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Aim: Synthesize literature on genetic structure within species to understand how geographic features and species traits influence past responses to climate change. Location: North America. Time Period: We synthesized phylogeographic studies from 1978 to 2023, which describe genetic lineages that diverged during the Pleistocene (≥11,700 years ago). Major Taxa Studied: Mammals. Methods: We conducted a literature review to map genetic breaks in species distributions, then tested a set of geographic hypotheses (e.g., mountains, rivers) to explain their position by comparing break locations to a grid within each species' sampled range using logistic regression. We then conducted a meta‐analysis using species‐specific model estimates to ask if life‐history traits explained variation in which barriers were most important in species' past response to climate change. Results: Our findings reveal heterogeneity in both where North American mammal phylogeography has been studied and the density of genetic breaks across 229 species. We found relatively high concordance among carnivores, ungulates and lagomorphs, where breaks were associated with mountains, major water bodies and relatively even terrain. In contrast, we found high variability within rodents and shrews, and no evidence that intrinsic factors related to dispersal ability explained the importance of hypothesized barriers across all species. Main Conclusions: Southern Mexico is a hotspot for genetic breaks that has yet to be integrated into the broader story of North American phylogeography. We show that mountains and major water bodies play particularly important roles as barriers, but substantial variation across species within orders suggests that there is more to the story besides shared climatic or phylogenetic histories. Thus, understanding the phylogeography of individual species will continue to be important given that our results suggest high variability in how species may respond to future global change. [ABSTRACT FROM AUTHOR]

For almost 200 years, the taxonomy of cutthroat trout (Oncorhynchus clarkii), a salmonid native to Western North America, has been in flux as ichthyologists and fisheries biologists have tried to describe the diversity within these fishes. Starting in the 1950s, Robert Behnke reexamined the cutthroat trout and identified 14 subspecies based on morphological traits, Pleistocene events, and modern geographic ranges. His designations became instrumental in recognizing and preserving the remaining diversity of cutthroat trout. Over time, molecular techniques (i.e. karyotypes, allozymes, mitochondrial DNA, SNPs, and microsatellite arrays) have largely reinforced Behnke's phylogenies, but have also revealed that some relationships are consistently weakly supported. To further resolve these relationships, we generated de novo transcriptomes for nine cutthroat subspecies, as well as a Bear River Bonneville form and two Colorado River lineages (blue and green). We present phylogenies of these subspecies generated from multiple sets of orthologous genes extracted from our transcriptomes. We confirm many of the relationships identified in previous morphological and molecular studies, as well as discuss the importance of significant differences apparent in our phylogenies from these studies within a geological perspective. Specific findings include three distinct clades: (1) Bear River Bonneville form and Yellowstone cutthroat trout; (2) Bonneville cutthroat trout (n = 2); and (3) Greenback and Rio Grande cutthroat trout. We also identify potential gene transfer between Bonneville cutthroat trout and a population of Colorado River green lineage cutthroat trout. Using these findings, it appears that additional groups warrant species‐level consideration if other recent species elevations are retained. [ABSTRACT FROM AUTHOR]

Lecidea varians is among the most common and abundant bark-dwelling crustose lichens in temperate eastern North America. As presently delimited, it is highly variable, including chemical and morphological diversity well beyond that currently accepted for most lichen species. The generic placement of L. varians has also been questioned for decades. It has long been recognized as aberrant in Lecidea and Pyrrhospora, excluded from Lecidella, and more recently transferred to Traponora. Drawing from the results of extensive chemical, molecular phylogenetic and morphological studies, we show that L. varians and its relatives represent a previously unrecognized lineage within the speciose lichen family Lecanoraceae. The lineage appears to occupy an isolated position, distinct from the aforementioned genera, and is newly described as the genus Xanthosyne (typified by L. varians). The chemical and morphological variation within L. varians is mirrored by, but not entirely correlated with, considerable molecular diversity. A new taxonomy is proposed for L. varians and its relatives to serve as a framework for future studies. Three species are recognized: X. varians (≡ Lecidea varians), common and widespread in parts of North America; X. granularis, a new species from the Atlantic Coast of eastern North America that differs morphologically from X. varians in having a leprose thallus; and X. sharnoffiorum, a new species also found mainly along the Atlantic Coast of eastern North America, which has a coarsely granular, non-leprose thallus and produces a unique, unidentified xanthone. Multiple well-supported lineages were recovered within X. varians that correlate to varying degrees with chemical and morphological variability, as well as geographic distribution. Eight subspecies are recognized to accommodate the variation within X. varians: X. varians subsp. exigua comb. nov. (≡ Lecidea exigua) characterized by the presence of atranorin and a consistent set of three xanthones, is widespread in southern Europe and western North America (coastal California); X. varians subsp. varians (≡ Lecidea varians) is distributed mainly in northeastern North America and produces thuringione and arthothelin; X. varians subsp. morsei subsp. nov. is morphologically and chemically variable, with one chemotype (thiophanic acid) with a northeastern distribution, and the other with a unique and unidentified xanthone, found mainly in the interior U.S.A.; X. varians subsp. obscura subsp. nov. occurs mainly in the central U.S.A. and North Temperate regions, produces a unique, unidentified xanthone and generally has black apothecia with green epihymenial pigments; X. varians subsp. pseudomorsei subsp. nov. and X. varians subsp. submorsei subsp. nov. resemble X. varians subsp. morsei but differ in molecular sequence characters; X. varians subsp. subtilis comb. nov. (≡ Lecidea subtilis) and X. varians subsp. subexigua subsp. nov. occur in the Appalachian Mountains, the former producing atranorin and the latter lacking atranorin, both with thiophanic acid with or without other xanthones. In an addendum, Lecidella subviridis is discussed with respect to the genus Xanthosyne. An identification key is provided for all species and their subspecies within Xanthosyne. [ABSTRACT FROM AUTHOR]

The taxonomic history of nominal subspecies of Danaus gilippus is reviewed. The historical record together with analysis of both morphological and molecular characters suggest that the current infraspecific nomenclature is in need of revision. The absence of DNA barcode differences and lack of consistent morphological differences in wing maculation in western and eastern populations in continental North America currently assigned to subspecies D. g. thersippus and D. g. berenice, respectively, raise the possibility that only a single subspecies, D. g. berenice, should be recognized. Recently published isotopic evidence for connectivity between eastern and western populations of D. gilippus, and potential ecological consequences of the relatively low numbers present in the spring and summer breeding range of the eastern migratory populations of the monarch, Danaus plexippus, are briefly discussed. [ABSTRACT FROM AUTHOR]

Northern bog lemmings, Mictomys (Synaptomys) borealis, are currently being assessed for protections under the U.S. Endangered Species Act. A major impediment to comprehensive evaluation is a deficiency of data towards understanding the biology of these rodents. Inherent rarity and scarce specimen sampling, despite a continent-wide distribution, has precluded our ability to implement modern methods for resolving taxonomy, evolutionary history, and investigating multiple other species traits. Here we use a maternally inherited locus (mitochondrial cytochrome b) and between 5939 and 11 513 nuclear loci from reduced representation sequencing (ddRADseq) to investigate the evolutionary history of northern bog lemmings. We (1) qualify evidence based on morphological and early molecular studies for the genus assignment of Mictomys, (2) test the validity of multiple sub-species designations, (3) provide spatial and temporal historical biogeographic perspectives, and (4) discuss how incomplete sampling might influence conservation efforts. Both mitochondrial and nuclear datasets exhibit deep divergence and paraphyly between two recognized species, the northern (Mictomys borealis) and southern (Synaptomys cooperi) bog lemmings. Based on mtDNA, the geographically isolated subspecies (M. b. sphagnicola) was found to be divergent from all other specimens. The remainder of the species exhibited shallow intra-specific differentiation in mtDNA, however, nuclear data supports genetic distinction consistent with four geographic subspecies. Recent coalescence of all northern bog lemmings (except for M. b. sphagnicola) reflects divergence in multiple refugia through the last glacial cycle, including a well-known coastal center of endemism and multiple regions south of continental ice sheets. Regional lineages across North America suggest strong latitudinal displacement with global climate change, coupled with isolation-reconnection dynamics. This taxon suffers from a lack of modern samples through most of its distribution, severely limiting the interpretation of ongoing evolutionary processes, particularly in southern portions of the species' range. Limited voucher specimen sampling of vulnerable populations could aid in rigorous conservation decision-making. [ABSTRACT FROM AUTHOR]

Context: Meaningful intraspecific taxonomy allows for robust classification of within-species diversity and effective conservation and management. Subspecies definitions broadly agree that subspecies are groups of populations that exhibit some degree of geographic separation, phenotypic distinctiveness, and unique evolutionary potential. The most powerful assessments of within-species taxonomy are those that employ multiple lines of evidence, including phenotypic, ecological, geographic and genetic, to delineate evolutionarily definable units. Aims: Here we describe how genetic data can be integrated into intraspecific taxonomy. Methods: We use our experiences incorporating genetic data to assess taxonomy within black-tailed and mule deer (Odocoileus hemionus), a widespread and highly mobile species with significant phenotypic variation and a complex evolutionary history. Key results: High-resolution sampling of individuals across the landscape and loci across the genome yielded accurate estimates of genetic variation in black-tailed and mule deer and better insight into the evolutionary processes that generate and maintain diversity. Conclusions: Integrating genetic data has informed meaningful intraspecific taxonomy within O. hemionus , showing support for the following five subspecies: two black-tailed deer subspecies (Columbian O. h. columbianus and Sitka O. h. sitkensis) and three mule deer subspecies (mainland O. h. hemionus and the two island subspecies, O. h. cerrosensis on Cedros Island and O. h. sheldoni on Tiburón Island). Implications: Our integrative approach provides a framework for incorporating genetic data in intraspecific taxonomy in other deer species. Meaningful classification of biodiversity through appropriate taxonomy provides the foundation for effective conservation and management. Integrating genetic data has helped inform within-species taxonomy by helping us understand how diversity is generated and maintained. We show how this integrative approach has worked well to resolve taxonomy in black-tailed and mule deer in North America, an example that provides a framework for assessing taxonomy in other species. [ABSTRACT FROM AUTHOR]

Jumping mice (subfamily Zapodinae) occur across most of North America (Zapus and Napaeozapus) and in confined regions in China (Eozapus). Recent molecular phylogenies have revised their taxonomy, raising some subspecies to full species and synonymizing others. This taxonomic revision has implications for subspecies conservation and management, since Z. hudsonius preblei and Z. h. luteus are legally protected by the United States federal Endangered Species Act (ESA), while Z. h. campestris and Z. trinotatus orarius are conserved in parts of their range. Several molecular studies have either synonymized Z. h. preblei with Z. h. campestris (and Z. h. intermedius) or grouped it with Z. h. alascensis and Z. h. tenellus as a widely distributed "Northern" lineage, arguing against its continued legal protection. However, genetic differentiation is a proxy for historical but not always adaptive distinctiveness, and the ESA considers both for conservation (i.e., Evolutionarily Significant Units). This study uses geometric morphometrics to compare adaptive distinctiveness of jumping mice subspecies. This compares scaled cranial shape, leading to insights that differ from linear measurements. For broader insights, cranial morphology was compared within jumping mice and with the closely related birch mice. Subspecies pairs within the three traditionally accepted Zapus species were ranked in order morphometric distinctiveness. The most distinct pair was found to be Z. h. preblei vs. Z. h. alascensis, members of the same genetic lineage. Other morphometrically distinct subspecies pairs were parts of the same or different genetic lineages, some having been elevated to full species. Other members of especially distinct pairs include Z. princeps oregonus, Z. p. saltator, Z. p. cinereus, Z. p. minor, Z. p. pacificus, and Z. p. idahoensis. Other aspects of adaptive distinctiveness should be examined in these subspecies for validation and to prioritize conservation efforts. [ABSTRACT FROM AUTHOR]

Salix vitellina L., or golden willow, was described by C. Linnaeus in 1753. It was later considered to be affiliated with S. alba, and its taxonomic rank has been changed to variety, subspecies, and form. A recent proposal designated it as a form of S. alba × S. fragilis. The goal of this study was to verify the taxonomic designation of S. vitellina using morphological characteristics including ovule number. A few specimens of S. vitellina from Europe and North America, including the lectotype LINN1158.13, were analyzed. It was recorded that S. vitellina has an ovule index of 6–10, with most valves with four and five ovules and less than 50% of valves with five ovules. These ovule parameters were similar to those of S. alba. The other floral characteristics also indicated that S. vitellina is associated with S. alba. No signs of androgyny or flower aberrations, commonly occurring in willow hybrids, were found in the specimens of S. vitellina. Thus, the analyses did not corroborate the hybrid origin of S. vitellina. The ovule analysis also confirmed that f. chermesina with orange–red stems is also a taxon of S. alba, which differs from f. vitellina by a greater ovule index of 12–16. [ABSTRACT FROM AUTHOR]

In North America, the population genetic structure of many raptor species has been shaped by patterns of post‐glacial population expansion and anthropogenic forces, such as the widespread use of the organochlorine pesticide dichlorodiphenyltrichloroethane (DDT) during the mid‐20th century. While common themes of post‐glacial avian population expansion have emerged, little is known about the genetic impacts of DDT on raptor species that experienced a population bottleneck but were not the focus of conservation efforts. We investigated how the combination of post‐Pleistocene environmental change and the DDT‐era population bottleneck have influenced the contemporary population structure of Merlins Falco columbarius in North America. We genotyped migrating Merlins across North America (n = 272) at 23 polymorphic microsatellite loci and generated sequence data for a 569‐base‐pair segment of the mitochondrial control region. We used hierarchical analysis of molecular variance, pairwise FST/ϕST comparisons and Bayesian clustering analyses to assess genetic differentiation between individuals from eastern and western North America, distinct migratory flyways, and three recognized North American subspecies. Across all analyses, we found low or no population differentiation, suggesting that North American Merlins largely comprise one panmictic population showing evidence of a post‐glacial population expansion with little genetic differentiation detected between regions. Furthermore, we did not detect a contemporary signal of a genetic bottleneck that could have resulted from the DDT‐era population decline with the markers used in this study. Consistent with other avian species, we found a correlation between allele length variation at a microsatellite isolated from the 3′ untranslated region of the ADCYAP1 gene and migratory versus sedentary characteristics in Merlin subspecies. We detected two common mitochondrial control region haplotypes in the geographical regions sampled, a unique pattern among other widespread North American raptor species. This study furthers our understanding of the genetic and demographic history of Merlins in North America and can inform future genomic studies of this species. [ABSTRACT FROM AUTHOR]

The Gray Wolf (Canis lupus) is viewed as one of the most diverse mammal species. In North America, the diversity of its forms is debated, with views conflicting on subspecies designation. The present study aimed to reinvestigate the skull morphometric variation among North American populations while attempting to unveil underlying causal factors. A large sample of vouchered museum skulls, collected from 12 ecogeographical populations spanning the North American range of the species, was examined and 21 craniodental characters were measured. Skull shape showed within-population variations but provided evidence for a high morphological affinity among populations. Allometric analyses also pointed to similar evolutionary paths among populations. However, significant size-related differentiation was revealed within and among populations. Skull size could be related to three insulin-like growth factor-1 gene (IGF-1) alleles. Ecological conditions that should determine prey type and availability accounted for most of the skull size variation. In contrast, no evidence of geographical isolation of populations was detected. The results support the existence of a single morphological pool of North American gray wolf populations that could be equated with one taxonomic unit. This study raises again the question of the diversity of forms in this species in North America and calls into question the validity of previously recognized species and subspecies based on genetics and morphology. [ABSTRACT FROM AUTHOR]

Simple Summary: Morphological characteristics related to sex-age class in introduced species during the early invasion stages, before further environmental adaptation, may indicate important information regarding their adaptability. For raccoons introduced to different regions in middle Japan, the results of multiple linear regression on body length showed that males were larger than females and body length increased with age class, while there was no difference between regions. The cranial size, which indicated different allometry in each sex, regressed positively according to increasing age class, body length, and body mass index in both sexes; however, it only differed between regions for females. Therefore, our results supported the hypothesis that older individuals with larger body sizes have an advantage in intrasexual selection and competition for food resources in raccoons. Considering the fact that multiple subspecies are sympatric in North America and the morphometrics of introduced raccoons in Japan were inconsistent with any of them, it is likely that hybridization occurred prior to introduction or naturalization. Further studies are necessary to demonstrate subspecific hybridization and its impact on morphological and ecological changes. Although the genetic distribution of introduced raccoons (Procyon lotor) in recent years is well known, few studies have examined their morphometrics, especially the relationships between sex and age in the introduced populations. The aim of this study was to describe the morphological characteristics of raccoons from parts of eastern and western Japan during their early invasion stages, focusing on the relationships between body length and the principal component of craniometrics, with region, sex, age class, body length, and body mass index using a regression model. The body length increased more in males than females and in the older age class, supporting the association with intrasexual selection and competition for food resources. Positive relationships for body length and body mass index were found in craniometric analyses, particularly regarding cranial size components, in addition to age class for both sexes, while cranial size also differed between regions for females. The relationship between body length and craniometrics was inconsistent with that of subspecies originating in North America. Given the sympatric distribution of haplotypes of multiple subspecies without reproductive-isolating barriers in North America and in several introduced areas, hybridization must have occurred prior to the introduction or naturalization of this species. [ABSTRACT FROM AUTHOR]

The gray wolf, Canis lupus , once inhabited much of the northern hemisphere worldwide; however, persecution drove its populations almost to extinction. In North America, diverse conservation programs have been implemented in the last decades to recover its populations in the wild, many of them guided by the historical distribution of the gray wolf subspecies. Over time, several authors have proposed different subspecies classifications. Nevertheless, most of them are mutually inconsistent regarding the number and distribution of subspecies, creating controversy when implementing conservation programs. This study used niche-based distribution models and cluster analysis to explore the bioclimatic profiles of C. lupus across North America and compare them with different subspecies classifications to identify environmental correlatives that support the proposed designations. Our cluster analysis results indicate that the optimal number of climatic groups was five, designated as Northern, Eastern, Western, Coastal, and Southern groups, with transitional overlap boundaries located at their peripheries, indicating climatic gradients between them and supporting the idea of intergrading zones. The geographic ranges of these groups mismatched to a different extent with all subspecies delimitations. In general, the boundaries of putative subspecies did not match the climatic patterns of North America. Our results may contribute to the recovery programs underway for this carnivore by identifying suitable areas for the release of individuals from specific lineages. New approaches to characterizing the intraspecific variation of the gray wolf should include all evidence available, including genetic, morphological, and ecological information. [ABSTRACT FROM AUTHOR]

Adaptation to local environments is common in widespread species and the basis of ecological speciation. The song sparrow (Melospiza melodia) is a widespread, polytypic passerine that occurs in shrubland habitats throughout North America. We examined the population structure of two parapatric subspecies that inhabit different environments: the Atlantic song sparrow (M. m. atlantica), a coastal specialist, and the eastern song sparrow (M. m. melodia), a shrubland generalist. These populations lacked clear mitochondrial population structure, yet coastal birds formed a distinct nuclear genetic cluster. We found weak overall genomic differentiation between these subspecies, suggesting either recent divergence, extensive gene flow, or a combination thereof. There was a steep genetic cline at the transition to coastal habitats, consistent with isolation by environment, not isolation by distance. A phenotype under divergent selection, bill size, varied with the amount of coastal ancestry in transitional areas, but larger bill size was maintained in coastal habitats regardless of ancestry, further supporting a role for selection in the maintenance of these subspecies. Demographic modeling suggested a divergence history of limited gene flow followed by secondary contact, which has emerged as a common theme in adaptive divergence across taxa. [ABSTRACT FROM AUTHOR]

Subalpine fir, Abies lasiocarpa, occurs throughout western North America, often in forest–tundra parkland. To resolve the presence of varieties in this species, we surveyed microsatellite genetic markers in 11 populations containing three putative varieties of Abies lasiocarpa: (1) var. lasiocarpa, (2) var. bifolia, and (3) var. arizonica. We tested primers from related taxa, and 13 of the best primer pairs were used for assays. Within populations, both heterozygosity and allelic richness were approximately 10% lower in var. lasiocarpa. The STRUCTURE procedure struggled to assign populations to groups correctly; at K = 3, individuals were assigned to their putative varieties with approximately 70% accuracy. Regardless, both lasiocarpa and bifolia were correctly assigned more than expected by chance, indicating that these taxa are distinct. A dendrogram of genetic distances showed var. arizonica to exhibit higher evolutionary distance from the other two varieties and serves as an outgroup. The dendrogram also showed a nesting of var. bifolia clades within var. lasiocarpa, indicating a complex relationship between var. lasiocarpa and var. bifolia. Comparisons among the STRUCTURE population assignments for K = 2, K = 3, and K = 4 identified populations with cryptic admixture and indicate a "lasiocarpa–bifolia" subspecies complex that warrants further study. [ABSTRACT FROM AUTHOR]

Plumage pigmentation is fundamental to a bird's phenotype, with pigment deposition causing relative crypsis or conspicuousness, depending on the environmental context. Geographic variation in plumage melanin tends to be predictable, suggesting that aspects of climate cause local matching of plumage to environment via genetic adaptation. Ecogeographic rules describe this predictability: Gloger's rule predicts that populations in wetter and warmer environments will be more pigmented; Bogert's Rule predicts more pigmentation in cold environments. The Great Horned Owl (Bubo virginianus) exhibits extensive geographic variation in the degree of melanin-based pigmentation. We examined fine-scale spatial variation in owl plumage melanism along environmental gradients in southwestern North America. We tested whether variation is explained by either of two non-mutually exclusive hypotheses: (1) a history of allopatric divergence between subspecies or (2) in situ local adaptation consistent with ecogeographic rules. The allopatric divergence hypothesis predicts a bimodal distribution of plumage melanism, with a geographic cline across a zone of secondary contact, whereas the local adaptation hypothesis predicts that climate explains variation independently of geography. Using a colorimeter, we measured coloration in 101 museum specimens of breeding-season Great Horned Owls that had been obtained from variable environments and elevations. Specimens previously identified as separate subspecies were distinguishable by colorimetry. Plumage lightness, however, was continuously distributed, rather than bimodal. While accounting for males having reduced pigmentation relative to females, linear models revealed that lighter plumage was associated with low latitude, low elevation, high temperature, and low precipitation. These findings suggest that variation in Great Horned Owl plumage pigmentation is best understood as continuous ecogeographic variation, consistent with ecogeographic predictions, and currently maintained in situ along multiple environmental gradients that characterize the "sky island" topography of the southwestern USA. [ABSTRACT FROM AUTHOR]

Vireo gilvus (Warbling Vireo) is the smallest bird species in North America known to eject Molothrus ater (Brown-headed Cowbird) eggs from their nests. Populations eject parasitic eggs in central North America and the Great Lakes region but not in western North America. The geographic differences in behavior may reflect the range distributions of 2 subspecies. However, experimental studies of egg ejection in eastern populations are currently lacking. To address this gap, I experimentally parasitized 3 Warbling Vireo nests in Massachusetts using real and model cowbird eggs. At all 3 nests, Warbling Vireos ejected the parasitic egg. To my knowledge, this is the first documented account of parasitic egg ejection by Warbling Vireos east of the Great Lakes region. [ABSTRACT FROM AUTHOR]

Although least chipmunks (Neotamias minimus) are a widely distributed North American species of least concern, the southernmost population, N. m. atristriatus (Peñasco least chipmunk), is imperiled and a candidate for federal listing as a subspecies. We conducted a phylogeographic analysis across the N. minimus range to assess genomic differentiation and distinctiveness of the N. m. atristriatus population. Additionally, we leveraged the historical component of sampling to conduct a temporal analysis of N. minimus genetic diversity and also considered climate change effects on range persistence probability by projecting a species distribution model into the IPCC5 RCP 2.6 and 8.5 scenarios. We identified three geographically structured groups (West, North, and South) that were supported by both mitochondrial and nuclear data. N. m. atristriatus grouped within a unique South subclade but were not reciprocally monophyletic from N. m. operarius, and nuclear genome analyses did not separate N. m. atristriatus, N. m. caryi, and N. m. operarius. Thus, while least chipmunks in the Southwest represent an evolutionary significant unit, subspecies distinctions were not supported and listing of the Peñasco population as a Distinct Population Segment of N. m. operarius may be warranted. Our results also support consideration of populations with North and West mitogenomes as two additional evolutionary significant units. We found that N. minimus genetic diversity declined by ~87% over the last century, and our models predicted substantial future habitat contraction, including the loss of the full contemporary ranges of N. m. atristriatus, N. m. arizonensis, and N. m. chuskaensis. [ABSTRACT FROM AUTHOR]

Aim: A central aim of biogeography is to understand how biodiversity is generated and maintained across landscapes. Here, we establish phylogenetic and population genetic patterns in a widespread reptile to quantify the influence of historical biogeography and current environmental variation on patterns of genetic diversity. Location: Western North America. Taxon: Western terrestrial garter snake, Thamnophis elegans. Methods: We used double‐digest RADseq to estimate phylogenetic relationships and characterize population genetic structure across the three widespread subspecies of T. elegans: T. e. vagrans (wandering garter snake), T. e. elegans (mountain garter snake) and T. e. terrestris (coast garter snake). We assessed patterns of dispersal and vicariance across biogeographic regions using ancestral area reconstruction (AAR) and deviations from isolation‐by‐distance across the landscape using estimated effective migration surfaces (EEMS). We identified environmental variables potentially shaping local adaptation in regional lineages using genetic‐environment association (GEA) analyses. Results: We recovered three well‐differentiated genetic groups that correspond to the three subspecies. AAR analyses inferred the eastern Cascade Range as the ancestral area, with dispersal to both the east and west across western North America. Populations of T. e. elegans displayed a latitudinal gradient in genetic variation across the Sierra Nevada and northern California, while populations of T. e. terrestris show discrete genetic breaks consistent with well‐known biogeographic barriers. Lastly, GEA analyses identified allele frequency shifts at loci associated with a common set of environmental variables in both T. e. elegans and T. e. terrestris. Main Conclusion: T. elegans is composed of distinct evolutionary lineages, each with its own geographic range and history of diversification. T. e. elegans and T. e. terrestris show unique patterns of diversification as populations dispersed from east to west and while adapting to the new environments they colonized. Historical events, landscape features and environmental variation have all contributed to patterns of differentiation in T. elegans. [ABSTRACT FROM AUTHOR]

The Salt Creek pupfish, Cyprinodon salinus salinus Miller, 1943 is endemic to Death Valley, California, USA, and resides as a single population within one of the most extreme inland aquatic environments capable of supporting fish. Here we report the sequencing of complete 16,499 base pair (bp) mitochondrion genomes from four C. salinus salinus individuals. The mitochondrial genome of C. salinus salinus comprises 13 protein-coding regions, 12S and 16S rRNAs, 22 tRNAs, and an 832 bp D-loop region. The first reported single nucleotide polymorphisms (SNPs) were identified within the mtDNA of C. salinus salinus, with the four mitogenomes exhibiting only 0.0485% nucleotide sequence divergence indicative of low intraspecific variation. These complete mitogenomes will facilitate future genetic analyses of intraspecific diversity between the two described subspecies of C. salinus as well as other Cyprinodon pupfishes in southwestern North America. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Integrated studies of the geographical, ecological, and historical factors that shape intraspecific phenotypic and genetic variation can help us to decipher the processes leading to geographic patterns of population divergence and speciation. We quantify and compare morphological and genetic variation in the Loggerhead Shrike (Lanius ludovicianus Linnaeus, 1766), a broadly distributed passerine in North America with both migratory and non-migratory populations that occupy a diversity of habitats and topographies. The geographic distributions and patterns of differentiation among subspecies suggest that migration has strongly impacted population divergence, including the habit of migrating itself, but also dispersal. Patterns of mitochondrial and nuclear genetic differentiation can be attributed to female-biased dispersal and to increased dispersal rates and distances in migratory populations. Weak phenotypic differentiation among migratory versus migratory and non-migratory populations suggest that migration may more strongly affect morphology than adaptation to local habitats. Our results generally support previous subspecific designations with two notable exceptions. We found little genetic differentiation between two subspecies (Lanius ludovicianus gambeli Ridgway, 1887 and Lanius ludovicianus mexicanus C.L. Brehm, 1854), but identify a new, distinct subspecies, which we refer to as Lanius ludovicianus centralis ssp. nov. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Avian and mammalian colours are thought to be constant in life and in museum specimens, but several early 20th-century taxonomists singled out the Canada Jay (Perisoreus canadensis (Linnaeus, 1766)) as having unstable feather pigments and warned against using old museum specimens for taxonomic purposes. One such error was Brisson's (1760) original naming of the species as "the Brown Jay of Canada". Another was Ridgway's (1899) naming of the "Gray Jay" as a new subspecies, Perisoreus (canadensis) griseus, through inappropriate comparison of fresh grey specimens with old brown ones. We discovered that browning of initially grey plumage also occurs between annual moults in living individuals of the Canada Jay's Pacific morphotype. We documented this change using photographs and re-sightings of colour-banded individuals and through spectral analysis of year-old (brown) and incoming (grey) rectrices collected from the same moulting individuals. To assess the distribution of this colour change, we compared September vs. May eBird photographs from across North America. We showed that seasonal colour change is normal in the Pacific morphotype but rare in the two other morphotypes. Collectively, these data have important implications for the taxonomy of the Canada Jay and are a cautionary tale for taxonomists studying animal colouration. [ABSTRACT FROM AUTHOR]

Clinostomus (Leuciscidae) is a wide‐ranging freshwater fish genus that occurs throughout eastern North America and southern portions of Canada with two species currently recognized: C. elongatus and C. funduloides. A previous taxonomic study of C. funduloides recognized two subspecies (estor and funduloides) and one diagnosed, but undescribed subspecies based on morphological characteristics and geographic distribution. In this study, we used three molecular markers (cytochrome b, S7 intron 1 and growth hormone intron 4) to test the three lineage hypothesis and evaluate genetic variation of C. funduloides across the range using Bayesian inference. Our results indicate that C. funduloides is not monophyletic, as individuals of C. elongatus nest within C. funduloides in both the mtDNA and nDNA phylogenetic analyses, although the position of C. elongatus varies between data sets. In addition, some of the recovered clades are deeply divergent from one another, further supporting the distinctiveness of many of the populations. Overall, these results suggest that subspecies designations are not warranted and a taxonomic revision is needed as Clinostomus is likely more diverse than is currently recognized. [ABSTRACT FROM AUTHOR]

As populations diverge many processes can shape genomic patterns of differentiation. Regions of high differentiation can arise due to divergent selection acting on selected loci, genetic hitchhiking of nearby loci, or through repeated selection against deleterious alleles (linked background selection); this divergence may then be further elevated in regions of reduced recombination. Atlantic salmon (Salmo salar) from Europe and North America diverged >600,000 years ago and despite some evidence of secondary contact, the majority of genetic data indicate substantial divergence between lineages. This deep divergence with potential gene flow provides an opportunity to investigate the role of different mechanisms that shape the genomic landscape during early speciation. Here, using 184,295 single nucleotide polymorphisms (SNPs) and 80 populations, we investigate the genomic landscape of differentiation across the Atlantic Ocean with a focus on highly differentiated regions and the processes shaping them. We found evidence of high (mean FST = 0.26) and heterogeneous genomic differentiation between continents. Genomic regions associated with high trans‐Atlantic differentiation ranged in size from single loci (SNPs) within important genes to large regions (1–3 Mbp) on four chromosomes (Ssa06, Ssa13, Ssa16 and Ssa19). These regions showed signatures consistent with selection, including high linkage disequilibrium, despite no significant reduction in recombination. Genes and functional enrichment of processes associated with differentiated regions may highlight continental differences in ocean navigation and parasite resistance. Our results provide insight into potential mechanisms underlying differences between continents, and evidence of near‐fixed and potentially adaptive trans‐Atlantic differences concurrent with a background of high genome‐wide differentiation supports subspecies designation in Atlantic salmon. [ABSTRACT FROM AUTHOR]

The common eastern North America and Gulf of Mexico olive shell, Americoliva nivosa (Marrat, 1871), is now known to comprise five separate subspecies that are distributed from Cape Hatteras to the Florida Keys, throughout the Gulf of Mexico to Isla Mujeres, and into the open Atlantic as far as Bermuda. The subspecies, which have disjunct distributions, include: Americoliva nivosa clenchi new subspecies (described here) which ranges from Cape Hatteras to Fort Pierce, Florida; Americoliva nivosa bollingi (Clench, 1934), which ranges from Palm Beach County, Florida south to the Florida Keys and Dry Tortugas; Americoliva nivosa choctaw Petuch and Myers, 2014, which ranges from Apalachicola to Pensacola along the Florida Panhandle of the northern Gulf of Mexico; Americoliva nivosa maya (Petuch and Sargent, 1986), which ranges from the Bay of Campeche to Isla Mujeres along the Yucatan Peninsula of Mexico; and Americoliva nivosa nivosa (Marrat, 1871), which is endemic to the island of Bermuda. All five of these distinct subspecies may have evolved from a common ancestor, the mid-Pleistocene (Ionian Age) Americoliva nivosa murielae (Olsson, 1967) from the Bermont Formation of southern Florida. A type locality is also designated for Marrat's non-localized Americoliva nivosa. [ABSTRACT FROM AUTHOR]

Genetic data indicate differences in speciation rate across latitudes, but underlying causes have been difficult to assess because a critical phase of the speciation process is initiated in allopatry, in which, by definition, individuals from different taxa do not interact. We conducted song playback experiments between 109 related pairs of mostly allopatric bird species or subspecies in Amazonia and North America to compare the rate of evolution of male discrimination of songs. Relative to local controls, the number of flyovers and approach to the speaker were higher in Amazonia. We estimate that responses to songs of relatives are being lost about 6 times more slowly in Amazonia than in North America. The slow loss of response holds even after accounting for differences in song frequency and song length. Amazonian species with year-round territories are losing aggressive responses especially slowly. We suggest the presence of many species and extensive interspecific territoriality favors recognition of songs sung by sympatric heterospecifics, which results in a broader window of recognition and hence an ongoing response to novel similar songs. These aggressive responses should slow the establishment of sympatry between recently diverged forms. If male responses to novel allopatric taxa reflect female responses, then premating reproductive isolation is also evolving more slowly in Amazonia. The findings are consistent with previously demonstrated slower recent rates of expansion of sister taxa into sympatry, slower rates of evolution of traits important for premating isolation, and slower rates of speciation in general in Amazonia than in temperate North America. The use of more than 100 song playback experiments reveals that birds give stronger responses to songs of closely related species in the Amazon than in temperate North America, suggesting that speciation is currently happening more slowly in the species-rich tropics than in species-poor temperate regions. [ABSTRACT FROM AUTHOR]

White-crowned Sparrow (Zonotrichia leucophrys) populations of western North America exhibit dramatic differences in life history strategies including migration behavior. However, individual migration strategies and population-level migratory patterns remain largely unknown for this species. Here, we focused on the long-distance migratory subspecies, Gambel's White-crowned Sparrow (Zonotrichia leucophrys gambelii). We used ringing, tracking and stable hydrogen isotope (δ2H) analysis of individuals migrating along the Pacific Flyway to assess individual phenology and routes as well as the pattern of connectivity between breeding and non-breeding sites. Results from all three methods, consisting of 79 ring recoveries, four light level geolocator tracks and 388 feather δ2H values, indicate low degrees of migratory connectivity. The isotope data provide evidence for leapfrog migration with the more southerly populations traveling greater distances to the breeding grounds than more centrally wintering individuals. Location estimates of four annual journeys revealed individually consistent migration strategies with relatively short flight bouts separated by two to three and two to six stopover sites during spring and autumn migration, respectively. However, combined results from all methods indicate high variability in migration distance among individuals. These findings confirm the phenotypic flexibility observed within this species and highlight the potential of White-crowned Sparrows for further investigations of evolutionary adaptations to ongoing changes in the environment. [ABSTRACT FROM AUTHOR]

Aluminum is increasingly globally bioavailable with acidification from industrial emissions and poor mining practices. This bioavailability increases uptake by flora, contaminating products such as fruit, pollen, and nectar. Concentrations of aluminum in fruit and pollen have been reported between 0.05 and 670mg/L in North America. This is particularly concerning for pollinators that ingest pollen and nectar. Honey bees represent a globally present species experiencing decline in Europe and North America. Region specific decline may be a result of differential toxicity of exposure between subspecies. We find that European honey bees (Apis mellifera mellifera) may have differential toxicity as compared to two allopatric Mediterranean subspecies (Apis mellifera carnica and Apis mellifera caucasica) which showed no within subspecies exposure differences. European honey bees were then used in a laboratory experiment and exposed to aluminum in their daily water supply to mimic nectar contamination at several concentrations. After approximately 3 weeks of aluminum ingestion these bees showed significantly shorter captive longevity than controls at concentrations as low as 10.4mg/L and showed a possible hormetic response in motility. We also compared European honey bees to Africanized/European hybrid bees (Apis mellifera mellifera/scutellata hybrid) in short-term free-flight experiments. Neither the European honey bee nor the hybrid showed immediate foraging deficits in flight time, color choice, or floral manipulation after aluminum exposure. We conclude that European honey bees are at the greatest risk of aluminum related decline from chronic ingestion as compared to other subspecies and offer new methods for future use in honey bee toxicology. [ABSTRACT FROM AUTHOR]

Recently evolved species typically share genetic variation across their genomes due to incomplete lineage sorting and/or ongoing gene flow. Given only subtle allele frequency differences at most loci and the expectation that divergent selection may affect only a tiny fraction of the genome, distinguishing closely related species based on multi‐locus data requires substantial genomic coverage. In this study, we used ddRAD‐seq to sample the genomes of five recently diverged, New World "mallards" (Anas spp.), a group of dabbling duck species characterized by diagnosable phenotypic differences but minimal genetic differentiation. With increased genomic sampling, we aimed to characterize population structure within this group and identify genomic regions that may have experienced divergent selection during speciation. We analyzed 3,017 autosomal ddRAD‐seq loci and 177 loci from the Z‐chromosome. In contrast to previous studies, the ddRAD‐seq data were sufficient to assign individuals to their respective species or subspecies and to generate estimates of gene flow in a phylogenetic framework. We find limited evidence of contemporary gene flow between the dichromatic mallard and several monochromatic taxa, but find evidence for historical gene flow between some monochromatic species pairs. We conclude that the overall genetic similarity of these taxa likely reflects retained ancestral polymorphism rather than recent and extensive gene flow. Thus, despite recurring cases of hybridization in this group, our results challenge the current dogma predicting the genetic extinction of the New World monochromatic dabbling ducks via introgressive hybridization with mallards. Moreover, ddRAD‐seq data were sufficient to identify previously unknown outlier regions across the Z‐chromosome and several autosomal chromosomes that may have been involved in the diversification of species in this recent radiation. [ABSTRACT FROM AUTHOR]

Accurate knowledge of geographic ranges and genetic relationships among populations is important when managing a species or population of conservation concern. Along the western coast of Canada, a subspecies of the northern goshawk (Accipiter gentilis laingi) is legally designated as Threatened. The range and distinctness of this form, in comparison with the broadly distributed North American subspecies (Accipiter gentilis atricapillus), is unclear. Given this morphological uncertainty, we analyzed genomic relationships in thousands of single nucleotide polymorphisms identified using genotyping‐by‐sequencing of high‐quality genetic samples. Results revealed a genetically distinct population of northern goshawks on the archipelago of Haida Gwaii and subtle structuring among other North American sampling regions. We then developed genotyping assays for ten loci that are highly differentiated between the two main genetic clusters, allowing inclusion of hundreds of low‐quality samples and confirming that the distinct genetic cluster is restricted to Haida Gwaii. As the laingi form was originally described as being based on Haida Gwaii (where the type specimen is from), further morphological analysis may result in this name being restricted to the Haida Gwaii genetic cluster. Regardless of taxonomic treatment, the distinct Haida Gwaii genetic cluster along with the small and declining population size of the Haida Gwaii population suggests a high risk of extinction of an ecologically and genetically distinct form of northern goshawk. Outside of Haida Gwaii, sampling regions along the coast of BC and southeast Alaska (often considered regions inhabited by laingi) show some subtle differentiation from other North American regions. These results will increase the effectiveness of conservation management of northern goshawks in northwestern North America. More broadly, other conservation‐related studies of genetic variation may benefit from the two‐step approach we employed that first surveys genomic variation using high‐quality samples and then genotypes low‐quality samples at particularly informative loci. [ABSTRACT FROM AUTHOR]

[Display omitted] • Retrospective use of integrative taxonomy in classical biological control. • Unintentional NA introduction of Rhinusa dieckmanni. • Genetic and morphological evaluation of species status. • Absence of genetic clustering between weevil populations on different Linaria spp. A seed-feeding weevil introduced to North America (NA) as a biological control agent of the invasive toadflax Linaria dalmatica (L.) Mill., identified then as Gymnetron antirrhini "Dalmatian host race" and subsequently confirmed as established, was revealed through our study to be a separate species, i.e., Rhinusa dieckmanni (Behne) (Coleoptera: Curculionidae). This weevil species was presumed to be endemic in its native range, with a distribution restricted to Mount Rila in southwestern Bulgaria. We conducted a comprehensive study of seed-feeding weevils associated with L. dalmatica , L. dalmatica ssp. macedonica (Griseb.) D.A. Sutton, L. genistifolia (L.) Mill., and L. grandiflora Desf. across a broad geographic area of their native range. Those results revealed that all four host plants were used by R. dieckmanni and thus the native geographic range of the species is wider than expected, encompassing the Balkans and the Anatolian Plateau. Our observations suggest that phenotypes of this weevil are highly variable and dependent on the seed capsule size of the Linaria host population. The haplotype network based on mitochondrial COII , 16S genes, and nuclear EF 1-α gene genealogy confirmed the conspecific nature of geographically distant weevil populations, that is, R. dieckmanni phenotypes utilizing L. genistifolia , L. dalmatica , and L. grandiflora for larval development. Specimens collected from L. dalmatica in the northwestern USA shared the same haplotypes as samples from L. dalmatica ssp. macedonica in southwestern North Macedonia, supporting the known introduction history of the North American population. Females from these populations have relatively short rostrums, which may limit their reproductive success on North American invasive L. dalmatica with larger seed capsules. [ABSTRACT FROM AUTHOR]

Nucleotide sequences from a segment of the mitochondrial cytochrome c oxidase subunit I (COI) gene were used to examine phylogeography, intraspecific relationships and taxonomy of the boll weevil Anthonomus grandis Boheman (Coleoptera: Curculionidae) collected from wild and cultivated cotton hosts in Mexico and USA. Phylogenetic trees and TCS haplotype networks showed that boll weevils partitioned into two clusters: 'western' and 'eastern'. In addition to infesting cultivated cotton, Gossypium hirsutum, both groups were found on several other species of the cotton tribe Gossypieae: wild Gossypium, Hampea, Cienfuegosia and Hibiscus pernambucensis (eastern group only). No evidence was found for host plant-associated genetic differentiation in either group. The level of genetic divergence and lack of shared COI haplotypes, combined with five apparent fixed nucleotide differences between the two groups and earlier evidence of reproductive isolation, together provide strong support for reinstating the subspecies name, Anthonomus grandis thurberiae Pierce, for the western lineage. Demographic tests suggested that both lineages have undergone population expansions dating to the Pleistocene. A possible vicariant role for the Trans-Mexican Volcanic Belt and the Sierra Madre Occidental in promoting genetic divergence, and a reassessment of dispersal scenarios during the postulated northward expansion of A. g. thurberiae are discussed. [ABSTRACT FROM AUTHOR]

Phragmites australis subsp. australis is an invasive and ecologically detrimental plant in multiple regions of North America. Its co-occurrence with the native subspecies, and multiple instances of hybridization, has created the need to differentiate Phragmites subspecies or haplotypes so that management can be appropriately targeted to the invader. We compiled a review of current genetic discrimination methods among the three Phragmites subspecies inhabiting the United States and Canada, and discussed how each method can contribute to control of the introduced subspecies while preserving the two endemic subspecies. We also discussed various control tools and the implications of Phragmites genetics for implementation. The Phragmites subspecies endemic to North America have environmental or infrastructure significance (e.g., habitat sustainability, biodiversity, storm surge and erosion protection). Thus, faster and more accurate differentiation among the endemic and introduced subspecies is needed. Additionally, more in-depth genetic information on Phragmites subspecies could support better management decisions, as well as the development of improved control treatments. This review highlights technologies and approaches currently available for genetic identification, recently collected genomic, transcriptomic and proteomic information, and implications for biological control and herbicide treatments. • Review of genetic discrimination methods among Phragmites australis lineages. • Development of a new nDNA PCR-RFLP method to differentiate P. australis hybrids. • Development of novel qPCR assays to differentiate three P. australis subspecies. • Information to support better management decisions and improved control treatments. • Discussion of future needs in the P. australis research and development community. [ABSTRACT FROM AUTHOR]

New taxa and nothotaxa are described within North American Rosa L. subg. Rosa. Rosa setigera Michx., formerly considered of Eurasian origin and placed in Rosa sect. Systylae DC., is segregated into the new Rosa sect. Americanae W. H. Lewis. Its origin is proposed to be in the Ozark Plateau of the south-central United States. One new species, R. memoryae W. H. Lewis, and one new subspecies, R. virginiana Mill. subsp. minidentata W. H. Lewis, are described. Twelve new Rosa nothospecies are described: Rosa × atlantica W. H. Lewis, Rosa × canadensis W. H. Lewis, Rosa × churchillii W. H. Lewis, Rosa × fernaldiorum W. H. Lewis, Rosa × gilmaniana W. H. Lewis, Rosa × hainesii W. H. Lewis, Rosa × harmsiana W. H. Lewis, Rosa × hodgdonii W. H. Lewis, Rosa × massiana W. H. Lewis, Rosa × oldhamii W. H. Lewis, Rosa × peraxeliana W. H. Lewis, and Rosa × victoriana W. H. Lewis. All of these are naturally produced hybrids rather than cultivated plants. The existing nothospecies Rosa × engelmannii S. Watson, of parentage R. acicularis Lindl. × R. nutkana C. Presl, is divided into three nothosubspecies: nothosubspecies engelmannii, nothosubspecies occidentalis W. H. Lewis, and nothosubspecies britannicae-columbiae W. H. Lewis, distinguished by parentage involving three different subspecies of R. nutkana. New hybrid introgressions identified in Canada and the United States are briefly discussed. [ABSTRACT FROM AUTHOR]

Genetic relationships within the Lygaeus kalmii complex were evaluated using specimens from multiple locations throughout the United States. Genes evaluated included the 18S ribosomal RNA (nuclear) and cytochrome oxidase subunit I (COI, mitochondrial). The 18S rRNA sequences were 100% conserved among all Lygaeus specimens, rendering the gene ineffective for inferring phylogenetic relationships for this project. However, the COI sequences were informative, and a COI-based phylogenetic tree revealed that L. reclivatus Say and both subspecies of L. kalmii (Stal) are closely related, with all falling within the same clade. Twelve different haplotypes of the COI gene were found among the sequences within the L. kalmii angustomarginatus, L. kalmii kalmii, and L. reclivatus clade. Each haplotype differed from other haplotypes by one to six nucleotides (0.13-0.77%), falling within the range of reported intraspecific divergence. Therefore, our data validate the nonspecific classification of L. kalmii angustomarginatus and L. kalmii kalmii and suggest that L. reclivatus is not a distinct species. The overlap of haplotypes also suggests possible gene flow among all three groups. [ABSTRACT FROM AUTHOR]

The article discusses a study on the evaluation of genetic evidence and population genetics of the subspecies of the semipalmated sandpiper, Calidris pusilla. The study involves the use of mitochondrial control region sequences and nuclear microsatellite loci in analyzing the DNA of the birds from seven locations in North America. It revealed that eastern group of semipalmated sandpiper was the source of the subspecies that colonized the western and central regions.

Premise of the study: Plant populations that face new environments adapt and diverge simultaneously, and both processes leave footprints in their genetic diversity. Arabidopsis lyrata is an excellent species for studying these processes. Pairs of populations and subspecies of A. lyrata represent different stages of divergence. These populations are also known to be locally adapted and display various stages of emerging reproductive isolation. Methods: We used nucleotide diversity data from 19 loci to estimate divergence times and levels of diversity among nine A. lyrata populations. Traditional distance-based methods and model-based clustering analysis were used to supplement pairwise coalescence-based analysis of divergence. Key results: Estimated divergence times varied from 130000 generations between North American and European subspecies to 39 000 generations between central European and Scandinavian populations. In concordance with previous studies, the highest level of diversity was found in Central Europe and the lowest in North America and a diverged Russian Karhumäki population. Local adaptation among Northern and central European populations has emerged during the last 39000 generations. Populations that are reproductively isolated by prezygotic mechanisms have been separated for a longer time period of ~70 000 generations but still have shared nucleotide polymorphism. Conclusions: In A. lyrata, reproductively isolated populations started to diverge ~70 000 generations ago and more closely related, locally adapted populations have been separate lineages for ~39 000 generations. However, based on the posterior distribution of divergence times, the processes leading to reproductive isolation and local adaptation are likely to temporally coincide. [ABSTRACT FROM AUTHOR]

Extrinsic factors such as physical barriers play an important role in shaping population genetic structure. A reduction in gene flow leading to population structuring may ultimately lead to population divergence. These divergent populations are often considered subspecies. Because genetic differentiation may represent differences between subspecies, patterns of genetic structure should reflect subspecies groupings. In this study, we examine the contemporary population genetic structure of muskrat (n = 331) and assess the relevance of 4 geographically distinct subspecies designations across northern North America using 9 microsatellite loci. We predicted that patterns of gene flow and genetic structure would reflect the described subspecies. We found evidence of genetic differentiation between western and eastern regions, and muskrats from Newfoundland (NF) showed significantly lower genetic diversity than central regions. A strong isolation by distance pattern was also detected within the eastern cluster. Our results did not differentiate Ondatra zibethicus spatulus (northwest) from O. z. albus (central), but they suggest a distinction between O. z. obscurus (NF) and O. z. zibethicus (east). This study highlights the need for more phylogenetic studies in order to better understand intraspecific divergence and the genetic characterization of subspecies. [ABSTRACT FROM PUBLISHER]

Five subspecies of the Greater White-fronted Goose, Anser albifrons (Scopoli, 1769), have been named, all on the basis of wintering birds, and up to six subspecies have been recognized. There has been confusion over the application of some names, particularly in North America, because of lack of knowledge of the breeding ranges and type localities, and incorrect taxonomic decisions. There is one clinally varying subspecies in Eurasia, one that breeds in Greenland, and three in North America, one newly named herein. [ABSTRACT FROM AUTHOR]

The article discusses a research study on the difference in wing formula of hermit thrush or Catharus guttatus in Eastern North America with the description in 1997 "Identification Guide to North American Birds," by Peter Pyle. Reseachers captured hermit thrushes, identified according to species and banded for wing formula measurements in a nonparametric statistical analysis. Comparison findings indicated that discrepancies in wing formula could be associated with subspecies of hermit thrush.

The article discusses a study completed in 2010 which sought to find out why the Hairy Woodpecker, Picoides villosus in Latin, have so many subspecies. It states that this genus has 21 subspecies, with more breeding grounds throughout North America than most others. It reports that researchers selected 296 birds from 89 locations and used ND2 sequencing on them. They found that those from the boreal and eastern zones and those from the western and southwestern zones are a relatively recent breed, suggesting a geographical basis for their diversity.

The carnivorous wetland plant, Sarracenia purpurea (the northern pitcher plant) is native to eastern and Midwestern North America. This species is abundant within its habitat but suitable habitat is increasingly scarce, raising interest in S. purpurea restoration and conservation. Complicating conservation planning, two controversial subspecies of S. purpurea are historically defined primarily on morphologic traits: S. purpurea subsp. purpurea distributed north of Maryland and S. purpurea subsp. venosa distributed south of Maryland. S. purpurea is also found in three distinct habitat types defined by substrate: acidic Sphagnum peatlands, acidic sandy savannahs, and alkaline marl wetlands. In species level studies, S. purpurea leaves have exhibited morphological plasticity in response to environmental variability, bringing into question the validity of subspecies definitions based on morphology alone. This study examined morphologic and genetic variation throughout S. purpurea's natural distribution, encompassing both the traditional subspecies and three unique habitat types testing the validity of traditional subspecies definitions. Genetic analysis indicated possible ecological significance of considering a new grouping of S. purpurea populations into Midwest, N. East Coast and S. East Coast populations (AMOVA % variation = 13.34, P = 0.0078) based on genetic differentiation. Morphological variation in leaf shape measurements supported this division as well as indicating plasticity associated with environmental variables. This study conservatively suggests that new, geographical area conservation units may be a more important conservation unit for preserving S. purpurea genetic variation and morphological plasticity than traditional subspecies definitions. [ABSTRACT FROM AUTHOR]

Aim We derived phylogenies, phylogeographies, and population demographies for two North American pitvipers, Agkistrodon contortrix (Linnaeus, 1766) and A. piscivorus (Lacépède, 1789) (Viperidae: Crotalinae), as a mechanism to evaluate the impact of rapid climatic change on these taxa. Location Midwestern and eastern North America. Methods We reconstructed maximum parsimony (MP) and maximum likelihood (ML) relationships based on 846 base pairs of mitochondrial DNA (mtDNA) ATPase 8 and ATPase 6 genes sequenced over 178 individuals. We quantified range expansions, demographic histories, divergence dates and potential size differences among clades since their last period of rapid expansion. We used the Shimodaira–Hasegawa (SH) test to compare our ML tree against three biogeographical hypotheses. Results A significant SH test supported diversification of A. contortrix from northeastern Mexico into midwestern–eastern North America, where its trajectory was sundered by two vicariant events. The first ( c. 5.1 Ma) segregated clades at 3.1% sequence divergence (SD) along a continental east–west moisture gradient. The second ( c. 1.4 Ma) segregated clades at 2.4% SD along the Mississippi River, coincident with the formation of the modern Ohio River as a major meltwater tributary. A single glacial refugium was detected within the Apalachicola region of southeastern North America. Significant support was also found for a hypothesis of trans-Gulf rafting by the common ancestor of A. piscivorus from eastern Mexico (possibly the Yucatan Peninsula) to northern Florida. There, a Mid–Late Pliocene marine transgression separated it at 4.8% SD from mainland North America. Significant range expansions followed compressive glacial effects in three (of four) A. contortrix clades and in two (of three) A. piscivorus clades, with the Florida A. piscivorus clade exhibiting significant distributional stasis. Main conclusions Pliocene glaciations, rapidly developing western aridity, and Pleistocene glacial meltwaters seemingly led to the diversification of A. contortrix and A. piscivorus in North America. Both species were pushed southwards by Pleistocene climate change, with subsequent northward expansions uninhibited topographically. The subspecific taxonomy used for A. contortrix and A. piscivorus today, however, appear non-representative. The monophyletic Florida subspecies of A. piscivorus may be a distinct species (at 4.8% SD), whereas two western subspecies of A. contortrix also appear to constitute a single distinct species, pending additional analyses. We conclude that both species of Agkistrodon can be used as suitable ectothermic models to gauge impacts of future climate change. [ABSTRACT FROM AUTHOR]

A set of DNA markers was developed that successfully identifies Bacillus thuringiensis ssp. kurstaki ( Btk) when screened against other Bacillus species and subspecies. These subspecies-specific primer sets allowed detection and characterization of Btk within an environmental background that contained many Bacillus species. Because Btk is used as an active ingredient in many commercial formulations, yet is not naturally widely distributed in North America or Europe, these markers will prove useful in investigations on the environmental persistence and ecological fate of Btk. [ABSTRACT FROM AUTHOR]

The article examines the level of concordance between the subspecies and microsatellite genotypes of Pacific Coast Song Sparrows in North America. Study shows that some populations recognized as subspecies are recognized to have the same subspecies. It suggests for the use of behavioral traits, multiple loci, and phenotypic characters in the evaluation of birds' geographic variation.

We examined the genetic structure of snowy plovers (Charadrius alexandrinus) in North America, the Caribbean, and the west coast of South America to quantify variation within and among breeding areas and to test the validity of three previously recognized subspecies. Sequences (676 bp) from domains I and II of the mitochondrial control region were analyzed for 166 snowy plovers from 20 breeding areas. Variation was also examined at 10 microsatellite loci for 144 snowy plovers from 14 breeding areas. The mtDNA and microsatellite data provided strong evidence that the Puerto Rican breeding group is genetically divergent from sites in the continental U.S. (net sequence divergence = 0.38%; FST for microsatellites = 0.190). Our data also revealed high levels of differentiation between sites from South America and North America (net sequence divergence = 0.81%; FST for microsatellites = 0.253). In contrast, there was little genetic structure among breeding sites within the continental U.S. Our results suggest that snowy plovers in Florida should be considered part of C. a. nivosus (rather than part of C. a. tenuirostris, where they are currently placed), whereas snowy plovers from Puerto Rico should be considered part of C. a. tenuirostris. Snowy plovers in South America should remain a separate subspecies (C. a. occidentalis). Although U.S. Pacific and Gulf Coast breeding areas were not genetically distinct from other continental U.S. sites, demographic isolation, unique coastal habitats, and recent population declines suggest they warrant special concern. [ABSTRACT FROM AUTHOR]

Abstract Complete ND2 and partial ND4 and cytochrome b mitochondrial DNA (mtDNA) sequences were analysed to evaluate the phylogeographic patterns of common garter snakes (Thamnophis sirtalis ) in western North America. This species is widely distributed throughout North America, and exhibits extensive phenotypic variation in the westernmost part of its range. The overall phylogeographic pattern based on mtDNA sequences is concordant with results from studies of other species in this region, implicating historical vicariant processes during the Pleistocene and indicating bottleneck effects of recent dispersal into postglacial habitat. Indeed, the topology is statistically consistent with the hypothesis of both southern (Great Basin and California) and northern (Haida Gwaii) refugia. Specifically, we identified genetic breaks among three major clades: Northwest Coastal populations, Intermountain populations, and all California populations. The California clade contained the only other well-supported branching patterns detected; relationships among populations within the two northern clades were indistinguishable. These molecular splits contrast sharply with all prior geographical analyses of phenotypic variation in T. sirtalis in this region. Our results suggest that the extensive phenotypic variation in western T. sirtalis has been shaped more by local evolutionary forces than by shared common ancestry. Consequently, we consider all morphologically based subspecies designations of T. sirtalis in this region invalid because they do not reflect reciprocal monophyly of the mtDNA sequences. [ABSTRACT FROM AUTHOR]

Hybridization can bring in single individuals alleles that were never designed to work together, which can result in unexpected or transgressive phenotypes. The Yellow-shafted (auratus group) and Red-shafted (cafer group) subspecies groups of the Northern Flicker (Colaptes auratus) differ conspicuously in the coloration of their flight feathers, but hybridize freely where their ranges overlap in western North America. The difference in color is largely the result of the Red-shafted form harboring ketolated products at C4(4′) of the carotenoids found in the Yellow-shafted form. Characterizing the carotenoid pigments in a series of birds of intermediate color (presumed hybrids) revealed that most accumulated a product of β-cryptoxanthin with a keto group on its hydroxylated ring (3-hydroxy-echinenone), while a few accumulated the product with a keto group on the unhydroxylated ring (3′-hydroxy-echinenone). Surprisingly, the latter group also had feather barbs that were noticeably yellower than the associated rachis, corresponding to a lower level of ketolation at C4(4′). We assessed possible biochemical explanations for the differences by probing the relative carotenoid concentration data in individuals of varying color. The difference between the hybrids could not be explained by the general level of ketolation of carotenoids or a particular selectivity of the 4-ketolase involved. We present a testable genetic explanation that invokes incompatibilities between divergent alleles of the two parental forms at interacting loci. Because the idiosyncrasies affect oxidation, they may be the product of mitonuclear incompatibilities. Unlabelled Image • Two forms of the Northern Flicker differ in the carotenoids of their flight feathers. • The forms hybridize where they meet resulting in birds of intermediate colors. • A subset of hybrids accumulate different carotenoids and have discordant feather parts. • We investigated possible explanations for the differences between hybrids. • Incompatibilities between genes of the two forms may explain the differences. [ABSTRACT FROM AUTHOR]

• Phylogenomics reveals hybrid origins of three Papilio lineages with fixed mtDNA. • Hybrid nuclear genomes primarily from a once-widespread ancestral paternal species. • A recent hybrid swarm has more diverse patterns of mitonuclear discordance. • Wide-ranging Papilio machaon and P. zelicaon are paraphyletic species. • Mediterranean relict Papilio hospiton is basal to the remainder of species group. Genomics has revolutionized our understanding of hybridization and introgression, but most of the early evidence for these processes came from studies of mitochondrial introgression. To expand these evolutionary insights from mitochondrial patterns, we evaluate phylogenetic discordance across the nuclear genomes of a hybridizing system, the Papilio machaon group of swallowtail butterflies. This species group contains three hybrid lineages (P. brevicauda , P. joanae , and P. m. kahli) that are geographically disjunct across North America and have complete fixation of a mitochondrial lineage that is otherwise primarily found in P. m. hudsonianus, a boreal subspecies of the Holarctic P. machaon. Genome-wide nuclear markers place the three hybrid lineages as a monophyletic group that is sister to P. polyxenes / P. zelicaon rather than P. machaon , although ancient hybridization between a subspecies of P. machaon and the ancestor of these three lineages is also shown by their greater nuclear affinity to P. m. hudsonianus than to other subspecies of P. machaon. Individuals from contemporary hybrid swarms in Alberta, where mitochondrial DNA fixation has not occurred, were more intermediate between their respective parent species, demonstrating diversity in mito-nuclear discordance following hybrid interactions. Our new phylogenetic findings for the P. machaon species group also include: subspecific paraphyly within P. machaon itself across its Holarctic distribution; paraphyly of P. zelicaon relative to P. polyxenes ; and more divergent placement of a Mediterranean species, P. hospiton. These results provide the first comprehensive genomic evaluation of relationships within this species group and provide insight into the evolutionary dynamics of hybridization and mitochondrial introgression. [ABSTRACT FROM AUTHOR]