Andrew Engilis

Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards

Speciation is a continuous and dynamic process, and studying organisms during the early stages of this process can aid in identifying speciation mechanisms. The mallard (Anas platyrhynchos) and Mexican duck (A. [p.] diazi) are two recently diverged taxa with a history of hybridization and controversial taxonomy. To understand their evolutionary history, we conducted genomic scans to characterize patterns of genetic diversity and divergence across the mitochondrial DNA (mtDNA) control region, 3523 autosomal loci and 172 Z‐linked sex chromosome loci. Between the two taxa, Z‐linked loci (ΦST = 0.088) were 5.2 times more differentiated than autosomal DNA (ΦST = 0.017) but comparable to mtDNA (ΦST = 0.092). This elevated Z differentiation deviated from neutral expectations inferred from simulated data that incorporated demographic history and differences in effective population sizes between marker types. Furthermore, 3% of Z‐linked loci, compared to <0.1% of autosomal loci, were detected as outlier loci under divergent selection with elevated relative (ΦST) and absolute (dXY) estimates of divergence. In contrast, the ratio of Z‐linked and autosomal differentiation among the seven Mexican duck sampling locations was close to 1:1 (ΦST = 0.018 for both markers). We conclude that between mallards and Mexican ducks, divergence at autosomal markers is largely neutral, whereas greater divergence on the Z chromosome (or some portions thereof) is likely the product of selection that has been important in speciation. Our results contribute to a growing body of literature indicating elevated divergence on the Z chromosome and its likely importance in avian speciation.

Genetic admixture supports an ancient hybrid origin of the endangered Hawaiian duck

Speciation is regarded primarily as a bifurcation from an ancestral species into two distinct taxonomic units, but gene flow can create complex signals of phylogenetic relationships, especially among different loci. We evaluated several hypotheses that could account for phylogenetic discord between mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) within Hawaiian duck (Anas wyvilliana), including stochastic lineage sorting, mtDNA capture and widespread genomic introgression. Our results best support the hypothesis that the contemporary Hawaiian duck is descended from an ancient hybridization event between the mallard (Anas platyrhynchos) and Laysan duck (Anas laysanensis). Whereas mtDNA clearly shows a sister relationship between Hawaiian duck and mallard, nuDNA is consistent with a genetic mosaic with nearly equal contributions from Laysan duck and mallard. In addition, coalescent analyses suggest that gene flow from either mallard or Laysan duck, depending on the predefined tree topology, is necessary to explain contemporary genetic diversity in Hawaiian ducks, and these estimates are more consistent with ancient, rather than contemporary, hybridization. Time since divergence estimates suggest that the genetic admixture event occurred around the Pleistocene–Holocene boundary, which is further supported by circumstantial evidence from the Hawaiian subfossil record. Although the extent of reproductive isolation from either putative parental taxon is not currently known, these species are phenotypically, genetically and ecologically different, and they meet primary criteria used in avian taxonomy for species designation. Thus, the available data are consistent with an admixed origin and support the hypothesis that the Hawaiian duck may represent a young hybrid species.

Summer vs. winter: Examining the temporal distribution of avian biodiversity to inform conservation

ABSTRACT Winter habitat quality plays a key role in avian population regulation, and conservation of winter habitat is a priority for waterfowl, shorebirds, and Neotropical migrant landbirds. Yet, there has been little discussion of the importance of conserving temperate wintering habitat for landbirds, including the billions of Neotemperate migratory landbirds that winter in the United States. The value and impact of conservation initiatives in the U.S. could be maximized by accommodating the habitat requirements of bird communities throughout the full annual cycle, particularly in the southern and western U.S. where winter species richness is concentrated. To estimate the degree to which winter bird communities should be a conservation priority, we examined the temporal distribution of avian diversity using riparian habitat in the lower Cosumnes River and lower Putah Creek watersheds in Californias Central Valley. We used hierarchical multispecies occupancy models to estimate seasonal species richness and phylogenetic diversity in each watershed. We found that total species richness was equally as high in winter as in summer, and that phylogenetic diversity was higher in winter, with a considerable proportion of the winter avian diversity attributable to boreal-breeding Neotemperate migrants. Our results provide evidence that maintaining and restoring high-quality riparian habitat for winter bird communities in California is an important conservation opportunity. Broader recognition of the diversity of temperate winter bird communities and additional research into the factors affecting body condition and survival would facilitate effective conservation of high-quality winter habitat, benefiting Neotemperate migrants and year-round residents during a season that can have important impacts on their population dynamics.

Foraging Behavior of Tufted Tit-Tyrants (Anairetes parulus) in Semiarid Northcentral Chile

Abstract We studied foraging behavior of Tufted Tit-Tyrants (Anairetes parulus) in Matorral (shrubland) habitat of northcentral Chile. This species is a generalist insectivore feeding in most shrubs of Matorral habitat at our study site, although they favored three of the dominant plant species. Their foraging is typical of small tyrannid flycatchers, using rapid perch gleans coupled with hover gleans and supplemented by flycatching. They use relatively long search periods (3–5 sec) followed by rapid gleans, which is typical for small tyrannids. Their active foraging (3.1 ± 1.8 prey attacks/min) coupled with a longer search time distinguishes them from parids or regulids of the Holarctic with which they often are compared. They generally forage singly or in pairs and aggressively defend what appears to be foraging territories in winter and summer. Densities of Tufted Tit-Tyrants at our study site were higher than reported in other studies from Chile and Argentina, presumably reflecting resource availability.

Avifauna of the Katavi-Rukwa Ecosystem, Tanzania

ABSTRACT We combined findings of an avian field survey conducted in 2003 with the efforts of other observers to develop a comprehensive species list for the Katavi-Rukwa ecosystem; a biologically rich area of western Tanzania. Our 2003 survey, during the dry season, yielded 222 species of birds, four of which had not been reported previously. In combination with other publications, field reports, and incidental observations we documented 458 species of birds occurring in this ecosystem. The confirmed presence of ten globally threatened species, 18 biome restricted species, one range restricted species (Tanzanian masked weaver Ploceus reichardi), and significant numbers of African skimmer (Rynchops flavirostris), a colonial waterbird, strongly reinforces the classification of the Katavi National Park as an Important Bird Area in Tanzania. A synopsis of species found in this area supports the view that the avifauna of the Katavi-Rukwa ecosystem is biogeographically affiliated with the Zambezian biome. These findings will provide a baseline for conservation, management, and future biodiversity and avian research efforts in the Katavi-Rukwa ecosystem.

New and extralimital records of breeding birds for Putah Creek, California

We report on extralimital and new breeding records from a 16-year study of birds along lower Putah creek, central Valley, california, that began in 1997. surveys for breeding birds have confirmed 74 species nesting on the creek, while nesting of 17 further species remains probable. Among rare or extralimital species, we documented nesting of the hooded Merganser (Lophodytes cucullatus), Selasphorus sp., Pileated Woodpecker (Dryocopus pileatus), Pacific-slope Flycatcher (Empidonax difficilis), Bell’s Vireo (Vireo bellii), Warbling Vireo (V. gilvus), chestnutbacked chickadee (Poecile rufescens), Brown creeper (Certhia americana), Wrentit (Chamaea fasciata), orange-crowned Warbler (Oreothlypis celata), dark-eyed Junco (Junco hyemalis), and Western Tanager (Piranga ludoviciana). The records of nesting of the Brown creeper, chestnut-backed chickadee, and Western Tanager are the first confirmed for those species on the central Valley floor. nine of these species have experienced recent expansions elsewhere in their california ranges, and Bell’s Vireo has begun to reoccupy a few other sites in the central Valley, from which it had been extirpated for decades. We also present evidence for probable breeding by the hairy Woodpecker (Picoides villosus), Western Wood-Pewee (Contopus sordidulus), california Thrasher (Toxostoma redivivum), yellow Warbler (Setophaga petechia), and yellow-breasted chat (Icteria virens). These breeding records attest to the pioneering nature of birds and to the importance of Putah creek in the maintenance of riparian species in the sacramento Valley. The primary interest of most bird inventories is to document the regularly occurring species, as these influential members of local ecosystems play a prominent role in ecogeographical studies. Very often less attention is paid to the scarce, rare, or irregularly occurring species as their role in community ecology seems to be slight or even negligible (Patten and Marantz 1996, Volume 48, number 3, 2017

A new Bent-toed gecko (Squamata: Gekkonidae) from the Mekongga Mountains, South East Sulawesi, Indonesia.

We describe Cyrtodactylus hitchi sp. nov., a new species of Bent-toed Gecko from montane forests in the Mekongga Mountains, South East Sulawesi, Indonesia. Although we cannot speculate about relationships, morphologically it shares several traits with C. batik, a large species known only from Mount Tompotika near the tip of Sulawesis Eastern Peninsula. The following unique combination of characters distinguishes it from all other congeners: absence of precloacal groove, absence of precloacal and femoral pores, absence of enlarged femoral scales, no abrupt contact between large and small postfemoral scales, 18-20 lamellae under the fourth toes, and transversely enlarged, median subcaudal scales arranged in a single row.

Evaluating Riparian Restoration Success: Long-Term Responses of the Breeding Bird Community in California's Lower Putah Creek Watershed

Restoration of river processes and riparian vegetation is a high priority, particularly in the western United States, where it provides critical habitat for fish and wildlife along with many other environmental and economic benefits, yet few studies have quantified long-term responses of wildlife. We evaluated responses of the breeding bird community to restoration and management of the lower Putah Creek watershed in the Central Valley of California following the establishment of the Putah Creek Accord in 2000, an historic agreement designed to improve ecosystem structure and function and protect the livelihoods of farmers and residents along the lower creek. We surveyed the breeding bird community at 14 sites distributed over 38 km of the creek between 1999 and 2012, and we detected significant increases in the abundance of 27 breeding bird species as well as increases in the size and diversity of the entire breeding bird community, which could not be accounted for by broader regional trends or the influence of local nest box installation. Further, changes in the watershed favored riparian and woodland-associated species over synanthropic species. However, in comparison with Central Valley Joint Venture density objectives for seven riparian focal bird species, there is still considerable room for improvement, particularly at sites farthest downstream. Overall, our results echo shifts in the Putah Creek fish community and provide evidence that the Putah Creek Accord and subsequent management actions have contributed to a long-term improvement in riparian ecosystem condition for both aquatic and terrestrial organisms.

Bats (Chiroptera) recorded in the lowland of Southeast Sulawesi, Indonesia with notes on taxonomic status and significant range extensions

Abstract This paper reports on a bat survey conducted in November 2011 in Mangolo Nature Park and Rawa Aopa Watumohai National Park, both lowland forests located in Southeast Sulawesi. We recorded 22 species of bats that represents nearly 1/3 of the total bat species known to occur on Sulawesi. Three of these are endemic to Sulawesi and adjacent islands, whereas one species, Myotis cf. ridleyi was identified as a new distributional record for this island and with further investigation could prove to be an undescribed species. Our record of Chironax melanocephalus tumulus provided a range extension to the southeastern arm of Sulawesi. Two specimens of Hipposideros boeadii were topotypes and represent the first collections after the description of the type specimen. Collections of Rhinolophus arcuatus from this survey were only the second record of this species from island and represent a range extension. Specimens of Megaderma spasma celebensis were the first records of this species from Southeast Sulawesi. Species are discussed individually with external, cranial and dental measurements summarized. Based on this survey, the number of bat species now documented from the lowlands of Southeast Sulawesi represents the highest diversity yet recorded from a site on Sulawesi. This region is therefore a high priority for conservation and a hotspot for bat research in Indonesia, especially Sulawesi.

Comparison of intraosseous pentobarbital administration and thoracic compression for euthanasia of anesthetized sparrows (Passer domesticus) and starlings (Sturnus vulgaris)

OBJECTIVE To compare intraosseous pentobarbital treatment (IPT) and thoracic compression (TC) on time to circulatory arrest and an isoelectric electroencephalogram (EEG) in anesthetized passerine birds. ANIMALS 30 wild-caught adult birds (17 house sparrows [Passer domesticus] and 13 European starlings [Sturnus vulgaris]). PROCEDURES Birds were assigned to receive IPT or TC (n = 6/species/group). Birds were anesthetized, and carotid arterial pulses were monitored by Doppler methodology. Five subdermal braided-wire electrodes were used for EEG. Anesthetic depth was adjusted until a continuous EEG pattern was maintained, then euthanasia was performed. Times from initiation of euthanasia to cessation of carotid pulse and irreversible isoelectric EEG (indicators of death) were measured. Data (medians and first to third quartiles) were summarized and compared between groups within species. Necropsies were performed for all birds included in experiments and for another 6 birds euthanized under anesthesia by TC (4 sparrows and 1 starling) or IPT (1 sparrow). RESULTS Median time to isoelectric EEG did not differ significantly between treatment groups for sparrows (19.0 and 6.0 seconds for TC and IPT, respectively) or starlings (88.5 and 77.5 seconds for TC and IPT, respectively). Median times to cessation of pulse were significantly shorter for TC than for IPT in sparrows (0.0 vs 18.5 seconds) and starlings (9.5 vs 151.0 seconds). On necropsy, most (14/17) birds that underwent TC had grossly visible coelomic, pericardial, or perihepatic hemorrhage. CONCLUSIONS AND CLINICAL RELEVANCE Results suggested that TC might be an efficient euthanasia method for small birds. Digital pressure directly over the heart during TC obstructed venous return, causing rapid circulatory arrest, with rupture of the atria or vena cava in several birds. The authors propose that cardiac compression is a more accurate description than TC for this procedure.