad Univ,C1428EGA, RA-2160 Buenos Aires, DF, Argentina Univ Estadual Paulista, Inst Biociencias, Dept Zool, Ave 24a,1515, Rio Claro, SP, Brazil Univ Calif Riverside, Dept Evolut Ecol & Organismal Biol, Riverside, CA 92521 USA Univ Estadual Paulista, Inst Biociencias, Dept Zool, Ave 24a,1515, Rio Claro, SP, Brazil FAPESP: 2012/17225-2

The validity of subspecies designations in the common and wide-ranging Neotropical white peacock butterfly, Anartia jatrophae, has been debated for decades and remains an unsettled and contentious taxonomic issue among lepidopterists. Originally described by Linnaeus in the mid-18th century from specimens obtained from northern South America (Suriname), subsequent authors proposed a variety of subspecies names based on differences in adult external morphology among geographical populations. Many of these differences, however, were subsequently found to occur seasonally within populations, leading some to conclude that only a single polymorphic species should be recognized. Here, we have analysed both new and publicly available mitochondrial DNA barcodes, obtained from specimens collected from southern USA to northern Argentina, to assess whether they could provide insight into this long-standing controversy. Our molecular analyses, using a combination of character-based (nucleotide composition), population genetic and phylogenetic approaches, indicated the presence of at least four distinct genetic lineages that we suggest are distinct at the subspecies level, namely A. j. jatrophae, A. j. luteipicta, A. j. saturata and A. j. semifusca. Justification for these assignments and the proposed geographical distribution of each subspecies within the Americas are discussed.

The application of evolutionary genetic research to investigate the potential for endangered species to adapt to changing environments is important for conservation biology. Effective population size (Ne) is informative for understanding adaptive potential as it refers to the genetic variation in breeding individuals who have contributed to contemporary and historic population diversity. We reconstruct fluctuations in Ne in three golden eagle subspecies (Japanese, Scottish, North American) using the pairwise sequential Markovian coalescent (PSMC) model based on whole-genome sequence data. Our results indicate the timing of subspeciation events and suggest significant ongoing demographic reductions since the start of the Last Glacial Period. Importantly, we find evidence for gene flow from continental populations into the ancestral Japanese population resulting in a short, sharp recovery in genetic diversity. Timing agrees with the palaeogeographic estimates of land bridge connections between the Japanese archipelago and Asian continent and matches a similar Ne spike in the Scottish population, but not in the North American population. Given contemporary declines in isolated Japanese and UK island populations, our study highlights a concerning loss of local genetic diversity, but also indicates the likely response of populations to genetic reinforcement from neighbouring subspecies, increasing management options and encouraging a range-wide species conservation approach.

Desert shrews of the genus Notiosorex comprise four species with morphological characteristics that are difficult to distinguish among the species. Indeed, N. cockrumi was described using only genetic markers. Based on molecular divergence documented in N. crawfordi, we hypothesize that a fifth species is present in the Baja California peninsula. Genetic variation at the species level was analyzed using individuals from locations west of the Colorado River in the Baja California peninsula, Mexico, and California, United States. Molecular markers of mitochondrial origin (cytochrome b, 1,140 bp; cytochrome c oxidase subunit I, 542 bp; and cytochrome c oxidase subunit III, 672 bp), as well as the nuclear intron 7 of the beta fibrinogen gene (385 bp) were used to construct a phylogeny for species of the genus Notiosorex. Genetic distances of 12.46–15.58% between west and east of the Colorado River were obtained using p-distance models. Our phylogenetic analyses showed almost identical topologies, placing populations from west of the Colorado River in three monophyletic clades with high bootstrap support values. Results of molecular phylogenetic identity among shrews of the genus Notiosorex support the existence of an undescribed, polytypic species of Notiosorex west of the Colorado River.

The kin structure of a species at relatively fine spatial scales impacts broad-scale patterns in genetic structure at the population level. However, kin structure rarely has been elucidated for migratory marine mammals. The Pacific walrus (Odobenus rosmarus divergens) exhibits migratory behavior linked to seasonal patterns in sea ice dynamics. Consequently, information on the spatial genetic structure of the subspecies, including kin structure, could aid wildlife managers in designing future studies to evaluate the impacts of sea ice loss on the subspecies. We sampled 8,303 individual walruses over a 5-year period and used 114 single-nucleotide polymorphisms to examine both broad-scale patterns in genetic structure and fine-scale patterns in relatedness. We did not detect any evidence of genetic structure at broad spatial scales, with low FST values (≤ 0.001) across all pairs of putative aggregations. To evaluate kin structure at fine spatial scales, we defined a walrus group as a cluster of resting individuals that were less than one walrus body length apart. We found weak evidence of kin structure at fine spatial scales, with 3.72% of groups exhibiting mean relatedness values greater than expected by chance, and a significantly higher overall observed mean value of relatedness within groups than expected by chance. Thus, the high spatiotemporal variation in the distribution of resources in the Pacific Arctic environment likely has favored a gregarious social system in Pacific walruses, with unrelated animals forming temporary associations.

The current outbreak of a novel severe acute respiratory syndrome‐like coronavirus, 2019_nCoV (now named SARS‐CoV‐2), illustrated difficulties in identifying a novel coronavirus and its natural host, as the coding sequences of various Betacoronavirus species can be highly diverse. By means of whole‐genome sequence comparisons, we demonstrate that the noncoding flanks of the viral genome can be used to correctly separate the recognized four betacoronavirus subspecies. The conservation would be sufficient to define target sequences that could, in theory, classify novel virus species into their subspecies. Only 253 upstream noncoding sequences of Sarbecovirus are sufficient to identify genetic similarities between species of this subgenus. Furthermore, it was investigated which bat species have commercial value in China, and would thus likely be handled for trading purposes. A number of coronavirus genomes have been published that were obtained from such bat species. These bats are used in Traditional Chinese Medicine, and their handling poses a potential risk to cause zoonotic coronavirus epidemics. Significance and Impact of the Study The noncoding upstream and downstream flanks of coronavirus genomes allow for rapid classification of novel Betacoronavirus species and correct identification of genetic relationships. Although bats are the likely natural host of 2019_nCoV, the exact bat species that serves as the natural host of the virus remains as yet unknown. Chinese bat species with commercial value were identified as natural reservoirs of coronaviruses and are used in Traditional Chinese Medicine. Since their trading provides a potential risk for spreading zoonoses, a change in these practices is highly recommended., Significance and Impact of the Study: The noncoding upstream and downstream flanks of coronavirus genomes allow for rapid classification of novel Betacoronavirus species and correct identification of genetic relationships. Although bats are the likely natural host of 2019_nCoV, the exact bat species that serves as the natural host of the virus remains as yet unknown. Chinese bat species with commercial value were identified as natural reservoirs of coronaviruses and are used in Traditional Chinese Medicine. Since their trading provides a potential risk for spreading zoonoses, a change in these practices is highly recommended.

Neusticomys peruviensis is a poorly known sigmodontine rodent of the tribe Ichthyomyini, represented in collections by only five specimens collected in five localities from lowland forests of central and southern Peru. Recent expeditions in Llanchama, in northern Peru, north of the Río Amazonas, and near Allpahuayo Mishana Natural Reserve (Loreto, Peru), were successful in obtaining three specimens of Neusticomys. Based on morphological and meristic data, we found the population at Llanchama is distinct from the allopatric populations of N. peruviensis, and other species of Neusticomys. A species distribution model also shows the population at Llanchama is not highly predicted by the set of variables of the known localities of N. peruviensis. However, sequence data from the mitochondrial cytochrome-b gene indicate that genetic distinctiveness is low. Because intraspecific variability is important to understand evolutionary and biogeographic processes, and in concordance with the polytypic species concept, we interpret the population at Llanchama to represent a new subspecies of N. peruviensis that we describe in this paper.

The complex topography, climate, and geological history of Western North America have shaped contemporary patterns of biodiversity and species distributions in the region. Pacific martens (Martes caurina) are distributed along the northern Pacific Coast of North America with disjunct populations found throughout the Northwestern Forested Mountains and Marine West Coast Forest ecoregions of the West Coast. Martes in this region have been classified into subspecies; however, the subspecific designation has been extensively debated. In this study, we use genomic data to delineate conservation units of Pacific marten in the Sierra-Cascade-Coastal montane belt in the western United States. We analyzed the mitochondrial genome for 94 individuals to evaluate the spatial distribution and divergence times of major lineages. We further genotyped 401 individuals at 13 microsatellite loci to investigate major patterns of population structure. Both nuclear and mitochondrial DNA suggest substantial genetic substructure concordant with historical subspecies designations. Our results revealed that the region contains 2 distinct mitochondrial lineages: a Cascades/Sierra lineage that diverged from the Cascades/coastal lineage 2.23 (1.48–3.14 mya), consistent with orogeny of the Cascade Mountain chain. Interestingly, Pacific Martes share phylogeographic patterns similar with other sympatric taxa, suggesting that the complex geological history has shaped the biota of this region. The information is critical for conservation and management efforts, and further investigation of adaptive diversity is warranted following appropriate revision of conservation management designations.

Aedes aegypti (L.) (Diptera: Culicidae) is a diurnal feeder that lives in close association with human populations. It is the principal vector of yellow fever, dengue fever and the Zika Virus. Issues of arboviral diseases have been on the ascendency in most countries including Ghana where Aedes mosquito is the main vector of yellow fever. A comparative study of the biting behavior of Ae. aegypti and the identification of subspecies were undertaken using molecular technique. Standard human landing technique was used to collect both indoor and outdoor biting mosquitoes at three zones located in the Upper East (Bolgatanga), Upper West (Nadowli), and Northern (Damongo) Regions of Ghana during the dry and rainy seasons between 0600 and 1800 Greenwich Mean Time (GMT). All collected mosquitoes were identified morphologically using taxonomic keys. random amplified polymorphic DNA polymerase chain reaction was used to categorize Ae. aegypti into subspecies. Adult female Aedes mosquitoes identified formed 62% (n = 1,206) of all female mosquitoes collected. Aedes aegypti 98% and Aedes vittatus 2% were the only Aedes species identified. Bolgatanga recorded the largest number of Ae. aegypti 42%, whereas Nadowli 22% recorded the least. Aedes vittatus was observed in Nadowli. Aedes aegypti exhibited a bimodal biting behavior peaking at 0600–0800 GMT and 1500–1600 h GMT. Molecular findings revealed 69% Ae. aegypti aegypti and 31% Ae. aegypti formosus as the two subspecies (n = 110). This information is important for implementing effective vector control programs in the three regions of the northern Ghana.

Management of the European gypsy moth [Lymantria dispar dispar (Linnaeus)] in North America has benefited from more than a century of research. The East Asian strains of the gypsy moth, however, bring new challenges including multiple subspecies (Lymantria dispar asiatica Vnukovskij and Lymantria dispar japonica Motschulsky), broad distributions across heterogeneous habitats, and a lack of data on the variation in the phenology of source populations, which may affect risk. To address these issues, published phenology parameters for eight populations of Asian gypsy moth were used to develop eight strain-specific agent-based phenological models. These models were applied to 47 ports in East Asia where the Asian gypsy moth is native, and output was compared with available trap data to assess the role of interpopulation variation in phenological parameters in predicting moth flight among varied locations, assess variation in the performance of models among years, and assess the importance of modeling phenology using parameters from a ‘local’ moth population. Variation in phenological parameters among the eight populations yielded variation in predicted flight times among the 47 ports analyzed, and the use of ‘local’ populations did not generally improve model fit. Model accuracy varied substantially among ports and among years within some ports. The larva-to-adult agent-based models described here have utility in estimating flight periods for some ports in their current form, but variation in model quality across the landscape suggests that there is potential for unsampled and unparameterized moth populations and factors that remain to be quantified.

We revise the taxonomy of the Sylvia cantillans complex, a group of phenotypically distinct warblers with mainly parapatric distributions around a large part of the Mediterranean basin. We redefine the species limits using a combination of mitochondrial and nuclear markers and we objectively link available names to the genetically defined lineages by genotyping the surviving type specimens. In addition, the study of archival documents clarifies the exact composition of type series and provides further evidence for the identification of lost types. These results support the recognition of three species-level taxa: Moltoni’s warbler, Sylvia subalpina (north-central Italy, Corsica, Sardinia and the Balearics); the western subalpine warbler, S. iberiae (North Africa, Iberia, southern France and extreme north-west Italy); and the eastern subalpine warbler, S. cantillans, with subspecies S. cantillans cantillans (southern Italy, Sicily) and S. cantillans albistriata (Balkans, Greece, western Turkey). We revise the taxonomy of the Sylvia cantillans complex, a group of phenotypically distinct warblers with mainly parapatric distributions around a large part of the Mediterranean basin. We redefine the species limits using a combination of mitochondrial and nuclear markers and we objectively link available names to the genetically defined lineages by genotyping the surviving type specimens. In addition, the study of archival documents clarifies the exact composition of type series and provides further evidence for the identification of lost types. These results support the recognition of three species-level taxa: Moltoni’s warbler, Sylvia subalpina (north-central Italy, Corsica, Sardinia and the Balearics); the western subalpine warbler, S. iberiae (North Africa, Iberia, southern France and extreme northwest Italy); and the eastern subalpine warbler, S. cantillans, with subspecies S. cantillans cantillans (southern Italy, Sicily) and S. cantillans albistriata (Balkans, Greece, western Turkey).

Conservation efforts rely on robust taxonomic assessments that should be based on critical assessment of interspecific boundaries, infraspecific variation, and potentially distinctive peripheral populations. The meadow vole (Microtus pennsylvanicus) is widely distributed across North America, including 28 morphologically defined subspecies and numerous isolated populations. Because some subspecies are of high conservation concern, we examined geographic variation across the range of the species to test existing infraspecific taxonomy in terms of local and regional diversification. We sequenced mitochondrial DNA (mtDNA) from 20 subspecies of M. pennsylvanicus and contextualized infraspecific variation through comparison of pairwise genetic distances derived from an extended data set of 63 species of Microtus. We found strong support for at least three divergent clades within M. pennsylvanicus, with observed intraspecific clade divergence exceeding that between several pairwise comparisons of sister species within Microtus. Six nuclear genes were then sequenced to test the validity of mtDNA structure and to further evaluate the possibility of cryptic, species-level diversity using Bayes factor species delimitation (BFD) analyses. BFD consistently and decisively supported multiple species based on the multilocus approach. We propose that taxonomic revision of the meadow vole is required, with the eastern clade now identified as M. pennsylvanicus (Ord 1815), the western clade as M. drummondii (Audubon and Bachman 1853), and the coastal Florida clade as M. dukecampbelli (Woods, Post, and Kilpatrick 1982). We suggest that such an arrangement would more closely reflect evolutionary history and provide critical context for further examination of distinctive southern peripheral populations that harbor novel evolutionary legacies and adaptive potential.

The mosquito Aedes aegypti (L.) is the primary vector of various infectious viruses and is typified by a polymorphic color and abundance of white scales on the body. It has been conventionally separated into two subspecies, Ae. aeg. formosus (Walker) (Aaf) and Ae. aeg. aegypti (L.) (Aaa), with Aaf considered a ‘sylvan’ form and Aaa a ‘domestic’ form. Because the two subspecies show different susceptibilities to dengue viruses it is important to understand their distribution. In this study, we collected larvae from artificial and natural habitats in southern Kenya and reared them to adults to morphologically identify subspecies. We describe the geographical distribution and relative abundance of Aaa and Aaf in Kenya, and estimate the environmental factors associated with their distributions by GIS using climate and environment data. A total of 5,243 Ae. aegypti adults were collected from 249 sites, with Aaa accounting for 22% of the specimens. The relative abundance of Aaa was higher in coastal areas versus sites in western Kenya. Aaa abundance was also higher in urbanized than forested areas, which is consistent with known ecology. In contrast and inconsistent with previous studies, both Aaa and Aaf were sympatric in artificial and natural habitats. The high relative abundance of Aaa in coastal areas might derive from old populated cities, climate, and/or introduction from abroad.

The crown-of-thorns starfish (COTS) is a coral predator that is widely distributed in Indo-Pacific Oceans. A previous phylogenetic study using partial mitochondrial sequences suggested that COTS had diverged into four distinct species, but a nuclear genome-based analysis to confirm this was not conducted. To address this, COTS species nuclear genome sequences were analysed here, sequencing Northern Indian Ocean (NIO) and Red Sea (RS) species genomes for the first time, followed by a comparative analysis with the Pacific Ocean (PO) species. Phylogenetic analysis and ADMIXTURE analysis revealed clear divergences between the three COTS species. Furthermore, within the PO species, the phylogenetic position of the Hawaiian sample was further away from the other Pacific-derived samples than expected based on the mitochondrial data, suggesting that it may be a PO subspecies. The pairwise sequentially Markovian coalescent model showed that the trajectories of the population size diverged by region during the Mid-Pleistocene transition when the sea-level was dramatically decreased, strongly suggesting that the three COTS species experienced allopatric speciation. Analysis of the orthologues indicated that there were remarkable genes with species-specific positive selection in the genomes of the PO and RS species, which suggested that there may be local adaptations in the COTS species.

Alpine Arianta populations from the Biellese Alps in Italy are characterized by imperforate, thin-shelled, dark brown shells without or with sparse light spots that resemble widespread phenotypes of Arianta arbustorum arbustorum found in calcium-deficient areas. Therefore, they were not considered a distinct taxon. However, molecular phylogenetic analyses show that they belong to a group of subspecies of A. arbustorum from the Western Alps and the Pyrenees. We classify them as a distinct subspecies, Arianta a. doriae (Paulucci, 1878), which reduces the geographical gap between the western group of subspecies of A. arbustorum and the Eastern Alps where Arianta originated. This subspecies survived the glacials in a peripheral mountain refuge at the southern margin of the Biellese Alps.

Universidade de S?o Paulo. Faculdade de Sa?de P?blica. Departamento de Epidemiologia. S?o Paulo, SP, Brazil / Instituto Oswaldo Cruz. Laborat?rio Interdisciplinar de Vigil?ncia Entomol?gica em D?ptera e Hemiptera. Rio de Janeiro, RJ, Brazil. Instituto Oswaldo Cruz. Laborat?rio Interdisciplinar de Vigil?ncia Entomol?gica em D?ptera e Hemiptera. Rio de Janeiro, RJ, Brazil. Instituto Oswaldo Cruz. Laborat?rio Interdisciplinar de Vigil?ncia Entomol?gica em D?ptera e Hemiptera. Rio de Janeiro, RJ, Brazil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Funda??o Oswaldo Cruz. Instituto Le?nidas and Maria Deane. Laborat?rio de Ecologia de doen?as transmiss?veis na Amaz?nia. Manaus, AM, Brasil. Secretaria Estadual de Sa?de de Rond?nia. Laborat?rio Central de Sa?de P?blica. Rond?nia, RO, Brazil. Instituto Oswaldo Cruz. Laborat?rio Interdisciplinar de Vigil?ncia Entomol?gica em D?ptera e Hemiptera. Rio de Janeiro, RJ, Brazil. Universidade de S?o Paulo. Faculdade de Sa?de P?blica. Departamento de Epidemiologia. S?o Paulo, SP, Brazil. Males of cryptic or closely related species present great morphological variation in their genitalia, whereas females, such as those of the Chagasi Series of the Psychodopygus Mangabeira, 1941 genus, are more similar. Therefore, our aim was to study the fine structure of the male genitalia of five species of the Chagasi Series to better understand the variation in their morphology and its influence on the copulatory process. The sand fly species were captured in the following Brazilian states: Psychodopygus chagasi (Costa Lima, 1941) (Rond?nia), Psychodopygus complexus (Mangabeira, 1941) (Tocantins), Psychodopygus squamiventris maripaensis (Floch & Abonnenc, 1946) (Amap?), Psychodopygus squamiventris squamiventris (Lutz & Neiva, 1912) (Amazonas), and Psychodopygus wellcomei Fraiha, Shaw & Lainson, 1971 (Par? and Cear?). Insects were stored in ethanol 70% (then dehydrated) and dry after they were sputtered with gold. The samples were observed under a scanning electron microscope. Microtrichiae, two types of trichoid sensilla, coeloconic and chaetic sensillae, were observed on the antenna of all species, with no difference between them. Only on the anepimeron of P. squamiventris squamiventris a modified ?racket?-like scale was observed. As for the male genitalia, the setae and structures of each species were fully described, such as the small setae on the paramere apex of the P. squamiventris subspecies, and the grooves present in this region and on the paramere lobe of P. complexus and P. wellcomei, which are impossible to observe with optic microscopy. New information is thus provided on the male genitalia, which can contribute to future bionomic studies of these species.

The long-tailed shrew, Sorex dispar Batchelder, 1911, and Gaspe shrew, S. gaspensis Anthony and Goodwin, 1924, from the Appalachian Mountains of North America have been characterized as genetically highly similar, and that one is morphologically a clinal variate of the other, i.e., there is a single species. I measured 24 characters of the skull on 196 shrews from throughout the range of the species. Geographic variation in skull shape and size was not gradual or continuous, but abrupt. These abrupt changes in morphology are associated with major water barriers, primarily the Connecticut River, middle Saint John River, and the Strait of Canso, which separates mainland Nova Scotia from Cape Breton Island. The morphological analyses presented here and previous genetic studies indicate that S. dispar and S. gaspensis are likely conspecific. Shrews with the largest skull occur from North Carolina north to Vermont and are referable to S. d. dispar with S. d. blitchi as a synonym. Shrews from New Hampshire northeast to southern New Brunswick and mainland Nova Scotia have a medium-sized skull and are referable to a new subspecies. Those from northern New Brunswick, Gaspe Peninsula of Quebec, and Cape Breton Island have a small skull and are referable to S. d. gaspensis. The skull morphology of S. d. gaspensis and the new subspecies are more similar to each other than to S. d. dispar. Results of this study differ from those of previous morphological studies because measurement error and within-group variation were reduced, which allowed for visibility of otherwise “hidden” between-group differences, or geographic variation.

Three subspecies of fin whales (Balaenoptera physalus) are currently recognized, including the northern fin whale (B. p. physalus), the southern fin whale (B. p. quoyi), and the pygmy fin whale (B. p. patachonica). The Northern Hemisphere subspecies encompasses fin whales in both the North Atlantic and North Pacific oceans. A recent analysis of 154 mitogenome sequences of fin whales from these two ocean basins and the Southern Hemisphere suggested that the North Pacific and North Atlantic populations should be treated as different subspecies. Using these mitogenome sequences, in this study, we conduct analyses on a larger mtDNA control region data set, and on 23 single-nucleotide polymorphisms (SNPs) from 144 of the 154 samples in the mitogenome data set. Our results reveal that North Pacific and North Atlantic fin whales can be correctly assigned to their ocean basin with 99% accuracy. Results of the SNP analysis indicate a correct classification rate of 95%, very low rates of gene flow among ocean basins, and that distinct mitogenome matrilines in the North Pacific are interbreeding. These results indicate that North Pacific fin whales should be recognized as a separate subspecies, with the name B. p. velifera Cope in Scammon 1869 as the oldest available name.

Theory suggests that different taxa having colonized a similar, challenging environment will show parallel or lineage-specific adaptations to shared selection pressures, but empirical examples of parallel evolution in independent taxa are exceedingly rare. We employed comparative genomics to identify parallel and lineage-specific responses to selection within and among four species of North American sparrows that represent four independent, post-Pleistocene colonization events by an ancestral, upland subspecies and a derived salt marsh specialist. We identified multiple cases of parallel adaptation in these independent comparisons following salt marsh colonization, including selection of 12 candidate genes linked to osmoregulation. In addition to detecting shared genetic targets of selection across multiple comparisons, we found many novel, species-specific signatures of selection, including evidence of selection of loci associated with both physiological and behavioral mechanisms of osmoregulation. Demographic reconstructions of all four species highlighted their recent divergence and small effective population sizes, as expected given their rapid radiation into saline environments. Our results highlight the interplay of both shared and lineage-specific selection pressures in the colonization of a biotically and abiotically challenging habitat and confirm theoretical expectations that steep environmental clines can drive repeated and rapid evolutionary diversification in birds.

Cylas formicarius F. and Euscepes batatae Waterhouse are the most damaging sweet potato insect pests globally. Both weevils are thought to have invaded the Pacific alongside the movement of sweet potato (Ipomoea batatas (L.) Lam. Convolvulaceae), with C. formicarius having originated in India and E. batatae in Central or South America. Here we compare the genetic relationships between populations of the pests, primarily in the Asia-Pacific, to understand better their contemporary population structure and their historical movement relative to that of sweet potato. Cylas formicarius has divergent mitochondrial lineages that indicate a more complex biogeographic and invasive history than is presently assumed for this insect, suggesting it was widespread across the Asia-Pacific before the arrival of sweet potato. Cylas formicarius must have originally fed on Ipomoea species other than I. batatas but the identity of these species is presently unknown. Cylas formicarius was formerly designated as three species or subspecies and the genetic data presented here suggests that these designations should be reinvestigated. Euscepes batatae has very low genetic diversity which is consistent with its historical association with sweet potato and a recent introduction to the Asia-Pacific from the Americas. The distribution of E. batatae may be narrower than that of C. formicarius in the Asia-Pacific because it has relied relatively more on human-assisted movement. Consequently, E. batatae may become more widespread in the future. Investigating the invasion history of both species will help to understand the probability and nature of future invasions.

The mitonuclear species concept hypothesizes that incompatibilities between interacting gene products of the nuclear and mitochondrial genomes are a major factor establishing and maintaining species boundaries. However, most of the data available to test this concept come from studies of genetic variation in mitochondrial DNA, and clines in the mitochondrial genome across contact zones can be produced by a variety of forces. Here, we show that using a combination of population genomic analyses of the nuclear and mitochondrial genomes and studies of mitochondrial function can provide insight into the relative roles of neutral processes, adaptive evolution, and mitonuclear incompatibility in establishing and maintaining mitochondrial clines, using Atlantic killifish (Fundulus heteroclitus) as a case study. There is strong evidence for a role of secondary contact following the last glaciation in shaping a steep mitochondrial cline across a contact zone between northern and southern subspecies of killifish, but there is also evidence for a role of adaptive evolution in driving differentiation between the subspecies in a variety of traits from the level of the whole organism to the level of mitochondrial function. In addition, studies are beginning to address the potential for mitonuclear incompatibilities in admixed populations. However, population genomic studies have failed to detect evidence for a strong and pervasive influence of mitonuclear incompatibilities, and we suggest that polygenic selection may be responsible for the complex patterns observed. This case study demonstrates that multiple forces can act together in shaping mitochondrial clines, and illustrates the challenge of disentangling their relative roles.

The genus Myotis is nearly cosmopolitan and the second-most speciose genus of mammals, but its Afrotropical members are few and poorly known. We analyzed phylogenetic and phylogeographic relationships of six of the eight known Afrotropical species using Cytb and sequences from four nuclear introns. Using Bayesian and maximum-likelihood approaches to generate single-locus, concatenated, and species trees, we confirmed prior evidence that the clade containing Afrotropical Myotis also contains both Palearctic and Indomalayan members. Additionally, we demonstrate that M. bocagii is sister to the Indian Ocean species M. anjouanensis, that this group is sister to M. tricolor and the Palearctic M. emarginatus, and find evidence suggesting that M. welwitschii is the earliest-diverging Afrotropical species and sister to the remainder. Although M. tricolor and M. welwitschii are both currently regarded as monotypic, both mitochondrial and nuclear data sets document significant, largely concordant geographic structure in each. Evidence for the distinction of two lineages within M. tricolor is particularly strong. On the other hand, geographic structure is lacking in M. bocagii, despite the current recognition of two subspecies in that species. Additional geographic sampling (especially at or near type localities), finer-scale sampling (especially in zones of sympatry), and integrative taxonomic assessments will be needed to better document this radiation and refine its nomenclature.

Male reproductive biology is described for the Southern Hemisphere long-finned pilot whale (Globicephala melas edwardii), a subspecies that regularly mass strands along the New Zealand coastline. Ten mass stranding events sampled over a 7-year period enabled assessments of key life history parameters. Sexual maturation in immature, maturing, and mature males was assessed using morphological data and histological examination of testicular tissue. Variation was observed in the age (11–15 years) and length (450–490 cm) at which individuals attained sexual maturity. Using Bayesian cumulative logit regression models, we estimated the average age and length at the attainment of sexual maturity to be 13.5 years and 472 cm, respectively. Combined testes weight, combined testes length, an index of testicular development (combined testes weight/combined testes length), and mean seminiferous tubule diameter were all good indicators of sexual maturity status. Combined testes length was the best nonhistological indicator, and all testicular measures were found to be better indicators of sexual maturation for G. m. edwardii than age or total body length. Sexual maturity was attained before physical maturity (> 40 years and 570 cm), and at a younger age and smaller body length than previously reported for Globicephala melas melas in the North Atlantic. Given the ease of collection, minimal processing, and applicability to suboptimal material collected from stranding events, future studies should assess the value of testicular size as an indicator of sexual maturity in pilot whales and other cetacean species. Estimates of the average age and length at sexual maturity for G. m. edwardii provided in this study may be used to inform population models required for conservation management of the subspecies, which is subject to high levels of stranding-related mortality.

Comparing mitochondrial and genomic phylogenies is an essential tool for investigating speciation processes, because each genome carries different inheritance properties and evolutionary characteristics. Furthermore, mitonuclear discordance may arise from ecological adaptation, historic isolation, population size changes, and sex-biased dispersal. Closely related taxa are expected to experience gene flow; however, this may not be true for insular populations or populations isolated in refugia. The four-lined snake Elaphe quatuorlineata has a fragmented distribution, separating populations of the Italian and Balkan Peninsulas, whereas several insular Aegean populations of significantly smaller body size (Cyclades island group and Skyros Island, Greece) are currently considered distinct subspecies. We constructed the species-tree phylogeny of this species utilizing genome-wide single nucleotide polymorphisms and a gene-tree based on complete cytochrome b sequences, aiming to detect convergence and discrepancies between biparentally and maternally inherited genomes. Population structuring, phylogenetic patterns and migration events among geographically defined lineages supported our hypothesis of isolation in multiple sub-refugia. Where biogeographical barriers did not restrict subsequent dispersal, extensive genetic exchange occurred between mainland Balkan populations. This process has led to the mitochondrial sweep of an ancestral mitolineage that survived only in peripheral (East Greece) and insular populations (North Cyclades and Skyros). The Central Cyclades represent an ancient lineage for both molecular markers that emerged almost 3.3 Mya. Considering their distinct morphology, insular E. quatuorlineata populations should be the future focus of an extensive sampling, especially since the mitonuclear discordance observed in this species could be related to ecological adaptations, such as the island-dwarfism phenomenon., P.K. was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant [grant number: 656006, project acronym: CoPhyMed]. This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 OD018174 Instrumentation Grant.

Recombination plays an integral role in the creation of novel genetic variation in sexually reproducing species. Despite this important role, the determinants and evolution of crossover hotspots have remained poorly understood in plants. Here, we present a comparative analysis of two rice (Oryza sativa) historical recombination maps from two subspecies (indica and japonica) using 150 resequenced genomes. Fine-scale recombination rates and crossover hotspots were validated by comparison with a consensus genetic map and empirically derived crossovers, respectively. Strikingly, nearly 80% of crossover hotspots were unique to each subspecies, despite their relatively recent divergence and broad-scale correlated recombination rates. Crossover hotspots were enriched with Stowaway and P instability factor (PIF)/Harbinger transposons and overlapped accessible chromatin regions. Increased nucleotide diversity and signatures of population differentiation augmented by Stowaway and PIF/Harbinger transposons were prevalent at subspecies-specific crossover hotspots. Motifs derived from lineage-specific indica and japonica crossover hotspots were nearly identical in the two subspecies, implicating a core set of crossover motifs in rice. Finally, Stowaway and PIF/Harbinger transposons were associated with stabilized G/C bias within highly active hotspots, suggesting that hotspot activity can be fueled by de novo variation. These results provide evolutionary insight into historical crossover hotspots as potentially powerful drivers of sequence and subspecies evolution in plants.

The number of Pithecia species has considerably increased in recent years. In the first comprehensive taxonomic revision for the genus, five species were recognized, among these, Pithecia irrorata, with two subspecies: P. irrorata irrorata and P. irrorata vanzolinii. These subspecies were elevated to full species in the most recent taxonomic revision of the genus, which was based primarily on pelage color. Additionally, it was proposed that P. irrorata was a group of undescribed species, and three additional species were described from P. irrorata: P. mittermeieri, P. rylandsi, and P. pissinattii. However, diagnoses and geographic distributions are not well defined for the species proposed, bringing confusion to subsequent studies. To address the current hypothesis on the species diversity in the P. irrorata species group, we conducted comparative analyses using the same source of evidence: pelage color variation. Material analyzed includes specimens throughout the distribution of the group in Peru, Bolivia, and Brazil. Based on our results, we recognize two groups that are morphologically diagnosable and correspond to geographically isolated populations. The senior names available for these groups are P. irrorata and P. vanzolinii. We recognize P. mittermeieri, P. rylandsi, and P. pissinattii as junior synonyms of P. irrorata. We also discuss some taxonomic inaccuracies regarding the type localities and type material for the senior and junior names, provide synonymy lists based on extensive literature review, and provide distribution maps for the valid species we recognized.

The Heermann's kangaroo rat (Dipodomys heermanni; Rodentia: Heteromyidae) is a Californian endemic primarily found in the dry, gravelly grassland and open chaparral habitats of the San Joaquin Valley. Current taxonomy (based on morphology and habitat use) recognizes nine subspecies within this kangaroo rat species. Management practices of D. heermanni primarily are based on this classification, but this taxonomy may not accurately reflect unique lineages in need of conservation. Using molecular and morphological data, we performed a phylogeographic assessment of D. heermanni across the full geographic range of the species. Phylogenetic and network analyses of mitochondrial data from over 90 museum specimens (representing all nine subspecies distributed across the range of the species) revealed no substantial genetic differentiation within D. heermanni. Similarly, a geometric morphometric analysis of the crania of over 200 adult D. heermanni museum specimens (again representing all subspecies across the geographic distribution of species) resulted in no apparent morphological clustering across geography. Our results indicate that recognition of none of the nine subspecies is warranted and that conservation and management practices of D. heermanni are in need of revision.

Disjunct distributions within a species are of great interest in systematics and biogeography. This separation can function as a barrier to gene flow when the distance among populations exceeds the dispersal capacity of individuals, and depending on the duration of the barrier, it may eventually lead to speciation. Here, we describe patterns of geographic differentiation of 2 disjunct populations of Diglossa brunneiventris separated by ∼1,000 km along the Andes. Diglossa brunneiventris vuilleumieriis isolated in northern Colombia, while Diglossa brunneiventris brunneiventris has a seemingly continuous distribution across Peru, Bolivia, and Chile. We sequenced mitochondrial and nuclear DNA of the 2 D. brunneiventris subspecies to evaluate whether they form a monophyletic clade, while including the other 3 species within the carbonaria complex (D. gloriosa, D. humeralis, and D. carbonaria). We also constructed ecological niche models for each D. brunneiventris subspecies to compare their climatic niches. We found that when using all available molecular data, the 2 D. brunneiventris subspecies are not sister lineages. In fact, each subspecies is more closely related to other species in the carbonaria complex. Our niche modeling analyses showed that the subspecies are occupying almost entirely different climatic niches. An additional and not expected result was that the carbonaria complex might encompass more cryptic species than previously considered. We suggest reevaluating the taxonomic status of these brunneiventris populations, especially the northern subspecies, given its highly restricted range and potential threatened status.LAY SUMMARYDiglossa brunneiventris has two disjunct populations separated by more than 1,000 km along the Andes (longer than the span of Ecuador).Although similar in coloration, the two populations exhibit differences in body size and wing length.Whether these two populations belong to the same species and how recently they were separated are still open questions.We provide molecular and climatic evidence that suggests the two populations are not sister taxa.Genetic evidence suggests the northern population is related to populations of Diglossa humeralis from the Eastern Andes in Colombia, while the southern population is more related to populations of D. humeralis from Ecuador and southern Colombia.The northern population has a restricted and fragmented range and its conservation status depends on evidence for its recognition as an independent lineage.

Seaside Sparrows (Ammospiza maritima) are tidal salt marsh endemic passerines found along the Atlantic and Gulf coasts of North America. Currently, there are 7 described subspecies, and “MacGillivray’s” Seaside Sparrow (A. m. macgillivraii) is the name given to the Atlantic coast subspecies breeding from North Carolina to northern Florida. In 2019 the US Fish and Wildlife Service received a petition to list this subspecies under the Endangered Species Act due to shrinking populations and loss of marsh habitat, which necessitated a Species Status Assessment. As part of the Species Status Assessment, we analyzed genetic (microsatellite and mitochondria) data from 464 Seaside Sparrows from Connecticut to Florida, USA, to infer population connectivity (gene flow) among Atlantic coast populations, and to assess the concordance of population genetic data with the putative ranges of the subspecies. Bayesian cluster analysis (program Structure) indicates three genetically distinct population segments: (1) Florida + Georgia, (2) Charleston, South Carolina, and (3) North Carolina to Connecticut. The population in Charleston, South Carolina was the most strongly differentiated based on microsatellite data, and harbored a unique mitochondrial haplotype not shared by other sampling locations, possibly reflecting long-standing isolation. Our results indicate population genetic discordance with currently described ranges of the subspecies of Seaside Sparrow and provide grounds for the consideration of separate management plans for the three populations.

Identifying population genetic structure is useful for inferring evolutionary process and comparing the resulting structure with subspecies boundaries can aid in species management. The American Kestrel (Falco sparverius) is a widespread and highly diverse species with 17 total subspecies, only 2 of which are found north of U.S./Mexico border (F. s. paulus is restricted to southeastern United States, while F. s. sparverius breeds across the remainder of the U.S. and Canadian distribution). In many parts of their U.S. and Canadian range, American Kestrels have been declining, but it has been difficult to interpret demographic trends without a clearer understanding of gene flow among populations. Here we sequence the first American Kestrel genome and scan the genome of 197 individuals from 12 sampling locations across the United States and Canada in order to identify population structure. To validate signatures of population structure and fill in sampling gaps across the U.S. and Canadian range, we screened 192 outlier loci in an additional 376 samples from 34 sampling locations. Overall, our analyses support the existence of 5 genetically distinct populations of American Kestrels—eastern, western, Texas, Florida, and Alaska. Interestingly, we found that while our genome-wide genetic data support the existence of previously described subspecies boundaries in the United States and Canada, genetic differences across the sampled range correlate more with putative migratory phenotypes (resident, long-distance, and short-distance migrants) rather than a priori described subspecies boundaries per se. Based on our results, we suggest the resulting 5 genetically distinct populations serve as the foundation for American Kestrel conservation and management in the face of future threats.

Four main challenges that can underpin ongoing, intransigent debates about species limits in birds are reviewed: allopatry (population subdivision vs. speciation), geographically widespread introgression of mitochondrial DNA (mtDNA), recent speciation, and selection. Examples from birds of the Australian region show how these challenges, their interplay, and the molecular-phenotypic discordance they generate can clarify or mislead species limits. Examples of how phylogenetic frameworks help reject or retain hypotheses of species limits under these challenges are given. Although mtDNA's strengths and limitations are well known, an underappreciated limitation of mtDNA is geographically widespread introgression that homogenizes mtDNA diversity across species, subspecies, or population boundaries and across hundreds of kilometers. The resulting discordance between mtDNA and phenotype can be profound. If undetected, the setting of species limits and evolutionarily significant units are misled. An example shows how recent genomic analyses can detect and solve the problem. Other examples concern legacy mtDNA-only datasets. These are often essentially unfinished studies leaving residual uncertainty in species limits. Examples illustrate when the possibility of large-scale introgression across species boundaries needs to be considered, and how genomic scale data offer solutions. Researchers must carefully parse 3 questions: has there been introgression of mtDNA and, if so, which population genetics-based driver has caused introgression, and do species limits need altering? Understanding of allopatry, mtDNA introgression, recent speciation, and selection must be properly integrated if species limits are to be robustly understood and applied with maximum benefit in downstream applications such as conservation and management.LAY SUMMARYBiologists still debate what species are and how we should best demarcate one species from another.The debates reflect a curious aspect of ongoing evolution: although we expect each species to have its own unique DNA, that is often not the case for many pieces of DNA that we look at.My paper reviews some of the major reasons why each species may not have its own unique DNA.I focus on birds of the Australian region but the lessons apply to ornithologists everywhere.This is important because we want to use DNA wisely to work out which populations and individuals belong to which species.Then we can best conserve and manage the biodiversity that nurtures us in so many ways.I hope my article will guide ornithologists everywhere in how they might deal with the thorny issues associated with these debates.

Despite the acknowledged importance of defining avian species limits to scientific research, conservation, and management, in practice, they often remain contentious. This is true even among practitioners of a single species concept and is inevitable owing to the continuous nature of the speciation process, our incomplete and changing understanding of individual cases, and differing interpretations of available data. This issue of Ornithology brings together several papers on species limits, some more theoretical and general, and others case studies of specific taxa. These are viewed primarily through the lens of the biological species concept (BSC), by far the most widely adopted species concept in influential ornithological works. The more conceptual contributions focus on the importance of the integrative approach in species delimitation; the importance of considering selection with the increasing use of genomic data; examinations of the effectiveness of the Tobias et al. character-scoring species limits criteria; a review of thorny issues in species delimitation using examples from Australo-Papuan birds; and a review of the process of speciation that addresses how population divergence poses challenges. Case studies include population genomics of the American Kestrel (Falco sparverius); an integrative taxonomic analysis of Graceful Prinia (Prinia gracilis) that suggests two species are involved; and a reevaluation of species limits in Caribbean Sharp-shinned Hawk (Accipiter striatus) taxa.LAY SUMMARYWe provide a brief overview of the science of biodiversity and how it is applied to categorize organisms, particularly at the species level.Speciation is a divergence process with an outcome that might produce species but often does not.This process is continuous, but our taxonomic categories are discrete, so it can be difficult to determine exactly where a divergent population fits in our categorization scheme.Ongoing changes in knowledge, sampling, data, and interpretation are leading to many improvements in the delimitation of bird species limits.A series of articles in this issue of Ornithology make it clear that progress (and changes) will continue to be made, especially when using approaches that integrate information from multiple datasets.

Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans, whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences—including a novel SC isolate—revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large-scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.