Garth M. Spellman

Phylogeography of the mountain chickadee (Poecile gambeli): diversification, introgression, and expansion in response to Quaternary climate change

Since the late 1990s, molecular techniques have fuelled debate about the role of Pleistocene glacial cycles in structuring contemporary avian diversity in North America. The debate is still heated; however, there is widespread agreement that the Pleistocene glacial cycles forced the repeated contraction, fragmentation, and expansion of the North American biota. These demographic processes should leave genetic ‘footprints’ in modern descendants, suggesting that detailed population genetic studies of contemporary species provide the key to elucidating the impact of the late Quaternary (late Pleistocene–Holocene). We present an analysis of mitochondrial DNA (mtDNA) variation in the mountain chickadee (Poecile gambeli) in an attempt to examine the genetic evidence of the impact of the late Quaternary glacial cycles. Phylogenetic analyses reveal two strongly supported clades of P. gambeli: an Eastern Clade (Rocky Mountains and Great Basin) and a Western Clade (Sierra Nevada and Cascades). Post‐glacial introgression is apparent between these two clades in the Mono Lake region of Central California. Within the Eastern Clade there is evidence of isolation‐by‐distance in the Rocky Mountain populations, and of limited gene flow into and around the Great Basin. Coalescent analysis of genetic variation in the Western Clade indicates that northern (Sierra Nevada/Cascades) and southern (Transverse/Peninsular Ranges) populations have been isolated and evolving independently for nearly 60 000 years.

Effect of antimicrobial compounds tylosin and chlortetracycline during batch anaerobic swine manure digestion.

Tylosin and chlortetracycline (CTC) are antimicrobial chemicals that are fed to >45% of the US swine herds at therapeutic and sub-therapeutic dosages to enhance growth rates and treat swine health problems. These compounds are poorly absorbed during digestion so that the bioactive compound or metabolites are excreted. This study investigated the degradation and stabilization of swine manure that contained no additives and compared the observed processes with those of manure containing either tylosin or CTC. The batch anaerobic incubation lasted 216 days. The breakdown of insoluble organic matter through anaerobic hydrolysis reactions was faster for manure containing CTC compared with tylosin or no-antimicrobial treatments. Volatile fatty acid (VFA) accumulation, including acetate, butyrate, and propionate, was greater for CTC-containing manure compared to tylosin and no-antimicrobial treatments. The relative abundance of two aceticlastic methanogens, Methanosaetaceae and Methanosarcinaceae spp., were less for CTC manure than manure with no-antimicrobial treatment. In addition, generation of methane and carbon dioxide was inhibited by 27.8% and 28.4%, respectively, due to the presence of CTC. Tylosin effects on manure degradation were limited, however the relative abundance of Methanosarcinaceae spp. was greater than found in the CTC or no-antimicrobial manures. These data suggest that acetate and other C-1 VFA compounds would be effectively utilized during methanogenesis in the presence of tylosin.

Cryptic diversity in a widespread North American songbird: Phylogeography of the Brown Creeper (Certhia americana)

The identification of species via morphological characteristics has traditionally left cryptic species undescribed in taxa under selection for morphological conservation (or a lack of selection for morphological change). Treecreepers (Genus: Certhia) have a conserved morphological appearance, making it difficult to ascertain relationships in the genus based on morphology alone. Recent genetic and song structure studies of Eurasian Treecreepers identified cryptic species within Old World Certhia that were previously undescribed using morphological characteristics. Here, we use mtDNA to investigate cryptic diversity and patterns of diversification in the Brown Creeper (Certhia americana), the single described Certhia species in the Americas. Phylogenetic analyses identified six well-supported geographically-structured clades; the basal divergence separates a northern and a southern lineage in the Brown Creeper, likely cryptic species previously characterized as many subspecies. Sympatry is prevalent between clades in western North America, where possible contact zones warrant further investigation. Allopatry appears to be the primary driver of deep phylogeographic structure within the Brown Creeper; however, within clade diversity is highly correlated with the life history traits of the populations that comprise the geographically structured phylogroups.

Phylogeography of the white‐breasted nuthatch (Sitta carolinensis): diversification in North American pine and oak woodlands

Pine and oak woodlands are common North American floral communities with distinct regional species composition. The white‐breasted nuthatch (Aves: Sitta carolinensis) is a common resident bird of North American pine and oak woodlands, and is distributed continentally across the highly disjunct distribution of these woodlands. We propose three historical hypotheses to explain the evolution of the white‐breasted nuthatch in its principal habitat. (i) The species evolved in situ in the regional pine–oak communities and the isolation of populations in these regions is captured in cryptic genetic variation. (ii) Migration of individuals between regions is frequent enough to maintain the widespread distributions and prevent regional divergence. (iii) The species have recently expanded to occupy their current distributions and an insufficient amount of time has passed for divergence to occur. Phylogenetic analysis of mitochondrial DNA (ND2 gene) variation (N = 216) in the white‐breasted nuthatch reveals four reciprocally monophyletic clades concordant with the distribution of the regional North American pine and oak woodlands, and supports hypothesis 1 of in situ evolution of populations in the regional pine and oak communities. Within‐clade population structure and demographic history are also discussed.

Testing hypotheses of Pleistocene population history using coalescent simulations: phylogeography of the pygmy nuthatch (Sitta pygmaea)

In this paper, we use mitochondrial NADH dehydrogenase subunit 2 sequences to test Pleistocene refugial hypotheses for the pygmy nuthatch (Sitta pygmaea). Pygmy nuthatches are a common resident of long-needle pine forests in western North America and demonstrate a particular affinity with ponderosa pine (Pinus ponderosa). Palaeoecological and genetic data indicate that ponderosa pine was isolated in two Pleistocene refugia corresponding to areas in the southern Sierra Nevada in the west and southern Arizona and New Mexico in the east. We use coalescent simulations to test the hypothesis that pygmy nuthatches tracked the Pleistocene history of their preferred habitat and persisted in two refugia during the periods of glacial maxima. Coalescent simulation of population history does not support the hypothesis of two Pleistocene refugia for the pygmy nuthatch. Instead, our data are consistent with a single refuge model. Nucleotide diversity is greatest in the western populations of southern and coastal California. We suggest that the pygmy nuthatch expanded from a far western glacial refuge into its current distribution since the most recent glacial maximum.

A hybrid zone revisited: molecular and morphological analysis of the maintenance, movement, and evolution of a Great Plains avian (Cardinalidae: Pheucticus) hybrid zone

Black‐headed grosbeaks (Pheucticus melanocephalus) and rose‐breasted grosbeaks (Pheucticus ludovicianus) are passerine bird species known to hybridize in the Great Plains of North America. Both extrinsic (environmental) and intrinsic factors (pre‐ and postzygotic reproductive isolation) have been credited for the generation and maintenance of the grosbeak hybrid zone, but little is known about the genetic characteristics of this hybrid zone. To investigate the stability and extent of the grosbeak hybrid zone, we constructed clines from both molecular sequence data (mtDNA, three autosomal intron loci, and one Z‐linked locus) and morphological data (morphometric analyses and hybrid index scores) to determined zone centre and width. Hybrid zone centre and width were also determined for samples collected across the zone 40 years ago from morphological data. The present and past clines were compared and provided support for stability in hybrid zone location and width, and the evolutionary implications of this are discussed. Three models of hybrid zone maintenance were investigated to consider the influence of intrinsic and extrinsic factors on this zone. Our results suggest low hybrid frequencies, a stable zone location and narrow width, and reduced hybrid fitness over the past 40 years best categorize the grosbeak hybrid zone as a tension zone.

Speciation in the White-breasted Nuthatch (Sitta carolinensis): a multilocus perspective.

Inferring the evolutionary and ecological processes that have shaped contemporary species distributions using the geographic distribution of gene lineages is the principal goal of phylogeographic research. Researchers in the field have recognized that inferences made from a single gene, often mitochondrial, can be informative regarding the pattern of diversification but lack conclusive information regarding the evolutionary mechanisms that led to the observed patterns. Here, we use a multilocus (20 loci) data set to explore the evolutionary history of the White‐breasted Nuthatch (Sitta carolinensis). A previous single‐locus study found S. carolinensis is comprised of four reciprocally monophyletic clades geographically restricted to the pine and oak forests of: (i) eastern North America, (ii) southern Rocky Mountain and Mexican Mountain ranges, (iii) Eastern Sierra Nevada and Northern Rocky Mountains and (iv) Pacific slope of North America. The diversification of the clades was attributed to the fragmentation of North American pine and oak woodlands in the Pliocene with subsequent divergences owing to the Pleistocene glacial cycles. Principal component, clustering and species tree analyses of the multilocus data resolved the same four groups or lineages found in the single‐locus study. Coalescent analyses and hypothesis testing of nested isolation and migration models indicate that isolation and not gene flow has been the major evolutionary mechanism responsible for shaping genetic variation, and all the divergence events within S. carolinensis have occurred in response to the Pleistocene glacial cycles.

Isolation-driven divergence: speciation in a widespread North American songbird (Aves: Certhiidae).

Lineage, or true ‘species’, trees may differ from gene trees because of stochastic processes in molecular evolution leading to gene‐tree heterogeneity. Problems with inferring species trees because of excessive incomplete lineage sorting may be exacerbated in lineages with rapid diversification or recent divergences necessitating the use of multiple loci and individuals. Many recent multilocus studies that investigate divergence times identify lineage splitting to be more recent than single‐locus studies, forcing the revision of biogeographic scenarios driving divergence. Here, we use 21 nuclear loci from regional populations to re‐evaluate hypotheses identified in an mtDNA phylogeographic study of the Brown Creeper (Certhia americana), as well as identify processes driving divergence. Nuclear phylogeographic analyses identified hierarchical genetic structure, supporting a basal split at approximately 32°N latitude, splitting northern and southern populations, with mixed patterns of genealogical concordance and discordance between data sets within the major lineages. Coalescent‐based analyses identify isolation, with little to no gene flow, as the primary driver of divergence between lineages. Recent isolation appears to have caused genetic bottlenecks in populations in the Sierra Madre Oriental and coastal mountain ranges of California, which may be targets for conservation concerns.

Clarifying the systematics of an enigmatic avian lineage : What is a bombycillid?

Avian Tree of Life (TOL) projects using multilocus sequence data have begun to reweave Sibley and Ahlquist’s (1990) “tapestry” of the systematic relationships among birds, which was based on DNA-DNA hybridization. Many of these studies have focused on relationships among members of the most species-rich avian order, Passeriformes, or the perching birds (e.g., Barker et al., 2002, 2004; Cibois and Cracraft, 2004; Voelker and Spellman, 2004; Alstrom et al., 2006). Bringing direct sequence-based character evidence to bear on the systematic relationships among passerine birds has demonstrated that monophyly cannot be assumed for many lineages (Barker et al., 2004), from suborder to tribe, proposed by Sibley and Ahlquist (1990) and Sibley and Monroe (1990). However, many of the paraphyletic passerine lineages identified by modern sequence-based studies represent taxa identified as difficult to place or otherwise problematic by Sibley and Ahlquist (1990). One of the consistently problematic groups has been the Bombycillidae (waxwings and allies). Sibley and Ahlquist (1990, p. 630) ultimately placed the Bombycillidae within the superfamily Muscicapoidea, but they were not confident of this placement. Recent studies have only confirmed the ambiguous placement of Bombycillidae, removing the family from the “core Muscicapoidea” because of poorly supported (low Bayesian credibility and bootstrap values) relationships with the core Muscicapoidea (Barker et al., 2002, 2004; Cibois and Cracraft, 2004; Voelker and Spellman, 2004), but keeping it in the superfamily. A potentially confounding factor for placing the Bombycillidae within the passerine phylogeny is that membership in and relationships among members of the family have long been controversial; therefore, a more thorough sampling of the group is desirable. Many early taxonomies recognized the morphological similarities among waxwings (Bombycilla, 3 spp.), silky-flycatchers (Phainopepla, Phainoptila, and Ptilogonys, 4 spp.), and the palmchat (Dulus, 1 sp.) and proposed them as members of a single family Bombycillidae (Arvey, 1951; Beecher, 1953). However, studies of egg white proteins in the waxwings, silky-flycatchers, and palmchat indicated a close relationship between the former two, but not the latter (Sibley, 1970). The DNA-DNA hybridization analyses of Sibley and Ahlquist (1990) supported the close association among these three groups as indicated by morphology, leading these authors and Sibley and Monroe (1990) to maintain these species as members of the Bombycillidae, while also recognizing their differences by labeling them as distinct tribes (Bombycillini, Ptilogonatini, and Dulini; Table 1). Other modern taxonomies of the bombycillids (Voous, 1977; Cramp, 1988; AOU, 1998) have followed Wetmore (1930) in emphasizing skeletal differences among the three groups and elevating each to the family level (Bombyicillidae, Ptilogonatidae, and Dulidae). If the waxwings, silky-flycatchers, and palmchat are considered the “core” bombycillids (but relationships among the core groups are still unknown), then the remaining ambiguity lies in placement of the only other species ever to be considered among the bombycillids, the grey hypocolius (Hypocolius ampelinus). The grey hypocolius is generally considered to belong to a monotypic family, Hypocoliidae; however, at various points in its taxonomic history it has been considered closely allied with shrikes of the families Prionopidae and Laniidae (morphological characters; Mayr and Amadon, 1951), cuckoo-shrikes (jaw musculature; Campephagidae, Beecher, 1953), bulbuls (morphology; Pycnonotidae, Sibley and Ahlquist, 1990; Sibley and Monroe, 1990; Clements, 1991), and the Bombycillidae (plumage and morphological characters; Lowe, 1947; Delacour and Amadon, 1949). The most recent taxonomic treatment of waxwings, silky-flycatchers, palmchat, and grey hypocolius listed each as a separate but closely related family (Bombycillidae, Ptilogonatidae, Dulidae, and Hypocoliidae), reflecting the continued ambiguity of relationships among the groups (del Hoyo, 2005). Table 1 Specimen information. In this study, we attempted to identify a monophyletic bombycillid lineage and to clarify the phylogenetic relationships among the members of this group. To identify membership within the bombycillid lineage, we first compared nuclear RAG-1 sequences from each putative bombycillid with the extensive RAG-1 dataset available for passerines (Barker et al., 2002; Barker et al., 2004). Then, to clarify relationships among bombycillid species, we analyzed sequence variation at three loci (RAG-1, RAG-2, and mtDNA).

A MOLECULAR EVALUATION OF THE NORTH AMERICAN "GRASSLAND" SPARROW CLADE

Abstract Because they share several morphological and ecological characters, the North American sparrow (Emberizidae) genera Ammodramus, Passerculus, and Xenospiza have historically been considered members of a well-defined “grassland” sparrow assemblage. Relationships among the 11 members of this group have been the subject of much taxonomic debate, yet no comprehensive molecular assessment of relationships has been done. We investigated these relationships using mitochondrial DNA sequence data that included complete cytochrome-b and ND2 genes. Phylogenetic reconstructions derived via parsimony, likelihood, and Bayesian methods were congruent. The grassland sparrows, as presently configured, are polyphyletic. Pooecetes gramineus, Amphispiza belli (but not A. quinquestriata and A. bilineata), Oriturus superciliosus, and all three species of Melospiza are included in a reconfigured clade, whereas the traditional forms of Ammodramus savannarum, humeralis, and aurifons are placed well outside of these. Within the clade of interest, Ammodramus remains polyphyletic, with leconteii, maritimus, nelsoni, and caudacutus forming a well-resolved clade apart from henslowii and bairdii. The latter are in another strongly supported clade that also includes Passerculus and a Xenospiza-Melozpiza sister pairing. Pooecetes, Amphispiza (belli), and Oriturus represent early lineages in this clade that today have no close living relatives. The polyphyly of the genus Ammodramus is likely the result of morphological convergence attributable to similar adaptive responses to the occupation of similar habitats. In general, the morphological and ecological factors that have defined the grassland sparrows are poor indicators of relatedness. Taxonomic revisions are suggested. Evaluación Molecular del Clado de Gorriones de Pastizales de Norte América